diff --git a/data/covid/preprints-summary.csv b/data/covid/preprints-summary.csv index 7f5f5559..f217a36f 100644 --- a/data/covid/preprints-summary.csv +++ b/data/covid/preprints-summary.csv @@ -1,51 +1,51 @@ -primary care research,biophysics,dermatology,month,allergy and immunology,neurology,hiv aids,evolutionary biology,biochemistry,respiratory medicine,cardiovascular medicine,genomics,genetic and genomic medicine,scientific communication and education,intensive care and critical care medicine,infectious diseases,pharmacology and therapeutics,occupational and environmental health,psychiatry and clinical psychology,obstetrics and gynecology,health policy,public and global health,Total,radiology and imaging,orthopedics,immunology,geriatric medicine,epidemiology,molecular biology,oncology,health systems and quality improvement,emergency medicine,microbiology,pediatrics,health economics,pathology,dentistry and oral medicine,ophthalmology,bioinformatics,surgery,health informatics -1,,,Mar-24,,,,,,,,,,,,,,,,,,,1,,,,,,,,,,,,,,,,,, -,,,Feb-24,,,,,,,,,,,,1,,,,,,2,4,,,,,1,,,,,,,,,,,,, -,,,Jan-24,,,,,,,,,,,,,,1,,,,2,3,,,,,,,,,,,,,,,,,, -,,,Dec-23,,1,,,,,1,,,,,,,1,,,,1,10,,,,,4,,,,,,,2,,,,,, -,,,Nov-23,,,,,,,,,,,,1,,,,,,,4,,,,,2,,1,,,,,,,,,,, -,,,Oct-23,,,,,,1,,,,,,1,,,,,,,5,,,1,,1,,,,,,,,,,,,,1 -,,,Sep-23,,,,,,,,,,,,1,,,,,,,1,,,,,,,,,,,,,,,,,, -1,,,Aug-23,,,,,,,,,,,,,,1,,,,1,7,,,,,4,,,,,,,,,,,,, -,,,Jul-23,,,,,,,,,1,,,,,,,,,1,7,,,,,3,,,2,,,,,,,,,, -,,,Jun-23,,,,,,,,,,1,,2,,1,,,,,7,,1,,,1,,,,,,,,,,,,,1 -,,,May-23,,,,,,1,,,,,,1,,,,,,1,5,,,1,,1,,,,,,,,,,,,, -,,,Apr-23,,,,,,,,,,,,1,,,,,,2,3,,,,,,,,,,,,,,,,,, -,,,Mar-23,,,,,,,,,,,,3,,1,1,,,2,8,,,,,1,,,,,,,,,,,,, -,,,Feb-23,,1,,,,1,,,,,,,,,,,,2,8,,,,,4,,,,,,,,,,,,, -,,,Jan-23,,,,,,,,,,,,1,,,,,,,6,,,,,5,,,,,,,,,,,,, -,,,Dec-22,,,,,,2,,,,,,4,,,,,1,1,12,,,,,3,,,,,,,,1,,,,, -,,,Nov-22,,,,,,,,,,,,4,,,,,,,4,,,,,,,,,,,,,,,,,, -,,,Oct-22,,,,,,,1,,,,,2,,,,,,2,6,,,,,1,,,,,,,,,,,,, -,,,Sep-22,,,,,,1,,,,,,2,,2,,,,1,8,,,,,1,,,,,1,,,,,,,, -,,,Aug-22,,,,,,,,,,,,2,,,,,,3,9,,,,,4,,,,,,,,,,,,, -,,,Jul-22,,,,,,,,,,,,3,,,,,,,8,,,1,,2,,,,,,1,,,,,,,1 -,,,Jun-22,,,,,,,,,1,,,4,,,5,,,1,18,,,,,6,,,,,,,,,,,,,1 -1,,,May-22,,,,,,,,,,,,5,,,2,,,1,13,,,,,1,,,1,,1,,1,,,,,, -,,,Apr-22,,,,,,1,1,,,,,3,,1,,,,1,16,,,,,5,,,2,,1,,1,,,,,, -,,,Mar-22,,,,1,,1,,,,,,5,,,1,,,,16,,,,,8,,,,,,,,,,,,, -,,,Feb-22,,1,,,,,,,,,,4,,,,,,1,12,,,,,6,,,,,,,,,,,,, -,,,Jan-22,,,,,,,1,,,,,3,,1,,,,1,14,,,1,,5,,,,,,,,,,,,,2 -1,,,Dec-21,,,,,,,1,,,,,8,,,,,,1,22,,,,,9,,,,,1,1,,,,,,, -1,1,,Nov-21,,1,,,,,,1,,,1,5,,,,,,3,24,,,,,9,,,2,,,,,,,,,, -,,,Oct-21,,,,,,,,,,,,3,,,2,,,,11,,,,1,4,,,,,,1,,,,,,, -,,,Sep-21,,,,,,,1,,,,1,5,1,,,,,2,17,,,,,6,,,,,,,,,,,,,1 -,,,Aug-21,,,,,,1,1,,,,1,3,,1,,,,3,12,,,,,1,,,,,,,,,,,,,1 -,,,Jul-21,,,,,,1,,,1,,1,12,,,,,,4,25,,,,,3,,1,,1,,1,,,,,,, -1,,,Jun-21,1,1,,,,,,,,,1,7,,1,1,,,4,28,,,1,,7,,,1,,,1,,,,,,,1 -,,1,May-21,,,,,,,,,1,,,7,,,1,,,1,23,,,,,11,,,,,,,,,,,,,1 -1,,,Apr-21,1,,,,,,,,,,,6,,2,,,,1,18,,,,,4,,,1,,1,,,,,,,,1 -,,,Mar-21,,1,,,1,,,,1,,,15,,,1,,,4,35,1,,,2,6,,,,,,1,,,,,,1,1 -,,,Feb-21,,,,,,,1,,,,,9,,,,,,1,24,,,,,9,,,1,,,,1,,,,,1,1 -1,,,Jan-21,,,,,,,,,,,1,8,,,1,,1,3,23,,,1,1,4,,,1,,,,,,1,,,, -1,,,Dec-20,,,,,,,2,2,,,,4,,,2,,,2,21,,,,,3,,,1,,1,,,,,,,,3 -,,,Nov-20,,,,,,,,,,,,12,,,,,1,5,27,,,1,,6,,,,,,,,,,,1,,1 -1,,,Oct-20,,,,,,,,,,,1,12,,,3,,1,,29,,,1,1,6,,1,,,,,,,,,1,,1 -1,,,Sep-20,,,1,,,,,,,,1,8,,,2,,,3,27,,,,,6,,,,3,1,,,,,,,,1 -,,,Aug-20,,,,,,,,,1,,,10,,,,1,,2,24,,,,,6,1,,1,2,,,,,,,,, -,,,Jul-20,,,,,,1,1,1,,,1,8,,,1,,,4,28,,,1,,10,,,,,,,,,,,,, -,,,Jun-20,,,,,,1,1,,,,3,10,,,4,,1,3,37,,,1,1,7,,1,1,,,,,,,1,1,,1 -,,,May-20,,,,,,1,2,,,,1,10,,1,,,,9,36,,,,1,7,,1,,,,,1,,,,1,,1 -,,,Apr-20,,,,,,,,1,2,,,6,,,,,,1,18,,,,,7,,,1,,,,,,,,,, -,,,Mar-20,,,,,,,,,,,,1,,,,,,3,8,,,,,4,,,,,,,,,,,,, -,,,Feb-20,,,,,,,,,,,,1,,,,,,2,7,,,,,4,,,,,,,,,,,,, +biochemistry,bioinformatics,molecular biology,cardiovascular medicine,orthopedics,health economics,health systems and quality improvement,pathology,neurology,biophysics,epidemiology,microbiology,public and global health,oncology,primary care research,month,immunology,infectious diseases,occupational and environmental health,pharmacology and therapeutics,dermatology,evolutionary biology,dentistry and oral medicine,genetic and genomic medicine,emergency medicine,obstetrics and gynecology,scientific communication and education,ophthalmology,genomics,pediatrics,health informatics,allergy and immunology,surgery,respiratory medicine,intensive care and critical care medicine,systems biology,Total,health policy,hiv aids,radiology and imaging,geriatric medicine,psychiatry and clinical psychology +,,,,,,,,,,,,,,1,Mar-24,,,,,,,,,,,,,,,,,,,,,1,,,,, +,,,,,,,,,,1,,2,,,Feb-24,,1,,,,,,,,,,,,,,,,,,,4,,,,, +,,,,,,,,,,,,2,,,Jan-24,,,1,,,,,,,,,,,,,,,,,,3,,,,, +,,,1,,2,,,1,,4,,1,,,Dec-23,,,1,,,,,,,,,,,,,,,,,,10,,,,, +,,,,,,,,,,2,,,,,Nov-23,,1,,,,,,,,,,,,,,,,,,,3,,,,, +,,,,,,,,,,1,,,,,Oct-23,1,1,,,,,,,,,,,,,1,,,1,,,5,,,,, +,,,,,,,,,,,,,,,Sep-23,,1,,,,,,,,,,,,,,,,,,,1,,,,, +,,,,,,,,,,4,,1,,1,Aug-23,,,1,,,,,,,,,,,,,,,,,,7,,,,, +,,,,,,2,,,,3,,1,,,Jul-23,,,,,,,,1,,,,,,,,,,,,,7,,,,, +,,,,1,,,,,,1,,,,,Jun-23,,2,1,,,,,,,,1,,,,1,,,,,,7,,,,, +,,,,,,,,,,2,,1,,,May-23,1,1,,,,,,,,,,,,,,,,1,,,6,,,,, +,,,,,,,,,,,,2,,,Apr-23,,1,,,,,,,,,,,,,,,,,,,3,,,,, +,,,,,,,,,,2,,2,,,Mar-23,,3,1,,,,,,,,,,,,,,,,,,9,,,,,1 +,,,,,,,,1,,4,,2,,,Feb-23,,,,,,,,,,,,,,,,,,1,,,8,,,,, +,,,,,,,,,,5,,,,,Jan-23,,1,,,,,,,,,,,,,,,,,,,6,,,,, +,,,,,,,1,,,3,,1,,,Dec-22,,4,,,,,,,,,,,,,,,,2,,,12,1,,,, +,,,,,,,,,,,,,,,Nov-22,,4,,,,,,,,,,,,,,,,,,,4,,,,, +,,,1,,,,,,,1,,2,,,Oct-22,,2,,,,,,,,,,,,,,,,,,,6,,,,, +,,,,,,,,,,1,1,1,,,Sep-22,,2,2,,,,,,,,,,,1,,,,1,,,9,,,,, +,,,,,,,,,,4,,3,,,Aug-22,,3,,,,,,,,,,,,,,,,,,,10,,,,, +,,,,,,,,,,2,,,,,Jul-22,1,3,,,,,,,,,,,,1,1,,,,,,8,,,,, +,,,,,,,,,,6,,1,,,Jun-22,,4,,,,,,1,,,,,,,1,,,,,,18,,,,,5 +,,,,,1,1,,,,1,1,1,,,May-22,,5,,,,,,,,,,,,,,,,,,,12,,,,,2 +,,,1,,1,2,,,,5,1,1,,,Apr-22,,3,1,,,,,,,,,,,,,,,1,,,16,,,,, +,,,,,,,,,,8,,,,1,Mar-22,,5,,,,1,,,,,,,,,,,,1,,,17,,,,,1 +,,,,,,,,1,,6,,1,,,Feb-22,,4,,,,,,,,,,,,,,,,,,,12,,,,, +,,,1,,,,,,,4,,1,,,Jan-22,1,3,1,,,,,,,,,,,,2,,,,,,13,,,,, +,,,1,,,,,1,,10,1,1,,1,Dec-21,,8,,,,,,,,,,,,1,,,,,,,24,,,,, +,,,,,,2,,1,1,9,,2,,1,Nov-21,,5,,,,,,,,,,,1,,,,,,1,,24,,,,,1 +,,,,,,,,,,4,,,,,Oct-21,,3,,,,,,,,,,,,1,,,,,,,11,,,,1,2 +,,,1,,,,,,,6,,2,,,Sep-21,,5,,1,,,,,,,,,,,1,,,,1,,17,,,,, +,,,1,,,,,,,2,,3,,,Aug-21,,3,1,,,,,,,,,,,,1,,,1,1,,13,,,,, +,,,,,,,,,,3,,4,1,,Jul-21,,11,,,,,,1,1,,,,,1,,,,2,1,,25,,,,, +,,,,,,1,,1,,7,,4,,1,Jun-21,1,7,1,,,,,,,,,,,1,1,1,,,1,,28,,,,,1 +,,,,,,,,,,9,,1,,,May-21,,8,,,1,,,1,,,,,,,1,,,,,,22,,,,,1 +,,,,,,1,,,,4,1,1,,1,Apr-21,,7,2,,,,,,,,,,,,1,1,,,,,20,,,,,1 +1,,,,,,,,1,,6,,5,,,Mar-21,,14,,,,,,1,,,,,,1,2,,1,,,,36,,,1,2,1 +,,,1,,1,1,,,,9,,1,,,Feb-21,,9,,,,,,,,,,,,,1,,1,,,,24,,,,, +,,,,,,1,,,,4,,3,,1,Jan-21,1,8,,,,,1,,,,,,,,,,,,1,,23,1,,,1,1 +,,,1,,,1,,,,4,1,3,,1,Dec-20,,3,,,,,,,,,,,2,,3,,,,,,21,,,,,2 +,1,,,,,,,,,6,,5,,,Nov-20,1,13,,,,,,,,,,,,,1,,,,,,28,1,,,, +,1,,,,,,,,,6,,,1,1,Oct-20,1,12,,,,,,,,,,,,,1,,,,1,1,30,1,,,1,3 +,,,,,,,,,,6,1,3,,1,Sep-20,,7,,,,,,,3,,,,,,1,,,,1,,26,,1,,,2 +,,1,,,,1,,,,6,,1,,,Aug-20,,12,1,,,,,1,2,1,,,,,,,,,,,26,,,,, +,,,1,,,,,,,10,,4,,,Jul-20,1,7,,,,,,,,,,,1,,,,,1,1,,27,,,,,1 +,1,,1,,,1,,,,7,,3,1,,Jun-20,1,10,,,,,,,,,,1,,,1,,,1,3,,37,1,,,1,4 +,1,,2,,1,,,,,8,,9,1,,May-20,,10,1,,,,,,,,,,,,1,,,1,1,,37,,,,1, +,,,,,,1,,,,7,,1,,,Apr-20,,7,,,,,,2,,,,,,,,,,,,,18,,,,, +,,,,,,,,,,4,,3,,,Mar-20,,1,,,,,,,,,,,,,,,,,,,8,,,,, +,,,,,,,,,,4,,2,,,Feb-20,,1,,,,,,,,,,,,,,,,,,,7,,,,, diff --git a/data/covid/preprints.csv b/data/covid/preprints.csv index dfd7b67b..edb3e88b 100644 --- a/data/covid/preprints.csv +++ b/data/covid/preprints.csv @@ -1,5 +1,11 @@ site,doi,date,link,title,authors,affiliations,abstract,category,match_type,author_similarity,affiliation_similarity -medRxiv,10.1101/2024.03.15.24304277,2024-03-16,https://medrxiv.org/cgi/content/short/2024.03.15.24304277,Comparative safety and effectiveness of Pfizer BA.4-5 versus Sanofi during the spring 2023 COVID-19 booster vaccination programme in England: a matched cohort study in OpenSAFELY-TPP,- The OpenSAFELY Collaborative; Colm D Andrews; Em Prestige; Edward P K Parker; Venexia Walker; Tom Palmer; Andrea L Schaffer; Amelia CA Green; Helen J Curtis; Alex J Walker; Rebecca M Smith; Christopher Wood; Christopher Bates; Amir Mehrkar; Brian MacKenna; Sebastian CJ Bacon; Ben Goldacre; Miguel A Hernan; Jonathan AC Sterne; William J Hulme,; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Bristol; University of Bristol; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Harvard University; University of Bristol; University of Oxford,"Introduction The spring 2023 COVID-19 booster vaccination programme in England used both Pfizer BA.4-5 and Sanofi vaccines. All people aged 75 years or over and the clinically vulnerable were eligible to receive a booster dose. Direct comparisons of the effectiveness of these two vaccines in boosting protection against severe COVID-19 events have not been made in trials or observational data. Methods With the approval of NHS England, we used the OpenSAFELY-TPP database to compare effectiveness of the Pfizer BA.4-5 and Sanofi vaccines during the spring 2023 booster programme, between 1 April and 30 June 2023. We investigated two cohorts separately: those aged 75 or over (75+); and those aged 50 or over and clinically vulnerable (CV). In each cohort, vaccine recipients were matched on date of vaccination, COVID-19 vaccine history, age, and other characteristics. Effectiveness outcomes were COVID-19 hospital admission, COVID-19 critical care admission, and COVID-19 death up to 16 weeks after vaccination. Safety outcomes were pericarditis and myocarditis up to 4 weeks after vaccination. We report the cumulative incidence of each outcome, and compare safety and effectiveness using risk differences (RD), relative risks (RR), and incidence rate ratios (IRRs). Results 492,642 people were 1-1 matched in the CV cohort, and 673,926 in the 75+ cohort, contributing a total of 7,423,251 and 10,173,230 person-weeks of follow-up, respectively. The incidence of COVID-19 hospital admission was higher for Sanofi than for Pfizer BA.4-5. In the CV cohort, 16-week risks per 10,000 people were 22.3 (95%CI 20.4 to 24.3) for Pfizer BA.4-5 and 26.4 (24.4 to 28.7) for Sanofi, with an IRR of 1.19 (95%CI 1.06 to 1.34). In the 75+ cohort, these were 17.5 (16.1 to 19.1) for Pfizer BA.4-5 and 20.4 (18.9 to 22.1) for Sanofi, with an IRR of 1.18 (1.05-1.32). These findings were similar across all pre-specified subgroups. More severe COVID-19 related outcomes (critical care admission and death), and safety outcomes at 4 weeks, were rare in both vaccines so we could not reliably compare effectiveness of the two vaccines. Conclusion This observational study comparing effectiveness of Pfizer BA.4-5 and Sanofi vaccine during the spring 2023 programme in England in the two main eligible cohorts - people aged 75 and over and in clinically vulnerable people - found some evidence of superior effectiveness against COVID-19 hospital admission for Pfizer BA.4-5 compared with Sanofi within 16 weeks after vaccination.",primary care research,fuzzy,100,100 +medRxiv,10.1101/2024.03.15.24304277,2024-03-16,https://medrxiv.org/cgi/content/short/2024.03.15.24304277,Comparative safety and effectiveness of Pfizer BA.4-5 versus Sanofi during the spring 2023 COVID-19 booster vaccination programme in England: a matched cohort study in OpenSAFELY-TPP,- The OpenSAFELY Collaborative; Colm D Andrews; Em Prestige; Edward P K Parker; Venexia Walker; Tom Palmer; Andrea L Schaffer; Amelia CA Green; Helen J Curtis; Alex J Walker; Rebecca M Smith; Christopher Wood; Christopher Bates; Amir Mehrkar; Brian MacKenna; Sebastian CJ Bacon; Ben Goldacre; Miguel A Hernan; Jonathan AC Sterne; William J Hulme,; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Bristol; University of Bristol; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Harvard University; University of Bristol; University of Oxford,"IntroductionThe spring 2023 COVID-19 booster vaccination programme in England used both Pfizer BA.4-5 and Sanofi vaccines. All people aged 75 years or over and the clinically vulnerable were eligible to receive a booster dose. Direct comparisons of the effectiveness of these two vaccines in boosting protection against severe COVID-19 events have not been made in trials or observational data. + +MethodsWith the approval of NHS England, we used the OpenSAFELY-TPP database to compare effectiveness of the Pfizer BA.4-5 and Sanofi vaccines during the spring 2023 booster programme, between 1 April and 30 June 2023. We investigated two cohorts separately: those aged 75 or over (75+); and those aged 50 or over and clinically vulnerable (CV). In each cohort, vaccine recipients were matched on date of vaccination, COVID-19 vaccine history, age, and other characteristics. Effectiveness outcomes were COVID-19 hospital admission, COVID-19 critical care admission, and COVID-19 death up to 16 weeks after vaccination. Safety outcomes were pericarditis and myocarditis up to 4 weeks after vaccination. We report the cumulative incidence of each outcome, and compare safety and effectiveness using risk differences (RD), relative risks (RR), and incidence rate ratios (IRRs). + +Results492,642 people were 1-1 matched in the CV cohort, and 673,926 in the 75+ cohort, contributing a total of 7,423,251 and 10,173,230 person-weeks of follow-up, respectively. The incidence of COVID-19 hospital admission was higher for Sanofi than for Pfizer BA.4-5. In the CV cohort, 16-week risks per 10,000 people were 22.3 (95%CI 20.4 to 24.3) for Pfizer BA.4-5 and 26.4 (24.4 to 28.7) for Sanofi, with an IRR of 1.19 (95%CI 1.06 to 1.34). In the 75+ cohort, these were 17.5 (16.1 to 19.1) for Pfizer BA.4-5 and 20.4 (18.9 to 22.1) for Sanofi, with an IRR of 1.18 (1.05-1.32). These findings were similar across all pre-specified subgroups. More severe COVID-19 related outcomes (critical care admission and death), and safety outcomes at 4 weeks, were rare in both vaccines so we could not reliably compare effectiveness of the two vaccines. + +ConclusionThis observational study comparing effectiveness of Pfizer BA.4-5 and Sanofi vaccine during the spring 2023 programme in England in the two main eligible cohorts - people aged 75 and over and in clinically vulnerable people - found some evidence of superior effectiveness against COVID-19 hospital admission for Pfizer BA.4-5 compared with Sanofi within 16 weeks after vaccination.",primary care research,fuzzy,100,100 medRxiv,10.1101/2024.02.23.24303274,2024-02-24,https://medrxiv.org/cgi/content/short/2024.02.23.24303274,A Population-Based Cross-Sectional Investigation of COVID-19 Hospitalizations and Mortality Among Autistic People,Dewy Nijhof; Filip Sosenko; Daniel MacKay; Michael Fleming; Bhautesh Dinesh Jani; Jill Pell; Chris Hatton; Deborah Cairns; Angela Henderson; Laura McKernan Ward; Ewelina Rydzewska; Maria Gardani; Elliot Millington; Craig Melville,"University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow School of Health and Wellbeing; University of Glasgow; Manchester Metropolitan University, Faculty of Health and Education; University of Glasgow; University of Glasgow; University of Dundee; University of Edinburgh; University of Edinburgh; University of Glasgow; University of Glasgow","BackgroundCurrent evidence suggests the possibility that autistic people may be at more risk of COVID-19 infection, hospitalisation, and mortality than the general population. Previous studies, however, are either limited in scale or do not investigate potential risk factors. Whilst many risk factors have been speculated to be responsible for severe COVID-19, this research has focused on general population samples. MethodsUsing data-linkage and a whole-country population, this study modelled associations between autism and COVID-19 hospitalisation and mortality risk in adults, investigating a multitude of clinical and demographic risk factors. @@ -128,7 +134,6 @@ FindingsWe identified a total of 55,465 people recorded to have long COVID over InterpretationEHR recorded long COVID remains very low compared and incident records of long COVID declined over 2022. We found the lowest rates of recorded long COVID in people with 3 or more vaccine doses. We summarised several sources of possible bias for researchers using EHRs to study long COVID.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.11.30.23299229,2023-12-01,https://medrxiv.org/cgi/content/short/2023.11.30.23299229,Population age as a key factor in the COVID-19 pandemic dynamics,Igor Nesteruk; Matt Keeling,"Institute of Hydromechanics National Academy of sciences of Ukraine; School of Life Sciences & Mathematics Institute, University of Warwick, UK","The population and governments of many countries are losing interest in the SARS-CoV-2 infection, the number of tests and the number of new cases detected is sharply decreasing. To compare the accumulated numbers CC of cases and deaths DC per million and to answer the question why the less vaccinated Africa has accumulated 36 times lower CC values and 15 times lower DC values than Europe, simple statistical analysis have been performed. CC and DC values demonstrated rather strong correlation with the median age of populations. One-year increment in the median year yields 12-18 thousand increase in CC values and 52-83 increase in DC values. Zero-COVID countries succeed to have much lower numbers of deaths per capita and case fatality ratios DC/CC.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.11.28.23299156,2023-11-29,https://medrxiv.org/cgi/content/short/2023.11.28.23299156,Examining the association of live virus neutralisation activity of capillary microsamples and risk of SARS-CoV-2 infections: a nested case control study within the Virus Watch community cohort,Alexei Yavlinsky; Vincent Nguyen; Sarah Beale; Emma Wall; Mary Y Wu; Isobel Braithwaite; Jana Kovar; Madhumita Shrotri; Annalan Mathew Dwight Navaratnam; Wing Lam Erica Fong; Thomas Edward Byrne; Francois Balloux; Ibrahim Abubakar; Benjamin J Cowling; Andrew Hayward; Robert W Aldridge,University College London; University College London; University College London; The Francis Crick Institute; The Francis Crick Institute; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; The University of Hong Kong; University College London; University College London,"Due to the proliferation of new SARS-CoV-2 variants, most COVID-19 cases are now caused by post-vaccine infections and a substantial proportion are reinfections. While prior research on correlates of protection has focused on the role of anti-spike antibodies, the results of the corresponding antibody assays may not accurately predict the risk of infection with new SARS-CoV-2 variants. In this study, we investigated the association between live virus neutralising antibody activity and SARS-CoV-2 infection risk using self-administered capillary microsample blood tests from VirusWatch participants. The study was conducted during the transition between the dominance of the B.1.617.2 (Delta) and B.1.1.529 (Omicron BA.1) SARS-CoV-2 variants, enabling us to investigate the association between variant-specific virus inhibition and subsequent infections within each dominance period. Greater inhibition of Omicron BA.1 live virus was associated with a reduction in infection risk during both the Delta and Omicron BA.1 dominance periods. Delta virus inhibition was associated with infection risk reduction during the Delta dominance period, but we found no association between Delta inhibition and protection against infection during the Omicron BA.1 dominance period. Our results are consistent with earlier findings and suggest that variant-specific serosurveillance of immunity and protection against SARS-CoV-2 infection at the population level could inform public health policy in near-real time using inexpensive and accessible home-based testing.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2023.11.24.23296021,2023-11-27,https://medrxiv.org/cgi/content/short/2023.11.24.23296021,Severe acute myositis and myocarditis upon initiation of six-weekly Pembrolizumab post-COVID-19 mRNA vaccination,Robert Aerwyn Watson; Weiyu Ye; Chelsea Alice Taylor; Rosalin Anisha Cooper; Orion Tong; Tim James; Brian Shine; Monika Hofer; Damian Jenkins; Robert Pell; Eleni Ieremia; Stephanie Jones; David Maldonado-Perez; Ian Roberts; Nicholas Coupe; Mark Ross Middleton; Miranda Jane Payne; Benjamin Peter Fairfax,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; University of Oxford; University of Oxford; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; University of Oxford; Oxford University Hospitals NHS Foundation Trust; University of Oxford,"We describe three cases of critical acute myositis with myocarditis occurring within 22 days of each other at a single institution, all within one month of receiving the initial cycle of the anti-PD-1 drug Pembrolizumab. Analysis of T cell receptor repertoires from peripheral blood and tissues revealed a high degree of clonal expansion and public clones between cases, with several T cell clones expanded within the skeletal muscle putatively recognising viral epitopes. All patients had recently received a COVID-19 mRNA booster vaccine prior to treatment and were positive for SARS-CoV2 Spike antibody. In conclusion, we report a series of unusually severe myositis and myocarditis following PD-1 blockade and the COVID-19 mRNA vaccination.",oncology,fuzzy,100,100 medRxiv,10.1101/2023.11.09.23298162,2023-11-10,https://medrxiv.org/cgi/content/short/2023.11.09.23298162,One year health outcomes associated with systemic corticosteroids for COVID-19: a longitudinal cohort study,Olivia C Leavy; Richard J Russell; Ewen M Harrison; Nazir I Lone; Steven Kerr; Annemarie B Docherty; Aziz Sheikh; Matthew Richardson; Omer Elneima; Neil J Greening; Victoria Claire Harris; Linzy Houchen-Wolloff; Hamish J C McAuley; Ruth M Saunders; Marco Sereno; Aarti Shikotra; Amisha Singapuri; Raminder Aul; Paul Beirne; Charlotte E Bolton; Jeremy S Brown; Gourab Choudhury; Nawar Diar Bakerly; Nicholas Easom; Carlos Echevarria; Jonathan Fuld; Nick Hart; John R Hurst; Mark Jones; Dhruv Parekh; Paul Pfeffer; Najib M Rahman; Sarah Rowland-Jones; Ajay M Shah; Dan G Wootton; Caroline Jolley; AA Roger Thompson; Trudie Chalder; Melanie J Davies; Anthony De Soyza; John R Geddes; William Greenhalf; Simon Heller; Luke Howard; Joseph Jacob; R Gisli Jenkins; Janet M Lord; Will D-C Man; Gerry P McCann; Stefan Neubauer; Peter JM Openshaw; Joanna Porter; Matthew J Rowland; Janet T Scott; Malcolm G Semple; Sally J Singh; David Thomas; Mark Toshner; Keir Lewis; Liam G Heaney; Andrew Briggs; Bang Zheng; Mathew Thorpe; Jennifer K Quint; James D Chalmers; Ling-Pei Ho; Alex Horsley; Michael Marks; Krisnah Poinasamy; Betty Raman; Louise V Wain; Christopher E Brightling; Rachael A Evans; - PHOSP-COVID Collaborative Group,"Department of Population Health Sciences, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; The Usher Institute, University of Edinburgh, Edinburgh, UK; Roslin Institute, University of Edinburgh, Edinburgh, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; The Usher Institute, University of Edinburgh, Edinburgh, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; Centre for Exercise and Rehabilitation Science, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; St Georges University Hospitals NHS Foundation Trust, London, UK; The Leeds Teaching Hospitals NHS Trust, Leeds, UK; University of Nottingham, Nottingham, UK; UCL Respiratory, Department of Medicine, University College London, Rayne Institute, London, UK; University of Edinburgh, Edinburgh, UK; Manchester Metropolitan University, Manchester, UK; Infection Research Group, Hull University Teaching Hospitals, Hull, UK; The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK; Department of Respiratory Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Lane Fox Respiratory Service, Guys and St Thomas NHS Foundation Trust, London, UK; University College London, London, UK; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK; University of Birmingham, Birmingham, UK; Barts Health NHS Trust, London, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK; University of Sheffield, Sheffield, UK; Kings College London, London, UK; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Kings College London, London, UK; University of Sheffield, Sheffield, UK; Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK; Diabetes Research Centre, University of Leicester, Leicester, UK; Population Health Sciences Institute, Newcastle University, Newcastle Upon Tyne, UK; NIHR Oxford Health Biomedical Research Centre, University of Oxford, Oxford, UK; University of Liverpool, Liverpool, UK; Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK; Imperial College Healthcare NHS Trust, London, UK; Centre for Medical Image Computing, University College London, London, UK; National Heart and Lung Institute, Imperial College London, London, UK; MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK; Royal Brompton and Harefield Clinical Group, Guys and St Thomas NHS Foundation Trust, London, UK; Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; National Heart and Lung Institute, Imperial College London, London, UK; UCL Respiratory, Department of Medicine, University College London, Rayne Institute, London, UK; Kadoorie Centre for Critical Care Research, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, U; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; Imperial College London, London, UK; Cambridge NIHR BRC, Cambridge, UK; Hywel Dda University Health Board, Wales, UK; Wellcome-Wolfson Institute for Experimental Medicine, Queens University Belfast, Belfast, UK; London School of Hygiene & Tropical Medicine, London, UK; London School of Hygiene & Tropical Medicine, London, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; NHLI, Imperial College London, London, UK; University of Dundee, Ninewells Hospital and Medical School, Dundee, UK; MRC Human Immunology Unit, University of Oxford, Oxford, UK; Division of Infection, Immunity & Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK; Asthma and Lung UK, London, UK; Radcliffe Department of Medicine, University of Oxford, Oxford, UK; Department of Population Health Sciences, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; ","BackgroundIn patients with COVID-19 requiring supplemental oxygen, dexamethasone reduces acute severity and improves survival, but longer-term effects are unknown. We hypothesised that systemic corticosteroid administration during acute COVID-19 would be associated with improved health-related quality of life (HRQoL) one year after discharge. MethodsAdults admitted to hospital between February 2020 and March 2021 for COVID-19 and meeting current guideline recommendations for dexamethasone treatment were included using two prospective UK cohort studies. HRQoL, assessed by EQ-5D-5L utility index, pre-hospital and one year after discharge were compared between those receiving corticosteroids or not after propensity weighting for treatment. Secondary outcomes included patient reported recovery, physical and mental health status, and measures of organ impairment. Sensitivity analyses were undertaken to account for survival and selection bias. @@ -379,6 +384,13 @@ ResultsAmong 20,112 observations across four population surveys, 13% reported ha ConclusionsLong COVID was associated with financial disruption in the UK. If our findings reflect causal effects, extending employment protection and financial support to people with long COVID may be warranted.",public and global health,fuzzy,100,100 bioRxiv,10.1101/2023.05.24.541920,2023-05-25,https://biorxiv.org/cgi/content/short/2023.05.24.541920,"Dichotomy of neutralizing antibody, B cell and T cell responses to SARS-CoV-2 vaccination and protection in healthy adults",Edward J Carr; Hermaleigh Townsley; Mary Y Wu; Katalin A Wilkinson; Philip S Hobson; Dina Levi; Sina Namjou; Harriet V Mears; Agnieszka Hobbs; Martina Ragno; Lou S Herman; Ruth Harvey; Chris Bailey; Ashley S Fowler; Emine Hatipoglu; Yenting Ngai; Bobbi Clayton; Murad Miah; Philip Bawumia; Mauro Miranda; Callie Smith; Chelsea Sawyer; Gavin Kelly; Viyaasan Mahalingasivam; Bang Zheng; Stephen JW Evans; Vincenzo Libri; Andrew Riddell; Jerome Nicod; Nicola O'Reilly; Michael Howell; Bryan Williams; Robert J Wilkinson; George Kassiotis; Charles Swanton; Sonia Gandhi; Rupert CL Beale; David LV Bauer; Emma C Wall,The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; Worldwide Influenza Centre; The Francis Crick Institute; The Francis Crick Institute; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; National Institute for Health Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre and NIHR UCLH Clinical Research Facility; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; UCL; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute,"Heterogeneity in SARS-CoV-2 vaccine responses is not understood. Here, we identify four patterns of live-virus neutralizing antibody responses: individuals with hybrid immunity (with confirmed prior infection); rare individuals with low responses (paucity of S1-binding antibodies); and surprisingly, two further groups with distinct serological repertoires. One group - broad responders - neutralize a range of SARS-CoV-2 variants, whereas the other - narrow responders - neutralize fewer, less divergent variants. This heterogeneity does not correlate with Ancestral S1-binding antibody, rather the quality of the serological response. Furthermore, IgDlowCD27-CD137+ B cells and CCR6+ CD4+ T cells are enriched in broad responders before dose 3. Notably, broad responders have significantly longer infection-free time after their third dose. Understanding the control and persistence of these serological profiles could allow personalized approaches to enhance serological breadth after vaccination.",immunology,fuzzy,100,100 +medRxiv,10.1101/2023.05.23.23289798,2023-05-24,https://medrxiv.org/cgi/content/short/2023.05.23.23289798,Primary Care Post-COVID syndrome Diagnosis and Referral Coding,Robert Willans; Gail Allsopp; Pall Jonsson; Fiona Glen; Felix Greaves; John Macleod; Yinghui Wei; Sebastian Bacon; Amir Mehrkar; Alex Walker; Brian MacKenna; Louis Fisher; Ben Goldacre; - The OpenSAFELY Collaborative; - The CONVALESCENCE Collaborative,"National Institute of Health and Care Excellence; Royal College of General Practitioners; National Institute of Health and Care Excellence; National Institute of Health and Care Excellence; National Institute of Health and Care Excellence; University of Bristol; University of Plymouth; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; ; ","IntroductionGuidelines for diagnosing and managing Post-COVID syndrome have been rapidly developed. Consistency of the application of these guidelines in primary care is unknown. Electronic health records provide an opportunity to review the use of codes relating to Post-COVID syndrome. This paper explores the use of primary care records as a surrogate uptake measure for NICEs rapid guideline ""managing the long-term effects of COVID-19"" by measuring the use of Post-COVID syndrome diagnosis and referral codes in the pathway. + +MethodWith the approval of NHS England we used routine clinical data from the OpenSafely-EMIS/-TPP platforms. Counts of Post-COVID syndrome diagnosis and referral codes were generated from a cohort of all adults, establishing numbers of diagnoses and referrals following diagnosis. The relationship between Post-COVID syndrome diagnosis and referral codes was explored with reference to NICEs rapid guideline. + +ResultsOf over 45 million patients, 69,220 (0.15%) had a Post-COVID syndrome diagnostic code, and 67,741 (0.15%) had a referral code. 78% of referral codes did not have an associated diagnosis code. 79% of diagnosis codes had no subsequent referral code. Only 18,633 (0.04%) had both. There were higher rates of both diagnosis and referral in those who were more deprived, female and some ethnic groups. + +DiscussionThis study demonstrates variation in diagnosis and referral coding rates for Post-COVID syndrome across different patient groups. The results, with limited crossover of referral and diagnostic codes, suggest only one type of code is usually recorded. Recording one code limits the use of routine data for monitoring Post-COVID syndrome diagnosis and management, but suggests several areas for improvement in coding. Post-COVID syndrome coding, particularly diagnosis coding, needs to improve before administrators and researchers can use it to evaluate care pathways.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.05.17.23290105,2023-05-24,https://medrxiv.org/cgi/content/short/2023.05.17.23290105,Within-host SARS-CoV-2 viral kinetics informed by complex life course exposures reveals different intrinsic properties of Omicron and Delta variants,Timothy W Russell; Hermaleigh Townsley; Sam Abbott; Joel Hellewell; Edward J Carr; Lloyd Chapman; Rachael Pung; Billy J Quilty; David Hodgson; Ashley Fowler; Lorin Adams; Christopher Bailey; Harriet V Mears; Ruth Harvey; Bobbi Clayton; Nicola O'Reilly; Yenting Ngai; Jerome Nicod; Steve Gamblin; Bryan Williams; Sonia Gandhi; Charles Swanton; Rupert Beale; David LV Bauer; Emma C Wall; Adam Kucharski,London School of Hygiene and Tropical Medicine; The Francis Crick Institute; London School of Hygiene and Tropical Medicine; European Molecular Biology Laboratory; The Francis Crick Institute; Lancaster University; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; National Institute for Health Research (NIHR) University College London Hospitals (UCLH); The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; London School of Hygiene and Tropical Medicine,"The emergence of successive SARS-CoV-2 variants of concern (VOC) during 2020-22, each exhibiting increased epidemic growth relative to earlier circulating variants, has created a need to understand the drivers of such growth. However, both pathogen biology and changing host characteristics - such as varying levels of immunity - can combine to influence replication and transmission of SARS-CoV-2 within and between hosts. Disentangling the role of variant and host in individual-level viral shedding of VOCs is essential to inform COVID-19 planning and response, and interpret past epidemic trends. Using data from a prospective observational cohort study of healthy adult volunteers undergoing weekly occupational health PCR screening, we developed a Bayesian hierarchical model to reconstruct individual-level viral kinetics and estimate how different factors shaped viral dynamics, measured by PCR cycle threshold (Ct) values over time. Jointly accounting for both inter-individual variation in Ct values and complex host characteristics - such as vaccination status, exposure history and age - we found that age and number of prior exposures had a strong influence on peak viral replication. Older individuals and those who had at least five prior antigen exposures to vaccination and/or infection typically had much lower levels of shedding. Moreover, we found evidence of a correlation between the speed of early shedding and duration of incubation period when comparing different VOCs and age groups. Our findings illustrate the value of linking information on participant characteristics, symptom profile and infecting variant with prospective PCR sampling, and the importance of accounting for increasingly complex population exposure landscapes when analysing the viral kinetics of VOCs.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.05.08.23289442,2023-05-11,https://medrxiv.org/cgi/content/short/2023.05.08.23289442,Cohort Profile: Post-hospitalisation COVID-19 study (PHOSP-COVID),Omer Elneima; Hamish J C McAuley; Olivia C Leavy; James D Chalmers; Alex Horsley; Ling-Pei Ho; Michael Marks; Krisnah Poinasamy; Betty Raman; Aarti Shikotra; Amisha Singapuri; Marco Sereno; Victoria C Harris; Linzy Houchen-Wolloff; Ruth M Saunders; Neil J Greening; Matthew Richardson; Jennifer K Quint; Andrew Briggs; Annemarie B Docherty; Steven Kerr; Ewen M Harrison; Nazir I Lone; Mathew Thorpe; Liam G Heaney; Keir E Lewis; Raminder Aul; Paul Beirne; Charlotte E Bolton; Jeremy S Brown; Gourab Choudhury; Nawar Diar Bakerly; Nicholas Easom; Carlos Echevarria; Jonathan Fuld; Nick Hart; John R Hurst; Mark G Jones; Dhruv Parekh; Paul E Pfeffer; Najib M Rahman; Sarah L Rowland-Jones; AA Roger Thompson; Caroline Jolley; Ajay M Shah; Dan G Wootton; Trudie Chalder; Melanie J Davies; Anthony De Soyza; John R Geddes; William Greenhalf; Simon Heller; Luke S Howard; Joseph Jacob; R Gisli Jenkins; Janet M Lord; William D-C Man; Gerry P McCann; Stefan Neubauer; Peter JM Openshaw; Joanna C Porter; Matthew J Rowland; Janet T Scott; Malcolm G Semple; Sally J Singh; David C Thomas; Mark Toshner; Aziz Sheikh; Chris E Brightling; Louise v Wain; Rachael A Evans; - on behalf of the PHOSP-COVID Collaborative Group,"The Institute for Lung Health, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; Department of Population Health Sciences, University of Leicester, Leicester, UK; University of Dundee, Ninewells Hospital and Medical School, Dundee, UK; Division of Infection, Immunity & Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; MRC Human Immunology Unit, University of Oxford, Oxford, UK; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK; Asthma and Lung UK, London, UK; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; Centre for Exercise and Rehabilitation Science, NIHR Leicester Biomedical Research Centre- Respiratory, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; National Heart and Lung Institute, Imperial College London, London, UK; London School of Hygiene & Tropical Medicine, London, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; The Roslin Institute, University of Edinburgh, Edinburgh, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; Wellcome-Wolfson Institute for Experimental Medicine, Queens University Belfast, Belfast, UK; Hywel Dda University Health Board, Wales, UK; St George's University Hospitals NHS Foundation Trust, London, UK; Leeds Teaching Hospitals NHS Trust, Leeds, UK; NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK; UCL Respiratory, Department of Medicine, University College London, London, UK; Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK; Salford Royal NHS Foundation Trust, Manchester, UK; Infection Research Group, Hull University Teaching Hospitals, Hull, UK; Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK; Department of Respiratory Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Lane Fox Respiratory Unit, Guy's and St Thomas' NHS Foundation Trust, London, UK; Royal Free London NHS Foundation Trust, London, UK; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK; Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK; Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; University of Sheffield, Sheffield, UK; University of Sheffield, Sheffield, UK; Centre for Human & Applied Physiological Sciences, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King's College London, London, UK; King's College London British Heart Foundation Centre, London, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK; Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; Population Health Sciences Institute, Newcastle University, Newcastle Upon Tyne, UK; NIHR Oxford Health Biomedical Research Centre, University of Oxford, Oxford, UK; The CRUK Liverpool Experimental Cancer Medicine Centre, Liverpool, UK; Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK; Imperial College Healthcare NHS Trust, London, UK; Centre for Medical Image Computing, University College London, London, UK; National Heart and Lung Institute, Imperial College London, London, UK; MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK; Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK; Department of Cardiovascular Sciences, University of Leicester and the NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester; NIHR Oxford Biomedical Research Centre, Oxford, UK; National Heart and Lung Institute, Imperial College London, London, UK; UCL Respiratory, Department of Medicine, University College London, London, UK; Kadoorie Centre for Critical Care Research, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; MRC-University of Glasgow Center for Virus research; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK; Centre for Exercise and Rehabilitation Science, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; Department of Immunology and Inflammation, Imperial College London, London, UK; NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; Department of Population Health Sciences, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; ","O_LIPHOSP-COVID is a national UK multi-centre cohort study of patients who were hospitalised for COVID-19 and subsequently discharged. C_LIO_LIPHOSP-COVID was established to investigate the medium- and long-term sequelae of severe COVID-19 requiring hospitalisation, understand the underlying mechanisms of these sequelae, evaluate the medium- and long-term effects of COVID-19 treatments, and to serve as a platform to enable future studies, including clinical trials. @@ -447,6 +459,13 @@ C_LI How this study might affect research, practice or policyO_LIThe findings contribute to the evidence base that long-COVID differences occur across industries and occupations, provides insights for employees, employers, occupational and healthcare for the industries and occupations that may need additional support for return- to-work policies and highlights sectors and occupations where further research is needed to understand the mechanisms resulting in long-COVID and how occupational factors influence the risk of developing long-COVID or interact with long-COVID to increase the impact on activities. C_LI",public and global health,fuzzy,100,100 +medRxiv,10.1101/2023.03.21.23287524,2023-03-22,https://medrxiv.org/cgi/content/short/2023.03.21.23287524,Employment outcomes of people with Long Covid symptoms: community-based cohort study,Daniel Ayoubkhani; Francesco Zaccardi; Koen B Pouwels; Ann Sarah Walker; Donald Houston; Nisreen A Alwan; Josh Martin; Kamlesh Khunti; Vahe Nafilyan,Office for National Statistics; University of Leicester; University of Oxford; University of Oxford; University of Portsmouth; University of Southampton; Bank of England; University of Leicester; Office for National Statistics,"BackgroundEvidence on the long-term employment consequences of SARS-CoV-2 infection is lacking. We used data from a large, community-based sample in the UK to estimate associations between Long Covid and subsequent employment outcomes. + +MethodsThis was an observational, longitudinal study using a pre-post design. We included survey participants from 3 February 2021 to 30 September 2022 when they were aged 16 to 64 years and not in full-time education. Using conditional logit modelling, we explored the time-varying relationship between Long Covid status [≥]12 weeks after a first test-confirmed SARS-CoV-2 infection (reference: pre-infection) and labour market inactivity (neither working nor looking for work) or workplace absence lasting [≥]4 weeks. + +ResultsOf 206,299 included participants (mean age 45 years, 54% female, 92% white), 15% were ever inactive in the labour market and 10% were ever long-term absent during follow-up. Compared with pre-infection, inactivity was higher in participants reporting Long Covid 30 to <40 weeks (adjusted odds ratio (aOR): 1.45; 95% CI: 1.17 to 1.81) or 40 to <52 weeks (1.34; 1.05 to 1.72) post-infection. Combining with official statistics on Long Covid prevalence, our estimates translate to 27,000 (95% CI: 6,000 to 47,000) working-age adults in the UK being inactive because of Long Covid in July 2022. + +ConclusionsLong Covid is likely to have contributed to reduced levels of participation in the UK labour market, though it is unlikely to be the sole driver. Further research is required to quantify the contribution of other factors, such as indirect health effects of the pandemic.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2023.03.15.23287300,2023-03-19,https://medrxiv.org/cgi/content/short/2023.03.15.23287300,Risk factors for SARS-CoV-2 infection: A test-negative case-control study with additional population controls,Marjut Sarjomaa; Chi Zhang; Yngvar Tveten; Hege Kersten; Harald Reiso; Randi Eikeland; Johny Kongerud; Kristine Karlsrud Berg; Carina Thilesen; Svein Arne Nordbo; Ingeborg Aaberge; Jan Vandenbroucke; Neil Pearce; Anne Kristin Fell,Telemark Hospital: Sykehuset Telemark HF; Norwegian Institute of Public Health: Folkehelseinstituttet; Telemark Hospital: Sykehuset Telemark HF; Telemark Hospital: Sykehuset Telemark HF; Sorlandet Hospital; Sorlandet Hospital; University of Oslo; Sorlandet Sykehus HF; Unilabs Laboratory Medicine; St Olavs Hospital; Norwegian Institute of Public Health; Leiden University Medical Center; London School of Hygiene and Tropical Medicine; Telemark Hospital: Sykehuset Telemark HF,"ObjectivesTo assess risk factors for SARS-CoV-2 infection by first comparing positive cases with negative controls as determined by polymerase chain reaction (PCR) testing and then comparing these two groups with an additional population control group. Design and settingTest-negative design (TND), multicentre case-control study with additional population controls in South Eastern Norway. @@ -865,6 +884,26 @@ FindingsOf 8,799,079 visits, 147,278 (1{middle dot}7%) were PCR-positive. Over t InterpretationChange-points in growth rates of SARS-CoV-2 can be detected in near real-time using ISR and second derivatives of GAMs. To increase certainty about changes in epidemic trajectories both methods could be run in parallel. Running either method in near real-time on different infection surveillance data streams could provide timely warnings of changing underlying epidemiology. FundingUK Health Security Agency, Department of Health and Social Care (UK), Welsh Government, Department of Health (on behalf of the Northern Ireland Government), Scottish Government, National Institute for Health Research.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2022.09.11.22279823,2022-09-12,https://medrxiv.org/cgi/content/short/2022.09.11.22279823,Effects of the COVID-19 pandemic on the mental health of clinically extremely vulnerable children and children living with clinically extremely vulnerable people in Wales: A data linkage study,Laura Elizabeth Cowley; Karen Hodgson; Jiao Song; Tony Whiffen; Jacinta Tan; Ann John; Amrita Bandyopadhyay; Alisha R Davies,Swansea University; Public Health Wales; Public Health Wales; Welsh Government; University of Oxford; Swansea University; Swansea University; Public Health Wales,"ObjectivesTo determine whether clinically extremely vulnerable (CEV) children or children living with a CEV person in Wales were at greater risk of presenting with anxiety or depression in primary or secondary care during the COVID-19 pandemic compared with children in the general population, and to compare patterns of anxiety and depression during the pandemic (23rd March 2020-31st January 2021, referred to as 2020/21) and before the pandemic (March 23rd 2019-January 31st 2020, referred to as 2019/20), between CEV children and the general population. + +DesignPopulation-based cross-sectional cohort study using anonymised, linked, routinely collected health and administrative data held in the Secure Anonymised Information Linkage Databank. CEV individuals were identified using the COVID-19 Shielded Patient List. + +SettingPrimary and secondary healthcare settings covering 80% of the population of Wales. + +ParticipantsChildren aged 2-17 in Wales: CEV (3,769); living with a CEV person (20,033); or neither (415,009). + +Primary outcome measureFirst record of anxiety or depression in primary or secondary healthcare in 2019/20 and 2020/21, identified using Read and ICD-10 codes. + +ResultsA Cox regression model adjusted for demographics and history of anxiety or depression revealed that only CEV children were at greater risk of presenting with anxiety or depression during the pandemic compared with the general population (Hazard Ratio=2.27, 95% Confidence Interval=1.94-2.66, p<0.001). Compared with the general population, the risk amongst CEV children was higher in 2020/21 (Risk Ratio 3.04) compared with 2019/20 (Risk Ratio 1.90). In 2020/21, the cumulative incidence of anxiety or depression increased slightly amongst CEV children, but declined amongst the general population. + +ConclusionsDifferences in the cumulative incidences of recorded anxiety or depression in healthcare between CEV children and the general population were largely driven by a reduction in presentations to healthcare services by children in the general population during the pandemic. + +Strengths and limitations of this studyO_LIStrengths of this study include its novelty, national focus and clinical relevance; to date this is the first population-based study examining the effects of the COVID-19 pandemic on healthcare use for anxiety or depression amongst clinically extremely vulnerable (CEV) children and children living with a CEV person in Wales +C_LIO_LIWe compared 2020/21 data with pre-pandemic 2019/20 data for CEV children and children in the general population, to place the impact of the COVID-19 pandemic in the context of longer-term patterns of healthcare use +C_LIO_LIWe used a novel approach and linked multiple datasets to identify a cohort of children living with a CEV person in Wales during the COVID-19 pandemic +C_LIO_LIThere was heterogeneity within the Shielded Patient List that was used to create the cohorts of children identified as CEV or living with a CEV person, in terms of the type and severity of individuals underlying conditions; the manner in which people were added to the list; the time point that people were added to the list; and the extent to which people followed the shielding guidance +C_LIO_LIRoutinely collected healthcare data does not capture self-reported health, and is likely to underestimate the burden of common mental disorders in the population +C_LI",pediatrics,fuzzy,100,100 medRxiv,10.1101/2022.09.09.22279754,2022-09-09,https://medrxiv.org/cgi/content/short/2022.09.09.22279754,Contact patterns of UK home delivery drivers and their use of protective measures during the COVID-19 pandemic: a cross-sectional study,Jessica R E Bridgen; Hua Wei; Carl A Whitfield; Yang Han; Ian Hall; Chris Jewell; Martie JA van Tongeren; Jonathan M Read,Lancaster University; The University of Manchester; University of Manchester; University of Manchester; University of Manchester; Lancaster University; University of Manchester; Lancaster University,"ObjectivesTo quantify contact patterns of UK home delivery drivers and identify protective measures adopted during the pandemic. MethodsWe conducted a cross-sectional online survey to measure the interactions of 170 UK delivery drivers during a working shift between 7 December 2020 and 31 March 2021. @@ -881,6 +920,27 @@ ResultsRelaxation of COVID-19 restrictions from April 2021 coincided with reduce ConclusionsRelaxation of COVID-19 restrictions coincided with decreased face covering use, increased social mixing and a rebound in ARI and asthma exacerbations. Associations between incident ARI and risk of moderate/severe asthma exacerbation were similar for non-COVID-19 ARI and COVID-19, both before and after emergence of the SARS-CoV-2 omicron variant. FundingBarts Charity, UKRI",respiratory medicine,fuzzy,100,100 +medRxiv,10.1101/2022.08.29.22279359,2022-08-31,https://medrxiv.org/cgi/content/short/2022.08.29.22279359,Prophylactic Treatment of COVID-19 in Care Homes Trial (PROTECT-CH),Philip M Bath; Jonathan Ball; Matthew Boyd; Heather Gage; Matthew Glover; Maureen Godfrey; Bruce Guthrie; Jonathan Hewitt; Robert Howard; Thomas Jaki; Edmund Juszczak; Daniel Lasserson; Paul Leighton; Val Leyland; Wei Shen Lim; Pip Logan; Garry Meakin; Alan Montgomery; Reuben Ogollah; Peter Passmore; Philip Quinlan; Caroline Rick; Simon Royal; Susan D Shenkin; Clare Upton; Adam L Gordon; - PROTECT-CH Trialists,University of Nottingham; University of Nottingham; University of Nottingham; University of Surrey; University of Surrey; Private person; University of Edinburgh; Llandough Hospital; University College London; University of Cambridge; University of Nottingham; University of Warwick; University of Nottingham; Private person; Nottingham University Hospitals NHS Trust; University of Nottingham; University of Nottingham; University of Nottingham; University of Nottingham; Queen's University Belfast; University of Nottingham; University of Nottingham; Cripps Health Centre; University of Edinburgh; University of Nottingham; University of Nottingham; ,"BackgroundCoronavirus disease 2019 (COVID-19) is associated with significant mortality and morbidity in care homes. Novel or repurposed antiviral drugs may reduce infection and disease severity through reducing viral replication and inflammation. + +ObjectiveTo compare the safety and efficacy of antiviral agents (ciclesonide, niclosamide) for preventing SARS-CoV-2 infection and COVID-19 severity in care home residents. + +DesignCluster-randomised open-label blinded endpoint platform clinical trial testing antiviral agents in a post-exposure prophylaxis paradigm. + +SettingCare homes across all four United Kingdom member countries. + +ParticipantsCare home residents 65 years of age or older. + +InterventionsCare homes were to be allocated at random by computer to 42 days of antiviral agent plus standard care versus standard of care and followed for 60 days after randomisation. + +Main outcome measuresThe primary four-level ordered categorical outcome with participants classified according to the most serious of all-cause mortality, all-cause hospitalisation, SARS-CoV-2 infection and no infection. Analysis using ordinal logistic regression was by intention to treat. Other outcomes included the components of the primary outcome and transmission. + +ResultsDelays in contracting between NIHR and the manufacturers of potential antiviral agents significantly delayed any potential start date. Having set up the trial (protocol, approvals, insurance, website, database, routine data algorithms, training materials), the trial was stopped in September 2021 prior to contracting of care homes and general practitioners in view of the success of vaccination in care homes with significantly reduced infections, hospitalisations and deaths. As a result, the sample size target (based on COVID-19 rates and deaths occurring in February-June 2020) became unfeasible. + +LimitationsCare home residents were not approached about the trial and so were not consented and did not receive treatment. Hence, the feasibility of screening, consent, treatment and data acquisition, and potential benefit of post exposure prophylaxis were never tested. Further, contracting between the University of Nottingham and the PIs, GPs and care homes was not completed, so the feasibility of contracting with all the different groups at the scale needed was not tested. + +ConclusionsThe role of post exposure prophylaxis of COVID-19 in care home residents was not tested because of changes in COVID-19 incidence, prevalence and virulence as a consequence of the vaccination programme that rendered the study unfeasible. Significant progress was made in describing and developing the infrastructure necessary for a large scale Clinical Trial of Investigational Medicinal Products in care homes in all four UK nations. + +Future workThe role of post-exposure prophylaxis of COVID-19 in care home residents remains to be defined. Significant logistical barriers to conducting research in care homes during a pandemic need to be removed before such studies are possible in the required short timescale.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2022.08.29.22279333,2022-08-30,https://medrxiv.org/cgi/content/short/2022.08.29.22279333,A case-crossover study of the effect of vaccination on SARS-CoV-2 transmission relevant behaviours during a period of national lockdown in England and Wales,Aimee Serisier; Sarah Beale; Yamina I Boukari; Susan J Hoskins; Vincent Nguyen; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Alexei Yavlinsky; Andrew Hayward; Robert W Aldridge,University College London; University College London; University College London; Univerity College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London,"BackgroundStudies of COVID-19 vaccine effectiveness show increases in COVID-19 cases within 14 days of a first dose, potentially reflecting post-vaccination behaviour changes associated with SARS-CoV-2 transmission before vaccine protection. However, direct evidence for a relationship between vaccination and behaviour is lacking. We aimed to examine the association between vaccination status and self-reported non-household contacts and non-essential activities during a national lockdown in England and Wales. MethodsParticipants (n=1,154) who had received the first dose of a COVID-19 vaccine reported non-household contacts and non-essential activities from February to March 2021 in monthly surveys during a national lockdown in England and Wales. We used a case-crossover study design and conditional logistic regression to examine the association between vaccination status (pre-vaccination vs. 14 days post-vaccination) and self-reported contacts and activities within individuals. Stratified subgroup analyses examined potential effect heterogeneity by sociodemographic characteristics such as sex, household income or age group. @@ -1170,22 +1230,14 @@ ResultsFollowing an initial plateau of 1.54% until mid-January, infection preval ConclusionHigh-resolution prevalence data fitted to P-splines allowed us to show that the lockdown was highly effective at reducing risk of infection with school holidays/closures playing a significant part.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2022.05.23.22275458,2022-05-25,https://medrxiv.org/cgi/content/short/2022.05.23.22275458,Covid-19 is a leading cause of death in children and young people ages 0-19 years in the United States,Seth Flaxman; Charles Whittaker; Elizaveta Semenova; Theo Rashid; Robbie Parks; Alexandra Blenkinsop; H Juliette T Unwin; Swapnil Mishra; Samir Bhatt; Deepti Gurdasani; Oliver Ratmann,"Oxford; Imperial College London; AstraZeneca; Imperial College London; Columbia University; Imperial College London; Imperial College London; University of Copenhagen; University of Copenhagen, Imperial College London; Queen Mary University of London; Imperial College London","Covid-19 has caused more than 1 million deaths in the US, including at least 1,204 deaths among children and young people (CYP) aged 0-19 years, with 796 occurring in the one year period April 1, 2021 - March 31, 2022. Deaths among US CYP are rare in general, and so we argue here that the mortality burden of Covid-19 in CYP is best understood in the context of all other causes of CYP death. Using publicly available data from CDC WONDER on NCHSs 113 Selected Causes of Death, and comparing to mortality in 2019, the immediate pre-pandemic period, we find that Covid-19 mortality is among the 10 leading causes of death in CYP aged 0-19 years in the US, ranking 8th among all causes of deaths, 5th in disease-related causes of deaths (excluding accidents, assault and suicide), and 1st in deaths caused by infectious or respiratory diseases. Covid-19 deaths constitute 2.3% of the 10 leading causes of death in this age group. Covid-19 caused substantially more deaths in CYP than major vaccine-preventable diseases did historically in the period before vaccines became available. Various factors including underreporting and Covid-19s role as a contributing cause of death from other diseases mean that our estimates may understate the true mortality burden of Covid-19. Our findings underscore the public health relevance of Covid-19 to CYP. In the likely future context of sustained SARS-CoV-2 circulation, pharmaceutical and non-pharmaceutical interventions will continue to play an important role in limiting transmission of the virus in CYP and mitigating severe disease.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2022.05.22.22275417,2022-05-23,https://medrxiv.org/cgi/content/short/2022.05.22.22275417,Comparative effectiveness of sotrovimab and molnupiravir for prevention of severe COVID-19 outcomes in non-hospitalised patients: an observational cohort study using the OpenSAFELY platform,Bang Zheng; Amelia CA Green; John Tazare; Helen J Curtis; Louis Fisher; Linda Nab; Anna Schultze; Viyaasan Mahalingasivam; Edward Parker; William J Hulme; Sebastian CJ Bacon; Nicholas J DeVito; Christopher Bates; David Evans; Peter Inglesby; Henry Drysdale; Simon Davy; Jonathan Cockburn; Caroline E Morton; George Hickman; Tom Ward; Rebecca M Smith; John Parry; Frank Hester; Sam Harper; Amir Mehrkar; Rosalind M Eggo; Alex J Walker; Stephen JW Evans; Ian J Douglas; Brian MacKenna; Ben Goldacre; Laurie A Tomlinson,London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Trop. Med.; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; TPP; TPP; University of Oxford; London School of Hygiene & Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine,"ObjectiveTo compare the effectiveness of sotrovimab (a neutralising monoclonal antibody) vs. molnupiravir (an antiviral) in preventing severe COVID-19 outcomes in non-hospitalised high-risk COVID-19 adult patients. - -DesignWith the approval of NHS England, we conducted a real-world cohort study using the OpenSAFELY-TPP platform. - -SettingPatient-level electronic health record data were obtained from 24 million people registered with a general practice in England that uses TPP software. The primary care data were securely linked with data on COVID-19 infection and therapeutics, hospital admission, and death within the OpenSAFELY-TPP platform, covering a period where both medications were frequently prescribed in community settings. - -ParticipantsNon-hospitalised adult COVID-19 patients at high risk of severe outcomes treated with sotrovimab or molnupiravir since December 16, 2021. - -InterventionsSotrovimab or molnupiravir administered in the community by COVID-19 Medicine Delivery Units. +medRxiv,10.1101/2022.05.21.22275368,2022-05-23,https://medrxiv.org/cgi/content/short/2022.05.21.22275368,"Variant-specific symptoms of COVID-19 among 1,542,510 people in England",Matthew Whitaker; Joshua Elliott; Barbara Bodinier; Wendy S Barclay; Helen Ward; Graham Cooke; Christl A Donnelly; Marc Chadeau-Hyam; Paul Elliott,Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London School of Public Health,"Infection with SARS-CoV-2 virus is associated with a wide range of symptoms. The REal-time Assessment of Community Transmission -1 (REACT-1) study has been monitoring the spread and clinical manifestation of SARS-CoV-2 among random samples of the population in England from 1 May 2020 to 31 March 2022. We show changing symptom profiles associated with the different variants over that period, with lower reporting of loss of sense of smell and taste for Omicron compared to previous variants, and higher reporting of cold-like and influenza-like symptoms, controlling for vaccination status. Contrary to the perception that recent variants have become successively milder, Omicron BA.2 was associated with reporting more symptoms, with greater disruption to daily activities, than BA.1. With restrictions lifted and routine testing limited in many countries, monitoring the changing symptom profiles associated with SARS-CoV-2 infection and induced changes in daily activities will become increasingly important.",infectious diseases,fuzzy,96,100 +medRxiv,10.1101/2022.05.19.22275214,2022-05-22,https://medrxiv.org/cgi/content/short/2022.05.19.22275214,Antibody levels following vaccination against SARS-CoV-2: associations with post-vaccination infection and risk factors,Nathan J Cheetham; Milla Kibble; Andrew Wong; Richard J Silverwood; Anika Knuppel; Dylan M Williams; Olivia K L Hamilton; Paul H Lee; Charis Bridger Staatz; Giorgio Di Gessa; Jingmin Zhu; Srinivasa Vittal Katikireddi; George B Ploubidis; Ellen J Thompson; Ruth C E Bowyer; Xinyuan Zhang; Golboo Abbasian; Maria Paz Garcia; Deborah Hart; Jeffrew Seow; Carl Graham; Neophytos Kouphou; Sam Acors; Michael H Malim; Ruth E Mitchell; Kate Northstone; Daniel Major-Smith; Sarah Matthews; Thomas Breeze; Michael Crawford; Lynn Molloy; Alex Siu Fung Kwong; Katie J Doores; Nishi Chaturvedi; Emma L Duncan; Nicholas J Timpson; Claire J Steves,King's College London; University of Cambridge; University College London; University College London; University College London; University College London; University of Glasgow; University of Leicester; University College London; University College London; University College London; University of Glasgow; University College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; King's College London; University College London; King's College London; University of Bristol; King's College London,"SARS-CoV-2 antibody levels can be used to assess humoral immune responses following SARS-CoV-2 infection or vaccination, and may predict risk of future infection. From cross-sectional antibody testing of 9,361 individuals from TwinsUK and ALSPAC UK population-based longitudinal studies (jointly in April-May 2021, and TwinsUK only in November 2021-January 2022), we tested associations between antibody levels following vaccination and: (1) SARS-CoV-2 infection following vaccination(s); (2) health, socio-demographic, SARS-CoV-2 infection and SARS-CoV-2 vaccination variables. -Main outcome measureCOVID-19 related hospitalisation or COVID-19 related death within 28 days after treatment initiation. +Within TwinsUK, single-vaccinated individuals with the lowest 20% of anti-Spike antibody levels at initial testing had 3-fold greater odds of SARS-CoV-2 infection over the next six to nine months, compared to the top 20%. In TwinsUK and ALSPAC, individuals identified as at increased risk of COVID-19 complication through the UK ""Shielded Patient List"" had consistently greater odds (2 to 4-fold) of having antibody levels in the lowest 10%. Third vaccination increased absolute antibody levels for almost all individuals, and reduced relative disparities compared with earlier vaccinations. -ResultsBetween December 16, 2021 and February 10, 2022, 3331 and 2689 patients were treated with sotrovimab and molnupiravir, with no substantial differences in their baseline characteristics. The mean age of all 6020 patients was 52 (SD=16) years; 59% were female, 89% White and 88% had three or more COVID-19 vaccinations. Within 28 days after treatment initiation, 87 (1.4%) COVID-19 related hospitalisations/deaths were observed (32 treated with sotrovimab and 55 with molnupiravir). Cox proportional hazards models stratified by area showed that after adjusting for demographics, high-risk cohort categories, vaccination status, calendar time, body mass index and other comorbidities, treatment with sotrovimab was associated with a substantially lower risk than treatment with molnupiravir (hazard ratio, HR=0.54, 95% CI: 0.33 to 0.88; P=0.014). Consistent results were obtained from propensity score weighted Cox models (HR=0.50, 95% CI: 0.31 to 0.81; P=0.005) and when restricted to fully vaccinated people (HR=0.53, 95% CI: 0.31 to 0.90; P=0.019). No substantial effect modifications by other characteristics were detected (all P values for interaction>0.10). Findings were similar in an exploratory analysis of patients treated between February 16 and May 1, 2022 when the Omicron BA.2 variant was dominant in England. +These findings quantify the association between antibody level and risk of subsequent infection, and support a policy of triple vaccination for the generation of protective antibodies. -ConclusionIn routine care of non-hospitalised high-risk adult patients with COVID-19 in England, those who received sotrovimab were at lower risk of severe COVID-19 outcomes than those receiving molnupiravir.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2022.05.21.22275368,2022-05-23,https://medrxiv.org/cgi/content/short/2022.05.21.22275368,"Variant-specific symptoms of COVID-19 among 1,542,510 people in England",Matthew Whitaker; Joshua Elliott; Barbara Bodinier; Wendy S Barclay; Helen Ward; Graham Cooke; Christl A Donnelly; Marc Chadeau-Hyam; Paul Elliott,Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London School of Public Health,"Infection with SARS-CoV-2 virus is associated with a wide range of symptoms. The REal-time Assessment of Community Transmission -1 (REACT-1) study has been monitoring the spread and clinical manifestation of SARS-CoV-2 among random samples of the population in England from 1 May 2020 to 31 March 2022. We show changing symptom profiles associated with the different variants over that period, with lower reporting of loss of sense of smell and taste for Omicron compared to previous variants, and higher reporting of cold-like and influenza-like symptoms, controlling for vaccination status. Contrary to the perception that recent variants have become successively milder, Omicron BA.2 was associated with reporting more symptoms, with greater disruption to daily activities, than BA.1. With restrictions lifted and routine testing limited in many countries, monitoring the changing symptom profiles associated with SARS-CoV-2 infection and induced changes in daily activities will become increasingly important.",infectious diseases,fuzzy,96,100 +Lay summaryIn this study, we analysed blood samples from 9,361 participants from two studies in the UK: an adult twin registry, TwinsUK (4,739 individuals); and the Avon Longitudinal Study of Parents and Children, ALSPAC (4,622 individuals). We did this work as part of the UK Government National Core Studies initiative researching COVID-19. We measured blood antibodies which are specific to SARS-CoV-2 (which causes COVID-19). Having a third COVID-19 vaccination boosted antibody levels. More than 90% of people from TwinsUK had levels after third vaccination that were greater than the average level after second vaccination. Importantly, this was the case even in individuals on the UK ""Shielded Patient List"". We found that people with lower antibody levels after first vaccination were more likely to report having COVID-19 later on, compared to people with higher antibody levels. People on the UK ""Shielded Patient List"", and individuals who reported that they had poorer general health, were more likely to have lower antibody levels after vaccination. In contrast, people who had had a previous COVID-19 infection were more likely to have higher antibody levels following vaccination compared to people without infection. People receiving the Oxford/AstraZeneca rather than the Pfizer BioNTech vaccine had lower antibody levels after one or two vaccinations. However, after a third vaccination, there was no difference in antibody levels between those who had Oxford/AstraZeneca and Pfizer BioNTech vaccines for their first two doses. These findings support having a third COVID-19 vaccination to boost antibodies.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2022.05.11.22274964,2022-05-16,https://medrxiv.org/cgi/content/short/2022.05.11.22274964,Mental health outcomes following COVID-19 infection: Evidence from 11 UK longitudinal population studies,Ellen J Thompson; Jean Stafford; Bettina Moltrecht; Charlotte F Huggins; Alex S F Kwong; Richard J Shaw; Paola Zaninotto; Kishan Patel; Richard J Silverwood; Eoin McElroy; Matthias Pierce; Michael J Green; Ruth Bowyer; Jane Maddock; Kate Tilling; Srinivasa Vittal Katikireddi; George B Ploubidis; Professor D Porteous; Nicholas J Timpson; Nish Chaturvedi; Claire Steves; Praveetha Patalay,"Department of Twin Research and Genetic Epidemiology Kings College London; MRC Unit for Lifelong Health and Ageing, UCL; Centre for Longitudinal Studies UCL Social Research Institute University College London; Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh; Division of Psychiatry, University of Edinburgh; Population Health Sciences, University of Bristol; MRC/CSO Social & Public Health Sciences Unit, Institute of Health & Wellbeing, University of Glasgow; Department of Epidemiology and Public Health UCL; MRC Unit for Lifelong Health and Ageing UCL; Centre for Longitudinal Studies UCL Social Research Institute University College London; School of Psychology Ulster University; Division of Psychology & Mental Health The University of Manchester; MRC CSO Social and Public Health Sciences Unit University of Glasgow; Department of Twin Research and Genetic Epidemiology King's College London; MRC Unit for Lifelong Health and Ageing UCL; MRC Integrative Epidemiology Unit University of Bristol; MRC CSO Social and Public Health Sciences UnitUniversity of Glasgow; Centre for Longitudinal Studies UCL Social Research Institute University College London; Centre for Genomic and Experimental Medicine University of Edinburgh; MRC Integrative Epidemiology Unit University of Bristol; MRC Unit for Lifelong Health and Ageing UCL; Department of Twin Research and Genetic Epidemiology King's College London; Centre for Longitudinal Studies and MRC Unit for Lifelong Health and Ageing University College London","BackgroundEvidence on associations between COVID-19 illness and mental health is mixed. We examined longitudinal associations between COVID-19 and mental health while considering: 1) pre-pandemic mental health, 2) time since infection; 3) subgroup differences; and 4) confirmation of infection via self-reported test, and serology data. MethodsUsing data from 11 UK longitudinal studies, involving 54,442 participants, with 2 to 8 repeated measures of mental health and COVID-19 between April 2020 and April 2021, we standardised continuous mental health scales within each study across time. We investigated associations between COVID-19 (self-report, test-confirmed, serology-confirmed) and mental health using multilevel generalised estimating equations. We examined whether associations varied by age, sex, ethnicity, education and pre-pandemic mental health. Effect-sizes were pooled in random-effects meta-analyses. @@ -1236,32 +1288,6 @@ In a mixed methods study, we therefore aim to: (1) describe the usual healthcare Methods and analysisA mixed methods study will address our aims. Qualitative data collection from patients and health professionals will be achieved through surveys, interviews and focus group discussions, to understand their experience and document the function of clinics. A patient cohort study will provide an understanding of outcomes and costs of care. Accessible data will be further analysed to understand the nature of Long Covid, and the care received. Ethics and disseminationEthical approval was obtained from South Central - Berkshire Research Ethics Committee (reference 303958). The dissemination plan will be decided by the patient and public involvement and engagement (PPIE) group members and study Co-Is, but will target 1) policy makers, and those responsible for commissioning and delivering Long Covid services, 2) patients and the public, and 3) academics.",health systems and quality improvement,fuzzy,100,100 -medRxiv,10.1101/2022.05.05.22273234,2022-05-07,https://medrxiv.org/cgi/content/short/2022.05.05.22273234,Changes in English medication safety indicators throughout the COVID-19 pandemic: a federated analysis of 57 million patients' primary care records in situ using OpenSAFELY,Louis Fisher; Lisa E M Hopcroft; Sarah Rodgers; James Barrett; Kerry Oliver; Anthony J Avery; Dai Evans; Helen Curtis; Richard Croker; Orla Macdonald; Jessica Morley; Amir Mehrkar; Seb Bacon; Simon Davy; Iain Dillingham; David Evans; George Hickman; Peter Inglesby; Caroline E Morton; Becky Smith; Tom Ward; William Hulme; Amelia Green; Jon Massey; Alex J Walker; Chris Bates; Jonathan Cockburn; John Parry; Frank Hester; Sam Harper; Shaun O'Hanlon; Alex Eavis; Richard Jarvis; Dima Avramov; Paul Griffiths; Aaron Fowles; Nasreen Parkes; Ben Goldacre; Brian MacKenna,"Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; PRIMIS, School of Medicine, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK; PRIMIS, School of Medicine, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK; PRIMIS, School of Medicine, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK; Centre for Academic Primary Care, School of Medicine, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK; PRIMIS, School of Medicine, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA; EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA; EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA; EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA; EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA; EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA; EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG","ObjectiveTo describe the impact of the COVID-19 pandemic on safe prescribing, using the PINCER prescribing indicators; to implement complex prescribing indicators at national scale using GP data. - -DesignPopulation based cohort study, with the approval of NHS England using the OpenSAFELY platform. - -SettingElectronic health record data from 56.8 million NHS patients general practice records. - -ParticipantsAll NHS patients registered at a GP practice using TPP or EMIS computer systems and recorded as at risk of at least one potentially hazardous PINCER indicator between September 2019 and September 2021. - -Main outcome measureMonthly trends and between-practice variation for compliance with 13 PINCER measures between September 2019 and September 2021. - -ResultsThe indicators were successfully implemented across GP data in OpenSAFELY. Hazardous prescribing remained largely unchanged during the COVID-19 pandemic, with only small reductions in achievement of the PINCER indicators. There were transient delays in blood test monitoring for some medications, particularly ACE inhibitors. All indicators exhibited substantial recovery by September 2021. We identified 1,813,058 patients at risk of at least one hazardous prescribing event. - -ConclusionGood performance was maintained during the COVID-19 pandemic across a diverse range of widely evaluated measures of safe prescribing. - -Summary box O_TEXTBOXWHAT IS ALREADY KNOWN ON THIS TOPICO_LIPrimary care services were substantially disrupted by the COVID-19 pandemic. -C_LIO_LIDisruption to safe prescribing during the pandemic has not previously been evaluated. -C_LIO_LIPINCER is a nationally adopted programme of activities that aims to identify and correct hazardous prescribing in GP practices, by conducting manual audit on subgroups of practices. -C_LI - -WHAT THIS STUDY ADDSO_LIFor the first time, we were able to successfully generate data on PINCER indicators for almost the whole population of England, in a single analysis. -C_LIO_LIOur study is the most comprehensive assessment of medication safety during the COVID-19 pandemic in England, covering 95% of the population using well-validated measures. -C_LIO_LIGood performance was maintained across many PINCER indicators throughout the pandemic. -C_LIO_LIDelays in delivering some medication-related blood test monitoring were evident though considerable recovery was made by the end of the study period. -C_LI - -C_TEXTBOX",primary care research,fuzzy,100,100 medRxiv,10.1101/2022.05.03.22274395,2022-05-05,https://medrxiv.org/cgi/content/short/2022.05.03.22274395,Development and evaluation of low-volume tests to detect and characterise antibodies to SARS-CoV-2,Alice Halliday; Anna E Long; Holly E Baum; Amy C Thomas; Kathryn L Shelley; Elizabeth Oliver; Kapil Gupta; Ore Francis; Maia Kavanagh Williamson; Natalie Di Bartolo; Matthew J Randell; Yassin Ben Khoud; Ilana Kelland; Georgina Mortimer; Olivia Ball; Charlie Plumptre; Kyla Chandler; Ulrike Obst; Massimiliano Secchi; Lorenzo Piemonti; Vito Lampasona; Joyce Smith; Michaela Gregorova; Lea Knezevic; Jane Metz; Rachael Barr; Begonia Morales-Aza; Jennifer Oliver; Lucy Collingwood; Benjamin Hitchings; Susan Ring; Linda Wooldridge; Laura Rivino; Nicholas J Timpson; Jorgen McKernon; Peter Muir; Fergus W Hamilton; David Arnold; Derek N Woolfson; Anu Goenka; Andrew D Davidson; Ashley Mark Toye; Imre Berger; Mick Bailey; Kathleen M Gillespie; Alistair JK Williams; Adam Finn,"University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; IRCCS Ospedale San Raffaele; IRCCS Ospedale San Raffaele; IRCCS Ospedale San Raffaele; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; National Infection Service, UK Health Security Agency, Southmead Hospital, Bristol, UK; National Infection Service, UK Health Security Agency, Southmead Hospital, Bristol, UK; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol","Low-volume antibody assays can be used to track SARS-CoV-2 infection rates in settings where active testing for virus is limited and remote sampling is optimal. We developed 12 ELISAs detecting total or antibody isotypes to SARS-CoV-2 nucleocapsid, spike protein or its receptor binding domain (RBD), 3 anti-RBD isotype specific luciferase immunoprecipitation system (LIPS) assays and a novel Spike-RBD bridging LIPS total-antibody assay. We utilised pre-pandemic (n=984) and confirmed/suspected recent COVID-19 sera taken pre-vaccination rollout in 2020 (n=269). Assays measuring total antibody discriminated best between pre-pandemic and COVID-19 sera and were selected for diagnostic evaluation. In the blind evaluation, two of these assays (Spike Pan ELISA and Spike-RBD Bridging LIPS assay) demonstrated >97% specificity and >92% sensitivity for samples from COVID- 19 patients taken >21 days post symptom onset or PCR test. These assays offered better sensitivity for the detection of COVID-19 cases than a commercial assay which requires 100-fold larger serum volumes. This study demonstrates that low-volume in- house antibody assays can provide good diagnostic performance, and highlights the importance of using well-characterised samples and controls for all stages of assay development and evaluation. These cost-effective assays may be particularly useful for seroprevalence studies in low and middle-income countries.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2022.05.03.22274602,2022-05-03,https://medrxiv.org/cgi/content/short/2022.05.03.22274602,Accident and emergency (AE) attendance in England following infection with SARS-CoV-2 Omicron or Delta,Daniel J Grint; Kevin Wing; Hamish P Gibbs; Stephen JW Evans; Elizabeth J Williamson; Krishnan Bhaskaran; Helen I McDonald; Alex J Walker; David Evans; George Hickman; Rohini Mathur; Anna Schultze; Christopher T Rentsch; John Tazare; Ian J Douglas; Helen J Curtis; Caroline E Morton; Sebastian CJ Bacon; Simon Davy; Brian MacKenna; Peter Inglesby; Richard Croker; John Parry; Frank Hester; Sam Harper; Nicholas J DeVito; William J Hulme; Christopher Bates; Jonathan Cockburn; Amir Mehrkar; Ben Goldacre; Rosalind M Eggo; Laurie Tomlinson,London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; TPP; TPP; University of Oxford; University of Oxford; TPP; TPP; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine,"The SARS-CoV-2 Omicron variant is increasing in prevalence around the world. Accurate estimation of disease severity associated with Omicron is critical for pandemic planning. We found lower risk of accident and emergency (AE) attendance following SARS-CoV-2 infection with Omicron compared to Delta (HR: 0.39 (95% CI: 0.30 - 0.51; P<.0001). For AE attendances that lead to hospital admission, Omicron was associated with an 85% lower hazard compared with Delta (HR: 0.14 (95% CI: 0.09 - 0.24; P<.0001)). @@ -1475,8 +1501,16 @@ ResultsThe baseline model (without any interventions) showed different workplace ConclusionThis work suggests that, without interventions, significant transmission could have occured in these workplaces, but that these posed minimal risk to customers. We found that identifying and isolating regular close-contacts of infectious individuals (i.e. house-share, carpools, or delivery pairs) is an efficient measure for stopping workplace outbreaks. Regular testing can make these isolation measures even more effective but also increases the number of staff isolating at one time. It is therefore more efficient to use these isolation measures in addition to social distancing and contact reduction interventions, rather than instead of, as these reduce both transmission and the number of people needing to isolate at one time. Author summaryDuring the COVID-19 pandemic the home-delivery sector was vital to maintaining peoples access to certain goods, and sustaining levels of economic activity for a variety of businesses. However, this important work necessarily involved contact with a large number of customers as well as colleagues. This means that questions have often been raised about whether enough was being done to keep customers and staff safe. Estimating the potential risk to customers and staff is complex, but here we tackle this problem by building a model of workplace and customer contacts, from which we simulate SARS-CoV-2 transmission. By involving industry representatives in the development of this model, we have simulated interventions that have either been applied or considered, and so the findings of this study are relevant to decisions made in that sector. Furthermore, we can learn generic lessons from this specific case study which apply to many types of shared workplace as well as highlighting implications of the highly stochastic nature of disease transmission in small populations.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2022.03.17.22272535,2022-03-18,https://medrxiv.org/cgi/content/short/2022.03.17.22272535,Comparison of the 2021 COVID-19 'Roadmap' Projections against Public Health Data,Matt J Keeling; Louise J Dyson; Michael Tildesley; Edward M Hill; Sam M Moore,University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick,"Control and mitigation of the COVID-19 pandemic in England has relied on a combination of vaccination and non-pharmaceutical interventions (NPIs). Some of these NPIs are extremely costly (economically and socially), so it was important to relax these promptly without overwhelming already burdened health services. The eventual policy was a Roadmap of four relaxation steps throughout 2021, taking England from lock-down to the cessation of all restrictions on social interaction. In a series of six Roadmap documents generated throughout 2021, models assessed the potential risk of each relaxation step. Here we show that the model projections generated a reliable estimation of medium-term hospital admission trends, with the data points up to September 2021 generally lying within our 95% prediction intervals. The greatest uncertainties in the modelled scenarios came from vaccine efficacy estimates against novel variants, and from assumptions about human behaviour in the face of changing restrictions and risk.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2022.03.15.22272362,2022-03-16,https://medrxiv.org/cgi/content/short/2022.03.15.22272362,Community-level characteristics of COVID-19 vaccine hesitancy in England: A nationwide cross-sectional study,Georges Bucyibaruta; Marta Blangialdo; Garyfallos Konstantinoudis,Imperial College London; Imperial College London; Imperial College London,"One year after the start of the COVID-19 vaccination programme in England, more than 43 million people older than 12 years old had received at least a first dose. Nevertheless, geographical differences persist, and vaccine hesitancy is still a major public health concern; understanding its determinants is crucial to managing the COVID-19 pandemic and preparing for future ones. In this cross-sectional population-based study we used cumulative data on the first dose of vaccine received by 01-01-2022 at Middle Super Output Area level in England. We used Bayesian hierarchical spatial models and investigated if the geographical differences in vaccination uptake can be explained by a range of community-level characteristics covering socio-demographics, political view, COVID-19 health risk awareness and targeting of high risk groups and accessibility. Deprivation is the covariate most strongly associated with vaccine uptake (Odds Ratio 0.55, 95%CI 0.54-0.57; most versus least deprived areas). The most ethnically diverse areas have a 38% (95%CI 36-40%) lower odds of vaccine uptake compared with those least diverse. Areas with the highest proportion of population between 12 and 24 years old had lower odds of vaccination (0.87, 95%CI 0.85-0.89). Finally increase in vaccine accessibility is associated with higher COVID-19 uptake (OR 1.07, 95%CI 1.03-1.12). Our results suggest that one year after the start of the vaccination programme, there is still evidence of inequalities in uptake, affecting particularly minorities and marginalised groups. Strategies including prioritising active outreach across communities and removing practical barriers and factors that make vaccines less accessible are needed to level up the differences.",epidemiology,fuzzy,94,100 +medRxiv,10.1101/2022.03.14.22272283,2022-03-14,https://medrxiv.org/cgi/content/short/2022.03.14.22272283,Migrants' primary care utilisation before and during the COVID-19 pandemic in England: An interrupted time series,Claire X Zhang; Yamina Boukari; Neha Pathak; Rohini Mathur; Srinivasa Vittal Katikireddi; Parth Patel; Inês Campos-Matos; Dan Lewer; Vincent Nguyen; Greg Hugenholtz; Rachel Burns; Amy R Mulick; Alasdair Henderson; Robert W Aldridge,UCL; University College London; University College London; London School of Hygiene and Tropical Medicine; University of Glasgow; University College London; Department of Health and Social Care; University College London; University College London; University College London; University College London; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; UCL,"BackgroundHow international migrants access and use primary care in England is poorly understood. We aimed to compare primary care consultation rates between international migrants and non-migrants in England before and during the COVID-19 pandemic (2015- 2020). + +MethodsUsing linked data from the Clinical Practice Research Datalink (CPRD) GOLD and the Office for National Statistics, we identified migrants using country-of-birth, visa-status or other codes indicating international migration. We ran a controlled interrupted time series (ITS) using negative binomial regression to compare rates before and during the pandemic. + +FindingsIn 262,644 individuals, pre-pandemic consultation rates per person-year were 4.35 (4.34-4.36) for migrants and 4.6 (4.59-4.6) for non-migrants (RR:0.94 [0.92-0.96]). Between 29 March and 26 December 2020, rates reduced to 3.54 (3.52-3.57) for migrants and 4.2 (4.17-4.23) for non-migrants (RR:0.84 [0.8-0.88]). Overall, this represents an 11% widening of the pre-pandemic difference in consultation rates between migrants and non-migrants during the first year of the pandemic (RR:0.89, 95%CI:0.84-0.94). This widening was greater for children, individuals whose first language was not English, and individuals of White British, White non-British and Black/African/Caribbean/Black British ethnicities. + +InterpretationMigrants were less likely to use primary care before the pandemic and the first year of the pandemic exacerbated this difference. As GP practices retain remote and hybrid models of service delivery, they must improve services and ensure they are accessible and responsive to migrants healthcare needs. + +FundingThis study was funded by the Medical Research Council (MR/V028375/1) and Wellcome Clinical Research Career Development Fellowship (206602).",primary care research,fuzzy,100,100 medRxiv,10.1101/2022.03.10.22272177,2022-03-13,https://medrxiv.org/cgi/content/short/2022.03.10.22272177,The Omicron SARS-CoV-2 epidemic in England during February 2022,Marc Chadeau-Hyam; David Tang; Oliver Eales; Barbara Bodinier; Haowei Wang; Jakob Jonnerby; Matthew Whitaker; Joshua Elliott; David Haw; Caroline E. Walters; Christina Atchinson; Peter J. Diggle; Andrew J. Page; Deborah Ashby; Wendy Barclay; Graham Taylor; Graham Cooke; Helen Ward; Ara Darzi; Christl A Donnelly; Paul Elliott,"School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UK; Imperial College Healthcare NHS Trust, UKDepartment of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; Quadram Institute, Norwich, UK; School of Public Health, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical; School of Public Health, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research; Imperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research Centre, UKInstitute of Global Health Innovation at ; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research","BackgroundThe third wave of COVID-19 in England peaked in January 2022 resulting from the rapid transmission of the Omicron variant. However, rates of hospitalisations and deaths were substantially lower than in the first and second waves MethodsIn the REal-time Assessment of Community Transmission-1 (REACT-1) study we obtained data from a random sample of 94,950 participants with valid throat and nose swab results by RT-PCR during round 18 (8 February to 1 March 2022). @@ -1507,6 +1541,31 @@ Research in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed, Added value of this studyThis study is among the first to provide a detailed analysis of a wide range of risk factors for breakthrough SARS-CoV-2 infection, both after the primary course of vaccination and after a booster dose. Our large study size and detailed data have allowed us to investigate associations with various sociodemographic, clinical, pharmacological, and nutritional factors. Monthly follow-up data have additionally given us the opportunity to consider the effects of behaviours that may have changed across the pandemic, while adjusting for local SARS-CoV-2 incidence. Implications of all the available evidenceOur findings add to growing evidence that risk factors for SARS-CoV-2 infection after primary or booster vaccinations can differ to those in unvaccinated populations, with effects attenuated for previously observed risk factors such as body-mass index and Asian ethnicity. The clear difference we observed between the efficacies of ChAdOx1 and BNT162b2 as the primary course of vaccination appears to have been reduced by the use of BNT162b2 boosters, but not by mNRA-1273 boosters. As more countries introduce booster vaccinations, future population-based studies with longer follow-up will be needed to investigate our findings further.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2022.03.13.22272176,2022-03-13,https://medrxiv.org/cgi/content/short/2022.03.13.22272176,Vaccination against SARS-CoV-2 in UK school-aged children and young people decreases infection rates and reduces COVID-19 symptoms,Erika Molteni; Liane S Canas; Kerstin Klaser; Jie Deng; Sunil S Bhopal; Robert C Hughes; Liyuan Chen; Benjamin Murray; Eric Kerfoot; Michela Antonelli; Carole Helene Sudre; Joan Capdevila Pujol; Lorenzo Polidori; Anna May; Alexander Hammers; Jonathan Wolf; Timothy Spector; Claire J Steves; Sebastien Ourselin; Michael Absoud; Marc Modat; Emma L Duncan,"King's College London; King's College London; King's College London; King's College London; Newcastle University; London School of Hygiene & Tropical Medicine, London; King's College London; King's College London; King's College London; King's College London; King's College London; Zoe Limited, London, UK; Zoe Limited, London, UK; Zoe Limited, London, UK; King's College London; Zoe Limited, London, UK; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London","BackgroundWe aimed to explore the effectiveness of one-dose BNT162b2 vaccination upon SARS-CoV-2 infection, its effect on COVID-19 presentation, and post-vaccination symptoms in children and young people (CYP) in the UK during periods of Delta and Omicron variant predominance. + +MethodsIn this prospective longitudinal cohort study, we analysed data from 115,775 CYP aged 12-17 years, proxy-reported through the Covid Symptom Study (CSS) smartphone application. We calculated post-vaccination infection risk after one dose of BNT162b2, and described the illness profile of CYP with post-vaccination SARS- CoV-2 infection, compared to unvaccinated CYP, and post-vaccination side-effects. + +FindingsBetween August 5, 2021 and February 14, 2022, 25,971 UK CYP aged 12-17 years received one dose of BNT162b2 vaccine. Vaccination reduced (proxy-reported) infection risk (-80{middle dot}4% and -53{middle dot}7% at 14-30 days with Delta and Omicron variants respectively, and -61{middle dot}5% and -63{middle dot}7% after 61-90 days). The probability of remaining infection-free diverged soon after vaccination, and was greater in CYP with prior SARS-CoV-2 infection. Vaccinated CYP who contracted SARS-CoV-2 during the Delta period had milder disease than unvaccinated CYP; during the Omicron period this was only evident in children aged 12-15 years. Overall disease profile was similar in both vaccinated and unvaccinated CYP. Post-vaccination local side-effects were common, systemic side-effects were uncommon, and both resolved quickly. + +InterpretationOne dose of BNT162b2 vaccine reduced risk of SARS-CoV-2 infection for at least 90 days in CYP aged 12-17 years. Vaccine protection varied for SARS-CoV-2 variant type (lower for Omicron than Delta variant), and was enhanced by pre-vaccination SARS-CoV-2 infection. Severity of COVID-19 presentation after vaccination was generally milder, although unvaccinated CYP also had generally mild disease. Overall, vaccination was well-tolerated. + +FundingUK Government Department of Health and Social Care, Chronic Disease Research Foundation, The Wellcome Trust, UK Engineering and Physical Sciences Research Council, UK Research and Innovation London Medical Imaging & Artificial Intelligence Centre for Value Based Healthcare, UK National Institute for Health Research, UK Medical Research Council, British Heart Foundation and Alzheimers Society, and ZOE Limited. + +Research in context + +Evidence before this studyWe searched PubMed database for peer-reviewed articles and medRxiv for preprint papers, published between January 1, 2021 and February 15, 2022 using keywords (""SARS-CoV-2"" OR ""COVID-19"") AND (child* OR p?ediatric* OR teenager*) AND (""vaccin*"" OR ""immunization campaign"") AND (""efficacy"" OR ""effectiveness"" OR ""symptoms"") AND (""delta"" or ""omicron"" OR ""B.1.617.2"" OR ""B.1.1.529""). The PubMed search retrieved 36 studies, of which fewer than 30% specifically investigated individuals <18 years. + +Eleven studies explored SARS-CoV-2 viral transmission: seroprevalence in children (n=4), including age-dependency of susceptibility to SARS-CoV-2 infection (n=1), SARS-CoV-2 transmission in schools (n=5), and the effect of school closure on viral transmission (n=1). + +Eighteen documents reported clinical aspects, including manifestation of infection (n=13), symptomatology, disease duration, and severity in children. Other studies estimated emergency department visits, hospitalization, need for intensive care, and/or deaths in children (n=4), and explored prognostic factors (n=1). + +Thirteen studies explored vaccination-related aspects, including vaccination of children within specific paediatric co-morbidity groups (e.g., children with Down syndrome, inflammatory bowel disease, and cancer survivors, n=4), mRNA vaccine efficacy in children and adolescents from the general population (n=7), and the relation between vaccination and severity of disease and hospitalization cases (n=2). Four clinical trials were conducted using mRNA vaccines in minors, also exploring side effects. Sixty percent of children were found to have side effects after BNT162b2 vaccination, and especially after the second dose; however, most symptoms were mild and transient apart from rare uncomplicated skin ulcers. Two studies focused on severe adverse effects and safety of SARS-CoV-2 vaccines in children, reporting on myocarditis episodes and two cases of Guillain-Barre syndrome. All other studies were beyond the scope of our research. + +Added value of this studyWe assessed multiple components of the UK vaccination campaign in a cohort of children and young people (CYP) aged 12-17 years drawn from a large UK community-based citizen-science study, who received a first dose of BNT162b2 vaccine. We describe a variant-dependent protective effect of the first dose against both Delta and Omicron, with additional protective effect of pre-vaccination SARS- CoV-2 infection on post-vaccination re-infection. We compare the illness profile in CYP infected post-vaccination with that of unvaccinated CYP, demonstrating overall milder disease with fewer symptoms for vaccinated CYP. We describe local and systemic side-effects during the first week following first-dose vaccination, confirming that local symptoms are common, systemic symptoms uncommon, and both usually transient. + +Implications of all the available evidenceOur data confirm that first dose BNT162b2 vaccination in CYP reduces risk of infection by SARS-CoV-2 variants, with generally local and brief side-effects. If infected after vaccination, COVID-19 is milder, if manifest at all. The study aims to contribute quantitative evidence to the risk-benefit evaluation of vaccination in CYP to inform discussion regarding rationale for their vaccination and the designing of national immunisation campaigns for this age group; and applies citizen-science approaches in the conduct of epidemiological surveillance and data collection in the UK community. + +Importantly, this study was conducted during Delta and Omicron predominance in UK; specificity of vaccine efficacy to variants is also illustrated; and results may not be generalizable to future SARS-CoV-2 strains.",epidemiology,fuzzy,94,100 medRxiv,10.1101/2022.03.10.22272081,2022-03-12,https://medrxiv.org/cgi/content/short/2022.03.10.22272081,Interstitial lung damage following COVID-19 hospitalisation: an interim analysis of the UKILD Post-COVID study.,I Stewart; J Jacob; PM George; PL Molyneaux; JC Porter; RJ Allen; JK Baillie; SL Barratt; P Beirne; SM Bianchi; JF Blaikley; J Chalmers; RC Chambers; N Chadhuri; C Coleman; G Collier; EK Denneny; A Docherty; O Elneima; RA Evans; L Fabbri; MA Gibbons; FV Gleeson; B Gooptu; NJ Greening; B Guillen Guio; IP Hall; NA Hanley; V Harris; E Harrison; M Heightman; TE Hillman; A Horsley; L Houchen-Wolloff; I Jarrold; SR Johnson; MG Jones; F Khan; R Lawson; OC Leavy; N Lone; M Marks; H McAuley; P Mehta; E Omer; D Parekh; K Piper Hanley; M Plate; J Pearl; K Poinasamy; JK Quint; B Raman; M Richardson; P Rivera-Ortega; L Saunders; R Saunders; MG Semple; M Sereno; A Shikotra; AJ Simpson; A Singapuri; DJF Smith; M Spears; LG Spencer; S Stanel; D Thickett; AAR Thompson; M Thorpe; R Thwaites; SLF Walsh; S Walker; ND Weatherley; M Weeks; JM Wild; DG Wootton; CE Brightling; LP Ho; LV Wain; RG Jenkins,"National Heart & Lung Institute, Imperial College London; Respiratory Medicine, University College London; Royal Brompton and Harefield NHS Foundation Trust; National Heart & Lung Institute, Imperial College London; University College London; University of Leicester; University of Edinburgh; North Bristol NHS Trust; Leeds Teaching Hospitals & University of Leeds; Sheffield Teaching Hospitals NHS Foundation Trust; University of Manchester; University of Dundee; Respiratory Medicine, University College London; University of Manchester; University of Nottingham; University of Sheffield; University College London; University of Edinburgh; University Hospitals of Leicester NHS Trust; University Hospitals of Leicester NHS Trust; National Heart & Lung Institute, Imperial College London; Royal Devon and Exeter NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; University of Leicester; University of Leicester; University of Leicester; University of Nottingham; University of Manchester; University Hospitals of Leicester NHS Trust; University of Edinburgh; University College London Hospital; University College London Hospital; University of Manchester; University Hospitals of Leicester NHS Trust; Asthma UK British Lung Foundation; University of Nottingham; Faculty of Medicine, University of Southampton; University of Nottingham; Sheffield Teaching Hospitals NHS Foundation Trust; University of Leicester; Usher Institute, University of Edinburgh; University College London Hospital; University of Leicester; University College London Hospital; University of Leicester; University of Birmingham; University of Manchester; University College London Hospital; University of Leicester; British Lung Foundation; National Heart & Lung Institute, Imperial College London; University of Oxford; University of Leicester; University of Manchester; University of Sheffield; University of Leicester; Liverpool University; University of Leicester; University Hospitals of Leicester NHS Trust; Newcastle University; University of Leicester; Royal Brompton and Harefield NHS Foundation Trust; Perth Royal Infirmary, NHS Tayside; Liverpool University Hospitals NHS Foundation Trust; University of Manchester; University of Birmingham; University of Sheffield; University of Edinburgh; National Heart & Lung Institute, Imperial College London; National Heart & Lung Institute, Imperial College London; Sheffield Teaching NHS Foundation Trust; Sheffield Teaching NHS Foundation Trust; National Heart & Lung Institute, Imperial College London; Sheffield Teaching NHS Foundation Trust; University of Liverpool; University Hospitals of Leicester NHS Trust; University of Oxford; University of Leicester; National Heart & Lung Institute, Imperial College London","IntroductionShared characteristics between COVID-19 and pulmonary fibrosis, including symptoms, genetic architecture, and circulating biomarkers, suggests interstitial lung disease (ILD) development may be associated with SARS-CoV-2 infection. MethodsThe UKILD Post-COVID study planned interim analysis was designed to stratify risk groups and estimate the prevalence of Post-COVID Interstitial Lung Damage (ILDam) using the Post-HOSPitalisation COVID-19 (PHOSP-COVID) Study. Demographics, radiological patterns and missing data were assessed descriptively. Bayes binomial regression was used to estimate the risk ratio of persistent lung damage >10% involvement in linked, clinically indicated CT scans. Indexing thresholds of percent predicted DLco, chest X-ray findings and severity of admission were used to generate risk strata. Number of cases within strata were used to estimate the amount of suspected Post-COVID ILDam. @@ -1753,7 +1812,6 @@ Method and FindingsThis multi-phase, prospective mixed-methods study took place ConclusionsThe SBQ-LC is a comprehensive patient-reported assessment of Long COVID symptom burden developed using modern psychometric methods. It measures symptoms of Long COVID important to individuals with lived experience and may be used to evaluate the impact of interventions and inform best practice in clinical management.",health informatics,fuzzy,100,100 medRxiv,10.1101/2022.01.13.22268948,2022-01-14,https://medrxiv.org/cgi/content/short/2022.01.13.22268948,Algorithmic Fairness and Bias Mitigation for Clinical Machine Learning: Insights from Rapid COVID-19 Diagnosis by Adversarial Learning,Jenny Yang; Andrew AS Soltan; Yang Yang; David A Clifton,The University of Oxford; University of Oxford; The University of Oxford; The University of Oxford,"Machine learning is becoming increasingly prominent in healthcare. Although its benefits are clear, growing attention is being given to how machine learning may exacerbate existing biases and disparities. In this study, we introduce an adversarial training framework that is capable of mitigating biases that may have been acquired through data collection or magnified during model development. For example, if one class is over-presented or errors/inconsistencies in practice are reflected in the training data, then a model can be biased by these. To evaluate our adversarial training framework, we used the statistical definition of equalized odds. We evaluated our model for the task of rapidly predicting COVID-19 for patients presenting to hospital emergency departments, and aimed to mitigate regional (hospital) and ethnic biases present. We trained our framework on a large, real-world COVID-19 dataset and demonstrated that adversarial training demonstrably improves outcome fairness (with respect to equalized odds), while still achieving clinically-effective screening performances (NPV>0.98). We compared our method to the benchmark set by related previous work, and performed prospective and external validation on four independent hospital cohorts. Our method can be generalized to any outcomes, models, and definitions of fairness.",health informatics,fuzzy,100,100 -medRxiv,10.1101/2022.01.05.21268323,2022-01-06,https://medrxiv.org/cgi/content/short/2022.01.05.21268323,Lineage replacement and evolution captured by the United Kingdom Covid Infection Survey,Katrina A Lythgoe; Tanya Golubchik; Matthew Hall; Thomas House; Roberto Cahuantzi; George MacIntyre-Cockett; Helen Fryer; Laura Thomson; Anel Nurtay; Mahan Ghafari; David Buck; Angie Green; Amy Trebes; Paolo Piazza; Lorne J Lonie; Ruth Studley; Emma Rourke; Darren Smith; Matthew Bashton; Andrew Nelson; Matthew Crown; Clare McCann; Gregory R Young; Rui Andre Nunes de Santos; Zack Richards; Adnan Tariq; - Wellcome Sanger Institute COVID-19 Surveillance Team; - COVID-19 Infection Survey Group; - The COVID-19 Genomics UK (COG-UK) consortium; Christophe Fraser; Ian Diamond; Jeff Barrett; Ann Sarah Walker; David Bonsall,University of Oxford; University of Oxford; University of Oxford; University of Manchester; University of Manchester; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Wellcome Sanger Institute; Office for National Statistics; ; University of Oxford; Office for National Statistics; Wellcome Sanger Institute; University of Oxford; University of Oxford,"The Office for National Statistics COVID-19 Infection Survey (ONS-CIS) is the largest surveillance study of SARS-CoV-2 positivity in the community, and collected data on the United Kingdom (UK) epidemic from April 2020 until March 2023 before being paused. Here, we report on the epidemiological and evolutionary dynamics of SARS-CoV-2 determined by analysing the sequenced samples collected by the ONS-CIS during this period. We observed a series of sweeps or partial sweeps, with each sweeping lineage having a distinct growth advantage compared to their predecessors. The sweeps also generated an alternating pattern in which most samples had either S-gene target failure (SGTF) or non- SGTF over time. Evolution was characterised by steadily increasing divergence and diversity within lineages, but with step increases in divergence associated with each sweeping major lineage. This led to a faster overall rate of evolution when measured at the between-lineage level compared to within lineages, and fluctuating levels of diversity. These observations highlight the value of viral sequencing integrated into community surveillance studies to monitor the viral epidemiology and evolution of SARS-CoV-2, and potentially other pathogens, particularly in the current phase of the pandemic with routine RT-PCR testing now ended in the community.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2022.01.01.21268131,2022-01-05,https://medrxiv.org/cgi/content/short/2022.01.01.21268131,Bayesian Estimation of real-time Epidemic Growth Rates using Gaussian Processes: local dynamics of SARS-CoV-2 in England,Laura Marcela Guzman Rincon; Edward M Hill; Louise Dyson; Michael J Tildesley; Matt J Keeling,University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick,"Quantitative assessments of the recent state of an epidemic and short-term projections into the near future are key public health tools that have substantial policy impacts, helping to determine if existing control measures are sufficient or need to be strengthened. Key to these quantitative assessments is the ability to rapidly and robustly measure the speed with which the epidemic is growing or decaying. Frequently, epidemiological trends are addressed in terms of the (time-varying) reproductive number R. Here, we take a more parsimonious approach and calculate the exponential growth rate, r, using a Bayesian hierarchical model to fit a Gaussian process to the epidemiological data. We show how the method can be employed when only case data from positive tests are available, and the improvement gained by including the total number of tests as a measure of heterogeneous testing effort. Although the methods are generic, we apply them to SARS-CoV-2 cases and testing in England, making use of the available high-resolution spatio-temporal data to determine long-term patterns of national growth, highlight regional growth and spatial heterogeneity.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.12.31.21268587,2022-01-02,https://medrxiv.org/cgi/content/short/2021.12.31.21268587,"The adverse impact of COVID-19 pandemic on cardiovascular disease prevention and management in England, Scotland and Wales: A population-scale descriptive analysis of trends in medication data",Caroline E Dale; Rohan Takhar; Ray Carragher; Fatemeh Torabi; Michalis Katsoulis; Stephen Duffield; Seamus Kent; Tanja Mueller; Amanj Kurdi; Stuart McTaggart; Hoda Abbasizanjani; Sam Hollings; Andrew Scourfield; Ronan Lyons; Rowena Griffiths; Jane Lyons; Gareth Davies; Dan Harris; Alex Handy; Mehrdad Alizadeh Mizani; Chris Tomlinson; Mark Ashworth; Spiros Denaxas; Amitava Banerjee; Jonathan Sterne; Kate Lovibond; Paul Brown; Ian Bullard; Rouven Priedon; Mamas A Mamas; Ann Slee; Paula Lorgelly; Munir Pirmohamed; Kamlesh Khunti; Naveed Sattar; Andrew Morris; Cathie Sudlow; Ashley Akbari; Marion Bennie; Reecha Sofat; - CVD-COVID-UK Consortium,"Institute of Health Informatics Research, University College London; Institute of Health Informatics Research, University College London; Strathclyde Institute of Pharmacy & Biomedical Sciences, University of Strathclyde; Swansea University; Institute of Health Informatics Research, University College London; NICE; NICE; University of Strathclyde; Strathclyde Institute of Pharmacy & Biomedical Sciences, University of Strathclyde; Public Health Scotland; Swansea University; NHS Digital, Leeds; UCLH NHS Foundation Trust; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Institute of Health Informatics Research, University College London; Institute of Health Informatics Research, University College London; Institute of Health Informatics Research, University College London; King's College London; Institute of Health Informatics Research, University College London; University College London; University of Bristol; Royal College of Physicians; NHS Digital, Leeds; NHS Digital; British Heart Foundation Data Science Centre, Health Data Research UK, London; Keele University; NHSX; Department of Applied Health Research, University College London; University of Liverpool; University of Leicester; University of Glasgow; Health Data Research UK; British Heart Foundation Data Science Centre, Health Data Research UK, London; Swansea University; University of Strathclyde; Institute of Health Informatics Research, University College London; ","ObjectivesTo estimate the impact of the COVID-19 pandemic on cardiovascular disease (CVD) and CVD management using routinely collected medication data as a proxy. @@ -1800,6 +1858,15 @@ Research in context panelO_ST_ABSEvidence before the studyC_ST_ABSThis study was Added value of this studyWe developed and validated two COVID-19 specific risk prediction scores. One to be used in the initial remote assessment of patients with acute COVID-19 to assess need for monitoring (RECAP-GP). The second one to assess the need for further treatment escalation and includes peripheral saturation of oxygen among the model predictors (RECAP-O2). To our knowledge, this is the first COVID-19 specific risk prediction score to assess and monitor COVID-19 patients risk of deterioration remotely. This will be a valuable resource to complement the use of oximetry in the community clinical decision-making when assessing a patient with acute COVID-19. Implications of all available evidenceTo manage pandemic waves and their demand on healthcare, acute COVID-19 patients require close monitoring in the community and prompt escalation of their treatment. Guidance available so far relies on unvalidated tools and clinician judgement to assess deterioration. COVID-19 specific community-based risk prediction scores such as RECAP may contribute to reducing the uncertainty in the assessment and monitoring of COVID-19 patients, increase safety in clinical practice and improve outcomes by facilitating appropriate treatment escalation.",primary care research,fuzzy,100,100 +medRxiv,10.1101/2021.12.22.21268252,2021-12-24,https://medrxiv.org/cgi/content/short/2021.12.22.21268252,Rapid increase in Omicron infections in England during December 2021: REACT-1 study,Paul Elliott; Barbara Bodinier; Oliver Eales; Haowei Wang; David Haw; Joshua Elliott; Matthew Whitaker; Jakob Jonnerby; David Tang; Caroline E. Walters; Christina Atchinson; Peter J. Diggle; Andrew J. Page; Alex Trotter; Deborah Ashby; Wendy Barclay; Graham Taylor; Helen Ward; Ara Darzi; Graham Cooke; Marc Chadeau-Hyam; Christl A Donnelly,"School of Public Health, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; Imperial College London; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; Imperial College London; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; Quadram Institute, Norwich, UK; Quadram Institute Bioscience; School of Public Health, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research; Imperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research Centre, UKInstitute of Global Health Innovation at ; Department of Infectious Disease, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency","BackgroundThe highest-ever recorded numbers of daily severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in England has been observed during December 2021 and have coincided with a rapid rise in the highly transmissible Omicron variant despite high levels of vaccination in the population. Although additional COVID-19 measures have been introduced in England and internationally to contain the epidemic, there remains uncertainty about the spread and severity of Omicron infections among the general population. + +MethodsThe REal-time Assessment of Community Transmission-1 (REACT-1) study has been monitoring the prevalence of SARS-CoV-2 infection in England since May 2020. REACT-1 obtains self-administered throat and nose swabs from a random sample of the population of England at ages 5 years and over. Swabs are tested for SARS-CoV-2 infection by reverse transcription polymerase chain reaction (RT-PCR) and samples testing positive are sent for viral genome sequencing. To date 16 rounds have been completed, each including [~]100,000 or more participants with data collected over a period of 2 to 3 weeks per month. Socio-demographic, lifestyle and clinical information (including previous history of COVID-19 and symptoms prior to swabbing) is collected by online or telephone questionnaire. Here we report results from round 14 (9-27 September 2021), round 15 (19 October - 05 November 2021) and round 16 (23 November - 14 December 2021) for a total of 297,728 participants with a valid RT-PCR test result, of whom 259,225 (87.1%) consented for linkage to their NHS records including detailed information on vaccination (vaccination status, date). We used these data to estimate community prevalence and trends by age and region, to evaluate vaccine effectiveness against infection in children ages 12 to 17 years, and effect of a third (booster) dose in adults, and to monitor the emergence of the Omicron variant in England. + +ResultsWe observed a high overall prevalence of 1.41% (1.33%, 1.51%) in the community during round 16. We found strong evidence of an increase in prevalence during round 16 with an estimated reproduction number R of 1.13 (1.06, 1.09) for the whole of round 16 and 1.27 (1.14, 1.40) when restricting to observations from 1 December onwards. The reproduction number in those aged 18-54 years was estimated at 1.23 (1.14, 1.33) for the whole of round 16 and 1.41 (1.23, 1.61) from 1 December. Our data also provide strong evidence of a steep increase in prevalence in London with an estimated R of 1.62 (1.34, 1.93) from 1 December onwards and a daily prevalence reaching 6.07% (4.06%, 9.00%) on 14 December 2021. As of 1 to 11 December 2021, of the 275 lineages determined, 11 (4.0%) corresponded to the Omicron variant. The first Omicron infection was detected in London on 3 December, and subsequent infections mostly appeared in the South of England. The 11 Omicron cases were all aged 18 to 54 years, double-vaccinated (reflecting the large numbers of people who have received two doses of vaccine in this age group) but not boosted, 9 were men, 5 lived in London and 7 were symptomatic (5 with classic COVID-19 symptoms: loss or change of sense of smell or taste, fever, persistent cough), 2 were asymptomatic, and symptoms were unknown for 2 cases. The proportion of Omicron (vs Delta or Delta sub-lineages) was found to increase rapidly with a daily increase of 66.0% (32.7%, 127.3%) in the odds of Omicron (vs. Delta) infection, conditional on swab positivity. Highest prevalence of swab positivity by age was observed in (unvaccinated) children aged 5 to 11 years (4.74% [4.15%, 5.40%]) similar to the prevalence observed at these ages in round 15. In contrast, prevalence in children aged 12 to 17 years more than halved from 5.35% (4.78%, 5.99%) in round 15 to 2.31% (1.91%, 2.80%) in round 16. As of 14 December 2021, 76.6% children at ages 12 to 17 years had received at least one vaccine dose; we estimated that vaccine effectiveness against infection was 57.9% (44.1%, 68.3%) in this age group. In addition, the prevalence of swab positivity in adults aged 65 years and over fell by over 40% from 0.84% (0.72%, 0.99%) in round 15 to 0.48% (0.39%,0.59%) in round 16 and for those aged 75 years and over it fell by two-thirds from 0.63% (0.48%,0.82%) to 0.21% (0.13%,0.32%). At these ages a high proportion of participants (>90%) had received a third vaccine dose; we estimated that adults having received a third vaccine dose had a three- to four-fold lower risk of testing positive compared to those who had received two doses. + +ConclusionA large fall in swab positivity from round 15 to round 16 among 12 to 17 year olds, most of whom have been vaccinated, contrasts with the continuing high prevalence among 5 to 11 year olds who have largely not been vaccinated. Likewise there were large falls in swab positivity among people aged 65 years and over, the vast majority of whom have had a third (booster) vaccine dose; these results reinforce the importance of the vaccine and booster campaign. However, the rapidly increasing prevalence of SARS-CoV-2 infections in England during December 2021, coincident with the rapid rise of Omicron infections, may lead to renewed pressure on health services. Additional measures beyond vaccination may be needed to control the current wave of infections and prevent health services (in England and other countries) from being overwhelmed. + +SummaryThe unprecedented rise in SARS-CoV-2 infections is concurrent with rapid spread of the Omicron variant in England and globally. We analysed prevalence of SARS-CoV-2 and its dynamics in England from end of November to mid-December 2021 among almost 100,000 participants from the REACT-1 study. Prevalence was high during December 2021 with rapid growth nationally and in London, and of the proportion of infections due to Omicron. We observed a large fall in swab positivity among mostly vaccinated older children (12-17 years) compared with unvaccinated younger children (5-11 years), and in adults who received a third vs. two doses of vaccine. Our results reiterate the importance of vaccination and booster campaigns; however, additional measures may be needed to control the rapid growth of the Omicron variant.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.12.21.21268214,2021-12-23,https://medrxiv.org/cgi/content/short/2021.12.21.21268214,Comparative effectiveness of ChAdOx1 versus BNT162b2 vaccines against SARS-CoV-2 infections in England and Wales: A cohort analysis using trial emulation in the Virus Watch community data,Vincent Grigori Nguyen; Alexei Yavlinsky; Sarah Beale; Susan J Hoskins; Vasileios Lampos; Isobel Braithwaite; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Annalan M D Navaratnam; Parth Patel; Madhumita Shrotri; Sophie Weber; Andrew Hayward; Robert W Aldridge,University College London; University College London; University College London; Univerity College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London,"IntroductionInfections of SARS-CoV-2 in vaccinated individuals have been increasing globally. Understanding the associations between vaccine type and a post-vaccination infection could help prevent further COVID-19 waves. In this paper, we use trial emulation to understand the impact of a phased introduction of the vaccine in the UK driven by vulnerability and exposure status. We estimate the comparative effectiveness of COVID-19 vaccines (ChAdOx1 versus BNT162b2) against post-vaccination infections of SARS-CoV-2 in a community setting in England and Wales. MethodTrial emulation was conducted by pooling results from six cohorts whose recruitment was staggered between 1st January 2021 and 31st March 2021 and followed until 12th November 2021. Eligibility for each trial was based upon age (18+ at the time of vaccination), without prior signs of infection or an infection within the first 14 days of the first dose. Time from vaccination of ChAdOx1 or BNT162b2 until SARS-CoV-2 infection (positive polymerase chain reaction or lateral flow test after 14 of the vaccination) was modelled using Cox proportional hazards model for each cohort and adjusted for age at vaccination, gender, minority ethnic status, clinically vulnerable status and index of multiple deprivation quintile. For those without SARS-CoV-2 infection during the study period, follow-up was until loss-of-follow-up or end of study (12th November 2021). Pooled hazard ratios were generated using random-effects meta-analysis. @@ -1947,6 +2014,13 @@ ResultsBased on analysis of 10475 adult participants including 874 infections ac ConclusionsA high proportion of the second wave of the pandemic was spent under conditions where people were being advised to work from home where possible, and to minimize exposure to shops, and a wide range of other businesses were subject to severe restrictions. Vaccines were being rolled out to high-risk groups. During this time, going to work was an important risk factor for infection but public transport use likely accounted for a lot of this risk. Only a minority of the cohort left home for work or used public or shared transport. By contrast, the majority of participants visited shops and this activity accounted for about one-third of non-household transmission.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.12.08.21267353,2021-12-08,https://medrxiv.org/cgi/content/short/2021.12.08.21267353,The challenge of limited vaccine supplies: impact of prior infection on anti-spike IgG antibody trajectories after a single COVID-19 vaccination,Jia Wei; Philippa Matthews; Nicole Stoesser; Ian Diamond; Ruth Studley; Emma Rourke; Duncan Cook; John Bell; John Newton; Jeremy Farrar; Alison Howarth; Brian Marsden; Sarah Hoosdally; Yvonne Jones; David Stuart; Derrick W Crook; tim E peto; Ann Sarah Walker; David W Eyre; Koen B Pouwels; - COVID-19 Infection Survey team,University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; NIHR Oxford Biomedical Research Centre; oxford university; University of Oxford; University of Oxford; University of Oxford; ,"Given high SARS-CoV-2 incidence, coupled with slow and inequitable vaccine roll-out, there is an urgent need for evidence to underpin optimum vaccine deployment, aiming to maximise global population immunity at speed. We evaluate whether a single vaccination in previously infected individuals generates similar initial and subsequent antibody responses to two vaccinations in those without prior infection. We compared anti-spike IgG antibody responses after a single dose of ChAdOx1, BNT162b2, or mRNA-1273 SARS-CoV-2 vaccines in the COVID-19 Infection Survey in the UK general population. In 100,849 adults who received at least one vaccination, 13,404 (13.3%) had serological and/or PCR evidence of prior infection. Prior infection significantly boosted antibody responses for all three vaccines, producing a higher peak level and longer half-life, and a response comparable to those without prior infection receiving two vaccinations. In those with prior infection, median time above the positivity threshold was estimated to last for >1 year after the first dose. Single-dose vaccination targeted to those previously infected may provide protection in populations with high rates of previous infection faced with limited vaccine supply, as an interim measure while vaccine campaigns are scaled up.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2021.12.03.21266112,2021-12-05,https://medrxiv.org/cgi/content/short/2021.12.03.21266112,Brain Injury in COVID-19 is Associated with Autoinflammation and Autoimmunity,Edward J Needham; Alex L Ren; Richard J Digby; Joanne G Outtrim; Dorothy A Chatfield; Virginia FJ Newcombe; Rainer Doffinger; Gabriela Barcenas-Morales; Claudia Fonseca; Michael J Taussig; Rowan M Burnstein; Cordelia Dunai; Nyarie Sithole; Nicholas J Ashton; Henrik Zetterberg; Magnus Gisslen; Eden Arvid; Emelie Marklund; Michael J Griffiths; Jonathan Cavanagh; Gerome Breen; Sarosh R Irani; Anne Elmer; Nathalie Kingston; John R Bradley; Leonie S Taams; Benedict D michael; Edward T Bullmore; Kenneth GC Smith; Paul A Lyons; Alasdair JC Coles; David K Menon; - Cambridge NeuroCOVID Group; - NIHR Cambridge Covid BioResource; - NIHR Cambridge Clinical Research Facility,"Department of Clinical Neurosciences, University of Cambridge, UK; Division of Anaesthesia, Department of Medicine, University of Cambridge, UK.; Division of Anaesthesia, Department of Medicine, University of Cambridge, UK.; Division of Anaesthesia, Department of Medicine, University of Cambridge, UK.; Division of Anaesthesia, Department of Medicine, University of Cambridge, UK.; Division of Anaesthesia, Department of Medicine, University of Cambridge, UK.; Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK.; Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK.; Cambridge Protein Arrays Ltd, Babraham Research Campus, Cambridge, UK; Cambridge Protein Arrays Ltd, Babraham Research Campus, Cambridge, UK; Division of Anaesthesia, Department of Medicine, University of Cambridge, UK.; Clinical Infection Microbiology and Neuroimmunology, Institute of Infection, Veterinary and Ecological Science, Liverpool, UK.; Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK.; Department of Psychiatry and Neurochemistry, Institute of Neuroscience & Physiology, the Sahlgrenska Academy at the University of Gothenburg, Molndal, Sweden.; Department of Psychiatry and Neurochemistry, Institute of Neuroscience & Physiology, the Sahlgrenska Academy at the University of Gothenburg, Molndal, Sweden; C; Department of Infectious Diseases, Institute of Biomedicine, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden; Region Vastra Gotaland; Department of Infectious Diseases, Institute of Biomedicine, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden; Region Vastra Gotaland; Department of Infectious Diseases, Institute of Biomnedicine, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden; Region Vastra Gotalan; Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK.; Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, U; Department of Social Genetic and Developmental Psychiatry, King's College London, London, UK.; Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Department of Neurology, Oxford University H; Cambridge Clinical Research Centre, NIHR Clinical Research Facility, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, UK ; NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge, UK.; NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge, UK; Department of Medicine, University of Cambridge, Ad; Centre for Inflammation Biology and Cancer Immunology and Dept Inflammation Biology, School of Immunology and Microbial Sciences, Kings College London, Guys Cam; Clinical Infection Microbiology and Neuroimmunology, Institute of Infection, Veterinary and Ecological Science, Liverpool, UK.; Department of Psychiatry, University of Cambridge, Herchel Smith Building for Brain and Mind Sciences, Cambridge Biomedical Campus, Cambridge, UK.; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Je; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Je; Department of Clinical Neurosciences, University of Cambridge, UK; Division of Anaesthesia, Department of Medicine, University of Cambridge, UK.; ; ; ","COVID-19 has been associated with many neurological complications including stroke, delirium and encephalitis. Furthermore, many individuals experience a protracted post-viral syndrome which is dominated by neuropsychiatric symptoms, and is seemingly unrelated to COVID-19 severity. The true frequency and underlying mechanisms of neurological injury are unknown, but exaggerated host inflammatory responses appear to be a key driver of severe COVID-19 more broadly. + +We sought to investigate the dynamics of, and relationship between, serum markers of brain injury (neurofilament light [NfL], Glial Fibrillary Acidic Protein [GFAP] and total Tau) and markers of dysregulated host response including measures of autoinflammation (proinflammatory cytokines) and autoimmunity. Brain injury biomarkers were measured using the Quanterix Simoa HDx platform, cytokine profiling by Luminex (R&D) and autoantibodies by a custom protein microarray. + +During hospitalisation, patients with COVID-19 demonstrated elevations of NfL and GFAP in a severity-dependant manner, and there was evidence of ongoing active brain injury at follow-up 4 months later. Raised NfL and GFAP were associated with both elevations of pro-inflammatory cytokines and the presence of autoantibodies; autoantibodies were commonly seen against lung surfactant proteins as well as brain proteins such as myelin associated glycoprotein, but reactivity was seen to a large number of different antigens. + +Furthermore, a distinct process characterised by elevation of serum total Tau was seen in patients at follow-up, which appeared to be independent of initial disease severity and was not associated with dysregulated immune responses in the same manner as NfL and GFAP.",neurology,fuzzy,100,100 medRxiv,10.1101/2021.11.24.21266818,2021-12-01,https://medrxiv.org/cgi/content/short/2021.11.24.21266818,Trends and associated factors for Covid-19 hospitalisation and fatality risk in 2.3 million adults in England,Thomas Beaney; Ana Luisa Neves; Ahmed Alboksmaty; Kelsey Flott; Aidan Fowler; Jonathan R Benger; Paul Aylin; Sarah Elkin; Ara Darzi; Jonathan Clarke,Imperial College London; Imperial College London; Imperial College London; Imperial College London; NHS England and Improvement; NHS Digital; Imperial College London; Imperial College London; Imperial College London; Imperial College London,"BackgroundThe Covid-19 case fatality ratio varies between countries and over time but it is unclear whether variation is explained by the underlying risk in those infected. This study aims to describe the trends and risk factors for admission and mortality rates over time in England. MethodsIn this retrospective cohort study, we included all adults ([≥]18 years) in England with a positive Covid-19 test result between 1st October 2020 and 30th April 2021. Data were linked to primary and secondary care electronic health records and death registrations. Our outcomes were i) one or more emergency hospital admissions and ii) death from any cause, within 28 days of a positive test. Multivariable multilevel logistic regression was used to model each outcome with patient risk factors and time. @@ -2045,18 +2119,14 @@ What this paper addsIn unvaccinated individuals the protection against hospitali Implications of all the available evidenceThe combination of natural infection and vaccination provides maximal protection against COVID-19: prior vaccination does not seriously impair this protection.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.11.19.21266529,2021-11-19,https://medrxiv.org/cgi/content/short/2021.11.19.21266529,Impact of the COVID-19 pandemic on community antibiotic prescribing and stewardship: a qualitative interview study with general practitioners in England,Aleksandra J Borek; Katherine Maitland; Monsey Mcleod; Anne Campbell; Benedict Hayhoe; Christopher C Butler; Liz Morrell; Laurence Roope; Alison Holmes; Ann Sarah Walker; Sarah Tonkin-Crine; - the STEP-UP study team,University of Oxford; University of Oxford; Imperial College London; Imperia College London; Imperial College London; University of Oxford; University of Oxford; University of Oxford; Imperial College London; University of Oxford; University of Oxford; ,"The COVID-19 pandemic has had a profound impact on the delivery of primary care services. We aimed to identify general practitioners (GPs) perceptions and experiences of how the COVID-19 pandemic influenced antibiotic prescribing and antimicrobial stewardship (AMS) in general practice in England. Twenty-four semi-structured interviews were conducted with 18 GPs at two time-points: autumn 2020 (14 interviews) and spring 2021 (10 interviews). Interviews were audio-recorded, transcribed and analysed thematically, taking a longitudinal approach. Participants reported a lower threshold for antibiotic prescribing (and fewer consultations) for respiratory infections and COVID-19 symptoms early in the pandemic, then returning to more usual (pre-pandemic) prescribing. They perceived less impact on antibiotic prescribing for urinary and skin infections. Participants perceived the changing ways of working and consulting (e.g., proportions of remote and in-person consultations), and the changing patient presentations and GP workload as influencing the fluctuations in antibiotic prescribing. This was compounded by decreased engagement with, and priority of, AMS due to COVID-19-related urgent priorities. Re-engagement with AMS is needed, e.g., through reviving antibiotic prescribing feedback and targets/incentives. While the pandemic disrupted the usual ways of working, it also produced opportunities, e.g., for re-organising ways of managing infections and AMS in the future.",primary care research,fuzzy,100,100 -medRxiv,10.1101/2021.11.15.21266255,2021-11-16,https://medrxiv.org/cgi/content/short/2021.11.15.21266255,"COVID-19 vaccination, risk-compensatory behaviours, and social contacts in four countries in the UK",John Buckell; Joel Jones; Philippa C Matthews; Ian Diamond; Emma Rourke; Ruth Studley; Duncan Cook; Ann Sarah Walker; Koen B Pouwels; - The COVID-19 Infection Survey Team,University of Oxford; Office for National Statistics; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; University of Oxford; ,"The physiological effects of vaccination against SARS-CoV-2 (COVID-19) are well documented, yet the behavioural effects are largely unknown. Risk compensation suggests that gains in personal safety, as a result of vaccination, are offset by increases in risky behaviour, such as socialising, commuting and working outside the home. This is potentially problematic because transmission of SARS-CoV-2 is driven by contacts, which could be amplified by vaccine-related risk compensation behaviours. Here, we show that behaviours were overall unrelated to personal vaccination, but - adjusting for variation in mitigation policies - were responsive to the level of vaccination in the wider population: individuals in the UK were risk compensating when rates of vaccination were rising. This effect was observed across four nations of the UK, each of which varied policies autonomously.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2021.11.10.21266124,2021-11-11,https://medrxiv.org/cgi/content/short/2021.11.10.21266124,Differences in COVID-19 vaccination coverage by occupation in England: a national linked data study,Vahe Nafilyan; Ted Dolby; Katie Finning; Jasper Morgan; Rhiannon Edge; Myer Glickman; Neil Pearce; Martie Van Tongeren,Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Lancaster University; Office for National Statistics; London School of Hygiene and Tropical Medicine; University of Manchester,"BackgroundMonitoring differences in COVID-19 vaccination uptake in different groups is crucial to help inform the policy response to the pandemic. A key gap is the absence of data on uptake by occupation. +medRxiv,10.1101/2021.11.15.21266264,2021-11-16,https://medrxiv.org/cgi/content/short/2021.11.15.21266264,Association of COVID-19 employment disruption with mental and social wellbeing: evidence from nine UK longitudinal studies,Jacques Wels; Charlotte Booth; Bozena Wielgoszewska; Michael J Green; Giorgio Di Gessa; Charlotte F Huggins; Gareth J Griffith; Alex Siu Fung Kwong; Ruth C E Bowyer; Jane Maddock; Praveetha Patalay; Richard J Silverwood; Emla Fitzsimons; Richard John Shaw; Ellen J Thompson; Andrew Steptoe; Alun Hughes; Nishi Chaturvedi; Claire J Steves; Srinivasa Vittal Katikireddi; George B Ploubidis,University College London; University College London; University College London; University of Glasgow; University College London; University of Edinburgh; University of Bristol; University of Bristol; King's College London; University College London; University College London; University College London; University College London; University of Glasgow; Kings College London; University College London; University College London; University College London; King's College London; University of Glasgow; University College London,"BackgroundThe COVID-19 pandemic has led to major economic disruptions. In March 2020, the UK implemented the Coronavirus Job Retention Scheme - known as furlough - to minimize the impact of job losses. We investigate associations between change in employment status and mental and social wellbeing during the early stages of the pandemic. -MethodsUsing nationwide population-level data, we calculated the proportion of people who had received two doses of a COVID-19 vaccine (assessed on 31 August 2021) by detailed occupational categories in adults aged 40-64 and estimated adjusted odds ratios to examine whether these differences were driven by occupation or other factors, such as education. We also examined whether vaccination rates differed by ability to work from home. +MethodsData were from 25,670 respondents, aged 17 to 66, across nine UK longitudinal studies. Furlough and other employment changes were defined using employment status pre-pandemic and during the first lockdown (April-June 2020). Mental and social wellbeing outcomes included psychological distress, life satisfaction, self-rated health, social contact, and loneliness. Study-specific modified Poisson regression estimates, adjusting for socio-demographic characteristics and pre-pandemic mental and social wellbeing measures, were pooled using meta-analysis. -ResultsOur study population included 14,298,147 adults 40-64. Vaccination rates differed markedly by occupation, being higher in administrative and secretarial occupations (90.8%); professional occupations (90.7%); and managers, directors and senior officials (90.6%); and lowest (83.1%) in people working in elementary occupations. We found substantial differences in vaccination rates looking at finer occupational groups even after adjusting for confounding factors, such as education. Vaccination rates were higher in occupations which can be done from home and lower in those which cannot. Many occupations with low vaccination rates also involved contact with the public or with vulnerable people +ResultsCompared to those who remained working, furloughed workers were at greater risk of psychological distress (adjusted risk ratio, ARR=1.12; 95% CI: 0.97, 1.29), low life satisfaction (ARR=1.14; 95% CI: 1.07, 1.22), loneliness (ARR=1.12; 95% CI: 1.01, 1.23), and poor self-rated health (ARR=1.26; 95% CI: 1.05, 1.50), but excess risk was less pronounced than that of those no longer employed (e.g., ARR for psychological distress=1.39; 95% CI: 1.21, 1.59) or in stable unemployment (ARR=1.33; 95% CI: 1.09, 1.62). -ConclusionsIncreasing vaccination coverage in occupations with low vaccination rates is crucial to help protecting the public and control infection, especially in occupations that cannot be done from home and involve contacts with the public. Policies such as work from home if you can may only have limited future impact on hospitalisations and deaths - -What is already known on this subject?Whilst several studies highlight differences in vaccination coverage by ethnicity, religion, socio-demographic factors and certain underlying health conditions, there is very little evidence on how vaccination coverage varies by occupation, in the UK and elsewhere. The few study looking at occupational differences in vaccine hesitancy focus on healthcare workers or only examined broad occupational groups. There is currently no large-scale study on occupational differences in COVID-19 vaccination coverage in the UK. - -What this study adds?Using population-level linked data combining the 2011 Census, primary care records, mortality and vaccination data, we found that the vaccination rates of adults aged 40 to 64 years in England differed markedly by occupation. Vaccination rates were high in administrative and secretarial occupations, professional occupations and managers, directors and senior officials and low in people working in elementary occupations. Adjusting for other factors likely to be linked to occupation and vaccination, such as education, did not substantially alter the results. Vaccination rates were also associated with the ability to work from home, with the vaccination rate being higher in occupations which can be done performed from home. Policies aiming to increase vaccination rates in occupations that cannot be done from home and involve contacts with the public should be priorities",public and global health,fuzzy,100,100 +ConclusionsDuring the early stages of the pandemic, those furloughed had increased risk for poor mental and social wellbeing. However, their excess risk was lower in magnitude than that of those who became or remained unemployed, suggesting that furlough may have partly mitigated poorer outcomes.",psychiatry and clinical psychology,fuzzy,100,100 +medRxiv,10.1101/2021.11.15.21266255,2021-11-16,https://medrxiv.org/cgi/content/short/2021.11.15.21266255,"COVID-19 vaccination, risk-compensatory behaviours, and social contacts in four countries in the UK",John Buckell; Joel Jones; Philippa C Matthews; Ian Diamond; Emma Rourke; Ruth Studley; Duncan Cook; Ann Sarah Walker; Koen B Pouwels; - The COVID-19 Infection Survey Team,University of Oxford; Office for National Statistics; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; University of Oxford; ,"The physiological effects of vaccination against SARS-CoV-2 (COVID-19) are well documented, yet the behavioural effects are largely unknown. Risk compensation suggests that gains in personal safety, as a result of vaccination, are offset by increases in risky behaviour, such as socialising, commuting and working outside the home. This is potentially problematic because transmission of SARS-CoV-2 is driven by contacts, which could be amplified by vaccine-related risk compensation behaviours. Here, we show that behaviours were overall unrelated to personal vaccination, but - adjusting for variation in mitigation policies - were responsive to the level of vaccination in the wider population: individuals in the UK were risk compensating when rates of vaccination were rising. This effect was observed across four nations of the UK, each of which varied policies autonomously.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.11.05.21265968,2021-11-09,https://medrxiv.org/cgi/content/short/2021.11.05.21265968,Waning of SARS-CoV-2 antibodies targeting the Spike protein in individuals post second dose of ChAdOx1 and BNT162b2 COVID-19 vaccines and risk of breakthrough infections: analysis of the Virus Watch community cohort.,Robert William Aldridge; Alexei Yavlinsky; Vincent Grigori Nguyen; Max T Eyre; Madhumita Shrotri; Annalan Mathew Dwight Navaratnam; Sarah Beale; Isobel Braithwaite; Thomas Edward Byrne; Jana Kovar; Ellen Fragaszy; Erica Wing Lam Fong; Cyril Roman Geismar; Parth Patel; Alison Rodger; Anne M Johnson; Andrew C Hayward,"University College London; University College London; University College London; Lancaster University, Liverpool School of Tropical Medicine; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London","BackgroundSARS-CoV-2 vaccines stimulate production of antibodies targeting the spike protein (anti-S). The level of antibodies following vaccination and trajectories of waning may differ between vaccines influencing the level of protection, how soon protection is reduced and, consequently the optimum timing of booster doses. MethodsWe measured SARS-CoV-2 anti-S titre in the context of seronegativity for SARS-CoV-2 anti-Nucleocapsid (anti-N), in samples collected between 1st July and 24th October 2021 in a subset of adults in the Virus Watch community cohort. We compared anti-S levels after BNT162b2 (BioNTech/Pfizer) or ChAdOx1 (AstraZeneca/Oxford) vaccination using time since second dose of vaccination, age, sex and clinical vulnerability to investigate antibody waning. To investigate the use of anti-S levels as a correlate of protection against SARS-CoV-2 infection, we undertook a survival analysis (Kaplan-Meier and Cox) with individuals entering 21 days after their second dose of vaccine, or first antibody test after 1st July (whichever was latest) and exiting with the outcome of SARS-Cov-2 infection or at the end of follow up 24th October 2021. We also undertook a negative test design case-control analysis of infections occurring after the second vaccine dose (breakthrough infections) to determine whether the type of vaccine affected the risk of becoming infected. @@ -2444,6 +2514,21 @@ ResultsWe studied 1489 participants returned valid results in both June and Sept DiscussionThese results do not follow the pattern reported from studies specifically designed to monitor seropositivity, which have found greater consistency over time and the influence of presence, timing and severity of symptoms on seroreversion. We suggest several factors that may have contributed to this difference: our low bar in defining initial seropositivity (single test); a non-quantitative test known to have relatively low sensitivity; participants carrying out testing. We would encourage other studies to use these real-world performance characteristics alongside those from laboratory studies to plan and analyse any antibody testing.",occupational and environmental health,fuzzy,100,100 medRxiv,10.1101/2021.08.18.21262237,2021-08-24,https://medrxiv.org/cgi/content/short/2021.08.18.21262237,Impact of Delta on viral burden and vaccine effectiveness against new SARS-CoV-2 infections in the UK,Koen B Pouwels; Emma Pritchard; Philippa Matthews; Nicole B Stoesser; David W Eyre; Karina-Doris Vihta; Thomas House; Jodie Hay; John Bell; John Newton; Jeremy Farrar; Derrick W Crook; Duncan Cook; Emma Rourke; Ruth Studley; Tim E Peto; Ian Diamond; Sarah Walker; - COVID-19 Infection Survey Team,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Manchester; Glasgow Lighthouse Laboratory; University of Oxford; Public Health England; Wellcome Trust; NIHR Oxford Biomedical Research Centre; Office for National Statistics; Office for National Statistics; Office for National Statistics; Oxford University; Office for National Statistics; University of Oxford; -,"The effectiveness of BNT162b2, ChAdOx1, and mRNA-1273 vaccines against new SARS-CoV-2 infections requires continuous re-evaluation, given the increasingly dominant Delta variant. We investigated the effectiveness of the vaccines in a large community-based survey of randomly selected households across the UK. We found that the effectiveness of BNT162b2 and ChAd0x1 against any infections (new PCR positives) and infections with symptoms or high viral burden is reduced with the Delta variant. A single dose of the mRNA-1273 vaccine had similar or greater effectiveness compared to a single dose of BNT162b2 or ChAdOx1. Effectiveness of two doses remains at least as great as protection afforded by prior natural infection. The dynamics of immunity following second doses differed significantly between BNT162b2 and ChAdOx1, with greater initial effectiveness against new PCR-positives but faster declines in protection against high viral burden and symptomatic infection with BNT162b2. There was no evidence that effectiveness varied by dosing interval, but protection was higher among those vaccinated following a prior infection and younger adults. With Delta, infections occurring following two vaccinations had similar peak viral burden to those in unvaccinated individuals. SARS-CoV-2 vaccination still reduces new infections, but effectiveness and attenuation of peak viral burden are reduced with Delta.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2021.08.23.21261779,2021-08-24,https://medrxiv.org/cgi/content/short/2021.08.23.21261779,Association of cerebral venous thrombosis with recent COVID-19 vaccination: case-crossover study using ascertainment through neuroimaging in Scotland.,Paul M McKeigue; Raj Burgul; Jennifer Bishop; Chris Robertson; Jim McMenamin; Maureen O'Leary; David A. McAllister; Helen M Colhoun,"University of Edinburgh; Forth Valley Royal Hospital; Public Health Scotland; Department of Mathematics and Statistics, University of Strathclyde; Public Health Scotland; Public Health Scotland; University of Glasgow; University of Edinburgh","ObjectivesTo investigate the association of primary acute cerebral venous thrombosis (CVT) with COVID-19 vaccination through complete ascertainment of all diagnosed CVT in the population of Scotland. + +DesignCase-crossover study comparing recent (1-14 days after vaccination) with less recent exposure to vaccination among cases of CVT. + +SettingNational data for Scotland from 1 December 2020, with diagnosed CVT case ascertainment through neuroimaging studies up to 17 May 2021 and diagnostic coding of hospital discharges up to 28 April 2021 and with linkage to vaccination records. + +Main outcome measurePrimary acute cerebral venous thrombosis + +ResultsOf 50 primary acute CVT cases, 29 were ascertained only from neuroimaging studies, 2 were ascertained only from hospital discharges, and 19 were ascertained from both sources. Of these 50 cases, 14 had received the Astra-Zeneca ChAdOx1 vaccine and 3 the Pfizer BNT162b2 vaccine. The incidence of CVT per million doses in the first 14 days after vaccination was 2.2 (95% credible interval 0.9 to 4.1) for ChAdOx1 and 1 (95% credible interval 0.1 to 2.9) for BNT162b2. The rate ratio for CVT associated with exposure to ChAdOx1 in the first 14 days compared with exposure 15-84 days after vaccination was 3.2 (95% credible interval 1.1 to 9.5). The 95% credible interval for the rate ratio associated with recent versus less recent exposure to BNT162b2 (0.6 to 95.8) was too wide for useful inference. + +ConclusionsThese findings support a causal association between CVT and the AstraZeneca vaccine. The absolute risk of post-vaccination CVT in this population-wide study in Scotland was lower than has been reported for populations in Scandinavia and Germany; the explanation for this is not clear. + +What is already known on this topicThe risk of cerebral venous thrombosis (CVT) within 28 days of receiving the AstraZeneca ChAdOx1 vaccine has been estimated as 18 to 25 per million doses in Germany and Scandinavia, but only 5 per million doses in the UK based on the Yellow Card reporting scheme. Risk estimates based on adverse event reporting systems are subject to under-ascertainment and other biases. + +What this study addsAll diagnosed cases of CVT in Scotland were ascertained by searching neuroimaging studies from December 2020 to May 2021 and linked to national vaccination records. The risk of CVT within 28 days of vaccination with ChAdOx1 was estimated as 3.5 per million doses with an upper bound of 6 per million doses, against a background incidence of about 12 per million adults per year. This indicates that the Yellow Card system has not seriously underestimated the risk in the UK; the explanation for higher risk in other European countries is not clear.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.08.19.21262231,2021-08-24,https://medrxiv.org/cgi/content/short/2021.08.19.21262231,Symptoms and SARS-CoV-2 positivity in the general population in the UK,Karina-Doris Vihta; Koen B. Pouwels; Tim Peto; Emma Pritchard; David W. Eyre; Thomas House; Owen Gethings; Ruth Studley; Emma Rourke; Duncan Cook; Ian Diamond; Derrick Crook; Philippa C. Matthews; Nicole Stoesser; Ann Sarah Walker; - COVID-19 Infection Survey team,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Manchester; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; University of Oxford; University of Oxford; University of Oxford; ,"BackgroundSeveral community-based studies have assessed the ability of different symptoms to identify COVID-19 infections, but few have compared symptoms over time (reflecting SARS-CoV-2 variants) and by vaccination status. MethodsUsing data and samples collected by the COVID-19 Infection Survey at regular visits to representative households across the UK, we compared symptoms in new PCR-positives and comparator test-negative controls. @@ -2574,6 +2659,21 @@ MethodsA nationally-representative cohort of U.S. adults (N=5,792) in the Unders ResultsVaccination was associated with a 0.09 decline in distress scores (95% CI:-0.15 to -0.04) (0-12 scale), a 5.7% relative decrease compared to mean scores in the wave prior to vaccination. Vaccination was also associated with an 8.44 percentage point reduction in perceived risk of infection (95% CI:-9.15% to -7.73%), a 7.44-point reduction in perceived risk of hospitalization (95% CI:-8.07% to -6.82%), and a 5.03-point reduction in perceived risk of death (95% CI:-5.57% to -4.49%). Adjusting for risk perceptions decreased the vaccination-distress association by two-thirds. Event study models suggest vaccinated and never vaccinated respondents followed similar PHQ-4 trends pre-vaccination, diverging significantly post-vaccination. Analyses were robust to individual and wave fixed effects, time-varying controls, and several alternative modelling strategies. Results were similar across sociodemographic groups. ConclusionReceiving a COVID-19 vaccination was associated with declines in distress and perceived risks of infection, hospitalization, and death. Vaccination campaigns could promote these additional benefits of being vaccinated.",public and global health,fuzzy,100,100 +medRxiv,10.1101/2021.07.21.21260906,2021-07-22,https://medrxiv.org/cgi/content/short/2021.07.21.21260906,Disentangling post-vaccination symptoms from early COVID-19,Liane S Canas; Marc F. Osterdahl; Jie Deng; Christina Hu; Somesh Selvachandran; Lorenzo Polidori; Anna May; Erika Molteni; Benjamin Murray; Liyuan Chen; Eric Kerfoot; Kerstin Klaser; Michela Antonelli; Alexander Hammers; Tim Spector; Sebastien Ourselin; Claire J. Steves; Carole H. Sudre; Marc Modat; Emma L. Duncan,"School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK; School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; ZOE Limited, London, UK; ZOE Limited, London, UK; ZOE Limited, London, UK; ZOE Limited, London, UK; School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; King's College London & Guy's and St Thomas' PET Centre, London, UK; Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK.; School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK.; School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; Medical Research Council Unit for Lifelong Health and Ageing, Departme; School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK.","BackgroundIdentifying and testing individuals likely to have SARS-CoV-2 is critical for infection control, including post-vaccination. Vaccination is a major public health strategy to reduce SARS-CoV-2 infection globally. Some individuals experience systemic symptoms post-vaccination, which overlap with COVID-19 symptoms. This study compared early post-vaccination symptoms in individuals who subsequently tested positive or negative for SARS-CoV-2, using data from the COVID Symptom Study (CSS) app. + +DesignWe conducted a prospective observational study in UK CSS participants who were asymptomatic when vaccinated with Pfizer-BioNTech mRNA vaccine (BNT162b2) or Oxford-AstraZeneca adenovirus-vectored vaccine (ChAdOx1 nCoV-19) between 8 December 2020 and 17 May 2021, who subsequently reported symptoms within seven days (other than local symptoms at injection site) and were tested for SARS-CoV-2, aiming to differentiate vaccination side-effects per se from superimposed SARS-CoV-2 infection. The post-vaccination symptoms and SARS-CoV-2 test results were contemporaneously logged by participants. Demographic and clinical information (including comorbidities) were also recorded. Symptom profiles in individuals testing positive were compared with a 1:1 matched population testing negative, including using machine learning and multiple models including UK testing criteria. + +FindingsDifferentiating post-vaccination side-effects alone from early COVID-19 was challenging, with a sensitivity in identification of individuals testing positive of 0.6 at best. A majority of these individuals did not have fever, persistent cough, or anosmia/dysosmia, requisite symptoms for accessing UK testing; and many only had systemic symptoms commonly seen post-vaccination in individuals negative for SARS-CoV-2 (headache, myalgia, and fatigue). + +InterpretationPost-vaccination side-effects per se cannot be differentiated from COVID-19 with clinical robustness, either using symptom profiles or machine-derived models. Individuals presenting with systemic symptoms post-vaccination should be tested for SARS-CoV-2, to prevent community spread. + +FundingZoe Limited, UK Government Department of Health and Social Care, Wellcome Trust, UK Engineering and Physical Sciences Research Council, UK National Institute for Health Research, UK Medical Research Council and British Heart Foundation, Alzheimers Society, Chronic Disease Research Foundation, Massachusetts Consortium on Pathogen Readiness (MassCPR). + +Research in contextO_ST_ABSEvidence before this studyC_ST_ABSThere are now multiple surveillance platforms internationally interrogating COVID-19 and/or post-vaccination side-effects. We designed a study to examine for differences between vaccination side-effects and early symptoms of COVID-19. We searched PubMed for peer-reviewed articles published between 1 January 2020 and 21 June 2021, using keywords: ""COVID-19"" AND ""Vaccination"" AND (""mobile application"" OR ""web tool"" OR ""digital survey"" OR ""early detection"" OR ""Self-reported symptoms"" OR ""side-effects""). Of 185 results, 25 studies attempted to differentiate symptoms of COVID-19 vs. post-vaccination side-effects; however, none used artificial intelligence (AI) technologies (""machine learning"") coupled with real-time data collection that also included comprehensive and systematic symptom assessment. Additionally, none of these studies attempt to discriminate the early signs of infection from side-effects of vaccination (specifically here: Pfizer-BioNTech mRNA vaccine (BNT162b2) and Oxford-AstraZeneca adenovirus-vectored vaccine (ChAdOx1 nCoV-19)). Further, none of these studies sought to provide comparisons with current testing criteria used by healthcare services. + +Added value of this studyThis study, in a uniquely large community-based cohort, uses prospective data capture in a novel effort to identify individuals with COVID-19 in the immediate post-vaccination period. Our results show that early symptoms of SARS-CoV-2 cannot be differentiated from vaccination side-effects robustly. Thus, post-vaccination systemic symptoms should not be ignored, and testing should be considered to prevent COVID-19 dissemination by vaccinated individuals. + +Implications of all the available evidenceOur study demonstrates the critical importance of testing symptomatic individuals - even if vaccinated - to ensure early detection of SARS-CoV-2 infection, helping to prevent future pandemic waves in the UK and elsewhere.",respiratory medicine,fuzzy,100,100 medRxiv,10.1101/2021.07.19.21260770,2021-07-22,https://medrxiv.org/cgi/content/short/2021.07.19.21260770,Uptake of infant and pre-school immunisations in Scotland and England during the COVID-19 pandemic: an observational study of routinely collected data,Fiona McQuaid; Rachel Mulholland; Yuma Sangpang Rai; Utkarsh Agrawal; Helen Bedford; Claire Cameron; Cheryl Gibbon; Partho Roy; Aziz Sheikh; Ting Shi; Colin Simpson; Judith Tait; Elise Tessier; Steve Turner; Jaime Villacampa Ortega; Joanne White; Rachael Wood,University of Edinburgh; University of Edinburgh; Public Health England; University of St Andrews; UCL Great Ormond Street Institute of Child Health; Public Health Scotland; Public Health Scotland; Public Health England; University of Edinburgh; University of Edinburgh; Victoria University of Wellington; Public Health Scotland; Public Health England; University of Aberdeen; Public Health Scotland; Public Health England; University of Edinburgh,"BackgroundIn 2020, the COVID-19 pandemic and control measures such as national lockdowns threatened to disrupt routine childhood immunisation programmes. Initial reports from the early weeks of lockdown in the UK and worldwide suggested that uptake could fall putting children at risk from multiple other infectious diseases. In Scotland and England, enhanced surveillance of national data for childhood immunisations was established to inform and rapidly assess the impact of the pandemic on infant and preschool immunisation uptake rates. Methods and findingsWe undertook an observational study using routinely collected data for the year prior to the pandemic (2019), and immediately before, during and after the first period of the UK lockdown in 2020. Data were obtained for Scotland from the Public Health Scotland ""COVID19 wider impacts on the health care system"" dashboard (https://scotland.shinyapps.io/phs-covid-wider-impact/) and for England from ImmForm. @@ -2711,25 +2811,6 @@ ResultsIn round 13 interim, we found 237 positives from 47,729 swabs giving a we DiscussionWe are entering a critical period with a number of important competing processes: continued vaccination rollout to the whole adult population in England, increased natural immunity through infection, reduced social mixing of children during school holidays, increased proportion of mixing occurring outdoors during summer, the intended full opening of hospitality and entertainment and cessation of mandated social distancing and mask wearing. Surveillance programmes are essential during this next phase of the epidemic to provide clear evidence to the government and the public on the levels and trends in prevalence of infections and their relationship to vaccine coverage, hospitalisations, deaths and Long COVID.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.07.02.21259897,2021-07-05,https://medrxiv.org/cgi/content/short/2021.07.02.21259897,Anti-spike antibody response to natural SARS-CoV-2 infection in the general population,Jia Wei; Philippa C Matthews; Nicole Stoesser; Thomas Maddox; Luke Lorenzi; Ruth Studley; John I Bell; John N Newton; Jeremy Farrar; Ian Diamond; Emma Rourke; Alison Howarth; Brian D Marsden; Sarah Hoosdally; E Yvonne Jones; David I Stuart; Derrick W Crook; Tim E.A. Peto; Koen B. Pouwels; A. Sarah Walker; David W Eyre,University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; Office for National Statistics; Office for National Statistics; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; NIHR Oxford Biomedical Research Centre; University of Oxford; University of Oxford; University of Oxford; University of Oxford,"We estimated the duration and determinants of antibody response after SARS-CoV-2 infection in the general population using representative data from 7,256 United Kingdom COVID-19 infection survey participants who had positive swab SARS-CoV-2 PCR tests from 26-April-2020 to 14-June-2021. A latent class model classified 24% of participants as non-responders not developing anti-spike antibodies. These seronegative non-responders were older, had higher SARS-CoV-2 cycle threshold values during infection (i.e. lower viral burden), and less frequently reported any symptoms. Among those who seroconverted, using Bayesian linear mixed models, the estimated anti-spike IgG peak level was 7.3-fold higher than the level previously associated with 50% protection against reinfection, with higher peak levels in older participants and those of non-white ethnicity. The estimated anti-spike IgG half-life was 184 days, being longer in females and those of white ethnicity. We estimated antibody levels associated with protection against reinfection likely last 1.5-2 years on average, with levels associated with protection from severe infection present for several years. These estimates could inform planning for vaccination booster strategies.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2021.06.28.21259452,2021-07-03,https://medrxiv.org/cgi/content/short/2021.06.28.21259452,"Persistent symptoms following SARS-CoV-2 infection in a random community sample of 508,707 people",Matthew Whitaker; Joshua Elliott; Marc Chadeau-Hyam; Steven Riley; Ara Darzi; Graham Cooke; Helen Ward; Paul Elliott,"Imperial College London; Imperial College London; Imperial College London; Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London School of Public Health","BackgroundLong COVID, describing the long-term sequelae after SARS-CoV-2 infection, remains a poorly defined syndrome. There is uncertainty about its predisposing factors and the extent of the resultant public health burden, with estimates of prevalence and duration varying widely. - -MethodsWithin rounds 3-5 of the REACT-2 study, 508,707 people in the community in England were asked about a prior history of COVID-19 and the presence and duration of 29 different symptoms. We used uni-and multivariable models to identify predictors of persistence of symptoms (12 weeks or more). We estimated the prevalence of symptom persistence at 12 weeks, and used unsupervised learning to cluster individuals by symptoms experienced. - -FindingsAmong the 508,707 participants, the weighted prevalence of self-reported COVID-19 was 19.2% (95% CI: 19.1,19.3). 37.7% of 76,155 symptomatic people post COVID-19 experienced at least one symptom, while 14.8% experienced three or more symptoms, lasting 12 weeks or more. This gives a weighted population prevalence of persistent symptoms of 5.75% (5.68, 5.81) for one and 2.22% (2.1, 2.26) for three or more symptoms. Almost a third of people (8,771/28,713 [30.5%]) with at least one symptom lasting 12 weeks or more reported having had severe COVID-19 symptoms (""significant effect on my daily life"") at the time of their illness, giving a weighted prevalence overall for this group of 1.72% (1.69,1.76). The prevalence of persistent symptoms was higher in women than men (OR: 1.51 [1.46,1.55]) and, conditional on reporting symptoms, risk of persistent symptoms increased linearly with age by 3.5 percentage points per decade of life. Obesity, smoking or vaping, hospitalisation, and deprivation were also associated with a higher probability of persistent symptoms, while Asian ethnicity was associated with a lower probability. Two stable clusters were identified based on symptoms that persisted for 12 weeks or more: in the largest cluster, tiredness predominated, while in the second there was a high prevalence of respiratory and related symptoms. - -InterpretationA substantial proportion of people with symptomatic COVID-19 go on to have persistent symptoms for 12 weeks or more, which is age-dependent. Clinicians need to be aware of the differing manifestations of Long COVID which may require tailored therapeutic approaches. Managing the long-term sequelae of SARS-CoV-2 infection in the population will remain a major challenge for health services in the next stage of the pandemic. - -FundingThe study was funded by the Department of Health and Social Care in England. - -Research in contextO_ST_ABSEvidence before this studyC_ST_ABSRecent systematic reviews have documented the wide range of symptoms and reported prevalence of persistent symptoms following COVID-19. A dynamic review of Long COVID studies (NIHR Evidence) in March 2021 summarised the literature on the prevalence of persistent symptoms after acute COVID19, and reported that most studies (14) were of hospitalised patients, with higher prevalence of persistent symptoms compared with two community-based studies. There was limited evidence from community studies beyond 12 weeks. Another systematic review reported a median of over 70% of people with symptoms lasting at least 60 days. A review of risk factors for Long COVID found consistent evidence for an increased risk amongst women and those with high body mass index (BMI) but inconsistent findings on the role of age and little evidence concerning risks among different socioeconomic or ethnic groups which are often not well captured in routine healthcare records. Long COVID is increasingly recognised as heterogenous, likely underpinned by differing biological mechanisms, but there is not yet consensus on defining subtypes of the condition. - -Added value of this studyThis community-based study of over half a million people was designed to be representative of the adult population of England. A random sample of adults ages 18 years and above registered with a GP were invited irrespective of previous access to services for COVID-19, providing an estimate of population prevalence that was representative of the whole population. The findings show substantial declines in symptom prevalence over the first 12 weeks following Covid-19, reported by nearly one fifth of respondents, of whom over a third remained symptomatic at 12 weeks and beyond, with little evidence for decline thereafter. - -Risk factors identified for persistent symptoms (12 weeks or more) suggestive of Long COVID confirm some previous findings - an increased risk in women, obese and overweight individuals and those hospitalised for COVID-19, with strong evidence for an increasing risk with age. Additional evidence was found for an increased risk in those with lower income, smoking or vaping and healthcare or care home workers. A lower risk was found in those of Asian ethnicity. - -Clustering identified two distinct groups of individuals with different symptom profiles at 12 weeks, highlighting the heterogeneity of clinical presentation. The smaller cluster had higher prevalence of respiratory and related symptoms, while for those in the larger cluster tiredness was the dominant symptom, with lower prevalence of organ-specific symptoms. - -Implications of available evidenceThere is a high prevalence of persistent symptoms beyond 12 weeks after acute COVID-19, with little evidence of decline thereafter. This highlights the needs for greater support for patients, both through specialised services and, for those from low-income settings, financial support. The understanding that there are distinct clusters of persistent symptoms, the most common of which is dominated by fatigue, is important for the recognition and clinical management of the condition outside of specialised services.",infectious diseases,fuzzy,96,100 medRxiv,10.1101/2021.06.28.21259529,2021-07-01,https://medrxiv.org/cgi/content/short/2021.06.28.21259529,Global patterns of genetic variation and association with clinical phenotypes at genes involved in SARS-CoV-2 infection,Chao Zhang; Anurag Verma; Yuanqing Feng; Marcelo C. R. Melo; Michael McQuillan; Matthew Hansen; Anastasia Lucas; Joseph Park; Alessia Ranciaro; Simon Thompson; Meghan A. Rubel; Michael C. Campbell; William Beggs; JIBRIL HIRBO; Sununguko Wata Mpoloka; Gaonyadiwe George Mokone; - Regeneron Genetic Center; Thomas Nyambo; Dawit Wolde Meskel; Gurja Belay; Charles Fokunang; Alfred K. Njamnshi; Sabah A. Omar; Scott Williams; Daniel Rader; Marylyn D Ritchie; Cesar de la Fuente Nunez; Giorgio Sirugo; Sarah Tishkoff,"University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; Perelman School of Medicine at the University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Howard; University of Pennsylvania; Vanderbilt University Medical Center; University of Botswana, Biological Sciences, Gaborone, Botswana; University of Botswana, Faculty of Medicine, Gaborone, Botswana; ; Department of Biochemistry, Kampala International University in Tanzania, Dar es Salaam, Tanzania; Addis Ababa University Department of Microbial Cellular and Molecular Biology, Addis Ababa, Ethiopia; Addis Ababa University Department of Microbial Cellular and Molecular Biology, Addis Ababa, Ethiopia; Department of Pharmacotoxicology and Pharmacokinetics, Faculty of Medicine and Biomedical Sciences, The University of Yaounde I, Yaounde, Cameroon; Department of Neurology, Central Hospital Yaounde; Brain Research Africa Initiative (BRAIN), Neuroscience Lab, Faculty of Medicine and Biomedical Sciences, The ; Center for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya; Case Western Reserve University; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania; University of Pennsylvania","We investigated global patterns of genetic variation and signatures of natural selection at host genes relevant to SARS-CoV-2 infection (ACE2, TMPRSS2, DPP4, and LY6E). We analyzed novel data from 2,012 ethnically diverse Africans and 15,997 individuals of European and African ancestry with electronic health records, and integrated with global data from the 1000GP. At ACE2, we identified 41 non-synonymous variants that were rare in most populations, several of which impact protein function. However, three non-synonymous variants were common among Central African hunter-gatherers from Cameroon and are on haplotypes that exhibit signatures of positive selection. We identify strong signatures of selection impacting variation at regulatory regions influencing ACE2 expression in multiple African populations. At TMPRSS2, we identified 13 amino acid changes that are adaptive and specific to the human lineage. Genetic variants that are targets of natural selection are associated with clinical phenotypes common in patients with COVID-19.",genetic and genomic medicine,fuzzy,100,100 medRxiv,10.1101/2021.06.23.21259400,2021-06-30,https://medrxiv.org/cgi/content/short/2021.06.23.21259400,Temporal trends in primary care-recorded self-harm during and beyond the first year of the COVID-19 pandemic: time series analysis of electronic healthcare records for 2.8 million patients in the Greater Manchester Care Record,Sarah Steeg; Lana Bojanić; George Tilston; Richard Williams; David A Jenkins; Matthew J Carr; Niels Peek; Darren M Ashcroft; Nav Kapur; Jennifer Voorhees; Roger T Webb,University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester; University of Manchester,"BackgroundSurveillance of clinically treated self-harm episode frequency is an important component of suicide prevention in the dynamic context of COVID-19. Studies published to date have investigated the initial months following the onset of the pandemic, despite national and regional restrictions persisting to Summer 2021. @@ -2995,19 +3076,6 @@ ConclusionPeak antibody responses after the second BNT162b2 vaccine are markedly What is already known on this topicThe BNT162b2 vaccine is highly effective against Covid-19 infection and was delivered with a 3-week time interval in registration studies. However, this interval has been extended in many countries in order to extend population coverage with a single vaccine. It is not known how immune responses after the second dose are influenced by delaying the second vaccine. What this study addsWe provide the first assessment of immune responses in the first 14 weeks after standard or extended interval BNT162b2 vaccination and show that delaying the second dose acts to strongly boost the peak antibody response in older people. The extended interval vaccination may offer a longer period of clinical protection. This information will be of value in optimizing vaccine regimens and help guide guide vaccination policies.",infectious diseases,fuzzy,100,92 -medRxiv,10.1101/2021.05.12.21257123,2021-05-17,https://medrxiv.org/cgi/content/short/2021.05.12.21257123,Occupation and COVID-19 mortality in England: a national linked data study of 14.3 million adults,Vahe Nafilyan; Piotr Pawelek; Daniel Ayoubkhani; Sarah Rhodes; Lucy Pembrey; Melissa Matz; Michel P Coleman; Claudia Allemani; Ben Windsor-Shellard; Martie van Tongeren; Neil Pearce,"Office for National Statistics; Office for National Statistics; Office for National Statistics; School of Health Sciences, University of Manchester; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine; Office for National Statistics; School of Health Sciences, University of Manchester; London School of Hygiene and Tropical Medicine","ObjectiveTo estimate occupational differences in COVID-19 mortality, and test whether these are confounded by factors, such as regional differences, ethnicity and education or due to non-workplace factors, such as deprivation or pre-pandemic health. - -DesignRetrospective cohort study - -SettingPeople living in private households England - -Participants14,295,900 people aged 40-64 years (mean age 52 years, 51% female) who were alive on 24 January 2020, living in private households in England in 2019, were employed in 2011, and completed the 2011 census. - -Main outcome measuresCOVID-19 related death, assessed between 24 January 2020 and 28 December 2020. We estimated age-standardised mortality rates per 100,000 person-years at risk (ASMR) stratified by sex and occupations. To estimate the effect of occupation due to work-related exposures, we used Cox proportional hazard models to adjust for confounding (region, ethnicity, education), as well as non-workplace factors that are related to occupation. - -ResultsThere is wide variation between occupations in COVID-19 mortality. Several occupations, particularly those involving contact with patients or the public, show three-fold or four-fold risks. These elevated risks were greatly attenuated after adjustment for confounding and mediating non-workplace factors. For example, the hazard ratio (HR) for men working as taxi and cab drivers or chauffeurs changed from 4.60 [95%CI 3.62-5.84] to 1.47 [1.14-1.89] after adjustment. More generally, the overall HR for men working in essential occupations compared with men in non-essential occupations changed from 1.45 [1.34 - 1.56] to 1.22 [1.13 - 1.32] after adjustment. For most occupations, confounding and other mediating factors explained about 70% to 80% of the age-adjusted hazard ratios. - -ConclusionsWorking conditions are likely to play a role in COVID-19 mortality, particularly in occupations involving contact with COVID-19 patients or the public. However, there is also a substantial contribution from non-workplace factors, including regional factors, socio-demographic factors, and pre-pandemic health.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2021.05.13.21257144,2021-05-17,https://medrxiv.org/cgi/content/short/2021.05.13.21257144,REACT-1 round 11 report: low prevalence of SARS-CoV-2 infection in the community prior to the third step of the English roadmap out of lockdown,Steven Riley; David J Haw; Caroline E Walters; Howei Wang; Oliver Eales; Kylie E C Ainslie; Christina Atchison; Claudio Fronterre; Peter J Diggle; Andrew J Page; Alexander J Trotter; Thanh Le Viet; Nabil-Fareed Alikhan; Justin O'Grady; - The COVID-19 Genomics UK (COG-UK) Consortium; Deborah Ashby; Christl Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands; Imperial College London; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; ; Imperial College London; University of Oxford; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London","BackgroundNational epidemic dynamics of SARS-CoV-2 infections are being driven by: the degree of recent indoor mixing (both social and workplace), vaccine coverage, intrinsic properties of the circulating lineages, and prior history of infection (via natural immunity). In England, infections, hospitalisations and deaths fell during the first two steps of the ""roadmap"" for exiting the third national lockdown. The third step of the roadmap in England takes place on 17 May 2021. MethodsWe report the most recent findings on community infections from the REal-time Assessment of Community Transmission-1 (REACT-1) study in which a swab is obtained from a representative cross-sectional sample of the population in England and tested using PCR. Round 11 of REACT-1 commenced self-administered swab-collection on 15 April 2021 and completed collections on 3 May 2021. We compare the results of REACT-1 round 11 to round 10, in which swabs were collected from 11 to 30 March 2021. @@ -3051,17 +3119,7 @@ MethodsAdults aged [≥]18 years from households enrolled in Virus Watch, a pro Results8,517 vaccinated participants (median age 65 years [IQR: 58, 71]), contributed 13,232 samples (8,115 following ChAdOx1, 5,008 following BNT162b2). Seropositivity to Spike was 96.42% (95%CI 96, 96.79) at 28-34 days following a single dose, reaching 99.08% (97.8, 99.62) at 7-14 days after a second dose. Seropositivity rates, and Spike-antibody levels rose more quickly following the first dose of BNT162b2, however, were equivalent for both vaccines by 4 and 8 weeks, respectively. There was evidence of lower S-antibody levels with increasing age (p=0.0001). In partially vaccinated 65-79 year-olds, lower S-antibody levels were observed in men (25.9 vs 42.3 U/ml, p<0.0001), those with a chronic condition (33.0 vs 41.2 U/ml, p<0.0001), diabetes (22.32 vs 36.01 U/ml, p<0.0001), cardiovascular disease (32.1 vs 36.7 U/ml, p=0.0002), or history of cancer (30.1 vs 35.7 U/ml, p=0.0001), particularly those with haematological rather than solid organ cancer (7.48 vs 31.68 U/ml, p<0.0001), and those currently on immunosuppressive therapy (21.7 vs 35.6 U/ml, p<0.0001). Following a second dose, high S-antibody titres ([≥]250U/ml) were observed for nearly all individuals. InterpretationA single dose of either BNT162b2 or ChAdOx1 leads to high Spike seropositivity rates in SARS-CoV-2-naive individuals. However, observed disparities in antibody levels after the first dose by vaccine type, age, and comorbidities highlight the importance of ongoing non-pharmaceutical preventative measures such as social distancing, for partially vaccinated adults, particularly those who are older and more clinically vulnerable.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2021.05.06.21256757,2021-05-14,https://medrxiv.org/cgi/content/short/2021.05.06.21256757,COVID-19 outbreak rates and infection attack rates associated with the workplace: a descriptive epidemiological study,Yiqun Chen; Timothy Aldridge; - UK COVID-19 National Core Studies Consortium; Claire F Ferraro; Fu-Meng Khaw,"Health and Safety Executive, UK; Health and Safety Executive, UK; ; National Infection Service, Public Health England, UK; Public Health England, UK","BackgroundA large number of COVID-19 outbreaks/clusters have been reported in a variety of workplace settings since the start of the pandemic. However, information on the rate of outbreak occurrences which helps to identify the type of workplaces that are more likely to experience an outbreak, or infection attack rates which estimates the potential extent of the virus transmission in an outbreak, has not yet been available to inform intervention strategies to limit transmission. - -ObjectivesTo link datasets on workplace settings and COVID-19 workplace outbreaks in England in order to: identify the geographical areas and workplace sectors with a high rate of outbreaks; and compare infection attack rates by workplace size and sector. - -MethodsWe analysed Public Health England (PHE) HPZone data on COVID-19 outbreaks in workplaces, covering the time period of 18 May - 12 October 2020. The workplaces analysed excluded care homes, hospitals and educational settings. We calculated the workplace outbreak rates by nine English regions, 151 Upper Tier Local Authorities (UTLAs) and twelve industrial sectors, using National Population Database (NPD) data extracted in May 2019 on the total number of the relevant workplaces as the denominator. We also calculated the infection attack rates by enterprise size (small, medium, large) and industrial sector, using PHE Situations of Interest (SOI) data on the number of test-confirmed COVID-19 cases in a workplace outbreak as the numerator, and using NPD data on the number employed in that workplace as the denominator. - -ResultsIn total, 1,317 confirmed workplace outbreaks were identified from HPZone data, of which 1,305 were available for estimation of outbreak rates. The average outbreak rate was 66 per 100,000 workplaces. Of the nine geographical regions in England, the North West had the highest workplace outbreak rate (155/100,000 workplaces), based on 351 outbreaks. Of the UTLAs, the highest workplace outbreak rate was Blackburn with Darwen (387/100,000 workplaces). The industrial sector with the highest workplace outbreak rate was manufacturers and packers of food (1,672/100,000), based on 117 outbreaks: this was consistent across seven of the regions. In addition, high outbreak rates in warehouses were observed in the East Midlands and the North West. - -In total, 390 outbreaks were identified from SOI data and 264 of them allowed for estimation of attack rates. The overall median attack rate was 3.4% of the employed persons with confirmed COVID-19 at a workplace with an outbreak. Most of these outbreaks (162) had an attack rate less than 6%. However, in a small number of outbreaks (57) the attack rate was over 15%. The attack rates increased as the size of the enterprise decreased. The highest attack rate was for outbreaks in close contact services (median 16.5%), which was followed by outbreaks in restaurants and catering (median 10.2%), and in manufacturers and packers of non-food products (median 6.7%). - -ConclusionsOur linked dataset analysis approach allows early identification of geographical regions and industrial sectors with higher rates of COVID-19 workplace outbreaks as well as estimation of attack rates by enterprise size and sector. This can be used to inform interventions to limit transmission of the virus. Our approach to analysing the workplace outbreak data can also be applied to calculation of outbreak rates and attack rates in other types of settings such as care homes, hospitals and educational settings.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2021.05.08.21256867,2021-05-14,https://medrxiv.org/cgi/content/short/2021.05.08.21256867,SARS-CoV-2 lineage dynamics in England from January to March 2021 inferred from representative community samples,Oliver Eales; Andrew Page; Sonja N. Tang; Caroline E. Walters; Haowei Wang; David Haw; Alexander J. Trotter; Thanh Le Viet; Ebenezer Foster-Nyarko; Sophie Prosolek; Christina Atchinson; Deborah Ashby; Graham Cooke; Wendy Barclay; Christl A Donnelly; Justin O'Grady; Erik Volz; - The COVID-19 Genomics UK (COG-UK) Consortium; Ara Darzi; Helen Ward; Paul Elliott; Steven Riley,"School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Quadram Institute, Norwich, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Quadram Institute, Norwich, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; ; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc","Genomic surveillance for SARS-CoV-2 lineages informs our understanding of possible future changes in transmissibility and vaccine efficacy. However, small changes in the frequency of one lineage over another are often difficult to interpret because surveillance samples are obtained from a variety of sources. Here, we describe lineage dynamics and phylogenetic relationships using sequences obtained from a random community sample who provided a throat and nose swab for rt-PCR during the first three months of 2021 as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. Overall, diversity decreased during the first quarter of 2021, with the B.1.1.7 lineage (first identified in Kent) predominant, driven by a 0.3 unit higher reproduction number over the prior wild type. During January, positive samples were more likely B.1.1.7 in younger and middle-aged adults (aged 18 to 54) than in other age groups. Although individuals infected with the B.1.1.7 lineage were no more likely to report one or more classic COVID-19 symptoms compared to those infected with wild type, they were more likely to be antibody positive 6 weeks after infection. Viral load was higher in B.1.1.7 infection as measured by cycle threshold (Ct) values, but did not account for the increased rate of testing positive for antibodies. The presence of infections with non-imported B.1.351 lineage (first identified in South Africa) during January, but not during February or March, suggests initial establishment in the community followed by fade-out. However, this occurred during a period of stringent social distancing and targeted public health interventions and does not immediately imply similar lineages could not become established in the future. Sequence data from representative community surveys such as REACT-1 can augment routine genomic surveillance.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.05.11.21257040,2021-05-13,https://medrxiv.org/cgi/content/short/2021.05.11.21257040,Trajectories of child emotional and behavioural difficulties before and during the COVID-19 pandemic in a longitudinal UK cohort,Elise Paul; Daphne Kounali; Alex Siu Fung Kwong; Daniel Smith; Ilaria Costantini; Deborah A Lawlor; Kapil Sayal; Helen Bould; Nicholas J Timpson; Kate Northstone; Melanie Lewcock; Kate J Tilling; Rebecca Pearson,University College London; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Nottingham; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol,"ImportanceCOVID-19 public health mitigation measures are likely to have detrimental effects on emotional and behavioural problems in children. However, longitudinal studies with pre-pandemic data are scarce. ObjectiveTo explore trajectories of childrens emotional and behavioural difficulties during the COVID-19 pandemic. @@ -3201,6 +3259,21 @@ The dry run showed four main sources of contamination that led to the modificati ConclusionCareful consideration of biosafety issues and contextual factors associated with care home are mandatory for safe use the POCT. Whilst POCT may have some utility for ruling out COVID-19, further diagnostic accuracy evaluations are needed to promote effective adoption.",health systems and quality improvement,fuzzy,90,100 medRxiv,10.1101/2021.04.22.21255911,2021-04-23,https://medrxiv.org/cgi/content/short/2021.04.22.21255911,The impact of SARS-CoV-2 vaccines on antibody responses in the general population in the United Kingdom,Jia Wei; Nicole Stoesser; Philippa C Matthews; Ruth Studley; Iain Bell; John I Bell; John N Newton; Jeremy Farrar; Ian Diamond; Emma Rourke; Alison Howarth; Brian D Marsden; Sarah Hoosdally; E Yvonne Jones; David I Stuart; Derrick W Crook; Tim EA Peto; Koen B Pouwels; David W Eyre; A Sarah Walker; - COVID-19 Infection Survey team,"University of Oxford; University of Oxford; University of Oxford; Office for National Statistics, UK; Office for National Statistics, UK; University of Oxford; Public Health England; Wellcome Trust; Office for National Statistics, UK; Office for National Statistics, UK; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; ","Real-world data on antibody response post-vaccination in the general population are limited. 45,965 adults in the UKs national COVID-19 Infection Survey receiving Pfizer-BioNTech or Oxford-AstraZeneca vaccines had 111,360 anti-spike IgG measurements. Without prior infection, seroconversion rates and quantitative antibody levels post single dose were lower in older individuals, especially >60y. Two doses achieved high responses across all ages, particularly increasing seroconversion in older people, to similar levels to those achieved after prior infection followed by a single dose. Antibody levels rose more slowly and to lower levels with Oxford-AstraZeneca vs Pfizer-BioNTech, but waned following a single Pfizer-BioNTech dose. Latent class models identified four responder phenotypes: older people, males, and those having long-term health conditions were more commonly low responders. Where supplies are limited, vaccines should be prioritised for those not previously infected, and second doses to individuals >60y. Further data on the relationship between vaccine-mediated protection and antibody responses are needed.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2021.04.22.21255913,2021-04-23,https://medrxiv.org/cgi/content/short/2021.04.22.21255913,Impact of vaccination on SARS-CoV-2 cases in the community: a population-based study using the UK COVID-19 Infection Survey,Emma Pritchard; Philippa Matthews; Nicole Stoesser; David Eyre; Owen Gethings; Karina-Doris Vitha; Joel Jones; Thomas House; Harper VanSteenhouse; Iain Bell; John Bell; John Newton; Jeremy Farrar; Ian Diamond; Emma Rourke; Ruth Studley; Derrick W Crook; tim E peto; Ann Sarah Walker; Koen B Pouwels,"University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; University of Oxford; Office for National Statistics; University of Manchester; Glasgow Lighthouse Laboratory; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; Office for National Statistics,; Office for National Statistics; Office for National Statistics; NIHR Oxford Biomedical Research Centre; oxford university; University of Oxford; University of Oxford","ObjectivesTo assess the effectiveness of COVID-19 vaccination in preventing SARS-CoV-2 infection in the community. + +DesignProspective cohort study. + +SettingThe UK population-representative longitudinal COVID-19 Infection Survey. + +Participants373,402 participants aged [≥]16 years contributing 1,610,562 RT-PCR results from nose and throat swabs between 1 December 2020 and 3 April 2021. + +Main outcome measuresNew RT-PCR-positive episodes for SARS-CoV-2 overall, by self-reported symptoms, by cycle threshold (Ct) value (<30 versus [≥]30), and by gene positivity (compatible with the B.1.1.7 variant versus not). + +ResultsOdds of new SARS-CoV-2 infection were reduced 65% (95% CI 60 to 70%; P<0.001) in those [≥]21 days since first vaccination with no second dose versus unvaccinated individuals without evidence of prior infection (RT-PCR or antibody). In those vaccinated, the largest reduction in odds was seen post second dose (70%, 95% CI 62 to 77%; P<0.001).There was no evidence that these benefits varied between Oxford-AstraZeneca and Pfizer-BioNTech vaccines (P>0.9).There was no evidence of a difference in odds of new SARS-CoV-2 infection for individuals having received two vaccine doses and with evidence of prior infection but not vaccinated (P=0.89). Vaccination had a greater impact on reducing SARS-CoV-2 infections with evidence of high viral shedding Ct<30 (88% reduction after two doses; 95% CI 80 to 93%; P<0.001) and with self-reported symptoms (90% reduction after two doses; 95% CI 82 to 94%; P<0.001); effects were similar for different gene positivity patterns. + +ConclusionVaccination with a single dose of Oxford-AstraZeneca or Pfizer-BioNTech vaccines, or two doses of Pfizer-BioNTech, significantly reduced new SARS-CoV-2 infections in this large community surveillance study. Greater reductions in symptomatic infections and/or infections with a higher viral burden are reflected in reduced rates of hospitalisations/deaths, but highlight the potential for limited ongoing transmission from asymptomatic infections in vaccinated individuals. + +RegistrationThe study is registered with the ISRCTN Registry, ISRCTN21086382.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.04.12.21255275,2021-04-19,https://medrxiv.org/cgi/content/short/2021.04.12.21255275,Children develop strong and sustained cross-reactive immune responses against spike protein following SARS-CoV-2 infection,Alexander C Dowell; Megan S. Butler; Elizabeth Jinks; Gokhan Tut; Tara Lancaster; Panagiota Sylla; Jusnara Begum; Rachel Bruton; Hayden Pearce; Kriti Verma; Nicola Logan; Grace Tyson; Eliska Spalkova; Sandra Margielewska-Davies; Graham S. Taylor; Eleni Syrimi; Frances Baawuah; Joanne Beckmann; Ifeanyichukwu Okike; Shazaad Ahmad; Joanna Garstang; Andrew Brent; Bernadette Brent; Georgina Ireland; Felicity Aiano; Zahin Amin-Chowdhury; Samuel Jones; Ray Borrow; Ezra Linley; Rafaq Azad; John Wright; Dagmar Waiblinger; Chris Davis; Emma C Thomson; Massimo Palmarini; Brian James Willett; Wendy S Barclay; John Poh; Vanessa Saliba; Gayatri Amirthalingam; Kevin Brown; Mary Ramsay; Jianmin Zuo; Paul Moss; Shamez Ladhani,"Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; University of Birmingham; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; University of Birmingham; MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61-1QH, UK; MRC-University of Glasgow Centre for Virus Research, 464 Bearsden Road, Glasgow G61-1QH, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; East London NHS Foundation Trust, 9 Allie Street, London E1 8DE, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK 4. University Hospitals of Derby and Burton NHS Foundation Trust, Uttoxeter New Road, Derby; Manchester University NHS Foundation Trust, Oxford Road, Manchester M13 9WL, UK; Birmingham Community Healthcare NHS Trust, Holt Street, Aston B7 4BN, UK; Oxford University Hospitals NHS Foundation Trust, Old Road, Oxford OX3 7HE University of Oxford, Wellington Square, Oxford OX1 2JD, UK; Oxford University Hospitals NHS Foundation Trust, Old Road, Oxford OX3 7HE; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Public Health England, Manchester Royal Infirmary, Manchester, United Kingdom; Public Health England, Manchester Royal Infirmary, Manchester, United Kingdom; Bradford Teaching Hospitals NHS Foundation Trust; Bradford Teaching Hospitals NHS Foundation Trust; Bradford Teaching Hospitals NHS Foundation Trust; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; Imperial College, London; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Institute of Immunology & Immunotherapy, Collage of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK; Public Health England, 61 Colindale Avenue, London NW9 5EQ, UK","SARS-CoV-2 infection is generally mild or asymptomatic in children but the biological basis for this is unclear. We studied the profile of antibody and cellular immunity in children aged 3-11 years in comparison with adults. Antibody responses against spike and receptor binding domain (RBD) were high in children and seroconversion boosted antibody responses against seasonal Beta-coronaviruses through cross-recognition of the S2 domain. Seroneutralisation assays against alpha, beta and delta SARS-CoV-2 variants demonstrated comparable neutralising activity between children and adults. T cell responses against spike were >2-fold higher in children compared to adults and displayed a TH1 cytokine profile. SARS-CoV-2 spike-specific T cells were also detected in many seronegative children, revealing pre-existing responses that were cross-reactive with seasonal Alpha and Beta-coronaviruses. Importantly, all children retained high antibody titres and cellular responses at 6 months after infection whilst relative antibody waning was seen in adults. Spike-specific responses in children also remained broadly stable beyond 12 months. Children thus distinctly generate robust, cross-reactive and sustained immune responses after SARS-CoV-2 infection with focussed specificity against spike protein. These observations demonstrate novel features of SARS-CoV-2-specific immune responses in children and may provide insight into their relative clinical protection. Furthermore, this information will help to guide the introduction of vaccination regimens in the paediatric population.",allergy and immunology,fuzzy,100,100 medRxiv,10.1101/2021.04.08.21255100,2021-04-15,https://medrxiv.org/cgi/content/short/2021.04.08.21255100,REACT-1 round 10 report: Level prevalence of SARS-CoV-2 swab-positivity in England during third national lockdown in March 2021,Steven Riley; Oliver Eales; David Haw; Caroline E. Walters; Haowei Wang; Kylie E. C. Ainslie; Christina Atchinson; Claudio Fronterre; Peter J. Diggle; Deborah Ashby; Christl A Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear","BackgroundIn England, hospitalisations and deaths due to SARS-CoV-2 have been falling consistently since January 2021 during the third national lockdown of the COVID-19 pandemic. The first significant relaxation of that lockdown occurred on 8 March when schools reopened. @@ -3282,6 +3355,15 @@ ResultsThirty-three papers met the inclusion criteria, only three of which were ConclusionsThe limited evidence suggests that health certification in relation to COVID-19 - outside of the context of international travel - has the potential for harm as well as benefit. Realising the benefits while minimising the harms will require real-time evaluations allowing modifications to maximise the potential contribution of certification to enable safer access to a range of activities.",public and global health,fuzzy,100,100 medRxiv,10.1101/2021.04.07.21254497,2021-04-09,https://medrxiv.org/cgi/content/short/2021.04.07.21254497,Characterising contact in disease outbreaks via a network model of spatial-temporal proximity,Ashleigh C Myall; Robert L Peach; Yu Wan; Siddharth Mookerjee; Elita Jauneikaite; Frankie Bolt; James Richard Price; Frances Davies; Andrea Yeong Wiesse; Alison Holmes; Mauricio Barahona,Imperial College London; Imperial College London; Imperial College London; Imperial College NHS Trust; Imperial College London; Imperial College London; Imperial College London; Imperial College NHS Trust; University of Edinburgh; Imperial College London; Imperial College London,"Contact tracing is a key tool in epidemiology to identify and control outbreaks of infectious diseases. Existing contact tracing methodologies produce contact maps of individuals based on a binary definition of contact which can be hampered by missing data and indirect contacts. Here, we present a Spatial-temporal Epidemiological Proximity (StEP) model to recover contact maps in disease outbreaks based on movement data. The StEP model accounts for imperfect data by considering probabilistic contacts between individuals based on spatial-temporal proximity of their movement trajectories, creating a robust movement network despite possible missing data and unseen transmission routes. Using real-world data we showcase the potential of StEP for contact tracing with outbreaks of multidrug-resistant bacteria and COVID-19 in a large hospital group in London, UK. In addition to the core structure of contacts that can be recovered using traditional methods of contact tracing, the StEP model reveals missing contacts that connect seemingly separate outbreaks. Comparison with genomic data further confirmed that these recovered contacts indeed improve characterisation of disease transmission and so highlights how the StEP framework can inform effective strategies of infection control and prevention.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2021.04.01.21254765,2021-04-07,https://medrxiv.org/cgi/content/short/2021.04.01.21254765,"Mental health inequalities in healthcare, economic, and housing disruption during COVID -19: an investigation in 12 longitudinal studies",Giorgio Di Gessa; Jane Maddock; Michael J Green; Ellen J Thompson; Eoin McElroy; Helena L Davies; Jessica Mundy; Anna J Stevenson; Alex S.F Kwong; Gareth J Griffith; Srinivasa Vittal Katikireddi; Claire L Niedzwiedz; George B Ploubidis; Emla Fitzsimons; Morag Henderson; Richard J. Silverwood; Nishi Chaturvedi; Gerome Breen; Claire J Steves; Andrew Steptoe; David J Porteous; Praveetha Patalay,"Institute of Epidemiology and Health Care, University College London; MRC Unit for Lifelong Health and Ageing, University College London; MRC/CSO Social & Public Health Sciences Unit, University of Glasgow; Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, Kings College London; Department of Neuroscience, Psychology and Behaviour, University of Leicester; Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, Kings College London; Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, Kings College London; Centre for Genomic and Experimental Medicine, University of Edinburgh; Division of Psychiatry, University of Edinburgh and MRC Integrative Epidemiology Unit, University of Bristol; MRC Integrative Epidemiology Unit, University of Bristol; MRC/CSO Social & Public Health Sciences Unit, University of Glasgow; Institute of Health & Wellbeing, University of Glasgow; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; MRC Unit for Lifelong Health and Ageing, University College London; Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, Kings College London and Maudsley Biomedical Research Cen; Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, Kings College London; Institute of Epidemiology and Health Care, University College London; Centre for Genomic and Experimental Medicine, University of Edinburgh; Centre for Longitudinal Studies and MRC Unit for Lifelong Health and Ageing, University College London","BackgroundThe COVID-19 pandemic and associated virus suppression measures have disrupted lives and livelihoods and people already experiencing mental ill-health may have been especially vulnerable. + +AimTo quantify mental health inequalities in disruptions to healthcare, economic activity and housing. + +Method59,482 participants in 12 UK longitudinal adult population studies with data collected prior to and during the COVID-19 pandemic. Within each study we estimated the association between psychological distress assessed pre-pandemic and disruptions since the start of the pandemic to three domains: healthcare (medication access, procedures, or appointments); economic activity (employment, income, or working hours); and housing (change of address or household composition). Meta-analyses were used to pool estimates across studies. + +ResultsAcross the analysed datasets, one to two-thirds of participants experienced at least one disruption, with 2.3-33.2% experiencing disruptions in two or more domains. One standard deviation higher pre-pandemic psychological distress was associated with: (i) increased odds of any healthcare disruptions (OR=1.30; [95% CI:1.20-1.40]) with fully adjusted ORs ranging from 1.24 [1.09-1.41] for disruption to procedures and 1.33 [1.20- 1.49] for disruptions to prescriptions or medication access; (ii) loss of employment (OR=1.13 [1.06-1.21]) and income (OR=1.12 [1.06 -1.19]) and reductions in working hours/furlough (OR=1.05 [1.00-1.09]); (iii) no associations with housing disruptions (OR=1.00 [0.97-1.03]); and (iv) increased likelihood of experiencing a disruption in at least two domains (OR=1.25 [1.18-1.32]) or in one domain (OR=1.11 [1.07-1.16]) relative to no disruption. + +ConclusionPeople experiencing psychological distress pre-pandemic have been more likely to experience healthcare and economic disruptions, and clusters of disruptions across multiple domains during the pandemic. Failing to address these disruptions risks further widening the existing inequalities in mental health.",psychiatry and clinical psychology,fuzzy,100,100 medRxiv,10.1101/2021.04.01.21254789,2021-04-07,https://medrxiv.org/cgi/content/short/2021.04.01.21254789,Mendelian randomisation identifies alternative splicing of the FAS death receptor as a mediator of severe COVID-19,Lucija Klaric; Jack S Gisby; Artemis Papadaki; Marisa D Muckian; Erin Macdonald-Dunlop; Jing Hua Zhao; Alex Tokolyi; Elodie Persyn; Erola Pairo-Castineira; Andrew P Morris; Anette Kalnapenkis; Anne Richmond; Arianna Landini; Ã…sa K Hedman; Bram Prins; Daniela Zanetti; Eleanor Wheeler; Charles Kooperberg; Chen Yao; John R Petrie; Jingyuan Fu; Lasse Folkersen; Mark Walker; Martin Magnusson; Niclas Eriksson; Niklas Mattsson-Carlgren; Paul RHJ Timmers; Shih-Jen Hwang; Stefan Enroth; Stefan Gustafsson; Urmo Vosa; Yan Chen; Agneta Siegbahn; Alexander Reiner; Ã…sa Johansson; Barbara Thorand; Bruna Gigante; Caroline Hayward; Christian Herder; Christian Gieger; Claudia Langenberg; Daniel Levy; Daria V Zhernakova; J Gustav Smith; Harry Campbell; Johan Sundstrom; John Danesh; Karl Michaëlsson; Karsten Suhre; Lars Lind; Lars Wallentin; Leonid Padyukov; Mikael Landén; Nicholas J Wareham; Andreas Göteson; Oskar Hansson; Per Eriksson; Rona J Strawbridge; Themistocles L Assimes; Tõnu Esko; Ulf Gyllensten; J Kenneth Baillie; Dirk S Paul; Peter K Joshi; Adam S Butterworth; Anders Mälarstig; Nicola Pirastu; James F Wilson; James E Peters,"MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, United Kingdom; Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, United Kingdom; Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, United Kingdom; Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, United Kingdom; Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, United Kingdom; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom; Department of Human Genetics, Wellcome Sanger Institute, Hinxton, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK; Centre for Genetics and Genomics Versus Arthritis, Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK; Institute of Genomics, University of Tartu, Tartu, Estonia; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, United Kingdom; Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, United Kingdom; Department of Medicine, Karolinska Institute, Stockholm, Sweden; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom; Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA; MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA; Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands; Danish National Genome Center, Copenhagen, Denmark.; Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK; Department of Clinical Sciences, Lund University, Malmö, Sweden; Uppsala Clinical Research Center (UCR), Uppsala University, Uppsala, Sweden; Clinical Memory Research Unit, Faculty of Medicine, Lund University, Lund, Sweden; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, United Kingdom; Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA; Department of Immunology, Genetics and Pathology, Uppsala University, Sweden; Department of Medical Sciences, Uppsala University, Uppsala, Sweden; Institute of Genomics, University of Tartu, Tartu, Estonia; Department of Medicine Solna, Karolinska Institutet; Department of Medical Sciences, Uppsala University, Uppsala, Sweden; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Department of Immunology, Genetics and Pathology, Uppsala University, Sweden; Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, München-Neuherberg, Germany; Division of Cardiovascular Medicine, Dept of Medicine, Karolinska Institutet, Stockholm, Sweden; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, United Kingdom; Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, München-Neuherberg, Germany; MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK; Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA; University of Groningen, University Medical Center Groningen, Department of Genetics, Groningen, the Netherlands; Department of Cardiology, Clinical Sciences, Lund University and SkÃ¥ne University Hospital, Lund, Sweden; Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, United Kingdom; Department of Medical Sciences, Uppsala University, Uppsala, Sweden; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom; Department of Surgcial Sciences, Unit of Medical Epidemiology, Uppsala University, Uppsala, Sweden; Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Doha, Qatar; Department of Medical Sciences, Uppsala University, Uppsala, Sweden; Department of Medical Sciences and Uppsala Clinical Research Center, Uppsala University, Uppsala, Sweden; Division of Rheumatology, Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden; Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden; MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK; Institute of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden; Clinical Memory Research Unit, Department of Clinical Sciences, Lund University, Lund, Sweden; Division of Cardiovascular Medicine, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden; Institute of Health and Wellbeing, College of Medicine, Veterinary and Life Sciences, University of Glasgow, UK; Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA; Institute of Genomics, University of Tartu, Tartu, Estonia; Department of Immunology, Genetics and Pathology, Uppsala University, Sweden; Roslin Institute, University of Edinburgh, Easter Bush, Edinburgh, EH25 9RG, UK; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK; Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, United Kingdom; British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom; Karolinska Institute, Stockholm, Sweden; Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, United Kingdom; Centre for Global Health Research, Usher Institute, University of Edinburgh, Teviot Place, Edinburgh, United Kingdom; Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, UK","Severe COVID-19 is characterised by immunopathology and epithelial injury. Proteomic studies have identified circulating proteins that are biomarkers of severe COVID-19, but cannot distinguish correlation from causation. To address this, we performed Mendelian randomisation (MR) to identify proteins that mediate severe COVID-19. Using protein quantitative trait loci (pQTL) data from the SCALLOP consortium, involving meta-analysis of up to 26,494 individuals, and COVID-19 genome-wide association data from the Host Genetics Initiative, we performed MR for 157 COVID-19 severity protein biomarkers. We identified significant MR results for five proteins: FAS, TNFRSF10A, CCL2, EPHB4 and LGALS9. Further evaluation of these candidates using sensitivity analyses and colocalization testing provided strong evidence to implicate the apoptosis-associated cytokine receptor FAS as a causal mediator of severe COVID-19. This effect was specific to severe disease. Using RNA-seq data from 4,778 individuals, we demonstrate that the pQTL at the FAS locus results from genetically influenced alternate splicing causing skipping of exon 6. We show that the risk allele for very severe COVID-19 increases the proportion of transcripts lacking exon 6, and thereby increases soluble FAS. Soluble FAS acts as a decoy receptor for FAS-ligand, inhibiting apoptosis induced through membrane-bound FAS. In summary, we demonstrate a novel genetic mechanism that contributes to risk of severe of COVID-19, highlighting a pathway that may be a promising therapeutic target.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.03.31.21254687,2021-04-05,https://medrxiv.org/cgi/content/short/2021.03.31.21254687,"SARS-CoV-2 infectivity by viral load, S gene variants and demographic factors and the utility of lateral flow devices to prevent transmission",Lennard YW Lee; Stefan Rozmanowski; Matthew Pang; Andre Charlett; Charlotte Anderson; Gareth J Hughes; Matthew Barnard; Leon Peto; Richard Vipond; Alex Sienkiewicz; Susan Hopkins; John Bell; Derrick W Crook; Nick Gent; A Sarah Walker; Tim EA Peto; David W Eyre,University of Oxford; UK Government Department of Health and Social Care; UK Government Department of Health and Social Care; Public Health England; Public Health England; Public Health England; UK Government Department of Health and Social Care; University of Oxford; Public Health England; Public Health England; Public Health England; University of Oxford; University of Oxford; Public Health England; University of Oxford; University of Oxford; University of Oxford,"BackgroundHow SARS-CoV-2 infectivity varies with viral load is incompletely understood. Whether rapid point-of-care antigen lateral flow devices (LFDs) detect most potential transmission sources despite imperfect sensitivity is unknown. @@ -3301,13 +3383,6 @@ FindingsWe recorded 446 incident cases of COVID-19 in 15,227 participants (2.9%) InterpretationAfter rigorous adjustment for factors influencing exposure to SARS-CoV-2, Asian/Asian British ethnicity and raised BMI were associated with increased risk of developing COVID-19, while atopic disease was associated with decreased risk. FundingBarts Charity, Health Data Research UK",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2021.03.21.21254061,2021-03-26,https://medrxiv.org/cgi/content/short/2021.03.21.21254061,Quantitative SARS-CoV-2 anti-spike responses to Pfizer-BioNTech and Oxford-AstraZeneca vaccines by previous infection status,David W Eyre; Sheila F Lumley; Jia Wei; Stuart Cox; Tim James; Anita Justice; Gerald Jesuthasan; Alison Howarth; Stephanie B Hatch; Brian D Marsden; E Yvonne Jones; David I Stuart; Daniel Ebner; Sarah Hoosdally; Derrick Crook; Tim EA Peto; Timothy M Walker; Nicole EA Stoesser; Philippa C Matthews; Koen B Pouwels; A Sarah Walker; Katie Jeffery,University of Oxford; University of Oxford; University of Oxford; Oxford University Hospitals; Oxford University Hospitals; Oxford University Hospitals; Oxford University Hospitals; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Oxford University Hospitals,"ObjectivesWe investigate determinants of SARS-CoV-2 anti-spike IgG responses in healthcare workers (HCWs) following one or two doses of Pfizer-BioNTech or Oxford-AstraZeneca vaccines. - -MethodsHCWs participating in regular SARS-CoV-2 PCR and antibody testing were invited for serological testing prior to first and second vaccination, and 4 weeks post-vaccination if receiving a 12-week dosing interval. Quantitative post-vaccination anti-spike antibody responses were measured using the Abbott SARS-CoV-2 IgG II Quant assay (detection threshold: [≥]50 AU/ml). We used multivariable logistic regression to identify predictors of seropositivity and generalised additive models to track antibody responses over time. - -ResultsVaccine uptake was 80%, but less in lower-paid roles and Black, south Asian and minority ethnic groups. 3570/3610(98.9%) HCWs were seropositive >14 days post-first vaccination and prior to second vaccination, 2706/2720(99.5%) after Pfizer-BioNTech and 864/890(97.1%) following Oxford-AstraZeneca vaccines. Previously infected and younger HCWs were more likely to test seropositive post-first vaccination, with no evidence of differences by sex or ethnicity. All 470 HCWs tested >14 days after second vaccine were seropositive. Quantitative antibody responses were higher after previous infection: median(IQR) >21 days post-first Pfizer-BioNTech 14,604(7644-22,291) AU/ml vs. 1028(564-1985) AU/ml without prior infection (p<0.001). Oxford-AstraZeneca vaccine recipients had lower readings post-first dose compared to Pfizer-BioNTech, with and without previous infection, 10,095(5354-17,096) and 435(203-962) AU/ml respectively (both p<0.001 vs. Pfizer-BioNTech). Antibody responses post-second vaccination were similar to those after prior infection and one vaccine dose. - -ConclusionsVaccination leads to detectable anti-spike antibodies in nearly all adult HCWs. Whether differences in response impact vaccine efficacy needs further study.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.03.21.21253968,2021-03-26,https://medrxiv.org/cgi/content/short/2021.03.21.21253968,Characteristics of Long Covid: findings from a social media surve,Nida Ziauddeen; Deepti Gurdasani; Margaret E O'Hara; Claire Hastie; Paul Roderick; Guiqing Yao; Nisreen A Alwan,"University of Southampton; Queen Mary University of London; Patient contributor, Long Covid Support: www.longcovid.org; Patient contributor, Long Covid Support: www.longcovid.org; University of Southampton; University of Leicester; University of Southampton","Many people are not recovering for months after being infected with SARS-CoV-2. Long Covid has emerged as a major public health concern that needs defining, quantifying, and describing. We aimed to explore the initial and ongoing symptoms of Long Covid following SARS-CoV-2 infection and describe its impact on daily life in people who were not admitted to hospital during the first two weeks of the illness. We co-produced a survey with people living with Long Covid. We collected the data through an online survey using convenience non-probability sampling, with the survey posted both specifically on Long Covid support groups and generally on social media. The criteria for inclusion were adults with lab-confirmed (PCR or antibody) or suspected COVID-19 managed in the community (non-hospitalised) in the first two weeks of illness. We used agglomerative hierarchical clustering to identify specific symptom clusters, and their demographic and functional correlates. We analysed data from 2550 participants with a median duration of illness of 7.7 months (interquartile range (IQR) 7.4-8.0). The mean age was 46.5 years (standard deviation 11 years) with 82.8% females and 79.9% of participants based in the UK. 89.5% described their health as good, very good or excellent before COVID-19. The most common initial symptoms that persisted were exhaustion, chest pressure/tightness, shortness of breath and headache. Cough, fever, and chills were common initial symptoms that became less prevalent later in the illness, whereas cognitive dysfunction and palpitations became more prevalent later in the illness. 26.5% reported lab-confirmation of infection. The biggest difference in ongoing symptoms between those who reported testing positive and those who did not was loss of smell/taste. Ongoing symptoms affected at least 3 organ systems in 83.5% of participants. @@ -3378,6 +3453,13 @@ ResultsWe observed a small proportion of care home residents with positive PCR t ConclusionsIncreased risk of infection after 21-days was associated with frailty. We found most infections occurred within 28-days of vaccination, suggesting extra precautions to reduce transmission risk should be taken in this time frame.",geriatric medicine,fuzzy,100,100 medRxiv,10.1101/2021.03.16.21253371,2021-03-24,https://medrxiv.org/cgi/content/short/2021.03.16.21253371,Axes of Prognosis: Identifying Subtypes of COVID-19 Outcomes,Emma Whitfield; Claire Coffey; Huayu Zhang; Ting Shi; Xiaodong Wu; Qiang Li; Honghan Wu,"Institute of Health Informatics, UCL, London, United Kingdom; University of Cambridge, Cambridge, United Kingdom; Usher Institute, University of Edinburgh, United Kingdom; Usher Institute, University of Edinburgh, United Kingdom; Shanghai East Hospital, Tongji University, Shanghai, China; Shanghai East Hospital, Tongji University, Shanghai, China; Institute of Health Informatics, UCL, London, United Kingdom","COVID-19 is a disease with vast impact, yet much remains unclear about patient outcomes. Most approaches to risk prediction of COVID-19 focus on binary or tertiary severity outcomes, despite the heterogeneity of the disease. In this work, we identify heterogeneous subtypes of COVID-19 outcomes by considering axes of prognosis. We propose two innovative clustering approaches - Layered Axes and Prognosis Space - to apply on patients outcome data. We then show how these clusters can help predict a patients deterioration pathway on their hospital admission, using random forest classification. We illustrate this methodology on a cohort from Wuhan in early 2020. We discover interesting subgroups of poor prognosis, particularly within respiratory patients, and predict respiratory subgroup membership with high accuracy. This work could assist clinicians in identifying appropriate treatments at patients hospital admission. Moreover, our method could be used to explore subtypes of long COVID and other diseases with heterogeneous outcomes.",health informatics,fuzzy,100,92 +medRxiv,10.1101/2021.03.16.21253377,2021-03-24,https://medrxiv.org/cgi/content/short/2021.03.16.21253377,First and second SARS-CoV-2 waves in inner London: A comparison of admission characteristics and the effects of the B.1.1.7 variant,Luke B Snell; Wenjuan Wang; Adela Alcolea-Medina; Themoula Charalampous; Gaia Nebbia; Rahul Batra; Leonardo de Jongh; Finola Higgins; Yanzhong Wang; Jonathan D Edgeworth; Vasa Curcin,"King's College London; School of Population Health and Environmental Sciences, King's College London, London, UK; Viapath, London, UK; Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK; Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK; Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK; NIHR Biomedical Research Centre, Guy's and St Thomas' NHS Foundation Trust; NIHR Biomedical Research Centre, Guy's and St Thomas' NHS Foundation Trust; School of Population Health and Environmental Sciences, King's College London, London, UK; Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK; School of Population Health and Environmental Sciences, King's College London, London, UK","IntroductionA second wave of SARS-CoV-2 infection spread across the UK in 2020 linked with emergence of the more transmissible B.1.1.7 variant. The emergence of new variants, particularly during relaxation of social distancing policies and implementation of mass vaccination, highlights the need for real-time integration of detailed patient clinical data alongside pathogen genomic data. We linked clinical data with viral genome sequence data to compare cases admitted during the first and second waves of SARS-CoV-2 infection. + +MethodsClinical, laboratory and demographic data from five electronic health record (EHR) systems was collected for all cases with a positive SARS-CoV-2 RNA test between March 13th 2020 and February 17th 2021. SARS-CoV-2 viral sequencing was performed using Oxford Nanopore Technology. Descriptive data are presented comparing cases between waves, and between cases of B.1.1.7 and non-B.1.1.7 variants. + +ResultsThere were 5810 SARS-CoV-2 RNA positive cases comprising inpatients (n=2341), healthcare workers (n=1549), outpatients (n=874), emergency department (ED) attenders not subsequently admitted (n=532), inter-hospital transfers (n=281) and nosocomial cases (n=233). There were two dominant waves of hospital admissions, with wave one starting from March 13th (n=838) and wave two from October 20th (n=1503), both with a temporally aligned rise in nosocomial cases (n=96 in wave one, n=137 in wave two). 1470 SARS-CoV-2 isolates were successfully sequenced, including 216/838 (26%) admitted cases from wave one, 472/1503 (31%) admitted cases in wave two and 121/233 (52%) nosocomial cases. The first B.1.1.7 variant was identified on 15th November 2020 and increased rapidly such that it comprised 400/472 (85%) of sequenced isolates from admitted cases in wave two. Females made up a larger proportion of admitted cases in wave two (47.3% vs 41.8%, p=0.011), and in those infected with the B.1.1.7 variant compared to non-B.1.1.7 variants (48.0% vs 41.8%, p=0.042). A diagnosis of frailty was less common in wave two (11.5% v 22.8%, p<0.001) and in the group infected with B.1.1.7 (14.5% v 22.4%, p=0.001). There was no difference in severity on admission between waves, as measured by hypoxia at admission (wave one: 64.3% vs wave two: 65.5%, p=0.67). However, a higher proportion of cases infected with the B.1.1.7 variant were hypoxic on admission compared to other variants (70.0% vs 62.5%, p=0.029). + +ConclusionsAutomated EHR data extraction linked with SARS-CoV-2 genome sequence data provides valuable insight into the evolving characteristics of cases admitted to hospital with COVID-19. The proportion of cases with hypoxia on admission was greater in those infected with the B.1.1.7 variant, which supports evidence the B.1.1.7 variant is associated with more severe disease. The number of nosocomial cases was similar in both waves despite introduction of many infection control interventions before wave two, an observation requiring further investigation.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.03.15.21253542,2021-03-24,https://medrxiv.org/cgi/content/short/2021.03.15.21253542,Comparison between one and two dose SARS-CoV-2 vaccine prioritisation for a fixed number of vaccine doses,Edward M Hill; Matt J Keeling,University of Warwick; University of Warwick,"The swift development of SARS-CoV-2 vaccines has been met with worldwide commendation. How-ever, in the context of an ongoing pandemic there is an interplay between infection and vaccination. Whilst infection can grow exponentially, vaccination rates are generally limited by supply and logistics. With the first SARS-CoV-2 vaccines receiving medical approval requiring two doses, there has been scrutiny on the spacing between doses; an elongated period between doses allows more of the population to receive a first vaccine dose in the short-term generating wide-spread partial immunity. Focusing on data from England, we investigated prioritisation of a one dose or two dose vaccination schedule given a fixed number of vaccine doses and with respect to a measure of maximising averted deaths. We optimised outcomes for two different estimates of population size and relative risk of mortality for at-risk groups within the Phase 1 vaccine priority order. Vaccines offering relatively high protection from the first dose favour strategies that prioritise giving more people one dose, although with increasing vaccine supply eventually those eligible and accepting vaccination will receive two doses. Whilst optimal dose timing can substantially reduce the overall mortality risk, there needs to be careful consideration of the logistics of vaccine delivery.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.03.18.21253888,2021-03-23,https://medrxiv.org/cgi/content/short/2021.03.18.21253888,"Long Covid in adults discharged from UK hospitals after Covid-19: A prospective, multicentre cohort study using the ISARIC WHO Clinical Characterisation Protocol.",Louise Sigfrid; Tom M Drake; Ellen Pauley; Edwin C Jesudason; Piero Olliaro; Wei Shen Lim; Annelise Gillesen; Colin Berry; David Lowe; Joanne McPeake; Nazir Lone; Muge Cevik; Daniel Munblit; Anna Casey; Peter Bannister; Clark D Russell; Lynsey Goodwin; Antonia Ho; Lance Turtle; Margret E O'Hara; Claire Hastie; Chloe Donohue; Rebecca Spencer; Cara Donegan; Alison Gummery; Janet Harrison; Hayley Hardwick; Claire E Hastie; Gail Carson; Laura Merson; John Kenneth Baillie; Peter Openshaw; Ewen M Harrison; Annemarie Docherty; Malcolm G Semple; Janet T Scott,"ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK; Centre for Medical Informatics, University of Edinburgh, Edinburgh, UK; University of Edinburgh Medical School, Edinburgh, UK.; NHS Lothian, Edinburgh, UK,; ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK.; Department of Respiratory Medicine, Nottingham University Hospitals NHS Trust, Nottingham, UK.; ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK.; Institute of Cardiovascular and Medical Sciences, University of Glasgow, UK; NHS Greater Glasgow and Clyde, Emergency Department, Glasgow, UK; School of Medicine, Dentistry and Nursing, University of Glasgow, UK; Usher Institute, University of Edinburgh, Edinburgh, UK; University of St Andrews; Sechenov First Moscow State Medical University, Imperial College London, Imperial College London, RSMU; Medical Student, Brighton and Sussex Medical School, UK; Brighton & Sussex Medical School, Brighton, UK; Centre for Inflammation Research, University of Edinburgh, UK; Institute of Infection, Veterinary and Ecological Studies, Univeristy of Liverpool. Tropical and Infectious Diseases Unit, North Manchester General Hospital, De; University of Glasgow, Glasgow, UK; NIHR Health Protection Research Unit in emerging and zoonotic infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, L; Long COVID Support, Birmingham, UK; Long COVID Support, Birmingham, UK; Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK; Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK.; Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK.; Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool, UK.; National Institute of Health Research (NIHR) Health Protection research Unit in Emerging and Zoonotic Infections, Liverpool, UK. 2. Institute of Infection and G; National Institute of Health Research (NIHR) Health Protection research Unit in Emerging and Zoonotic Infections, Liverpool, UK. 2. Institute of Infection and G; Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK.; ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK.; ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, UK; Roslin Institute, University of Edinburgh, Edinburgh, UK; National Heart and Lung Institute, Imperial College, London UK.; Director Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK.; Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, UK. 2. Intensive Care Unit, Royal Infirmary Edinburgh, Edinburgh, UK; Health Protection Research Unit In Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, UK 2. ; MRC-University of Glasgow Center for Virus research","Structured AbstractO_ST_ABSObjectivesC_ST_ABSThe long-term consequences of severe Covid-19 requiring hospital admission are not well characterised. The objective of this study was to establish the long-term effects of Covid-19 following hospitalisation and the impact these may have on patient reported outcome measures. @@ -3411,7 +3493,21 @@ FindingsOf 6,775 participants in UKB who had tested positive for infection with InterpretationShorter LTL, indicative of older biological age, is associated with higher risk of adverse COVID-19 outcomes, independent of several major risk factors for COVID-19 including chronological age. Further data are needed to determine whether this association reflects causality. FundingUK Medical Research Council, Biotechnology and Biological Sciences Research Council and British Heart Foundation.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2021.03.11.21253275,2021-03-21,https://medrxiv.org/cgi/content/short/2021.03.11.21253275,Effect of vaccination on transmission of COVID-19: an observational study in healthcare workers and their households,Anoop Shah; Ciara Gribben; Jennifer Bishop; Peter Hanlon; David Caldwell; Rachael Wood; Martin Reid; Jim McMenamin; David Goldberg; Diane Stockton; Sharon Hutchinson; Chris Robertson; Paul M McKeigue; Helen M Colhoun; David McAllister,London School of Hygiene and Tropical Medicine; Public Health Scotland; Public Health Scotland; University of Glasgow; Public Health Scotland; PublicHealth Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; University of Glasgow,"BackgroundThe effect of vaccination for COVID-19 on onward transmission is unknown. + +MethodsA national record linkage study determined documented COVID-19 cases and hospitalisations in unvaccinated household members of vaccinated and unvaccinated healthcare workers from 8th December 2020 to 3rd March 2021. The primary endpoint was COVID-19 14 days following the first dose. + +ResultsThe cohort comprised of 194,362 household members (mean age 31{middle dot}1 {+/-} 20{middle dot}9 years) and 144,525 healthcare workers (mean age 44{middle dot}4 {+/-} 11{middle dot}4 years). 113,253 (78{middle dot}3%) of healthcare workers received at least one dose of the BNT162b2 mRNA or ChAdOx1 nCoV-19 vaccine and 36,227 (25{middle dot}1%) received a second dose. There were 3,123 and 4,343 documented COVID-19 cases and 175 and 177 COVID-19 hospitalisations in household members of healthcare workers and healthcare workers respectively. Household members of vaccinated healthcare workers had a lower risk of COVID-19 case compared to household members of unvaccinated healthcare worker (rate per 100 person-years 9{middle dot}40 versus 5{middle dot}93; HR 0{middle dot}70, 95% confidence interval [CI] 0{middle dot}63 to 0{middle dot}78). The effect size for COVID-19 hospitalisation was similar, with the confidence interval crossing the null (HR 0{middle dot}77 [95% CI 0{middle dot}53 to 1{middle dot}10]). The rate per 100 person years was lower in vaccinated compared to unvaccinated healthcare workers for documented (20{middle dot}13 versus 8{middle dot}51; HR 0{middle dot}45 [95% CI 0{middle dot}42 to 0{middle dot}49]) and hospitalized COVID-19 (0{middle dot}97 versus 0{middle dot}14; HR 0{middle dot}16 [95% CI 0{middle dot}09 to 0{middle dot}27]). Compared to the period before the first dose, the risk of documented COVID-19 case was lower at [≥] 14 days after the second dose for household members (HR 0{middle dot}46 [95% CI 0{middle dot}30to 0{middle dot}70]) and healthcare workers (HR 0{middle dot}08 [95% CI 0{middle dot}04 to 0{middle dot}17]). + +InterpretationVaccination of health care workers was associated with a substantial reduction in COVID-19 cases in household contacts consistent with an effect of vaccination on transmission.",public and global health,fuzzy,100,100 medRxiv,10.1101/2021.03.17.21253853,2021-03-20,https://medrxiv.org/cgi/content/short/2021.03.17.21253853,"Modelling the impact of rapid tests, tracing and distancing in lower-income countries suggest optimal policies varies with rural-urban settings",Xilin Jiang; Wenfeng Gong; Zlatina Dobreva; Ya Gao; Matthew Quaife; Christophe Fraser; Chris Holmes,"University of Oxford; Bill & Melinda Gates Foundation; Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine, London, UK; Department of International Health, Johns Hopkins University; Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine, London, UK; University of Oxford; University of Oxford","Low- and middle-income countries (LMICs) remain of high potential for hotspots for COVID-19 deaths and emerging variants given the inequality of vaccine distribution and their vulnerable healthcare systems. We aim to evaluate containment strategies that are sustainable and effective for LMICs. We constructed synthetic populations with varying contact and household structures to capture LMIC demographic characteristics that vary across communities. Using an agent- based model, we explored the optimal containment strategies for rural and urban communities by designing and simulating setting-specific strategies that deploy rapid diagnostic tests, symptom screening, contact tracing and physical distancing. In low-density rural communities, we found implementing either high quality (sensitivity > 50%) antigen rapid diagnostic tests or moderate physical distancing could contain the transmission. In urban communities, we demonstrated that both physical distancing and case finding are essential for containing COVID-19 (average infection rate < 10%). In high density communities that resemble slums and squatter settlements, physical distancing is less effective compared to rural and urban communities. Lastly, we demonstrated contact tracing is essential for effective containment. Our findings suggested that rapid diagnostic tests could be prioritised for control and monitor COVID-19 transmission and highlighted that contact survey data could guide strategy design to save resources for LMICs. An accompanying open source R package is available for simulating COVID-19 transmission based on contact network models.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2021.03.18.21253443,2021-03-20,https://medrxiv.org/cgi/content/short/2021.03.18.21253443,Intensity of COVID-19 in care homes following Hospital Discharge in the early stages of the UK epidemic,Joe Hollinghurst; Laura North; Chris Emmerson; Ashley Akbari; Fatemeh Torabi; Ronan A Lyons; Alan G Hawkes; Ed Bennett; Mike B Gravenor; Richard Fry,Swansea University; Swansea University; Public Health Wales; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University,"BackgroundA defining feature of the COVID-19 pandemic in many countries was the tragic extent to which care home residents were affected, and the difficulty preventing introduction and subsequent spread of infection. Management of risk in care homes requires good evidence on the most important transmission pathways. One hypothesised route at the start of the pandemic, prior to widespread testing, was transfer of patients from hospitals, which were experiencing high levels of nosocomial events. + +MethodsWe tested the hypothesis that hospital discharge events increased the intensity of care home cases using a national individually linked health record cohort in Wales, UK. We monitored 186,772 hospital discharge events over the period March to July 2020, tracking individuals to 923 care homes and recording the daily case rate in the homes populated by 15,772 residents. We estimated the risk of an increase in cases rates following exposure to a hospital discharge using multi-level hierarchical logistic regression, and a novel stochastic Hawkes process outbreak model. + +FindingsIn regression analysis, after adjusting for care home size, we found no significant association between hospital discharge and subsequent increases in care home case numbers (odds ratio: 0.99, 95% CI 0.82, 1.90). Risk factors for increased cases included care home size, care home resident density, and provision of nursing care. Using our outbreak model, we found a significant effect of hospital discharge on the subsequent intensity of cases. However, the effect was small, and considerably less than the effect of care home size, suggesting the highest risk of introduction came from interaction with the community. We estimated approximately 1.8% of hospital discharged patients may have been infected. + +InterpretationThere is growing evidence in the UK that the risk of transfer of COVID-19 from the high-risk hospital setting to the high-risk care home setting during the early stages of the pandemic was relatively small. Although access to testing was limited to initial symptomatic cases in each care home at this time, our results suggest that reduced numbers of discharges, selection of patients, and action taken within care homes following transfer all may have contributed to mitigation. The precise key transmission routes from the community remain to be quantified.",health informatics,fuzzy,100,100 medRxiv,10.1101/2021.03.15.21253590,2021-03-17,https://medrxiv.org/cgi/content/short/2021.03.15.21253590,"An integrated analysis of contact tracing and genomics to assess the efficacy of travel restrictions on SARS-CoV-2 introduction and transmission in England from June to September, 2020",Dinesh Aggarwal; Andrew J Page; Ulf Schaefer; George M Savva; Richard Myers; Erik Volz; Nicholas Ellaby; Steven Platt; Natalie Groves; Eileen Gallaghar; Niamh M. Tumelty; Thanh Le-Viet; Gareth J. Hughes; Cong Chen; Charlie Turner; Sophie Logan; Abbie Harrison; - The COVID-19 Genomics UK (COG-UK) Consortium; Sharon J. Peacock; Meera Chand; Ewan M. Harrison,"University of Cambridge, Department of Medicine, Cambridge, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK; Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK; Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK; Imperial College London; Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK; Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK; Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK; Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK; University of Cambridge, Cambridge University Libraries, Cambridge, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, UK; Public Health England National Infections Service, Field Service, Leeds, UK; Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK; Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK; Public Health England, National Infections Service, Field Service, Nottingham, UK; Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK; ; University of Cambridge, Department of Medicine, Cambridge, UK; Public Health England, 61 Colindale Ave, London, NW9 5EQ, UK; University of Cambridge, Department of Medicine, Cambridge","BackgroundMitigation of SARS-CoV-2 transmission from international travel is a priority. Travellers from countries with travel restrictions (closed travel-corridors) were required to quarantine for 14 days over Summer 2020 in England. We describe the genomic epidemiology of travel-related cases in England and evaluate the effectiveness of this travel policy. MethodsBetween 27/05/2020 and 13/09/2020, probable travel-related SARS-CoV-2 cases and their contacts were identified and combined with UK SARS-CoV-2 sequencing data. The epidemiology and demographics of cases was identified, and the number of contacts per case modelled using negative binomial regression to estimate the effect of travel restriction, and any variation by age, sex and calendar date. Unique travel-related SARS-CoV-2 genomes in the COG-UK dataset were identified to estimate the effect travel restrictions on cluster size generated from these. The Polecat Clustering Tool was used to identify a travel-related SARS-CoV-2 cluster of infection. @@ -3484,15 +3580,6 @@ medRxiv,10.1101/2021.03.11.21253106,2021-03-12,https://medrxiv.org/cgi/content/s Method and resultsWe used data from the CAPACITY-COVID registry and LEOSS study. Multivariable Poisson regression models were fitted to assess the association between different types of pre-existent heart disease and in-hospital mortality. 16,511 patients with COVID-19 were included (21.1% aged 66 - 75 years; 40.2% female) and 31.5% had a history of heart disease. Patients with heart disease were older, predominantly male and often had other comorbid conditions when compared to those without. Mortality was higher in patients with cardiac disease (29.7%; n=1545 versus 15.9%; n=1797). However, following multivariable adjustment this difference was not significant (adjusted risk ratio (aRR) 1.08 [95% CI 1.02 - 1.15; p-value 0.12 (corrected for multiple testing)]). Associations with in-hospital mortality by heart disease subtypes differed considerably, with the strongest association for heart failure aRR (1.19 [1.10 - 1.30]; p-value <0.018) particularly for severe NYHA III/IV) heart failure (aRR 1.41 [95% CI 1.20 - 1.64; p-value <0.018]. None of the other heart disease subtypes, including ischemic heart disease, remained significant after multivariable adjustment. Serious cardiac complications were diagnosed in <1% of patients. ConclusionConsiderable heterogeneity exists in the strength of association between heart disease subtypes and in-hospital mortality. Of all patients with heart disease, those with heart failure are at greatest risk of death when hospitalized with COVID-19. Serious cardiac complications are rare.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2021.03.09.21253218,2021-03-12,https://medrxiv.org/cgi/content/short/2021.03.09.21253218,An observational cohort study on the incidence of SARS-CoV-2 infection and B.1.1.7 variant infection in healthcare workers by antibody and vaccination status,Sheila F Lumley; Gillian Rodger; Bede Constantinides; Nicholas Sanderson; Kevin K Chau; Teresa L Street; Alison Howarth; Stephanie B Hatch; Brian D Marsden; Stuart Cox; Tim James; Fiona Warren; Liam J Peck; Thomas G Ritter; Zoe de Toledo; Laura Warren; David Axten; Richard J Cornall; E Yvonne Jones; David I Stuart; Gavin Screaton; Daniel Ebner; Sarah Hoosdally; Meera Chand; - Oxford University Hospitals Staff Testing Group; Derrick Crook; Christopher P Conlon; Koen B Pouwels; A Sarah Walker; Tim EA Peto; Susan Hopkins; Timothy M Walker; Nicole EA Stoesser; Philippa C Matthews; Katie Jeffery; David W Eyre,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Oxford University Hospitals; Oxford University Hospitals; Oxford University Hospitals; University of Oxford; University of Oxford; University of Oxford; Oxford University Hospitals; Oxford University Hospitals; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Public Health England; ; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Public Health England; University of Oxford; University of Oxford; University of Oxford; Oxford University Hospitals; University of Oxford,"BackgroundNatural and vaccine-induced immunity will play a key role in controlling the SARS-CoV-2 pandemic. SARS-CoV-2 variants have the potential to evade natural and vaccine-induced immunity. - -MethodsIn a longitudinal cohort study of healthcare workers (HCWs) in Oxfordshire, UK, we investigated the protection from symptomatic and asymptomatic PCR-confirmed SARS-CoV-2 infection conferred by vaccination (Pfizer-BioNTech BNT162b2, Oxford-AstraZeneca ChAdOx1 nCOV-19) and prior infection (determined using anti-spike antibody status), using Poisson regression adjusted for age, sex, temporal changes in incidence and role. We estimated protection conferred after one versus two vaccinations and from infections with the B.1.1.7 variant identified using whole genome sequencing. - -Results13,109 HCWs participated; 8285 received the Pfizer-BioNTech vaccine (1407 two doses) and 2738 the Oxford-AstraZeneca vaccine (49 two doses). Compared to unvaccinated seronegative HCWs, natural immunity and two vaccination doses provided similar protection against symptomatic infection: no HCW vaccinated twice had symptomatic infection, and incidence was 98% lower in seropositive HCWs (adjusted incidence rate ratio 0.02 [95%CI <0.01-0.18]). Two vaccine doses or seropositivity reduced the incidence of any PCR-positive result with or without symptoms by 90% (0.10 [0.02-0.38]) and 85% (0.15 [0.08-0.26]) respectively. Single-dose vaccination reduced the incidence of symptomatic infection by 67% (0.33 [0.21-0.52]) and any PCR-positive result by 64% (0.36 [0.26-0.50]). There was no evidence of differences in immunity induced by natural infection and vaccination for infections with S-gene target failure and B.1.1.7. - -ConclusionNatural infection resulting in detectable anti-spike antibodies and two vaccine doses both provide robust protection against SARS-CoV-2 infection, including against the B.1.1.7 variant. - -SummaryNatural infection resulting in detectable anti-spike antibodies and two vaccine doses both provided [≥] 85% protection against symptomatic and asymptomatic SARS-CoV-2 infection in healthcare workers, including against the B.1.1.7 variant. Single dose vaccination reduced symptomatic infection by 67%.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.03.08.21253110,2021-03-10,https://medrxiv.org/cgi/content/short/2021.03.08.21253110,Incidence of SARS-CoV-2 infection according to baseline antibody status in staff and residents of 100 Long Term Care Facilities (VIVALDI study),Maria Krutikov; Tom Palmer; Gokhan Tut; Chris Fuller; Madhumita Shrotri; Haydn Williams; Daniel Davies; Aidan Irwin-Singer; James Robson; Andrew Hayward; Paul Moss; Andrew Copas; Laura J Shallcross,UCL; UCL; University of Birmingham; UCL; UCL; Four Seasons Healthcare Group; Palantir Ltd; UK Department of Health and Social Care; Four Seasons Healthcare Group; UCL; University of Birmingham; UCL; UCL,"BackgroundSARS-CoV-2 infection represents a major challenge for Long Term Care Facilities (LTCFs) and many residents and staff are now sero-positive following persistent outbreaks. We investigated the relationship between the presence of SARS-CoV-2 specific antibodies and subsequent infection in this population. MethodsProspective cohort study of infection in staff and residents in 100 LTCFs in England between October 2020 and February 2021. Blood samples were collected at baseline (June 2020), 2 and 4 months and tested for IgG antibodies to nucleocapsid and spike protein. PCR testing for SARS-CoV-2 was undertaken weekly in staff and monthly in residents. The primary analysis estimated the relative hazard of a PCR-positive test by baseline antibody status, from Cox regression adjusted for age and gender, and stratified by LTCF. @@ -3548,7 +3635,6 @@ Funding statementN/A",public and global health,fuzzy,100,100 medRxiv,10.1101/2021.03.04.21252931,2021-03-08,https://medrxiv.org/cgi/content/short/2021.03.04.21252931,A common TMPRSS2 variant protects against severe COVID-19,"Alessia David; Nicholas Parkinson; Thomas P Peacock; Erola Pairo-Castineira; Tarun Khanna; Aurelie Cobat; Albert Tenesa; Vanessa Sancho-Shimizu; - GenOMICC Investigators, ISARIC4C Investigators; Jean-Laurent Casanova; Laurent Abel; Wendy S Barclay; J Kenneth Baillie; Michael J.E. Sternberg","Centre for Integrative System Biology and Bioinformatics, Imperial College London, London; Roslin Institute, University of Edinburgh; Department of Infectious Diseases, Imperial College London; Roslin Institute, University of Edinburgh; Centre for Integrative System Biology and Bioinformatics, Imperial College London; Laboratory of Human Genetics of Infectious Diseases, INSERM; Roslin Institute, University of Edinburgh; Department of Paediatric Infectious Diseases & Virology, Imperial College London; ; St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University; Laboratory of Human Genetics of Infectious Diseases, INSERM; Department of Infectious Diseases, Imperial College London; Roslin Institute, University of Edinburgh; Centre for Integrative System Biology and Bioinformatics, Imperial College London","Infection with SARS-CoV-2 has a wide range of clinical presentations, from asymptomatic to life-threatening. Old age is the strongest factor associated with increased COVID19-related mortality, followed by sex and pre-existing conditions. The importance of genetic and immunological factors on COVID19 outcome is also starting to emerge, as demonstrated by population studies and the discovery of damaging variants in genes controlling type I IFN immunity and of autoantibodies that neutralize type I IFNs. The human protein transmembrane protease serine type 2 (TMPRSS2) plays a key role in SARS-CoV-2 infection, as it is required to activate the virus spike protein, facilitating entry into target cells. We focused on the only common TMPRSS2 non-synonymous variant predicted to be damaging (rs12329760), which has a minor allele frequency of [~]25% in the population. In a large population of SARS-CoV-2 positive patients, we show that this variant is associated with a reduced likelihood of developing severe COVID19 (OR 0.87, 95%CI:0.79-0.97, p=0.01). This association was stronger in homozygous individuals when compared to the general population (OR 0.65, 95%CI:0.50-0.84, p=1.3x10-3). We demonstrate in vitro that this variant, which causes the amino acid substitution valine to methionine, impacts the catalytic activity of TMPRSS2 and is less able to support SARS-CoV-2 spike-mediated entry into cells. TMPRSS2 rs12329760 is a common variant associated with a significantly decreased risk of severe COVID19. Further studies are needed to assess the expression of the TMPRSS2 across different age groups. Moreover, our results identify TMPRSS2 as a promising drug target, with a potential role for camostat mesilate, a drug approved for the treatment of chronic pancreatitis and postoperative reflux esophagitis, in the treatment of COVID19. Clinical trials are needed to confirm this.",genetic and genomic medicine,fuzzy,100,100 -medRxiv,10.1101/2021.03.04.21252528,2021-03-08,https://medrxiv.org/cgi/content/short/2021.03.04.21252528,Case fatality risk of the SARS-CoV-2 variant of concern B.1.1.7 in England,Daniel J Grint; Kevin Wing; Elizabeth Williamson; Helen I McDonald; Krishnan Bhaskaran; David Evans; Stephen JW Evans; Alex J Walker; George Hickman; Emily Nightingale; Anna Schultze; Christopher T Rentsch; Chris Bates; Jonathan Cockburn; Helen J Curtis; Caroline E Morton; Sebastian Bacon; Simon Davy; Angel YS Wong; Amir Mehrkar; Laurie Tomlinson; Ian J Douglas; Rohini Mathur; Paula Blomquist; Brian MacKenna; Peter Ingelsby; Richard Croker; John Parry; Frank Hester; Sam Harper; Nicolas J DeVito; Will Hulme; John Tazare; Ben Goldacre; Liam Smeeth; Rosalind M Eggo,"Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Faculty of Public Health and Policy, London School of Hygiene & Tropical Medicine, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, UK; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; COVID-19 Outbreak Surveillance Team, Public Health England, London, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, UK; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, UK; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK",The B.1.1.7 variant of concern (VOC) is increasing in prevalence across Europe. Accurate estimation of disease severity associated with this VOC is critical for pandemic planning. We found increased risk of death for VOC compared with non-VOC cases in England (HR: 1.67 (95% CI: 1.34 - 2.09; P<.0001). Absolute risk of death by 28-days increased with age and comorbidities. VOC has potential to spread faster with higher mortality than the pandemic to date.,infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.03.08.21253112,2021-03-08,https://medrxiv.org/cgi/content/short/2021.03.08.21253112,OpenSAFELY: Risks of COVID-19 hospital admission and death for people with learning disabilities - a cohort study.,Elizabeth Williamson; Helen I McDonald; Krishnan Bhaskaran; Alex J Walker; Sebastian Bacon; Simon Davy; Anna Schultze; Laurie Tomlinson; Chris Bates; Mary Ramsay; Helen J Curtis; Harriet Forbes; Kevin Wing; Caroline Minassian; John Tazare; Caroline E Morton; Emily Nightingale; Amir Mehrkar; Dave Evans; Peter Inglesby; Brian MacKenna; Jonathan Cockburn; Christopher T Rentsch; Rohini Mathur; Angel Wong; Rosalind M Eggo; William J Hulme; Richard Croker; John Parry; Frank Hester; Sam Harper; Ian Douglas; Stephen JW Evans; Liam Smeeth; Ben Goldacre; Hannah Kuper,"London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; NIHR Health Protection Research Unit (HPRU) in Immunisation; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; Public Health England, London; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT","ObjectivesTo assess the association between learning disability and risk of hospitalisation and mortality from COVID-19 in England among adults and children. DesignWorking on behalf of NHS England, two cohort studies using patient-level data for >17 million people from primary care electronic health records were linked with death data from the Office for National Statistics and hospitalization data from NHS Secondary Uses Service using the OpenSAFELY platform. @@ -3605,6 +3691,21 @@ MethodsA cross-sectional community survey in England undertaken between 26 Janua ResultsThe survey comprised 172,099 people, with valid IgG antibody results from 155,172. The overall prevalence of antibodies (weighted to be representative of the population of England and adjusted for test sensitivity and specificity) in England was 13.9% (95% CI 13.7, 14.1) overall, 37.9% (37.2, 38.7) in vaccinated and 9.8% (9.6, 10.0) in unvaccinated people. The prevalence of antibodies (weighted) in unvaccinated people was highest in London at 16.9% (16.3, 17.5), and higher in people of Black (22.4%, 20.8, 24.1) and Asian (20.0%, 19.0, 21.0) ethnicity compared to white (8.5%, 8.3, 8.7) people. The uptake of vaccination by age was highest in those aged 80 years or older (93.5%). Vaccine confidence was high with 92.0% (91.9, 92.1) of people saying that they had accepted or intended to accept the offer. Vaccine confidence varied by age and ethnicity, with lower confidence in young people and those of Black ethnicity. Particular concerns were identified around pregnancy, fertility and allergies. In 971 individuals who received two doses of the Pfizer-BioNTech vaccine, the proportion testing positive was high across all age groups. Following a single dose of Pfizer-BioNTech vaccine after 21 days or more, 84.1% (82.2, 85.9) of people under 60 years tested positive (unadjusted) with a decreasing trend with increasing age, but high responses to a single dose in those with confirmed or suspected prior COVID at 90.1% (87.2, 92.4) across all age groups. ConclusionsThere is uneven distribution of SARS-CoV-2 antibodies in the population with a higher burden in key workers and some minority ethnic groups, similar to the pattern in the first wave. Confidence in the vaccine programme is high overall although it was lower in some of the higher prevalence groups which suggests the need for improved communication about specific perceived risks. Two doses of Pfizer-BioNTech vaccine, or a single dose following previous infection, confers high levels of antibody positivity across all ages. Further work is needed to understand the relationship between antibody positivity, clinical outcomes such as hospitalisation, and transmission.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2021.02.25.21252433,2021-03-01,https://medrxiv.org/cgi/content/short/2021.02.25.21252433,Predicting COVID-19 related death using the OpenSAFELY platform,Elizabeth J Williamson; John Tazare; Krishnan Bhaskaran; Helen I McDonald; Alex J Walker; Laurie Tomlinson; Kevin Wing; Sebastian Bacon; Chris Bates; Helen J Curtis; Harriet Forbes; Caroline Minassian; Caroline E Morton; Emily Nightingale; Amir Mehrkar; Dave Evans; Brian D Nicholson; Dave Leon; Peter Inglesby; Brian MacKenna; Nicholas G Davies; Nicholas J DeVito; Henry Drysdale; Jonathan Cockburn; William J Hulme; Jessica Morley; Ian Douglas; Christopher T Rentsch; Rohini Mathur; Angel Wong; Anna Schultze; Richard Croker; John Parry; Frank Hester; Sam Harper; Richard Grieve; David A Harrison; Ewout W Steyerberg; Rosalind M Eggo; Karla Diaz-Ordaz; Ruth Keogh; Stephen JW Evans; Liam Smeeth; Ben Goldacre,"London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; NIHR Health Protection Research Unit (HPRU) in Immunisation; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; Intensive Care National Audit & Research Centre (ICNARC), 24 High Holborn, Holborn, London WC1V 6AZ; Leiden University Medical Center, Leiden, the Netherlands; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG","ObjectivesTo compare approaches for obtaining relative and absolute estimates of risk of 28-day COVID-19 mortality for adults in the general population of England in the context of changing levels of circulating infection. + +DesignThree designs were compared. (A) case-cohort which does not explicitly account for the time-changing prevalence of COVID-19 infection, (B) 28-day landmarking, a series of sequential overlapping sub-studies incorporating time-updating proxy measures of the prevalence of infection, and (C) daily landmarking. Regression models were fitted to predict 28-day COVID-19 mortality. + +SettingWorking on behalf of NHS England, we used clinical data from adult patients from all regions of England held in the TPP SystmOne electronic health record system, linked to Office for National Statistics (ONS) mortality data, using the OpenSAFELY platform. + +ParticipantsEligible participants were adults aged 18 or over, registered at a general practice using TPP software on 1st March 2020 with recorded sex, postcode and ethnicity. 11,972,947 individuals were included, and 7,999 participants experienced a COVID-19 related death. The study period lasted 100 days, ending 8th June 2020. + +PredictorsA range of demographic characteristics and comorbidities were used as potential predictors. Local infection prevalence was estimated with three proxies: modelled based on local prevalence and other key factors; rate of A&E COVID-19 related attendances; and rate of suspected COVID-19 cases in primary care. + +Main outcome measuresCOVID-19 related death. + +ResultsAll models discriminated well between patients who did and did not experience COVID-19 related death, with C-statistics ranging from 0.92-0.94. Accurate estimates of absolute risk required data on local infection prevalence, with modelled estimates providing the best performance. + +ConclusionsReliable estimates of absolute risk need to incorporate changing local prevalence of infection. Simple models can provide very good discrimination and may simplify implementation of risk prediction tools in practice.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2021.02.25.21252402,2021-02-28,https://medrxiv.org/cgi/content/short/2021.02.25.21252402,Racial and ethnic differences in COVID-19 vaccine hesitancy and uptake,Long H. Nguyen; Amit D. Joshi; David A. Drew; Jordi Merino; Wenjie Ma; Sohee Kwon; Kai Wang; Mark S. Graham; Lorenzo Polidori; Cristina Menni; Carole H. Sudre; Adjoa Anyane-Yeboa; Christina M. Astley; Erica T. Warner; Christina Hu; Somesh Selvachandran; Richard Davies; Denis Nash; Paul W. Franks; Jonathhan Wolf; Sebastien Ourselin; Claire J Steves; Tim D. Spector; Andrew T. Chan; - COPE Consortium,Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital and Harvard Medical School; Massachusetts General Hospital and Harvard Medical School; King's College London; Zoe Global Ltd.; King's College London; King's College London; Massachusetts General Hospital and Harvard Medical School; Broad Institute of MIT and Harvard; Massachusetts General Hospital and Harvard Medical School; Zoe Global Ltd.; Zoe Global Ltd.; Zoe Global Ltd.; City University of New York; Lund University; Zoe Global Ltd.; King's College London; King's College London; King's College London; Massachusetts General Hospital and Harvard Medical School; ,"BackgroundRacial and ethnic minorities have been disproportionately impacted by COVID-19. In the initial phase of population-based vaccination in the United States (U.S.) and United Kingdom (U.K.), vaccine hesitancy and limited access may result in disparities in uptake. MethodsWe performed a cohort study among U.S. and U.K. participants in the smartphone-based COVID Symptom Study (March 24, 2020-February 16, 2021). We used logistic regression to estimate odds ratios (ORs) of COVID-19 vaccine hesitancy (unsure/not willing) and receipt. @@ -4107,6 +4208,7 @@ Added value of this studyTranslating current knowledge and uncertainty of vaccin Implications of all the available evidenceVaccination is likely to provide substantial individual protection to those receiving two doses, but the degree of protection to the wider population is still uncertain. While substantial immunisation of the most vulnerable groups will allow for some relaxation of controls, this must be done gradually to prevent large scale public health consequences.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.12.30.20248603,2021-01-01,https://medrxiv.org/cgi/content/short/2020.12.30.20248603,SARS-CoV-2 positivity in asymptomatic-screened dental patients,David I Conway; Shauna Culshaw; Maura Edwards; Claire Clark; Chris Watling; Chris Robertson; Raymond Braid; Emma O'Keefe; Niall McGoldrick; Jacky Burns; Stacey Provan; Harper VanSteenhouse; Jodie Hay; Rory Gunson; - Dental COVID-19 Surveillance Survey Group,University of Glasgow and Public Health Scotland; University of Glasgow; NHS Ayrshire and Arran; Public Health Scotland; Public Health Scotland; Strathclyde University and Public Health Scotland; Public Health Scotland; NHS Fife; NHS Fife; NHS Fife; NHS Greater Glasgow & Clyde; BioClavis Ltd; University of Glasgow; NHS Greater Glasgow & Clyde; ,"Enhanced community surveillance is a key pillar of the public health response to COVID-19. Asymptomatic carriage of SARS-CoV-2 is a potentially significant source of transmission, yet remains relatively poorly understood. Disruption of dental services continues with significantly reduced capacity. Ongoing precautions include pre- and/or at appointment COVID-19 symptom screening and use of enhanced personal protective equipment (PPE). This study aimed to investigate SARS-CoV-2 infection in dental patients to inform community surveillance and improve understanding of risks in the dental setting. Thirty-one dental care centres across Scotland invited asymptomatic screened patients over 5-years-old to participate. Following verbal consent and completion of sociodemographic and symptom history questionnaire, trained dental teams took a combined oropharyngeal and nasal swab sample using standardised VTM-containing testkits. Samples were processed by the Lighthouse Lab and patients informed of their results by SMS/e-mail with appropriate self-isolation guidance in the event of a positive test. Over a 13-week period (from 3August to 31October2020) n=4,032 patients, largely representative of the population, were tested. Of these n=22 (0.5%; 95%CI 0.5%, 0.8%) tested positive for SARS-CoV-2. The positivity rate increased over the period, commensurate with uptick in community prevalence identified across all national testing monitoring data streams. All positive cases were successfully followed up by the national contact tracing program. To the best of our knowledge this is the first report of a COVID-19 testing survey in asymptomatic-screened patients presenting in a dental setting. The positivity rate in this patient group reflects the underlying prevalence in community at the time. These data are a salient reminder, particularly when community infection levels are rising, of the importance of appropriate ongoing Infection Prevention Control and PPE vigilance, which is relevant as healthcare team fatigue increases as the pandemic continues. Dental settings are a valuable location for public health surveillance.",dentistry and oral medicine,fuzzy,100,100 +medRxiv,10.1101/2020.12.24.20248822,2020-12-26,https://medrxiv.org/cgi/content/short/2020.12.24.20248822,Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England,Nicholas G Davies; Sam Abbott; Rosanna C. Barnard; Christopher I. Jarvis; Adam J. Kucharski; James D Munday; Carl A. B. Pearson; Timothy Russell; Damien Tully; Alex D. Washburne; Tom Wenseleers; Amy Gimma; William Waites; Kerry L. M. Wong; Kevin van Zandvoort; Justin D. Silverman; - CMMID COVID-19 Working Group; - The COVID-19 Genomics UK (COG-UK) Consortium; Karla Diaz-Ordaz; Ruth H Keogh; Rosalind M Eggo; Sebastian Funk; Mark Jit; Katherine E. Atkins; W. John Edmunds,"London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Selva Analytics LLC; KU Leuven; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; College of Information Science and Technology, Pennsylvania State University; ; ; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine","A novel SARS-CoV-2 variant, VOC 202012/01 (lineage B.1.1.7), emerged in southeast England in November 2020 and is rapidly spreading towards fixation. Using a variety of statistical and dynamic modelling approaches, we estimate that this variant has a 43-90% (range of 95% credible intervals 38-130%) higher reproduction number than preexisting variants. A fitted two-strain dynamic transmission model shows that VOC 202012/01 will lead to large resurgences of COVID-19 cases. Without stringent control measures, including limited closure of educational institutions and a greatly accelerated vaccine roll-out, COVID-19 hospitalisations and deaths across England in 2021 will exceed those in 2020. Concerningly, VOC 202012/01 has spread globally and exhibits a similar transmission increase (59-74%) in Denmark, Switzerland, and the United States.",epidemiology,fuzzy,100,100 bioRxiv,10.1101/2020.12.23.424229,2020-12-25,https://biorxiv.org/cgi/content/short/2020.12.23.424229,Patterns of within-host genetic diversity in SARS-CoV-2,Gerry Tonkin-Hill; Inigo Martincorena; Roberto Amato; Andrew R J Lawson; Moritz Gerstung; Ian Johnston; David K Jackson; Naomi R Park; Stefanie V Lensing; Michael A Quail; Sónia Gonçalves; Cristina Ariani; Michael Spencer Chapman; William L Hamilton; Luke W Meredith; Grant Hall; Aminu S Jahun; Yasmin Chaudhry; Myra Hosmillo; Malte L Pinckert; Iliana Georgana; Anna Yakovleva; Laura G Caller; Sarah L Caddy; Theresa Feltwell; Fahad A Khokhar; Charlotte J Houldcroft; Martin D Curran; Surendra Parmar; - The COVID-19 Genomics UK (COG-UK) Consortium; Alex Alderton; Rachel Nelson; Ewan Harrison; John Sillitoe; Stephen D Bentley; Jeffrey C Barrett; M. Estee Torok; Ian G Goodfellow; Cordelia Langford; Dominic Kwiatkowski; - Wellcome Sanger Institute COVID-19 Surveillance Team,"Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; European Bioinformatics Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge; Department of Pathology, University of Cambridge and The Francis Crick Institute; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Department of Medicine, University of Cambridge and Cambridge Institute of Therapeutic Immunology and Infectious Disease; Department of Medicine, University of Cambridge; Public Health England; Public Health England; COG-UK; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute and European Bioinformatics Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Wellcome Sanger Institute; Department of Medicine, University of Cambridge; Department of Pathology, University of Cambridge; Wellcome Sanger Institute; Wellcome Sanger Institute and Oxford University; ","Monitoring the spread of SARS-CoV-2 and reconstructing transmission chains has become a major public health focus for many governments around the world. The modest mutation rate and rapid transmission of SARS-CoV-2 prevents the reconstruction of transmission chains from consensus genome sequences, but within-host genetic diversity could theoretically help identify close contacts. Here we describe the patterns of within-host diversity in 1,181 SARS-CoV-2 samples sequenced to high depth in duplicate. 95% of samples show within-host mutations at detectable allele frequencies. Analyses of the mutational spectra revealed strong strand asymmetries suggestive of damage or RNA editing of the plus strand, rather than replication errors, dominating the accumulation of mutations during the SARS-CoV-2 pandemic. Within and between host diversity show strong purifying selection, particularly against nonsense mutations. Recurrent within-host mutations, many of which coincide with known phylogenetic homoplasies, display a spectrum and patterns of purifying selection more suggestive of mutational hotspots than recombination or convergent evolution. While allele frequencies suggest that most samples result from infection by a single lineage, we identify multiple putative examples of co-infection. Integrating these results into an epidemiological inference framework, we find that while sharing of within-host variants between samples could help the reconstruction of transmission chains, mutational hotspots and rare cases of superinfection can confound these analyses.",genomics,fuzzy,100,100 medRxiv,10.1101/2020.12.21.20248607,2020-12-22,https://medrxiv.org/cgi/content/short/2020.12.21.20248607,Time use and social mixing during and around festive periods: Potential changes in the age distribution of COVID-19 cases from increased intergenerational interactions,Edwin van Leeuwen; Frank G. Sandmann; Rosalind M. Eggo; - PHE Joint modelling group; Peter J. White,Public Health England; Public Health England; London School of Hygiene &Tropical Medicine; London School of Hygiene & Tropical Medicine; ; Public Health England; Imperial College London,"RationaleAmid the ongoing coronavirus disease 2019 (COVID-19) pandemic in which many countries have adopted physical distancing measures, tiered restrictions, and episodic ""lockdowns,"" the impact of potentially increased social mixing during festive holidays on the age distribution of new COVID-19 cases remains unclear. @@ -4187,15 +4289,6 @@ MethodsREACT-1 is a series of community surveys of SARS-CoV-2 RT-PCR swab-positi ResultsBetween 13th November and 3rd December (round 7) there were 1,299 positive swabs out of 168,181 giving a weighted prevalence of 0.94% (95% CI 0.87%, 1.01%) or 94 per 10,000 people infected in the community in England. This compares with a prevalence of 1.30% (1.21%, 1.39%) from 16th October to 2nd November 2020 (round 6), a decline of 28%. Prevalence during the latter half of round 7 was 0.91% (95% CI, 0.81%, 1.03%) compared with 0.96% (0.87%, 1.05%) in the first half. The national R number in round 7 was estimated at 0.96 (0.88, 1.03) with a decline in prevalence observed during the first half of this period no longer apparent during the second half at the end of lockdown. During round 7 there was a marked fall in prevalence in West Midlands, a levelling off in some regions and a rise in London. R numbers at regional level ranged from 0.60 (0.41, 0.80) in West Midlands up to 1.27 (1.04, 1.54) in London, where prevalence was highest in the east and south-east of the city. Nationally, between 13th November and 3rd December, the highest prevalence was in school-aged children especially at ages 13-17 years at 2.04% (1.69%, 2.46%), or approximately 1 in 50. ConclusionBetween the previous round and round 7 (during lockdown), there was a fall in prevalence of SARS-CoV-2 swab-positivity nationally, but it did not fall uniformly over time or by geography. Continued vigilance is required to reduce rates of infection until effective immunity at the population level can be achieved through the vaccination programme.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2020.12.10.20245944,2020-12-14,https://medrxiv.org/cgi/content/short/2020.12.10.20245944,"Azithromycin in Hospitalised Patients with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial",Peter W Horby; Alistair Roddick; Enti Spata; Natalie Staplin; Jonathan R Emberson; Guilherme Pessoa-Amorim; Leon Peto; Mark Campbell; Christopher Brightling; Ben Prudon; David Chadwick; Andrew Ustianowski; Abdul Ashish; Stacy Todd; Bryan Yates; Robert Buttery; Stephen Scott; Diego Maseda; J Kenneth Baillie; Maya H Buch; Lucy C Chappell; Jeremy N Day; Saul N Faust; Thomas Jaki; Katie Jeffery; Edmund Juszczak; Wei Shen Lim; Alan Montgomery; Andrew Mumford; Kathryn Rowan; Guy Thwaites; Marion Mafham; Richard Haynes; Martin J Landray,"Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, United Kingdom; Department of Respiratory Medicine, North Tees & Hartlepool NHS Foundation Trust, Stockton-on-Tees, United Kingdom; Centre for Clinical Infection, James Cook University Hospital, Middlesbrough, United Kingdom; North Manchester General Hospital & University of Manchester, Manchester, United Kingdom; Wrightington Wigan and Leigh NHS Foundation Trust, Wigan, United Kingdom; Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom; Northumbria Healthcare NHS Foundation Trust, North Tyneside, United Kingdom; North West Anglia NHS Foundation Trust, Peterborough, United Kingdom; The Countess of Chester Hospital NHS Foundation Trust, Chester, United Kingdom; Mid Cheshire Hospitals NHS Foundation Trust, Crewe, United Kingdom; Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom; Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom; School of Life Sciences, King's College London, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, ; Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom; MRC Biostatistics Unit, University of Cambridge, Cambridge, United Ki; Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; Respiratory Medicine Department, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol, United kingdom; Intensive Care National Audit & Research Centre, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom","BackgroundAzithromycin has been proposed as a treatment for COVID-19 on the basis of its immunomodulatory actions. We evaluated the efficacy and safety of azithromycin in hospitalised patients with COVID-19. - -MethodsIn this randomised, controlled, open-label, adaptive platform trial, several possible treatments were compared with usual care in patients hospitalised with COVID-19 in the UK. Eligible and consenting patients were randomly allocated to either usual standard of care alone or usual standard of care plus azithromycin 500 mg once daily by mouth or intravenously for 10 days or until discharge (or one of the other treatment arms). Patients were twice as likely to be randomised to usual care as to any of the active treatment groups. The primary outcome was 28-day mortality. The trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936). - -FindingsBetween 7 April and 27 November 2020, 2582 patients were randomly allocated to receive azithromycin and 5182 patients to receive usual care alone. Overall, 496 (19%) patients allocated to azithromycin and 997 (19%) patients allocated to usual care died within 28 days (rate ratio 1{middle dot}00; 95% confidence interval [CI] 0{middle dot}90-1{middle dot}12; p=0{middle dot}99). Consistent results were seen in all pre-specified subgroups of patients. There was no difference in duration of hospitalisation (median 12 days vs. 13 days) or the proportion of patients discharged from hospital alive within 28 days (60% vs. 59%; rate ratio 1{middle dot}03; 95% CI 0{middle dot}97-1{middle dot}10; p=0{middle dot}29). Among those not on invasive mechanical ventilation at baseline, there was no difference in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (21% vs. 22%; risk ratio 0{middle dot}97; 95% CI 0{middle dot}89-1{middle dot}07; p=0{middle dot}54). - -InterpretationIn patients hospitalised with COVID-19, azithromycin did not provide any clinical benefit. Azithromycin use in patients hospitalised with COVID-19 should be restricted to patients where there is a clear antimicrobial indication. - -FundingUK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant ref: MC_PC_19056).",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.12.11.20247742,2020-12-14,https://medrxiv.org/cgi/content/short/2020.12.11.20247742,Changes in cardiovascular disease monitoring in English primary care during the COVID-19 pandemic: an observational cohort study,Clare R Bankhead; Sarah Lay-Flurrie; Brian D Nicholson; James P Sheppard; Chris P Gale; Harshana Liyanage; Dylan McGagh; Mark Minchin; Rafael Perera; Julian Sherlock; Margaret Smith; Nicholas PB Thomas; Cynthia Wright Drakesmith; Simon D de Lusignan; Richard Hobbs,University of Oxford; University of Oxford; Nuffield Department of Primary Care Health Sciences; University of Oxford; University of Leeds; University of Oxford; University of Oxford; National Institute for Health and Care Excellence; University of Oxford; University of Oxford; University of Oxford; Royal College of General Practitioners; University of Oxford; University of Oxford; University of Oxford,"ObjectiveTo quantify the impact and recovery in cardiovascular disease monitoring in primary care associated with the first COVID-19 lockdown. DesignRetrospective nationwide primary care cohort study, utilising data from 1st January 2018 to 27th September 2020. @@ -4215,6 +4308,13 @@ Following the immediate drop, rates of recorded tests increased on average by 5- ConclusionsCardiovascular disease monitoring in English primary care declined substantially from the time of the first UK lockdown. Despite a consistent recovery in activity, there is still a substantial shortfall in the numbers of recorded measurements to those expected. Strategies are required to ensure cardiovascular disease monitoring is maintained during the COVID-19 pandemic.",primary care research,fuzzy,100,100 medRxiv,10.1101/2020.12.10.20247155,2020-12-14,https://medrxiv.org/cgi/content/short/2020.12.10.20247155,Self-harm presentations to Emergency Departments and Place of Safety during the first wave of the UK COVID-19 pandemic: South London and Maudsley data on service use from February to June 2020.,Eleanor Nuzum; Evangelia Martin; Gemma Morgan; Rina Dutta; Christoph Mueller; Catherine Polling; Megan Pritchard; Sumithra Velupillai; Robert Stewart,South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London,"The lockdown and social distancing policy imposed due to the COVID-19 pandemic has had a substantial impact on both mental health service delivery, and the ways in which people are accessing these services. Previous reports from the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for around 1.2m residents in South London) have highlighted increased use of virtual contacts by mental health teams, with dropping numbers of face-to-face contacts over the first wave of the pandemic. There has been concern that the impact of the COVID-19 pandemic would lead to higher mental health emergencies, particularly instances of self-harm. However, with people advised to stay at home during the first wave lockdown, it is as yet unclear whether this impacted mental health service presentations. Taking advantage of SLaMs Clinical Records Interactive Search (CRIS) data resource with daily updates of information from its electronic mental health records, this paper describes overall presentations to Emergency Department (ED) mental health liaison teams, and those with self-harm. The paper focussed on three periods: i) a pre-lockdown period 1st February to 15th March, ii) a lockdown period 16th March to 10th May and iii) a post-lockdown period 11th May to 28th June. In summary, all attendances to EDs for mental health support decreased during the lockdown period, including those with self-harm. All types of self-harm decreased during lockdown, with self-poisoning remaining the most common. Attendances to EDs for mental health support increased post-lockdown, although were only just approaching pre-lockdown levels by the end of June 2020.",psychiatry and clinical psychology,fuzzy,100,100 medRxiv,10.1101/2020.12.05.20241927,2020-12-11,https://medrxiv.org/cgi/content/short/2020.12.05.20241927,Neutralising antibodies drive Spike mediated SARS-CoV-2 evasion,Steven A Kemp; Dami A Collier; Rawlings Datir; Isabella ATM Ferreira; Salma Gayed; Aminu Jahun; Myra Hosmillo; Chloe Rees-Spear; Petra Mlcochova; Ines Ushiro Lumb; David Roberts; Anita Chandra; Nigel Temperton; - The COVID-19 Genomics UK (COG-UK) Consortium; Katherine Sharrocks; Elizabeth Blane; - The CITIID-NIHR BioResource COVID-19 Collaboration; John A Briggs; Marit van Gils; Ken G Smith; John R Bradley; Chris Smith; Rainer Doffinger; Lourdes Ceron-Gutierrez; Gabriela Barcenas-Morales; David Pollock; Richard Goldstein; Anna Smielewska; Jordan P Skittrall; Theo Gouliouris; Ian G Goodfellow; Effrossyni Gkrania-Klotsas; Chris JR Illingworth; Laura E McCoy; Ravindra K Gupta,"Division of Infection and Immunity, University College London, London, UK; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.; Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK.; Department of Pathology, University of Cambridge, Cambridge; Department of Pathology, University of Cambridge, Cambridge; Division of Infection and Immunity, University College London, London, UK.; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.; Public Health England, Colindale, London, UK; Public Health England, Colindale, London, UK; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.; Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, UK; -; Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK.; Department of Medicine, University of Cambridge, Cambridge, UK.; -; Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.; University of Amsterdam; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.; NIHR Cambridge Clinical Research Facility, Cambridge, UK.; Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK; Addenbrookes Hospital; Addenbrookes Hospital; Addenbrookes Hospital; University of Colorado School of Medicine; Division of Infection & Immunity, University College London, UK; Department of Virology, Cambridge University NHS Hospitals Foundation Trust; Clinical Microbiology and Public Health Laboratory, Addenbrookes Hospital, Cambridge, UK; Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK.; Department of Pathology, University of Cambridge, Cambridge; Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK.; MRC Biostatistics Unit, University of Cambridge, Cambridge, UK; Division of Infection and Immunity, University College London, London, UK; Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.","SARS-CoV-2 Spike protein is critical for virus infection via engagement of ACE2, and amino acid variation in Spike is increasingly appreciated. Given both vaccines and therapeutics are designed around Wuhan-1 Spike, this raises the theoretical possibility of virus escape, particularly in immunocompromised individuals where prolonged viral replication occurs. Here we report chronic SARS-CoV-2 with reduced sensitivity to neutralising antibodies in an immune suppressed individual treated with convalescent plasma, generating whole genome ultradeep sequences by both short and long read technologies over 23 time points spanning 101 days. Although little change was observed in the overall viral population structure following two courses of remdesivir over the first 57 days, N501Y in Spike was transiently detected at day 55 and V157L in RdRp emerged. However, following convalescent plasma we observed large, dynamic virus population shifts, with the emergence of a dominant viral strain bearing D796H in S2 and{Delta} H69/{Delta}V70 in the S1 N-terminal domain NTD of the Spike protein. As passively transferred serum antibodies diminished, viruses with the escape genotype diminished in frequency, before returning during a final, unsuccessful course of convalescent plasma. In vitro, the Spike escape double mutant bearing{Delta} H69/{Delta}V70 and D796H conferred decreased sensitivity to convalescent plasma, whilst maintaining infectivity similar to wild type. D796H appeared to be the main contributor to decreased susceptibility, but incurred an infectivity defect. The{Delta} H69/{Delta}V70 single mutant had two-fold higher infectivity compared to wild type and appeared to compensate for the reduced infectivity of D796H. Consistent with the observed mutations being outside the RBD, monoclonal antibodies targeting the RBD were not impacted by either or both mutations, but a non RBD binding monoclonal antibody was less potent against{Delta} H69/{Delta}V70 and the double mutant. These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy associated with emergence of viral variants with reduced susceptibility to neutralising antibodies.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2020.12.08.20246231,2020-12-11,https://medrxiv.org/cgi/content/short/2020.12.08.20246231,Artificial intelligence-enabled analysis of UK and US public attitudes on Facebook and Twitter towards COVID-19 vaccinations,Amir Hussain; Ahsen Tahir; Zain Hussain; Zakariya Sheikh; Mandar Gogate; Kia Dashtipour; Azhar Ali; Aziz Sheikh,"Edinburgh Napier University, UK; Edinburgh Napier University, UK; Edinburgh Medical School, College of Medicine and Veterinary Medicine, University of Edinburgh, UK; Edinburgh Medical School, College of Medicine and Veterinary Medicine, University of Edinburgh, UK; Edinburgh Napier University, UK; Edinburgh Napier University, UK; NHS Forth Medical Group, UK & Harvard T.H. Chan School of Public Health, USA; Usher Institute, Edinburgh Medical School, University of Edinburgh, UK","BackgroundGlobal efforts towards the development and deployment of a vaccine for SARS-CoV-2 are rapidly advancing. We developed and applied an artificial-intelligence (AI)-based approach to analyse social-media public sentiment in the UK and the US towards COVID-19 vaccinations, to understand public attitude and identify topics of concern. + +MethodsOver 300,000 social-media posts related to COVID-19 vaccinations were extracted, including 23,571 Facebook-posts from the UK and 144,864 from the US, along with 40,268 tweets from the UK and 98,385 from the US respectively, from 1st March - 22nd November 2020. We used natural language processing and deep learning based techniques to predict average sentiments, sentiment trends and topics of discussion. These were analysed longitudinally and geo-spatially, and a manual reading of randomly selected posts around points of interest helped identify underlying themes and validated insights from the analysis. + +ResultsWe found overall averaged positive, negative and neutral sentiment in the UK to be 58%, 22% and 17%, compared to 56%, 24% and 18% in the US, respectively. Public optimism over vaccine development, effectiveness and trials as well as concerns over safety, economic viability and corporation control were identified. We compared our findings to national surveys in both countries and found them to correlate broadly. + +ConclusionsAI-enabled social-media analysis should be considered for adoption by institutions and governments, alongside surveys and other conventional methods of assessing public attitude. This could enable real-time assessment, at scale, of public confidence and trust in COVID-19 vaccinations, help address concerns of vaccine-sceptics and develop more effective policies and communication strategies to maximise uptake.",public and global health,fuzzy,100,100 medRxiv,10.1101/2020.12.03.20242941,2020-12-07,https://medrxiv.org/cgi/content/short/2020.12.03.20242941,Contrasting factors associated with COVID-19-related ICU and death outcomes: interpretable multivariable analyses of the UK CHESS dataset.,Massimo Cavallaro; Haseeb Moiz; Matt J Keeling; Noel D McCarthy,University of Warwick; University of Warwick; University of Warwick; University of Warwick,"Identification of those at greatest risk of death due to the substantial threat of COVID-19 can benefit from novel approaches to epidemiology that leverage large datasets and complex machine-learning models, provide data-driven intelligence, and guide decisions such as intensive-care unit admission (ICUA). The objective of this study is two-fold, one substantive and one methodological: substantively to evaluate the association of demographic and health records with two related, yet different, outcomes of severe COVID-19 (viz., death and ICUA); methodologically to compare interpretations based on logistic regression and on gradient-boosted decision tree (GBDT) predictions interpreted by means of the Shapley impacts of covariates. Very different association of some factors, e.g., obesity and chronic respiratory diseases, with death and ICUA may guide review of practice. Shapley explanation of GBDTs identified varying effects of some factors among patients, thus emphasising the importance of individual patient assessment. The results of this study are also relevant for the evaluation of complex automated clinical decision systems, which should optimise prediction scores whilst remaining interpretable to clinicians and mitigating potential biases. Author summaryThe design is a retrospective cohort study of 13954 in-patients of ages ranging from 1 to 105 year (IQR: 56, 70, 81) with a confirmed diagnosis of COVID-19 by 28th June 2020. This study used multivariable logistic regression to generate odd ratios (ORs) multiply adjusted for 37 covariates (comorbidities, demographic, and others) selected on the basis of clinical interest and prior findings. Results were supplemented by gradient-boosted decision tree (GBDT) classification to generate Shapley values in order to evaluate the impact of the covariates on model output for all patients. Factors are differentially associated with death and ICUA and among patients. @@ -4232,15 +4332,6 @@ MethodsWe conducted a cohort study of consecutive adults hospitalised for severe FindingsAmong 1,721 patients (median age 71 years, 57% male), 349 (20.3%) had pre-existing CVD (CVD), 888 (51.6%) had CV risk factors without CVD (RF-CVD), 484 (28.1%) had neither. Patients with CVD were older with a higher burden of non-CV comorbidities. During follow-up, 438 (25.5%) patients died: 37% with CVD, 25.7% with RF-CVD and 16.5% with neither. CVD was independently associated with in-hospital mortality among patients <70 years of age (adjusted HR 2.43 [95%CI 1.16-5.07]), but not in those [≥]70 years (aHR 1.14 [95%CI 0.77-1.69]). RF-CVD were not independently associated with mortality in either age group (<70y aHR 1.21 [95%CI 0.72-2.01], [≥]70y aHR 1.07 [95%CI 0.76-1.52]). Most CV complications occurred in patients with CVD (66%) versus RF-CVD (17%) or neither (11%; p<0.001). 213 [12.4%] patients developed venous thromboembolism (VTE). CVD was not an independent predictor of VTE. InterpretationIn patients hospitalised with COVID-19, pre-existing established CVD appears to be a more important contributor to mortality than CV risk factors in the absence of CVD. CVD-related hazard may be mediated, in part, by new CV complications. Optimal care and vigilance for destabilised CVD are essential in this patient group.",cardiovascular medicine,fuzzy,100,100 -medRxiv,10.1101/2020.12.03.20243535,2020-12-04,https://medrxiv.org/cgi/content/short/2020.12.03.20243535,OpenSAFELY: impact of national guidance on switching from warfarin to direct oral anticoagulants (DOACs) in early phase of COVID-19 pandemic in England,Helen J Curtis; Brian MacKenna; Alex J Walker; Richard Croker; Amir Mehrkar; Caroline E Morton; Seb Bacon; George Hickman; Peter Inglesby; Chris Bates; David Evans; Tom Ward; Jonathan Cockburn; Simon Davy; Krishnan Bhaskaran; Anna Schultze; Christopher T Rentsch; Elizabeth Williamson; William Hulme; Helen I McDonald; Laurie Tomlinson; Rohini Mathur; Henry Drysdale; Rosalind M Eggo; Kevin Wing; Angel Wong; Harriet Forbes; John Parry; Frank Hester; Sam Harper; Stephen JW Evans; Ian J Douglas; Liam Smeeth; Ben Goldacre,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; TPP; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP; TPP; TPP; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford,"BackgroundEarly in the COVID-19 pandemic the NHS recommended that appropriate patients anticoagulated with warfarin should be switched to direct acting oral anticoagulants (DOACs), requiring less frequent blood testing. Subsequently, a national safety alert was issued regarding patients being inappropriately co-prescribed two anticoagulants following a medication change, and associated monitoring. - -ObjectiveTo describe which people were switched from warfarin to DOACs; identify potentially unsafe co-prescribing of anticoagulants; and assess whether abnormal clotting results have become more frequent during the pandemic. - -MethodsWorking on behalf of NHS England we conducted a population cohort based study using routine clinical data from >17 million adults in England. - -Results20,000 of 164,000 warfarin patients (12.2%) switched to DOACs between March and May 2020, most commonly to edoxaban and apixaban. Factors associated with switching included: older age, recent renal function test, higher number of recent INR tests recorded, atrial fibrillation diagnosis and care home residency. There was a sharp rise in co-prescribing of warfarin and DOACs from typically 50-100 per month to 246 in April 2020, 0.06% of all people receiving a DOAC or warfarin. INR testing fell by 14% to 506.8 patients tested per 1000 warfarin patients each month. We observed a very small increase in elevated INRs (n=470) during April compared with January (n=420). - -ConclusionsIncreased switching of anticoagulants from warfarin to DOACs was observed at the outset of the COVID-19 pandemic in England following national guidance. There was a small but substantial number of people co-prescribed warfarin and DOACs during this period. Despite a national safety alert on the issue, a widespread rise in elevated INR test results was not found. Primary care has responded rapidly to changes in patient care during the COVID-19 pandemic.",cardiovascular medicine,fuzzy,100,100 medRxiv,10.1101/2020.11.30.20240010,2020-12-03,https://medrxiv.org/cgi/content/short/2020.11.30.20240010,Is Point-of-Care testing feasible and safe in care homes in England? An exploratory usability and accuracy evaluation of Point-of-Care Polymerase Chain Reaction test for SARS-COV-2,Massimo Micocci; Adam Gordon; Mikyung Kelly Seo; Joy A Allen; Kerrie Davies; Dan Lasserson; Carl Thompson; Karen Spilsbury; Cyd Akrill; Ros Heath; Anita Astle; Claire Sharpe; Rafael Perera; Gail Hayward; Peter Buckle,"NIHR London In Vitro Diagnostics Co-operative, Dept of Surgery and Cancer, Faculty of Medicine, Imperial College London St. Mary's Hospital London; Division of Medical Sciences and Graduate Entry Medicine, University of Nottingham, Nottingham, UK;NIHR Applied Research Collaboration-East Midlands (ARC-EM), N; NIHR London In Vitro Diagnostics Co-operative, Dept of Surgery and Cancer, Faculty of Medicine, Imperial College London St. Mary's Hospital London; NIHR Newcastle In Vitro Diagnostics Co-operative, Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK; Healthcare Associated Infections Research Group, University of Leeds and Leeds Teaching Hospitals NHS Trust, Leeds, UK; Warwick Medical School, University of Warwick, UK; School of Healthcare, University of Leeds, Leeds, UK; School of Healthcare, University of Leeds, Leeds, UK; NIHR Applied Research Collaboration Yorkshire and Humber, UK; Springfield Healthcare, Leeds, UK; Landermeads Nursing Home, Nottingham, UK; Wren Hall Nursing Home, Selston, UK; Ashmere Nottinghamshire Ltd, Notts, UK; Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; NIHR Community Healthcare MedTech and IVD Co-operative,Oxford,UK; NIHR London In Vitro Diagnostics Co-operative, Dept of Surgery and Cancer, Faculty of Medicine, Imperial College London St. Mary's Hospital London","IntroductionReliable rapid testing on COVID-19 is needed in care homes to reduce the risk of outbreaks and enable timely care. Point-of-care testing (POCT) in care homes could provide rapid actionable results. This study aimed to examine the usability and test performance of point of care polymerase chain reaction (PCR) for COVID-19 in care homes. MethodsPoint-of-care PCR for detection of SARS-COV2 was evaluated in a purposeful sample of four UK care homes. Test agreement with laboratory real-time PCR and usability and use errors were assessed. @@ -4316,6 +4407,13 @@ MethodsREACT-1 is a series of community surveys of SARS-CoV-2 RT-PCR swab-positi ResultsOverall weighted prevalence of infection in the community in England was 1.3% or 130 people per 10,000 infected, up from 60 people per 10,000 in the round 5 report (18th September to 5th October 2020), doubling every 24 days on average since the prior round. The corresponding R number was estimated to be 1.2. Prevalence of infection was highest in North West (2.4%, up from 1.2%), followed by Yorkshire and The Humber (2.3% up from 0.84%), West Midlands (1.6% up from 0.60%), North East (1.5% up from 1.1%), East Midlands (1.3% up from 0.56%), London (0.97%, up from 0.54%), South West (0.80% up from 0.33%), South East (0.69% up from 0.29%), and East of England (0.69% up from 0.30%). Rapid growth in the South observed in the first half of round 6 was no longer apparent in the second half of round 6. We also observed a decline in prevalence in Yorkshire and The Humber during this period. Comparing the first and second halves of round 6, there was a suggestion of decline in weighted prevalence in participants aged 5 to 12 years and in those aged 25 to 44 years. While prevalence remained high, in the second half of round 6 there was suggestion of a slight fall then rise that was seen nationally and also separately in both the North and the South. ConclusionThe impact of the second national lockdown in England is not yet known. We provide here a detailed description of swab-positivity patterns at national, regional and local scales for the period immediately preceding lockdown, against which future trends in prevalence can be evaluated.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2020.11.18.20230649,2020-11-20,https://medrxiv.org/cgi/content/short/2020.11.18.20230649,A network modelling approach to assess non-pharmaceutical disease controls in a worker population: An application to SARS-CoV-2,Edward M Hill; Benjamin D Atkins; Matt J Keeling; Louise Dyson; Michael J Tildesley,University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick,"BackgroundAs part of a concerted pandemic response to protect public health, businesses can enact non-pharmaceutical controls to minimise exposure to pathogens in workplaces and premises open to the public. Amendments to working practices can lead to the amount, duration and/or proximity of interactions being changed, ultimately altering the dynamics of disease spread. These modifications could be specific to the type of business being operated. + +MethodsWe use a data-driven approach to parameterise an individual-based network model for transmission of SARS-CoV-2 amongst the working population, stratified into work sectors. The network is comprised of layered contacts to consider the risk of spread in multiple encounter settings (workplaces, households, social and other). We analyse several interventions targeted towards working practices: mandating a fraction of the population to work from home; using temporally asynchronous work patterns; and introducing measures to create COVID-secure workplaces. We also assess the general role of adherence to (or effectiveness of) isolation and test and trace measures and demonstrate the impact of all these interventions across a variety of relevant metrics. + +ResultsThe progress of the epidemic can be significantly hindered by instructing a significant proportion of the workforce to work from home. Furthermore, if required to be present at the workplace, asynchronous work patterns can help to reduce infections when compared with scenarios where all workers work on the same days, particularly for longer working weeks. When assessing COVID-secure workplace measures, we found that smaller work teams and a greater reduction in transmission risk reduced the probability of large, prolonged outbreaks. Finally, following isolation guidance and engaging with contact tracing without other measures is an effective tool to curb transmission, but is highly sensitive to adherence levels. + +ConclusionsIn the absence of sufficient adherence to non-pharmaceutical interventions, our results indicate a high likelihood of SARS-CoV-2 spreading widely throughout a worker population. Given the heterogeneity of demographic attributes across worker roles, in addition to the individual nature of controls such as contact tracing, we demonstrate the utility of a network model approach to investigate workplace-targeted intervention strategies and the role of test, trace and isolation in tackling disease spread.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.11.18.20225029,2020-11-20,https://medrxiv.org/cgi/content/short/2020.11.18.20225029,The Invasive Respiratory Infection Surveillance (IRIS) Initiative reveals significant reductions in invasive bacterial infections during the COVID-19 pandemic,Angela B Brueggemann; Melissa J Jansen van Rensburg; David Shaw; Noel D McCarthy; Keith A Jolley; Martin CJ Maiden; Mark PG van der Linden,University of Oxford; University of Oxford; University of Oxford; University of Warwick; University of Oxford; University of Oxford; University Hospital RWTH Aachen,"BackgroundStreptococcus pneumoniae, Haemophilus influenzae and Neisseria meningitidis are leading causes of invasive diseases including bacteraemic pneumonia and meningitis, and of secondary infections post-viral respiratory disease. They are typically transmitted via respiratory droplets. We investigated rates of invasive disease due to these pathogens during the early phase of the COVID-19 pandemic. MethodsLaboratories in 26 countries across six continents submitted data on cases of invasive disease due to S pneumoniae, H influenzae and N meningitidis from 1 January 2018 to 31 May 2020. Weekly cases in 2020 vs 2018-2019 were compared. Streptococcus agalactiae data were collected from nine laboratories for comparison to a non-respiratory pathogen. The stringency of COVID-19 containment measures was quantified by the Oxford COVID-19 Government Response Tracker. Changes in population movements were assessed by Google COVID-19 Community Mobility Reports. Interrupted time series modelling quantified changes in rates of invasive disease in 2020 relative to when containment measures were imposed. @@ -4472,6 +4570,7 @@ RESULTS IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSA small study in 47 Added value of this studyTo our knowledge this is the first study to explore changes in healthcare contacts for acute physical and mental health conditions in a large population representative of the UK. We used electronic primary care health records of nearly 10 million individuals across the UK to investigate the indirect impact of COVID-19 on primary care contacts for mental health, acute alcohol-related events, asthma/chronic obstructive pulmonary disease (COPD) exacerbations, and cardiovascular and diabetic emergencies up to July 2020. For all conditions studied, we found primary care contacts dropped dramatically following the introduction of population-wide restriction measures in March 2020. By July 2020, with the exception of unstable angina and acute alcohol-related events, primary care contacts for all conditions studied had not recovered to pre-lockdown levels. In the general population, estimates of the absolute reduction in the number of primary care contacts up to July 2020, compared to what we would expect from previous years varied from fewer than 10 contacts per million for some cardiovascular outcomes, to 12,800 per million for depression and 6,600 for anxiety. In people with COPD, we estimated there were 43,900 per million fewer contacts for COPD exacerbations up to July 2020 than what we would expect from previous years. Implicatins of all the available evidenceWhile our results may represent some genuine reduction in disease frequency (e.g. the restriction measures may have improved diabetic glycaemic control due to more regular daily routines at home), it is more likely the reduced primary care conatcts we saw represent a substantial burden of unmet need (particularly for mental health conditions) that may be reflected in subsequent increased mortality and morbidity. Health service providers should take steps to prepare for increased demand in the coming months and years due to the short and longterm ramifications of reduced access to care for severe acute physical and mental health conditions. Maintaining access to primary care is key to future public health planning in relation to the pandemic.",primary care research,fuzzy,100,100 +bioRxiv,10.1101/2020.10.26.356014,2020-10-28,https://biorxiv.org/cgi/content/short/2020.10.26.356014,"COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms",Marek Ostaszewski; Anna Niarakis; Alexander Mazein; Inna Kuperstein; Robert Phair; Aurelio Orta-Resendiz; Vidisha Singh; Sara Sadat Aghamiri; Marcio Luis Acencio; Enrico Glaab; Andreas Ruepp; Gisela Fobo; Corinna Montrone; Barbara Brauner; Goar Frishman; Julia Somers; Matti Hoch; Shailendra Kumar Gupta; Julia Scheel; Hanna Borlinghaus; Tobias Czauderna; Falk Schreiber; Arnau Montagud; Miguel Ponce de Leon; Akira Funahashi; Yusuke Hiki; Noriko Hiroi; Takahiro G Yamada; Andreas Drager; Alina Renz; Muhammad Naveez; Zsolt Bocskei; Daniela Bornigen; Liam Fergusson; Marta Conti; Marius Rameil; Vanessa Nakonecnij; Jakob Vanhoefer; Leonard Schmiester; Muying Wang; Emily E Ackerman; Jason E Shoemaker; Jeremy Zucker; Kristie L Oxford; Jeremy Teuton; Ebru Kocakaya; Gokce Yagmur Summak; Kristina Hanspers; Martina Kutmon; Susan Coort; Lars Eijssen; Friederike Ehrhart; Rex D. A. B.; Denise Slenter; Marvin Martens; Nhung Pham; Robin Haw; Bijay Jassal; Lisa Matthews; Marija Orlic-Milacic; Andrea Senff-Ribeiro; Karen Rothfels; Veronica Shamovsky; Ralf Stephan; Cristoffer Sevilla; Thawfeek Mohamed Varusai; Jean-Marie Ravel; Vera Ortseifen; Silvia Marchesi; Piotr Gawron; Ewa Smula; Laurent Heirendt; Venkata Satagopam; Guanming Wu; Anders Riutta; Martin Golebiewski; Stuart Owen; Carole Goble; Xiaoming Hu; Rupert Overall; Dieter Maier; Angela Bauch; Benjamin M Gyori; John A Bachman; Carlos Vega; Valentin Groues; Miguel Vazquez; Pablo Porras; Luana Licata; Marta Iannuccelli; Francesca Sacco; Denes Turei; Augustin Luna; Ozgun Babur; Sylvain Soliman; Alberto Valdeolivas; Marina Esteban-Medina; Maria Pena-Chilet; Kinza Rian; Tomas Helikar; Bhanwar Lal Puniya; Anastasia Nesterova; Anton Yuryev; Anita de Waard; Dezso Modos; Agatha Treveil; Marton Laszlo Olbei; Bertrand De Meulder; Aurelien Naldi; Aurelien Dugourd; Laurence Calzone; Chris Sander; Emek Demir; Tamas Korcsmaros; Tom C Freeman; Franck Auge; Jacques S Beckmann; Jan Hasenauer; Olaf Wolkenhauer; Egon Willighagen; Alexander R Pico; Chris Evelo; Lincoln D Stein; Henning Hermjakob; Julio Saez-Rodriguez; Joaquin Dopazo; Alfonso Valencia; Hiroaki Kitano; Emmanuel Barillot; Charles Auffray; Rudi Balling; Reinhard Schneider; - the COVID-19 Disease Map Community,"Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; Department of Biology, Univ. Evry, University of Paris-Saclay, GenHotel, Genopole, 91025, Evry, France; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; Institut Curie, PSL Research University, Paris, France.; Integrative Bioinformatics, Inc., 346 Paul Ave, Mountain View, CA, USA; Institut Pasteur, HIV, Inflammation and Persistence Unit, Paris, France; Laboratoire Europeen de Recherche pour la Polyarthrite Rhumatoide - Genhotel, Univ Evry, Universite Paris-Saclay, 2, rue Gaston Cremieux, 91057 EVRY-GENOPOLE ce; Inserm- Institut national de la sante et de la recherche medicale. Saint-Louis Hospital 1 avenue Claude Vellefaux Pavillon Bazin 75475 Paris; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; Institute of Experimental Genetics (IEG), Helmholtz Zentrum Munchen-German Research Center for Environmental Health (GmbH), Ingolstadter Landstrasse 1, D-85764 ; Institute of Experimental Genetics (IEG), Helmholtz Zentrum Munchen-German Research Center for Environmental Health (GmbH), Ingolstadter Landstrasse 1, D-85764 ; Institute of Experimental Genetics (IEG), Helmholtz Zentrum Munchen-German Research Center for Environmental Health (GmbH), Ingolstadter Landstrasse 1, D-85764 ; Institute of Experimental Genetics (IEG), Helmholtz Zentrum Munchen-German Research Center for Environmental Health (GmbH), Ingolstadter Landstrasse 1, D-85764 ; Institute of Experimental Genetics (IEG), Helmholtz Zentrum Munchen-German Research Center for Environmental Health (GmbH), Ingolstadter Landstrasse 1, D-85764 ; Oregong Health & Sciences Univerity; Department of Molecular and Medical Genetics; 3222 SW Research Drive, Portland, Oregon, U.S.A 97239; Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany; Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany; Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany; Department of Computer and Information Science, University of Konstanz, Konstanz, Germany; Monash University, Faculty of Information Technology, Department of Human-Centred Computing, Wellington Rd, Clayton VIC 3800, Australia; Department of Computer and Information Science, University of Konstanz, Konstanz, Germany; Barcelona Supercomputing Center (BSC), Barcelona, Spain; Barcelona Supercomputing Center (BSC), Barcelona, Spain; Keio University, Department of Biosciences and Informatics, 3-14-1 Hiyoshi Kouhoku-ku Yokohama Japan 223-8522; Keio University, Department of Biosciences and Informatics, 3-14-1 Hiyoshi Kouhoku-ku Yokohama Japan 223-8522; Sanyo-Onoda City University, Faculty of Pharmaceutical Sciences, University St.1-1-1, Yamaguchi, Japan 756-0884; Keio University, Department of Biosciences and Informatics, 3-14-1 Hiyoshi Kouhoku-ku Yokohama Japan 223-8522; Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tu; Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tu; Riga Technical University, Institute of Applied Computer Systems,1 Kalku Street, LV-1658 Riga, Latvia; Sanofi R&D Translational Sciences; Bioinformatics Core Facility, Universitaetsklinikum Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany; The University of Edinburgh, Royal (Dick) School of Veterinary Medicine, Easter Bush Campus, Midlothian, EH25 9RG; Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany; University of Bonn, Germany; Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany; Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany; Helmholtz Zentrum Munchen - German Research Center for Environmental Health, Institute of Computational Biology, 85764 Neuherberg, Germany; Department of Chemical Engineering, University of Pittsburgh; University of Pittsburgh, Department of Chemical and Petroleum Engineering; Dept. of Chemical & Petroleum Engineering, University of Pittsburgh; Pacific Northwest National Laboratory; Pacific Northwest National Laboratory; Pacific Northwest National Laboratory; Ankara University, Stem Cell Institute, Ceyhun Atif Kansu St. No: 169 06520 Cevizlidere/ANKARA/TURKEY; Ankara University, Stem Cell Institute, Ceyhun Atif Kansu St. No: 169 06520 Cevizlidere/ANKARA/TURKEY; Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands; Maastricht University, NUTRIM, Bioinformatics-BiGCaT, PO Box 616, 6200 MD, Maastricht, the Netherlands; Department of Bioninformatics-BiGCaT, NUTRIM, Maastricht University, Universiteitssingel 60, 6229 ER Maastricht, The Netherlands; Maastricht University, Department of Bioinformatics, NUTRIM, Universiteitssingel 60; 6229 ER Maastricht; The Netherlands; Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore 575018, India; Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, 6229 ER Maastricht, The Netherlands; Maastricht University, NUTRIM, Bioinformatics-BiGCaT, PO Box 616, 6200 MD, Maastricht, the Netherlands; Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3; Ontario Institute for Cancer Research (OICR), 661 University Ave Suite 510, Toronto, ON M5G 0A3, Canada; NYU Grossman School of Medicine, New York NY 10016 USA; Ontario Institute for Cancer Research, Department of Computational Biology, MaRS Centre, South Tower, 661 University Avenue, Suite 500, Toronto, Ontario, Canada; Ontario Institute for Cancer Research (OICR) (Canada); Ontario Institute for Cancer Research, Department of Computational Biology, MaRS Centre, South Tower, 661 University Avenue, Suite 500, Toronto, Ontario, Canada; NYU Langone Medical Center, New York, USA; Ontario Institute for Cancer Research, MaRS Centre, 661 University Ave, Suite 510, Toronto, Ontario, Canada; EMBL-EBI, Molecular Systems, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD; Reactome, EMBL-EBI, Cambridge, UK; University of Lorraine, INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, F-54000 Nancy, France.; Senior Research Group in Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitaetsstrasse 27, 33615 Bielefeld,; Uppsala University - Sweden; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239-3098, USA; Gladstone Institutes, Institute for Data Science and Biotechnology, 1650 Owens St., San Francisco, CA 94131, USA; Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg (Germany); The University of Manchester, Department of Computer Science, Oxford Road, Manchester, M13 9PL, UK; The University of Manchester, Department of Computer Science, Oxford Road, Manchester, M13 9PL, UK; Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg (Germany); German Center for Neurodegenerative Diseases (DZNE) Dresden, Tatzberg 41, 01307 Dresden, Germany.; Biomax Informatics AG, Robert-Koch-Str. 2, 82152 Planegg, Germany; Biomax Informatics AG, Robert-Koch-Str. 2, 82152 Planegg, Germany; Harvard Medical School, Laboratory of Systems Pharmacology, 200 Longwood Avenue, Boston, MA; Harvard Medical School, Laboratory of Systems Pharmacology, 200 Longwood Avenue, Boston, MA; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; Barcelona Supercomputing Center (BSC), Barcelona, Spain; EMBL-EBI, Molecular Systems, Wellcome Genome Campus, CB10 1SD, Hinxton, UK; University of Rome Tor Vergata, Department of Biology, Via della Ricerca Scientifica 1, 00133 Rome, Italy; University of Rome Tor Vergata, Department of Biology, Via della Ricerca Scientifica 1, 00133 Rome, Italy; University of Rome Tor Vergata, Department of Biology, Via della Ricerca Scientifica 1, 00133 Rome, Italy; Heidelberg Univarsity, Institute for Computational Biomedicine, BQ 0053, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany; cBio Center, Divisions of Biostatistics and Computational Biology, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.; University of Massachusetts Boston, Computer Science Department, 100 William T, Morrissey Blvd, Boston, MA 02125; Inria Saclay Ile-de-France; Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany; Clinical Bioinformatics Area. Fundacion Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain.; Clinical Bioinformatics Area. Fundacion Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain.; Clinical Bioinformatics Area. Fundacion Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain.; University of Nebraska-Lincoln, Department of Biochemistry, 1901 Vine St., Lincoln, NE, 68588, USA; University of Nebraska-Lincoln, Department of Biochemistry, 1901 Vine St., Lincoln, NE, 68588, USA; Elsevier, Life Science Department; Elsevier, Professional Services, 1600 John F Kennedy Blvd #1800, Philadelphia, PA 19103; Elsevier, Research Collaborations Unit, 71 Hanley Lane, Jericho, VT 05465; Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom; Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom; Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom; Association EISBM; Inria Saclay - Ile de France, Lifeware group, 91120 Palaiseau, France; Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany; Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, F-75005, Paris, France.; cBio Center, Divisions of Biostatistics and Computational Biology, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.; Oregon Health and Science University, Department of Molecular and Medical Genetics, 3222 SW Research Drive, Mail Code: L103, Portland, Oregon, U.S.A. 97239; Earlham Institute, Norwich Research Park, NR4 7UZ, Norwich, UK; The Roslin Institute, University of Edinburgh EH25 9RG; Sanofi R&D, Translational Sciences, 1 av Pierre Brossolette 91395 Chilly-Mazarin France; University of Lausanne, Lausanne, Switzerland; Interdisciplinary Research Unit Mathematics and Life Sciences, University of Bonn, Germany; University of Rostock, Dept of Systems Biology & Bioinformatics; Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands; Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA; Dept. Bioinformatics - BiGCaT, Maastricht University, The Netherlands; Ontario Institute for Cancer Research, Adaptive Oncology Theme, 661 University Ave, Toronto, ON M5G 1M1 Canada; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK; Institute for Computational Biomedicine Heidelberg University, Faculty of Medicine, Im Neuenheimer Feld 267, 69120 Heidelberg; Clinical Bioinformatics Area. Fundacion Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio. 41013. Sevilla. Spain.; Barcelona Supercomputing Center (BSC), Barcelona, Spain; Systems Biology Institute, Tokyo Japan; Institut Curie, PSL Research University, Paris, France.; European Institute for Systems Biology and Medicine (EISBM), Vourles, France; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; -","We describe a large-scale community effort to build an open-access, interoperable, and computable repository of COVID-19 molecular mechanisms - the COVID-19 Disease Map. We discuss the tools, platforms, and guidelines necessary for the distributed development of its contents by a multi-faceted community of biocurators, domain experts, bioinformaticians, and computational biologists. We highlight the role of relevant databases and text mining approaches in enrichment and validation of the curated mechanisms. We describe the contents of the Map and their relevance to the molecular pathophysiology of COVID-19 and the analytical and computational modelling approaches that can be applied for mechanistic data interpretation and predictions. We conclude by demonstrating concrete applications of our work through several use cases and highlight new testable hypotheses.",systems biology,fuzzy,100,100 medRxiv,10.1101/2020.10.25.20219048,2020-10-27,https://medrxiv.org/cgi/content/short/2020.10.25.20219048,Viral load in community SARS-CoV-2 cases varies widely and temporally,Ann Sarah Walker; Emma Pritchard; Thomas House; Julie V Robotham; Paul J Birrell; Iain Bell; John I Bell; John N Newton; Jeremy Farrar; Ian Diamond; Ruth Studley; Jodie Hay; Karina-Doris Vihta; Timothy EA Peto; Nicole Stoesser; Philippa C Matthews; David W Eyre; Koen Pouwels; - the COVID-19 Infection Survey team,University of Oxford; University of Oxford; University of Manchester; Public Health England; Public Health England; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; Office for National Statistics; Office for National Statistics; University of Glasgow; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; ,"Information on SARS-CoV-2 in representative community surveillance is limited, particularly cycle threshold (Ct) values (a proxy for viral load). Of 3,312,159 nose and throat swabs taken 26-April-2020 to 13-March-2021 in the UKs national COVID-19 Infection Survey, 27,902(0.83%) were RT-PCR-positive, 10,317(37%), 11,012(40%) and 6,550(23%) for 3, 2 or 1 of the N, S and ORF1ab genes respectively, with median Ct=29.2 ([~]215 copies/ml; IQR Ct=21.9-32.8, 14-56,400 copies/ml). Independent predictors of lower Cts (i.e. higher viral load) included self-reported symptoms and more genes detected, with at most small effects of sex, ethnicity and age. Single-gene positives almost invariably had Ct>30, but Cts varied widely in triple-gene positives, including without symptoms. Population-level Cts changed over time, with declining Ct preceding increasing SARS-CoV-2 positivity. Of 6,189 participants with IgG S-antibody tests post-first RT-PCR-positive, 4,808(78%) were ever antibody-positive; Cts were significantly higher in those remaining antibody-negative. Community SARS-CoV-2 Ct values could be a useful epidemiological early-warning indicator. IMPACT STATEMENTCt values from SARS-CoV-2 RT-PCR tests vary widely and over calendar time. They have the potential to be used more broadly in public testing programmes as an ""early-warning"" system for shifts in infectious load and hence transmission.",infectious diseases,fuzzy,100,100 @@ -4766,27 +4865,6 @@ Research in contextO_ST_ABSEvidence before this studyC_ST_ABSPublished trials an Added value of this studyIn this cohort study representing 40% of the population of England, we investigated whether routine use of hydroxychloroquine prior to the COVID-19 outbreak prevented COVID-19 mortality. Using robust pharmacoepidemiological methods, we found no evidence to support a substantial benefit of hydroxychloroquine in preventing COVID-19 mortality. At the same time, we have shown no significant harm, and this generates the equipoise to justify continuing randomised trials. We have demonstrated in this study that it is feasible to address specific hypotheses about medicines in a rapid and transparent manner to inform interim clinical decision making and support the need for large-scale, randomised trial data. Implications of all the available evidenceThis is the first study to investigate the ongoing routine use of hydroxychloroquine and risk of COVID-19 mortality in a general population. While we found no evidence of any protective benefit, due to the observational nature of the study, residual confounding remains a possibility. Completion of trials for prevention of severe outcomes is warranted, but prior to the completion of these, we found no evidence to support the use of hydroxychloroquine for prevention of COVID-19 mortality.",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2020.09.05.20188821,2020-09-08,https://medrxiv.org/cgi/content/short/2020.09.05.20188821,Ethnicity and clinical outcomes in COVID-19A Systematic Review and Meta-analysis,Shirley Sze; Daniel Pan; Laura J Gray; Clareece R Nevill; Christopher A Martin; Joshua Nazareth; Jatinder S Minhas; Pip Divall; Kamlesh Khunti; Keith Abrams; Laura B Nellums; Manish Pareek,University of Leicester; University of Leicester; University of Leicester; University of Leicester; University of Leicester; University of Leicester; University of Leicester; University Hospitals of Leicester NHS Trust; University of Leicester; University of Leicester; University of Nottingham; University of Leicester,"ImportanceThe association of ethnicity with outcomes in patients with COVID-19 is unclear. - -ObjectiveTo determine whether the risk of SARS-CoV-2 infection, COVID-19 intensive care unit (ICU) admission and mortality are associated with ethnicity. - -Data SourcesWe searched all English language articles published 1st December 2019 - 30th June 2020 within MEDLINE, EMBASE, PROSPERO and the Cochrane library using indexing terms for COVID-19 and ethnicity, as well as manuscripts awaiting peer review on MedRxiv during the same period. - -Study SelectionIncluded studies reported original clinical data, disaggregated by ethnicity, on patients with confirmed or suspected COVID-19. We excluded correspondence, area level, modelling and basic science articles. Two independent reviewers screened articles for inclusion. Of 926 identified articles, 35 were included in the meta-analyses. - -Data Extraction and SynthesisThe review was conducted according to PRISMA guidelines. Reviewers independently extracted data using a piloted form on: (1) rates of infection, ICU admission and mortality by ethnicity; and (2) unadjusted and adjusted data comparing ethnic minority and White groups. Data were pooled using random effects models. - -Main Outcomes and MeasuresOutcomes were: (1) infection with SARS-CoV-2 confirmed on molecular testing; (2) ICU admission; and (3) mortality in COVID-19 confirmed and suspected cases. - -Results13,535,562 patients from 35 studies were included in the meta-analyses. Black, Asian and Hispanic individuals had a greater risk of infection compared to White individuals (Black: pooled adjusted RR: 2.06, 95% CI: 1.59-2.67; Asian: 1.35, 95%CI: 1.15-1.59; Hispanic: 1.77, 95% CI: 1.39-2.25). Black individuals were significantly more likely to be admitted to ICU than White individuals (pooled adjusted RR: 1.61, 95% CI: 1.02-2.55). Risk of mortality was similar across ethnicities among hospitalised patients, but increased among Asian and Mixed ethnic groups in the general population. - -ConclusionsBlack, Asian and Hispanic ethnic groups are at increased risk of SARS-CoV-2 infection. Black individuals may be more likely to require ICU admission for COVID-19. There may also be disparities in risk of death from COVID-19 at a population level. Our findings are of critical public health importance and should inform policy on minimising SARS-CoV-2 exposure in ethnic minority groups. - -KEY POINTSO_ST_ABSQuestionC_ST_ABSIs ethnicity associated with vulnerability to, and outcomes from, coronavirus disease 2019 (COVID-19)? - -FindingsIn this systematic review and meta-analysis, rates of infection and outcomes from COVID-19 were compared between ethnic groups. Individuals from Black, Asian and Hispanic ethnicity were significantly more vulnerable to SARS-CoV-2 infection than those of White ethnicity. Black individuals were more likely to need intensive care unit (ICU) admission for COVID-19 than White individuals. Risk of mortality was similar across ethnicities among hospitalised patients, but increased among Asian and Mixed ethnic groups in the general population. - -MeaningThere is strong evidence for an increased risk of SARS-CoV-2 infection amongst ethnic minorities, and targeted public health policies are required to reduce this risk.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.09.02.20185892,2020-09-07,https://medrxiv.org/cgi/content/short/2020.09.02.20185892,Prognostic accuracy of emergency department triage tools for adults with suspected COVID-19: The PRIEST observational cohort study,Ben Thomas; Steve Goodacre; Ellen Lee; Laura Sutton; Amanda Loban; Simon Waterhouse; Richard Simmonds; Katie Biggs; Carl Marincowitz; Jose Schutter; Sarah Connelly; Elena Sheldon; Jamie Hall; Emma Young; Andrew Bentley; Kirsty Challen; Chris Fitzsimmons; Tim Harris; Fiona Lecky; Andrew Lee; Ian Maconochie; Darren Walter,University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; University of Sheffield; Manchester University NHS Foundation Trust; Lancashire Teaching Hospitals NHS Foundation Trust; Sheffield Children's NHS Foundation Trust; Barts Health NHS Trust; University of Sheffield; University of Sheffield; Imperial College Healthcare NHS Trust; Manchester University NHS Foundation Trust,"ObjectivesThe World Health Organisation (WHO) and National Institute for Health and Care Excellence (NICE) recommend various triage tools to assist decision-making for patients with suspected COVID-19. We aimed to estimate the accuracy of triage tools for predicting severe illness in adults presenting to the emergency department (ED) with suspected COVID-19 infection. MethodsWe undertook a mixed prospective and retrospective observational cohort study in 70 EDs across the United Kingdom (UK). We collected data from people attending with suspected COVID-19 between 26 March 2020 and 28 May 2020, and used presenting data to determine the results of assessment with the following triage tools: the WHO algorithm, NEWS2, CURB-65, CRB-65, PMEWS and the swine flu adult hospital pathway (SFAHP). We used 30-day outcome data (death or receipt of respiratory, cardiovascular or renal support) to determine prognostic accuracy for adverse outcome. @@ -4892,7 +4970,6 @@ MethodsWe developed a simple, interactive tool to assess the impact of different ResultsWith sensitivity of 80%, infection prevalence of 1 in 2,000, and specificity 99.9% on all tests, PPV in the tested population of 100,000 will be only 29% with one test, increasing to > 99.5% (100% when rounded to the nearest %) with repeat testing in strategies 2 or 3. More realistically, if specificity is 95% for the first and 99.9% for subsequent tests, single test PPV will be only 1%, increasing to 86% with repeat testing in strategy 2, or 79% with strategy 3 (albeit with 6 fewer false negatives than strategy 2). In the whole population, or in particular individuals, PPV increases as infection becomes more common in the population but falls to unacceptably low levels with lower test specificity. ConclusionTo avoid multiple unnecessary restrictions on whole populations, and in particular individuals, from widespread population testing for SARS-CoV-2, the crucial roles of extremely high test specificity and of confirmatory testing must be fully appreciated and incorporated into policy decisions.",epidemiology,fuzzy,100,100 -medRxiv,10.1101/2020.08.17.20175117,2020-08-21,https://medrxiv.org/cgi/content/short/2020.08.17.20175117,Real-time spatial health surveillance: mapping the UK COVID-19 epidemic,Richard Fry; Joe Hollinghurst; Helen R Stagg; Daniel A Thompson; Claudio Fronterre; Chris Orton; Ronan A Lyons; David V Ford; Aziz Sheikh; Peter J Diggle,Swansea University; Swansea University; Edinburgh University; Swansea University; Lancaster University; Swansea University; Swansea University; Swansea University; Edinburgh University; Lancaster University,"The COVID-19 pandemic has highlighted the need for robust data linkage systems and methods for identifying outbreaks of disease in near real-time. Using self-reported app data and the Secure Anonymised Information Linkage (SAIL) Databank, we demonstrate the use of sophisticated spatial modelling for near-real-time prediction of COVID-19 prevalence at small-area resolution to inform strategic government policy areas. A pre-requisite to an effective control strategy is that predictions need to be accompanied by estimates of their precision, to guard against over-reaction to potentially spurious features of best guess predictions. In the UK, important emerging risk-factors such as social deprivation or ethnicity vary over small distances, hence risk needs to be modelled at fine spatial resolution to avoid aggregation bias. We demonstrate that existing geospatial statistical methods originally developed for global health applications are well-suited to this task and can be used in an anonymised databank environment, thus preserving the privacy of the individuals who contribute their data.",public and global health,fuzzy,100,100 medRxiv,10.1101/2020.08.17.20161760,2020-08-19,https://medrxiv.org/cgi/content/short/2020.08.17.20161760,"SARS-CoV-2 (COVID-19) infection in pregnant women: characterization of symptoms and syndromes predictive of disease and severity through real-time, remote participatory epidemiology.",Erika Molteni; Christina M Astley; Wenjie Ma; Carole Helene Sudre; Laura A Magee; Benjamin Murray; Tove Fall; Maria F Gomez; Neli Tsereteli; Paul W Franks; John S Brownstein; Richard Davies; Jonathan Wolf; Timothy Spector; Sebastien Ourselin; Claire Steves; Andrew T Chan; Marc Modat,"King's College London; Boston Children's Hospital and Harvard Medical School; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA; King's College London; Department of Women and Childrens Health, School of Life Course Sciences and the Institute of Women and Childrens Health, Kings College London, London, United K; School of Biomedical Engineering & Imaging Sciences, Kings College London, London, United Kingdom; Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Sweden; Department of Clinical Sciences, Lund University Diabetes Centre, Jan Waldenstroems gata 35, SE-21428, Malmo, Sweden; Department of Clinical Sciences, Lund University Diabetes Centre, Jan Waldenstroems gata 35, SE-21428, Malmo, Sweden; Department of Clinical Sciences, Lund University Diabetes Centre, Jan Waldenstroems gata 35, SE-21428, Malmo, Sweden.; Boston Childrens Hospital and Harvard Medical School, Boston, MA, USA; Zoe Global Limited, London, United Kingdom; Zoe Global Limited, London, United Kingdom; King's College London; School of Biomedical Engineering & Imaging Sciences, Kings College London, London, United Kingdom; King's College London; Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA; School of Biomedical Engineering & Imaging Sciences, Kings College London, London, United Kingdom","BackgroundFrom the beginning of COVID-19 pandemic, pregnant women have been considered at greater risk of severe morbidity and mortality. However, data on hospitalized pregnant women show that the symptom profile and risk factors for severe disease are similar to those among women who are not pregnant, although preterm birth, Cesarean delivery, and stillbirth may be more frequent and vertical transmission is possible. Limited data are available for the cohort of pregnant women that gave rise to these hospitalized cases, hindering our ability to quantify risk of COVID-19 sequelae for pregnant women in the community. ObjectiveTo test the hypothesis that pregnant women in community differ in their COVID-19 symptoms profile and disease severity compared to non-pregnant women. This was assessed in two community-based cohorts of women aged 18-44 years in the United Kingdom, Sweden and the United States of America. @@ -4911,6 +4988,19 @@ FindingsUnsupervised clustering identified distinct sub-groups. First, a core sy InterpretationThe large scale of the ISARIC-4C study enabled robust, granular discovery and replication of patient clusters. Clinical interpretation is necessary to determine which of these observations have practical utility. We propose that four patterns are usefully distinct from the core symptom groups: gastro-intestinal disease, productive cough, confusion, and pauci-symptomatic presentations. Importantly, each is associated with an in-hospital mortality which differs from that of patients with core symptoms. These observations deepen our understanding of COVID-19 and will influence clinical diagnosis, risk prediction, and future mechanistic and clinical studies. FundingMedical Research Council; National Institute Health Research; Well-come Trust; Department for International Development; Bill and Melinda Gates Foundation; Liverpool Experimental Cancer Medicine Centre.",infectious diseases,fuzzy,94,100 +medRxiv,10.1101/2020.08.13.20174193,2020-08-15,https://medrxiv.org/cgi/content/short/2020.08.13.20174193,CovidNudge: diagnostic accuracy of a novel lab-free point-of-care diagnostic for SARS-CoV-2,Malick M Gibani; Christofer Toumazou; Mohammadreza Sohbati; Rashmita Sahoo; Maria Karvela; Tsz-Kin Hon; Sara De Mateo; Alison Burdett; K Y Felice Leung; Jake Barnett; Arman Orbeladze; Song Luan; Stavros Pournias; Jiayang Sun; Barnaby Flower; Judith Bedzo-Nutakor; Maisarah Amran; Rachael Quinlan; Keira Skolimowska; Robert Klaber; Gary Davies; David Muir; Paul Randell; Derrick W M Crook; Graham P Taylor; Wendy Barclay; Nabeela Mughal; Luke S P Moore; Katie Jeffery; Graham S Cooke,"Imperial College London; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; Department of Infectious Disease, Imperial College London, United Kingdom; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; Imperial College Healthcare NHS Trust, United Kingdom.; Department of Infectious Disease, Imperial College London, United Kingdom; Imperial College Healthcare NHS Trust, United Kingdom; Imperial College Healthcare NHS Trust, United Kingdom; Chelsea & Westminster NHS Foundation Trust, London; Imperial College Healthcare NHS Trust, United Kingdom; Imperial College Healthcare NHS Trust, United Kingdom; NIHR Oxford Biomedical Research Centre; Department of Infectious Disease, Imperial College London, United Kingdom; Department of Infectious Disease, Imperial College London, United Kingdom; Chelsea & Westminster NHS Foundation Trust, London; Chelsea & Westminster NHS Foundation Trust, London; Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; Department of Infectious Disease, Imperial College London, United Kingdom","3.BackgroundAccess to rapid diagnosis is key to the control and management of SARS-CoV-2. Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) testing usually requires a centralised laboratory and significant infrastructure. We describe the development and diagnostic accuracy assessment of a novel, rapid point-of-care RT-PCR test, the DnaNudge(R) platform CovidNudge test, which requires no laboratory handling or sample pre-processing. + +MethodsNasopharyngeal swabs are inserted directly into a cartridge which contains all reagents and components required for RT-PCR reactions, including multiple technical replicates of seven SARS-CoV-2 gene targets (rdrp1, rdrp2, e-gene, n-gene, n1, n2 and n3) and human ribonuclease P (RNaseP) as positive control. Between April and May 2020, swab samples were tested in parallel using the CovidNudge direct-to-cartridge platform and standard laboratory RT-PCR using swabs in viral transport medium. Samples were collected from three groups: self-referred healthcare workers with suspected COVID-19 (Group 1, n=280/386; 73%); patients attending the emergency department with suspected COVID-19 (Group 2, n=15/386; 4%) and hospital inpatient admissions with or without suspected COVID-19 (Group 3, n=91/386; 23%). + +ResultsOf 386 paired samples tested across all groups, 67 tested positive on the CovidNudge platform and 71 with standard laboratory RT-PCR. The sensitivity of the test varied by group (Group 1 93% [84-98%], Group 2 100% [48-100%] and Group 3 100% [29-100%], giving an average sensitivity of 94.4% (95% confidence interval 86-98%) and an overall specificity of 100% (95%CI 99-100%; Group 1 100% [98-100%]; Group 2 100% [69-100%] and Group 3 100% [96-100%]). Point of care testing performance was comparable during a period of high (25%) and low (3%) background prevalence. Amplification of the viral nucleocapsid (n1, n2, n3) targets were most sensitive for detection of SARS-CoV2, with the assay able to detect 1x104 viral particles in a single swab. + +ConclusionsThe CovidNudge platform offers a sensitive, specific and rapid point of care test for the presence of SARS-CoV-2 without laboratory handling or sample pre-processing. The implementation of such a device could be used to enable rapid decisions for clinical care and testing programs. + +4. RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSThe WHO has highlighted the development of rapid, point-of-care diagnostics for detection of SARS-CoV-2 as a key priority to tackle COVID-19. The Foundation for Innovative Diagnostics (FIND) has identified over 90 point-of-care, near patient or mobile tests for viral detection of SARS-CoV-2. However, the most widely available rapid tests to date require some sample handling which limits their use at point-of-care. In addition, pressure on supply chains is restricting access to current diagnostics and alternatives are needed urgently. + +Added value of this studyWe describe the development and clinical validation of COVID nudge, a novel point-of-care RT-PCR diagnostic, evaluated during the first wave of the SARS-CoV-2 epidemic. The platform is able to achieve high analytic sensitivity and specificity from dry swabs within a self-contained cartridge. The lack of downstream sample handling makes it suitable for use in a range of clinical settings, without need for a laboratory or specialized operator. Multiplexed assays within the cartridge allow inclusion of a positive human control, which reduces the false negative testing rate due to insufficient sampling. + +Implication of the available evidencePoint-of-care testing can relieve pressure on centralized laboratories and increase overall testing capacity, complementing existing approaches. These findings support a role for COVID Nudge as part of strategies to improve access to rapid diagnostics to SARS-CoV-2. Since May 2020, the system has been implemented in UK hospitals and is being rolled out nationwide.",infectious diseases,fuzzy,92,100 medRxiv,10.1101/2020.08.12.20173690,2020-08-14,https://medrxiv.org/cgi/content/short/2020.08.12.20173690,"Antibody prevalence for SARS-CoV-2 in England following first peak of the pandemic: REACT2 study in 100,000 adults",Helen Ward; Christina J Atchison; Matthew Whitaker; Kylie E. C. Ainslie; Joshua Elliott; Lucy C Okell; Rozlyn Redd; Deborah Ashby; Christl A. Donnelly; Wendy Barclay; Ara Darzi; Graham Cooke; Steven Riley; Paul Elliott,"Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Dept Inf Dis Epi, Imperial College; Imperial College London","BackgroundEngland, UK has experienced a large outbreak of SARS-CoV-2 infection. As in USA and elsewhere, disadvantaged communities have been disproportionately affected. MethodsNational REal-time Assessment of Community Transmission-2 (REACT-2) prevalence study using a self-administered lateral flow immunoassay (LFIA) test for IgG among a random population sample of 100,000 adults over 18 years in England, 20 June to 13 July 2020. @@ -4918,6 +5008,7 @@ MethodsNational REal-time Assessment of Community Transmission-2 (REACT-2) preva ResultsData were available for 109,076 participants, yielding 5,544 IgG positive results; adjusted (for test performance) and re-weighted (for sampling) prevalence was 6.0% (95% Cl: 5.8, 6.1). Highest prevalence was in London (13.0% [12.3, 13.6]), among people of Black or Asian (mainly South Asian) ethnicity (17.3% [15.8, 19.1] and 11.9% [11.0, 12.8] respectively) and those aged 18-24 years (7.9% [7.3, 8.5]). Adjusted odds ratio for care home workers with client-facing roles was 3.1 (2.5, 3.8) compared with non-essential workers. One third (32.2%, [31.0-33.4]) of antibody positive individuals reported no symptoms. Among symptomatic cases, most (78.8%) reported symptoms during the peak of the epidemic in England in March (31.3%) and April (47.5%) 2020. We estimate that 3.36 million (3.21, 3.51) people have been infected with SARS-CoV-2 in England to end June 2020, with an overall infection fatality ratio (IFR) of 0.90% (0.86, 0.94); age-specific IFR was similar among people of different ethnicities. ConclusionThe SARS-CoV-2 pandemic in England disproportionately affected ethnic minority groups and health and care home workers. The higher risk of infection in minority ethnic groups may explain their increased risk of hospitalisation and mortality from COVID-19.",infectious diseases,fuzzy,100,100 +medRxiv,10.1101/2020.08.13.20174227,2020-08-14,https://medrxiv.org/cgi/content/short/2020.08.13.20174227,Long-Term Exposure to Outdoor Air Pollution and COVID-19 Mortality: an ecological analysis in England,Zhiqiang Feng; Mark Cherrie; Chris DIBBEN,University of Edinburgh; University of Edinburgh; University of Edinburgh,"There is an urgent need to examine what individual and environmental risk factors are associated with COVID-19 mortality. This objective of this study is to investigate the association between long term exposure to air pollution and COVID-19 mortality. We conducted a nationwide, ecological study using zero-inflated negative binomial models to estimate the association between long term (2014-2018) small area level exposure to NOx, PM2.5, PM10 and SO2 and COVID-19 mortality rates in England adjusting for socioeconomic factors and infection exposure. We found that all four pollutant concentrations were positively associated with COVID-19 mortality. The increase in mortality risk ratio per inter quarter range increase was for PM2.5:11%, 95%CIs 6%-17%), PM10 (5%; 95%CIs 1%-11%), NOx (11%, 95%CIs 6%-15%) and SO2 (7%, 95%CIs 3%-11%) were respectively in adjusted models. Public health intervention may need to protect people who are in highly polluted areas from COVID-19 infections.",occupational and environmental health,fuzzy,100,100 medRxiv,10.1101/2020.08.12.20171405,2020-08-14,https://medrxiv.org/cgi/content/short/2020.08.12.20171405,OpenSAFELY: Do adults prescribed Non-steroidal anti-inflammatory drugs have an increased risk of death from COVID-19?,Angel YS Wong; Brian MacKenna; Caroline Morton; Anna Schultze; Alex J Walker; Krishnan Bhaskaran; Jeremy Brown; Christopher T. Rentsch; Elizabeth Williamson; Henry Drysdale; Richard Croker; Seb Bacon; William Hulme; Chris Bates; Helen J Curtis; Amir Mehrkar; David Evans; Peter Inglesby; Jonathan Cockburn; Helen McDonald; Laurie Tomlinson; Rohini Mathur; Kevin Wing; Harriet Forbes; John Parry; Frank Hester; Sam Harper; Stephen Evans; Liam Smeeth; Ian Douglas; Ben Goldacre,"London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; US Department of Veterans Affairs, London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP; TPP; TPP; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford","ImportanceThere has been speculation that non-steroidal anti-inflammatory drugs (NSAIDs) may negatively affect coronavirus disease 2019 (COVID-19) outcomes, yet clinical evidence is limited. ObjectiveTo assess the association between NSAID use and deaths from COVID-19 using OpenSAFELY, a secure analytical platform. @@ -5006,6 +5097,9 @@ Statistical methodsWe estimated hazard ratios (HRs) for ethnic minority groups c ResultsIn the age-adjusted models, people from all ethnic minority groups were at elevated risk of COVID-19 mortality; the HRs for Black males and females were 3.13 [95% confidence interval: 2.93 to 3.34] and 2.40 [2.20 to 2.61] respectively. However, in the fully adjusted model for females, the HRs were close to unity for all ethnic groups except Black (1.29 [1.18 to 1.42]). For males, COVID-19 mortality risk remained elevated for the Black (1.76 [1.63 to 1.90]), Bangladeshi/Pakistani (1.35 [1.21 to 1.49]) and Indian (1.30 [1.19 to 1.43]) groups. The HRs decreased after lockdown for all ethnic groups, particularly Black and Bangladeshi/Pakistani females. ConclusionsDifferences in COVID-19 mortality between ethnic groups were largely attenuated by geographical and socio-economic factors, although some residual differences remained. Lockdown was associated with reductions in excess mortality risk in ethnic minority populations, which has major implications for a second wave of infection or local spikes. Further research is needed to understand the causal mechanisms underpinning observed differences in COVID-19 mortality between ethnic groups.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2020.08.04.20163782,2020-08-04,https://medrxiv.org/cgi/content/short/2020.08.04.20163782,Fitting models to the COVID-19 outbreak and estimating R,Matt J Keeling; Louise Dyson; Glen Guyver-Fletcher; Alex Holmes; Malcolm G Semple; - ISARIC4C Investigators; Michael J Tildesley; Edward M Hill,University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Liverpool; ; University of Warwick; University of Warwick,"The COVID-19 pandemic has brought to the fore the need for policy makers to receive timely and ongoing scientific guidance in response to this recently emerged human infectious disease. Fitting mathematical models of infectious disease transmission to the available epidemiological data provides a key statistical tool for understanding the many quantities of interest that are not explicit in the underlying epidemiological data streams. Of these, the effective reproduction number, R, has taken on special significance in terms of the general understanding of whether the epidemic is under control (R < 1). Unfortunately, none of the epidemiological data streams are designed for modelling, hence assimilating information from multiple (often changing) sources of data is a major challenge that is particularly stark in novel disease outbreaks. + +Here, focusing on the dynamics of the first-wave (March-June 2020), we present in some detail the inference scheme employed for calibrating the Warwick COVID-19 model to the available public health data streams, which span hospitalisations, critical care occupancy, mortality and serological testing. We then perform computational simulations, making use of the acquired parameter posterior distributions, to assess how the accuracy of short-term predictions varied over the timecourse of the outbreak. To conclude, we compare how refinements to data streams and model structure impact estimates of epidemiological measures, including the estimated growth rate and daily incidence.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.07.30.20165464,2020-08-02,https://medrxiv.org/cgi/content/short/2020.07.30.20165464,Risk stratification of patients admitted to hospital with covid-19 using the ISARIC WHO Clinical Characterisation Protocol: development and validation of the 4C Mortality Score,Stephen R Knight; Antonia Ho; Riinu Pius; Iain Buchan; Gail Carson; Thomas M Drake; Jake Dunning; Cameron J Fairfield; Carrol Gamble; Christopher A Green; Rishi K Gupta; Sophie Halpin; Hayley Hardwick; Karl Holden; Peter W Horby; Clare Jackson; Kenneth A McLean; Laura Merson; Jonathan S Nguyen-Van-Tam; Lisa Norman; Mahdad Noursadeghi; Piero L Olliaro; Mark G Pritchard; Clark D Russell; Catherine A Shaw; Aziz Sheikh; Tom Solomon; Cathie Sudlow; Olivia V Swann; Lance Turtle; Peter JM Openshaw; J Kenneth Baillie; Malcolm Gracie Semple; Annemarie B Docherty; Ewen M Harrison,"Centre for Medical Informatics, The Usher Institute, University of Edinburgh; Medical Research Council University of Glasgow Centre for Virus Research, Glasgow, UK; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK; Institute of Population Health Sciences, University of Liverpool; University of Oxford; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK; National Infection Service Public Health England; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK; Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK; Institute of Microbiology & Infection, University of Birmingham; University College London; Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections and Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and ; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections and Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and ; ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Liverpool Clinical Trials Centre, University of Liverpool, Liverpool, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh; ISARIC Global Support Centre, Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Division of Epidemiology and Public Health, University of Nottingham School of Medicine, Nottingham, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh; Division of Infection and Immunity, University College London, Gower Street, London, WC1E 6BT; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, United Kingdom; Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7LF, United Kingdom; Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK; Department of Clinical Surgery, University of Edinburgh; Centre for Medical Informatics, The Usher Institute, University of Edinburgh; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections and Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and ; Health Data Research UK, Gibbs Building, 215 Euston Road, London, NW1 2BE; Department of Child Life and Health, University of Edinburgh, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections and Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and ; National Heart and Lung Institute, Imperial College London, London, UK; Roslin Institute, University of Edinburgh; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections and Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and ; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK; Centre for Medical Informatics, Usher Institute, University of Edinburgh, UK","ObjectivesTo develop and validate a pragmatic risk score to predict mortality for patients admitted to hospital with covid-19. DesignProspective observational cohort study: ISARIC WHO CCP-UK study (ISARIC Coronavirus Clinical Characterisation Consortium [4C]). Model training was performed on a cohort of patients recruited between 6 February and 20 May 2020, with validation conducted on a second cohort of patients recruited between 21 May and 29 June 2020. @@ -5170,21 +5264,6 @@ ConclusionsIn patients hospitalized with COVID-19, hydroxychloroquine was not as FundingMedical Research Council and NIHR (Grant ref: MC_PC_19056). Trial registrationsThe trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936).",infectious diseases,fuzzy,100,100 -medRxiv,10.1101/2020.07.13.20152793,2020-07-14,https://medrxiv.org/cgi/content/short/2020.07.13.20152793,At what times during infection is SARS-CoV-2 detectable and no longer detectable using RT-PCR based tests?: A systematic review of individual participant data,Sue Mallett; Joy Allen; Sara Graziadio; Stuart A Taylor; Naomi S Sakai; Kile Green; Jana Suklan; Chris Hyde; Bethany Shinkins; Zhivko Zhelev; Jaime Peters; Philip Turner; Nia W Roberts; Lavinia Ferrante di Ruffano; Robert Wolff; Penny Whiting; Amanda Winter; Gauraang Bhatnagar; Brian D Nicholson; Steve Halligan,"University College London, UK; Newcastle University, UK; Newcastle upon Tyne Hospitals NHS Foundation Trust, UK; University College London, UK; University College London, UK; Newcastle University, UK; Newcastle University, UK; University of Exeter, UK; University of Leeds, UK; University of Exeter, UK; University of Exeter, UK; University of Oxford, UK; University of Oxford, UK; University of Birmingham, UK; Kleijnen Systematic Reviews Ltd, UK; University of Bristol, UK; Newcastle University, UK; Frimley Health NHS Foundation Trust, UK; University of Oxford, UK; University College London, UK","STRUCTURED SUMMARYO_ST_ABSBackgroundC_ST_ABSTests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral ribonucleic acid (RNA), using reverse transcription polymerase chain reaction (RT-PCR) are pivotal to detecting current coronavirus disease (COVID-19) and duration of detectable virus indicating potential for infectivity. - -MethodsWe conducted an individual participant data (IPD) systematic review of longitudinal studies of RT-PCR test results in symptomatic SARS-CoV-2. We searched PubMed, LitCOVID, medRxiv and COVID-19 Living Evidence databases. We assessed risk of bias using a QUADAS- 2 adaptation. Outcomes were the percentage of positive test results by time and the duration of detectable virus, by anatomical sampling sites. - -FindingsOf 5078 studies screened, we included 32 studies with 1023 SARS-CoV-2 infected participants and 1619 test results, from -6 to 66 days post-symptom onset and hospitalisation. The highest percentage virus detection was from nasopharyngeal sampling between 0 to 4 days post-symptom onset at 89% (95% confidence interval (CI) 83 to 93) dropping to 54% (95% CI 47 to 61) after 10 to 14 days. On average, duration of detectable virus was longer with lower respiratory tract (LRT) sampling than upper respiratory tract (URT). Duration of faecal and respiratory tract virus detection varied greatly within individual participants. In some participants, virus was still detectable at 46 days post- symptom onset. - -InterpretationRT-PCR misses detection of people with SARS-CoV-2 infection; early sampling minimises false negative diagnoses. Beyond ten days post-symptom onset, lower RT or faecal testing may be preferred sampling sites. The included studies are open to substantial risk of bias so the positivity rates are probably overestimated. - -PANEL: RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSThere are numerous reports of negative severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse transcription polymerase chain reaction (RT-PCR) test results in participants with known SARS-CoV-2 infection, and increasing awareness that the ability of RT-PCR tests to detect virus depends on the timing of sample retrieval and anatomical sampling site. - -Individual studies suggest that positive test results from RT-PCR with nasopharyngeal sampling declines within a week of symptoms and that a positive test later in the disease course is more likely from sputum, bronchoalveolar lavage (BAL) or stool, but data are inconsistent. - -Added value of this studyWe searched 5078 titles and abstracts for longitudinal studies reporting individual participant data (IPD) for RT-PCR for participants with COVID-19 linked to either time since symptom onset or time since hospitalisation. Search included SARS-CoV-2 and RT-PCR keywords and MeSH terms. Each included study was subject to careful assessment of risk of bias. This IPD systematic review (SR) addresses RT-PCR test detection rates at different times since symptom onset and hospitalisation for different sampling sites, and summarises the duration of detectable virus. To our knowledge, this is the first rapid SR addressing this topic. We identified 32 studies available as published articles or pre-prints between January 1st and April 24th 2020, including participants sampled at 11 different sampling sites and some participants sampled at more than one site. At earlier time points, nasopharyngeal sampling had the highest virus detection, but the duration of shedding was shorter compared to lower respiratory tract sampling. At 10 to 14 days post-symptom onset, the percentage of positive nasopharyngeal test results was 54% compared to 89% at day 0 to 4. Presence and duration of faecal detection varied by participant, and in nearly half duration was shorter than respiratory sample detection. Virus detection varies for participants and can continue to be detected up to 46 days post-symptom onset or hospitalisation. The included studies were open to substantial risk of bias, so the detection rates are probably overestimates. There was also poor reporting of sampling methods and sparse data on sampling methods that are becoming more widely implemented, such as self-sampling and short nasal swab sampling (anterior nares/mid turbinate). - -Implications of all the available evidenceResults from this IPD SR of SARS-CoV-2 testing at different time points and using different anatomical sample sites are important to inform strategies of testing. For prevention of ongoing transmission of SARS-CoV-2, samples for RT-PCR testing need to be taken as soon as possible post-symptom onset, as we confirm that RT-PCR misses more people with infection if sampling is delayed. The percentage of positive RT-PCR tests is also highly dependent on the anatomical site sampled in infected people. Sampling at more than one anatomical site may be advisable as there is variation between individuals in the sites that are infected, as well as the timing of SARS-CoV-2 virus detection at an anatomical site. Testing ten days after symptom onset will lead to a higher frequency of negative tests, particularly if using only upper respiratory tract sampling. However, our estimates may considerably understate the frequency of negative RT-PCR results in people with SARS-CoV- 2 infection. Further investment in this IPD approach is recommended as the amount data available was small given the scale of the pandemic and the importance of the question. More studies, learning from our observations about risk of bias and strengths of example studies (Box 1, Box 2) are urgently needed to inform the optimal sampling strategy by including self-collected samples such as saliva and short nasal swabs. Better reporting of anatomical sampling sites with a detailed methodology on sample collection is also urgently needed.",infectious diseases,fuzzy,92,100 medRxiv,10.1101/2020.07.13.20152710,2020-07-14,https://medrxiv.org/cgi/content/short/2020.07.13.20152710,Excess mortality in mental health service users during the COVID-19 pandemic described by ethnic group: South London and Maudsley data,Robert Stewart; Matthew Broadbent; Jayati Das-Munshi,King's College London; South London and Maudsley NHS Foundation Trust; King's College London,"The COVID-19 pandemic in the UK was accompanied by excess all-cause mortality at a national level, only part of which was accounted for by known infections. Excess mortality has previously been described in people who had received care from the South London and Maudsley NHS Foundation Trust (SLaM), a large mental health service provider for 1.2m residents in south London. SLaMs Clinical Record Interactive Search (CRIS) data resource receives 24-hourly updates from its full electronic health record, including regularly sourced national mortality on all past and present SLaM service users. SLaMs urban catchment has high levels of deprivation and is ethnically diverse, so the objective of the descriptive analyses reported in this manuscript was to compare mortality in SLaM service users from 16th March to 15th May 2020 to that for the same period in 2019 within specific ethnic groups: i) White British, ii) Other White, iii) Black African/Caribbean, iv) South Asian, v) Other, and vi) missing/not stated. For Black African/Caribbean patients (the largest minority ethnic group) this ratio was 3.33, compared to 2.47 for White British patients. Considering premature mortality (restricting to deaths below age 70), these ratios were 2.74 and 1.96 respectively. Ratios were also high for those from Other ethnic groups (2.63 for all mortality, 3.07 for premature mortality).",psychiatry and clinical psychology,fuzzy,100,100 medRxiv,10.1101/2020.07.11.20147157,2020-07-14,https://medrxiv.org/cgi/content/short/2020.07.11.20147157,Effects of environmental factors on severity and mortality of COVID-19,Domagoj Kifer; Dario Bugada; Judit Villar-Garcia; Ivan Gudelj; Cristina Menni; Carole Helene Sudre; Frano Vuckovic; Ivo Ugrina; Luca F Lorini; Silvia Bettinelli; Nicola Ughi; Alessandro Maloberti; Oscar Epis; Cristina Giannattasio; Claudio Rossetti; Livije Kalogjera; Jasminka Persec; Luke Ollivere; Benjamin Ollivere; Huadong Yan; Ting Cai; Guruprasad Aithal; Claire Steves; Anu Kantele; Mikael Kajova; Olli Vapalahti; Antti Sajantila; Rafal Wojtowicz; Waldemar Wierzba; Zbigniew Krol; Artur Zaczynski; Katarzyna Zycinska; Marek Postula; Ivica Luksic; Rok Civljak; Alemka Markotic; Christian Mahnkopf; Andreas Markl; Johannes Brachmann; Benjamin Murray; Sebastien Ourselin; Julio Pascual; Ana M Valdes; Margarita Posso; Juan Horcajada; Xavier Castells; Massimo Allegri; Dragan Primorac; Timothy Spector; Clara Barrios; Gordan Lauc,"University of Zagreb; Emergency and Intensive Care Department - ASST Papa Giovanni XXII Hospital - Bergamo - Italy; Hospital del Mar-IMIM, Barcelona, Spain; Genos; King's College London; KCL; Genos; Genos; Emergency and Intensive Care Department - ASST Papa Giovanni XXII Hospital - Bergamo - Italy; Emergency and Intensive Care Department - ASST Papa Giovanni XXII Hospital - Bergamo - Italy; ASST GOM Niguarda; ASST GOM Niguarda; ASST GOM Niguarda; ASST GOM Niguarda; ASST GOM Niguarda; School of Medicine, University Hospital ""Sestre milosrdnice"" Zagreb, Croatia; University Hospital Dubrava Zagreb, Croatia, University of Zagreb School of Dental Medicine; Nottingham University Trust; University of Nottingham, School of Medicine; Department of Infectious Diseases, Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Hwamei Hospital, University of Chi; Hwa Mei Hospital, University of Chinese Academy of Sciences; School of Medicine, University of Nottingham; King's College London; Inflammation Centre, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Inflammation Centre, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; University of Helsinki; Department of Forensic Medicine, University of Helsinki, Finland; Central Clinical Hospital of the Ministry of the Interior and Administration in Warsaw, Poland; Central Clinical Hospital of the Ministry of the Interior and Administration in Warsaw, Poland; Central Clinical Hospital of the Ministry of the Interior and Administration in Warsaw, Poland; Central Clinical Hospital of the Ministry of the Interior and Administration in Warsaw, Poland; Medical University of Warsaw, Warsaw, Poland; Medical University of Warsaw, Warsaw, Poland; Clinical Hospital Dubrava, Zagreb; Hospital for Infectious Diseases, Zagreb, Croatia; Hospital for Infectious Diseases; REGIOMED-KLINIKEN GmbH, Gustav-Hirschfeld-Ring 3, 96450 Coburg, Germany; REGIOMED-KLINIKEN GmbH, Gustav-Hirschfeld-Ring 3, 96450 Coburg, Germany; REGIOMED Kliniken; School of Biomedical Engineering & Imaging Sciences, King's College London; School of Biomedical Engineering & Imaging Sciences, King's College London; Department of Nephrology, Hospital del Mar, Barcelona, Spain; University of Nottingham, School of Medicine, Nottingham NIHR BRC; Department of Epidemiology and Evaluation, Hospital del Mar-IMIM, Barcelona, Spain; Department of Infectious Diseases, Hospital del Mar. Barcelona, Spain; Department of Epidemiology and Evaluation, Hospital del Mar-IMIM, Barcelona, Spain; Pain Therapy Service Policlinico of Monza Hospital - Monza Italy & Italian Pain Group - Milan - Italy; St. Catherine Hospital; King's College London; Hospital del Mar. Barcelona, Spain; University of Zagreb","BackgroundMost respiratory viruses show pronounced seasonality, but for SARS-CoV-2 this still needs to be documented. @@ -5867,6 +5946,21 @@ We illustrate how the potential for the relaxation of restrictions interacts wit We find that the outcome of any future policy is strongly influenced by the contact matrix between segments and the relationships between physical distancing measures and transmission rates. These relationships are difficult to quantify so close monitoring of the epidemic would be essential during and after the exit from lockdown. More generally, S&S has potential applications for any infectious disease for which there are defined proportions of the population who cannot be treated or who are at risk of severe outcomes.",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2020.05.06.20092999,2020-05-07,https://medrxiv.org/cgi/content/short/2020.05.06.20092999,OpenSAFELY: factors associated with COVID-19-related hospital death in the linked electronic health records of 17 million adult NHS patients.,- The OpenSAFELY Collaborative; Elizabeth Williamson; Alex J Walker; Krishnan J Bhaskaran; Seb Bacon; Chris Bates; Caroline E Morton; Helen J Curtis; Amir Mehrkar; David Evans; Peter Inglesby; Jonathan Cockburn; Helen I Mcdonald; Brian MacKenna; Laurie Tomlinson; Ian J Douglas; Christopher T Rentsch; Rohini Mathur; Angel Wong; Richard Grieve; David Harrison; Harriet Forbes; Anna Schultze; Richard T Croker; John Parry; Frank Hester; Sam Harper; Rafael Perera; Stephen Evans; Liam Smeeth; Ben Goldacre,; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; TPP; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; ICNARC; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; TPP; TPP; TPP; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford,"BackgroundEstablishing who is at risk from a novel rapidly arising cause of death, and why, requires a new approach to epidemiological research with very large datasets and timely data. Working on behalf of NHS England we therefore set out to deliver a secure and pseudonymised analytics platform inside the data centre of a major primary care electronic health records vendor establishing coverage across detailed primary care records for a substantial proportion of all patients in England. The following results are preliminary. + +Data sourcesPrimary care electronic health records managed by the electronic health record vendor TPP, pseudonymously linked to patient-level data from the COVID-19 Patient Notification System (CPNS) for death of hospital inpatients with confirmed COVID-19, using the new OpenSAFELY platform. + +Population17,425,445 adults. + +Time period1st Feb 2020 to 25th April 2020. + +Primary outcomeDeath in hospital among people with confirmed COVID-19. + +MethodsCohort study analysed by Cox-regression to generate hazard ratios: age and sex adjusted, and multiply adjusted for co-variates selected prospectively on the basis of clinical interest and prior findings. + +ResultsThere were 5683 deaths attributed to COVID-19. In summary after full adjustment, death from COVID-19 was strongly associated with: being male (hazard ratio 1.99, 95%CI 1.88-2.10); older age and deprivation (both with a strong gradient); uncontrolled diabetes (HR 2.36 95% CI 2.18-2.56); severe asthma (HR 1.25 CI 1.08-1.44); and various other prior medical conditions. Compared to people with ethnicity recorded as white, black people were at higher risk of death, with only partial attenuation in hazard ratios from the fully adjusted model (age-sex adjusted HR 2.17 95% CI 1.84-2.57; fully adjusted HR 1.71 95% CI 1.44-2.02); with similar findings for Asian people (age-sex adjusted HR 1.95 95% CI 1.73-2.18; fully adjusted HR 1.62 95% CI 1.431.82). + +ConclusionsWe have quantified a range of clinical risk factors for death from COVID-19, some of which were not previously well characterised, in the largest cohort study conducted by any country to date. People from Asian and black groups are at markedly increased risk of in-hospital death from COVID-19, and contrary to some prior speculation this is only partially attributable to pre-existing clinical risk factors or deprivation; further research into the drivers of this association is therefore urgently required. Deprivation is also a major risk factor with, again, little of the excess risk explained by co-morbidity or other risk factors. The findings for clinical risk factors are concordant with policies in the UK for protecting those at highest risk. Our OpenSAFELY platform is rapidly adding further NHS patients records; we will update and extend these results regularly.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.05.02.20078642,2020-05-06,https://medrxiv.org/cgi/content/short/2020.05.02.20078642,Impact of ethnicity on outcome of severe COVID-19 infection. Data from an ethnically diverse UK tertiary centre,James T Teo; Daniel Bean; Rebecca Bendayan; Richard Dobson; Ajay Shah,Kings College Hospital NHS Foundation Trust; King's College London; King's College London; Kings College London; King's College London,"During the current COVID-19 pandemic, it has been suggested that BAME background patients may be disproportionately affected compared to White but few detailed data are available. We took advantage of near real-time hospital data access and analysis pipelines to look at the impact of ethnicity in 1200 consecutive patients admitted between 1st March 2020 and 12th May 2020 to Kings College Hospital NHS Trust in London (UK). Our key findings are firstly that BAME patients are significantly younger and have different co-morbidity profiles than White individuals. Secondly, there is no significant independent effect of ethnicity on severe outcomes (death or ITU admission) within 14-days of symptom onset, after adjustment for age, sex and comorbidities.",intensive care and critical care medicine,fuzzy,100,100 @@ -5944,13 +6038,6 @@ C_LIO_LIRisk stratification was improved by the addition of routinely-measured b C_LIO_LIThis improvement over NEWS2 alone was maintained across multiple hospital trusts but the model tended to be miscalibrated with risks of severe outcomes underestimated in most sites. C_LIO_LIWe benefited from existing pipelines for informatics at KCH such as CogStack that allowed rapid extraction and processing of electronic health records. This methodological approach provided rapid insights and allowed us to overcome the complications associated with slow data centralisation approaches. C_LI",infectious diseases,fuzzy,100,100 -bioRxiv,10.1101/2020.04.28.066977,2020-04-29,https://biorxiv.org/cgi/content/short/2020.04.28.066977,"Controlling the SARS-CoV-2 outbreak, insights from large scale whole genome sequences generated across the world",Jody Phelan; Wouter Deelder; Daniel Ward; Susana Campino; Martin L Hibberd; Taane G Clark,London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine,"BackgroundSARS-CoV-2 most likely evolved from a bat beta-coronavirus and started infecting humans in December 2019. Since then it has rapidly infected people around the world, with more than 4.5 million confirmed cases by the middle of May 2020. Early genome sequencing of the virus has enabled the development of molecular diagnostics and the commencement of therapy and vaccine development. The analysis of the early sequences showed relatively few evolutionary selection pressures. However, with the rapid worldwide expansion into diverse human populations, significant genetic variations are becoming increasingly likely. The current limitations on social movement between countries also offers the opportunity for these viral variants to become distinct strains with potential implications for diagnostics, therapies and vaccines. - -MethodsWe used the current sequencing archives (NCBI and GISAID) to investigate 15,487 whole genomes, looking for evidence of strain diversification and selective pressure. - -ResultsWe used 6,294 SNPs to build a phylogenetic tree of SARS-CoV-2 diversity and noted strong evidence for the existence of two major clades and six sub-clades, unevenly distributed across the world. We also noted that convergent evolution has potentially occurred across several locations in the genome, showing selection pressures, including on the spike glycoprotein where we noted a potentially critical mutation that could affect its binding to the ACE2 receptor. We also report on mutations that could prevent current molecular diagnostics from detecting some of the sub-clades. - -ConclusionThe worldwide whole genome sequencing effort is revealing the challenge of developing SARS-CoV-2 containment tools suitable for everyone and the need for data to be continually evaluated to ensure accuracy in outbreak estimations.",genomics,fuzzy,100,100 medRxiv,10.1101/2020.04.23.20076521,2020-04-27,https://medrxiv.org/cgi/content/short/2020.04.23.20076521,"Geo-social gradients in predicted COVID-19 prevalence and severity in Great Britain: results from 2,266,235 users of the COVID-19 Symptoms Tracker app",Ruth Bowyer; Thomas Varsavsky; Carole H Sudre; Benjamin Murray; Maxim Freidin; Darioush Yarand; Sajaysurya Ganesh; Joan Capdevila; Ellen J Thompson; Elco Bakker; M Jorge Cardoso; Richard Davies; Jonathan Wolf; Tim D Spector; Sebastien Ourselin; Claire J Steves; Cristina Menni,King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Zoe Global Limited; Zoe Global Limited; King's College London; Zoe Global Limited; King's College London; King's College London; Zoe Global Limited; King's College London; King's College London; King's College London; King's College London,"Understanding the geographical distribution of COVID-19 through the general population is key to the provision of adequate healthcare services. Using self-reported data from 2,266,235 unique GB users of the COVID Symptom Tracker app, we find that COVID-19 prevalence and severity became rapidly distributed across the UK within a month of the WHO declaration of the pandemic, with significant evidence of ""urban hot-spots"". We found a geo-social gradient associated with disease severity and prevalence suggesting resources should focus on urban areas and areas of higher deprivation. Our results demonstrate use of self-reported data to inform public health policy and resource allocation.",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.04.22.20075663,2020-04-27,https://medrxiv.org/cgi/content/short/2020.04.22.20075663,Ethnic and socioeconomic differences in SARS-CoV2 infection in the UK Biobank cohort study,Claire L Niedzwiedz; Bhautesh D Jani; Evangelia Demou; Frederick K Ho; Carlos Celis-Morales; Barbara I Nicholl; Frances Mair; Paul Welsh; Naveed Sattar; Jill Pell; Srinivasa Vittal Katikireddi,University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow; University Of Glasgow; University of Glasgow; University of Glasgow; University of Glasgow,"BackgroundUnderstanding of the role of ethnicity and socioeconomic position in the risk of developing SARS-CoV-2 infection is limited. We investigated this in the UK Biobank study. @@ -6077,6 +6164,9 @@ C_LI",epidemiology,fuzzy,100,100 medRxiv,10.1101/2020.04.02.20051334,2020-04-06,https://medrxiv.org/cgi/content/short/2020.04.02.20051334,Rapid implementation of mobile technology for real-time epidemiology of COVID-19,David A. Drew; Long H. Nguyen; Claire J. Steves; Jonathan Wolf; Tim D. Spector; Andrew T. Chan; COPE Consortium,Massachusetts General Hospital; Massachusetts General Hospital; King's College London; Zoe Global Limited; King's College London; Massachusetts General Hospital; ,"The rapid pace of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic (COVID-19) presents challenges to the robust collection of population-scale data to address this global health crisis. We established the COronavirus Pandemic Epidemiology (COPE) consortium to bring together scientists with expertise in big data research and epidemiology to develop a COVID-19 Symptom Tracker mobile application that we launched in the UK on March 24, 2020 and the US on March 29, 2020 garnering more than 2.25 million users to date. This mobile application offers data on risk factors, herald symptoms, clinical outcomes, and geographical hot spots. This initiative offers critical proof-of-concept for the repurposing of existing approaches to enable rapidly scalable epidemiologic data collection and analysis which is critical for a data-driven response to this public health challenge. One Sentence SummaryCOVID-19 symptom tracker for smartphones",epidemiology,fuzzy,100,100 +medRxiv,10.1101/2020.04.02.20051284,2020-04-06,https://medrxiv.org/cgi/content/short/2020.04.02.20051284,Building an International Consortium for Tracking Coronavirus Health Status,Eran Segal; Feng Zhang; Xihong Lin; Gary King; Ophir Shalem; Smadar Shilo; William E. Allen; Yonatan H. Grad; Casey S. Greene; Faisal Alquaddoomi; Simon Anders; Ran Balicer; Tal Bauman; Ximena Bonilla; Gisel Booman; Andrew T. Chan; Ori Ori Cohen; Silvano Coletti; Natalie Davidson; Yuval Dor; David A. Drew; Olivier Elemento; Georgina Evans; Phil Ewels; Joshua Gale; Amir Gavrieli; Benjamin Geiger; Iman Hajirasouliha; Roman Jerala; Andre Kahles; Olli Kallioniemi; Ayya Keshet; Gregory Landua; Tomer Meir; Aline Muller; Long H. Nguyen; Matej Oresic; Svetlana Ovchinnikova; Hedi Peterson; Jay Rajagopal; Gunnar Ratsch; Hagai Rossman; Johan Rung; Andrea Sboner; Alexandros Sigaras; Tim Spector; Ron Steinherz; Irene Stevens; Jaak Vilo; Paul Wilmes; CCC (Coronavirus Census Collective),"Weizmann Institute of Science; Howard Hughes Medical Institute, Core Member, Broad Institute of MIT and Harvard, United States; Departments of Biostatistics and Statistics, Harvard T.H. Chan School of Public Health; Albert J. Weatherhead III University, Institute for Quantitative Social Science, Harvard University; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, United States; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Society of Fellows, Harvard University, United States; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, United States; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, United States; ETH Zurich, NEXUS Personalized Health Technologies, Zurich, Switzerland; Center for Molecular Biology (ZMBH), University of Heidelberg, Germany; Clalit Research Institute, Clalit Health Services, Israel; Mapping and Geo-Information Engineering, Civil and Environmental Engineering Faculty, The Technion, Israel; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich, ; Regen Network, Argentina; Massachusetts General Hospital (MGH), United States; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Chelonia Applied Science, Switzerland; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich, ; School of Medicine-IMRIC-Developmental Biology and Cancer Research, The Hebrew University; Massachusetts General Hospital (MGH), United States; Englander Institute for Precision Medicine and Department of Physiology and Biophysics, Weill Cornell Medicine, USA; Institute for Quantitative Social Science, Harvard University; Science for Life Laboratory (SciLifeLab), Department of Biochemistry and Biophysics, Stockholm University, Sweden; symptometrics.org; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Department of immunology, Weizmann Institute of Science, Israel; Englander Institute for Precision Medicine and Department of Physiology and Biophysics, Weill Cornell Medicine, USA; Department of Synthetic biology and Immunology, National Institute of Chemistry, Slovenia; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich, ; Science for Life Laboratory (SciLifeLab), Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Regen Network, United States; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Luxembourg Institute of Socio-Economic Research and University of Luxembourg, Luxembourg; Massachusetts General Hospital (MGH), United States; School of Medical Sciences, Orebro University, Orebro, Sweden, and Turku Bioscience Centre, University of Turku and Abo Akademi University, Turku, Finland; Center for Molecular Biology (ZMBH), University of Heidelberg, Germany; Institute of Computer Science, University of Tartu, Estonia, Estonia; Internal Medicine, Harvard Medical School, Department of Pulmonary Medicine and Critical Care, Massachusetts General Hospital (MGH), United States; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich a; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Science for Life Laboratory (SciLifeLab), Department of Immunology, Genetics and Pathology, Uppsala university, Sweden; Englander Institute for Precision Medicine and Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, USA; Englander Institute for Precision Medicine and Department of Physiology and Biophysics, Weill Cornell Medicine, USA; Kings College, United Kingdom; Regen Network, United States; Science for Life Laboratory (SciLifeLab), Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Sweden; Institute of Computer Science, University of Tartu, Estonia, Estonia; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg; ","Information is the most potent protective weapon we have to combat a pandemic, at both the individual and global level. For individuals, information can help us make personal decisions and provide a sense of security. For the global community, information can inform policy decisions and offer critical insights into the epidemic of COVID-19 disease. Fully leveraging the power of information, however, requires large amounts of data and access to it. To achieve this, we are making steps to form an international consortium, Coronavirus Census Collective (CCC, coronaviruscensuscollective.org), that will serve as a hub for integrating information from multiple data sources that can be utilized to understand, monitor, predict, and combat global pandemics. These sources may include self-reported health status through surveys (including mobile apps), results of diagnostic laboratory tests, and other static and real-time geospatial data. This collective effort to track and share information will be invaluable in predicting hotspots of disease outbreak, identifying which factors control the rate of spreading, informing immediate policy decisions, evaluating the effectiveness of measures taken by health organizations on pandemic control, and providing critical insight on the etiology of COVID-19. It will also help individuals stay informed on this rapidly evolving situation and contribute to other global efforts to slow the spread of disease. + +In the past few weeks, several initiatives across the globe have surfaced to use daily self-reported symptoms as a means to track disease spread, predict outbreak locations, guide population measures and help in the allocation of healthcare resources. The aim of this paper is to put out a call to standardize these efforts and spark a collaborative effort to maximize the global gain while protecting participant privacy.",infectious diseases,fuzzy,100,100 medRxiv,10.1101/2020.04.01.20049908,2020-04-06,https://medrxiv.org/cgi/content/short/2020.04.01.20049908,"The effect of non-pharmaceutical interventions on COVID-19 cases, deaths and demand for hospital services in the UK: a modelling study",Nicholas G Davies; Adam J Kucharski; Rosalind M Eggo; Amy Gimma; - CMMID COVID-19 Working Group; W. John Edmunds,London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene & Tropical Medicine; -; London School of Hygiene & Tropical Medicine,"BackgroundNon-pharmaceutical interventions have been implemented to reduce transmission of SARS-CoV-2 in the UK. Projecting the size of an unmitigated epidemic and the potential effect of different control measures has been critical to support evidence-based policymaking during the early stages of the epidemic. MethodsWe used a stochastic age-structured transmission model to explore a range of intervention scenarios, including the introduction of school closures, social distancing, shielding of elderly groups, self-isolation of symptomatic cases, and extreme ""lockdown""-type restrictions. We simulated different durations of interventions and triggers for introduction, as well as combinations of interventions. For each scenario, we projected estimated new cases over time, patients requiring inpatient and critical care (intensive care unit, ICU) treatment, and deaths. diff --git a/data/covid/preprints.exact.csv b/data/covid/preprints.exact.csv index 1399e42c..cf533855 100644 --- a/data/covid/preprints.exact.csv +++ b/data/covid/preprints.exact.csv @@ -65,7 +65,6 @@ InterpretationIncidence of mental illness is elevated for up to a year following FundingMedical Research Council (MC_PC_20059) and NIHR (COV-LT-0009).",epidemiology,exact,100,100 medRxiv,10.1101/2023.11.28.23299156,2023-11-29,https://medrxiv.org/cgi/content/short/2023.11.28.23299156,Examining the association of live virus neutralisation activity of capillary microsamples and risk of SARS-CoV-2 infections: a nested case control study within the Virus Watch community cohort,Alexei Yavlinsky; Vincent Nguyen; Sarah Beale; Emma Wall; Mary Y Wu; Isobel Braithwaite; Jana Kovar; Madhumita Shrotri; Annalan Mathew Dwight Navaratnam; Wing Lam Erica Fong; Thomas Edward Byrne; Francois Balloux; Ibrahim Abubakar; Benjamin J Cowling; Andrew Hayward; Robert W Aldridge,University College London; University College London; University College London; The Francis Crick Institute; The Francis Crick Institute; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; The University of Hong Kong; University College London; University College London,"Due to the proliferation of new SARS-CoV-2 variants, most COVID-19 cases are now caused by post-vaccine infections and a substantial proportion are reinfections. While prior research on correlates of protection has focused on the role of anti-spike antibodies, the results of the corresponding antibody assays may not accurately predict the risk of infection with new SARS-CoV-2 variants. In this study, we investigated the association between live virus neutralising antibody activity and SARS-CoV-2 infection risk using self-administered capillary microsample blood tests from VirusWatch participants. The study was conducted during the transition between the dominance of the B.1.617.2 (Delta) and B.1.1.529 (Omicron BA.1) SARS-CoV-2 variants, enabling us to investigate the association between variant-specific virus inhibition and subsequent infections within each dominance period. Greater inhibition of Omicron BA.1 live virus was associated with a reduction in infection risk during both the Delta and Omicron BA.1 dominance periods. Delta virus inhibition was associated with infection risk reduction during the Delta dominance period, but we found no association between Delta inhibition and protection against infection during the Omicron BA.1 dominance period. Our results are consistent with earlier findings and suggest that variant-specific serosurveillance of immunity and protection against SARS-CoV-2 infection at the population level could inform public health policy in near-real time using inexpensive and accessible home-based testing.",epidemiology,exact,100,100 -medRxiv,10.1101/2023.11.24.23296021,2023-11-27,https://medrxiv.org/cgi/content/short/2023.11.24.23296021,Severe acute myositis and myocarditis upon initiation of six-weekly Pembrolizumab post-COVID-19 mRNA vaccination,Robert Aerwyn Watson; Weiyu Ye; Chelsea Alice Taylor; Rosalin Anisha Cooper; Orion Tong; Tim James; Brian Shine; Monika Hofer; Damian Jenkins; Robert Pell; Eleni Ieremia; Stephanie Jones; David Maldonado-Perez; Ian Roberts; Nicholas Coupe; Mark Ross Middleton; Miranda Jane Payne; Benjamin Peter Fairfax,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; University of Oxford; University of Oxford; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; University of Oxford; Oxford University Hospitals NHS Foundation Trust; University of Oxford,"We describe three cases of critical acute myositis with myocarditis occurring within 22 days of each other at a single institution, all within one month of receiving the initial cycle of the anti-PD-1 drug Pembrolizumab. Analysis of T cell receptor repertoires from peripheral blood and tissues revealed a high degree of clonal expansion and public clones between cases, with several T cell clones expanded within the skeletal muscle putatively recognising viral epitopes. All patients had recently received a COVID-19 mRNA booster vaccine prior to treatment and were positive for SARS-CoV2 Spike antibody. In conclusion, we report a series of unusually severe myositis and myocarditis following PD-1 blockade and the COVID-19 mRNA vaccination.",oncology,exact,100,100 medRxiv,10.1101/2023.11.09.23298162,2023-11-10,https://medrxiv.org/cgi/content/short/2023.11.09.23298162,One year health outcomes associated with systemic corticosteroids for COVID-19: a longitudinal cohort study,Olivia C Leavy; Richard J Russell; Ewen M Harrison; Nazir I Lone; Steven Kerr; Annemarie B Docherty; Aziz Sheikh; Matthew Richardson; Omer Elneima; Neil J Greening; Victoria Claire Harris; Linzy Houchen-Wolloff; Hamish J C McAuley; Ruth M Saunders; Marco Sereno; Aarti Shikotra; Amisha Singapuri; Raminder Aul; Paul Beirne; Charlotte E Bolton; Jeremy S Brown; Gourab Choudhury; Nawar Diar Bakerly; Nicholas Easom; Carlos Echevarria; Jonathan Fuld; Nick Hart; John R Hurst; Mark Jones; Dhruv Parekh; Paul Pfeffer; Najib M Rahman; Sarah Rowland-Jones; Ajay M Shah; Dan G Wootton; Caroline Jolley; AA Roger Thompson; Trudie Chalder; Melanie J Davies; Anthony De Soyza; John R Geddes; William Greenhalf; Simon Heller; Luke Howard; Joseph Jacob; R Gisli Jenkins; Janet M Lord; Will D-C Man; Gerry P McCann; Stefan Neubauer; Peter JM Openshaw; Joanna Porter; Matthew J Rowland; Janet T Scott; Malcolm G Semple; Sally J Singh; David Thomas; Mark Toshner; Keir Lewis; Liam G Heaney; Andrew Briggs; Bang Zheng; Mathew Thorpe; Jennifer K Quint; James D Chalmers; Ling-Pei Ho; Alex Horsley; Michael Marks; Krisnah Poinasamy; Betty Raman; Louise V Wain; Christopher E Brightling; Rachael A Evans; - PHOSP-COVID Collaborative Group,"Department of Population Health Sciences, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; The Usher Institute, University of Edinburgh, Edinburgh, UK; Roslin Institute, University of Edinburgh, Edinburgh, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; The Usher Institute, University of Edinburgh, Edinburgh, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; Centre for Exercise and Rehabilitation Science, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; St Georges University Hospitals NHS Foundation Trust, London, UK; The Leeds Teaching Hospitals NHS Trust, Leeds, UK; University of Nottingham, Nottingham, UK; UCL Respiratory, Department of Medicine, University College London, Rayne Institute, London, UK; University of Edinburgh, Edinburgh, UK; Manchester Metropolitan University, Manchester, UK; Infection Research Group, Hull University Teaching Hospitals, Hull, UK; The Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK; Department of Respiratory Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Lane Fox Respiratory Service, Guys and St Thomas NHS Foundation Trust, London, UK; University College London, London, UK; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK; University of Birmingham, Birmingham, UK; Barts Health NHS Trust, London, UK; Oxford University Hospitals NHS Foundation Trust, Oxford, UK; University of Sheffield, Sheffield, UK; Kings College London, London, UK; Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Kings College London, London, UK; University of Sheffield, Sheffield, UK; Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK; Diabetes Research Centre, University of Leicester, Leicester, UK; Population Health Sciences Institute, Newcastle University, Newcastle Upon Tyne, UK; NIHR Oxford Health Biomedical Research Centre, University of Oxford, Oxford, UK; University of Liverpool, Liverpool, UK; Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK; Imperial College Healthcare NHS Trust, London, UK; Centre for Medical Image Computing, University College London, London, UK; National Heart and Lung Institute, Imperial College London, London, UK; MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK; Royal Brompton and Harefield Clinical Group, Guys and St Thomas NHS Foundation Trust, London, UK; Department of Cardiovascular Sciences, University of Leicester, Leicester, UK; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; National Heart and Lung Institute, Imperial College London, London, UK; UCL Respiratory, Department of Medicine, University College London, Rayne Institute, London, UK; Kadoorie Centre for Critical Care Research, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; MRC-University of Glasgow Centre for Virus Research, Glasgow, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, U; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; Imperial College London, London, UK; Cambridge NIHR BRC, Cambridge, UK; Hywel Dda University Health Board, Wales, UK; Wellcome-Wolfson Institute for Experimental Medicine, Queens University Belfast, Belfast, UK; London School of Hygiene & Tropical Medicine, London, UK; London School of Hygiene & Tropical Medicine, London, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; NHLI, Imperial College London, London, UK; University of Dundee, Ninewells Hospital and Medical School, Dundee, UK; MRC Human Immunology Unit, University of Oxford, Oxford, UK; Division of Infection, Immunity & Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK; Asthma and Lung UK, London, UK; Radcliffe Department of Medicine, University of Oxford, Oxford, UK; Department of Population Health Sciences, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; ","BackgroundIn patients with COVID-19 requiring supplemental oxygen, dexamethasone reduces acute severity and improves survival, but longer-term effects are unknown. We hypothesised that systemic corticosteroid administration during acute COVID-19 would be associated with improved health-related quality of life (HRQoL) one year after discharge. MethodsAdults admitted to hospital between February 2020 and March 2021 for COVID-19 and meeting current guideline recommendations for dexamethasone treatment were included using two prospective UK cohort studies. HRQoL, assessed by EQ-5D-5L utility index, pre-hospital and one year after discharge were compared between those receiving corticosteroids or not after propensity weighting for treatment. Secondary outcomes included patient reported recovery, physical and mental health status, and measures of organ impairment. Sensitivity analyses were undertaken to account for survival and selection bias. @@ -167,6 +166,13 @@ MethodsWe estimated associations between long COVID (derived using self-reported ResultsAmong 20,112 observations across four population surveys, 13% reported having COVID-19 with symptoms that impeded their ability to function normally - 10.7% had such symptoms for <4 weeks (acute COVID-19), 1.2% had such symptoms for 4-12 weeks (ongoing symptomatic COVID-19) and 0.6% had such symptoms for >12 weeks (post-COVID-19 syndrome). We found that post-COVID-19 syndrome was associated with worse subjective financial well-being (adjusted relative risk ratios (aRRR)=1.57, 95% confidence interval (CI)=1.25, 1.96) and new benefit claims (aRRR=1.79, CI=1.27, 2.53). Associations were broadly similar across sexes and education levels. These results were not meaningfully altered when scaled to represent the population by age. ConclusionsLong COVID was associated with financial disruption in the UK. If our findings reflect causal effects, extending employment protection and financial support to people with long COVID may be warranted.",public and global health,exact,100,100 +medRxiv,10.1101/2023.05.23.23289798,2023-05-24,https://medrxiv.org/cgi/content/short/2023.05.23.23289798,Primary Care Post-COVID syndrome Diagnosis and Referral Coding,Robert Willans; Gail Allsopp; Pall Jonsson; Fiona Glen; Felix Greaves; John Macleod; Yinghui Wei; Sebastian Bacon; Amir Mehrkar; Alex Walker; Brian MacKenna; Louis Fisher; Ben Goldacre; - The OpenSAFELY Collaborative; - The CONVALESCENCE Collaborative,"National Institute of Health and Care Excellence; Royal College of General Practitioners; National Institute of Health and Care Excellence; National Institute of Health and Care Excellence; National Institute of Health and Care Excellence; University of Bristol; University of Plymouth; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; ; ","IntroductionGuidelines for diagnosing and managing Post-COVID syndrome have been rapidly developed. Consistency of the application of these guidelines in primary care is unknown. Electronic health records provide an opportunity to review the use of codes relating to Post-COVID syndrome. This paper explores the use of primary care records as a surrogate uptake measure for NICEs rapid guideline ""managing the long-term effects of COVID-19"" by measuring the use of Post-COVID syndrome diagnosis and referral codes in the pathway. + +MethodWith the approval of NHS England we used routine clinical data from the OpenSafely-EMIS/-TPP platforms. Counts of Post-COVID syndrome diagnosis and referral codes were generated from a cohort of all adults, establishing numbers of diagnoses and referrals following diagnosis. The relationship between Post-COVID syndrome diagnosis and referral codes was explored with reference to NICEs rapid guideline. + +ResultsOf over 45 million patients, 69,220 (0.15%) had a Post-COVID syndrome diagnostic code, and 67,741 (0.15%) had a referral code. 78% of referral codes did not have an associated diagnosis code. 79% of diagnosis codes had no subsequent referral code. Only 18,633 (0.04%) had both. There were higher rates of both diagnosis and referral in those who were more deprived, female and some ethnic groups. + +DiscussionThis study demonstrates variation in diagnosis and referral coding rates for Post-COVID syndrome across different patient groups. The results, with limited crossover of referral and diagnostic codes, suggest only one type of code is usually recorded. Recording one code limits the use of routine data for monitoring Post-COVID syndrome diagnosis and management, but suggests several areas for improvement in coding. Post-COVID syndrome coding, particularly diagnosis coding, needs to improve before administrators and researchers can use it to evaluate care pathways.",epidemiology,exact,100,100 medRxiv,10.1101/2023.05.17.23290105,2023-05-24,https://medrxiv.org/cgi/content/short/2023.05.17.23290105,Within-host SARS-CoV-2 viral kinetics informed by complex life course exposures reveals different intrinsic properties of Omicron and Delta variants,Timothy W Russell; Hermaleigh Townsley; Sam Abbott; Joel Hellewell; Edward J Carr; Lloyd Chapman; Rachael Pung; Billy J Quilty; David Hodgson; Ashley Fowler; Lorin Adams; Christopher Bailey; Harriet V Mears; Ruth Harvey; Bobbi Clayton; Nicola O'Reilly; Yenting Ngai; Jerome Nicod; Steve Gamblin; Bryan Williams; Sonia Gandhi; Charles Swanton; Rupert Beale; David LV Bauer; Emma C Wall; Adam Kucharski,London School of Hygiene and Tropical Medicine; The Francis Crick Institute; London School of Hygiene and Tropical Medicine; European Molecular Biology Laboratory; The Francis Crick Institute; Lancaster University; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; National Institute for Health Research (NIHR) University College London Hospitals (UCLH); The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; The Francis Crick Institute; London School of Hygiene and Tropical Medicine,"The emergence of successive SARS-CoV-2 variants of concern (VOC) during 2020-22, each exhibiting increased epidemic growth relative to earlier circulating variants, has created a need to understand the drivers of such growth. However, both pathogen biology and changing host characteristics - such as varying levels of immunity - can combine to influence replication and transmission of SARS-CoV-2 within and between hosts. Disentangling the role of variant and host in individual-level viral shedding of VOCs is essential to inform COVID-19 planning and response, and interpret past epidemic trends. Using data from a prospective observational cohort study of healthy adult volunteers undergoing weekly occupational health PCR screening, we developed a Bayesian hierarchical model to reconstruct individual-level viral kinetics and estimate how different factors shaped viral dynamics, measured by PCR cycle threshold (Ct) values over time. Jointly accounting for both inter-individual variation in Ct values and complex host characteristics - such as vaccination status, exposure history and age - we found that age and number of prior exposures had a strong influence on peak viral replication. Older individuals and those who had at least five prior antigen exposures to vaccination and/or infection typically had much lower levels of shedding. Moreover, we found evidence of a correlation between the speed of early shedding and duration of incubation period when comparing different VOCs and age groups. Our findings illustrate the value of linking information on participant characteristics, symptom profile and infecting variant with prospective PCR sampling, and the importance of accounting for increasingly complex population exposure landscapes when analysing the viral kinetics of VOCs.",epidemiology,exact,100,100 medRxiv,10.1101/2023.05.08.23289442,2023-05-11,https://medrxiv.org/cgi/content/short/2023.05.08.23289442,Cohort Profile: Post-hospitalisation COVID-19 study (PHOSP-COVID),Omer Elneima; Hamish J C McAuley; Olivia C Leavy; James D Chalmers; Alex Horsley; Ling-Pei Ho; Michael Marks; Krisnah Poinasamy; Betty Raman; Aarti Shikotra; Amisha Singapuri; Marco Sereno; Victoria C Harris; Linzy Houchen-Wolloff; Ruth M Saunders; Neil J Greening; Matthew Richardson; Jennifer K Quint; Andrew Briggs; Annemarie B Docherty; Steven Kerr; Ewen M Harrison; Nazir I Lone; Mathew Thorpe; Liam G Heaney; Keir E Lewis; Raminder Aul; Paul Beirne; Charlotte E Bolton; Jeremy S Brown; Gourab Choudhury; Nawar Diar Bakerly; Nicholas Easom; Carlos Echevarria; Jonathan Fuld; Nick Hart; John R Hurst; Mark G Jones; Dhruv Parekh; Paul E Pfeffer; Najib M Rahman; Sarah L Rowland-Jones; AA Roger Thompson; Caroline Jolley; Ajay M Shah; Dan G Wootton; Trudie Chalder; Melanie J Davies; Anthony De Soyza; John R Geddes; William Greenhalf; Simon Heller; Luke S Howard; Joseph Jacob; R Gisli Jenkins; Janet M Lord; William D-C Man; Gerry P McCann; Stefan Neubauer; Peter JM Openshaw; Joanna C Porter; Matthew J Rowland; Janet T Scott; Malcolm G Semple; Sally J Singh; David C Thomas; Mark Toshner; Aziz Sheikh; Chris E Brightling; Louise v Wain; Rachael A Evans; - on behalf of the PHOSP-COVID Collaborative Group,"The Institute for Lung Health, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; Department of Population Health Sciences, University of Leicester, Leicester, UK; University of Dundee, Ninewells Hospital and Medical School, Dundee, UK; Division of Infection, Immunity & Respiratory Medicine, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; MRC Human Immunology Unit, University of Oxford, Oxford, UK; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK; Asthma and Lung UK, London, UK; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; Centre for Exercise and Rehabilitation Science, NIHR Leicester Biomedical Research Centre- Respiratory, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; National Heart and Lung Institute, Imperial College London, London, UK; London School of Hygiene & Tropical Medicine, London, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; The Roslin Institute, University of Edinburgh, Edinburgh, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; Wellcome-Wolfson Institute for Experimental Medicine, Queens University Belfast, Belfast, UK; Hywel Dda University Health Board, Wales, UK; St George's University Hospitals NHS Foundation Trust, London, UK; Leeds Teaching Hospitals NHS Trust, Leeds, UK; NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK; UCL Respiratory, Department of Medicine, University College London, London, UK; Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK; Salford Royal NHS Foundation Trust, Manchester, UK; Infection Research Group, Hull University Teaching Hospitals, Hull, UK; Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK; Department of Respiratory Medicine, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK; Lane Fox Respiratory Unit, Guy's and St Thomas' NHS Foundation Trust, London, UK; Royal Free London NHS Foundation Trust, London, UK; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK; Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK; Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK; NIHR Oxford Biomedical Research Centre, Oxford, UK; University of Sheffield, Sheffield, UK; University of Sheffield, Sheffield, UK; Centre for Human & Applied Physiological Sciences, School of Basic & Medical Biosciences, Faculty of Life Sciences & Medicine, King's College London, London, UK; King's College London British Heart Foundation Centre, London, UK; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK; Department of Psychological Medicine, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK; NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK; Population Health Sciences Institute, Newcastle University, Newcastle Upon Tyne, UK; NIHR Oxford Health Biomedical Research Centre, University of Oxford, Oxford, UK; The CRUK Liverpool Experimental Cancer Medicine Centre, Liverpool, UK; Department of Oncology and Metabolism, University of Sheffield, Sheffield, UK; Imperial College Healthcare NHS Trust, London, UK; Centre for Medical Image Computing, University College London, London, UK; National Heart and Lung Institute, Imperial College London, London, UK; MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK; Royal Brompton & Harefield Hospitals, Guy's and St. Thomas' NHS Foundation Trust, London, UK; Department of Cardiovascular Sciences, University of Leicester and the NIHR Leicester Biomedical Research Centre, Glenfield Hospital, Leicester; NIHR Oxford Biomedical Research Centre, Oxford, UK; National Heart and Lung Institute, Imperial College London, London, UK; UCL Respiratory, Department of Medicine, University College London, London, UK; Kadoorie Centre for Critical Care Research, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; MRC-University of Glasgow Center for Virus research; NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK; Centre for Exercise and Rehabilitation Science, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; Department of Immunology and Inflammation, Imperial College London, London, UK; NIHR Cambridge Biomedical Research Centre, Cambridge, United Kingdom; Centre for Medical Informatics, The Usher Institute, University of Edinburgh, Edinburgh, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; Department of Population Health Sciences, University of Leicester, Leicester, UK; The Institute for Lung Health, NIHR Leicester Biomedical Research Centre-Respiratory, University of Leicester, Leicester, UK; ","O_LIPHOSP-COVID is a national UK multi-centre cohort study of patients who were hospitalised for COVID-19 and subsequently discharged. C_LIO_LIPHOSP-COVID was established to investigate the medium- and long-term sequelae of severe COVID-19 requiring hospitalisation, understand the underlying mechanisms of these sequelae, evaluate the medium- and long-term effects of COVID-19 treatments, and to serve as a platform to enable future studies, including clinical trials. @@ -503,6 +509,26 @@ FindingsOf 8,799,079 visits, 147,278 (1{middle dot}7%) were PCR-positive. Over t InterpretationChange-points in growth rates of SARS-CoV-2 can be detected in near real-time using ISR and second derivatives of GAMs. To increase certainty about changes in epidemic trajectories both methods could be run in parallel. Running either method in near real-time on different infection surveillance data streams could provide timely warnings of changing underlying epidemiology. FundingUK Health Security Agency, Department of Health and Social Care (UK), Welsh Government, Department of Health (on behalf of the Northern Ireland Government), Scottish Government, National Institute for Health Research.",epidemiology,exact,100,100 +medRxiv,10.1101/2022.09.11.22279823,2022-09-12,https://medrxiv.org/cgi/content/short/2022.09.11.22279823,Effects of the COVID-19 pandemic on the mental health of clinically extremely vulnerable children and children living with clinically extremely vulnerable people in Wales: A data linkage study,Laura Elizabeth Cowley; Karen Hodgson; Jiao Song; Tony Whiffen; Jacinta Tan; Ann John; Amrita Bandyopadhyay; Alisha R Davies,Swansea University; Public Health Wales; Public Health Wales; Welsh Government; University of Oxford; Swansea University; Swansea University; Public Health Wales,"ObjectivesTo determine whether clinically extremely vulnerable (CEV) children or children living with a CEV person in Wales were at greater risk of presenting with anxiety or depression in primary or secondary care during the COVID-19 pandemic compared with children in the general population, and to compare patterns of anxiety and depression during the pandemic (23rd March 2020-31st January 2021, referred to as 2020/21) and before the pandemic (March 23rd 2019-January 31st 2020, referred to as 2019/20), between CEV children and the general population. + +DesignPopulation-based cross-sectional cohort study using anonymised, linked, routinely collected health and administrative data held in the Secure Anonymised Information Linkage Databank. CEV individuals were identified using the COVID-19 Shielded Patient List. + +SettingPrimary and secondary healthcare settings covering 80% of the population of Wales. + +ParticipantsChildren aged 2-17 in Wales: CEV (3,769); living with a CEV person (20,033); or neither (415,009). + +Primary outcome measureFirst record of anxiety or depression in primary or secondary healthcare in 2019/20 and 2020/21, identified using Read and ICD-10 codes. + +ResultsA Cox regression model adjusted for demographics and history of anxiety or depression revealed that only CEV children were at greater risk of presenting with anxiety or depression during the pandemic compared with the general population (Hazard Ratio=2.27, 95% Confidence Interval=1.94-2.66, p<0.001). Compared with the general population, the risk amongst CEV children was higher in 2020/21 (Risk Ratio 3.04) compared with 2019/20 (Risk Ratio 1.90). In 2020/21, the cumulative incidence of anxiety or depression increased slightly amongst CEV children, but declined amongst the general population. + +ConclusionsDifferences in the cumulative incidences of recorded anxiety or depression in healthcare between CEV children and the general population were largely driven by a reduction in presentations to healthcare services by children in the general population during the pandemic. + +Strengths and limitations of this studyO_LIStrengths of this study include its novelty, national focus and clinical relevance; to date this is the first population-based study examining the effects of the COVID-19 pandemic on healthcare use for anxiety or depression amongst clinically extremely vulnerable (CEV) children and children living with a CEV person in Wales +C_LIO_LIWe compared 2020/21 data with pre-pandemic 2019/20 data for CEV children and children in the general population, to place the impact of the COVID-19 pandemic in the context of longer-term patterns of healthcare use +C_LIO_LIWe used a novel approach and linked multiple datasets to identify a cohort of children living with a CEV person in Wales during the COVID-19 pandemic +C_LIO_LIThere was heterogeneity within the Shielded Patient List that was used to create the cohorts of children identified as CEV or living with a CEV person, in terms of the type and severity of individuals underlying conditions; the manner in which people were added to the list; the time point that people were added to the list; and the extent to which people followed the shielding guidance +C_LIO_LIRoutinely collected healthcare data does not capture self-reported health, and is likely to underestimate the burden of common mental disorders in the population +C_LI",pediatrics,exact,100,100 medRxiv,10.1101/2022.09.01.22279473,2022-09-02,https://medrxiv.org/cgi/content/short/2022.09.01.22279473,Rebound in asthma exacerbations following relaxation of COVID-19 restrictions: a longitudinal population-based study (COVIDENCE UK),Florence Tydeman; Paul Pfeffer; Giulia Vivaldi; Hayley Holt; Mohammad Talaei; David Jolliffe; Gwyneth Davies; Ronan Lyons; Chris Griffiths; Frank Kee; Aziz Sheikh; Seif Shaheen; Adrian R Martineau,Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Queen Mary University of London; Swansea University; Swansea University; Queen Mary University of London; Queen's University Belfast; Edinburgh University; Queen Mary University of London; Queen Mary University of London,"BackgroundThe imposition of restrictions on social mixing early in the COVID-19 pandemic was followed by a reduction in asthma exacerbations in multiple settings internationally. Temporal trends in social mixing, incident acute respiratory infections (ARI) and asthma exacerbations following relaxation of COVID-19 restrictions have not yet been described. MethodsWe conducted a population-based longitudinal study in 2,312 UK adults with asthma between November 2020 and April 2022. Details of face covering use, social mixing, incident ARI and moderate/severe asthma exacerbations were collected via monthly on-line questionnaires. Temporal changes in these parameters were visualised using Poisson generalised additive models. Multilevel logistic regression was used to test for associations between incident ARI and risk of asthma exacerbations, adjusting for potential confounders. @@ -512,6 +538,27 @@ ResultsRelaxation of COVID-19 restrictions from April 2021 coincided with reduce ConclusionsRelaxation of COVID-19 restrictions coincided with decreased face covering use, increased social mixing and a rebound in ARI and asthma exacerbations. Associations between incident ARI and risk of moderate/severe asthma exacerbation were similar for non-COVID-19 ARI and COVID-19, both before and after emergence of the SARS-CoV-2 omicron variant. FundingBarts Charity, UKRI",respiratory medicine,exact,100,100 +medRxiv,10.1101/2022.08.29.22279359,2022-08-31,https://medrxiv.org/cgi/content/short/2022.08.29.22279359,Prophylactic Treatment of COVID-19 in Care Homes Trial (PROTECT-CH),Philip M Bath; Jonathan Ball; Matthew Boyd; Heather Gage; Matthew Glover; Maureen Godfrey; Bruce Guthrie; Jonathan Hewitt; Robert Howard; Thomas Jaki; Edmund Juszczak; Daniel Lasserson; Paul Leighton; Val Leyland; Wei Shen Lim; Pip Logan; Garry Meakin; Alan Montgomery; Reuben Ogollah; Peter Passmore; Philip Quinlan; Caroline Rick; Simon Royal; Susan D Shenkin; Clare Upton; Adam L Gordon; - PROTECT-CH Trialists,University of Nottingham; University of Nottingham; University of Nottingham; University of Surrey; University of Surrey; Private person; University of Edinburgh; Llandough Hospital; University College London; University of Cambridge; University of Nottingham; University of Warwick; University of Nottingham; Private person; Nottingham University Hospitals NHS Trust; University of Nottingham; University of Nottingham; University of Nottingham; University of Nottingham; Queen's University Belfast; University of Nottingham; University of Nottingham; Cripps Health Centre; University of Edinburgh; University of Nottingham; University of Nottingham; ,"BackgroundCoronavirus disease 2019 (COVID-19) is associated with significant mortality and morbidity in care homes. Novel or repurposed antiviral drugs may reduce infection and disease severity through reducing viral replication and inflammation. + +ObjectiveTo compare the safety and efficacy of antiviral agents (ciclesonide, niclosamide) for preventing SARS-CoV-2 infection and COVID-19 severity in care home residents. + +DesignCluster-randomised open-label blinded endpoint platform clinical trial testing antiviral agents in a post-exposure prophylaxis paradigm. + +SettingCare homes across all four United Kingdom member countries. + +ParticipantsCare home residents 65 years of age or older. + +InterventionsCare homes were to be allocated at random by computer to 42 days of antiviral agent plus standard care versus standard of care and followed for 60 days after randomisation. + +Main outcome measuresThe primary four-level ordered categorical outcome with participants classified according to the most serious of all-cause mortality, all-cause hospitalisation, SARS-CoV-2 infection and no infection. Analysis using ordinal logistic regression was by intention to treat. Other outcomes included the components of the primary outcome and transmission. + +ResultsDelays in contracting between NIHR and the manufacturers of potential antiviral agents significantly delayed any potential start date. Having set up the trial (protocol, approvals, insurance, website, database, routine data algorithms, training materials), the trial was stopped in September 2021 prior to contracting of care homes and general practitioners in view of the success of vaccination in care homes with significantly reduced infections, hospitalisations and deaths. As a result, the sample size target (based on COVID-19 rates and deaths occurring in February-June 2020) became unfeasible. + +LimitationsCare home residents were not approached about the trial and so were not consented and did not receive treatment. Hence, the feasibility of screening, consent, treatment and data acquisition, and potential benefit of post exposure prophylaxis were never tested. Further, contracting between the University of Nottingham and the PIs, GPs and care homes was not completed, so the feasibility of contracting with all the different groups at the scale needed was not tested. + +ConclusionsThe role of post exposure prophylaxis of COVID-19 in care home residents was not tested because of changes in COVID-19 incidence, prevalence and virulence as a consequence of the vaccination programme that rendered the study unfeasible. Significant progress was made in describing and developing the infrastructure necessary for a large scale Clinical Trial of Investigational Medicinal Products in care homes in all four UK nations. + +Future workThe role of post-exposure prophylaxis of COVID-19 in care home residents remains to be defined. Significant logistical barriers to conducting research in care homes during a pandemic need to be removed before such studies are possible in the required short timescale.",infectious diseases,exact,100,100 medRxiv,10.1101/2022.08.29.22279333,2022-08-30,https://medrxiv.org/cgi/content/short/2022.08.29.22279333,A case-crossover study of the effect of vaccination on SARS-CoV-2 transmission relevant behaviours during a period of national lockdown in England and Wales,Aimee Serisier; Sarah Beale; Yamina I Boukari; Susan J Hoskins; Vincent Nguyen; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Alexei Yavlinsky; Andrew Hayward; Robert W Aldridge,University College London; University College London; University College London; Univerity College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London,"BackgroundStudies of COVID-19 vaccine effectiveness show increases in COVID-19 cases within 14 days of a first dose, potentially reflecting post-vaccination behaviour changes associated with SARS-CoV-2 transmission before vaccine protection. However, direct evidence for a relationship between vaccination and behaviour is lacking. We aimed to examine the association between vaccination status and self-reported non-household contacts and non-essential activities during a national lockdown in England and Wales. MethodsParticipants (n=1,154) who had received the first dose of a COVID-19 vaccine reported non-household contacts and non-essential activities from February to March 2021 in monthly surveys during a national lockdown in England and Wales. We used a case-crossover study design and conditional logistic regression to examine the association between vaccination status (pre-vaccination vs. 14 days post-vaccination) and self-reported contacts and activities within individuals. Stratified subgroup analyses examined potential effect heterogeneity by sociodemographic characteristics such as sex, household income or age group. @@ -678,6 +725,13 @@ ResultsFollowing an initial plateau of 1.54% until mid-January, infection preval ConclusionHigh-resolution prevalence data fitted to P-splines allowed us to show that the lockdown was highly effective at reducing risk of infection with school holidays/closures playing a significant part.",infectious diseases,exact,100,100 medRxiv,10.1101/2022.05.23.22275458,2022-05-25,https://medrxiv.org/cgi/content/short/2022.05.23.22275458,Covid-19 is a leading cause of death in children and young people ages 0-19 years in the United States,Seth Flaxman; Charles Whittaker; Elizaveta Semenova; Theo Rashid; Robbie Parks; Alexandra Blenkinsop; H Juliette T Unwin; Swapnil Mishra; Samir Bhatt; Deepti Gurdasani; Oliver Ratmann,"Oxford; Imperial College London; AstraZeneca; Imperial College London; Columbia University; Imperial College London; Imperial College London; University of Copenhagen; University of Copenhagen, Imperial College London; Queen Mary University of London; Imperial College London","Covid-19 has caused more than 1 million deaths in the US, including at least 1,204 deaths among children and young people (CYP) aged 0-19 years, with 796 occurring in the one year period April 1, 2021 - March 31, 2022. Deaths among US CYP are rare in general, and so we argue here that the mortality burden of Covid-19 in CYP is best understood in the context of all other causes of CYP death. Using publicly available data from CDC WONDER on NCHSs 113 Selected Causes of Death, and comparing to mortality in 2019, the immediate pre-pandemic period, we find that Covid-19 mortality is among the 10 leading causes of death in CYP aged 0-19 years in the US, ranking 8th among all causes of deaths, 5th in disease-related causes of deaths (excluding accidents, assault and suicide), and 1st in deaths caused by infectious or respiratory diseases. Covid-19 deaths constitute 2.3% of the 10 leading causes of death in this age group. Covid-19 caused substantially more deaths in CYP than major vaccine-preventable diseases did historically in the period before vaccines became available. Various factors including underreporting and Covid-19s role as a contributing cause of death from other diseases mean that our estimates may understate the true mortality burden of Covid-19. Our findings underscore the public health relevance of Covid-19 to CYP. In the likely future context of sustained SARS-CoV-2 circulation, pharmaceutical and non-pharmaceutical interventions will continue to play an important role in limiting transmission of the virus in CYP and mitigating severe disease.",infectious diseases,exact,100,100 +medRxiv,10.1101/2022.05.19.22275214,2022-05-22,https://medrxiv.org/cgi/content/short/2022.05.19.22275214,Antibody levels following vaccination against SARS-CoV-2: associations with post-vaccination infection and risk factors,Nathan J Cheetham; Milla Kibble; Andrew Wong; Richard J Silverwood; Anika Knuppel; Dylan M Williams; Olivia K L Hamilton; Paul H Lee; Charis Bridger Staatz; Giorgio Di Gessa; Jingmin Zhu; Srinivasa Vittal Katikireddi; George B Ploubidis; Ellen J Thompson; Ruth C E Bowyer; Xinyuan Zhang; Golboo Abbasian; Maria Paz Garcia; Deborah Hart; Jeffrew Seow; Carl Graham; Neophytos Kouphou; Sam Acors; Michael H Malim; Ruth E Mitchell; Kate Northstone; Daniel Major-Smith; Sarah Matthews; Thomas Breeze; Michael Crawford; Lynn Molloy; Alex Siu Fung Kwong; Katie J Doores; Nishi Chaturvedi; Emma L Duncan; Nicholas J Timpson; Claire J Steves,King's College London; University of Cambridge; University College London; University College London; University College London; University College London; University of Glasgow; University of Leicester; University College London; University College London; University College London; University of Glasgow; University College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; King's College London; University College London; King's College London; University of Bristol; King's College London,"SARS-CoV-2 antibody levels can be used to assess humoral immune responses following SARS-CoV-2 infection or vaccination, and may predict risk of future infection. From cross-sectional antibody testing of 9,361 individuals from TwinsUK and ALSPAC UK population-based longitudinal studies (jointly in April-May 2021, and TwinsUK only in November 2021-January 2022), we tested associations between antibody levels following vaccination and: (1) SARS-CoV-2 infection following vaccination(s); (2) health, socio-demographic, SARS-CoV-2 infection and SARS-CoV-2 vaccination variables. + +Within TwinsUK, single-vaccinated individuals with the lowest 20% of anti-Spike antibody levels at initial testing had 3-fold greater odds of SARS-CoV-2 infection over the next six to nine months, compared to the top 20%. In TwinsUK and ALSPAC, individuals identified as at increased risk of COVID-19 complication through the UK ""Shielded Patient List"" had consistently greater odds (2 to 4-fold) of having antibody levels in the lowest 10%. Third vaccination increased absolute antibody levels for almost all individuals, and reduced relative disparities compared with earlier vaccinations. + +These findings quantify the association between antibody level and risk of subsequent infection, and support a policy of triple vaccination for the generation of protective antibodies. + +Lay summaryIn this study, we analysed blood samples from 9,361 participants from two studies in the UK: an adult twin registry, TwinsUK (4,739 individuals); and the Avon Longitudinal Study of Parents and Children, ALSPAC (4,622 individuals). We did this work as part of the UK Government National Core Studies initiative researching COVID-19. We measured blood antibodies which are specific to SARS-CoV-2 (which causes COVID-19). Having a third COVID-19 vaccination boosted antibody levels. More than 90% of people from TwinsUK had levels after third vaccination that were greater than the average level after second vaccination. Importantly, this was the case even in individuals on the UK ""Shielded Patient List"". We found that people with lower antibody levels after first vaccination were more likely to report having COVID-19 later on, compared to people with higher antibody levels. People on the UK ""Shielded Patient List"", and individuals who reported that they had poorer general health, were more likely to have lower antibody levels after vaccination. In contrast, people who had had a previous COVID-19 infection were more likely to have higher antibody levels following vaccination compared to people without infection. People receiving the Oxford/AstraZeneca rather than the Pfizer BioNTech vaccine had lower antibody levels after one or two vaccinations. However, after a third vaccination, there was no difference in antibody levels between those who had Oxford/AstraZeneca and Pfizer BioNTech vaccines for their first two doses. These findings support having a third COVID-19 vaccination to boost antibodies.",epidemiology,exact,100,100 medRxiv,10.1101/2022.05.10.22274890,2022-05-10,https://medrxiv.org/cgi/content/short/2022.05.10.22274890,Biopsychosocial response to the COVID-19 lockdown in people with major depressive disorder and multiple sclerosis.,Sara Siddi; Iago Gine Vazquez; Raquel Bailon; Faith Matcham; Femke Lamers; Spyridon Kontaxis; Estela Laporta Puyal; Esther Garcia; Belen Arranz; Gloria Dallacosta; Anna Isabel Guerrero Perez; Anna Zabalza; Mathias Buron; Giancarlo Comi; Letizia Leocani; Peter Annas; Matthew Hotopf; Brenda Penninx; Melinda Magyari; Per Sorensen; Xavier Montalban; Grace Lavalle; Alina Ivan; Carolin Oetzmann; Katie White; Sonia Difrancesco; Patrick Locatelli; Jordi Aguilo; Vaibhav Narayan; Amos Folarin; Richard Dobson; Judith Anne Dineley; Daniel Leightley; Nicholas Cummins; Yarharth Ranjan; Zulqarnain Rashid; Aki Rintala; Giovanni De Girolamo; Antonio Preti; Sara Simblett; Til Wykes; Inez Myin-Germeys; Josep Maria Haro,"Parc Sanitari Sant Joan de Deu Cibersam; Parc Sanitari Sant Joan de Deu Cibersam; Universidad de Zaragoza; King's College London; Amsterdam UMC Locatie AMC, Amsterdam, North Holland, NL; Universidad de Zaragoza; Universidad de Zaragoza; Universitat Autonoma de Barcelona; Parc Sanitari Sant Joan de Deu Cibersam; Istituto di Ricovero e Cura a Carattere Scientifico Ospedale San Raffaele Milano; Vall d'Hebron Institut de Recerca; Vall d'Hebron Institut de Recerca; Copenhagen University Hospital Kobenhavn; Istituto di Ricovero e Cura a Carattere Scientifico Ospedale San Raffaele Milano; Istituto di Ricovero e Cura a Carattere Scientifico Ospedale San Raffaele Milano; H Lundbeck AS Valby; Institute of Psychiatry, Psychological Medicine; Amsterdam UMC Locatie AMC, Amsterdam, North Holland, NL; Copenhagen University Hospital Kobenhavn; Copenhagen University Hospital Kobenhavn; Vall d'Hebron Institut de Recerca; King's College London; King's College London; King's College London; King's College London; Amsterdam UMC Locatie AMC, Amsterdam, North Holland, NL; University of Bergamo; Universitat Autonoma de Barcelona; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Katholieke Universiteit Leuven; Centro San Giovanni di Dio Fatebenefratelli; Universita degli Studi di Torino; King's College London; King's College London; KU Leuven; Parc Sanitari Sant Joan de Deu Cibersam","BackgroundChanges in lifestyle, finances and work status during COVID-19 lockdowns may have led to biopsychosocial changes in people with pre-existing vulnerabilities such as Major Depressive Disorders (MDD) and Multiple Sclerosis (MS). MethodsData were collected as a part of the RADAR-CNS (Remote Assessment of Disease and Relapse - Central Nervous System) programme. We analyzed the following data from long-term participants in a decentralized multinational study: symptoms of depression, heart rate (HR) during the day and night; social activity; sedentary state, steps and physical activity of varying intensity. Linear mixed-effects regression analyses with repeated measures were fitted to assess the changes among three time periods (pre, during and post-lockdown) across the groups, adjusting for depression severity before the pandemic and gender. @@ -946,7 +1000,6 @@ ResultsBetween October-2020 and April-2022, 120,995 SARS-CoV-2 PCR-positive epis ConclusionsIncreases in sore throat (also common in the general community), and a marked reduction in loss of taste/smell, make Omicron harder to detect with symptom-based testing algorithms, with implications for institutional and national testing policies. SummaryIn a UK community study, loss of taste/smell was markedly less commonly reported with Omicron BA.1/BA.2 than Delta SARS-CoV-2 infections, with smaller declines in reported shortness of breath, myalgia and fatigue/weakness, but increases in sore throat, challenging symptom-based testing algorithms.",epidemiology,exact,100,100 -medRxiv,10.1101/2022.01.05.21268323,2022-01-06,https://medrxiv.org/cgi/content/short/2022.01.05.21268323,Lineage replacement and evolution captured by the United Kingdom Covid Infection Survey,Katrina A Lythgoe; Tanya Golubchik; Matthew Hall; Thomas House; Roberto Cahuantzi; George MacIntyre-Cockett; Helen Fryer; Laura Thomson; Anel Nurtay; Mahan Ghafari; David Buck; Angie Green; Amy Trebes; Paolo Piazza; Lorne J Lonie; Ruth Studley; Emma Rourke; Darren Smith; Matthew Bashton; Andrew Nelson; Matthew Crown; Clare McCann; Gregory R Young; Rui Andre Nunes de Santos; Zack Richards; Adnan Tariq; - Wellcome Sanger Institute COVID-19 Surveillance Team; - COVID-19 Infection Survey Group; - The COVID-19 Genomics UK (COG-UK) consortium; Christophe Fraser; Ian Diamond; Jeff Barrett; Ann Sarah Walker; David Bonsall,University of Oxford; University of Oxford; University of Oxford; University of Manchester; University of Manchester; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Wellcome Sanger Institute; Office for National Statistics; ; University of Oxford; Office for National Statistics; Wellcome Sanger Institute; University of Oxford; University of Oxford,"The Office for National Statistics COVID-19 Infection Survey (ONS-CIS) is the largest surveillance study of SARS-CoV-2 positivity in the community, and collected data on the United Kingdom (UK) epidemic from April 2020 until March 2023 before being paused. Here, we report on the epidemiological and evolutionary dynamics of SARS-CoV-2 determined by analysing the sequenced samples collected by the ONS-CIS during this period. We observed a series of sweeps or partial sweeps, with each sweeping lineage having a distinct growth advantage compared to their predecessors. The sweeps also generated an alternating pattern in which most samples had either S-gene target failure (SGTF) or non- SGTF over time. Evolution was characterised by steadily increasing divergence and diversity within lineages, but with step increases in divergence associated with each sweeping major lineage. This led to a faster overall rate of evolution when measured at the between-lineage level compared to within lineages, and fluctuating levels of diversity. These observations highlight the value of viral sequencing integrated into community surveillance studies to monitor the viral epidemiology and evolution of SARS-CoV-2, and potentially other pathogens, particularly in the current phase of the pandemic with routine RT-PCR testing now ended in the community.",epidemiology,exact,100,100 medRxiv,10.1101/2021.12.31.21268587,2022-01-02,https://medrxiv.org/cgi/content/short/2021.12.31.21268587,"The adverse impact of COVID-19 pandemic on cardiovascular disease prevention and management in England, Scotland and Wales: A population-scale descriptive analysis of trends in medication data",Caroline E Dale; Rohan Takhar; Ray Carragher; Fatemeh Torabi; Michalis Katsoulis; Stephen Duffield; Seamus Kent; Tanja Mueller; Amanj Kurdi; Stuart McTaggart; Hoda Abbasizanjani; Sam Hollings; Andrew Scourfield; Ronan Lyons; Rowena Griffiths; Jane Lyons; Gareth Davies; Dan Harris; Alex Handy; Mehrdad Alizadeh Mizani; Chris Tomlinson; Mark Ashworth; Spiros Denaxas; Amitava Banerjee; Jonathan Sterne; Kate Lovibond; Paul Brown; Ian Bullard; Rouven Priedon; Mamas A Mamas; Ann Slee; Paula Lorgelly; Munir Pirmohamed; Kamlesh Khunti; Naveed Sattar; Andrew Morris; Cathie Sudlow; Ashley Akbari; Marion Bennie; Reecha Sofat; - CVD-COVID-UK Consortium,"Institute of Health Informatics Research, University College London; Institute of Health Informatics Research, University College London; Strathclyde Institute of Pharmacy & Biomedical Sciences, University of Strathclyde; Swansea University; Institute of Health Informatics Research, University College London; NICE; NICE; University of Strathclyde; Strathclyde Institute of Pharmacy & Biomedical Sciences, University of Strathclyde; Public Health Scotland; Swansea University; NHS Digital, Leeds; UCLH NHS Foundation Trust; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Institute of Health Informatics Research, University College London; Institute of Health Informatics Research, University College London; Institute of Health Informatics Research, University College London; King's College London; Institute of Health Informatics Research, University College London; University College London; University of Bristol; Royal College of Physicians; NHS Digital, Leeds; NHS Digital; British Heart Foundation Data Science Centre, Health Data Research UK, London; Keele University; NHSX; Department of Applied Health Research, University College London; University of Liverpool; University of Leicester; University of Glasgow; Health Data Research UK; British Heart Foundation Data Science Centre, Health Data Research UK, London; Swansea University; University of Strathclyde; Institute of Health Informatics Research, University College London; ","ObjectivesTo estimate the impact of the COVID-19 pandemic on cardiovascular disease (CVD) and CVD management using routinely collected medication data as a proxy. DesignDescriptive and interrupted time series analysis using anonymised individual-level population-scale data for 1.32 billion records of dispensed CVD medications across 15.8 million individuals in England, Scotland and Wales. @@ -978,6 +1031,15 @@ Implications of all the available evidenceWe find evidence that four vaccines, u medRxiv,10.1101/2021.12.23.21268276,2021-12-25,https://medrxiv.org/cgi/content/short/2021.12.23.21268276,Risk of myocarditis following sequential COVID-19 vaccinations by age and sex,Martina Patone; Winnie Xue Mei; Lahiru Handunnetthi; Sharon Dixon; Francesco Zaccardi; Manu Shankar-Hari; Peter Watkinson; Kamlesh Khunti; Anthony Harnden; Carol AC Coupland; Keith M. Channon; Nicholas L Mills; Aziz Sheikh; Julia Hippisley-Cox,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Leicester; University of Edinburgh; University of Oxford; University of Leicester; University of Oxford; University of Oxford; University of Oxford; University of Edinburgh; University of Edinburgh; University of Oxford,"In an updated self-controlled case series analysis of 42,200,614 people aged 13 years or more, we evaluate the association between COVID-19 vaccination and myocarditis, stratified by age and sex, including 10,978,507 people receiving a third vaccine dose. Myocarditis risk was increased during 1-28 days following a third dose of BNT162b2 (IRR 2.02, 95%CI 1.40, 2.91). Associations were strongest in males younger than 40 years for all vaccine types with an additional 3 (95%CI 1, 5) and 12 (95% CI 1,17) events per million estimated in the 1-28 days following a first dose of BNT162b2 and mRNA-1273, respectively; 14 (95%CI 8, 17), 12 (95%CI 1, 7) and 101 (95%CI 95, 104) additional events following a second dose of ChAdOx1, BNT162b2 and mRNA-1273, respectively; and 13 (95%CI 7, 15) additional events following a third dose of BNT162b2, compared with 7 (95%CI 2, 11) additional events following COVID-19 infection. An association between COVID-19 infection and myocarditis was observed in all ages for both sexes but was substantially higher in those older than 40 years. These findings have important implications for public health and vaccination policy. FundingHealth Data Research UK.",epidemiology,exact,100,100 +medRxiv,10.1101/2021.12.22.21268252,2021-12-24,https://medrxiv.org/cgi/content/short/2021.12.22.21268252,Rapid increase in Omicron infections in England during December 2021: REACT-1 study,Paul Elliott; Barbara Bodinier; Oliver Eales; Haowei Wang; David Haw; Joshua Elliott; Matthew Whitaker; Jakob Jonnerby; David Tang; Caroline E. Walters; Christina Atchinson; Peter J. Diggle; Andrew J. Page; Alex Trotter; Deborah Ashby; Wendy Barclay; Graham Taylor; Helen Ward; Ara Darzi; Graham Cooke; Marc Chadeau-Hyam; Christl A Donnelly,"School of Public Health, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; Imperial College London; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; Imperial College London; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; Quadram Institute, Norwich, UK; Quadram Institute Bioscience; School of Public Health, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research; Imperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research Centre, UKInstitute of Global Health Innovation at ; Department of Infectious Disease, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency","BackgroundThe highest-ever recorded numbers of daily severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in England has been observed during December 2021 and have coincided with a rapid rise in the highly transmissible Omicron variant despite high levels of vaccination in the population. Although additional COVID-19 measures have been introduced in England and internationally to contain the epidemic, there remains uncertainty about the spread and severity of Omicron infections among the general population. + +MethodsThe REal-time Assessment of Community Transmission-1 (REACT-1) study has been monitoring the prevalence of SARS-CoV-2 infection in England since May 2020. REACT-1 obtains self-administered throat and nose swabs from a random sample of the population of England at ages 5 years and over. Swabs are tested for SARS-CoV-2 infection by reverse transcription polymerase chain reaction (RT-PCR) and samples testing positive are sent for viral genome sequencing. To date 16 rounds have been completed, each including [~]100,000 or more participants with data collected over a period of 2 to 3 weeks per month. Socio-demographic, lifestyle and clinical information (including previous history of COVID-19 and symptoms prior to swabbing) is collected by online or telephone questionnaire. Here we report results from round 14 (9-27 September 2021), round 15 (19 October - 05 November 2021) and round 16 (23 November - 14 December 2021) for a total of 297,728 participants with a valid RT-PCR test result, of whom 259,225 (87.1%) consented for linkage to their NHS records including detailed information on vaccination (vaccination status, date). We used these data to estimate community prevalence and trends by age and region, to evaluate vaccine effectiveness against infection in children ages 12 to 17 years, and effect of a third (booster) dose in adults, and to monitor the emergence of the Omicron variant in England. + +ResultsWe observed a high overall prevalence of 1.41% (1.33%, 1.51%) in the community during round 16. We found strong evidence of an increase in prevalence during round 16 with an estimated reproduction number R of 1.13 (1.06, 1.09) for the whole of round 16 and 1.27 (1.14, 1.40) when restricting to observations from 1 December onwards. The reproduction number in those aged 18-54 years was estimated at 1.23 (1.14, 1.33) for the whole of round 16 and 1.41 (1.23, 1.61) from 1 December. Our data also provide strong evidence of a steep increase in prevalence in London with an estimated R of 1.62 (1.34, 1.93) from 1 December onwards and a daily prevalence reaching 6.07% (4.06%, 9.00%) on 14 December 2021. As of 1 to 11 December 2021, of the 275 lineages determined, 11 (4.0%) corresponded to the Omicron variant. The first Omicron infection was detected in London on 3 December, and subsequent infections mostly appeared in the South of England. The 11 Omicron cases were all aged 18 to 54 years, double-vaccinated (reflecting the large numbers of people who have received two doses of vaccine in this age group) but not boosted, 9 were men, 5 lived in London and 7 were symptomatic (5 with classic COVID-19 symptoms: loss or change of sense of smell or taste, fever, persistent cough), 2 were asymptomatic, and symptoms were unknown for 2 cases. The proportion of Omicron (vs Delta or Delta sub-lineages) was found to increase rapidly with a daily increase of 66.0% (32.7%, 127.3%) in the odds of Omicron (vs. Delta) infection, conditional on swab positivity. Highest prevalence of swab positivity by age was observed in (unvaccinated) children aged 5 to 11 years (4.74% [4.15%, 5.40%]) similar to the prevalence observed at these ages in round 15. In contrast, prevalence in children aged 12 to 17 years more than halved from 5.35% (4.78%, 5.99%) in round 15 to 2.31% (1.91%, 2.80%) in round 16. As of 14 December 2021, 76.6% children at ages 12 to 17 years had received at least one vaccine dose; we estimated that vaccine effectiveness against infection was 57.9% (44.1%, 68.3%) in this age group. In addition, the prevalence of swab positivity in adults aged 65 years and over fell by over 40% from 0.84% (0.72%, 0.99%) in round 15 to 0.48% (0.39%,0.59%) in round 16 and for those aged 75 years and over it fell by two-thirds from 0.63% (0.48%,0.82%) to 0.21% (0.13%,0.32%). At these ages a high proportion of participants (>90%) had received a third vaccine dose; we estimated that adults having received a third vaccine dose had a three- to four-fold lower risk of testing positive compared to those who had received two doses. + +ConclusionA large fall in swab positivity from round 15 to round 16 among 12 to 17 year olds, most of whom have been vaccinated, contrasts with the continuing high prevalence among 5 to 11 year olds who have largely not been vaccinated. Likewise there were large falls in swab positivity among people aged 65 years and over, the vast majority of whom have had a third (booster) vaccine dose; these results reinforce the importance of the vaccine and booster campaign. However, the rapidly increasing prevalence of SARS-CoV-2 infections in England during December 2021, coincident with the rapid rise of Omicron infections, may lead to renewed pressure on health services. Additional measures beyond vaccination may be needed to control the current wave of infections and prevent health services (in England and other countries) from being overwhelmed. + +SummaryThe unprecedented rise in SARS-CoV-2 infections is concurrent with rapid spread of the Omicron variant in England and globally. We analysed prevalence of SARS-CoV-2 and its dynamics in England from end of November to mid-December 2021 among almost 100,000 participants from the REACT-1 study. Prevalence was high during December 2021 with rapid growth nationally and in London, and of the proportion of infections due to Omicron. We observed a large fall in swab positivity among mostly vaccinated older children (12-17 years) compared with unvaccinated younger children (5-11 years), and in adults who received a third vs. two doses of vaccine. Our results reiterate the importance of vaccination and booster campaigns; however, additional measures may be needed to control the rapid growth of the Omicron variant.",epidemiology,exact,100,100 medRxiv,10.1101/2021.12.21.21268214,2021-12-23,https://medrxiv.org/cgi/content/short/2021.12.21.21268214,Comparative effectiveness of ChAdOx1 versus BNT162b2 vaccines against SARS-CoV-2 infections in England and Wales: A cohort analysis using trial emulation in the Virus Watch community data,Vincent Grigori Nguyen; Alexei Yavlinsky; Sarah Beale; Susan J Hoskins; Vasileios Lampos; Isobel Braithwaite; Thomas Edward Byrne; Wing Lam Erica Fong; Ellen Fragaszy; Cyril Geismar; Jana Kovar; Annalan M D Navaratnam; Parth Patel; Madhumita Shrotri; Sophie Weber; Andrew Hayward; Robert W Aldridge,University College London; University College London; University College London; Univerity College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London; University College London,"IntroductionInfections of SARS-CoV-2 in vaccinated individuals have been increasing globally. Understanding the associations between vaccine type and a post-vaccination infection could help prevent further COVID-19 waves. In this paper, we use trial emulation to understand the impact of a phased introduction of the vaccine in the UK driven by vulnerability and exposure status. We estimate the comparative effectiveness of COVID-19 vaccines (ChAdOx1 versus BNT162b2) against post-vaccination infections of SARS-CoV-2 in a community setting in England and Wales. MethodTrial emulation was conducted by pooling results from six cohorts whose recruitment was staggered between 1st January 2021 and 31st March 2021 and followed until 12th November 2021. Eligibility for each trial was based upon age (18+ at the time of vaccination), without prior signs of infection or an infection within the first 14 days of the first dose. Time from vaccination of ChAdOx1 or BNT162b2 until SARS-CoV-2 infection (positive polymerase chain reaction or lateral flow test after 14 of the vaccination) was modelled using Cox proportional hazards model for each cohort and adjusted for age at vaccination, gender, minority ethnic status, clinically vulnerable status and index of multiple deprivation quintile. For those without SARS-CoV-2 infection during the study period, follow-up was until loss-of-follow-up or end of study (12th November 2021). Pooled hazard ratios were generated using random-effects meta-analysis. @@ -1121,18 +1183,14 @@ Key pointsO_ST_ABSQuestionC_ST_ABSIs COVID-19 associated with higher long-term i FindingsIn this cohort study of 48 million adults in England and Wales, COVID-19 was associated with higher incidence, that declined with time since diagnosis, of both arterial thromboses [week 1: adjusted HR [aHR] 21.7 (95% CI 21.0-22.4) weeks 27-49: aHR 1.34 (1.21-1.48)] and venous thromboembolism [week 1: aHR 33.2 (31.3-35.2), weeks 27-49 1.80 (1.50-2.17)]. aHRs were higher, for longer, after hospitalised than non-hospitalised COVID-19. The estimated excess number of arterial thromboses and venous thromboembolisms was 10,500. MeaningAvoidance of COVID-19 infection through vaccination, and use of secondary preventive agents after infection in high-risk patients, may reduce post-COVID-19 acute vascular diseases.",infectious diseases,exact,100,100 -medRxiv,10.1101/2021.11.15.21266255,2021-11-16,https://medrxiv.org/cgi/content/short/2021.11.15.21266255,"COVID-19 vaccination, risk-compensatory behaviours, and social contacts in four countries in the UK",John Buckell; Joel Jones; Philippa C Matthews; Ian Diamond; Emma Rourke; Ruth Studley; Duncan Cook; Ann Sarah Walker; Koen B Pouwels; - The COVID-19 Infection Survey Team,University of Oxford; Office for National Statistics; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; University of Oxford; ,"The physiological effects of vaccination against SARS-CoV-2 (COVID-19) are well documented, yet the behavioural effects are largely unknown. Risk compensation suggests that gains in personal safety, as a result of vaccination, are offset by increases in risky behaviour, such as socialising, commuting and working outside the home. This is potentially problematic because transmission of SARS-CoV-2 is driven by contacts, which could be amplified by vaccine-related risk compensation behaviours. Here, we show that behaviours were overall unrelated to personal vaccination, but - adjusting for variation in mitigation policies - were responsive to the level of vaccination in the wider population: individuals in the UK were risk compensating when rates of vaccination were rising. This effect was observed across four nations of the UK, each of which varied policies autonomously.",infectious diseases,exact,100,100 -medRxiv,10.1101/2021.11.10.21266124,2021-11-11,https://medrxiv.org/cgi/content/short/2021.11.10.21266124,Differences in COVID-19 vaccination coverage by occupation in England: a national linked data study,Vahe Nafilyan; Ted Dolby; Katie Finning; Jasper Morgan; Rhiannon Edge; Myer Glickman; Neil Pearce; Martie Van Tongeren,Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Lancaster University; Office for National Statistics; London School of Hygiene and Tropical Medicine; University of Manchester,"BackgroundMonitoring differences in COVID-19 vaccination uptake in different groups is crucial to help inform the policy response to the pandemic. A key gap is the absence of data on uptake by occupation. - -MethodsUsing nationwide population-level data, we calculated the proportion of people who had received two doses of a COVID-19 vaccine (assessed on 31 August 2021) by detailed occupational categories in adults aged 40-64 and estimated adjusted odds ratios to examine whether these differences were driven by occupation or other factors, such as education. We also examined whether vaccination rates differed by ability to work from home. - -ResultsOur study population included 14,298,147 adults 40-64. Vaccination rates differed markedly by occupation, being higher in administrative and secretarial occupations (90.8%); professional occupations (90.7%); and managers, directors and senior officials (90.6%); and lowest (83.1%) in people working in elementary occupations. We found substantial differences in vaccination rates looking at finer occupational groups even after adjusting for confounding factors, such as education. Vaccination rates were higher in occupations which can be done from home and lower in those which cannot. Many occupations with low vaccination rates also involved contact with the public or with vulnerable people +medRxiv,10.1101/2021.11.15.21266264,2021-11-16,https://medrxiv.org/cgi/content/short/2021.11.15.21266264,Association of COVID-19 employment disruption with mental and social wellbeing: evidence from nine UK longitudinal studies,Jacques Wels; Charlotte Booth; Bozena Wielgoszewska; Michael J Green; Giorgio Di Gessa; Charlotte F Huggins; Gareth J Griffith; Alex Siu Fung Kwong; Ruth C E Bowyer; Jane Maddock; Praveetha Patalay; Richard J Silverwood; Emla Fitzsimons; Richard John Shaw; Ellen J Thompson; Andrew Steptoe; Alun Hughes; Nishi Chaturvedi; Claire J Steves; Srinivasa Vittal Katikireddi; George B Ploubidis,University College London; University College London; University College London; University of Glasgow; University College London; University of Edinburgh; University of Bristol; University of Bristol; King's College London; University College London; University College London; University College London; University College London; University of Glasgow; Kings College London; University College London; University College London; University College London; King's College London; University of Glasgow; University College London,"BackgroundThe COVID-19 pandemic has led to major economic disruptions. In March 2020, the UK implemented the Coronavirus Job Retention Scheme - known as furlough - to minimize the impact of job losses. We investigate associations between change in employment status and mental and social wellbeing during the early stages of the pandemic. -ConclusionsIncreasing vaccination coverage in occupations with low vaccination rates is crucial to help protecting the public and control infection, especially in occupations that cannot be done from home and involve contacts with the public. Policies such as work from home if you can may only have limited future impact on hospitalisations and deaths +MethodsData were from 25,670 respondents, aged 17 to 66, across nine UK longitudinal studies. Furlough and other employment changes were defined using employment status pre-pandemic and during the first lockdown (April-June 2020). Mental and social wellbeing outcomes included psychological distress, life satisfaction, self-rated health, social contact, and loneliness. Study-specific modified Poisson regression estimates, adjusting for socio-demographic characteristics and pre-pandemic mental and social wellbeing measures, were pooled using meta-analysis. -What is already known on this subject?Whilst several studies highlight differences in vaccination coverage by ethnicity, religion, socio-demographic factors and certain underlying health conditions, there is very little evidence on how vaccination coverage varies by occupation, in the UK and elsewhere. The few study looking at occupational differences in vaccine hesitancy focus on healthcare workers or only examined broad occupational groups. There is currently no large-scale study on occupational differences in COVID-19 vaccination coverage in the UK. +ResultsCompared to those who remained working, furloughed workers were at greater risk of psychological distress (adjusted risk ratio, ARR=1.12; 95% CI: 0.97, 1.29), low life satisfaction (ARR=1.14; 95% CI: 1.07, 1.22), loneliness (ARR=1.12; 95% CI: 1.01, 1.23), and poor self-rated health (ARR=1.26; 95% CI: 1.05, 1.50), but excess risk was less pronounced than that of those no longer employed (e.g., ARR for psychological distress=1.39; 95% CI: 1.21, 1.59) or in stable unemployment (ARR=1.33; 95% CI: 1.09, 1.62). -What this study adds?Using population-level linked data combining the 2011 Census, primary care records, mortality and vaccination data, we found that the vaccination rates of adults aged 40 to 64 years in England differed markedly by occupation. Vaccination rates were high in administrative and secretarial occupations, professional occupations and managers, directors and senior officials and low in people working in elementary occupations. Adjusting for other factors likely to be linked to occupation and vaccination, such as education, did not substantially alter the results. Vaccination rates were also associated with the ability to work from home, with the vaccination rate being higher in occupations which can be done performed from home. Policies aiming to increase vaccination rates in occupations that cannot be done from home and involve contacts with the public should be priorities",public and global health,exact,100,100 +ConclusionsDuring the early stages of the pandemic, those furloughed had increased risk for poor mental and social wellbeing. However, their excess risk was lower in magnitude than that of those who became or remained unemployed, suggesting that furlough may have partly mitigated poorer outcomes.",psychiatry and clinical psychology,exact,100,100 +medRxiv,10.1101/2021.11.15.21266255,2021-11-16,https://medrxiv.org/cgi/content/short/2021.11.15.21266255,"COVID-19 vaccination, risk-compensatory behaviours, and social contacts in four countries in the UK",John Buckell; Joel Jones; Philippa C Matthews; Ian Diamond; Emma Rourke; Ruth Studley; Duncan Cook; Ann Sarah Walker; Koen B Pouwels; - The COVID-19 Infection Survey Team,University of Oxford; Office for National Statistics; University of Oxford; Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; University of Oxford; University of Oxford; ,"The physiological effects of vaccination against SARS-CoV-2 (COVID-19) are well documented, yet the behavioural effects are largely unknown. Risk compensation suggests that gains in personal safety, as a result of vaccination, are offset by increases in risky behaviour, such as socialising, commuting and working outside the home. This is potentially problematic because transmission of SARS-CoV-2 is driven by contacts, which could be amplified by vaccine-related risk compensation behaviours. Here, we show that behaviours were overall unrelated to personal vaccination, but - adjusting for variation in mitigation policies - were responsive to the level of vaccination in the wider population: individuals in the UK were risk compensating when rates of vaccination were rising. This effect was observed across four nations of the UK, each of which varied policies autonomously.",infectious diseases,exact,100,100 medRxiv,10.1101/2021.11.09.21266054,2021-11-09,https://medrxiv.org/cgi/content/short/2021.11.09.21266054,"Time varying association between deprivation, ethnicity and SARS-CoV-2 infections in England: a space-time study",Tullia Padellini; Radka Jersakova; Peter J Diggle; Chris Holmes; Ruairidh King; Brieuc Lehmann; Ann-Marie Mallon; George Nicholson; Sylvia Richardson; Marta Blangiardo,Imperial College London; The Alan Turing Institute; Lancaster University; The Alan Turing Institute; MRC Harwell; University of Oxford; MRC Harwell; University of Oxford; University of Cambridge; Imperial College London,"BackgroundEthnically diverse and socio-economically deprived communities have been differentially affected by the COVID-19 pandemic in the UK. MethodUsing a multilevel regression model we assess the time-varying association between SARS-CoV-2 infections and areal level deprivation and ethnicity. We separately consider weekly test positivity rate (number of positive tests over the total number of tests) and estimated unbiased prevalence (proportion of individuals in the population who would test positive) at the Lower Tier Local Authority (LTLA) level. The model also adjusts for age, urbanicity, vaccine uptake and spatio-temporal correlation structure. @@ -1524,19 +1582,6 @@ FindingsWe included results from 8213 swabbed illnesses, 944 of which tested pos InterpretationCOVID-19 is difficult to distinguish from other respiratory infections and common ailments on the basis of symptoms. Broadening the list of symptoms used to encourage engagement with TTI could moderately increase the number of infections identified and shorten delays to isolation, but with a large increase in the number of tests needed and the number of unwell individuals and contacts who are advised to self-isolate whilst awaiting results, and subsequently test negative for SARS-CoV-2.",epidemiology,exact,100,100 medRxiv,10.1101/2021.05.17.21256818,2021-05-18,https://medrxiv.org/cgi/content/short/2021.05.17.21256818,Local prevalence of transmissible SARS-CoV-2 infection : an integrative causal model for debiasing fine-scale targeted testing data,George Nicholson; Brieuc CL Lehmann; Tullia Padellini; Koen B Pouwels; Radka Jersakova; James Lomax; Ruairidh E King; Ann-Marie Mallon; Peter J Diggle; Sylvia Richardson; Marta Blangiardo; Chris Holmes,University of Oxford; University of Oxford; Imperial College London; University of Oxford; The Alan Turing Institute; The Alan Turing Institute; MRC Harwell Institute; MRC Harwell Institute; Lancaster University; MRC Biostatistics Unit; Imperial College London; University of Oxford,"Targeted surveillance testing schemes for SARS-CoV-2 focus on certain subsets of the population, such as individuals experiencing one or more of a prescribed list of symptoms. These schemes have routinely been used to monitor the spread of SARS-CoV-2 in countries across the world. The number of positive tests in a given region can provide local insights into important epidemiological parameters, such as prevalence and effective reproduction number. Moreover, targeted testing data has been used inform the deployment of localised non-pharmaceutical interventions. However, surveillance schemes typically suffer from ascertainment bias; the individuals who are tested are not necessarily representative of the wider population of interest. Here, we show that data from randomised testing schemes, such as the REACT study in the UK, can be used to debias fine-scale targeted testing data in order to provide accurate localised estimates of the number of infectious individuals. We develop a novel, integrative causal framework that explicitly models the process underlying the selection of individuals for targeted testing. The output from our model can readily be incorporated into longitudinal analyses to provide local estimates of the reproduction number. We apply our model to characterise the size of the infectious population in England between June 2020 and January 2021. Our local estimates of the effective reproduction number are predictive of future changes in positive case numbers. We also capture local increases in both prevalence and effective reproductive number in the South East from November 2020 to December 2020, reflecting the spread of the Kent variant. Our results illustrate the complementary roles of randomised and targeted testing schemes. Preparations for future epidemics should ensure the rapid deployment of both types of schemes to accurately monitor the spread of emerging and ongoing infectious diseases.",infectious diseases,exact,100,100 -medRxiv,10.1101/2021.05.12.21257123,2021-05-17,https://medrxiv.org/cgi/content/short/2021.05.12.21257123,Occupation and COVID-19 mortality in England: a national linked data study of 14.3 million adults,Vahe Nafilyan; Piotr Pawelek; Daniel Ayoubkhani; Sarah Rhodes; Lucy Pembrey; Melissa Matz; Michel P Coleman; Claudia Allemani; Ben Windsor-Shellard; Martie van Tongeren; Neil Pearce,"Office for National Statistics; Office for National Statistics; Office for National Statistics; School of Health Sciences, University of Manchester; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine; Office for National Statistics; School of Health Sciences, University of Manchester; London School of Hygiene and Tropical Medicine","ObjectiveTo estimate occupational differences in COVID-19 mortality, and test whether these are confounded by factors, such as regional differences, ethnicity and education or due to non-workplace factors, such as deprivation or pre-pandemic health. - -DesignRetrospective cohort study - -SettingPeople living in private households England - -Participants14,295,900 people aged 40-64 years (mean age 52 years, 51% female) who were alive on 24 January 2020, living in private households in England in 2019, were employed in 2011, and completed the 2011 census. - -Main outcome measuresCOVID-19 related death, assessed between 24 January 2020 and 28 December 2020. We estimated age-standardised mortality rates per 100,000 person-years at risk (ASMR) stratified by sex and occupations. To estimate the effect of occupation due to work-related exposures, we used Cox proportional hazard models to adjust for confounding (region, ethnicity, education), as well as non-workplace factors that are related to occupation. - -ResultsThere is wide variation between occupations in COVID-19 mortality. Several occupations, particularly those involving contact with patients or the public, show three-fold or four-fold risks. These elevated risks were greatly attenuated after adjustment for confounding and mediating non-workplace factors. For example, the hazard ratio (HR) for men working as taxi and cab drivers or chauffeurs changed from 4.60 [95%CI 3.62-5.84] to 1.47 [1.14-1.89] after adjustment. More generally, the overall HR for men working in essential occupations compared with men in non-essential occupations changed from 1.45 [1.34 - 1.56] to 1.22 [1.13 - 1.32] after adjustment. For most occupations, confounding and other mediating factors explained about 70% to 80% of the age-adjusted hazard ratios. - -ConclusionsWorking conditions are likely to play a role in COVID-19 mortality, particularly in occupations involving contact with COVID-19 patients or the public. However, there is also a substantial contribution from non-workplace factors, including regional factors, socio-demographic factors, and pre-pandemic health.",epidemiology,exact,100,100 medRxiv,10.1101/2021.05.13.21257144,2021-05-17,https://medrxiv.org/cgi/content/short/2021.05.13.21257144,REACT-1 round 11 report: low prevalence of SARS-CoV-2 infection in the community prior to the third step of the English roadmap out of lockdown,Steven Riley; David J Haw; Caroline E Walters; Howei Wang; Oliver Eales; Kylie E C Ainslie; Christina Atchison; Claudio Fronterre; Peter J Diggle; Andrew J Page; Alexander J Trotter; Thanh Le Viet; Nabil-Fareed Alikhan; Justin O'Grady; - The COVID-19 Genomics UK (COG-UK) Consortium; Deborah Ashby; Christl Donnelly; Graham Cooke; Wendy Barclay; Helen Ward; Ara Darzi; Paul Elliott,"Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands; Imperial College London; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; ; Imperial College London; University of Oxford; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London","BackgroundNational epidemic dynamics of SARS-CoV-2 infections are being driven by: the degree of recent indoor mixing (both social and workplace), vaccine coverage, intrinsic properties of the circulating lineages, and prior history of infection (via natural immunity). In England, infections, hospitalisations and deaths fell during the first two steps of the ""roadmap"" for exiting the third national lockdown. The third step of the roadmap in England takes place on 17 May 2021. MethodsWe report the most recent findings on community infections from the REal-time Assessment of Community Transmission-1 (REACT-1) study in which a swab is obtained from a representative cross-sectional sample of the population in England and tested using PCR. Round 11 of REACT-1 commenced self-administered swab-collection on 15 April 2021 and completed collections on 3 May 2021. We compare the results of REACT-1 round 11 to round 10, in which swabs were collected from 11 to 30 March 2021. @@ -1551,17 +1596,7 @@ MethodsThe Virus Watch study is an online, prospective, community cohort study f ResultsOut of 24,887 illnesses reported, 915 tested positive for SARS-CoV-2 and 186 likely infector-infectee pairs in 186 households amongst 372 individuals were identified. The mean COVID-19 serial interval was 3.18 (95%CI: 2.55 - 3.81) days. There was no significant difference (p=0.267) between the mean serial interval for Variants of Concern (VOC) hotspots (mean = 3.64 days, (95%CI: 2.55 - 4.73)) days and non-VOC hotspots, (mean = 2.72 days, (95%CI: 1.48 - 3.96)). ConclusionsOur estimates of the average serial interval of COVID-19 are broadly similar to estimates from previous studies and we find no evidence that B.1.1.7 is associated with a change in serial intervals. Alternative explanations such as increased viral load, longer period of viral shedding or improved receptor binding may instead explain the increased transmissibility and rapid spread and should undergo further investigation.",epidemiology,exact,100,100 -medRxiv,10.1101/2021.05.06.21256757,2021-05-14,https://medrxiv.org/cgi/content/short/2021.05.06.21256757,COVID-19 outbreak rates and infection attack rates associated with the workplace: a descriptive epidemiological study,Yiqun Chen; Timothy Aldridge; - UK COVID-19 National Core Studies Consortium; Claire F Ferraro; Fu-Meng Khaw,"Health and Safety Executive, UK; Health and Safety Executive, UK; ; National Infection Service, Public Health England, UK; Public Health England, UK","BackgroundA large number of COVID-19 outbreaks/clusters have been reported in a variety of workplace settings since the start of the pandemic. However, information on the rate of outbreak occurrences which helps to identify the type of workplaces that are more likely to experience an outbreak, or infection attack rates which estimates the potential extent of the virus transmission in an outbreak, has not yet been available to inform intervention strategies to limit transmission. - -ObjectivesTo link datasets on workplace settings and COVID-19 workplace outbreaks in England in order to: identify the geographical areas and workplace sectors with a high rate of outbreaks; and compare infection attack rates by workplace size and sector. - -MethodsWe analysed Public Health England (PHE) HPZone data on COVID-19 outbreaks in workplaces, covering the time period of 18 May - 12 October 2020. The workplaces analysed excluded care homes, hospitals and educational settings. We calculated the workplace outbreak rates by nine English regions, 151 Upper Tier Local Authorities (UTLAs) and twelve industrial sectors, using National Population Database (NPD) data extracted in May 2019 on the total number of the relevant workplaces as the denominator. We also calculated the infection attack rates by enterprise size (small, medium, large) and industrial sector, using PHE Situations of Interest (SOI) data on the number of test-confirmed COVID-19 cases in a workplace outbreak as the numerator, and using NPD data on the number employed in that workplace as the denominator. - -ResultsIn total, 1,317 confirmed workplace outbreaks were identified from HPZone data, of which 1,305 were available for estimation of outbreak rates. The average outbreak rate was 66 per 100,000 workplaces. Of the nine geographical regions in England, the North West had the highest workplace outbreak rate (155/100,000 workplaces), based on 351 outbreaks. Of the UTLAs, the highest workplace outbreak rate was Blackburn with Darwen (387/100,000 workplaces). The industrial sector with the highest workplace outbreak rate was manufacturers and packers of food (1,672/100,000), based on 117 outbreaks: this was consistent across seven of the regions. In addition, high outbreak rates in warehouses were observed in the East Midlands and the North West. - -In total, 390 outbreaks were identified from SOI data and 264 of them allowed for estimation of attack rates. The overall median attack rate was 3.4% of the employed persons with confirmed COVID-19 at a workplace with an outbreak. Most of these outbreaks (162) had an attack rate less than 6%. However, in a small number of outbreaks (57) the attack rate was over 15%. The attack rates increased as the size of the enterprise decreased. The highest attack rate was for outbreaks in close contact services (median 16.5%), which was followed by outbreaks in restaurants and catering (median 10.2%), and in manufacturers and packers of non-food products (median 6.7%). - -ConclusionsOur linked dataset analysis approach allows early identification of geographical regions and industrial sectors with higher rates of COVID-19 workplace outbreaks as well as estimation of attack rates by enterprise size and sector. This can be used to inform interventions to limit transmission of the virus. Our approach to analysing the workplace outbreak data can also be applied to calculation of outbreak rates and attack rates in other types of settings such as care homes, hospitals and educational settings.",epidemiology,exact,100,100 +medRxiv,10.1101/2021.05.08.21256867,2021-05-14,https://medrxiv.org/cgi/content/short/2021.05.08.21256867,SARS-CoV-2 lineage dynamics in England from January to March 2021 inferred from representative community samples,Oliver Eales; Andrew Page; Sonja N. Tang; Caroline E. Walters; Haowei Wang; David Haw; Alexander J. Trotter; Thanh Le Viet; Ebenezer Foster-Nyarko; Sophie Prosolek; Christina Atchinson; Deborah Ashby; Graham Cooke; Wendy Barclay; Christl A Donnelly; Justin O'Grady; Erik Volz; - The COVID-19 Genomics UK (COG-UK) Consortium; Ara Darzi; Helen Ward; Paul Elliott; Steven Riley,"School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Quadram Institute, Norwich, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Quadram Institute, Norwich, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; ; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc","Genomic surveillance for SARS-CoV-2 lineages informs our understanding of possible future changes in transmissibility and vaccine efficacy. However, small changes in the frequency of one lineage over another are often difficult to interpret because surveillance samples are obtained from a variety of sources. Here, we describe lineage dynamics and phylogenetic relationships using sequences obtained from a random community sample who provided a throat and nose swab for rt-PCR during the first three months of 2021 as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. Overall, diversity decreased during the first quarter of 2021, with the B.1.1.7 lineage (first identified in Kent) predominant, driven by a 0.3 unit higher reproduction number over the prior wild type. During January, positive samples were more likely B.1.1.7 in younger and middle-aged adults (aged 18 to 54) than in other age groups. Although individuals infected with the B.1.1.7 lineage were no more likely to report one or more classic COVID-19 symptoms compared to those infected with wild type, they were more likely to be antibody positive 6 weeks after infection. Viral load was higher in B.1.1.7 infection as measured by cycle threshold (Ct) values, but did not account for the increased rate of testing positive for antibodies. The presence of infections with non-imported B.1.351 lineage (first identified in South Africa) during January, but not during February or March, suggests initial establishment in the community followed by fade-out. However, this occurred during a period of stringent social distancing and targeted public health interventions and does not immediately imply similar lineages could not become established in the future. Sequence data from representative community surveys such as REACT-1 can augment routine genomic surveillance.",infectious diseases,exact,100,100 medRxiv,10.1101/2021.05.06.21256755,2021-05-13,https://medrxiv.org/cgi/content/short/2021.05.06.21256755,Clinical coding of long COVID in English primary care: a federated analysis of 58 million patient records in situ using OpenSAFELY,- The OpenSAFELY Collaborative; Alex J Walker; Brian MacKenna; Peter Inglesby; Christopher T Rentsch; Helen J Curtis; Caroline E Morton; Jessica Morley; Amir Mehrkar; Sebastian CJ Bacon; George Hickman; Christopher Bates; Richard Croker; David Evans; Tom Ward; Jonathan Cockburn; Simon Davy; Krishnan Bhaskaran; Anna Schultze; Elizabeth J Williamson; William J Hulme; Helen I McDonald; Laurie Tomlinson; Rohini Mathur; Rosalind M Eggo; Kevin Wing; Angel YS Wong; Harriet Forbes; John Tazare; John Parry; Frank Hester; Sam Harper; Shaun O'Hanlon; Alex Eavis; Richard Jarvis; Dima Avramov; Paul Griffiths; Aaron Fowles; Nasreen Parkes; Ian J Douglas; Stephen JW Evans; Liam Smeeth; Ben Goldacre,; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP; TPP; TPP; EMIS; EMIS; EMIS; EMIS; EMIS; EMIS; EMIS; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford,"BackgroundLong COVID is a term to describe new or persistent symptoms at least four weeks after onset of acute COVID-19. Clinical codes to describe this phenomenon were released in November 2020 in the UK, but it is not known how these codes have been used in practice. MethodsWorking on behalf of NHS England, we used OpenSAFELY data encompassing 96% of the English population. We measured the proportion of people with a recorded code for long COVID, overall and by demographic factors, electronic health record software system, and week. We also measured variation in recording amongst practices. @@ -1626,6 +1661,21 @@ Added value of this studyThe ATOMIC2 trial was uniquely-designed to assess azith Implications of all the available evidenceOur findings, taken together with existing data, suggest there is no evidence that azithromycin reduces hospitalisation, respiratory failure or death compared with standard care, either in early disease in the community, or those hospitalised with severe disease, or in those with moderate disease managed on an ambulatory pathway.",infectious diseases,exact,100,100 medRxiv,10.1101/2021.04.22.21255911,2021-04-23,https://medrxiv.org/cgi/content/short/2021.04.22.21255911,The impact of SARS-CoV-2 vaccines on antibody responses in the general population in the United Kingdom,Jia Wei; Nicole Stoesser; Philippa C Matthews; Ruth Studley; Iain Bell; John I Bell; John N Newton; Jeremy Farrar; Ian Diamond; Emma Rourke; Alison Howarth; Brian D Marsden; Sarah Hoosdally; E Yvonne Jones; David I Stuart; Derrick W Crook; Tim EA Peto; Koen B Pouwels; David W Eyre; A Sarah Walker; - COVID-19 Infection Survey team,"University of Oxford; University of Oxford; University of Oxford; Office for National Statistics, UK; Office for National Statistics, UK; University of Oxford; Public Health England; Wellcome Trust; Office for National Statistics, UK; Office for National Statistics, UK; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; ","Real-world data on antibody response post-vaccination in the general population are limited. 45,965 adults in the UKs national COVID-19 Infection Survey receiving Pfizer-BioNTech or Oxford-AstraZeneca vaccines had 111,360 anti-spike IgG measurements. Without prior infection, seroconversion rates and quantitative antibody levels post single dose were lower in older individuals, especially >60y. Two doses achieved high responses across all ages, particularly increasing seroconversion in older people, to similar levels to those achieved after prior infection followed by a single dose. Antibody levels rose more slowly and to lower levels with Oxford-AstraZeneca vs Pfizer-BioNTech, but waned following a single Pfizer-BioNTech dose. Latent class models identified four responder phenotypes: older people, males, and those having long-term health conditions were more commonly low responders. Where supplies are limited, vaccines should be prioritised for those not previously infected, and second doses to individuals >60y. Further data on the relationship between vaccine-mediated protection and antibody responses are needed.",infectious diseases,exact,100,100 +medRxiv,10.1101/2021.04.22.21255913,2021-04-23,https://medrxiv.org/cgi/content/short/2021.04.22.21255913,Impact of vaccination on SARS-CoV-2 cases in the community: a population-based study using the UK COVID-19 Infection Survey,Emma Pritchard; Philippa Matthews; Nicole Stoesser; David Eyre; Owen Gethings; Karina-Doris Vitha; Joel Jones; Thomas House; Harper VanSteenhouse; Iain Bell; John Bell; John Newton; Jeremy Farrar; Ian Diamond; Emma Rourke; Ruth Studley; Derrick W Crook; tim E peto; Ann Sarah Walker; Koen B Pouwels,"University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; University of Oxford; Office for National Statistics; University of Manchester; Glasgow Lighthouse Laboratory; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; Office for National Statistics,; Office for National Statistics; Office for National Statistics; NIHR Oxford Biomedical Research Centre; oxford university; University of Oxford; University of Oxford","ObjectivesTo assess the effectiveness of COVID-19 vaccination in preventing SARS-CoV-2 infection in the community. + +DesignProspective cohort study. + +SettingThe UK population-representative longitudinal COVID-19 Infection Survey. + +Participants373,402 participants aged [≥]16 years contributing 1,610,562 RT-PCR results from nose and throat swabs between 1 December 2020 and 3 April 2021. + +Main outcome measuresNew RT-PCR-positive episodes for SARS-CoV-2 overall, by self-reported symptoms, by cycle threshold (Ct) value (<30 versus [≥]30), and by gene positivity (compatible with the B.1.1.7 variant versus not). + +ResultsOdds of new SARS-CoV-2 infection were reduced 65% (95% CI 60 to 70%; P<0.001) in those [≥]21 days since first vaccination with no second dose versus unvaccinated individuals without evidence of prior infection (RT-PCR or antibody). In those vaccinated, the largest reduction in odds was seen post second dose (70%, 95% CI 62 to 77%; P<0.001).There was no evidence that these benefits varied between Oxford-AstraZeneca and Pfizer-BioNTech vaccines (P>0.9).There was no evidence of a difference in odds of new SARS-CoV-2 infection for individuals having received two vaccine doses and with evidence of prior infection but not vaccinated (P=0.89). Vaccination had a greater impact on reducing SARS-CoV-2 infections with evidence of high viral shedding Ct<30 (88% reduction after two doses; 95% CI 80 to 93%; P<0.001) and with self-reported symptoms (90% reduction after two doses; 95% CI 82 to 94%; P<0.001); effects were similar for different gene positivity patterns. + +ConclusionVaccination with a single dose of Oxford-AstraZeneca or Pfizer-BioNTech vaccines, or two doses of Pfizer-BioNTech, significantly reduced new SARS-CoV-2 infections in this large community surveillance study. Greater reductions in symptomatic infections and/or infections with a higher viral burden are reflected in reduced rates of hospitalisations/deaths, but highlight the potential for limited ongoing transmission from asymptomatic infections in vaccinated individuals. + +RegistrationThe study is registered with the ISRCTN Registry, ISRCTN21086382.",infectious diseases,exact,100,100 medRxiv,10.1101/2021.04.08.21255099,2021-04-14,https://medrxiv.org/cgi/content/short/2021.04.08.21255099,Occupational risks of COVID-19 in NHS workers in England,Diana van der Plaat; Ira Madan; David Coggon; Martie van Tongeren; Rhiannon Edge; Rupert Muiry; Vaughan Parsons; Paul Cullinan,Imperial College London; Guy's and St Thomas' NHS Foundation Trust; Southampton General Hospital; University of Manchester; Lancaster University; Guy's and St Thomas NHS Foundation Trust; Guy's and St Thomas NHS Foundation Trust; Imperial College London,"ObjectiveTo quantify occupational risks of Covid-19 among healthcare staff during the first wave of the pandemic in England MethodsUsing pseudonymised data on 902,813 individuals continuously employed by 191 National Health Service trusts during 1.1.19 to 31.7.20, we explored demographic and occupational risk factors for sickness absence ascribed to Covid-19 during 9.3.20 to 31.7.20 (n = 92,880). We estimated odds ratios (ORs) by multivariable logistic regression. @@ -1724,7 +1774,28 @@ MethodsWe used Cox proportional hazards models to estimate hazard ratios (HRs) f ResultsWe observed a small proportion of care home residents with positive PCR tests following vaccination 1.05% (N=148), with 90% of infections occurring within 28-days. For the 7-day landmark analysis we found a reduced risk of SARS-CoV-2 infection for vaccinated individuals who had a previous infection; HR (95% confidence interval) 0.54 (0.30,0.95), and an increased HR for those receiving the Pfizer-BioNTECH vaccine compared to the Oxford-AstraZeneca; 3.83 (2.45,5.98). For the 21-day landmark analysis we observed high HRs for individuals with low and intermediate frailty compared to those without; 4.59 (1.23,17.12) and 4.85 (1.68,14.04) respectively. ConclusionsIncreased risk of infection after 21-days was associated with frailty. We found most infections occurred within 28-days of vaccination, suggesting extra precautions to reduce transmission risk should be taken in this time frame.",geriatric medicine,exact,100,100 +medRxiv,10.1101/2021.03.16.21253377,2021-03-24,https://medrxiv.org/cgi/content/short/2021.03.16.21253377,First and second SARS-CoV-2 waves in inner London: A comparison of admission characteristics and the effects of the B.1.1.7 variant,Luke B Snell; Wenjuan Wang; Adela Alcolea-Medina; Themoula Charalampous; Gaia Nebbia; Rahul Batra; Leonardo de Jongh; Finola Higgins; Yanzhong Wang; Jonathan D Edgeworth; Vasa Curcin,"King's College London; School of Population Health and Environmental Sciences, King's College London, London, UK; Viapath, London, UK; Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK; Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK; Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK; NIHR Biomedical Research Centre, Guy's and St Thomas' NHS Foundation Trust; NIHR Biomedical Research Centre, Guy's and St Thomas' NHS Foundation Trust; School of Population Health and Environmental Sciences, King's College London, London, UK; Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK; School of Population Health and Environmental Sciences, King's College London, London, UK","IntroductionA second wave of SARS-CoV-2 infection spread across the UK in 2020 linked with emergence of the more transmissible B.1.1.7 variant. The emergence of new variants, particularly during relaxation of social distancing policies and implementation of mass vaccination, highlights the need for real-time integration of detailed patient clinical data alongside pathogen genomic data. We linked clinical data with viral genome sequence data to compare cases admitted during the first and second waves of SARS-CoV-2 infection. + +MethodsClinical, laboratory and demographic data from five electronic health record (EHR) systems was collected for all cases with a positive SARS-CoV-2 RNA test between March 13th 2020 and February 17th 2021. SARS-CoV-2 viral sequencing was performed using Oxford Nanopore Technology. Descriptive data are presented comparing cases between waves, and between cases of B.1.1.7 and non-B.1.1.7 variants. + +ResultsThere were 5810 SARS-CoV-2 RNA positive cases comprising inpatients (n=2341), healthcare workers (n=1549), outpatients (n=874), emergency department (ED) attenders not subsequently admitted (n=532), inter-hospital transfers (n=281) and nosocomial cases (n=233). There were two dominant waves of hospital admissions, with wave one starting from March 13th (n=838) and wave two from October 20th (n=1503), both with a temporally aligned rise in nosocomial cases (n=96 in wave one, n=137 in wave two). 1470 SARS-CoV-2 isolates were successfully sequenced, including 216/838 (26%) admitted cases from wave one, 472/1503 (31%) admitted cases in wave two and 121/233 (52%) nosocomial cases. The first B.1.1.7 variant was identified on 15th November 2020 and increased rapidly such that it comprised 400/472 (85%) of sequenced isolates from admitted cases in wave two. Females made up a larger proportion of admitted cases in wave two (47.3% vs 41.8%, p=0.011), and in those infected with the B.1.1.7 variant compared to non-B.1.1.7 variants (48.0% vs 41.8%, p=0.042). A diagnosis of frailty was less common in wave two (11.5% v 22.8%, p<0.001) and in the group infected with B.1.1.7 (14.5% v 22.4%, p=0.001). There was no difference in severity on admission between waves, as measured by hypoxia at admission (wave one: 64.3% vs wave two: 65.5%, p=0.67). However, a higher proportion of cases infected with the B.1.1.7 variant were hypoxic on admission compared to other variants (70.0% vs 62.5%, p=0.029). + +ConclusionsAutomated EHR data extraction linked with SARS-CoV-2 genome sequence data provides valuable insight into the evolving characteristics of cases admitted to hospital with COVID-19. The proportion of cases with hypoxia on admission was greater in those infected with the B.1.1.7 variant, which supports evidence the B.1.1.7 variant is associated with more severe disease. The number of nosocomial cases was similar in both waves despite introduction of many infection control interventions before wave two, an observation requiring further investigation.",infectious diseases,exact,100,100 +medRxiv,10.1101/2021.03.11.21253275,2021-03-21,https://medrxiv.org/cgi/content/short/2021.03.11.21253275,Effect of vaccination on transmission of COVID-19: an observational study in healthcare workers and their households,Anoop Shah; Ciara Gribben; Jennifer Bishop; Peter Hanlon; David Caldwell; Rachael Wood; Martin Reid; Jim McMenamin; David Goldberg; Diane Stockton; Sharon Hutchinson; Chris Robertson; Paul M McKeigue; Helen M Colhoun; David McAllister,London School of Hygiene and Tropical Medicine; Public Health Scotland; Public Health Scotland; University of Glasgow; Public Health Scotland; PublicHealth Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; University of Glasgow,"BackgroundThe effect of vaccination for COVID-19 on onward transmission is unknown. + +MethodsA national record linkage study determined documented COVID-19 cases and hospitalisations in unvaccinated household members of vaccinated and unvaccinated healthcare workers from 8th December 2020 to 3rd March 2021. The primary endpoint was COVID-19 14 days following the first dose. + +ResultsThe cohort comprised of 194,362 household members (mean age 31{middle dot}1 {+/-} 20{middle dot}9 years) and 144,525 healthcare workers (mean age 44{middle dot}4 {+/-} 11{middle dot}4 years). 113,253 (78{middle dot}3%) of healthcare workers received at least one dose of the BNT162b2 mRNA or ChAdOx1 nCoV-19 vaccine and 36,227 (25{middle dot}1%) received a second dose. There were 3,123 and 4,343 documented COVID-19 cases and 175 and 177 COVID-19 hospitalisations in household members of healthcare workers and healthcare workers respectively. Household members of vaccinated healthcare workers had a lower risk of COVID-19 case compared to household members of unvaccinated healthcare worker (rate per 100 person-years 9{middle dot}40 versus 5{middle dot}93; HR 0{middle dot}70, 95% confidence interval [CI] 0{middle dot}63 to 0{middle dot}78). The effect size for COVID-19 hospitalisation was similar, with the confidence interval crossing the null (HR 0{middle dot}77 [95% CI 0{middle dot}53 to 1{middle dot}10]). The rate per 100 person years was lower in vaccinated compared to unvaccinated healthcare workers for documented (20{middle dot}13 versus 8{middle dot}51; HR 0{middle dot}45 [95% CI 0{middle dot}42 to 0{middle dot}49]) and hospitalized COVID-19 (0{middle dot}97 versus 0{middle dot}14; HR 0{middle dot}16 [95% CI 0{middle dot}09 to 0{middle dot}27]). Compared to the period before the first dose, the risk of documented COVID-19 case was lower at [≥] 14 days after the second dose for household members (HR 0{middle dot}46 [95% CI 0{middle dot}30to 0{middle dot}70]) and healthcare workers (HR 0{middle dot}08 [95% CI 0{middle dot}04 to 0{middle dot}17]). + +InterpretationVaccination of health care workers was associated with a substantial reduction in COVID-19 cases in household contacts consistent with an effect of vaccination on transmission.",public and global health,exact,100,100 medRxiv,10.1101/2021.03.17.21253853,2021-03-20,https://medrxiv.org/cgi/content/short/2021.03.17.21253853,"Modelling the impact of rapid tests, tracing and distancing in lower-income countries suggest optimal policies varies with rural-urban settings",Xilin Jiang; Wenfeng Gong; Zlatina Dobreva; Ya Gao; Matthew Quaife; Christophe Fraser; Chris Holmes,"University of Oxford; Bill & Melinda Gates Foundation; Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine, London, UK; Department of International Health, Johns Hopkins University; Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine, London, UK; University of Oxford; University of Oxford","Low- and middle-income countries (LMICs) remain of high potential for hotspots for COVID-19 deaths and emerging variants given the inequality of vaccine distribution and their vulnerable healthcare systems. We aim to evaluate containment strategies that are sustainable and effective for LMICs. We constructed synthetic populations with varying contact and household structures to capture LMIC demographic characteristics that vary across communities. Using an agent- based model, we explored the optimal containment strategies for rural and urban communities by designing and simulating setting-specific strategies that deploy rapid diagnostic tests, symptom screening, contact tracing and physical distancing. In low-density rural communities, we found implementing either high quality (sensitivity > 50%) antigen rapid diagnostic tests or moderate physical distancing could contain the transmission. In urban communities, we demonstrated that both physical distancing and case finding are essential for containing COVID-19 (average infection rate < 10%). In high density communities that resemble slums and squatter settlements, physical distancing is less effective compared to rural and urban communities. Lastly, we demonstrated contact tracing is essential for effective containment. Our findings suggested that rapid diagnostic tests could be prioritised for control and monitor COVID-19 transmission and highlighted that contact survey data could guide strategy design to save resources for LMICs. An accompanying open source R package is available for simulating COVID-19 transmission based on contact network models.",epidemiology,exact,100,100 +medRxiv,10.1101/2021.03.18.21253443,2021-03-20,https://medrxiv.org/cgi/content/short/2021.03.18.21253443,Intensity of COVID-19 in care homes following Hospital Discharge in the early stages of the UK epidemic,Joe Hollinghurst; Laura North; Chris Emmerson; Ashley Akbari; Fatemeh Torabi; Ronan A Lyons; Alan G Hawkes; Ed Bennett; Mike B Gravenor; Richard Fry,Swansea University; Swansea University; Public Health Wales; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University,"BackgroundA defining feature of the COVID-19 pandemic in many countries was the tragic extent to which care home residents were affected, and the difficulty preventing introduction and subsequent spread of infection. Management of risk in care homes requires good evidence on the most important transmission pathways. One hypothesised route at the start of the pandemic, prior to widespread testing, was transfer of patients from hospitals, which were experiencing high levels of nosocomial events. + +MethodsWe tested the hypothesis that hospital discharge events increased the intensity of care home cases using a national individually linked health record cohort in Wales, UK. We monitored 186,772 hospital discharge events over the period March to July 2020, tracking individuals to 923 care homes and recording the daily case rate in the homes populated by 15,772 residents. We estimated the risk of an increase in cases rates following exposure to a hospital discharge using multi-level hierarchical logistic regression, and a novel stochastic Hawkes process outbreak model. + +FindingsIn regression analysis, after adjusting for care home size, we found no significant association between hospital discharge and subsequent increases in care home case numbers (odds ratio: 0.99, 95% CI 0.82, 1.90). Risk factors for increased cases included care home size, care home resident density, and provision of nursing care. Using our outbreak model, we found a significant effect of hospital discharge on the subsequent intensity of cases. However, the effect was small, and considerably less than the effect of care home size, suggesting the highest risk of introduction came from interaction with the community. We estimated approximately 1.8% of hospital discharged patients may have been infected. + +InterpretationThere is growing evidence in the UK that the risk of transfer of COVID-19 from the high-risk hospital setting to the high-risk care home setting during the early stages of the pandemic was relatively small. Although access to testing was limited to initial symptomatic cases in each care home at this time, our results suggest that reduced numbers of discharges, selection of patients, and action taken within care homes following transfer all may have contributed to mitigation. The precise key transmission routes from the community remain to be quantified.",health informatics,exact,100,100 medRxiv,10.1101/2021.03.04.21252931,2021-03-08,https://medrxiv.org/cgi/content/short/2021.03.04.21252931,A common TMPRSS2 variant protects against severe COVID-19,"Alessia David; Nicholas Parkinson; Thomas P Peacock; Erola Pairo-Castineira; Tarun Khanna; Aurelie Cobat; Albert Tenesa; Vanessa Sancho-Shimizu; - GenOMICC Investigators, ISARIC4C Investigators; Jean-Laurent Casanova; Laurent Abel; Wendy S Barclay; J Kenneth Baillie; Michael J.E. Sternberg","Centre for Integrative System Biology and Bioinformatics, Imperial College London, London; Roslin Institute, University of Edinburgh; Department of Infectious Diseases, Imperial College London; Roslin Institute, University of Edinburgh; Centre for Integrative System Biology and Bioinformatics, Imperial College London; Laboratory of Human Genetics of Infectious Diseases, INSERM; Roslin Institute, University of Edinburgh; Department of Paediatric Infectious Diseases & Virology, Imperial College London; ; St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University; Laboratory of Human Genetics of Infectious Diseases, INSERM; Department of Infectious Diseases, Imperial College London; Roslin Institute, University of Edinburgh; Centre for Integrative System Biology and Bioinformatics, Imperial College London","Infection with SARS-CoV-2 has a wide range of clinical presentations, from asymptomatic to life-threatening. Old age is the strongest factor associated with increased COVID19-related mortality, followed by sex and pre-existing conditions. The importance of genetic and immunological factors on COVID19 outcome is also starting to emerge, as demonstrated by population studies and the discovery of damaging variants in genes controlling type I IFN immunity and of autoantibodies that neutralize type I IFNs. The human protein transmembrane protease serine type 2 (TMPRSS2) plays a key role in SARS-CoV-2 infection, as it is required to activate the virus spike protein, facilitating entry into target cells. We focused on the only common TMPRSS2 non-synonymous variant predicted to be damaging (rs12329760), which has a minor allele frequency of [~]25% in the population. In a large population of SARS-CoV-2 positive patients, we show that this variant is associated with a reduced likelihood of developing severe COVID19 (OR 0.87, 95%CI:0.79-0.97, p=0.01). This association was stronger in homozygous individuals when compared to the general population (OR 0.65, 95%CI:0.50-0.84, p=1.3x10-3). We demonstrate in vitro that this variant, which causes the amino acid substitution valine to methionine, impacts the catalytic activity of TMPRSS2 and is less able to support SARS-CoV-2 spike-mediated entry into cells. TMPRSS2 rs12329760 is a common variant associated with a significantly decreased risk of severe COVID19. Further studies are needed to assess the expression of the TMPRSS2 across different age groups. Moreover, our results identify TMPRSS2 as a promising drug target, with a potential role for camostat mesilate, a drug approved for the treatment of chronic pancreatitis and postoperative reflux esophagitis, in the treatment of COVID19. Clinical trials are needed to confirm this.",genetic and genomic medicine,exact,100,100 @@ -2017,15 +2088,6 @@ bioRxiv,10.1101/2020.12.23.424229,2020-12-25,https://biorxiv.org/cgi/content/sho medRxiv,10.1101/2020.12.18.20248477,2020-12-20,https://medrxiv.org/cgi/content/short/2020.12.18.20248477,Face covering adherence is positively associated with better mental health and wellbeing: a longitudinal analysis of the CovidLife surveys,Drew M Altschul; Chloe Fawns-Ritchie; Alex Kwong; Louise Hartley; Clifford Nangle; Rachel Edwards; Rebecca Dawson; Christie Levein; Archie Campbell; Robin Flaig; Andrew McIntosh; Ian Deary; Riccardo Marioni; Caroline Hayward; Cathie Sudlow; Elaine Douglas; David Bell; David Porteous,The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; The University of Edinburgh; University of Stirling; University of Stirling; The University of Edinburgh,"Face masks or coverings are effective at reducing airborne infection rates, yet pandemic mitigation measures, including wearing face coverings, have been suggested to contribute to reductions in quality of life and poorer mental health. Longitudinal analyses of more than 11,000 participants across the UK found no association between lower adherence to face covering guidelines and poorer mental health. The opposite appears to be true. Even after controlling for behavioral, social, and psychological confounds, including measures of pre-pandemic mental health, individuals who wore face coverings ""most of the time"" or ""always"" had better mental health and wellbeing than those who did not. These results suggest that wearing face coverings more often will not negatively impact mental health.",psychiatry and clinical psychology,exact,100,100 medRxiv,10.1101/2020.12.10.20247155,2020-12-14,https://medrxiv.org/cgi/content/short/2020.12.10.20247155,Self-harm presentations to Emergency Departments and Place of Safety during the first wave of the UK COVID-19 pandemic: South London and Maudsley data on service use from February to June 2020.,Eleanor Nuzum; Evangelia Martin; Gemma Morgan; Rina Dutta; Christoph Mueller; Catherine Polling; Megan Pritchard; Sumithra Velupillai; Robert Stewart,South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; South London and Maudsley NHS Foundation Trust; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London,"The lockdown and social distancing policy imposed due to the COVID-19 pandemic has had a substantial impact on both mental health service delivery, and the ways in which people are accessing these services. Previous reports from the South London and Maudsley NHS Trust (SLaM; a large mental health service provider for around 1.2m residents in South London) have highlighted increased use of virtual contacts by mental health teams, with dropping numbers of face-to-face contacts over the first wave of the pandemic. There has been concern that the impact of the COVID-19 pandemic would lead to higher mental health emergencies, particularly instances of self-harm. However, with people advised to stay at home during the first wave lockdown, it is as yet unclear whether this impacted mental health service presentations. Taking advantage of SLaMs Clinical Records Interactive Search (CRIS) data resource with daily updates of information from its electronic mental health records, this paper describes overall presentations to Emergency Department (ED) mental health liaison teams, and those with self-harm. The paper focussed on three periods: i) a pre-lockdown period 1st February to 15th March, ii) a lockdown period 16th March to 10th May and iii) a post-lockdown period 11th May to 28th June. In summary, all attendances to EDs for mental health support decreased during the lockdown period, including those with self-harm. All types of self-harm decreased during lockdown, with self-poisoning remaining the most common. Attendances to EDs for mental health support increased post-lockdown, although were only just approaching pre-lockdown levels by the end of June 2020.",psychiatry and clinical psychology,exact,100,100 medRxiv,10.1101/2020.12.07.20245183,2020-12-07,https://medrxiv.org/cgi/content/short/2020.12.07.20245183,"Indicators of COVID-19 status in a cohort study of university staff and post-graduate research students, including results from home antibody testing",Katrina A S Davis; Ewan Carr; Daniel Leightley; Valentina Vitiello; Gabriella Bergin Cartwright; Grace Lavelle; Alice Wickersham; Michael H Malim; Carolin Oetzmann; Catherine Polling; Sharon A.M. Stevelink; Reza Razavi; Matthew Hotopf; - KCL-CHECK research team,"KCL Institute of Psychiatry, Psychology and Neuroscience; KCL Institute of Psychiatry Psychology and Neuroscience; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; ","Background Definitive diagnosis of COVID-19 requires resources frequently restricted to the severely ill. Cohort studies must rely on surrogate indicators to define cases of COVID-19 in the community. We describe the prevalence and overlap of potential indicators including self-reported symptoms, suspicion, and routine test results, plus home antibody testing. Methods An occupational cohort of 2807 staff and postgraduate students at a large London university. Repeated surveys covering March to June 2020. Antibody test results from 'lateral flow' IgG/IgM cassettes in June 2020. Results 1882 participants had valid antibody test results, and 124 (7%) were positive. Core symptoms of COVID-19 were common (770 participants positive, 41%), although fewer met criteria on a symptom algorithm (n=297, 16%). Suspicion of COVID-19 (n=509, 27%) was much higher than positive external tests (n=39, 2%). Positive antibody tests were rare in people who had no suspicion (n=4, 1%) or no core symptoms (n=10, 2%). In those who reported external antibody tests, 15% were positive on the study antibody test, compared with 24% on earlier external antibody tests. Discussion Our results demonstrate the agreement between different COVID indicators. Antibody testing using lateral flow devices at home can detect asymptomatic cases and provide greater certainty to self-report; but due to weak and waning antibody responses to mild infection, may under-ascertain. Multiple indicators used in combination can provide a more complete story than one used alone. Cohort studies need to consider how they deal with different, sometimes conflicting, indicators of COVID-19 illness to understand its long-term outcomes.",epidemiology,exact,100,100 -medRxiv,10.1101/2020.12.03.20243535,2020-12-04,https://medrxiv.org/cgi/content/short/2020.12.03.20243535,OpenSAFELY: impact of national guidance on switching from warfarin to direct oral anticoagulants (DOACs) in early phase of COVID-19 pandemic in England,Helen J Curtis; Brian MacKenna; Alex J Walker; Richard Croker; Amir Mehrkar; Caroline E Morton; Seb Bacon; George Hickman; Peter Inglesby; Chris Bates; David Evans; Tom Ward; Jonathan Cockburn; Simon Davy; Krishnan Bhaskaran; Anna Schultze; Christopher T Rentsch; Elizabeth Williamson; William Hulme; Helen I McDonald; Laurie Tomlinson; Rohini Mathur; Henry Drysdale; Rosalind M Eggo; Kevin Wing; Angel Wong; Harriet Forbes; John Parry; Frank Hester; Sam Harper; Stephen JW Evans; Ian J Douglas; Liam Smeeth; Ben Goldacre,University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; TPP; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP; TPP; TPP; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford,"BackgroundEarly in the COVID-19 pandemic the NHS recommended that appropriate patients anticoagulated with warfarin should be switched to direct acting oral anticoagulants (DOACs), requiring less frequent blood testing. Subsequently, a national safety alert was issued regarding patients being inappropriately co-prescribed two anticoagulants following a medication change, and associated monitoring. - -ObjectiveTo describe which people were switched from warfarin to DOACs; identify potentially unsafe co-prescribing of anticoagulants; and assess whether abnormal clotting results have become more frequent during the pandemic. - -MethodsWorking on behalf of NHS England we conducted a population cohort based study using routine clinical data from >17 million adults in England. - -Results20,000 of 164,000 warfarin patients (12.2%) switched to DOACs between March and May 2020, most commonly to edoxaban and apixaban. Factors associated with switching included: older age, recent renal function test, higher number of recent INR tests recorded, atrial fibrillation diagnosis and care home residency. There was a sharp rise in co-prescribing of warfarin and DOACs from typically 50-100 per month to 246 in April 2020, 0.06% of all people receiving a DOAC or warfarin. INR testing fell by 14% to 506.8 patients tested per 1000 warfarin patients each month. We observed a very small increase in elevated INRs (n=470) during April compared with January (n=420). - -ConclusionsIncreased switching of anticoagulants from warfarin to DOACs was observed at the outset of the COVID-19 pandemic in England following national guidance. There was a small but substantial number of people co-prescribed warfarin and DOACs during this period. Despite a national safety alert on the issue, a widespread rise in elevated INR test results was not found. Primary care has responded rapidly to changes in patient care during the COVID-19 pandemic.",cardiovascular medicine,exact,100,100 medRxiv,10.1101/2020.11.27.20238147,2020-12-02,https://medrxiv.org/cgi/content/short/2020.11.27.20238147,"Ethnicity, Household Composition and COVID-19 Mortality: A National Linked Data Study",Vahe Nafilyan; Nazrul Islam; Daniel Ayoubkhani; Clare Gilles; Srinivasa Vittal Katikireddi; Rohini Mathur; Annabel Summerfield; Karen Tingay; Miqdad Asaria; Ann John; Peter Goldblatt; Amitava Banerjee; Myer Glickman; Kamlesh Khunti,"Office for National Statistics; Nuffield Department of Population Health, Big Data Institute, University of Oxford; Office for National Statistics; Diabetes Research Centre, University of Leicester; University of Glasgow; London School of Hygiene and Tropical Medicine; Office for National Statistics; Office for National Statistics; London School of Economics and Political Sciences; Swansea University; UCL Institute of Health Equity, University College London; University College London; Office for National Statistics; Diabetes Research Centre, University of Leicester","BackgroundEthnic minorities have experienced disproportionate COVID-19 mortality rates. We estimated associations between household composition and COVID-19 mortality in older adults ([≥] 65 years) using a newly linked census-based dataset, and investigated whether living in a multi-generational household explained some of the elevated COVID-19 mortality amongst ethnic minority groups. MethodsUsing retrospective data from the 2011 Census linked to Hospital Episode Statistics (2017-2019) and death registration data (up to 27th July 2020), we followed adults aged 65 years or over living in private households in England from 2 March 2020 until 27 July 2020 (n=10,078,568). We estimated hazard ratios (HRs) for COVID-19 death for people living in a multi-generational household compared with people living with another older adult, adjusting for geographical factors, socio-economic characteristics and pre-pandemic health. We conducted a causal mediation analysis to estimate the proportion of ethnic inequalities explained by living in a multi-generational household. @@ -2356,7 +2418,6 @@ MethodsWe developed a simple, interactive tool to assess the impact of different ResultsWith sensitivity of 80%, infection prevalence of 1 in 2,000, and specificity 99.9% on all tests, PPV in the tested population of 100,000 will be only 29% with one test, increasing to > 99.5% (100% when rounded to the nearest %) with repeat testing in strategies 2 or 3. More realistically, if specificity is 95% for the first and 99.9% for subsequent tests, single test PPV will be only 1%, increasing to 86% with repeat testing in strategy 2, or 79% with strategy 3 (albeit with 6 fewer false negatives than strategy 2). In the whole population, or in particular individuals, PPV increases as infection becomes more common in the population but falls to unacceptably low levels with lower test specificity. ConclusionTo avoid multiple unnecessary restrictions on whole populations, and in particular individuals, from widespread population testing for SARS-CoV-2, the crucial roles of extremely high test specificity and of confirmatory testing must be fully appreciated and incorporated into policy decisions.",epidemiology,exact,100,100 -medRxiv,10.1101/2020.08.17.20175117,2020-08-21,https://medrxiv.org/cgi/content/short/2020.08.17.20175117,Real-time spatial health surveillance: mapping the UK COVID-19 epidemic,Richard Fry; Joe Hollinghurst; Helen R Stagg; Daniel A Thompson; Claudio Fronterre; Chris Orton; Ronan A Lyons; David V Ford; Aziz Sheikh; Peter J Diggle,Swansea University; Swansea University; Edinburgh University; Swansea University; Lancaster University; Swansea University; Swansea University; Swansea University; Edinburgh University; Lancaster University,"The COVID-19 pandemic has highlighted the need for robust data linkage systems and methods for identifying outbreaks of disease in near real-time. Using self-reported app data and the Secure Anonymised Information Linkage (SAIL) Databank, we demonstrate the use of sophisticated spatial modelling for near-real-time prediction of COVID-19 prevalence at small-area resolution to inform strategic government policy areas. A pre-requisite to an effective control strategy is that predictions need to be accompanied by estimates of their precision, to guard against over-reaction to potentially spurious features of best guess predictions. In the UK, important emerging risk-factors such as social deprivation or ethnicity vary over small distances, hence risk needs to be modelled at fine spatial resolution to avoid aggregation bias. We demonstrate that existing geospatial statistical methods originally developed for global health applications are well-suited to this task and can be used in an anonymised databank environment, thus preserving the privacy of the individuals who contribute their data.",public and global health,exact,100,100 medRxiv,10.1101/2020.08.12.20173690,2020-08-14,https://medrxiv.org/cgi/content/short/2020.08.12.20173690,"Antibody prevalence for SARS-CoV-2 in England following first peak of the pandemic: REACT2 study in 100,000 adults",Helen Ward; Christina J Atchison; Matthew Whitaker; Kylie E. C. Ainslie; Joshua Elliott; Lucy C Okell; Rozlyn Redd; Deborah Ashby; Christl A. Donnelly; Wendy Barclay; Ara Darzi; Graham Cooke; Steven Riley; Paul Elliott,"Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Imperial College London; Dept Inf Dis Epi, Imperial College; Imperial College London","BackgroundEngland, UK has experienced a large outbreak of SARS-CoV-2 infection. As in USA and elsewhere, disadvantaged communities have been disproportionately affected. MethodsNational REal-time Assessment of Community Transmission-2 (REACT-2) prevalence study using a self-administered lateral flow immunoassay (LFIA) test for IgG among a random population sample of 100,000 adults over 18 years in England, 20 June to 13 July 2020. @@ -2804,6 +2865,21 @@ MethodsPatients with confirmed SARS-CoV-2 infection requiring admission to Unive ResultsAll patients admitted to UHB with COVID-19 during the study period were included (2217 in total). Fifty-eight percent were male, 69.5% White and the majority (80.2%) had co-morbidities. Eighteen and a half percent were of South Asian ethnicity, and these patients were more likely to be younger, have no co-morbidities but twice the prevalence of diabetes than White patients. SAR and SMR suggested more admissions and deaths in South Asian patients than would be predicted and they were more likely to present with severe disease despite no delay in presentation since symptom onset. South Asian ethnicity was associated with an increased risk of death; both by Cox regression (Hazard Ratio 1.4 (95%CI 1.2-1.8) after adjusting for age, sex, deprivation and comorbidities and by propensity score matching, matching for the same factors but categorising ethnicity into South Asian or not (Hazard ratio 1.3 (1.0-1.6)). ConclusionsThose of South Asian ethnicity appear at risk of worse COVID-19 outcomes, further studies need to establish the underlying mechanistic pathways.",infectious diseases,exact,100,100 +medRxiv,10.1101/2020.05.06.20092999,2020-05-07,https://medrxiv.org/cgi/content/short/2020.05.06.20092999,OpenSAFELY: factors associated with COVID-19-related hospital death in the linked electronic health records of 17 million adult NHS patients.,- The OpenSAFELY Collaborative; Elizabeth Williamson; Alex J Walker; Krishnan J Bhaskaran; Seb Bacon; Chris Bates; Caroline E Morton; Helen J Curtis; Amir Mehrkar; David Evans; Peter Inglesby; Jonathan Cockburn; Helen I Mcdonald; Brian MacKenna; Laurie Tomlinson; Ian J Douglas; Christopher T Rentsch; Rohini Mathur; Angel Wong; Richard Grieve; David Harrison; Harriet Forbes; Anna Schultze; Richard T Croker; John Parry; Frank Hester; Sam Harper; Rafael Perera; Stephen Evans; Liam Smeeth; Ben Goldacre,; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; TPP; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; ICNARC; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; TPP; TPP; TPP; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford,"BackgroundEstablishing who is at risk from a novel rapidly arising cause of death, and why, requires a new approach to epidemiological research with very large datasets and timely data. Working on behalf of NHS England we therefore set out to deliver a secure and pseudonymised analytics platform inside the data centre of a major primary care electronic health records vendor establishing coverage across detailed primary care records for a substantial proportion of all patients in England. The following results are preliminary. + +Data sourcesPrimary care electronic health records managed by the electronic health record vendor TPP, pseudonymously linked to patient-level data from the COVID-19 Patient Notification System (CPNS) for death of hospital inpatients with confirmed COVID-19, using the new OpenSAFELY platform. + +Population17,425,445 adults. + +Time period1st Feb 2020 to 25th April 2020. + +Primary outcomeDeath in hospital among people with confirmed COVID-19. + +MethodsCohort study analysed by Cox-regression to generate hazard ratios: age and sex adjusted, and multiply adjusted for co-variates selected prospectively on the basis of clinical interest and prior findings. + +ResultsThere were 5683 deaths attributed to COVID-19. In summary after full adjustment, death from COVID-19 was strongly associated with: being male (hazard ratio 1.99, 95%CI 1.88-2.10); older age and deprivation (both with a strong gradient); uncontrolled diabetes (HR 2.36 95% CI 2.18-2.56); severe asthma (HR 1.25 CI 1.08-1.44); and various other prior medical conditions. Compared to people with ethnicity recorded as white, black people were at higher risk of death, with only partial attenuation in hazard ratios from the fully adjusted model (age-sex adjusted HR 2.17 95% CI 1.84-2.57; fully adjusted HR 1.71 95% CI 1.44-2.02); with similar findings for Asian people (age-sex adjusted HR 1.95 95% CI 1.73-2.18; fully adjusted HR 1.62 95% CI 1.431.82). + +ConclusionsWe have quantified a range of clinical risk factors for death from COVID-19, some of which were not previously well characterised, in the largest cohort study conducted by any country to date. People from Asian and black groups are at markedly increased risk of in-hospital death from COVID-19, and contrary to some prior speculation this is only partially attributable to pre-existing clinical risk factors or deprivation; further research into the drivers of this association is therefore urgently required. Deprivation is also a major risk factor with, again, little of the excess risk explained by co-morbidity or other risk factors. The findings for clinical risk factors are concordant with policies in the UK for protecting those at highest risk. Our OpenSAFELY platform is rapidly adding further NHS patients records; we will update and extend these results regularly.",epidemiology,exact,100,100 medRxiv,10.1101/2020.05.02.20078642,2020-05-06,https://medrxiv.org/cgi/content/short/2020.05.02.20078642,Impact of ethnicity on outcome of severe COVID-19 infection. Data from an ethnically diverse UK tertiary centre,James T Teo; Daniel Bean; Rebecca Bendayan; Richard Dobson; Ajay Shah,Kings College Hospital NHS Foundation Trust; King's College London; King's College London; Kings College London; King's College London,"During the current COVID-19 pandemic, it has been suggested that BAME background patients may be disproportionately affected compared to White but few detailed data are available. We took advantage of near real-time hospital data access and analysis pipelines to look at the impact of ethnicity in 1200 consecutive patients admitted between 1st March 2020 and 12th May 2020 to Kings College Hospital NHS Trust in London (UK). Our key findings are firstly that BAME patients are significantly younger and have different co-morbidity profiles than White individuals. Secondly, there is no significant independent effect of ethnicity on severe outcomes (death or ITU admission) within 14-days of symptom onset, after adjustment for age, sex and comorbidities.",intensive care and critical care medicine,exact,100,100 @@ -2829,13 +2905,6 @@ C_LIO_LIRisk stratification was improved by the addition of routinely-measured b C_LIO_LIThis improvement over NEWS2 alone was maintained across multiple hospital trusts but the model tended to be miscalibrated with risks of severe outcomes underestimated in most sites. C_LIO_LIWe benefited from existing pipelines for informatics at KCH such as CogStack that allowed rapid extraction and processing of electronic health records. This methodological approach provided rapid insights and allowed us to overcome the complications associated with slow data centralisation approaches. C_LI",infectious diseases,exact,100,100 -bioRxiv,10.1101/2020.04.28.066977,2020-04-29,https://biorxiv.org/cgi/content/short/2020.04.28.066977,"Controlling the SARS-CoV-2 outbreak, insights from large scale whole genome sequences generated across the world",Jody Phelan; Wouter Deelder; Daniel Ward; Susana Campino; Martin L Hibberd; Taane G Clark,London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine,"BackgroundSARS-CoV-2 most likely evolved from a bat beta-coronavirus and started infecting humans in December 2019. Since then it has rapidly infected people around the world, with more than 4.5 million confirmed cases by the middle of May 2020. Early genome sequencing of the virus has enabled the development of molecular diagnostics and the commencement of therapy and vaccine development. The analysis of the early sequences showed relatively few evolutionary selection pressures. However, with the rapid worldwide expansion into diverse human populations, significant genetic variations are becoming increasingly likely. The current limitations on social movement between countries also offers the opportunity for these viral variants to become distinct strains with potential implications for diagnostics, therapies and vaccines. - -MethodsWe used the current sequencing archives (NCBI and GISAID) to investigate 15,487 whole genomes, looking for evidence of strain diversification and selective pressure. - -ResultsWe used 6,294 SNPs to build a phylogenetic tree of SARS-CoV-2 diversity and noted strong evidence for the existence of two major clades and six sub-clades, unevenly distributed across the world. We also noted that convergent evolution has potentially occurred across several locations in the genome, showing selection pressures, including on the spike glycoprotein where we noted a potentially critical mutation that could affect its binding to the ACE2 receptor. We also report on mutations that could prevent current molecular diagnostics from detecting some of the sub-clades. - -ConclusionThe worldwide whole genome sequencing effort is revealing the challenge of developing SARS-CoV-2 containment tools suitable for everyone and the need for data to be continually evaluated to ensure accuracy in outbreak estimations.",genomics,exact,100,100 medRxiv,10.1101/2020.04.22.20072124,2020-04-24,https://medrxiv.org/cgi/content/short/2020.04.22.20072124,"Self-reported symptoms of covid-19 including symptoms most predictive of SARS-CoV-2 infection, are heritable",Frances MK Williams; Maxim Freydin; Massimo Mangino; Simon Couvreur; Alessia Visconti; Ruth CE Bowyer; Caroline I Le Roy; Mario Falchi; Carole Sudre; Richard Davies; Christopher Hammond; Cristina Menni; Claire Steves; Tim Spector,King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; Zoe Global Ltd; King's College London; King's College London; King's College London; King's College London,"Susceptibility to infection such as SARS-CoV-2 may be influenced by host genotype. TwinsUK volunteers (n=2633) completing the C-19 Covid symptom tracker app allowed classical twin studies of covid-19 symptoms including predicted covid-19, a symptom-based algorithm predicting true infection derived in app users tested for SARS-CoV-2. We found heritability for fever = 41 (95% confidence intervals 12-70)%; anosmia 47 (27-67)%; delirium 49 (24-75)%; and predicted covid-19 gave heritability = 50 (29-70)%.",genetic and genomic medicine,exact,100,100 medRxiv,10.1101/2020.04.21.20073049,2020-04-24,https://medrxiv.org/cgi/content/short/2020.04.21.20073049,What can trends in hospital deaths from COVID-19 tell us about the progress and peak of the pandemic? An analysis of death counts from England announced up to 20 April 2020,David A Leon; Christopher I Jarvis; Anne M Johnson; Liam Smeeth; Vladimir M Shkolnikov,London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; University College London; London School of Hygiene & Tropical Medicine; Max Planck Institute for Demographic Research,"BackgroundReporting of daily hospital COVID-19 deaths in the UK are promoted by the government and scientific advisers alike as a key metric for assessing the progress in the control of the epidemic. These data, however, have certain limitations, among which one of the most significant concerns the fact that the daily totals span deaths that have occurred between 1 and 10 days or more in the past. @@ -2924,6 +2993,9 @@ What this study addsO_LIAmong individuals showing symptoms severe enough to be g C_LIO_LIWe developed a mathematical model combining symptoms to predict individuals likely to be COVID-19 positive and applied this to over 400,000 individuals in the general population presenting some of the COVID-19 symptoms. C_LIO_LIWe find that [~]13% of those presenting symptoms are likely to have or have had a COVID-19 infection. The proportion was slightly higher in women than in men but is comparable in all age groups, and corresponds to 3.4% of those who filled the app report. C_LI",epidemiology,exact,100,100 +medRxiv,10.1101/2020.04.02.20051284,2020-04-06,https://medrxiv.org/cgi/content/short/2020.04.02.20051284,Building an International Consortium for Tracking Coronavirus Health Status,Eran Segal; Feng Zhang; Xihong Lin; Gary King; Ophir Shalem; Smadar Shilo; William E. Allen; Yonatan H. Grad; Casey S. Greene; Faisal Alquaddoomi; Simon Anders; Ran Balicer; Tal Bauman; Ximena Bonilla; Gisel Booman; Andrew T. Chan; Ori Ori Cohen; Silvano Coletti; Natalie Davidson; Yuval Dor; David A. Drew; Olivier Elemento; Georgina Evans; Phil Ewels; Joshua Gale; Amir Gavrieli; Benjamin Geiger; Iman Hajirasouliha; Roman Jerala; Andre Kahles; Olli Kallioniemi; Ayya Keshet; Gregory Landua; Tomer Meir; Aline Muller; Long H. Nguyen; Matej Oresic; Svetlana Ovchinnikova; Hedi Peterson; Jay Rajagopal; Gunnar Ratsch; Hagai Rossman; Johan Rung; Andrea Sboner; Alexandros Sigaras; Tim Spector; Ron Steinherz; Irene Stevens; Jaak Vilo; Paul Wilmes; CCC (Coronavirus Census Collective),"Weizmann Institute of Science; Howard Hughes Medical Institute, Core Member, Broad Institute of MIT and Harvard, United States; Departments of Biostatistics and Statistics, Harvard T.H. Chan School of Public Health; Albert J. Weatherhead III University, Institute for Quantitative Social Science, Harvard University; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, United States; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Society of Fellows, Harvard University, United States; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, United States; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, United States; ETH Zurich, NEXUS Personalized Health Technologies, Zurich, Switzerland; Center for Molecular Biology (ZMBH), University of Heidelberg, Germany; Clalit Research Institute, Clalit Health Services, Israel; Mapping and Geo-Information Engineering, Civil and Environmental Engineering Faculty, The Technion, Israel; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich, ; Regen Network, Argentina; Massachusetts General Hospital (MGH), United States; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Chelonia Applied Science, Switzerland; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich, ; School of Medicine-IMRIC-Developmental Biology and Cancer Research, The Hebrew University; Massachusetts General Hospital (MGH), United States; Englander Institute for Precision Medicine and Department of Physiology and Biophysics, Weill Cornell Medicine, USA; Institute for Quantitative Social Science, Harvard University; Science for Life Laboratory (SciLifeLab), Department of Biochemistry and Biophysics, Stockholm University, Sweden; symptometrics.org; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Department of immunology, Weizmann Institute of Science, Israel; Englander Institute for Precision Medicine and Department of Physiology and Biophysics, Weill Cornell Medicine, USA; Department of Synthetic biology and Immunology, National Institute of Chemistry, Slovenia; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich, ; Science for Life Laboratory (SciLifeLab), Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Regen Network, United States; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Luxembourg Institute of Socio-Economic Research and University of Luxembourg, Luxembourg; Massachusetts General Hospital (MGH), United States; School of Medical Sciences, Orebro University, Orebro, Sweden, and Turku Bioscience Centre, University of Turku and Abo Akademi University, Turku, Finland; Center for Molecular Biology (ZMBH), University of Heidelberg, Germany; Institute of Computer Science, University of Tartu, Estonia, Estonia; Internal Medicine, Harvard Medical School, Department of Pulmonary Medicine and Critical Care, Massachusetts General Hospital (MGH), United States; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich a; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Science for Life Laboratory (SciLifeLab), Department of Immunology, Genetics and Pathology, Uppsala university, Sweden; Englander Institute for Precision Medicine and Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, USA; Englander Institute for Precision Medicine and Department of Physiology and Biophysics, Weill Cornell Medicine, USA; Kings College, United Kingdom; Regen Network, United States; Science for Life Laboratory (SciLifeLab), Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Sweden; Institute of Computer Science, University of Tartu, Estonia, Estonia; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg; ","Information is the most potent protective weapon we have to combat a pandemic, at both the individual and global level. For individuals, information can help us make personal decisions and provide a sense of security. For the global community, information can inform policy decisions and offer critical insights into the epidemic of COVID-19 disease. Fully leveraging the power of information, however, requires large amounts of data and access to it. To achieve this, we are making steps to form an international consortium, Coronavirus Census Collective (CCC, coronaviruscensuscollective.org), that will serve as a hub for integrating information from multiple data sources that can be utilized to understand, monitor, predict, and combat global pandemics. These sources may include self-reported health status through surveys (including mobile apps), results of diagnostic laboratory tests, and other static and real-time geospatial data. This collective effort to track and share information will be invaluable in predicting hotspots of disease outbreak, identifying which factors control the rate of spreading, informing immediate policy decisions, evaluating the effectiveness of measures taken by health organizations on pandemic control, and providing critical insight on the etiology of COVID-19. It will also help individuals stay informed on this rapidly evolving situation and contribute to other global efforts to slow the spread of disease. + +In the past few weeks, several initiatives across the globe have surfaced to use daily self-reported symptoms as a means to track disease spread, predict outbreak locations, guide population measures and help in the allocation of healthcare resources. The aim of this paper is to put out a call to standardize these efforts and spark a collaborative effort to maximize the global gain while protecting participant privacy.",infectious diseases,exact,100,100 medRxiv,10.1101/2020.03.30.20047217,2020-03-30,https://medrxiv.org/cgi/content/short/2020.03.30.20047217,"Physical interventions to interrupt or reduce the spread of respiratory viruses. Part 1 - Face masks, eye protection and person distancing: systematic review and meta-analysis",Tom Jefferson; Mark Jones; Lubna A Al Ansari; Ghada Bawazeer; Elaine Beller; Justin Clark; John Conly; Chris Del Mar; Elisabeth Dooley; Eliana Ferroni; Paul Glasziou; Tammy Hoffman; Sarah Thorning; Mieke Van Driel,"University of Oxford; Bond University, Australia; Kind Saud University, Saudi Arabia; King Saud, University, Saudi Arabia; Bond University, Australia; Bond University, Australia; Department of Medicine, Microbiology, Immunology & Infectious Diseases, Cumming School of Medicine, University of Calgary and Alberta Health Services , Calgary,; Bond University, Australia; Bond University, Australia; Regione Veneto, Italy; Bond University, Australia; Bond University, Australia; Bond University, Australia; Primary Care Clinical Unit, Faculty of Medicine, University of Queensland, Australia","OBJECTIVETo examine the effectiveness of eye protection, face masks, or person distancing on interrupting or reducing the spread of respiratory viruses. DESIGNUpdate of a Cochrane review that included a meta-analysis of observational studies during the SARS outbreak of 2003. diff --git a/data/covid/preprints.exact.json b/data/covid/preprints.exact.json index 4d74f226..875952a4 100644 --- a/data/covid/preprints.exact.json +++ b/data/covid/preprints.exact.json @@ -111,20 +111,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2023.11.24.23296021", - "date": "2023-11-27", - "link": "https://medrxiv.org/cgi/content/short/2023.11.24.23296021", - "title": "Severe acute myositis and myocarditis upon initiation of six-weekly Pembrolizumab post-COVID-19 mRNA vaccination", - "authors": "Robert Aerwyn Watson; Weiyu Ye; Chelsea Alice Taylor; Rosalin Anisha Cooper; Orion Tong; Tim James; Brian Shine; Monika Hofer; Damian Jenkins; Robert Pell; Eleni Ieremia; Stephanie Jones; David Maldonado-Perez; Ian Roberts; Nicholas Coupe; Mark Ross Middleton; Miranda Jane Payne; Benjamin Peter Fairfax", - "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; University of Oxford; University of Oxford; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; University of Oxford; Oxford University Hospitals NHS Foundation Trust; University of Oxford", - "abstract": "We describe three cases of critical acute myositis with myocarditis occurring within 22 days of each other at a single institution, all within one month of receiving the initial cycle of the anti-PD-1 drug Pembrolizumab. Analysis of T cell receptor repertoires from peripheral blood and tissues revealed a high degree of clonal expansion and public clones between cases, with several T cell clones expanded within the skeletal muscle putatively recognising viral epitopes. All patients had recently received a COVID-19 mRNA booster vaccine prior to treatment and were positive for SARS-CoV2 Spike antibody. In conclusion, we report a series of unusually severe myositis and myocarditis following PD-1 blockade and the COVID-19 mRNA vaccination.", - "category": "oncology", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2023.11.09.23298162", @@ -321,6 +307,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2023.05.23.23289798", + "date": "2023-05-24", + "link": "https://medrxiv.org/cgi/content/short/2023.05.23.23289798", + "title": "Primary Care Post-COVID syndrome Diagnosis and Referral Coding", + "authors": "Robert Willans; Gail Allsopp; Pall Jonsson; Fiona Glen; Felix Greaves; John Macleod; Yinghui Wei; Sebastian Bacon; Amir Mehrkar; Alex Walker; Brian MacKenna; Louis Fisher; Ben Goldacre; - The OpenSAFELY Collaborative; - The CONVALESCENCE Collaborative", + "affiliations": "National Institute of Health and Care Excellence; Royal College of General Practitioners; National Institute of Health and Care Excellence; National Institute of Health and Care Excellence; National Institute of Health and Care Excellence; University of Bristol; University of Plymouth; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; ; ", + "abstract": "IntroductionGuidelines for diagnosing and managing Post-COVID syndrome have been rapidly developed. Consistency of the application of these guidelines in primary care is unknown. Electronic health records provide an opportunity to review the use of codes relating to Post-COVID syndrome. This paper explores the use of primary care records as a surrogate uptake measure for NICEs rapid guideline \"managing the long-term effects of COVID-19\" by measuring the use of Post-COVID syndrome diagnosis and referral codes in the pathway.\n\nMethodWith the approval of NHS England we used routine clinical data from the OpenSafely-EMIS/-TPP platforms. Counts of Post-COVID syndrome diagnosis and referral codes were generated from a cohort of all adults, establishing numbers of diagnoses and referrals following diagnosis. The relationship between Post-COVID syndrome diagnosis and referral codes was explored with reference to NICEs rapid guideline.\n\nResultsOf over 45 million patients, 69,220 (0.15%) had a Post-COVID syndrome diagnostic code, and 67,741 (0.15%) had a referral code. 78% of referral codes did not have an associated diagnosis code. 79% of diagnosis codes had no subsequent referral code. Only 18,633 (0.04%) had both. There were higher rates of both diagnosis and referral in those who were more deprived, female and some ethnic groups.\n\nDiscussionThis study demonstrates variation in diagnosis and referral coding rates for Post-COVID syndrome across different patient groups. The results, with limited crossover of referral and diagnostic codes, suggest only one type of code is usually recorded. Recording one code limits the use of routine data for monitoring Post-COVID syndrome diagnosis and management, but suggests several areas for improvement in coding. Post-COVID syndrome coding, particularly diagnosis coding, needs to improve before administrators and researchers can use it to evaluate care pathways.", + "category": "epidemiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2023.05.17.23290105", @@ -797,6 +797,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.09.11.22279823", + "date": "2022-09-12", + "link": "https://medrxiv.org/cgi/content/short/2022.09.11.22279823", + "title": "Effects of the COVID-19 pandemic on the mental health of clinically extremely vulnerable children and children living with clinically extremely vulnerable people in Wales: A data linkage study", + "authors": "Laura Elizabeth Cowley; Karen Hodgson; Jiao Song; Tony Whiffen; Jacinta Tan; Ann John; Amrita Bandyopadhyay; Alisha R Davies", + "affiliations": "Swansea University; Public Health Wales; Public Health Wales; Welsh Government; University of Oxford; Swansea University; Swansea University; Public Health Wales", + "abstract": "ObjectivesTo determine whether clinically extremely vulnerable (CEV) children or children living with a CEV person in Wales were at greater risk of presenting with anxiety or depression in primary or secondary care during the COVID-19 pandemic compared with children in the general population, and to compare patterns of anxiety and depression during the pandemic (23rd March 2020-31st January 2021, referred to as 2020/21) and before the pandemic (March 23rd 2019-January 31st 2020, referred to as 2019/20), between CEV children and the general population.\n\nDesignPopulation-based cross-sectional cohort study using anonymised, linked, routinely collected health and administrative data held in the Secure Anonymised Information Linkage Databank. CEV individuals were identified using the COVID-19 Shielded Patient List.\n\nSettingPrimary and secondary healthcare settings covering 80% of the population of Wales.\n\nParticipantsChildren aged 2-17 in Wales: CEV (3,769); living with a CEV person (20,033); or neither (415,009).\n\nPrimary outcome measureFirst record of anxiety or depression in primary or secondary healthcare in 2019/20 and 2020/21, identified using Read and ICD-10 codes.\n\nResultsA Cox regression model adjusted for demographics and history of anxiety or depression revealed that only CEV children were at greater risk of presenting with anxiety or depression during the pandemic compared with the general population (Hazard Ratio=2.27, 95% Confidence Interval=1.94-2.66, p<0.001). Compared with the general population, the risk amongst CEV children was higher in 2020/21 (Risk Ratio 3.04) compared with 2019/20 (Risk Ratio 1.90). In 2020/21, the cumulative incidence of anxiety or depression increased slightly amongst CEV children, but declined amongst the general population.\n\nConclusionsDifferences in the cumulative incidences of recorded anxiety or depression in healthcare between CEV children and the general population were largely driven by a reduction in presentations to healthcare services by children in the general population during the pandemic.\n\nStrengths and limitations of this studyO_LIStrengths of this study include its novelty, national focus and clinical relevance; to date this is the first population-based study examining the effects of the COVID-19 pandemic on healthcare use for anxiety or depression amongst clinically extremely vulnerable (CEV) children and children living with a CEV person in Wales\nC_LIO_LIWe compared 2020/21 data with pre-pandemic 2019/20 data for CEV children and children in the general population, to place the impact of the COVID-19 pandemic in the context of longer-term patterns of healthcare use\nC_LIO_LIWe used a novel approach and linked multiple datasets to identify a cohort of children living with a CEV person in Wales during the COVID-19 pandemic\nC_LIO_LIThere was heterogeneity within the Shielded Patient List that was used to create the cohorts of children identified as CEV or living with a CEV person, in terms of the type and severity of individuals underlying conditions; the manner in which people were added to the list; the time point that people were added to the list; and the extent to which people followed the shielding guidance\nC_LIO_LIRoutinely collected healthcare data does not capture self-reported health, and is likely to underestimate the burden of common mental disorders in the population\nC_LI", + "category": "pediatrics", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.09.01.22279473", @@ -811,6 +825,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.08.29.22279359", + "date": "2022-08-31", + "link": "https://medrxiv.org/cgi/content/short/2022.08.29.22279359", + "title": "Prophylactic Treatment of COVID-19 in Care Homes Trial (PROTECT-CH)", + "authors": "Philip M Bath; Jonathan Ball; Matthew Boyd; Heather Gage; Matthew Glover; Maureen Godfrey; Bruce Guthrie; Jonathan Hewitt; Robert Howard; Thomas Jaki; Edmund Juszczak; Daniel Lasserson; Paul Leighton; Val Leyland; Wei Shen Lim; Pip Logan; Garry Meakin; Alan Montgomery; Reuben Ogollah; Peter Passmore; Philip Quinlan; Caroline Rick; Simon Royal; Susan D Shenkin; Clare Upton; Adam L Gordon; - PROTECT-CH Trialists", + "affiliations": "University of Nottingham; University of Nottingham; University of Nottingham; University of Surrey; University of Surrey; Private person; University of Edinburgh; Llandough Hospital; University College London; University of Cambridge; University of Nottingham; University of Warwick; University of Nottingham; Private person; Nottingham University Hospitals NHS Trust; University of Nottingham; University of Nottingham; University of Nottingham; University of Nottingham; Queen's University Belfast; University of Nottingham; University of Nottingham; Cripps Health Centre; University of Edinburgh; University of Nottingham; University of Nottingham; ", + "abstract": "BackgroundCoronavirus disease 2019 (COVID-19) is associated with significant mortality and morbidity in care homes. Novel or repurposed antiviral drugs may reduce infection and disease severity through reducing viral replication and inflammation.\n\nObjectiveTo compare the safety and efficacy of antiviral agents (ciclesonide, niclosamide) for preventing SARS-CoV-2 infection and COVID-19 severity in care home residents.\n\nDesignCluster-randomised open-label blinded endpoint platform clinical trial testing antiviral agents in a post-exposure prophylaxis paradigm.\n\nSettingCare homes across all four United Kingdom member countries.\n\nParticipantsCare home residents 65 years of age or older.\n\nInterventionsCare homes were to be allocated at random by computer to 42 days of antiviral agent plus standard care versus standard of care and followed for 60 days after randomisation.\n\nMain outcome measuresThe primary four-level ordered categorical outcome with participants classified according to the most serious of all-cause mortality, all-cause hospitalisation, SARS-CoV-2 infection and no infection. Analysis using ordinal logistic regression was by intention to treat. Other outcomes included the components of the primary outcome and transmission.\n\nResultsDelays in contracting between NIHR and the manufacturers of potential antiviral agents significantly delayed any potential start date. Having set up the trial (protocol, approvals, insurance, website, database, routine data algorithms, training materials), the trial was stopped in September 2021 prior to contracting of care homes and general practitioners in view of the success of vaccination in care homes with significantly reduced infections, hospitalisations and deaths. As a result, the sample size target (based on COVID-19 rates and deaths occurring in February-June 2020) became unfeasible.\n\nLimitationsCare home residents were not approached about the trial and so were not consented and did not receive treatment. Hence, the feasibility of screening, consent, treatment and data acquisition, and potential benefit of post exposure prophylaxis were never tested. Further, contracting between the University of Nottingham and the PIs, GPs and care homes was not completed, so the feasibility of contracting with all the different groups at the scale needed was not tested.\n\nConclusionsThe role of post exposure prophylaxis of COVID-19 in care home residents was not tested because of changes in COVID-19 incidence, prevalence and virulence as a consequence of the vaccination programme that rendered the study unfeasible. Significant progress was made in describing and developing the infrastructure necessary for a large scale Clinical Trial of Investigational Medicinal Products in care homes in all four UK nations.\n\nFuture workThe role of post-exposure prophylaxis of COVID-19 in care home residents remains to be defined. Significant logistical barriers to conducting research in care homes during a pandemic need to be removed before such studies are possible in the required short timescale.", + "category": "infectious diseases", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.08.29.22279333", @@ -1077,6 +1105,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.05.19.22275214", + "date": "2022-05-22", + "link": "https://medrxiv.org/cgi/content/short/2022.05.19.22275214", + "title": "Antibody levels following vaccination against SARS-CoV-2: associations with post-vaccination infection and risk factors", + "authors": "Nathan J Cheetham; Milla Kibble; Andrew Wong; Richard J Silverwood; Anika Knuppel; Dylan M Williams; Olivia K L Hamilton; Paul H Lee; Charis Bridger Staatz; Giorgio Di Gessa; Jingmin Zhu; Srinivasa Vittal Katikireddi; George B Ploubidis; Ellen J Thompson; Ruth C E Bowyer; Xinyuan Zhang; Golboo Abbasian; Maria Paz Garcia; Deborah Hart; Jeffrew Seow; Carl Graham; Neophytos Kouphou; Sam Acors; Michael H Malim; Ruth E Mitchell; Kate Northstone; Daniel Major-Smith; Sarah Matthews; Thomas Breeze; Michael Crawford; Lynn Molloy; Alex Siu Fung Kwong; Katie J Doores; Nishi Chaturvedi; Emma L Duncan; Nicholas J Timpson; Claire J Steves", + "affiliations": "King's College London; University of Cambridge; University College London; University College London; University College London; University College London; University of Glasgow; University of Leicester; University College London; University College London; University College London; University of Glasgow; University College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; King's College London; University College London; King's College London; University of Bristol; King's College London", + "abstract": "SARS-CoV-2 antibody levels can be used to assess humoral immune responses following SARS-CoV-2 infection or vaccination, and may predict risk of future infection. From cross-sectional antibody testing of 9,361 individuals from TwinsUK and ALSPAC UK population-based longitudinal studies (jointly in April-May 2021, and TwinsUK only in November 2021-January 2022), we tested associations between antibody levels following vaccination and: (1) SARS-CoV-2 infection following vaccination(s); (2) health, socio-demographic, SARS-CoV-2 infection and SARS-CoV-2 vaccination variables.\n\nWithin TwinsUK, single-vaccinated individuals with the lowest 20% of anti-Spike antibody levels at initial testing had 3-fold greater odds of SARS-CoV-2 infection over the next six to nine months, compared to the top 20%. In TwinsUK and ALSPAC, individuals identified as at increased risk of COVID-19 complication through the UK \"Shielded Patient List\" had consistently greater odds (2 to 4-fold) of having antibody levels in the lowest 10%. Third vaccination increased absolute antibody levels for almost all individuals, and reduced relative disparities compared with earlier vaccinations.\n\nThese findings quantify the association between antibody level and risk of subsequent infection, and support a policy of triple vaccination for the generation of protective antibodies.\n\nLay summaryIn this study, we analysed blood samples from 9,361 participants from two studies in the UK: an adult twin registry, TwinsUK (4,739 individuals); and the Avon Longitudinal Study of Parents and Children, ALSPAC (4,622 individuals). We did this work as part of the UK Government National Core Studies initiative researching COVID-19. We measured blood antibodies which are specific to SARS-CoV-2 (which causes COVID-19). Having a third COVID-19 vaccination boosted antibody levels. More than 90% of people from TwinsUK had levels after third vaccination that were greater than the average level after second vaccination. Importantly, this was the case even in individuals on the UK \"Shielded Patient List\". We found that people with lower antibody levels after first vaccination were more likely to report having COVID-19 later on, compared to people with higher antibody levels. People on the UK \"Shielded Patient List\", and individuals who reported that they had poorer general health, were more likely to have lower antibody levels after vaccination. In contrast, people who had had a previous COVID-19 infection were more likely to have higher antibody levels following vaccination compared to people without infection. People receiving the Oxford/AstraZeneca rather than the Pfizer BioNTech vaccine had lower antibody levels after one or two vaccinations. However, after a third vaccination, there was no difference in antibody levels between those who had Oxford/AstraZeneca and Pfizer BioNTech vaccines for their first two doses. These findings support having a third COVID-19 vaccination to boost antibodies.", + "category": "epidemiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.05.10.22274890", @@ -1441,20 +1483,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.01.05.21268323", - "date": "2022-01-06", - "link": "https://medrxiv.org/cgi/content/short/2022.01.05.21268323", - "title": "Lineage replacement and evolution captured by the United Kingdom Covid Infection Survey", - "authors": "Katrina A Lythgoe; Tanya Golubchik; Matthew Hall; Thomas House; Roberto Cahuantzi; George MacIntyre-Cockett; Helen Fryer; Laura Thomson; Anel Nurtay; Mahan Ghafari; David Buck; Angie Green; Amy Trebes; Paolo Piazza; Lorne J Lonie; Ruth Studley; Emma Rourke; Darren Smith; Matthew Bashton; Andrew Nelson; Matthew Crown; Clare McCann; Gregory R Young; Rui Andre Nunes de Santos; Zack Richards; Adnan Tariq; - Wellcome Sanger Institute COVID-19 Surveillance Team; - COVID-19 Infection Survey Group; - The COVID-19 Genomics UK (COG-UK) consortium; Christophe Fraser; Ian Diamond; Jeff Barrett; Ann Sarah Walker; David Bonsall", - "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Manchester; University of Manchester; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Wellcome Sanger Institute; Office for National Statistics; ; University of Oxford; Office for National Statistics; Wellcome Sanger Institute; University of Oxford; University of Oxford", - "abstract": "The Office for National Statistics COVID-19 Infection Survey (ONS-CIS) is the largest surveillance study of SARS-CoV-2 positivity in the community, and collected data on the United Kingdom (UK) epidemic from April 2020 until March 2023 before being paused. Here, we report on the epidemiological and evolutionary dynamics of SARS-CoV-2 determined by analysing the sequenced samples collected by the ONS-CIS during this period. We observed a series of sweeps or partial sweeps, with each sweeping lineage having a distinct growth advantage compared to their predecessors. The sweeps also generated an alternating pattern in which most samples had either S-gene target failure (SGTF) or non- SGTF over time. Evolution was characterised by steadily increasing divergence and diversity within lineages, but with step increases in divergence associated with each sweeping major lineage. This led to a faster overall rate of evolution when measured at the between-lineage level compared to within lineages, and fluctuating levels of diversity. These observations highlight the value of viral sequencing integrated into community surveillance studies to monitor the viral epidemiology and evolution of SARS-CoV-2, and potentially other pathogens, particularly in the current phase of the pandemic with routine RT-PCR testing now ended in the community.", - "category": "epidemiology", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.12.31.21268587", @@ -1497,6 +1525,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.12.22.21268252", + "date": "2021-12-24", + "link": "https://medrxiv.org/cgi/content/short/2021.12.22.21268252", + "title": "Rapid increase in Omicron infections in England during December 2021: REACT-1 study", + "authors": "Paul Elliott; Barbara Bodinier; Oliver Eales; Haowei Wang; David Haw; Joshua Elliott; Matthew Whitaker; Jakob Jonnerby; David Tang; Caroline E. Walters; Christina Atchinson; Peter J. Diggle; Andrew J. Page; Alex Trotter; Deborah Ashby; Wendy Barclay; Graham Taylor; Helen Ward; Ara Darzi; Graham Cooke; Marc Chadeau-Hyam; Christl A Donnelly", + "affiliations": "School of Public Health, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; Imperial College London; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; Imperial College London; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; Quadram Institute, Norwich, UK; Quadram Institute Bioscience; School of Public Health, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research; Imperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research Centre, UKInstitute of Global Health Innovation at ; Department of Infectious Disease, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency", + "abstract": "BackgroundThe highest-ever recorded numbers of daily severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in England has been observed during December 2021 and have coincided with a rapid rise in the highly transmissible Omicron variant despite high levels of vaccination in the population. Although additional COVID-19 measures have been introduced in England and internationally to contain the epidemic, there remains uncertainty about the spread and severity of Omicron infections among the general population.\n\nMethodsThe REal-time Assessment of Community Transmission-1 (REACT-1) study has been monitoring the prevalence of SARS-CoV-2 infection in England since May 2020. REACT-1 obtains self-administered throat and nose swabs from a random sample of the population of England at ages 5 years and over. Swabs are tested for SARS-CoV-2 infection by reverse transcription polymerase chain reaction (RT-PCR) and samples testing positive are sent for viral genome sequencing. To date 16 rounds have been completed, each including [~]100,000 or more participants with data collected over a period of 2 to 3 weeks per month. Socio-demographic, lifestyle and clinical information (including previous history of COVID-19 and symptoms prior to swabbing) is collected by online or telephone questionnaire. Here we report results from round 14 (9-27 September 2021), round 15 (19 October - 05 November 2021) and round 16 (23 November - 14 December 2021) for a total of 297,728 participants with a valid RT-PCR test result, of whom 259,225 (87.1%) consented for linkage to their NHS records including detailed information on vaccination (vaccination status, date). We used these data to estimate community prevalence and trends by age and region, to evaluate vaccine effectiveness against infection in children ages 12 to 17 years, and effect of a third (booster) dose in adults, and to monitor the emergence of the Omicron variant in England.\n\nResultsWe observed a high overall prevalence of 1.41% (1.33%, 1.51%) in the community during round 16. We found strong evidence of an increase in prevalence during round 16 with an estimated reproduction number R of 1.13 (1.06, 1.09) for the whole of round 16 and 1.27 (1.14, 1.40) when restricting to observations from 1 December onwards. The reproduction number in those aged 18-54 years was estimated at 1.23 (1.14, 1.33) for the whole of round 16 and 1.41 (1.23, 1.61) from 1 December. Our data also provide strong evidence of a steep increase in prevalence in London with an estimated R of 1.62 (1.34, 1.93) from 1 December onwards and a daily prevalence reaching 6.07% (4.06%, 9.00%) on 14 December 2021. As of 1 to 11 December 2021, of the 275 lineages determined, 11 (4.0%) corresponded to the Omicron variant. The first Omicron infection was detected in London on 3 December, and subsequent infections mostly appeared in the South of England. The 11 Omicron cases were all aged 18 to 54 years, double-vaccinated (reflecting the large numbers of people who have received two doses of vaccine in this age group) but not boosted, 9 were men, 5 lived in London and 7 were symptomatic (5 with classic COVID-19 symptoms: loss or change of sense of smell or taste, fever, persistent cough), 2 were asymptomatic, and symptoms were unknown for 2 cases. The proportion of Omicron (vs Delta or Delta sub-lineages) was found to increase rapidly with a daily increase of 66.0% (32.7%, 127.3%) in the odds of Omicron (vs. Delta) infection, conditional on swab positivity. Highest prevalence of swab positivity by age was observed in (unvaccinated) children aged 5 to 11 years (4.74% [4.15%, 5.40%]) similar to the prevalence observed at these ages in round 15. In contrast, prevalence in children aged 12 to 17 years more than halved from 5.35% (4.78%, 5.99%) in round 15 to 2.31% (1.91%, 2.80%) in round 16. As of 14 December 2021, 76.6% children at ages 12 to 17 years had received at least one vaccine dose; we estimated that vaccine effectiveness against infection was 57.9% (44.1%, 68.3%) in this age group. In addition, the prevalence of swab positivity in adults aged 65 years and over fell by over 40% from 0.84% (0.72%, 0.99%) in round 15 to 0.48% (0.39%,0.59%) in round 16 and for those aged 75 years and over it fell by two-thirds from 0.63% (0.48%,0.82%) to 0.21% (0.13%,0.32%). At these ages a high proportion of participants (>90%) had received a third vaccine dose; we estimated that adults having received a third vaccine dose had a three- to four-fold lower risk of testing positive compared to those who had received two doses.\n\nConclusionA large fall in swab positivity from round 15 to round 16 among 12 to 17 year olds, most of whom have been vaccinated, contrasts with the continuing high prevalence among 5 to 11 year olds who have largely not been vaccinated. Likewise there were large falls in swab positivity among people aged 65 years and over, the vast majority of whom have had a third (booster) vaccine dose; these results reinforce the importance of the vaccine and booster campaign. However, the rapidly increasing prevalence of SARS-CoV-2 infections in England during December 2021, coincident with the rapid rise of Omicron infections, may lead to renewed pressure on health services. Additional measures beyond vaccination may be needed to control the current wave of infections and prevent health services (in England and other countries) from being overwhelmed.\n\nSummaryThe unprecedented rise in SARS-CoV-2 infections is concurrent with rapid spread of the Omicron variant in England and globally. We analysed prevalence of SARS-CoV-2 and its dynamics in England from end of November to mid-December 2021 among almost 100,000 participants from the REACT-1 study. Prevalence was high during December 2021 with rapid growth nationally and in London, and of the proportion of infections due to Omicron. We observed a large fall in swab positivity among mostly vaccinated older children (12-17 years) compared with unvaccinated younger children (5-11 years), and in adults who received a third vs. two doses of vaccine. Our results reiterate the importance of vaccination and booster campaigns; however, additional measures may be needed to control the rapid growth of the Omicron variant.", + "category": "epidemiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.12.21.21268214", @@ -1721,6 +1763,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.11.15.21266264", + "date": "2021-11-16", + "link": "https://medrxiv.org/cgi/content/short/2021.11.15.21266264", + "title": "Association of COVID-19 employment disruption with mental and social wellbeing: evidence from nine UK longitudinal studies", + "authors": "Jacques Wels; Charlotte Booth; Bozena Wielgoszewska; Michael J Green; Giorgio Di Gessa; Charlotte F Huggins; Gareth J Griffith; Alex Siu Fung Kwong; Ruth C E Bowyer; Jane Maddock; Praveetha Patalay; Richard J Silverwood; Emla Fitzsimons; Richard John Shaw; Ellen J Thompson; Andrew Steptoe; Alun Hughes; Nishi Chaturvedi; Claire J Steves; Srinivasa Vittal Katikireddi; George B Ploubidis", + "affiliations": "University College London; University College London; University College London; University of Glasgow; University College London; University of Edinburgh; University of Bristol; University of Bristol; King's College London; University College London; University College London; University College London; University College London; University of Glasgow; Kings College London; University College London; University College London; University College London; King's College London; University of Glasgow; University College London", + "abstract": "BackgroundThe COVID-19 pandemic has led to major economic disruptions. In March 2020, the UK implemented the Coronavirus Job Retention Scheme - known as furlough - to minimize the impact of job losses. We investigate associations between change in employment status and mental and social wellbeing during the early stages of the pandemic.\n\nMethodsData were from 25,670 respondents, aged 17 to 66, across nine UK longitudinal studies. Furlough and other employment changes were defined using employment status pre-pandemic and during the first lockdown (April-June 2020). Mental and social wellbeing outcomes included psychological distress, life satisfaction, self-rated health, social contact, and loneliness. Study-specific modified Poisson regression estimates, adjusting for socio-demographic characteristics and pre-pandemic mental and social wellbeing measures, were pooled using meta-analysis.\n\nResultsCompared to those who remained working, furloughed workers were at greater risk of psychological distress (adjusted risk ratio, ARR=1.12; 95% CI: 0.97, 1.29), low life satisfaction (ARR=1.14; 95% CI: 1.07, 1.22), loneliness (ARR=1.12; 95% CI: 1.01, 1.23), and poor self-rated health (ARR=1.26; 95% CI: 1.05, 1.50), but excess risk was less pronounced than that of those no longer employed (e.g., ARR for psychological distress=1.39; 95% CI: 1.21, 1.59) or in stable unemployment (ARR=1.33; 95% CI: 1.09, 1.62).\n\nConclusionsDuring the early stages of the pandemic, those furloughed had increased risk for poor mental and social wellbeing. However, their excess risk was lower in magnitude than that of those who became or remained unemployed, suggesting that furlough may have partly mitigated poorer outcomes.", + "category": "psychiatry and clinical psychology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.11.15.21266255", @@ -1735,20 +1791,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.11.10.21266124", - "date": "2021-11-11", - "link": "https://medrxiv.org/cgi/content/short/2021.11.10.21266124", - "title": "Differences in COVID-19 vaccination coverage by occupation in England: a national linked data study", - "authors": "Vahe Nafilyan; Ted Dolby; Katie Finning; Jasper Morgan; Rhiannon Edge; Myer Glickman; Neil Pearce; Martie Van Tongeren", - "affiliations": "Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Lancaster University; Office for National Statistics; London School of Hygiene and Tropical Medicine; University of Manchester", - "abstract": "BackgroundMonitoring differences in COVID-19 vaccination uptake in different groups is crucial to help inform the policy response to the pandemic. A key gap is the absence of data on uptake by occupation.\n\nMethodsUsing nationwide population-level data, we calculated the proportion of people who had received two doses of a COVID-19 vaccine (assessed on 31 August 2021) by detailed occupational categories in adults aged 40-64 and estimated adjusted odds ratios to examine whether these differences were driven by occupation or other factors, such as education. We also examined whether vaccination rates differed by ability to work from home.\n\nResultsOur study population included 14,298,147 adults 40-64. Vaccination rates differed markedly by occupation, being higher in administrative and secretarial occupations (90.8%); professional occupations (90.7%); and managers, directors and senior officials (90.6%); and lowest (83.1%) in people working in elementary occupations. We found substantial differences in vaccination rates looking at finer occupational groups even after adjusting for confounding factors, such as education. Vaccination rates were higher in occupations which can be done from home and lower in those which cannot. Many occupations with low vaccination rates also involved contact with the public or with vulnerable people\n\nConclusionsIncreasing vaccination coverage in occupations with low vaccination rates is crucial to help protecting the public and control infection, especially in occupations that cannot be done from home and involve contacts with the public. Policies such as work from home if you can may only have limited future impact on hospitalisations and deaths\n\nWhat is already known on this subject?Whilst several studies highlight differences in vaccination coverage by ethnicity, religion, socio-demographic factors and certain underlying health conditions, there is very little evidence on how vaccination coverage varies by occupation, in the UK and elsewhere. The few study looking at occupational differences in vaccine hesitancy focus on healthcare workers or only examined broad occupational groups. There is currently no large-scale study on occupational differences in COVID-19 vaccination coverage in the UK.\n\nWhat this study adds?Using population-level linked data combining the 2011 Census, primary care records, mortality and vaccination data, we found that the vaccination rates of adults aged 40 to 64 years in England differed markedly by occupation. Vaccination rates were high in administrative and secretarial occupations, professional occupations and managers, directors and senior officials and low in people working in elementary occupations. Adjusting for other factors likely to be linked to occupation and vaccination, such as education, did not substantially alter the results. Vaccination rates were also associated with the ability to work from home, with the vaccination rate being higher in occupations which can be done performed from home. Policies aiming to increase vaccination rates in occupations that cannot be done from home and involve contacts with the public should be priorities", - "category": "public and global health", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.11.09.21266054", @@ -2435,20 +2477,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.05.12.21257123", - "date": "2021-05-17", - "link": "https://medrxiv.org/cgi/content/short/2021.05.12.21257123", - "title": "Occupation and COVID-19 mortality in England: a national linked data study of 14.3 million adults", - "authors": "Vahe Nafilyan; Piotr Pawelek; Daniel Ayoubkhani; Sarah Rhodes; Lucy Pembrey; Melissa Matz; Michel P Coleman; Claudia Allemani; Ben Windsor-Shellard; Martie van Tongeren; Neil Pearce", - "affiliations": "Office for National Statistics; Office for National Statistics; Office for National Statistics; School of Health Sciences, University of Manchester; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine; Office for National Statistics; School of Health Sciences, University of Manchester; London School of Hygiene and Tropical Medicine", - "abstract": "ObjectiveTo estimate occupational differences in COVID-19 mortality, and test whether these are confounded by factors, such as regional differences, ethnicity and education or due to non-workplace factors, such as deprivation or pre-pandemic health.\n\nDesignRetrospective cohort study\n\nSettingPeople living in private households England\n\nParticipants14,295,900 people aged 40-64 years (mean age 52 years, 51% female) who were alive on 24 January 2020, living in private households in England in 2019, were employed in 2011, and completed the 2011 census.\n\nMain outcome measuresCOVID-19 related death, assessed between 24 January 2020 and 28 December 2020. We estimated age-standardised mortality rates per 100,000 person-years at risk (ASMR) stratified by sex and occupations. To estimate the effect of occupation due to work-related exposures, we used Cox proportional hazard models to adjust for confounding (region, ethnicity, education), as well as non-workplace factors that are related to occupation.\n\nResultsThere is wide variation between occupations in COVID-19 mortality. Several occupations, particularly those involving contact with patients or the public, show three-fold or four-fold risks. These elevated risks were greatly attenuated after adjustment for confounding and mediating non-workplace factors. For example, the hazard ratio (HR) for men working as taxi and cab drivers or chauffeurs changed from 4.60 [95%CI 3.62-5.84] to 1.47 [1.14-1.89] after adjustment. More generally, the overall HR for men working in essential occupations compared with men in non-essential occupations changed from 1.45 [1.34 - 1.56] to 1.22 [1.13 - 1.32] after adjustment. For most occupations, confounding and other mediating factors explained about 70% to 80% of the age-adjusted hazard ratios.\n\nConclusionsWorking conditions are likely to play a role in COVID-19 mortality, particularly in occupations involving contact with COVID-19 patients or the public. However, there is also a substantial contribution from non-workplace factors, including regional factors, socio-demographic factors, and pre-pandemic health.", - "category": "epidemiology", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.05.13.21257144", @@ -2479,14 +2507,14 @@ }, { "site": "medRxiv", - "doi": "10.1101/2021.05.06.21256757", + "doi": "10.1101/2021.05.08.21256867", "date": "2021-05-14", - "link": "https://medrxiv.org/cgi/content/short/2021.05.06.21256757", - "title": "COVID-19 outbreak rates and infection attack rates associated with the workplace: a descriptive epidemiological study", - "authors": "Yiqun Chen; Timothy Aldridge; - UK COVID-19 National Core Studies Consortium; Claire F Ferraro; Fu-Meng Khaw", - "affiliations": "Health and Safety Executive, UK; Health and Safety Executive, UK; ; National Infection Service, Public Health England, UK; Public Health England, UK", - "abstract": "BackgroundA large number of COVID-19 outbreaks/clusters have been reported in a variety of workplace settings since the start of the pandemic. However, information on the rate of outbreak occurrences which helps to identify the type of workplaces that are more likely to experience an outbreak, or infection attack rates which estimates the potential extent of the virus transmission in an outbreak, has not yet been available to inform intervention strategies to limit transmission.\n\nObjectivesTo link datasets on workplace settings and COVID-19 workplace outbreaks in England in order to: identify the geographical areas and workplace sectors with a high rate of outbreaks; and compare infection attack rates by workplace size and sector.\n\nMethodsWe analysed Public Health England (PHE) HPZone data on COVID-19 outbreaks in workplaces, covering the time period of 18 May - 12 October 2020. The workplaces analysed excluded care homes, hospitals and educational settings. We calculated the workplace outbreak rates by nine English regions, 151 Upper Tier Local Authorities (UTLAs) and twelve industrial sectors, using National Population Database (NPD) data extracted in May 2019 on the total number of the relevant workplaces as the denominator. We also calculated the infection attack rates by enterprise size (small, medium, large) and industrial sector, using PHE Situations of Interest (SOI) data on the number of test-confirmed COVID-19 cases in a workplace outbreak as the numerator, and using NPD data on the number employed in that workplace as the denominator.\n\nResultsIn total, 1,317 confirmed workplace outbreaks were identified from HPZone data, of which 1,305 were available for estimation of outbreak rates. The average outbreak rate was 66 per 100,000 workplaces. Of the nine geographical regions in England, the North West had the highest workplace outbreak rate (155/100,000 workplaces), based on 351 outbreaks. Of the UTLAs, the highest workplace outbreak rate was Blackburn with Darwen (387/100,000 workplaces). The industrial sector with the highest workplace outbreak rate was manufacturers and packers of food (1,672/100,000), based on 117 outbreaks: this was consistent across seven of the regions. In addition, high outbreak rates in warehouses were observed in the East Midlands and the North West.\n\nIn total, 390 outbreaks were identified from SOI data and 264 of them allowed for estimation of attack rates. The overall median attack rate was 3.4% of the employed persons with confirmed COVID-19 at a workplace with an outbreak. Most of these outbreaks (162) had an attack rate less than 6%. However, in a small number of outbreaks (57) the attack rate was over 15%. The attack rates increased as the size of the enterprise decreased. The highest attack rate was for outbreaks in close contact services (median 16.5%), which was followed by outbreaks in restaurants and catering (median 10.2%), and in manufacturers and packers of non-food products (median 6.7%).\n\nConclusionsOur linked dataset analysis approach allows early identification of geographical regions and industrial sectors with higher rates of COVID-19 workplace outbreaks as well as estimation of attack rates by enterprise size and sector. This can be used to inform interventions to limit transmission of the virus. Our approach to analysing the workplace outbreak data can also be applied to calculation of outbreak rates and attack rates in other types of settings such as care homes, hospitals and educational settings.", - "category": "epidemiology", + "link": "https://medrxiv.org/cgi/content/short/2021.05.08.21256867", + "title": "SARS-CoV-2 lineage dynamics in England from January to March 2021 inferred from representative community samples", + "authors": "Oliver Eales; Andrew Page; Sonja N. Tang; Caroline E. Walters; Haowei Wang; David Haw; Alexander J. Trotter; Thanh Le Viet; Ebenezer Foster-Nyarko; Sophie Prosolek; Christina Atchinson; Deborah Ashby; Graham Cooke; Wendy Barclay; Christl A Donnelly; Justin O'Grady; Erik Volz; - The COVID-19 Genomics UK (COG-UK) Consortium; Ara Darzi; Helen Ward; Paul Elliott; Steven Riley", + "affiliations": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Quadram Institute, Norwich, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Quadram Institute, Norwich, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; ; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc", + "abstract": "Genomic surveillance for SARS-CoV-2 lineages informs our understanding of possible future changes in transmissibility and vaccine efficacy. However, small changes in the frequency of one lineage over another are often difficult to interpret because surveillance samples are obtained from a variety of sources. Here, we describe lineage dynamics and phylogenetic relationships using sequences obtained from a random community sample who provided a throat and nose swab for rt-PCR during the first three months of 2021 as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. Overall, diversity decreased during the first quarter of 2021, with the B.1.1.7 lineage (first identified in Kent) predominant, driven by a 0.3 unit higher reproduction number over the prior wild type. During January, positive samples were more likely B.1.1.7 in younger and middle-aged adults (aged 18 to 54) than in other age groups. Although individuals infected with the B.1.1.7 lineage were no more likely to report one or more classic COVID-19 symptoms compared to those infected with wild type, they were more likely to be antibody positive 6 weeks after infection. Viral load was higher in B.1.1.7 infection as measured by cycle threshold (Ct) values, but did not account for the increased rate of testing positive for antibodies. The presence of infections with non-imported B.1.351 lineage (first identified in South Africa) during January, but not during February or March, suggests initial establishment in the community followed by fade-out. However, this occurred during a period of stringent social distancing and targeted public health interventions and does not immediately imply similar lineages could not become established in the future. Sequence data from representative community surveys such as REACT-1 can augment routine genomic surveillance.", + "category": "infectious diseases", "match_type": "exact", "author_similarity": 100, "affiliation_similarity": 100 @@ -2589,6 +2617,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.04.22.21255913", + "date": "2021-04-23", + "link": "https://medrxiv.org/cgi/content/short/2021.04.22.21255913", + "title": "Impact of vaccination on SARS-CoV-2 cases in the community: a population-based study using the UK COVID-19 Infection Survey", + "authors": "Emma Pritchard; Philippa Matthews; Nicole Stoesser; David Eyre; Owen Gethings; Karina-Doris Vitha; Joel Jones; Thomas House; Harper VanSteenhouse; Iain Bell; John Bell; John Newton; Jeremy Farrar; Ian Diamond; Emma Rourke; Ruth Studley; Derrick W Crook; tim E peto; Ann Sarah Walker; Koen B Pouwels", + "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; University of Oxford; Office for National Statistics; University of Manchester; Glasgow Lighthouse Laboratory; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; Office for National Statistics,; Office for National Statistics; Office for National Statistics; NIHR Oxford Biomedical Research Centre; oxford university; University of Oxford; University of Oxford", + "abstract": "ObjectivesTo assess the effectiveness of COVID-19 vaccination in preventing SARS-CoV-2 infection in the community.\n\nDesignProspective cohort study.\n\nSettingThe UK population-representative longitudinal COVID-19 Infection Survey.\n\nParticipants373,402 participants aged [≥]16 years contributing 1,610,562 RT-PCR results from nose and throat swabs between 1 December 2020 and 3 April 2021.\n\nMain outcome measuresNew RT-PCR-positive episodes for SARS-CoV-2 overall, by self-reported symptoms, by cycle threshold (Ct) value (<30 versus [≥]30), and by gene positivity (compatible with the B.1.1.7 variant versus not).\n\nResultsOdds of new SARS-CoV-2 infection were reduced 65% (95% CI 60 to 70%; P<0.001) in those [≥]21 days since first vaccination with no second dose versus unvaccinated individuals without evidence of prior infection (RT-PCR or antibody). In those vaccinated, the largest reduction in odds was seen post second dose (70%, 95% CI 62 to 77%; P<0.001).There was no evidence that these benefits varied between Oxford-AstraZeneca and Pfizer-BioNTech vaccines (P>0.9).There was no evidence of a difference in odds of new SARS-CoV-2 infection for individuals having received two vaccine doses and with evidence of prior infection but not vaccinated (P=0.89). Vaccination had a greater impact on reducing SARS-CoV-2 infections with evidence of high viral shedding Ct<30 (88% reduction after two doses; 95% CI 80 to 93%; P<0.001) and with self-reported symptoms (90% reduction after two doses; 95% CI 82 to 94%; P<0.001); effects were similar for different gene positivity patterns.\n\nConclusionVaccination with a single dose of Oxford-AstraZeneca or Pfizer-BioNTech vaccines, or two doses of Pfizer-BioNTech, significantly reduced new SARS-CoV-2 infections in this large community surveillance study. Greater reductions in symptomatic infections and/or infections with a higher viral burden are reflected in reduced rates of hospitalisations/deaths, but highlight the potential for limited ongoing transmission from asymptomatic infections in vaccinated individuals.\n\nRegistrationThe study is registered with the ISRCTN Registry, ISRCTN21086382.", + "category": "infectious diseases", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.04.08.21255099", @@ -2729,6 +2771,34 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.03.16.21253377", + "date": "2021-03-24", + "link": "https://medrxiv.org/cgi/content/short/2021.03.16.21253377", + "title": "First and second SARS-CoV-2 waves in inner London: A comparison of admission characteristics and the effects of the B.1.1.7 variant", + "authors": "Luke B Snell; Wenjuan Wang; Adela Alcolea-Medina; Themoula Charalampous; Gaia Nebbia; Rahul Batra; Leonardo de Jongh; Finola Higgins; Yanzhong Wang; Jonathan D Edgeworth; Vasa Curcin", + "affiliations": "King's College London; School of Population Health and Environmental Sciences, King's College London, London, UK; Viapath, London, UK; Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK; Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK; Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK; NIHR Biomedical Research Centre, Guy's and St Thomas' NHS Foundation Trust; NIHR Biomedical Research Centre, Guy's and St Thomas' NHS Foundation Trust; School of Population Health and Environmental Sciences, King's College London, London, UK; Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK; School of Population Health and Environmental Sciences, King's College London, London, UK", + "abstract": "IntroductionA second wave of SARS-CoV-2 infection spread across the UK in 2020 linked with emergence of the more transmissible B.1.1.7 variant. The emergence of new variants, particularly during relaxation of social distancing policies and implementation of mass vaccination, highlights the need for real-time integration of detailed patient clinical data alongside pathogen genomic data. We linked clinical data with viral genome sequence data to compare cases admitted during the first and second waves of SARS-CoV-2 infection.\n\nMethodsClinical, laboratory and demographic data from five electronic health record (EHR) systems was collected for all cases with a positive SARS-CoV-2 RNA test between March 13th 2020 and February 17th 2021. SARS-CoV-2 viral sequencing was performed using Oxford Nanopore Technology. Descriptive data are presented comparing cases between waves, and between cases of B.1.1.7 and non-B.1.1.7 variants.\n\nResultsThere were 5810 SARS-CoV-2 RNA positive cases comprising inpatients (n=2341), healthcare workers (n=1549), outpatients (n=874), emergency department (ED) attenders not subsequently admitted (n=532), inter-hospital transfers (n=281) and nosocomial cases (n=233). There were two dominant waves of hospital admissions, with wave one starting from March 13th (n=838) and wave two from October 20th (n=1503), both with a temporally aligned rise in nosocomial cases (n=96 in wave one, n=137 in wave two). 1470 SARS-CoV-2 isolates were successfully sequenced, including 216/838 (26%) admitted cases from wave one, 472/1503 (31%) admitted cases in wave two and 121/233 (52%) nosocomial cases. The first B.1.1.7 variant was identified on 15th November 2020 and increased rapidly such that it comprised 400/472 (85%) of sequenced isolates from admitted cases in wave two. Females made up a larger proportion of admitted cases in wave two (47.3% vs 41.8%, p=0.011), and in those infected with the B.1.1.7 variant compared to non-B.1.1.7 variants (48.0% vs 41.8%, p=0.042). A diagnosis of frailty was less common in wave two (11.5% v 22.8%, p<0.001) and in the group infected with B.1.1.7 (14.5% v 22.4%, p=0.001). There was no difference in severity on admission between waves, as measured by hypoxia at admission (wave one: 64.3% vs wave two: 65.5%, p=0.67). However, a higher proportion of cases infected with the B.1.1.7 variant were hypoxic on admission compared to other variants (70.0% vs 62.5%, p=0.029).\n\nConclusionsAutomated EHR data extraction linked with SARS-CoV-2 genome sequence data provides valuable insight into the evolving characteristics of cases admitted to hospital with COVID-19. The proportion of cases with hypoxia on admission was greater in those infected with the B.1.1.7 variant, which supports evidence the B.1.1.7 variant is associated with more severe disease. The number of nosocomial cases was similar in both waves despite introduction of many infection control interventions before wave two, an observation requiring further investigation.", + "category": "infectious diseases", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, + { + "site": "medRxiv", + "doi": "10.1101/2021.03.11.21253275", + "date": "2021-03-21", + "link": "https://medrxiv.org/cgi/content/short/2021.03.11.21253275", + "title": "Effect of vaccination on transmission of COVID-19: an observational study in healthcare workers and their households", + "authors": "Anoop Shah; Ciara Gribben; Jennifer Bishop; Peter Hanlon; David Caldwell; Rachael Wood; Martin Reid; Jim McMenamin; David Goldberg; Diane Stockton; Sharon Hutchinson; Chris Robertson; Paul M McKeigue; Helen M Colhoun; David McAllister", + "affiliations": "London School of Hygiene and Tropical Medicine; Public Health Scotland; Public Health Scotland; University of Glasgow; Public Health Scotland; PublicHealth Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; University of Glasgow", + "abstract": "BackgroundThe effect of vaccination for COVID-19 on onward transmission is unknown.\n\nMethodsA national record linkage study determined documented COVID-19 cases and hospitalisations in unvaccinated household members of vaccinated and unvaccinated healthcare workers from 8th December 2020 to 3rd March 2021. The primary endpoint was COVID-19 14 days following the first dose.\n\nResultsThe cohort comprised of 194,362 household members (mean age 31{middle dot}1 {+/-} 20{middle dot}9 years) and 144,525 healthcare workers (mean age 44{middle dot}4 {+/-} 11{middle dot}4 years). 113,253 (78{middle dot}3%) of healthcare workers received at least one dose of the BNT162b2 mRNA or ChAdOx1 nCoV-19 vaccine and 36,227 (25{middle dot}1%) received a second dose. There were 3,123 and 4,343 documented COVID-19 cases and 175 and 177 COVID-19 hospitalisations in household members of healthcare workers and healthcare workers respectively. Household members of vaccinated healthcare workers had a lower risk of COVID-19 case compared to household members of unvaccinated healthcare worker (rate per 100 person-years 9{middle dot}40 versus 5{middle dot}93; HR 0{middle dot}70, 95% confidence interval [CI] 0{middle dot}63 to 0{middle dot}78). The effect size for COVID-19 hospitalisation was similar, with the confidence interval crossing the null (HR 0{middle dot}77 [95% CI 0{middle dot}53 to 1{middle dot}10]). The rate per 100 person years was lower in vaccinated compared to unvaccinated healthcare workers for documented (20{middle dot}13 versus 8{middle dot}51; HR 0{middle dot}45 [95% CI 0{middle dot}42 to 0{middle dot}49]) and hospitalized COVID-19 (0{middle dot}97 versus 0{middle dot}14; HR 0{middle dot}16 [95% CI 0{middle dot}09 to 0{middle dot}27]). Compared to the period before the first dose, the risk of documented COVID-19 case was lower at [≥] 14 days after the second dose for household members (HR 0{middle dot}46 [95% CI 0{middle dot}30to 0{middle dot}70]) and healthcare workers (HR 0{middle dot}08 [95% CI 0{middle dot}04 to 0{middle dot}17]).\n\nInterpretationVaccination of health care workers was associated with a substantial reduction in COVID-19 cases in household contacts consistent with an effect of vaccination on transmission.", + "category": "public and global health", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.03.17.21253853", @@ -2743,6 +2813,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.03.18.21253443", + "date": "2021-03-20", + "link": "https://medrxiv.org/cgi/content/short/2021.03.18.21253443", + "title": "Intensity of COVID-19 in care homes following Hospital Discharge in the early stages of the UK epidemic", + "authors": "Joe Hollinghurst; Laura North; Chris Emmerson; Ashley Akbari; Fatemeh Torabi; Ronan A Lyons; Alan G Hawkes; Ed Bennett; Mike B Gravenor; Richard Fry", + "affiliations": "Swansea University; Swansea University; Public Health Wales; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University", + "abstract": "BackgroundA defining feature of the COVID-19 pandemic in many countries was the tragic extent to which care home residents were affected, and the difficulty preventing introduction and subsequent spread of infection. Management of risk in care homes requires good evidence on the most important transmission pathways. One hypothesised route at the start of the pandemic, prior to widespread testing, was transfer of patients from hospitals, which were experiencing high levels of nosocomial events.\n\nMethodsWe tested the hypothesis that hospital discharge events increased the intensity of care home cases using a national individually linked health record cohort in Wales, UK. We monitored 186,772 hospital discharge events over the period March to July 2020, tracking individuals to 923 care homes and recording the daily case rate in the homes populated by 15,772 residents. We estimated the risk of an increase in cases rates following exposure to a hospital discharge using multi-level hierarchical logistic regression, and a novel stochastic Hawkes process outbreak model.\n\nFindingsIn regression analysis, after adjusting for care home size, we found no significant association between hospital discharge and subsequent increases in care home case numbers (odds ratio: 0.99, 95% CI 0.82, 1.90). Risk factors for increased cases included care home size, care home resident density, and provision of nursing care. Using our outbreak model, we found a significant effect of hospital discharge on the subsequent intensity of cases. However, the effect was small, and considerably less than the effect of care home size, suggesting the highest risk of introduction came from interaction with the community. We estimated approximately 1.8% of hospital discharged patients may have been infected.\n\nInterpretationThere is growing evidence in the UK that the risk of transfer of COVID-19 from the high-risk hospital setting to the high-risk care home setting during the early stages of the pandemic was relatively small. Although access to testing was limited to initial symptomatic cases in each care home at this time, our results suggest that reduced numbers of discharges, selection of patients, and action taken within care homes following transfer all may have contributed to mitigation. The precise key transmission routes from the community remain to be quantified.", + "category": "health informatics", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.03.04.21252931", @@ -3163,20 +3247,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.12.03.20243535", - "date": "2020-12-04", - "link": "https://medrxiv.org/cgi/content/short/2020.12.03.20243535", - "title": "OpenSAFELY: impact of national guidance on switching from warfarin to direct oral anticoagulants (DOACs) in early phase of COVID-19 pandemic in England", - "authors": "Helen J Curtis; Brian MacKenna; Alex J Walker; Richard Croker; Amir Mehrkar; Caroline E Morton; Seb Bacon; George Hickman; Peter Inglesby; Chris Bates; David Evans; Tom Ward; Jonathan Cockburn; Simon Davy; Krishnan Bhaskaran; Anna Schultze; Christopher T Rentsch; Elizabeth Williamson; William Hulme; Helen I McDonald; Laurie Tomlinson; Rohini Mathur; Henry Drysdale; Rosalind M Eggo; Kevin Wing; Angel Wong; Harriet Forbes; John Parry; Frank Hester; Sam Harper; Stephen JW Evans; Ian J Douglas; Liam Smeeth; Ben Goldacre", - "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; TPP; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP; TPP; TPP; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford", - "abstract": "BackgroundEarly in the COVID-19 pandemic the NHS recommended that appropriate patients anticoagulated with warfarin should be switched to direct acting oral anticoagulants (DOACs), requiring less frequent blood testing. Subsequently, a national safety alert was issued regarding patients being inappropriately co-prescribed two anticoagulants following a medication change, and associated monitoring.\n\nObjectiveTo describe which people were switched from warfarin to DOACs; identify potentially unsafe co-prescribing of anticoagulants; and assess whether abnormal clotting results have become more frequent during the pandemic.\n\nMethodsWorking on behalf of NHS England we conducted a population cohort based study using routine clinical data from >17 million adults in England.\n\nResults20,000 of 164,000 warfarin patients (12.2%) switched to DOACs between March and May 2020, most commonly to edoxaban and apixaban. Factors associated with switching included: older age, recent renal function test, higher number of recent INR tests recorded, atrial fibrillation diagnosis and care home residency. There was a sharp rise in co-prescribing of warfarin and DOACs from typically 50-100 per month to 246 in April 2020, 0.06% of all people receiving a DOAC or warfarin. INR testing fell by 14% to 506.8 patients tested per 1000 warfarin patients each month. We observed a very small increase in elevated INRs (n=470) during April compared with January (n=420).\n\nConclusionsIncreased switching of anticoagulants from warfarin to DOACs was observed at the outset of the COVID-19 pandemic in England following national guidance. There was a small but substantial number of people co-prescribed warfarin and DOACs during this period. Despite a national safety alert on the issue, a widespread rise in elevated INR test results was not found. Primary care has responded rapidly to changes in patient care during the COVID-19 pandemic.", - "category": "cardiovascular medicine", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.11.27.20238147", @@ -3779,20 +3849,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.08.17.20175117", - "date": "2020-08-21", - "link": "https://medrxiv.org/cgi/content/short/2020.08.17.20175117", - "title": "Real-time spatial health surveillance: mapping the UK COVID-19 epidemic", - "authors": "Richard Fry; Joe Hollinghurst; Helen R Stagg; Daniel A Thompson; Claudio Fronterre; Chris Orton; Ronan A Lyons; David V Ford; Aziz Sheikh; Peter J Diggle", - "affiliations": "Swansea University; Swansea University; Edinburgh University; Swansea University; Lancaster University; Swansea University; Swansea University; Swansea University; Edinburgh University; Lancaster University", - "abstract": "The COVID-19 pandemic has highlighted the need for robust data linkage systems and methods for identifying outbreaks of disease in near real-time. Using self-reported app data and the Secure Anonymised Information Linkage (SAIL) Databank, we demonstrate the use of sophisticated spatial modelling for near-real-time prediction of COVID-19 prevalence at small-area resolution to inform strategic government policy areas. A pre-requisite to an effective control strategy is that predictions need to be accompanied by estimates of their precision, to guard against over-reaction to potentially spurious features of best guess predictions. In the UK, important emerging risk-factors such as social deprivation or ethnicity vary over small distances, hence risk needs to be modelled at fine spatial resolution to avoid aggregation bias. We demonstrate that existing geospatial statistical methods originally developed for global health applications are well-suited to this task and can be used in an anonymised databank environment, thus preserving the privacy of the individuals who contribute their data.", - "category": "public and global health", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.08.12.20173690", @@ -4493,6 +4549,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.05.06.20092999", + "date": "2020-05-07", + "link": "https://medrxiv.org/cgi/content/short/2020.05.06.20092999", + "title": "OpenSAFELY: factors associated with COVID-19-related hospital death in the linked electronic health records of 17 million adult NHS patients.", + "authors": "- The OpenSAFELY Collaborative; Elizabeth Williamson; Alex J Walker; Krishnan J Bhaskaran; Seb Bacon; Chris Bates; Caroline E Morton; Helen J Curtis; Amir Mehrkar; David Evans; Peter Inglesby; Jonathan Cockburn; Helen I Mcdonald; Brian MacKenna; Laurie Tomlinson; Ian J Douglas; Christopher T Rentsch; Rohini Mathur; Angel Wong; Richard Grieve; David Harrison; Harriet Forbes; Anna Schultze; Richard T Croker; John Parry; Frank Hester; Sam Harper; Rafael Perera; Stephen Evans; Liam Smeeth; Ben Goldacre", + "affiliations": "; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; TPP; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; ICNARC; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; TPP; TPP; TPP; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford", + "abstract": "BackgroundEstablishing who is at risk from a novel rapidly arising cause of death, and why, requires a new approach to epidemiological research with very large datasets and timely data. Working on behalf of NHS England we therefore set out to deliver a secure and pseudonymised analytics platform inside the data centre of a major primary care electronic health records vendor establishing coverage across detailed primary care records for a substantial proportion of all patients in England. The following results are preliminary.\n\nData sourcesPrimary care electronic health records managed by the electronic health record vendor TPP, pseudonymously linked to patient-level data from the COVID-19 Patient Notification System (CPNS) for death of hospital inpatients with confirmed COVID-19, using the new OpenSAFELY platform.\n\nPopulation17,425,445 adults.\n\nTime period1st Feb 2020 to 25th April 2020.\n\nPrimary outcomeDeath in hospital among people with confirmed COVID-19.\n\nMethodsCohort study analysed by Cox-regression to generate hazard ratios: age and sex adjusted, and multiply adjusted for co-variates selected prospectively on the basis of clinical interest and prior findings.\n\nResultsThere were 5683 deaths attributed to COVID-19. In summary after full adjustment, death from COVID-19 was strongly associated with: being male (hazard ratio 1.99, 95%CI 1.88-2.10); older age and deprivation (both with a strong gradient); uncontrolled diabetes (HR 2.36 95% CI 2.18-2.56); severe asthma (HR 1.25 CI 1.08-1.44); and various other prior medical conditions. Compared to people with ethnicity recorded as white, black people were at higher risk of death, with only partial attenuation in hazard ratios from the fully adjusted model (age-sex adjusted HR 2.17 95% CI 1.84-2.57; fully adjusted HR 1.71 95% CI 1.44-2.02); with similar findings for Asian people (age-sex adjusted HR 1.95 95% CI 1.73-2.18; fully adjusted HR 1.62 95% CI 1.431.82).\n\nConclusionsWe have quantified a range of clinical risk factors for death from COVID-19, some of which were not previously well characterised, in the largest cohort study conducted by any country to date. People from Asian and black groups are at markedly increased risk of in-hospital death from COVID-19, and contrary to some prior speculation this is only partially attributable to pre-existing clinical risk factors or deprivation; further research into the drivers of this association is therefore urgently required. Deprivation is also a major risk factor with, again, little of the excess risk explained by co-morbidity or other risk factors. The findings for clinical risk factors are concordant with policies in the UK for protecting those at highest risk. Our OpenSAFELY platform is rapidly adding further NHS patients records; we will update and extend these results regularly.", + "category": "epidemiology", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.05.02.20078642", @@ -4535,20 +4605,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "bioRxiv", - "doi": "10.1101/2020.04.28.066977", - "date": "2020-04-29", - "link": "https://biorxiv.org/cgi/content/short/2020.04.28.066977", - "title": "Controlling the SARS-CoV-2 outbreak, insights from large scale whole genome sequences generated across the world", - "authors": "Jody Phelan; Wouter Deelder; Daniel Ward; Susana Campino; Martin L Hibberd; Taane G Clark", - "affiliations": "London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine", - "abstract": "BackgroundSARS-CoV-2 most likely evolved from a bat beta-coronavirus and started infecting humans in December 2019. Since then it has rapidly infected people around the world, with more than 4.5 million confirmed cases by the middle of May 2020. Early genome sequencing of the virus has enabled the development of molecular diagnostics and the commencement of therapy and vaccine development. The analysis of the early sequences showed relatively few evolutionary selection pressures. However, with the rapid worldwide expansion into diverse human populations, significant genetic variations are becoming increasingly likely. The current limitations on social movement between countries also offers the opportunity for these viral variants to become distinct strains with potential implications for diagnostics, therapies and vaccines.\n\nMethodsWe used the current sequencing archives (NCBI and GISAID) to investigate 15,487 whole genomes, looking for evidence of strain diversification and selective pressure.\n\nResultsWe used 6,294 SNPs to build a phylogenetic tree of SARS-CoV-2 diversity and noted strong evidence for the existence of two major clades and six sub-clades, unevenly distributed across the world. We also noted that convergent evolution has potentially occurred across several locations in the genome, showing selection pressures, including on the spike glycoprotein where we noted a potentially critical mutation that could affect its binding to the ACE2 receptor. We also report on mutations that could prevent current molecular diagnostics from detecting some of the sub-clades.\n\nConclusionThe worldwide whole genome sequencing effort is revealing the challenge of developing SARS-CoV-2 containment tools suitable for everyone and the need for data to be continually evaluated to ensure accuracy in outbreak estimations.", - "category": "genomics", - "match_type": "exact", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.04.22.20072124", @@ -4661,6 +4717,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.04.02.20051284", + "date": "2020-04-06", + "link": "https://medrxiv.org/cgi/content/short/2020.04.02.20051284", + "title": "Building an International Consortium for Tracking Coronavirus Health Status", + "authors": "Eran Segal; Feng Zhang; Xihong Lin; Gary King; Ophir Shalem; Smadar Shilo; William E. Allen; Yonatan H. Grad; Casey S. Greene; Faisal Alquaddoomi; Simon Anders; Ran Balicer; Tal Bauman; Ximena Bonilla; Gisel Booman; Andrew T. Chan; Ori Ori Cohen; Silvano Coletti; Natalie Davidson; Yuval Dor; David A. Drew; Olivier Elemento; Georgina Evans; Phil Ewels; Joshua Gale; Amir Gavrieli; Benjamin Geiger; Iman Hajirasouliha; Roman Jerala; Andre Kahles; Olli Kallioniemi; Ayya Keshet; Gregory Landua; Tomer Meir; Aline Muller; Long H. Nguyen; Matej Oresic; Svetlana Ovchinnikova; Hedi Peterson; Jay Rajagopal; Gunnar Ratsch; Hagai Rossman; Johan Rung; Andrea Sboner; Alexandros Sigaras; Tim Spector; Ron Steinherz; Irene Stevens; Jaak Vilo; Paul Wilmes; CCC (Coronavirus Census Collective)", + "affiliations": "Weizmann Institute of Science; Howard Hughes Medical Institute, Core Member, Broad Institute of MIT and Harvard, United States; Departments of Biostatistics and Statistics, Harvard T.H. Chan School of Public Health; Albert J. Weatherhead III University, Institute for Quantitative Social Science, Harvard University; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, United States; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Society of Fellows, Harvard University, United States; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, United States; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, United States; ETH Zurich, NEXUS Personalized Health Technologies, Zurich, Switzerland; Center for Molecular Biology (ZMBH), University of Heidelberg, Germany; Clalit Research Institute, Clalit Health Services, Israel; Mapping and Geo-Information Engineering, Civil and Environmental Engineering Faculty, The Technion, Israel; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich, ; Regen Network, Argentina; Massachusetts General Hospital (MGH), United States; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Chelonia Applied Science, Switzerland; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich, ; School of Medicine-IMRIC-Developmental Biology and Cancer Research, The Hebrew University; Massachusetts General Hospital (MGH), United States; Englander Institute for Precision Medicine and Department of Physiology and Biophysics, Weill Cornell Medicine, USA; Institute for Quantitative Social Science, Harvard University; Science for Life Laboratory (SciLifeLab), Department of Biochemistry and Biophysics, Stockholm University, Sweden; symptometrics.org; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Department of immunology, Weizmann Institute of Science, Israel; Englander Institute for Precision Medicine and Department of Physiology and Biophysics, Weill Cornell Medicine, USA; Department of Synthetic biology and Immunology, National Institute of Chemistry, Slovenia; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich, ; Science for Life Laboratory (SciLifeLab), Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Regen Network, United States; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Luxembourg Institute of Socio-Economic Research and University of Luxembourg, Luxembourg; Massachusetts General Hospital (MGH), United States; School of Medical Sciences, Orebro University, Orebro, Sweden, and Turku Bioscience Centre, University of Turku and Abo Akademi University, Turku, Finland; Center for Molecular Biology (ZMBH), University of Heidelberg, Germany; Institute of Computer Science, University of Tartu, Estonia, Estonia; Internal Medicine, Harvard Medical School, Department of Pulmonary Medicine and Critical Care, Massachusetts General Hospital (MGH), United States; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich a; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Science for Life Laboratory (SciLifeLab), Department of Immunology, Genetics and Pathology, Uppsala university, Sweden; Englander Institute for Precision Medicine and Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, USA; Englander Institute for Precision Medicine and Department of Physiology and Biophysics, Weill Cornell Medicine, USA; Kings College, United Kingdom; Regen Network, United States; Science for Life Laboratory (SciLifeLab), Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Sweden; Institute of Computer Science, University of Tartu, Estonia, Estonia; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg; ", + "abstract": "Information is the most potent protective weapon we have to combat a pandemic, at both the individual and global level. For individuals, information can help us make personal decisions and provide a sense of security. For the global community, information can inform policy decisions and offer critical insights into the epidemic of COVID-19 disease. Fully leveraging the power of information, however, requires large amounts of data and access to it. To achieve this, we are making steps to form an international consortium, Coronavirus Census Collective (CCC, coronaviruscensuscollective.org), that will serve as a hub for integrating information from multiple data sources that can be utilized to understand, monitor, predict, and combat global pandemics. These sources may include self-reported health status through surveys (including mobile apps), results of diagnostic laboratory tests, and other static and real-time geospatial data. This collective effort to track and share information will be invaluable in predicting hotspots of disease outbreak, identifying which factors control the rate of spreading, informing immediate policy decisions, evaluating the effectiveness of measures taken by health organizations on pandemic control, and providing critical insight on the etiology of COVID-19. It will also help individuals stay informed on this rapidly evolving situation and contribute to other global efforts to slow the spread of disease.\n\nIn the past few weeks, several initiatives across the globe have surfaced to use daily self-reported symptoms as a means to track disease spread, predict outbreak locations, guide population measures and help in the allocation of healthcare resources. The aim of this paper is to put out a call to standardize these efforts and spark a collaborative effort to maximize the global gain while protecting participant privacy.", + "category": "infectious diseases", + "match_type": "exact", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.03.30.20047217", diff --git a/data/covid/preprints.json b/data/covid/preprints.json index 7f2adbc8..88f39531 100644 --- a/data/covid/preprints.json +++ b/data/covid/preprints.json @@ -7,7 +7,7 @@ "title": "Comparative safety and effectiveness of Pfizer BA.4-5 versus Sanofi during the spring 2023 COVID-19 booster vaccination programme in England: a matched cohort study in OpenSAFELY-TPP", "authors": "- The OpenSAFELY Collaborative; Colm D Andrews; Em Prestige; Edward P K Parker; Venexia Walker; Tom Palmer; Andrea L Schaffer; Amelia CA Green; Helen J Curtis; Alex J Walker; Rebecca M Smith; Christopher Wood; Christopher Bates; Amir Mehrkar; Brian MacKenna; Sebastian CJ Bacon; Ben Goldacre; Miguel A Hernan; Jonathan AC Sterne; William J Hulme", "affiliations": "; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Bristol; University of Bristol; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Harvard University; University of Bristol; University of Oxford", - "abstract": "Introduction The spring 2023 COVID-19 booster vaccination programme in England used both Pfizer BA.4-5 and Sanofi vaccines. All people aged 75 years or over and the clinically vulnerable were eligible to receive a booster dose. Direct comparisons of the effectiveness of these two vaccines in boosting protection against severe COVID-19 events have not been made in trials or observational data. Methods With the approval of NHS England, we used the OpenSAFELY-TPP database to compare effectiveness of the Pfizer BA.4-5 and Sanofi vaccines during the spring 2023 booster programme, between 1 April and 30 June 2023. We investigated two cohorts separately: those aged 75 or over (75+); and those aged 50 or over and clinically vulnerable (CV). In each cohort, vaccine recipients were matched on date of vaccination, COVID-19 vaccine history, age, and other characteristics. Effectiveness outcomes were COVID-19 hospital admission, COVID-19 critical care admission, and COVID-19 death up to 16 weeks after vaccination. Safety outcomes were pericarditis and myocarditis up to 4 weeks after vaccination. We report the cumulative incidence of each outcome, and compare safety and effectiveness using risk differences (RD), relative risks (RR), and incidence rate ratios (IRRs). Results 492,642 people were 1-1 matched in the CV cohort, and 673,926 in the 75+ cohort, contributing a total of 7,423,251 and 10,173,230 person-weeks of follow-up, respectively. The incidence of COVID-19 hospital admission was higher for Sanofi than for Pfizer BA.4-5. In the CV cohort, 16-week risks per 10,000 people were 22.3 (95%CI 20.4 to 24.3) for Pfizer BA.4-5 and 26.4 (24.4 to 28.7) for Sanofi, with an IRR of 1.19 (95%CI 1.06 to 1.34). In the 75+ cohort, these were 17.5 (16.1 to 19.1) for Pfizer BA.4-5 and 20.4 (18.9 to 22.1) for Sanofi, with an IRR of 1.18 (1.05-1.32). These findings were similar across all pre-specified subgroups. More severe COVID-19 related outcomes (critical care admission and death), and safety outcomes at 4 weeks, were rare in both vaccines so we could not reliably compare effectiveness of the two vaccines. Conclusion This observational study comparing effectiveness of Pfizer BA.4-5 and Sanofi vaccine during the spring 2023 programme in England in the two main eligible cohorts - people aged 75 and over and in clinically vulnerable people - found some evidence of superior effectiveness against COVID-19 hospital admission for Pfizer BA.4-5 compared with Sanofi within 16 weeks after vaccination.", + "abstract": "IntroductionThe spring 2023 COVID-19 booster vaccination programme in England used both Pfizer BA.4-5 and Sanofi vaccines. All people aged 75 years or over and the clinically vulnerable were eligible to receive a booster dose. Direct comparisons of the effectiveness of these two vaccines in boosting protection against severe COVID-19 events have not been made in trials or observational data.\n\nMethodsWith the approval of NHS England, we used the OpenSAFELY-TPP database to compare effectiveness of the Pfizer BA.4-5 and Sanofi vaccines during the spring 2023 booster programme, between 1 April and 30 June 2023. We investigated two cohorts separately: those aged 75 or over (75+); and those aged 50 or over and clinically vulnerable (CV). In each cohort, vaccine recipients were matched on date of vaccination, COVID-19 vaccine history, age, and other characteristics. Effectiveness outcomes were COVID-19 hospital admission, COVID-19 critical care admission, and COVID-19 death up to 16 weeks after vaccination. Safety outcomes were pericarditis and myocarditis up to 4 weeks after vaccination. We report the cumulative incidence of each outcome, and compare safety and effectiveness using risk differences (RD), relative risks (RR), and incidence rate ratios (IRRs).\n\nResults492,642 people were 1-1 matched in the CV cohort, and 673,926 in the 75+ cohort, contributing a total of 7,423,251 and 10,173,230 person-weeks of follow-up, respectively. The incidence of COVID-19 hospital admission was higher for Sanofi than for Pfizer BA.4-5. In the CV cohort, 16-week risks per 10,000 people were 22.3 (95%CI 20.4 to 24.3) for Pfizer BA.4-5 and 26.4 (24.4 to 28.7) for Sanofi, with an IRR of 1.19 (95%CI 1.06 to 1.34). In the 75+ cohort, these were 17.5 (16.1 to 19.1) for Pfizer BA.4-5 and 20.4 (18.9 to 22.1) for Sanofi, with an IRR of 1.18 (1.05-1.32). These findings were similar across all pre-specified subgroups. More severe COVID-19 related outcomes (critical care admission and death), and safety outcomes at 4 weeks, were rare in both vaccines so we could not reliably compare effectiveness of the two vaccines.\n\nConclusionThis observational study comparing effectiveness of Pfizer BA.4-5 and Sanofi vaccine during the spring 2023 programme in England in the two main eligible cohorts - people aged 75 and over and in clinically vulnerable people - found some evidence of superior effectiveness against COVID-19 hospital admission for Pfizer BA.4-5 compared with Sanofi within 16 weeks after vaccination.", "category": "primary care research", "match_type": "fuzzy", "author_similarity": 100, @@ -265,20 +265,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2023.11.24.23296021", - "date": "2023-11-27", - "link": "https://medrxiv.org/cgi/content/short/2023.11.24.23296021", - "title": "Severe acute myositis and myocarditis upon initiation of six-weekly Pembrolizumab post-COVID-19 mRNA vaccination", - "authors": "Robert Aerwyn Watson; Weiyu Ye; Chelsea Alice Taylor; Rosalin Anisha Cooper; Orion Tong; Tim James; Brian Shine; Monika Hofer; Damian Jenkins; Robert Pell; Eleni Ieremia; Stephanie Jones; David Maldonado-Perez; Ian Roberts; Nicholas Coupe; Mark Ross Middleton; Miranda Jane Payne; Benjamin Peter Fairfax", - "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; University of Oxford; University of Oxford; Oxford University Hospitals NHS Foundation Trust; Oxford University Hospitals NHS Foundation Trust; University of Oxford; Oxford University Hospitals NHS Foundation Trust; University of Oxford", - "abstract": "We describe three cases of critical acute myositis with myocarditis occurring within 22 days of each other at a single institution, all within one month of receiving the initial cycle of the anti-PD-1 drug Pembrolizumab. Analysis of T cell receptor repertoires from peripheral blood and tissues revealed a high degree of clonal expansion and public clones between cases, with several T cell clones expanded within the skeletal muscle putatively recognising viral epitopes. All patients had recently received a COVID-19 mRNA booster vaccine prior to treatment and were positive for SARS-CoV2 Spike antibody. In conclusion, we report a series of unusually severe myositis and myocarditis following PD-1 blockade and the COVID-19 mRNA vaccination.", - "category": "oncology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2023.11.09.23298162", @@ -713,6 +699,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2023.05.23.23289798", + "date": "2023-05-24", + "link": "https://medrxiv.org/cgi/content/short/2023.05.23.23289798", + "title": "Primary Care Post-COVID syndrome Diagnosis and Referral Coding", + "authors": "Robert Willans; Gail Allsopp; Pall Jonsson; Fiona Glen; Felix Greaves; John Macleod; Yinghui Wei; Sebastian Bacon; Amir Mehrkar; Alex Walker; Brian MacKenna; Louis Fisher; Ben Goldacre; - The OpenSAFELY Collaborative; - The CONVALESCENCE Collaborative", + "affiliations": "National Institute of Health and Care Excellence; Royal College of General Practitioners; National Institute of Health and Care Excellence; National Institute of Health and Care Excellence; National Institute of Health and Care Excellence; University of Bristol; University of Plymouth; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford; ; ", + "abstract": "IntroductionGuidelines for diagnosing and managing Post-COVID syndrome have been rapidly developed. Consistency of the application of these guidelines in primary care is unknown. Electronic health records provide an opportunity to review the use of codes relating to Post-COVID syndrome. This paper explores the use of primary care records as a surrogate uptake measure for NICEs rapid guideline \"managing the long-term effects of COVID-19\" by measuring the use of Post-COVID syndrome diagnosis and referral codes in the pathway.\n\nMethodWith the approval of NHS England we used routine clinical data from the OpenSafely-EMIS/-TPP platforms. Counts of Post-COVID syndrome diagnosis and referral codes were generated from a cohort of all adults, establishing numbers of diagnoses and referrals following diagnosis. The relationship between Post-COVID syndrome diagnosis and referral codes was explored with reference to NICEs rapid guideline.\n\nResultsOf over 45 million patients, 69,220 (0.15%) had a Post-COVID syndrome diagnostic code, and 67,741 (0.15%) had a referral code. 78% of referral codes did not have an associated diagnosis code. 79% of diagnosis codes had no subsequent referral code. Only 18,633 (0.04%) had both. There were higher rates of both diagnosis and referral in those who were more deprived, female and some ethnic groups.\n\nDiscussionThis study demonstrates variation in diagnosis and referral coding rates for Post-COVID syndrome across different patient groups. The results, with limited crossover of referral and diagnostic codes, suggest only one type of code is usually recorded. Recording one code limits the use of routine data for monitoring Post-COVID syndrome diagnosis and management, but suggests several areas for improvement in coding. Post-COVID syndrome coding, particularly diagnosis coding, needs to improve before administrators and researchers can use it to evaluate care pathways.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2023.05.17.23290105", @@ -825,6 +825,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2023.03.21.23287524", + "date": "2023-03-22", + "link": "https://medrxiv.org/cgi/content/short/2023.03.21.23287524", + "title": "Employment outcomes of people with Long Covid symptoms: community-based cohort study", + "authors": "Daniel Ayoubkhani; Francesco Zaccardi; Koen B Pouwels; Ann Sarah Walker; Donald Houston; Nisreen A Alwan; Josh Martin; Kamlesh Khunti; Vahe Nafilyan", + "affiliations": "Office for National Statistics; University of Leicester; University of Oxford; University of Oxford; University of Portsmouth; University of Southampton; Bank of England; University of Leicester; Office for National Statistics", + "abstract": "BackgroundEvidence on the long-term employment consequences of SARS-CoV-2 infection is lacking. We used data from a large, community-based sample in the UK to estimate associations between Long Covid and subsequent employment outcomes.\n\nMethodsThis was an observational, longitudinal study using a pre-post design. We included survey participants from 3 February 2021 to 30 September 2022 when they were aged 16 to 64 years and not in full-time education. Using conditional logit modelling, we explored the time-varying relationship between Long Covid status [≥]12 weeks after a first test-confirmed SARS-CoV-2 infection (reference: pre-infection) and labour market inactivity (neither working nor looking for work) or workplace absence lasting [≥]4 weeks.\n\nResultsOf 206,299 included participants (mean age 45 years, 54% female, 92% white), 15% were ever inactive in the labour market and 10% were ever long-term absent during follow-up. Compared with pre-infection, inactivity was higher in participants reporting Long Covid 30 to <40 weeks (adjusted odds ratio (aOR): 1.45; 95% CI: 1.17 to 1.81) or 40 to <52 weeks (1.34; 1.05 to 1.72) post-infection. Combining with official statistics on Long Covid prevalence, our estimates translate to 27,000 (95% CI: 6,000 to 47,000) working-age adults in the UK being inactive because of Long Covid in July 2022.\n\nConclusionsLong Covid is likely to have contributed to reduced levels of participation in the UK labour market, though it is unlikely to be the sole driver. Further research is required to quantify the contribution of other factors, such as indirect health effects of the pandemic.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2023.03.15.23287300", @@ -1497,6 +1511,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.09.11.22279823", + "date": "2022-09-12", + "link": "https://medrxiv.org/cgi/content/short/2022.09.11.22279823", + "title": "Effects of the COVID-19 pandemic on the mental health of clinically extremely vulnerable children and children living with clinically extremely vulnerable people in Wales: A data linkage study", + "authors": "Laura Elizabeth Cowley; Karen Hodgson; Jiao Song; Tony Whiffen; Jacinta Tan; Ann John; Amrita Bandyopadhyay; Alisha R Davies", + "affiliations": "Swansea University; Public Health Wales; Public Health Wales; Welsh Government; University of Oxford; Swansea University; Swansea University; Public Health Wales", + "abstract": "ObjectivesTo determine whether clinically extremely vulnerable (CEV) children or children living with a CEV person in Wales were at greater risk of presenting with anxiety or depression in primary or secondary care during the COVID-19 pandemic compared with children in the general population, and to compare patterns of anxiety and depression during the pandemic (23rd March 2020-31st January 2021, referred to as 2020/21) and before the pandemic (March 23rd 2019-January 31st 2020, referred to as 2019/20), between CEV children and the general population.\n\nDesignPopulation-based cross-sectional cohort study using anonymised, linked, routinely collected health and administrative data held in the Secure Anonymised Information Linkage Databank. CEV individuals were identified using the COVID-19 Shielded Patient List.\n\nSettingPrimary and secondary healthcare settings covering 80% of the population of Wales.\n\nParticipantsChildren aged 2-17 in Wales: CEV (3,769); living with a CEV person (20,033); or neither (415,009).\n\nPrimary outcome measureFirst record of anxiety or depression in primary or secondary healthcare in 2019/20 and 2020/21, identified using Read and ICD-10 codes.\n\nResultsA Cox regression model adjusted for demographics and history of anxiety or depression revealed that only CEV children were at greater risk of presenting with anxiety or depression during the pandemic compared with the general population (Hazard Ratio=2.27, 95% Confidence Interval=1.94-2.66, p<0.001). Compared with the general population, the risk amongst CEV children was higher in 2020/21 (Risk Ratio 3.04) compared with 2019/20 (Risk Ratio 1.90). In 2020/21, the cumulative incidence of anxiety or depression increased slightly amongst CEV children, but declined amongst the general population.\n\nConclusionsDifferences in the cumulative incidences of recorded anxiety or depression in healthcare between CEV children and the general population were largely driven by a reduction in presentations to healthcare services by children in the general population during the pandemic.\n\nStrengths and limitations of this studyO_LIStrengths of this study include its novelty, national focus and clinical relevance; to date this is the first population-based study examining the effects of the COVID-19 pandemic on healthcare use for anxiety or depression amongst clinically extremely vulnerable (CEV) children and children living with a CEV person in Wales\nC_LIO_LIWe compared 2020/21 data with pre-pandemic 2019/20 data for CEV children and children in the general population, to place the impact of the COVID-19 pandemic in the context of longer-term patterns of healthcare use\nC_LIO_LIWe used a novel approach and linked multiple datasets to identify a cohort of children living with a CEV person in Wales during the COVID-19 pandemic\nC_LIO_LIThere was heterogeneity within the Shielded Patient List that was used to create the cohorts of children identified as CEV or living with a CEV person, in terms of the type and severity of individuals underlying conditions; the manner in which people were added to the list; the time point that people were added to the list; and the extent to which people followed the shielding guidance\nC_LIO_LIRoutinely collected healthcare data does not capture self-reported health, and is likely to underestimate the burden of common mental disorders in the population\nC_LI", + "category": "pediatrics", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.09.09.22279754", @@ -1525,6 +1553,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.08.29.22279359", + "date": "2022-08-31", + "link": "https://medrxiv.org/cgi/content/short/2022.08.29.22279359", + "title": "Prophylactic Treatment of COVID-19 in Care Homes Trial (PROTECT-CH)", + "authors": "Philip M Bath; Jonathan Ball; Matthew Boyd; Heather Gage; Matthew Glover; Maureen Godfrey; Bruce Guthrie; Jonathan Hewitt; Robert Howard; Thomas Jaki; Edmund Juszczak; Daniel Lasserson; Paul Leighton; Val Leyland; Wei Shen Lim; Pip Logan; Garry Meakin; Alan Montgomery; Reuben Ogollah; Peter Passmore; Philip Quinlan; Caroline Rick; Simon Royal; Susan D Shenkin; Clare Upton; Adam L Gordon; - PROTECT-CH Trialists", + "affiliations": "University of Nottingham; University of Nottingham; University of Nottingham; University of Surrey; University of Surrey; Private person; University of Edinburgh; Llandough Hospital; University College London; University of Cambridge; University of Nottingham; University of Warwick; University of Nottingham; Private person; Nottingham University Hospitals NHS Trust; University of Nottingham; University of Nottingham; University of Nottingham; University of Nottingham; Queen's University Belfast; University of Nottingham; University of Nottingham; Cripps Health Centre; University of Edinburgh; University of Nottingham; University of Nottingham; ", + "abstract": "BackgroundCoronavirus disease 2019 (COVID-19) is associated with significant mortality and morbidity in care homes. Novel or repurposed antiviral drugs may reduce infection and disease severity through reducing viral replication and inflammation.\n\nObjectiveTo compare the safety and efficacy of antiviral agents (ciclesonide, niclosamide) for preventing SARS-CoV-2 infection and COVID-19 severity in care home residents.\n\nDesignCluster-randomised open-label blinded endpoint platform clinical trial testing antiviral agents in a post-exposure prophylaxis paradigm.\n\nSettingCare homes across all four United Kingdom member countries.\n\nParticipantsCare home residents 65 years of age or older.\n\nInterventionsCare homes were to be allocated at random by computer to 42 days of antiviral agent plus standard care versus standard of care and followed for 60 days after randomisation.\n\nMain outcome measuresThe primary four-level ordered categorical outcome with participants classified according to the most serious of all-cause mortality, all-cause hospitalisation, SARS-CoV-2 infection and no infection. Analysis using ordinal logistic regression was by intention to treat. Other outcomes included the components of the primary outcome and transmission.\n\nResultsDelays in contracting between NIHR and the manufacturers of potential antiviral agents significantly delayed any potential start date. Having set up the trial (protocol, approvals, insurance, website, database, routine data algorithms, training materials), the trial was stopped in September 2021 prior to contracting of care homes and general practitioners in view of the success of vaccination in care homes with significantly reduced infections, hospitalisations and deaths. As a result, the sample size target (based on COVID-19 rates and deaths occurring in February-June 2020) became unfeasible.\n\nLimitationsCare home residents were not approached about the trial and so were not consented and did not receive treatment. Hence, the feasibility of screening, consent, treatment and data acquisition, and potential benefit of post exposure prophylaxis were never tested. Further, contracting between the University of Nottingham and the PIs, GPs and care homes was not completed, so the feasibility of contracting with all the different groups at the scale needed was not tested.\n\nConclusionsThe role of post exposure prophylaxis of COVID-19 in care home residents was not tested because of changes in COVID-19 incidence, prevalence and virulence as a consequence of the vaccination programme that rendered the study unfeasible. Significant progress was made in describing and developing the infrastructure necessary for a large scale Clinical Trial of Investigational Medicinal Products in care homes in all four UK nations.\n\nFuture workThe role of post-exposure prophylaxis of COVID-19 in care home residents remains to be defined. Significant logistical barriers to conducting research in care homes during a pandemic need to be removed before such studies are possible in the required short timescale.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.08.29.22279333", @@ -2029,20 +2071,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.05.22.22275417", - "date": "2022-05-23", - "link": "https://medrxiv.org/cgi/content/short/2022.05.22.22275417", - "title": "Comparative effectiveness of sotrovimab and molnupiravir for prevention of severe COVID-19 outcomes in non-hospitalised patients: an observational cohort study using the OpenSAFELY platform", - "authors": "Bang Zheng; Amelia CA Green; John Tazare; Helen J Curtis; Louis Fisher; Linda Nab; Anna Schultze; Viyaasan Mahalingasivam; Edward Parker; William J Hulme; Sebastian CJ Bacon; Nicholas J DeVito; Christopher Bates; David Evans; Peter Inglesby; Henry Drysdale; Simon Davy; Jonathan Cockburn; Caroline E Morton; George Hickman; Tom Ward; Rebecca M Smith; John Parry; Frank Hester; Sam Harper; Amir Mehrkar; Rosalind M Eggo; Alex J Walker; Stephen JW Evans; Ian J Douglas; Brian MacKenna; Ben Goldacre; Laurie A Tomlinson", - "affiliations": "London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; London School of Hygiene and Trop. Med.; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; TPP; TPP; University of Oxford; London School of Hygiene & Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; University of Oxford; London School of Hygiene and Tropical Medicine", - "abstract": "ObjectiveTo compare the effectiveness of sotrovimab (a neutralising monoclonal antibody) vs. molnupiravir (an antiviral) in preventing severe COVID-19 outcomes in non-hospitalised high-risk COVID-19 adult patients.\n\nDesignWith the approval of NHS England, we conducted a real-world cohort study using the OpenSAFELY-TPP platform.\n\nSettingPatient-level electronic health record data were obtained from 24 million people registered with a general practice in England that uses TPP software. The primary care data were securely linked with data on COVID-19 infection and therapeutics, hospital admission, and death within the OpenSAFELY-TPP platform, covering a period where both medications were frequently prescribed in community settings.\n\nParticipantsNon-hospitalised adult COVID-19 patients at high risk of severe outcomes treated with sotrovimab or molnupiravir since December 16, 2021.\n\nInterventionsSotrovimab or molnupiravir administered in the community by COVID-19 Medicine Delivery Units.\n\nMain outcome measureCOVID-19 related hospitalisation or COVID-19 related death within 28 days after treatment initiation.\n\nResultsBetween December 16, 2021 and February 10, 2022, 3331 and 2689 patients were treated with sotrovimab and molnupiravir, with no substantial differences in their baseline characteristics. The mean age of all 6020 patients was 52 (SD=16) years; 59% were female, 89% White and 88% had three or more COVID-19 vaccinations. Within 28 days after treatment initiation, 87 (1.4%) COVID-19 related hospitalisations/deaths were observed (32 treated with sotrovimab and 55 with molnupiravir). Cox proportional hazards models stratified by area showed that after adjusting for demographics, high-risk cohort categories, vaccination status, calendar time, body mass index and other comorbidities, treatment with sotrovimab was associated with a substantially lower risk than treatment with molnupiravir (hazard ratio, HR=0.54, 95% CI: 0.33 to 0.88; P=0.014). Consistent results were obtained from propensity score weighted Cox models (HR=0.50, 95% CI: 0.31 to 0.81; P=0.005) and when restricted to fully vaccinated people (HR=0.53, 95% CI: 0.31 to 0.90; P=0.019). No substantial effect modifications by other characteristics were detected (all P values for interaction>0.10). Findings were similar in an exploratory analysis of patients treated between February 16 and May 1, 2022 when the Omicron BA.2 variant was dominant in England.\n\nConclusionIn routine care of non-hospitalised high-risk adult patients with COVID-19 in England, those who received sotrovimab were at lower risk of severe COVID-19 outcomes than those receiving molnupiravir.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.05.21.22275368", @@ -2057,6 +2085,20 @@ "author_similarity": 96, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.05.19.22275214", + "date": "2022-05-22", + "link": "https://medrxiv.org/cgi/content/short/2022.05.19.22275214", + "title": "Antibody levels following vaccination against SARS-CoV-2: associations with post-vaccination infection and risk factors", + "authors": "Nathan J Cheetham; Milla Kibble; Andrew Wong; Richard J Silverwood; Anika Knuppel; Dylan M Williams; Olivia K L Hamilton; Paul H Lee; Charis Bridger Staatz; Giorgio Di Gessa; Jingmin Zhu; Srinivasa Vittal Katikireddi; George B Ploubidis; Ellen J Thompson; Ruth C E Bowyer; Xinyuan Zhang; Golboo Abbasian; Maria Paz Garcia; Deborah Hart; Jeffrew Seow; Carl Graham; Neophytos Kouphou; Sam Acors; Michael H Malim; Ruth E Mitchell; Kate Northstone; Daniel Major-Smith; Sarah Matthews; Thomas Breeze; Michael Crawford; Lynn Molloy; Alex Siu Fung Kwong; Katie J Doores; Nishi Chaturvedi; Emma L Duncan; Nicholas J Timpson; Claire J Steves", + "affiliations": "King's College London; University of Cambridge; University College London; University College London; University College London; University College London; University of Glasgow; University of Leicester; University College London; University College London; University College London; University of Glasgow; University College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; University of Bristol; King's College London; University College London; King's College London; University of Bristol; King's College London", + "abstract": "SARS-CoV-2 antibody levels can be used to assess humoral immune responses following SARS-CoV-2 infection or vaccination, and may predict risk of future infection. From cross-sectional antibody testing of 9,361 individuals from TwinsUK and ALSPAC UK population-based longitudinal studies (jointly in April-May 2021, and TwinsUK only in November 2021-January 2022), we tested associations between antibody levels following vaccination and: (1) SARS-CoV-2 infection following vaccination(s); (2) health, socio-demographic, SARS-CoV-2 infection and SARS-CoV-2 vaccination variables.\n\nWithin TwinsUK, single-vaccinated individuals with the lowest 20% of anti-Spike antibody levels at initial testing had 3-fold greater odds of SARS-CoV-2 infection over the next six to nine months, compared to the top 20%. In TwinsUK and ALSPAC, individuals identified as at increased risk of COVID-19 complication through the UK \"Shielded Patient List\" had consistently greater odds (2 to 4-fold) of having antibody levels in the lowest 10%. Third vaccination increased absolute antibody levels for almost all individuals, and reduced relative disparities compared with earlier vaccinations.\n\nThese findings quantify the association between antibody level and risk of subsequent infection, and support a policy of triple vaccination for the generation of protective antibodies.\n\nLay summaryIn this study, we analysed blood samples from 9,361 participants from two studies in the UK: an adult twin registry, TwinsUK (4,739 individuals); and the Avon Longitudinal Study of Parents and Children, ALSPAC (4,622 individuals). We did this work as part of the UK Government National Core Studies initiative researching COVID-19. We measured blood antibodies which are specific to SARS-CoV-2 (which causes COVID-19). Having a third COVID-19 vaccination boosted antibody levels. More than 90% of people from TwinsUK had levels after third vaccination that were greater than the average level after second vaccination. Importantly, this was the case even in individuals on the UK \"Shielded Patient List\". We found that people with lower antibody levels after first vaccination were more likely to report having COVID-19 later on, compared to people with higher antibody levels. People on the UK \"Shielded Patient List\", and individuals who reported that they had poorer general health, were more likely to have lower antibody levels after vaccination. In contrast, people who had had a previous COVID-19 infection were more likely to have higher antibody levels following vaccination compared to people without infection. People receiving the Oxford/AstraZeneca rather than the Pfizer BioNTech vaccine had lower antibody levels after one or two vaccinations. However, after a third vaccination, there was no difference in antibody levels between those who had Oxford/AstraZeneca and Pfizer BioNTech vaccines for their first two doses. These findings support having a third COVID-19 vaccination to boost antibodies.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.05.11.22274964", @@ -2141,20 +2183,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.05.05.22273234", - "date": "2022-05-07", - "link": "https://medrxiv.org/cgi/content/short/2022.05.05.22273234", - "title": "Changes in English medication safety indicators throughout the COVID-19 pandemic: a federated analysis of 57 million patients' primary care records in situ using OpenSAFELY", - "authors": "Louis Fisher; Lisa E M Hopcroft; Sarah Rodgers; James Barrett; Kerry Oliver; Anthony J Avery; Dai Evans; Helen Curtis; Richard Croker; Orla Macdonald; Jessica Morley; Amir Mehrkar; Seb Bacon; Simon Davy; Iain Dillingham; David Evans; George Hickman; Peter Inglesby; Caroline E Morton; Becky Smith; Tom Ward; William Hulme; Amelia Green; Jon Massey; Alex J Walker; Chris Bates; Jonathan Cockburn; John Parry; Frank Hester; Sam Harper; Shaun O'Hanlon; Alex Eavis; Richard Jarvis; Dima Avramov; Paul Griffiths; Aaron Fowles; Nasreen Parkes; Ben Goldacre; Brian MacKenna", - "affiliations": "Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; PRIMIS, School of Medicine, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK; PRIMIS, School of Medicine, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK; PRIMIS, School of Medicine, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK; Centre for Academic Primary Care, School of Medicine, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK; PRIMIS, School of Medicine, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA; EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA; EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA; EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA; EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA; EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA; EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG", - "abstract": "ObjectiveTo describe the impact of the COVID-19 pandemic on safe prescribing, using the PINCER prescribing indicators; to implement complex prescribing indicators at national scale using GP data.\n\nDesignPopulation based cohort study, with the approval of NHS England using the OpenSAFELY platform.\n\nSettingElectronic health record data from 56.8 million NHS patients general practice records.\n\nParticipantsAll NHS patients registered at a GP practice using TPP or EMIS computer systems and recorded as at risk of at least one potentially hazardous PINCER indicator between September 2019 and September 2021.\n\nMain outcome measureMonthly trends and between-practice variation for compliance with 13 PINCER measures between September 2019 and September 2021.\n\nResultsThe indicators were successfully implemented across GP data in OpenSAFELY. Hazardous prescribing remained largely unchanged during the COVID-19 pandemic, with only small reductions in achievement of the PINCER indicators. There were transient delays in blood test monitoring for some medications, particularly ACE inhibitors. All indicators exhibited substantial recovery by September 2021. We identified 1,813,058 patients at risk of at least one hazardous prescribing event.\n\nConclusionGood performance was maintained during the COVID-19 pandemic across a diverse range of widely evaluated measures of safe prescribing.\n\nSummary box O_TEXTBOXWHAT IS ALREADY KNOWN ON THIS TOPICO_LIPrimary care services were substantially disrupted by the COVID-19 pandemic.\nC_LIO_LIDisruption to safe prescribing during the pandemic has not previously been evaluated.\nC_LIO_LIPINCER is a nationally adopted programme of activities that aims to identify and correct hazardous prescribing in GP practices, by conducting manual audit on subgroups of practices.\nC_LI\n\nWHAT THIS STUDY ADDSO_LIFor the first time, we were able to successfully generate data on PINCER indicators for almost the whole population of England, in a single analysis.\nC_LIO_LIOur study is the most comprehensive assessment of medication safety during the COVID-19 pandemic in England, covering 95% of the population using well-validated measures.\nC_LIO_LIGood performance was maintained across many PINCER indicators throughout the pandemic.\nC_LIO_LIDelays in delivering some medication-related blood test monitoring were evident though considerable recovery was made by the end of the study period.\nC_LI\n\nC_TEXTBOX", - "category": "primary care research", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.05.03.22274395", @@ -2505,20 +2533,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.03.17.22272535", - "date": "2022-03-18", - "link": "https://medrxiv.org/cgi/content/short/2022.03.17.22272535", - "title": "Comparison of the 2021 COVID-19 'Roadmap' Projections against Public Health Data", - "authors": "Matt J Keeling; Louise J Dyson; Michael Tildesley; Edward M Hill; Sam M Moore", - "affiliations": "University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick", - "abstract": "Control and mitigation of the COVID-19 pandemic in England has relied on a combination of vaccination and non-pharmaceutical interventions (NPIs). Some of these NPIs are extremely costly (economically and socially), so it was important to relax these promptly without overwhelming already burdened health services. The eventual policy was a Roadmap of four relaxation steps throughout 2021, taking England from lock-down to the cessation of all restrictions on social interaction. In a series of six Roadmap documents generated throughout 2021, models assessed the potential risk of each relaxation step. Here we show that the model projections generated a reliable estimation of medium-term hospital admission trends, with the data points up to September 2021 generally lying within our 95% prediction intervals. The greatest uncertainties in the modelled scenarios came from vaccine efficacy estimates against novel variants, and from assumptions about human behaviour in the face of changing restrictions and risk.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.03.15.22272362", @@ -2533,6 +2547,20 @@ "author_similarity": 94, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.03.14.22272283", + "date": "2022-03-14", + "link": "https://medrxiv.org/cgi/content/short/2022.03.14.22272283", + "title": "Migrants' primary care utilisation before and during the COVID-19 pandemic in England: An interrupted time series", + "authors": "Claire X Zhang; Yamina Boukari; Neha Pathak; Rohini Mathur; Srinivasa Vittal Katikireddi; Parth Patel; In\u00eas Campos-Matos; Dan Lewer; Vincent Nguyen; Greg Hugenholtz; Rachel Burns; Amy R Mulick; Alasdair Henderson; Robert W Aldridge", + "affiliations": "UCL; University College London; University College London; London School of Hygiene and Tropical Medicine; University of Glasgow; University College London; Department of Health and Social Care; University College London; University College London; University College London; University College London; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; UCL", + "abstract": "BackgroundHow international migrants access and use primary care in England is poorly understood. We aimed to compare primary care consultation rates between international migrants and non-migrants in England before and during the COVID-19 pandemic (2015- 2020).\n\nMethodsUsing linked data from the Clinical Practice Research Datalink (CPRD) GOLD and the Office for National Statistics, we identified migrants using country-of-birth, visa-status or other codes indicating international migration. We ran a controlled interrupted time series (ITS) using negative binomial regression to compare rates before and during the pandemic.\n\nFindingsIn 262,644 individuals, pre-pandemic consultation rates per person-year were 4.35 (4.34-4.36) for migrants and 4.6 (4.59-4.6) for non-migrants (RR:0.94 [0.92-0.96]). Between 29 March and 26 December 2020, rates reduced to 3.54 (3.52-3.57) for migrants and 4.2 (4.17-4.23) for non-migrants (RR:0.84 [0.8-0.88]). Overall, this represents an 11% widening of the pre-pandemic difference in consultation rates between migrants and non-migrants during the first year of the pandemic (RR:0.89, 95%CI:0.84-0.94). This widening was greater for children, individuals whose first language was not English, and individuals of White British, White non-British and Black/African/Caribbean/Black British ethnicities.\n\nInterpretationMigrants were less likely to use primary care before the pandemic and the first year of the pandemic exacerbated this difference. As GP practices retain remote and hybrid models of service delivery, they must improve services and ensure they are accessible and responsive to migrants healthcare needs.\n\nFundingThis study was funded by the Medical Research Council (MR/V028375/1) and Wellcome Clinical Research Career Development Fellowship (206602).", + "category": "primary care research", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.03.10.22272177", @@ -2561,6 +2589,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2022.03.13.22272176", + "date": "2022-03-13", + "link": "https://medrxiv.org/cgi/content/short/2022.03.13.22272176", + "title": "Vaccination against SARS-CoV-2 in UK school-aged children and young people decreases infection rates and reduces COVID-19 symptoms", + "authors": "Erika Molteni; Liane S Canas; Kerstin Klaser; Jie Deng; Sunil S Bhopal; Robert C Hughes; Liyuan Chen; Benjamin Murray; Eric Kerfoot; Michela Antonelli; Carole Helene Sudre; Joan Capdevila Pujol; Lorenzo Polidori; Anna May; Alexander Hammers; Jonathan Wolf; Timothy Spector; Claire J Steves; Sebastien Ourselin; Michael Absoud; Marc Modat; Emma L Duncan", + "affiliations": "King's College London; King's College London; King's College London; King's College London; Newcastle University; London School of Hygiene & Tropical Medicine, London; King's College London; King's College London; King's College London; King's College London; King's College London; Zoe Limited, London, UK; Zoe Limited, London, UK; Zoe Limited, London, UK; King's College London; Zoe Limited, London, UK; King's College London; King's College London; King's College London; King's College London; King's College London; King's College London", + "abstract": "BackgroundWe aimed to explore the effectiveness of one-dose BNT162b2 vaccination upon SARS-CoV-2 infection, its effect on COVID-19 presentation, and post-vaccination symptoms in children and young people (CYP) in the UK during periods of Delta and Omicron variant predominance.\n\nMethodsIn this prospective longitudinal cohort study, we analysed data from 115,775 CYP aged 12-17 years, proxy-reported through the Covid Symptom Study (CSS) smartphone application. We calculated post-vaccination infection risk after one dose of BNT162b2, and described the illness profile of CYP with post-vaccination SARS- CoV-2 infection, compared to unvaccinated CYP, and post-vaccination side-effects.\n\nFindingsBetween August 5, 2021 and February 14, 2022, 25,971 UK CYP aged 12-17 years received one dose of BNT162b2 vaccine. Vaccination reduced (proxy-reported) infection risk (-80{middle dot}4% and -53{middle dot}7% at 14-30 days with Delta and Omicron variants respectively, and -61{middle dot}5% and -63{middle dot}7% after 61-90 days). The probability of remaining infection-free diverged soon after vaccination, and was greater in CYP with prior SARS-CoV-2 infection. Vaccinated CYP who contracted SARS-CoV-2 during the Delta period had milder disease than unvaccinated CYP; during the Omicron period this was only evident in children aged 12-15 years. Overall disease profile was similar in both vaccinated and unvaccinated CYP. Post-vaccination local side-effects were common, systemic side-effects were uncommon, and both resolved quickly.\n\nInterpretationOne dose of BNT162b2 vaccine reduced risk of SARS-CoV-2 infection for at least 90 days in CYP aged 12-17 years. Vaccine protection varied for SARS-CoV-2 variant type (lower for Omicron than Delta variant), and was enhanced by pre-vaccination SARS-CoV-2 infection. Severity of COVID-19 presentation after vaccination was generally milder, although unvaccinated CYP also had generally mild disease. Overall, vaccination was well-tolerated.\n\nFundingUK Government Department of Health and Social Care, Chronic Disease Research Foundation, The Wellcome Trust, UK Engineering and Physical Sciences Research Council, UK Research and Innovation London Medical Imaging & Artificial Intelligence Centre for Value Based Healthcare, UK National Institute for Health Research, UK Medical Research Council, British Heart Foundation and Alzheimers Society, and ZOE Limited.\n\nResearch in context\n\nEvidence before this studyWe searched PubMed database for peer-reviewed articles and medRxiv for preprint papers, published between January 1, 2021 and February 15, 2022 using keywords (\"SARS-CoV-2\" OR \"COVID-19\") AND (child* OR p?ediatric* OR teenager*) AND (\"vaccin*\" OR \"immunization campaign\") AND (\"efficacy\" OR \"effectiveness\" OR \"symptoms\") AND (\"delta\" or \"omicron\" OR \"B.1.617.2\" OR \"B.1.1.529\"). The PubMed search retrieved 36 studies, of which fewer than 30% specifically investigated individuals <18 years.\n\nEleven studies explored SARS-CoV-2 viral transmission: seroprevalence in children (n=4), including age-dependency of susceptibility to SARS-CoV-2 infection (n=1), SARS-CoV-2 transmission in schools (n=5), and the effect of school closure on viral transmission (n=1).\n\nEighteen documents reported clinical aspects, including manifestation of infection (n=13), symptomatology, disease duration, and severity in children. Other studies estimated emergency department visits, hospitalization, need for intensive care, and/or deaths in children (n=4), and explored prognostic factors (n=1).\n\nThirteen studies explored vaccination-related aspects, including vaccination of children within specific paediatric co-morbidity groups (e.g., children with Down syndrome, inflammatory bowel disease, and cancer survivors, n=4), mRNA vaccine efficacy in children and adolescents from the general population (n=7), and the relation between vaccination and severity of disease and hospitalization cases (n=2). Four clinical trials were conducted using mRNA vaccines in minors, also exploring side effects. Sixty percent of children were found to have side effects after BNT162b2 vaccination, and especially after the second dose; however, most symptoms were mild and transient apart from rare uncomplicated skin ulcers. Two studies focused on severe adverse effects and safety of SARS-CoV-2 vaccines in children, reporting on myocarditis episodes and two cases of Guillain-Barre syndrome. All other studies were beyond the scope of our research.\n\nAdded value of this studyWe assessed multiple components of the UK vaccination campaign in a cohort of children and young people (CYP) aged 12-17 years drawn from a large UK community-based citizen-science study, who received a first dose of BNT162b2 vaccine. We describe a variant-dependent protective effect of the first dose against both Delta and Omicron, with additional protective effect of pre-vaccination SARS- CoV-2 infection on post-vaccination re-infection. We compare the illness profile in CYP infected post-vaccination with that of unvaccinated CYP, demonstrating overall milder disease with fewer symptoms for vaccinated CYP. We describe local and systemic side-effects during the first week following first-dose vaccination, confirming that local symptoms are common, systemic symptoms uncommon, and both usually transient.\n\nImplications of all the available evidenceOur data confirm that first dose BNT162b2 vaccination in CYP reduces risk of infection by SARS-CoV-2 variants, with generally local and brief side-effects. If infected after vaccination, COVID-19 is milder, if manifest at all. The study aims to contribute quantitative evidence to the risk-benefit evaluation of vaccination in CYP to inform discussion regarding rationale for their vaccination and the designing of national immunisation campaigns for this age group; and applies citizen-science approaches in the conduct of epidemiological surveillance and data collection in the UK community.\n\nImportantly, this study was conducted during Delta and Omicron predominance in UK; specificity of vaccine efficacy to variants is also illustrated; and results may not be generalizable to future SARS-CoV-2 strains.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 94, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2022.03.10.22272081", @@ -2967,20 +3009,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2022.01.05.21268323", - "date": "2022-01-06", - "link": "https://medrxiv.org/cgi/content/short/2022.01.05.21268323", - "title": "Lineage replacement and evolution captured by the United Kingdom Covid Infection Survey", - "authors": "Katrina A Lythgoe; Tanya Golubchik; Matthew Hall; Thomas House; Roberto Cahuantzi; George MacIntyre-Cockett; Helen Fryer; Laura Thomson; Anel Nurtay; Mahan Ghafari; David Buck; Angie Green; Amy Trebes; Paolo Piazza; Lorne J Lonie; Ruth Studley; Emma Rourke; Darren Smith; Matthew Bashton; Andrew Nelson; Matthew Crown; Clare McCann; Gregory R Young; Rui Andre Nunes de Santos; Zack Richards; Adnan Tariq; - Wellcome Sanger Institute COVID-19 Surveillance Team; - COVID-19 Infection Survey Group; - The COVID-19 Genomics UK (COG-UK) consortium; Christophe Fraser; Ian Diamond; Jeff Barrett; Ann Sarah Walker; David Bonsall", - "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Manchester; University of Manchester; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; Office for National Statistics; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Northumbria University; Wellcome Sanger Institute; Office for National Statistics; ; University of Oxford; Office for National Statistics; Wellcome Sanger Institute; University of Oxford; University of Oxford", - "abstract": "The Office for National Statistics COVID-19 Infection Survey (ONS-CIS) is the largest surveillance study of SARS-CoV-2 positivity in the community, and collected data on the United Kingdom (UK) epidemic from April 2020 until March 2023 before being paused. Here, we report on the epidemiological and evolutionary dynamics of SARS-CoV-2 determined by analysing the sequenced samples collected by the ONS-CIS during this period. We observed a series of sweeps or partial sweeps, with each sweeping lineage having a distinct growth advantage compared to their predecessors. The sweeps also generated an alternating pattern in which most samples had either S-gene target failure (SGTF) or non- SGTF over time. Evolution was characterised by steadily increasing divergence and diversity within lineages, but with step increases in divergence associated with each sweeping major lineage. This led to a faster overall rate of evolution when measured at the between-lineage level compared to within lineages, and fluctuating levels of diversity. These observations highlight the value of viral sequencing integrated into community surveillance studies to monitor the viral epidemiology and evolution of SARS-CoV-2, and potentially other pathogens, particularly in the current phase of the pandemic with routine RT-PCR testing now ended in the community.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2022.01.01.21268131", @@ -3065,6 +3093,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.12.22.21268252", + "date": "2021-12-24", + "link": "https://medrxiv.org/cgi/content/short/2021.12.22.21268252", + "title": "Rapid increase in Omicron infections in England during December 2021: REACT-1 study", + "authors": "Paul Elliott; Barbara Bodinier; Oliver Eales; Haowei Wang; David Haw; Joshua Elliott; Matthew Whitaker; Jakob Jonnerby; David Tang; Caroline E. Walters; Christina Atchinson; Peter J. Diggle; Andrew J. Page; Alex Trotter; Deborah Ashby; Wendy Barclay; Graham Taylor; Helen Ward; Ara Darzi; Graham Cooke; Marc Chadeau-Hyam; Christl A Donnelly", + "affiliations": "School of Public Health, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; Imperial College London; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; Imperial College London; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency; School of Public Health, Imperial College London, UK; CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK; Quadram Institute, Norwich, UK; Quadram Institute Bioscience; School of Public Health, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research; Imperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research Centre, UKInstitute of Global Health Innovation at ; Department of Infectious Disease, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency", + "abstract": "BackgroundThe highest-ever recorded numbers of daily severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in England has been observed during December 2021 and have coincided with a rapid rise in the highly transmissible Omicron variant despite high levels of vaccination in the population. Although additional COVID-19 measures have been introduced in England and internationally to contain the epidemic, there remains uncertainty about the spread and severity of Omicron infections among the general population.\n\nMethodsThe REal-time Assessment of Community Transmission-1 (REACT-1) study has been monitoring the prevalence of SARS-CoV-2 infection in England since May 2020. REACT-1 obtains self-administered throat and nose swabs from a random sample of the population of England at ages 5 years and over. Swabs are tested for SARS-CoV-2 infection by reverse transcription polymerase chain reaction (RT-PCR) and samples testing positive are sent for viral genome sequencing. To date 16 rounds have been completed, each including [~]100,000 or more participants with data collected over a period of 2 to 3 weeks per month. Socio-demographic, lifestyle and clinical information (including previous history of COVID-19 and symptoms prior to swabbing) is collected by online or telephone questionnaire. Here we report results from round 14 (9-27 September 2021), round 15 (19 October - 05 November 2021) and round 16 (23 November - 14 December 2021) for a total of 297,728 participants with a valid RT-PCR test result, of whom 259,225 (87.1%) consented for linkage to their NHS records including detailed information on vaccination (vaccination status, date). We used these data to estimate community prevalence and trends by age and region, to evaluate vaccine effectiveness against infection in children ages 12 to 17 years, and effect of a third (booster) dose in adults, and to monitor the emergence of the Omicron variant in England.\n\nResultsWe observed a high overall prevalence of 1.41% (1.33%, 1.51%) in the community during round 16. We found strong evidence of an increase in prevalence during round 16 with an estimated reproduction number R of 1.13 (1.06, 1.09) for the whole of round 16 and 1.27 (1.14, 1.40) when restricting to observations from 1 December onwards. The reproduction number in those aged 18-54 years was estimated at 1.23 (1.14, 1.33) for the whole of round 16 and 1.41 (1.23, 1.61) from 1 December. Our data also provide strong evidence of a steep increase in prevalence in London with an estimated R of 1.62 (1.34, 1.93) from 1 December onwards and a daily prevalence reaching 6.07% (4.06%, 9.00%) on 14 December 2021. As of 1 to 11 December 2021, of the 275 lineages determined, 11 (4.0%) corresponded to the Omicron variant. The first Omicron infection was detected in London on 3 December, and subsequent infections mostly appeared in the South of England. The 11 Omicron cases were all aged 18 to 54 years, double-vaccinated (reflecting the large numbers of people who have received two doses of vaccine in this age group) but not boosted, 9 were men, 5 lived in London and 7 were symptomatic (5 with classic COVID-19 symptoms: loss or change of sense of smell or taste, fever, persistent cough), 2 were asymptomatic, and symptoms were unknown for 2 cases. The proportion of Omicron (vs Delta or Delta sub-lineages) was found to increase rapidly with a daily increase of 66.0% (32.7%, 127.3%) in the odds of Omicron (vs. Delta) infection, conditional on swab positivity. Highest prevalence of swab positivity by age was observed in (unvaccinated) children aged 5 to 11 years (4.74% [4.15%, 5.40%]) similar to the prevalence observed at these ages in round 15. In contrast, prevalence in children aged 12 to 17 years more than halved from 5.35% (4.78%, 5.99%) in round 15 to 2.31% (1.91%, 2.80%) in round 16. As of 14 December 2021, 76.6% children at ages 12 to 17 years had received at least one vaccine dose; we estimated that vaccine effectiveness against infection was 57.9% (44.1%, 68.3%) in this age group. In addition, the prevalence of swab positivity in adults aged 65 years and over fell by over 40% from 0.84% (0.72%, 0.99%) in round 15 to 0.48% (0.39%,0.59%) in round 16 and for those aged 75 years and over it fell by two-thirds from 0.63% (0.48%,0.82%) to 0.21% (0.13%,0.32%). At these ages a high proportion of participants (>90%) had received a third vaccine dose; we estimated that adults having received a third vaccine dose had a three- to four-fold lower risk of testing positive compared to those who had received two doses.\n\nConclusionA large fall in swab positivity from round 15 to round 16 among 12 to 17 year olds, most of whom have been vaccinated, contrasts with the continuing high prevalence among 5 to 11 year olds who have largely not been vaccinated. Likewise there were large falls in swab positivity among people aged 65 years and over, the vast majority of whom have had a third (booster) vaccine dose; these results reinforce the importance of the vaccine and booster campaign. However, the rapidly increasing prevalence of SARS-CoV-2 infections in England during December 2021, coincident with the rapid rise of Omicron infections, may lead to renewed pressure on health services. Additional measures beyond vaccination may be needed to control the current wave of infections and prevent health services (in England and other countries) from being overwhelmed.\n\nSummaryThe unprecedented rise in SARS-CoV-2 infections is concurrent with rapid spread of the Omicron variant in England and globally. We analysed prevalence of SARS-CoV-2 and its dynamics in England from end of November to mid-December 2021 among almost 100,000 participants from the REACT-1 study. Prevalence was high during December 2021 with rapid growth nationally and in London, and of the proportion of infections due to Omicron. We observed a large fall in swab positivity among mostly vaccinated older children (12-17 years) compared with unvaccinated younger children (5-11 years), and in adults who received a third vs. two doses of vaccine. Our results reiterate the importance of vaccination and booster campaigns; however, additional measures may be needed to control the rapid growth of the Omicron variant.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.12.21.21268214", @@ -3303,6 +3345,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.12.03.21266112", + "date": "2021-12-05", + "link": "https://medrxiv.org/cgi/content/short/2021.12.03.21266112", + "title": "Brain Injury in COVID-19 is Associated with Autoinflammation and Autoimmunity", + "authors": "Edward J Needham; Alex L Ren; Richard J Digby; Joanne G Outtrim; Dorothy A Chatfield; Virginia FJ Newcombe; Rainer Doffinger; Gabriela Barcenas-Morales; Claudia Fonseca; Michael J Taussig; Rowan M Burnstein; Cordelia Dunai; Nyarie Sithole; Nicholas J Ashton; Henrik Zetterberg; Magnus Gisslen; Eden Arvid; Emelie Marklund; Michael J Griffiths; Jonathan Cavanagh; Gerome Breen; Sarosh R Irani; Anne Elmer; Nathalie Kingston; John R Bradley; Leonie S Taams; Benedict D michael; Edward T Bullmore; Kenneth GC Smith; Paul A Lyons; Alasdair JC Coles; David K Menon; - Cambridge NeuroCOVID Group; - NIHR Cambridge Covid BioResource; - NIHR Cambridge Clinical Research Facility", + "affiliations": "Department of Clinical Neurosciences, University of Cambridge, UK; Division of Anaesthesia, Department of Medicine, University of Cambridge, UK.; Division of Anaesthesia, Department of Medicine, University of Cambridge, UK.; Division of Anaesthesia, Department of Medicine, University of Cambridge, UK.; Division of Anaesthesia, Department of Medicine, University of Cambridge, UK.; Division of Anaesthesia, Department of Medicine, University of Cambridge, UK.; Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK.; Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK.; Cambridge Protein Arrays Ltd, Babraham Research Campus, Cambridge, UK; Cambridge Protein Arrays Ltd, Babraham Research Campus, Cambridge, UK; Division of Anaesthesia, Department of Medicine, University of Cambridge, UK.; Clinical Infection Microbiology and Neuroimmunology, Institute of Infection, Veterinary and Ecological Science, Liverpool, UK.; Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK.; Department of Psychiatry and Neurochemistry, Institute of Neuroscience & Physiology, the Sahlgrenska Academy at the University of Gothenburg, Molndal, Sweden.; Department of Psychiatry and Neurochemistry, Institute of Neuroscience & Physiology, the Sahlgrenska Academy at the University of Gothenburg, Molndal, Sweden; C; Department of Infectious Diseases, Institute of Biomedicine, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden; Region Vastra Gotaland; Department of Infectious Diseases, Institute of Biomedicine, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden; Region Vastra Gotaland; Department of Infectious Diseases, Institute of Biomnedicine, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden; Region Vastra Gotalan; Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK.; Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, U; Department of Social Genetic and Developmental Psychiatry, King's College London, London, UK.; Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Department of Neurology, Oxford University H; Cambridge Clinical Research Centre, NIHR Clinical Research Facility, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, UK ; NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge, UK.; NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge, UK; Department of Medicine, University of Cambridge, Ad; Centre for Inflammation Biology and Cancer Immunology and Dept Inflammation Biology, School of Immunology and Microbial Sciences, Kings College London, Guys Cam; Clinical Infection Microbiology and Neuroimmunology, Institute of Infection, Veterinary and Ecological Science, Liverpool, UK.; Department of Psychiatry, University of Cambridge, Herchel Smith Building for Brain and Mind Sciences, Cambridge Biomedical Campus, Cambridge, UK.; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Je; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Je; Department of Clinical Neurosciences, University of Cambridge, UK; Division of Anaesthesia, Department of Medicine, University of Cambridge, UK.; ; ; ", + "abstract": "COVID-19 has been associated with many neurological complications including stroke, delirium and encephalitis. Furthermore, many individuals experience a protracted post-viral syndrome which is dominated by neuropsychiatric symptoms, and is seemingly unrelated to COVID-19 severity. The true frequency and underlying mechanisms of neurological injury are unknown, but exaggerated host inflammatory responses appear to be a key driver of severe COVID-19 more broadly.\n\nWe sought to investigate the dynamics of, and relationship between, serum markers of brain injury (neurofilament light [NfL], Glial Fibrillary Acidic Protein [GFAP] and total Tau) and markers of dysregulated host response including measures of autoinflammation (proinflammatory cytokines) and autoimmunity. Brain injury biomarkers were measured using the Quanterix Simoa HDx platform, cytokine profiling by Luminex (R&D) and autoantibodies by a custom protein microarray.\n\nDuring hospitalisation, patients with COVID-19 demonstrated elevations of NfL and GFAP in a severity-dependant manner, and there was evidence of ongoing active brain injury at follow-up 4 months later. Raised NfL and GFAP were associated with both elevations of pro-inflammatory cytokines and the presence of autoantibodies; autoantibodies were commonly seen against lung surfactant proteins as well as brain proteins such as myelin associated glycoprotein, but reactivity was seen to a large number of different antigens.\n\nFurthermore, a distinct process characterised by elevation of serum total Tau was seen in patients at follow-up, which appeared to be independent of initial disease severity and was not associated with dysregulated immune responses in the same manner as NfL and GFAP.", + "category": "neurology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.11.24.21266818", @@ -3443,6 +3499,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.11.15.21266264", + "date": "2021-11-16", + "link": "https://medrxiv.org/cgi/content/short/2021.11.15.21266264", + "title": "Association of COVID-19 employment disruption with mental and social wellbeing: evidence from nine UK longitudinal studies", + "authors": "Jacques Wels; Charlotte Booth; Bozena Wielgoszewska; Michael J Green; Giorgio Di Gessa; Charlotte F Huggins; Gareth J Griffith; Alex Siu Fung Kwong; Ruth C E Bowyer; Jane Maddock; Praveetha Patalay; Richard J Silverwood; Emla Fitzsimons; Richard John Shaw; Ellen J Thompson; Andrew Steptoe; Alun Hughes; Nishi Chaturvedi; Claire J Steves; Srinivasa Vittal Katikireddi; George B Ploubidis", + "affiliations": "University College London; University College London; University College London; University of Glasgow; University College London; University of Edinburgh; University of Bristol; University of Bristol; King's College London; University College London; University College London; University College London; University College London; University of Glasgow; Kings College London; University College London; University College London; University College London; King's College London; University of Glasgow; University College London", + "abstract": "BackgroundThe COVID-19 pandemic has led to major economic disruptions. In March 2020, the UK implemented the Coronavirus Job Retention Scheme - known as furlough - to minimize the impact of job losses. We investigate associations between change in employment status and mental and social wellbeing during the early stages of the pandemic.\n\nMethodsData were from 25,670 respondents, aged 17 to 66, across nine UK longitudinal studies. Furlough and other employment changes were defined using employment status pre-pandemic and during the first lockdown (April-June 2020). Mental and social wellbeing outcomes included psychological distress, life satisfaction, self-rated health, social contact, and loneliness. Study-specific modified Poisson regression estimates, adjusting for socio-demographic characteristics and pre-pandemic mental and social wellbeing measures, were pooled using meta-analysis.\n\nResultsCompared to those who remained working, furloughed workers were at greater risk of psychological distress (adjusted risk ratio, ARR=1.12; 95% CI: 0.97, 1.29), low life satisfaction (ARR=1.14; 95% CI: 1.07, 1.22), loneliness (ARR=1.12; 95% CI: 1.01, 1.23), and poor self-rated health (ARR=1.26; 95% CI: 1.05, 1.50), but excess risk was less pronounced than that of those no longer employed (e.g., ARR for psychological distress=1.39; 95% CI: 1.21, 1.59) or in stable unemployment (ARR=1.33; 95% CI: 1.09, 1.62).\n\nConclusionsDuring the early stages of the pandemic, those furloughed had increased risk for poor mental and social wellbeing. However, their excess risk was lower in magnitude than that of those who became or remained unemployed, suggesting that furlough may have partly mitigated poorer outcomes.", + "category": "psychiatry and clinical psychology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.11.15.21266255", @@ -3457,20 +3527,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.11.10.21266124", - "date": "2021-11-11", - "link": "https://medrxiv.org/cgi/content/short/2021.11.10.21266124", - "title": "Differences in COVID-19 vaccination coverage by occupation in England: a national linked data study", - "authors": "Vahe Nafilyan; Ted Dolby; Katie Finning; Jasper Morgan; Rhiannon Edge; Myer Glickman; Neil Pearce; Martie Van Tongeren", - "affiliations": "Office for National Statistics; Office for National Statistics; Office for National Statistics; Office for National Statistics; Lancaster University; Office for National Statistics; London School of Hygiene and Tropical Medicine; University of Manchester", - "abstract": "BackgroundMonitoring differences in COVID-19 vaccination uptake in different groups is crucial to help inform the policy response to the pandemic. A key gap is the absence of data on uptake by occupation.\n\nMethodsUsing nationwide population-level data, we calculated the proportion of people who had received two doses of a COVID-19 vaccine (assessed on 31 August 2021) by detailed occupational categories in adults aged 40-64 and estimated adjusted odds ratios to examine whether these differences were driven by occupation or other factors, such as education. We also examined whether vaccination rates differed by ability to work from home.\n\nResultsOur study population included 14,298,147 adults 40-64. Vaccination rates differed markedly by occupation, being higher in administrative and secretarial occupations (90.8%); professional occupations (90.7%); and managers, directors and senior officials (90.6%); and lowest (83.1%) in people working in elementary occupations. We found substantial differences in vaccination rates looking at finer occupational groups even after adjusting for confounding factors, such as education. Vaccination rates were higher in occupations which can be done from home and lower in those which cannot. Many occupations with low vaccination rates also involved contact with the public or with vulnerable people\n\nConclusionsIncreasing vaccination coverage in occupations with low vaccination rates is crucial to help protecting the public and control infection, especially in occupations that cannot be done from home and involve contacts with the public. Policies such as work from home if you can may only have limited future impact on hospitalisations and deaths\n\nWhat is already known on this subject?Whilst several studies highlight differences in vaccination coverage by ethnicity, religion, socio-demographic factors and certain underlying health conditions, there is very little evidence on how vaccination coverage varies by occupation, in the UK and elsewhere. The few study looking at occupational differences in vaccine hesitancy focus on healthcare workers or only examined broad occupational groups. There is currently no large-scale study on occupational differences in COVID-19 vaccination coverage in the UK.\n\nWhat this study adds?Using population-level linked data combining the 2011 Census, primary care records, mortality and vaccination data, we found that the vaccination rates of adults aged 40 to 64 years in England differed markedly by occupation. Vaccination rates were high in administrative and secretarial occupations, professional occupations and managers, directors and senior officials and low in people working in elementary occupations. Adjusting for other factors likely to be linked to occupation and vaccination, such as education, did not substantially alter the results. Vaccination rates were also associated with the ability to work from home, with the vaccination rate being higher in occupations which can be done performed from home. Policies aiming to increase vaccination rates in occupations that cannot be done from home and involve contacts with the public should be priorities", - "category": "public and global health", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.11.05.21265968", @@ -4087,6 +4143,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.08.23.21261779", + "date": "2021-08-24", + "link": "https://medrxiv.org/cgi/content/short/2021.08.23.21261779", + "title": "Association of cerebral venous thrombosis with recent COVID-19 vaccination: case-crossover study using ascertainment through neuroimaging in Scotland.", + "authors": "Paul M McKeigue; Raj Burgul; Jennifer Bishop; Chris Robertson; Jim McMenamin; Maureen O'Leary; David A. McAllister; Helen M Colhoun", + "affiliations": "University of Edinburgh; Forth Valley Royal Hospital; Public Health Scotland; Department of Mathematics and Statistics, University of Strathclyde; Public Health Scotland; Public Health Scotland; University of Glasgow; University of Edinburgh", + "abstract": "ObjectivesTo investigate the association of primary acute cerebral venous thrombosis (CVT) with COVID-19 vaccination through complete ascertainment of all diagnosed CVT in the population of Scotland.\n\nDesignCase-crossover study comparing recent (1-14 days after vaccination) with less recent exposure to vaccination among cases of CVT.\n\nSettingNational data for Scotland from 1 December 2020, with diagnosed CVT case ascertainment through neuroimaging studies up to 17 May 2021 and diagnostic coding of hospital discharges up to 28 April 2021 and with linkage to vaccination records.\n\nMain outcome measurePrimary acute cerebral venous thrombosis\n\nResultsOf 50 primary acute CVT cases, 29 were ascertained only from neuroimaging studies, 2 were ascertained only from hospital discharges, and 19 were ascertained from both sources. Of these 50 cases, 14 had received the Astra-Zeneca ChAdOx1 vaccine and 3 the Pfizer BNT162b2 vaccine. The incidence of CVT per million doses in the first 14 days after vaccination was 2.2 (95% credible interval 0.9 to 4.1) for ChAdOx1 and 1 (95% credible interval 0.1 to 2.9) for BNT162b2. The rate ratio for CVT associated with exposure to ChAdOx1 in the first 14 days compared with exposure 15-84 days after vaccination was 3.2 (95% credible interval 1.1 to 9.5). The 95% credible interval for the rate ratio associated with recent versus less recent exposure to BNT162b2 (0.6 to 95.8) was too wide for useful inference.\n\nConclusionsThese findings support a causal association between CVT and the AstraZeneca vaccine. The absolute risk of post-vaccination CVT in this population-wide study in Scotland was lower than has been reported for populations in Scandinavia and Germany; the explanation for this is not clear.\n\nWhat is already known on this topicThe risk of cerebral venous thrombosis (CVT) within 28 days of receiving the AstraZeneca ChAdOx1 vaccine has been estimated as 18 to 25 per million doses in Germany and Scandinavia, but only 5 per million doses in the UK based on the Yellow Card reporting scheme. Risk estimates based on adverse event reporting systems are subject to under-ascertainment and other biases.\n\nWhat this study addsAll diagnosed cases of CVT in Scotland were ascertained by searching neuroimaging studies from December 2020 to May 2021 and linked to national vaccination records. The risk of CVT within 28 days of vaccination with ChAdOx1 was estimated as 3.5 per million doses with an upper bound of 6 per million doses, against a background incidence of about 12 per million adults per year. This indicates that the Yellow Card system has not seriously underestimated the risk in the UK; the explanation for higher risk in other European countries is not clear.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.08.19.21262231", @@ -4311,6 +4381,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.07.21.21260906", + "date": "2021-07-22", + "link": "https://medrxiv.org/cgi/content/short/2021.07.21.21260906", + "title": "Disentangling post-vaccination symptoms from early COVID-19", + "authors": "Liane S Canas; Marc F. Osterdahl; Jie Deng; Christina Hu; Somesh Selvachandran; Lorenzo Polidori; Anna May; Erika Molteni; Benjamin Murray; Liyuan Chen; Eric Kerfoot; Kerstin Klaser; Michela Antonelli; Alexander Hammers; Tim Spector; Sebastien Ourselin; Claire J. Steves; Carole H. Sudre; Marc Modat; Emma L. Duncan", + "affiliations": "School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK; School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; ZOE Limited, London, UK; ZOE Limited, London, UK; ZOE Limited, London, UK; ZOE Limited, London, UK; School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; King's College London & Guy's and St Thomas' PET Centre, London, UK; Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK.; School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK.; School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; Medical Research Council Unit for Lifelong Health and Ageing, Departme; School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK.", + "abstract": "BackgroundIdentifying and testing individuals likely to have SARS-CoV-2 is critical for infection control, including post-vaccination. Vaccination is a major public health strategy to reduce SARS-CoV-2 infection globally. Some individuals experience systemic symptoms post-vaccination, which overlap with COVID-19 symptoms. This study compared early post-vaccination symptoms in individuals who subsequently tested positive or negative for SARS-CoV-2, using data from the COVID Symptom Study (CSS) app.\n\nDesignWe conducted a prospective observational study in UK CSS participants who were asymptomatic when vaccinated with Pfizer-BioNTech mRNA vaccine (BNT162b2) or Oxford-AstraZeneca adenovirus-vectored vaccine (ChAdOx1 nCoV-19) between 8 December 2020 and 17 May 2021, who subsequently reported symptoms within seven days (other than local symptoms at injection site) and were tested for SARS-CoV-2, aiming to differentiate vaccination side-effects per se from superimposed SARS-CoV-2 infection. The post-vaccination symptoms and SARS-CoV-2 test results were contemporaneously logged by participants. Demographic and clinical information (including comorbidities) were also recorded. Symptom profiles in individuals testing positive were compared with a 1:1 matched population testing negative, including using machine learning and multiple models including UK testing criteria.\n\nFindingsDifferentiating post-vaccination side-effects alone from early COVID-19 was challenging, with a sensitivity in identification of individuals testing positive of 0.6 at best. A majority of these individuals did not have fever, persistent cough, or anosmia/dysosmia, requisite symptoms for accessing UK testing; and many only had systemic symptoms commonly seen post-vaccination in individuals negative for SARS-CoV-2 (headache, myalgia, and fatigue).\n\nInterpretationPost-vaccination side-effects per se cannot be differentiated from COVID-19 with clinical robustness, either using symptom profiles or machine-derived models. Individuals presenting with systemic symptoms post-vaccination should be tested for SARS-CoV-2, to prevent community spread.\n\nFundingZoe Limited, UK Government Department of Health and Social Care, Wellcome Trust, UK Engineering and Physical Sciences Research Council, UK National Institute for Health Research, UK Medical Research Council and British Heart Foundation, Alzheimers Society, Chronic Disease Research Foundation, Massachusetts Consortium on Pathogen Readiness (MassCPR).\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThere are now multiple surveillance platforms internationally interrogating COVID-19 and/or post-vaccination side-effects. We designed a study to examine for differences between vaccination side-effects and early symptoms of COVID-19. We searched PubMed for peer-reviewed articles published between 1 January 2020 and 21 June 2021, using keywords: \"COVID-19\" AND \"Vaccination\" AND (\"mobile application\" OR \"web tool\" OR \"digital survey\" OR \"early detection\" OR \"Self-reported symptoms\" OR \"side-effects\"). Of 185 results, 25 studies attempted to differentiate symptoms of COVID-19 vs. post-vaccination side-effects; however, none used artificial intelligence (AI) technologies (\"machine learning\") coupled with real-time data collection that also included comprehensive and systematic symptom assessment. Additionally, none of these studies attempt to discriminate the early signs of infection from side-effects of vaccination (specifically here: Pfizer-BioNTech mRNA vaccine (BNT162b2) and Oxford-AstraZeneca adenovirus-vectored vaccine (ChAdOx1 nCoV-19)). Further, none of these studies sought to provide comparisons with current testing criteria used by healthcare services.\n\nAdded value of this studyThis study, in a uniquely large community-based cohort, uses prospective data capture in a novel effort to identify individuals with COVID-19 in the immediate post-vaccination period. Our results show that early symptoms of SARS-CoV-2 cannot be differentiated from vaccination side-effects robustly. Thus, post-vaccination systemic symptoms should not be ignored, and testing should be considered to prevent COVID-19 dissemination by vaccinated individuals.\n\nImplications of all the available evidenceOur study demonstrates the critical importance of testing symptomatic individuals - even if vaccinated - to ensure early detection of SARS-CoV-2 infection, helping to prevent future pandemic waves in the UK and elsewhere.", + "category": "respiratory medicine", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.07.19.21260770", @@ -4535,20 +4619,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.06.28.21259452", - "date": "2021-07-03", - "link": "https://medrxiv.org/cgi/content/short/2021.06.28.21259452", - "title": "Persistent symptoms following SARS-CoV-2 infection in a random community sample of 508,707 people", - "authors": "Matthew Whitaker; Joshua Elliott; Marc Chadeau-Hyam; Steven Riley; Ara Darzi; Graham Cooke; Helen Ward; Paul Elliott", - "affiliations": "Imperial College London; Imperial College London; Imperial College London; Dept Inf Dis Epi, Imperial College; Imperial College London; Imperial College London; Imperial College London; Imperial College London School of Public Health", - "abstract": "BackgroundLong COVID, describing the long-term sequelae after SARS-CoV-2 infection, remains a poorly defined syndrome. There is uncertainty about its predisposing factors and the extent of the resultant public health burden, with estimates of prevalence and duration varying widely.\n\nMethodsWithin rounds 3-5 of the REACT-2 study, 508,707 people in the community in England were asked about a prior history of COVID-19 and the presence and duration of 29 different symptoms. We used uni-and multivariable models to identify predictors of persistence of symptoms (12 weeks or more). We estimated the prevalence of symptom persistence at 12 weeks, and used unsupervised learning to cluster individuals by symptoms experienced.\n\nFindingsAmong the 508,707 participants, the weighted prevalence of self-reported COVID-19 was 19.2% (95% CI: 19.1,19.3). 37.7% of 76,155 symptomatic people post COVID-19 experienced at least one symptom, while 14.8% experienced three or more symptoms, lasting 12 weeks or more. This gives a weighted population prevalence of persistent symptoms of 5.75% (5.68, 5.81) for one and 2.22% (2.1, 2.26) for three or more symptoms. Almost a third of people (8,771/28,713 [30.5%]) with at least one symptom lasting 12 weeks or more reported having had severe COVID-19 symptoms (\"significant effect on my daily life\") at the time of their illness, giving a weighted prevalence overall for this group of 1.72% (1.69,1.76). The prevalence of persistent symptoms was higher in women than men (OR: 1.51 [1.46,1.55]) and, conditional on reporting symptoms, risk of persistent symptoms increased linearly with age by 3.5 percentage points per decade of life. Obesity, smoking or vaping, hospitalisation, and deprivation were also associated with a higher probability of persistent symptoms, while Asian ethnicity was associated with a lower probability. Two stable clusters were identified based on symptoms that persisted for 12 weeks or more: in the largest cluster, tiredness predominated, while in the second there was a high prevalence of respiratory and related symptoms.\n\nInterpretationA substantial proportion of people with symptomatic COVID-19 go on to have persistent symptoms for 12 weeks or more, which is age-dependent. Clinicians need to be aware of the differing manifestations of Long COVID which may require tailored therapeutic approaches. Managing the long-term sequelae of SARS-CoV-2 infection in the population will remain a major challenge for health services in the next stage of the pandemic.\n\nFundingThe study was funded by the Department of Health and Social Care in England.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSRecent systematic reviews have documented the wide range of symptoms and reported prevalence of persistent symptoms following COVID-19. A dynamic review of Long COVID studies (NIHR Evidence) in March 2021 summarised the literature on the prevalence of persistent symptoms after acute COVID19, and reported that most studies (14) were of hospitalised patients, with higher prevalence of persistent symptoms compared with two community-based studies. There was limited evidence from community studies beyond 12 weeks. Another systematic review reported a median of over 70% of people with symptoms lasting at least 60 days. A review of risk factors for Long COVID found consistent evidence for an increased risk amongst women and those with high body mass index (BMI) but inconsistent findings on the role of age and little evidence concerning risks among different socioeconomic or ethnic groups which are often not well captured in routine healthcare records. Long COVID is increasingly recognised as heterogenous, likely underpinned by differing biological mechanisms, but there is not yet consensus on defining subtypes of the condition.\n\nAdded value of this studyThis community-based study of over half a million people was designed to be representative of the adult population of England. A random sample of adults ages 18 years and above registered with a GP were invited irrespective of previous access to services for COVID-19, providing an estimate of population prevalence that was representative of the whole population. The findings show substantial declines in symptom prevalence over the first 12 weeks following Covid-19, reported by nearly one fifth of respondents, of whom over a third remained symptomatic at 12 weeks and beyond, with little evidence for decline thereafter.\n\nRisk factors identified for persistent symptoms (12 weeks or more) suggestive of Long COVID confirm some previous findings - an increased risk in women, obese and overweight individuals and those hospitalised for COVID-19, with strong evidence for an increasing risk with age. Additional evidence was found for an increased risk in those with lower income, smoking or vaping and healthcare or care home workers. A lower risk was found in those of Asian ethnicity.\n\nClustering identified two distinct groups of individuals with different symptom profiles at 12 weeks, highlighting the heterogeneity of clinical presentation. The smaller cluster had higher prevalence of respiratory and related symptoms, while for those in the larger cluster tiredness was the dominant symptom, with lower prevalence of organ-specific symptoms.\n\nImplications of available evidenceThere is a high prevalence of persistent symptoms beyond 12 weeks after acute COVID-19, with little evidence of decline thereafter. This highlights the needs for greater support for patients, both through specialised services and, for those from low-income settings, financial support. The understanding that there are distinct clusters of persistent symptoms, the most common of which is dominated by fatigue, is important for the recognition and clinical management of the condition outside of specialised services.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 96, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.06.28.21259529", @@ -5095,20 +5165,6 @@ "author_similarity": 100, "affiliation_similarity": 92 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.05.12.21257123", - "date": "2021-05-17", - "link": "https://medrxiv.org/cgi/content/short/2021.05.12.21257123", - "title": "Occupation and COVID-19 mortality in England: a national linked data study of 14.3 million adults", - "authors": "Vahe Nafilyan; Piotr Pawelek; Daniel Ayoubkhani; Sarah Rhodes; Lucy Pembrey; Melissa Matz; Michel P Coleman; Claudia Allemani; Ben Windsor-Shellard; Martie van Tongeren; Neil Pearce", - "affiliations": "Office for National Statistics; Office for National Statistics; Office for National Statistics; School of Health Sciences, University of Manchester; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine; Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine; Office for National Statistics; School of Health Sciences, University of Manchester; London School of Hygiene and Tropical Medicine", - "abstract": "ObjectiveTo estimate occupational differences in COVID-19 mortality, and test whether these are confounded by factors, such as regional differences, ethnicity and education or due to non-workplace factors, such as deprivation or pre-pandemic health.\n\nDesignRetrospective cohort study\n\nSettingPeople living in private households England\n\nParticipants14,295,900 people aged 40-64 years (mean age 52 years, 51% female) who were alive on 24 January 2020, living in private households in England in 2019, were employed in 2011, and completed the 2011 census.\n\nMain outcome measuresCOVID-19 related death, assessed between 24 January 2020 and 28 December 2020. We estimated age-standardised mortality rates per 100,000 person-years at risk (ASMR) stratified by sex and occupations. To estimate the effect of occupation due to work-related exposures, we used Cox proportional hazard models to adjust for confounding (region, ethnicity, education), as well as non-workplace factors that are related to occupation.\n\nResultsThere is wide variation between occupations in COVID-19 mortality. Several occupations, particularly those involving contact with patients or the public, show three-fold or four-fold risks. These elevated risks were greatly attenuated after adjustment for confounding and mediating non-workplace factors. For example, the hazard ratio (HR) for men working as taxi and cab drivers or chauffeurs changed from 4.60 [95%CI 3.62-5.84] to 1.47 [1.14-1.89] after adjustment. More generally, the overall HR for men working in essential occupations compared with men in non-essential occupations changed from 1.45 [1.34 - 1.56] to 1.22 [1.13 - 1.32] after adjustment. For most occupations, confounding and other mediating factors explained about 70% to 80% of the age-adjusted hazard ratios.\n\nConclusionsWorking conditions are likely to play a role in COVID-19 mortality, particularly in occupations involving contact with COVID-19 patients or the public. However, there is also a substantial contribution from non-workplace factors, including regional factors, socio-demographic factors, and pre-pandemic health.", - "category": "epidemiology", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.05.13.21257144", @@ -5167,14 +5223,14 @@ }, { "site": "medRxiv", - "doi": "10.1101/2021.05.06.21256757", + "doi": "10.1101/2021.05.08.21256867", "date": "2021-05-14", - "link": "https://medrxiv.org/cgi/content/short/2021.05.06.21256757", - "title": "COVID-19 outbreak rates and infection attack rates associated with the workplace: a descriptive epidemiological study", - "authors": "Yiqun Chen; Timothy Aldridge; - UK COVID-19 National Core Studies Consortium; Claire F Ferraro; Fu-Meng Khaw", - "affiliations": "Health and Safety Executive, UK; Health and Safety Executive, UK; ; National Infection Service, Public Health England, UK; Public Health England, UK", - "abstract": "BackgroundA large number of COVID-19 outbreaks/clusters have been reported in a variety of workplace settings since the start of the pandemic. However, information on the rate of outbreak occurrences which helps to identify the type of workplaces that are more likely to experience an outbreak, or infection attack rates which estimates the potential extent of the virus transmission in an outbreak, has not yet been available to inform intervention strategies to limit transmission.\n\nObjectivesTo link datasets on workplace settings and COVID-19 workplace outbreaks in England in order to: identify the geographical areas and workplace sectors with a high rate of outbreaks; and compare infection attack rates by workplace size and sector.\n\nMethodsWe analysed Public Health England (PHE) HPZone data on COVID-19 outbreaks in workplaces, covering the time period of 18 May - 12 October 2020. The workplaces analysed excluded care homes, hospitals and educational settings. We calculated the workplace outbreak rates by nine English regions, 151 Upper Tier Local Authorities (UTLAs) and twelve industrial sectors, using National Population Database (NPD) data extracted in May 2019 on the total number of the relevant workplaces as the denominator. We also calculated the infection attack rates by enterprise size (small, medium, large) and industrial sector, using PHE Situations of Interest (SOI) data on the number of test-confirmed COVID-19 cases in a workplace outbreak as the numerator, and using NPD data on the number employed in that workplace as the denominator.\n\nResultsIn total, 1,317 confirmed workplace outbreaks were identified from HPZone data, of which 1,305 were available for estimation of outbreak rates. The average outbreak rate was 66 per 100,000 workplaces. Of the nine geographical regions in England, the North West had the highest workplace outbreak rate (155/100,000 workplaces), based on 351 outbreaks. Of the UTLAs, the highest workplace outbreak rate was Blackburn with Darwen (387/100,000 workplaces). The industrial sector with the highest workplace outbreak rate was manufacturers and packers of food (1,672/100,000), based on 117 outbreaks: this was consistent across seven of the regions. In addition, high outbreak rates in warehouses were observed in the East Midlands and the North West.\n\nIn total, 390 outbreaks were identified from SOI data and 264 of them allowed for estimation of attack rates. The overall median attack rate was 3.4% of the employed persons with confirmed COVID-19 at a workplace with an outbreak. Most of these outbreaks (162) had an attack rate less than 6%. However, in a small number of outbreaks (57) the attack rate was over 15%. The attack rates increased as the size of the enterprise decreased. The highest attack rate was for outbreaks in close contact services (median 16.5%), which was followed by outbreaks in restaurants and catering (median 10.2%), and in manufacturers and packers of non-food products (median 6.7%).\n\nConclusionsOur linked dataset analysis approach allows early identification of geographical regions and industrial sectors with higher rates of COVID-19 workplace outbreaks as well as estimation of attack rates by enterprise size and sector. This can be used to inform interventions to limit transmission of the virus. Our approach to analysing the workplace outbreak data can also be applied to calculation of outbreak rates and attack rates in other types of settings such as care homes, hospitals and educational settings.", - "category": "epidemiology", + "link": "https://medrxiv.org/cgi/content/short/2021.05.08.21256867", + "title": "SARS-CoV-2 lineage dynamics in England from January to March 2021 inferred from representative community samples", + "authors": "Oliver Eales; Andrew Page; Sonja N. Tang; Caroline E. Walters; Haowei Wang; David Haw; Alexander J. Trotter; Thanh Le Viet; Ebenezer Foster-Nyarko; Sophie Prosolek; Christina Atchinson; Deborah Ashby; Graham Cooke; Wendy Barclay; Christl A Donnelly; Justin O'Grady; Erik Volz; - The COVID-19 Genomics UK (COG-UK) Consortium; Ara Darzi; Helen Ward; Paul Elliott; Steven Riley", + "affiliations": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Quadram Institute, Norwich, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; Quadram Institute, Norwich, UK; School of Public Health, Imperial College London, UK; School of Public Health, Imperial College London, UK; Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic; Department of Infectious Disease, Imperial College London, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; Quadram Institute, Norwich, UK; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc; ; Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear; School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc", + "abstract": "Genomic surveillance for SARS-CoV-2 lineages informs our understanding of possible future changes in transmissibility and vaccine efficacy. However, small changes in the frequency of one lineage over another are often difficult to interpret because surveillance samples are obtained from a variety of sources. Here, we describe lineage dynamics and phylogenetic relationships using sequences obtained from a random community sample who provided a throat and nose swab for rt-PCR during the first three months of 2021 as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. Overall, diversity decreased during the first quarter of 2021, with the B.1.1.7 lineage (first identified in Kent) predominant, driven by a 0.3 unit higher reproduction number over the prior wild type. During January, positive samples were more likely B.1.1.7 in younger and middle-aged adults (aged 18 to 54) than in other age groups. Although individuals infected with the B.1.1.7 lineage were no more likely to report one or more classic COVID-19 symptoms compared to those infected with wild type, they were more likely to be antibody positive 6 weeks after infection. Viral load was higher in B.1.1.7 infection as measured by cycle threshold (Ct) values, but did not account for the increased rate of testing positive for antibodies. The presence of infections with non-imported B.1.351 lineage (first identified in South Africa) during January, but not during February or March, suggests initial establishment in the community followed by fade-out. However, this occurred during a period of stringent social distancing and targeted public health interventions and does not immediately imply similar lineages could not become established in the future. Sequence data from representative community surveys such as REACT-1 can augment routine genomic surveillance.", + "category": "infectious diseases", "match_type": "fuzzy", "author_similarity": 100, "affiliation_similarity": 100 @@ -5375,6 +5431,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.04.22.21255913", + "date": "2021-04-23", + "link": "https://medrxiv.org/cgi/content/short/2021.04.22.21255913", + "title": "Impact of vaccination on SARS-CoV-2 cases in the community: a population-based study using the UK COVID-19 Infection Survey", + "authors": "Emma Pritchard; Philippa Matthews; Nicole Stoesser; David Eyre; Owen Gethings; Karina-Doris Vitha; Joel Jones; Thomas House; Harper VanSteenhouse; Iain Bell; John Bell; John Newton; Jeremy Farrar; Ian Diamond; Emma Rourke; Ruth Studley; Derrick W Crook; tim E peto; Ann Sarah Walker; Koen B Pouwels", + "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; Office for National Statistics; University of Oxford; Office for National Statistics; University of Manchester; Glasgow Lighthouse Laboratory; Office for National Statistics; University of Oxford; Public Health England; Wellcome Trust; Office for National Statistics,; Office for National Statistics; Office for National Statistics; NIHR Oxford Biomedical Research Centre; oxford university; University of Oxford; University of Oxford", + "abstract": "ObjectivesTo assess the effectiveness of COVID-19 vaccination in preventing SARS-CoV-2 infection in the community.\n\nDesignProspective cohort study.\n\nSettingThe UK population-representative longitudinal COVID-19 Infection Survey.\n\nParticipants373,402 participants aged [≥]16 years contributing 1,610,562 RT-PCR results from nose and throat swabs between 1 December 2020 and 3 April 2021.\n\nMain outcome measuresNew RT-PCR-positive episodes for SARS-CoV-2 overall, by self-reported symptoms, by cycle threshold (Ct) value (<30 versus [≥]30), and by gene positivity (compatible with the B.1.1.7 variant versus not).\n\nResultsOdds of new SARS-CoV-2 infection were reduced 65% (95% CI 60 to 70%; P<0.001) in those [≥]21 days since first vaccination with no second dose versus unvaccinated individuals without evidence of prior infection (RT-PCR or antibody). In those vaccinated, the largest reduction in odds was seen post second dose (70%, 95% CI 62 to 77%; P<0.001).There was no evidence that these benefits varied between Oxford-AstraZeneca and Pfizer-BioNTech vaccines (P>0.9).There was no evidence of a difference in odds of new SARS-CoV-2 infection for individuals having received two vaccine doses and with evidence of prior infection but not vaccinated (P=0.89). Vaccination had a greater impact on reducing SARS-CoV-2 infections with evidence of high viral shedding Ct<30 (88% reduction after two doses; 95% CI 80 to 93%; P<0.001) and with self-reported symptoms (90% reduction after two doses; 95% CI 82 to 94%; P<0.001); effects were similar for different gene positivity patterns.\n\nConclusionVaccination with a single dose of Oxford-AstraZeneca or Pfizer-BioNTech vaccines, or two doses of Pfizer-BioNTech, significantly reduced new SARS-CoV-2 infections in this large community surveillance study. Greater reductions in symptomatic infections and/or infections with a higher viral burden are reflected in reduced rates of hospitalisations/deaths, but highlight the potential for limited ongoing transmission from asymptomatic infections in vaccinated individuals.\n\nRegistrationThe study is registered with the ISRCTN Registry, ISRCTN21086382.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.04.12.21255275", @@ -5501,6 +5571,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.04.01.21254765", + "date": "2021-04-07", + "link": "https://medrxiv.org/cgi/content/short/2021.04.01.21254765", + "title": "Mental health inequalities in healthcare, economic, and housing disruption during COVID -19: an investigation in 12 longitudinal studies", + "authors": "Giorgio Di Gessa; Jane Maddock; Michael J Green; Ellen J Thompson; Eoin McElroy; Helena L Davies; Jessica Mundy; Anna J Stevenson; Alex S.F Kwong; Gareth J Griffith; Srinivasa Vittal Katikireddi; Claire L Niedzwiedz; George B Ploubidis; Emla Fitzsimons; Morag Henderson; Richard J. Silverwood; Nishi Chaturvedi; Gerome Breen; Claire J Steves; Andrew Steptoe; David J Porteous; Praveetha Patalay", + "affiliations": "Institute of Epidemiology and Health Care, University College London; MRC Unit for Lifelong Health and Ageing, University College London; MRC/CSO Social & Public Health Sciences Unit, University of Glasgow; Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, Kings College London; Department of Neuroscience, Psychology and Behaviour, University of Leicester; Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, Kings College London; Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, Kings College London; Centre for Genomic and Experimental Medicine, University of Edinburgh; Division of Psychiatry, University of Edinburgh and MRC Integrative Epidemiology Unit, University of Bristol; MRC Integrative Epidemiology Unit, University of Bristol; MRC/CSO Social & Public Health Sciences Unit, University of Glasgow; Institute of Health & Wellbeing, University of Glasgow; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; Centre for Longitudinal Studies, UCL Social Research Institute, University College London; MRC Unit for Lifelong Health and Ageing, University College London; Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, Kings College London and Maudsley Biomedical Research Cen; Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, Kings College London; Institute of Epidemiology and Health Care, University College London; Centre for Genomic and Experimental Medicine, University of Edinburgh; Centre for Longitudinal Studies and MRC Unit for Lifelong Health and Ageing, University College London", + "abstract": "BackgroundThe COVID-19 pandemic and associated virus suppression measures have disrupted lives and livelihoods and people already experiencing mental ill-health may have been especially vulnerable.\n\nAimTo quantify mental health inequalities in disruptions to healthcare, economic activity and housing.\n\nMethod59,482 participants in 12 UK longitudinal adult population studies with data collected prior to and during the COVID-19 pandemic. Within each study we estimated the association between psychological distress assessed pre-pandemic and disruptions since the start of the pandemic to three domains: healthcare (medication access, procedures, or appointments); economic activity (employment, income, or working hours); and housing (change of address or household composition). Meta-analyses were used to pool estimates across studies.\n\nResultsAcross the analysed datasets, one to two-thirds of participants experienced at least one disruption, with 2.3-33.2% experiencing disruptions in two or more domains. One standard deviation higher pre-pandemic psychological distress was associated with: (i) increased odds of any healthcare disruptions (OR=1.30; [95% CI:1.20-1.40]) with fully adjusted ORs ranging from 1.24 [1.09-1.41] for disruption to procedures and 1.33 [1.20- 1.49] for disruptions to prescriptions or medication access; (ii) loss of employment (OR=1.13 [1.06-1.21]) and income (OR=1.12 [1.06 -1.19]) and reductions in working hours/furlough (OR=1.05 [1.00-1.09]); (iii) no associations with housing disruptions (OR=1.00 [0.97-1.03]); and (iv) increased likelihood of experiencing a disruption in at least two domains (OR=1.25 [1.18-1.32]) or in one domain (OR=1.11 [1.07-1.16]) relative to no disruption.\n\nConclusionPeople experiencing psychological distress pre-pandemic have been more likely to experience healthcare and economic disruptions, and clusters of disruptions across multiple domains during the pandemic. Failing to address these disruptions risks further widening the existing inequalities in mental health.", + "category": "psychiatry and clinical psychology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.04.01.21254789", @@ -5543,20 +5627,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.03.21.21254061", - "date": "2021-03-26", - "link": "https://medrxiv.org/cgi/content/short/2021.03.21.21254061", - "title": "Quantitative SARS-CoV-2 anti-spike responses to Pfizer-BioNTech and Oxford-AstraZeneca vaccines by previous infection status", - "authors": "David W Eyre; Sheila F Lumley; Jia Wei; Stuart Cox; Tim James; Anita Justice; Gerald Jesuthasan; Alison Howarth; Stephanie B Hatch; Brian D Marsden; E Yvonne Jones; David I Stuart; Daniel Ebner; Sarah Hoosdally; Derrick Crook; Tim EA Peto; Timothy M Walker; Nicole EA Stoesser; Philippa C Matthews; Koen B Pouwels; A Sarah Walker; Katie Jeffery", - "affiliations": "University of Oxford; University of Oxford; University of Oxford; Oxford University Hospitals; Oxford University Hospitals; Oxford University Hospitals; Oxford University Hospitals; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Oxford University Hospitals", - "abstract": "ObjectivesWe investigate determinants of SARS-CoV-2 anti-spike IgG responses in healthcare workers (HCWs) following one or two doses of Pfizer-BioNTech or Oxford-AstraZeneca vaccines.\n\nMethodsHCWs participating in regular SARS-CoV-2 PCR and antibody testing were invited for serological testing prior to first and second vaccination, and 4 weeks post-vaccination if receiving a 12-week dosing interval. Quantitative post-vaccination anti-spike antibody responses were measured using the Abbott SARS-CoV-2 IgG II Quant assay (detection threshold: [≥]50 AU/ml). We used multivariable logistic regression to identify predictors of seropositivity and generalised additive models to track antibody responses over time.\n\nResultsVaccine uptake was 80%, but less in lower-paid roles and Black, south Asian and minority ethnic groups. 3570/3610(98.9%) HCWs were seropositive >14 days post-first vaccination and prior to second vaccination, 2706/2720(99.5%) after Pfizer-BioNTech and 864/890(97.1%) following Oxford-AstraZeneca vaccines. Previously infected and younger HCWs were more likely to test seropositive post-first vaccination, with no evidence of differences by sex or ethnicity. All 470 HCWs tested >14 days after second vaccine were seropositive. Quantitative antibody responses were higher after previous infection: median(IQR) >21 days post-first Pfizer-BioNTech 14,604(7644-22,291) AU/ml vs. 1028(564-1985) AU/ml without prior infection (p<0.001). Oxford-AstraZeneca vaccine recipients had lower readings post-first dose compared to Pfizer-BioNTech, with and without previous infection, 10,095(5354-17,096) and 435(203-962) AU/ml respectively (both p<0.001 vs. Pfizer-BioNTech). Antibody responses post-second vaccination were similar to those after prior infection and one vaccine dose.\n\nConclusionsVaccination leads to detectable anti-spike antibodies in nearly all adult HCWs. Whether differences in response impact vaccine efficacy needs further study.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.03.21.21253968", @@ -5669,6 +5739,20 @@ "author_similarity": 100, "affiliation_similarity": 92 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.03.16.21253377", + "date": "2021-03-24", + "link": "https://medrxiv.org/cgi/content/short/2021.03.16.21253377", + "title": "First and second SARS-CoV-2 waves in inner London: A comparison of admission characteristics and the effects of the B.1.1.7 variant", + "authors": "Luke B Snell; Wenjuan Wang; Adela Alcolea-Medina; Themoula Charalampous; Gaia Nebbia; Rahul Batra; Leonardo de Jongh; Finola Higgins; Yanzhong Wang; Jonathan D Edgeworth; Vasa Curcin", + "affiliations": "King's College London; School of Population Health and Environmental Sciences, King's College London, London, UK; Viapath, London, UK; Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK; Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK; Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK; NIHR Biomedical Research Centre, Guy's and St Thomas' NHS Foundation Trust; NIHR Biomedical Research Centre, Guy's and St Thomas' NHS Foundation Trust; School of Population Health and Environmental Sciences, King's College London, London, UK; Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK; School of Population Health and Environmental Sciences, King's College London, London, UK", + "abstract": "IntroductionA second wave of SARS-CoV-2 infection spread across the UK in 2020 linked with emergence of the more transmissible B.1.1.7 variant. The emergence of new variants, particularly during relaxation of social distancing policies and implementation of mass vaccination, highlights the need for real-time integration of detailed patient clinical data alongside pathogen genomic data. We linked clinical data with viral genome sequence data to compare cases admitted during the first and second waves of SARS-CoV-2 infection.\n\nMethodsClinical, laboratory and demographic data from five electronic health record (EHR) systems was collected for all cases with a positive SARS-CoV-2 RNA test between March 13th 2020 and February 17th 2021. SARS-CoV-2 viral sequencing was performed using Oxford Nanopore Technology. Descriptive data are presented comparing cases between waves, and between cases of B.1.1.7 and non-B.1.1.7 variants.\n\nResultsThere were 5810 SARS-CoV-2 RNA positive cases comprising inpatients (n=2341), healthcare workers (n=1549), outpatients (n=874), emergency department (ED) attenders not subsequently admitted (n=532), inter-hospital transfers (n=281) and nosocomial cases (n=233). There were two dominant waves of hospital admissions, with wave one starting from March 13th (n=838) and wave two from October 20th (n=1503), both with a temporally aligned rise in nosocomial cases (n=96 in wave one, n=137 in wave two). 1470 SARS-CoV-2 isolates were successfully sequenced, including 216/838 (26%) admitted cases from wave one, 472/1503 (31%) admitted cases in wave two and 121/233 (52%) nosocomial cases. The first B.1.1.7 variant was identified on 15th November 2020 and increased rapidly such that it comprised 400/472 (85%) of sequenced isolates from admitted cases in wave two. Females made up a larger proportion of admitted cases in wave two (47.3% vs 41.8%, p=0.011), and in those infected with the B.1.1.7 variant compared to non-B.1.1.7 variants (48.0% vs 41.8%, p=0.042). A diagnosis of frailty was less common in wave two (11.5% v 22.8%, p<0.001) and in the group infected with B.1.1.7 (14.5% v 22.4%, p=0.001). There was no difference in severity on admission between waves, as measured by hypoxia at admission (wave one: 64.3% vs wave two: 65.5%, p=0.67). However, a higher proportion of cases infected with the B.1.1.7 variant were hypoxic on admission compared to other variants (70.0% vs 62.5%, p=0.029).\n\nConclusionsAutomated EHR data extraction linked with SARS-CoV-2 genome sequence data provides valuable insight into the evolving characteristics of cases admitted to hospital with COVID-19. The proportion of cases with hypoxia on admission was greater in those infected with the B.1.1.7 variant, which supports evidence the B.1.1.7 variant is associated with more severe disease. The number of nosocomial cases was similar in both waves despite introduction of many infection control interventions before wave two, an observation requiring further investigation.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.03.15.21253542", @@ -5711,6 +5795,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.03.11.21253275", + "date": "2021-03-21", + "link": "https://medrxiv.org/cgi/content/short/2021.03.11.21253275", + "title": "Effect of vaccination on transmission of COVID-19: an observational study in healthcare workers and their households", + "authors": "Anoop Shah; Ciara Gribben; Jennifer Bishop; Peter Hanlon; David Caldwell; Rachael Wood; Martin Reid; Jim McMenamin; David Goldberg; Diane Stockton; Sharon Hutchinson; Chris Robertson; Paul M McKeigue; Helen M Colhoun; David McAllister", + "affiliations": "London School of Hygiene and Tropical Medicine; Public Health Scotland; Public Health Scotland; University of Glasgow; Public Health Scotland; PublicHealth Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; Public Health Scotland; University of Glasgow", + "abstract": "BackgroundThe effect of vaccination for COVID-19 on onward transmission is unknown.\n\nMethodsA national record linkage study determined documented COVID-19 cases and hospitalisations in unvaccinated household members of vaccinated and unvaccinated healthcare workers from 8th December 2020 to 3rd March 2021. The primary endpoint was COVID-19 14 days following the first dose.\n\nResultsThe cohort comprised of 194,362 household members (mean age 31{middle dot}1 {+/-} 20{middle dot}9 years) and 144,525 healthcare workers (mean age 44{middle dot}4 {+/-} 11{middle dot}4 years). 113,253 (78{middle dot}3%) of healthcare workers received at least one dose of the BNT162b2 mRNA or ChAdOx1 nCoV-19 vaccine and 36,227 (25{middle dot}1%) received a second dose. There were 3,123 and 4,343 documented COVID-19 cases and 175 and 177 COVID-19 hospitalisations in household members of healthcare workers and healthcare workers respectively. Household members of vaccinated healthcare workers had a lower risk of COVID-19 case compared to household members of unvaccinated healthcare worker (rate per 100 person-years 9{middle dot}40 versus 5{middle dot}93; HR 0{middle dot}70, 95% confidence interval [CI] 0{middle dot}63 to 0{middle dot}78). The effect size for COVID-19 hospitalisation was similar, with the confidence interval crossing the null (HR 0{middle dot}77 [95% CI 0{middle dot}53 to 1{middle dot}10]). The rate per 100 person years was lower in vaccinated compared to unvaccinated healthcare workers for documented (20{middle dot}13 versus 8{middle dot}51; HR 0{middle dot}45 [95% CI 0{middle dot}42 to 0{middle dot}49]) and hospitalized COVID-19 (0{middle dot}97 versus 0{middle dot}14; HR 0{middle dot}16 [95% CI 0{middle dot}09 to 0{middle dot}27]). Compared to the period before the first dose, the risk of documented COVID-19 case was lower at [≥] 14 days after the second dose for household members (HR 0{middle dot}46 [95% CI 0{middle dot}30to 0{middle dot}70]) and healthcare workers (HR 0{middle dot}08 [95% CI 0{middle dot}04 to 0{middle dot}17]).\n\nInterpretationVaccination of health care workers was associated with a substantial reduction in COVID-19 cases in household contacts consistent with an effect of vaccination on transmission.", + "category": "public and global health", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.03.17.21253853", @@ -5725,6 +5823,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.03.18.21253443", + "date": "2021-03-20", + "link": "https://medrxiv.org/cgi/content/short/2021.03.18.21253443", + "title": "Intensity of COVID-19 in care homes following Hospital Discharge in the early stages of the UK epidemic", + "authors": "Joe Hollinghurst; Laura North; Chris Emmerson; Ashley Akbari; Fatemeh Torabi; Ronan A Lyons; Alan G Hawkes; Ed Bennett; Mike B Gravenor; Richard Fry", + "affiliations": "Swansea University; Swansea University; Public Health Wales; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University; Swansea University", + "abstract": "BackgroundA defining feature of the COVID-19 pandemic in many countries was the tragic extent to which care home residents were affected, and the difficulty preventing introduction and subsequent spread of infection. Management of risk in care homes requires good evidence on the most important transmission pathways. One hypothesised route at the start of the pandemic, prior to widespread testing, was transfer of patients from hospitals, which were experiencing high levels of nosocomial events.\n\nMethodsWe tested the hypothesis that hospital discharge events increased the intensity of care home cases using a national individually linked health record cohort in Wales, UK. We monitored 186,772 hospital discharge events over the period March to July 2020, tracking individuals to 923 care homes and recording the daily case rate in the homes populated by 15,772 residents. We estimated the risk of an increase in cases rates following exposure to a hospital discharge using multi-level hierarchical logistic regression, and a novel stochastic Hawkes process outbreak model.\n\nFindingsIn regression analysis, after adjusting for care home size, we found no significant association between hospital discharge and subsequent increases in care home case numbers (odds ratio: 0.99, 95% CI 0.82, 1.90). Risk factors for increased cases included care home size, care home resident density, and provision of nursing care. Using our outbreak model, we found a significant effect of hospital discharge on the subsequent intensity of cases. However, the effect was small, and considerably less than the effect of care home size, suggesting the highest risk of introduction came from interaction with the community. We estimated approximately 1.8% of hospital discharged patients may have been infected.\n\nInterpretationThere is growing evidence in the UK that the risk of transfer of COVID-19 from the high-risk hospital setting to the high-risk care home setting during the early stages of the pandemic was relatively small. Although access to testing was limited to initial symptomatic cases in each care home at this time, our results suggest that reduced numbers of discharges, selection of patients, and action taken within care homes following transfer all may have contributed to mitigation. The precise key transmission routes from the community remain to be quantified.", + "category": "health informatics", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.03.15.21253590", @@ -5837,20 +5949,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.03.09.21253218", - "date": "2021-03-12", - "link": "https://medrxiv.org/cgi/content/short/2021.03.09.21253218", - "title": "An observational cohort study on the incidence of SARS-CoV-2 infection and B.1.1.7 variant infection in healthcare workers by antibody and vaccination status", - "authors": "Sheila F Lumley; Gillian Rodger; Bede Constantinides; Nicholas Sanderson; Kevin K Chau; Teresa L Street; Alison Howarth; Stephanie B Hatch; Brian D Marsden; Stuart Cox; Tim James; Fiona Warren; Liam J Peck; Thomas G Ritter; Zoe de Toledo; Laura Warren; David Axten; Richard J Cornall; E Yvonne Jones; David I Stuart; Gavin Screaton; Daniel Ebner; Sarah Hoosdally; Meera Chand; - Oxford University Hospitals Staff Testing Group; Derrick Crook; Christopher P Conlon; Koen B Pouwels; A Sarah Walker; Tim EA Peto; Susan Hopkins; Timothy M Walker; Nicole EA Stoesser; Philippa C Matthews; Katie Jeffery; David W Eyre", - "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Oxford University Hospitals; Oxford University Hospitals; Oxford University Hospitals; University of Oxford; University of Oxford; University of Oxford; Oxford University Hospitals; Oxford University Hospitals; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Public Health England; ; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; Public Health England; University of Oxford; University of Oxford; University of Oxford; Oxford University Hospitals; University of Oxford", - "abstract": "BackgroundNatural and vaccine-induced immunity will play a key role in controlling the SARS-CoV-2 pandemic. SARS-CoV-2 variants have the potential to evade natural and vaccine-induced immunity.\n\nMethodsIn a longitudinal cohort study of healthcare workers (HCWs) in Oxfordshire, UK, we investigated the protection from symptomatic and asymptomatic PCR-confirmed SARS-CoV-2 infection conferred by vaccination (Pfizer-BioNTech BNT162b2, Oxford-AstraZeneca ChAdOx1 nCOV-19) and prior infection (determined using anti-spike antibody status), using Poisson regression adjusted for age, sex, temporal changes in incidence and role. We estimated protection conferred after one versus two vaccinations and from infections with the B.1.1.7 variant identified using whole genome sequencing.\n\nResults13,109 HCWs participated; 8285 received the Pfizer-BioNTech vaccine (1407 two doses) and 2738 the Oxford-AstraZeneca vaccine (49 two doses). Compared to unvaccinated seronegative HCWs, natural immunity and two vaccination doses provided similar protection against symptomatic infection: no HCW vaccinated twice had symptomatic infection, and incidence was 98% lower in seropositive HCWs (adjusted incidence rate ratio 0.02 [95%CI <0.01-0.18]). Two vaccine doses or seropositivity reduced the incidence of any PCR-positive result with or without symptoms by 90% (0.10 [0.02-0.38]) and 85% (0.15 [0.08-0.26]) respectively. Single-dose vaccination reduced the incidence of symptomatic infection by 67% (0.33 [0.21-0.52]) and any PCR-positive result by 64% (0.36 [0.26-0.50]). There was no evidence of differences in immunity induced by natural infection and vaccination for infections with S-gene target failure and B.1.1.7.\n\nConclusionNatural infection resulting in detectable anti-spike antibodies and two vaccine doses both provide robust protection against SARS-CoV-2 infection, including against the B.1.1.7 variant.\n\nSummaryNatural infection resulting in detectable anti-spike antibodies and two vaccine doses both provided [≥] 85% protection against symptomatic and asymptomatic SARS-CoV-2 infection in healthcare workers, including against the B.1.1.7 variant. Single dose vaccination reduced symptomatic infection by 67%.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.03.08.21253110", @@ -5921,20 +6019,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2021.03.04.21252528", - "date": "2021-03-08", - "link": "https://medrxiv.org/cgi/content/short/2021.03.04.21252528", - "title": "Case fatality risk of the SARS-CoV-2 variant of concern B.1.1.7 in England", - "authors": "Daniel J Grint; Kevin Wing; Elizabeth Williamson; Helen I McDonald; Krishnan Bhaskaran; David Evans; Stephen JW Evans; Alex J Walker; George Hickman; Emily Nightingale; Anna Schultze; Christopher T Rentsch; Chris Bates; Jonathan Cockburn; Helen J Curtis; Caroline E Morton; Sebastian Bacon; Simon Davy; Angel YS Wong; Amir Mehrkar; Laurie Tomlinson; Ian J Douglas; Rohini Mathur; Paula Blomquist; Brian MacKenna; Peter Ingelsby; Richard Croker; John Parry; Frank Hester; Sam Harper; Nicolas J DeVito; Will Hulme; John Tazare; Ben Goldacre; Liam Smeeth; Rosalind M Eggo", - "affiliations": "Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Faculty of Public Health and Policy, London School of Hygiene & Tropical Medicine, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, UK; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; COVID-19 Outbreak Surveillance Team, Public Health England, London, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, UK; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, UK; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK; Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK", - "abstract": "The B.1.1.7 variant of concern (VOC) is increasing in prevalence across Europe. Accurate estimation of disease severity associated with this VOC is critical for pandemic planning. We found increased risk of death for VOC compared with non-VOC cases in England (HR: 1.67 (95% CI: 1.34 - 2.09; P<.0001). Absolute risk of death by 28-days increased with age and comorbidities. VOC has potential to spread faster with higher mortality than the pandemic to date.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2021.03.08.21253112", @@ -6019,6 +6103,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2021.02.25.21252433", + "date": "2021-03-01", + "link": "https://medrxiv.org/cgi/content/short/2021.02.25.21252433", + "title": "Predicting COVID-19 related death using the OpenSAFELY platform", + "authors": "Elizabeth J Williamson; John Tazare; Krishnan Bhaskaran; Helen I McDonald; Alex J Walker; Laurie Tomlinson; Kevin Wing; Sebastian Bacon; Chris Bates; Helen J Curtis; Harriet Forbes; Caroline Minassian; Caroline E Morton; Emily Nightingale; Amir Mehrkar; Dave Evans; Brian D Nicholson; Dave Leon; Peter Inglesby; Brian MacKenna; Nicholas G Davies; Nicholas J DeVito; Henry Drysdale; Jonathan Cockburn; William J Hulme; Jessica Morley; Ian Douglas; Christopher T Rentsch; Rohini Mathur; Angel Wong; Anna Schultze; Richard Croker; John Parry; Frank Hester; Sam Harper; Richard Grieve; David A Harrison; Ewout W Steyerberg; Rosalind M Eggo; Karla Diaz-Ordaz; Ruth Keogh; Stephen JW Evans; Liam Smeeth; Ben Goldacre", + "affiliations": "London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; NIHR Health Protection Research Unit (HPRU) in Immunisation; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; Intensive Care National Audit & Research Centre (ICNARC), 24 High Holborn, Holborn, London WC1V 6AZ; Leiden University Medical Center, Leiden, the Netherlands; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG", + "abstract": "ObjectivesTo compare approaches for obtaining relative and absolute estimates of risk of 28-day COVID-19 mortality for adults in the general population of England in the context of changing levels of circulating infection.\n\nDesignThree designs were compared. (A) case-cohort which does not explicitly account for the time-changing prevalence of COVID-19 infection, (B) 28-day landmarking, a series of sequential overlapping sub-studies incorporating time-updating proxy measures of the prevalence of infection, and (C) daily landmarking. Regression models were fitted to predict 28-day COVID-19 mortality.\n\nSettingWorking on behalf of NHS England, we used clinical data from adult patients from all regions of England held in the TPP SystmOne electronic health record system, linked to Office for National Statistics (ONS) mortality data, using the OpenSAFELY platform.\n\nParticipantsEligible participants were adults aged 18 or over, registered at a general practice using TPP software on 1st March 2020 with recorded sex, postcode and ethnicity. 11,972,947 individuals were included, and 7,999 participants experienced a COVID-19 related death. The study period lasted 100 days, ending 8th June 2020.\n\nPredictorsA range of demographic characteristics and comorbidities were used as potential predictors. Local infection prevalence was estimated with three proxies: modelled based on local prevalence and other key factors; rate of A&E COVID-19 related attendances; and rate of suspected COVID-19 cases in primary care.\n\nMain outcome measuresCOVID-19 related death.\n\nResultsAll models discriminated well between patients who did and did not experience COVID-19 related death, with C-statistics ranging from 0.92-0.94. Accurate estimates of absolute risk required data on local infection prevalence, with modelled estimates providing the best performance.\n\nConclusionsReliable estimates of absolute risk need to incorporate changing local prevalence of infection. Simple models can provide very good discrimination and may simplify implementation of risk prediction tools in practice.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2021.02.25.21252402", @@ -6677,6 +6775,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.12.24.20248822", + "date": "2020-12-26", + "link": "https://medrxiv.org/cgi/content/short/2020.12.24.20248822", + "title": "Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England", + "authors": "Nicholas G Davies; Sam Abbott; Rosanna C. Barnard; Christopher I. Jarvis; Adam J. Kucharski; James D Munday; Carl A. B. Pearson; Timothy Russell; Damien Tully; Alex D. Washburne; Tom Wenseleers; Amy Gimma; William Waites; Kerry L. M. Wong; Kevin van Zandvoort; Justin D. Silverman; - CMMID COVID-19 Working Group; - The COVID-19 Genomics UK (COG-UK) Consortium; Karla Diaz-Ordaz; Ruth H Keogh; Rosalind M Eggo; Sebastian Funk; Mark Jit; Katherine E. Atkins; W. John Edmunds", + "affiliations": "London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene & Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; Selva Analytics LLC; KU Leuven; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; College of Information Science and Technology, Pennsylvania State University; ; ; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine", + "abstract": "A novel SARS-CoV-2 variant, VOC 202012/01 (lineage B.1.1.7), emerged in southeast England in November 2020 and is rapidly spreading towards fixation. Using a variety of statistical and dynamic modelling approaches, we estimate that this variant has a 43-90% (range of 95% credible intervals 38-130%) higher reproduction number than preexisting variants. A fitted two-strain dynamic transmission model shows that VOC 202012/01 will lead to large resurgences of COVID-19 cases. Without stringent control measures, including limited closure of educational institutions and a greatly accelerated vaccine roll-out, COVID-19 hospitalisations and deaths across England in 2021 will exceed those in 2020. Concerningly, VOC 202012/01 has spread globally and exhibits a similar transmission increase (59-74%) in Denmark, Switzerland, and the United States.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "bioRxiv", "doi": "10.1101/2020.12.23.424229", @@ -6803,20 +6915,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.12.10.20245944", - "date": "2020-12-14", - "link": "https://medrxiv.org/cgi/content/short/2020.12.10.20245944", - "title": "Azithromycin in Hospitalised Patients with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial", - "authors": "Peter W Horby; Alistair Roddick; Enti Spata; Natalie Staplin; Jonathan R Emberson; Guilherme Pessoa-Amorim; Leon Peto; Mark Campbell; Christopher Brightling; Ben Prudon; David Chadwick; Andrew Ustianowski; Abdul Ashish; Stacy Todd; Bryan Yates; Robert Buttery; Stephen Scott; Diego Maseda; J Kenneth Baillie; Maya H Buch; Lucy C Chappell; Jeremy N Day; Saul N Faust; Thomas Jaki; Katie Jeffery; Edmund Juszczak; Wei Shen Lim; Alan Montgomery; Andrew Mumford; Kathryn Rowan; Guy Thwaites; Marion Mafham; Richard Haynes; Martin J Landray", - "affiliations": "Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, United Kingdom; Department of Respiratory Medicine, North Tees & Hartlepool NHS Foundation Trust, Stockton-on-Tees, United Kingdom; Centre for Clinical Infection, James Cook University Hospital, Middlesbrough, United Kingdom; North Manchester General Hospital & University of Manchester, Manchester, United Kingdom; Wrightington Wigan and Leigh NHS Foundation Trust, Wigan, United Kingdom; Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom; Northumbria Healthcare NHS Foundation Trust, North Tyneside, United Kingdom; North West Anglia NHS Foundation Trust, Peterborough, United Kingdom; The Countess of Chester Hospital NHS Foundation Trust, Chester, United Kingdom; Mid Cheshire Hospitals NHS Foundation Trust, Crewe, United Kingdom; Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom; Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom; School of Life Sciences, King's College London, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, ; Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom; MRC Biostatistics Unit, University of Cambridge, Cambridge, United Ki; Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; Respiratory Medicine Department, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom; School of Medicine, University of Nottingham, Nottingham, United Kingdom; School of Cellular and Molecular Medicine, University of Bristol, Bristol, United kingdom; Intensive Care National Audit & Research Centre, London, United Kingdom; Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom", - "abstract": "BackgroundAzithromycin has been proposed as a treatment for COVID-19 on the basis of its immunomodulatory actions. We evaluated the efficacy and safety of azithromycin in hospitalised patients with COVID-19.\n\nMethodsIn this randomised, controlled, open-label, adaptive platform trial, several possible treatments were compared with usual care in patients hospitalised with COVID-19 in the UK. Eligible and consenting patients were randomly allocated to either usual standard of care alone or usual standard of care plus azithromycin 500 mg once daily by mouth or intravenously for 10 days or until discharge (or one of the other treatment arms). Patients were twice as likely to be randomised to usual care as to any of the active treatment groups. The primary outcome was 28-day mortality. The trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936).\n\nFindingsBetween 7 April and 27 November 2020, 2582 patients were randomly allocated to receive azithromycin and 5182 patients to receive usual care alone. Overall, 496 (19%) patients allocated to azithromycin and 997 (19%) patients allocated to usual care died within 28 days (rate ratio 1{middle dot}00; 95% confidence interval [CI] 0{middle dot}90-1{middle dot}12; p=0{middle dot}99). Consistent results were seen in all pre-specified subgroups of patients. There was no difference in duration of hospitalisation (median 12 days vs. 13 days) or the proportion of patients discharged from hospital alive within 28 days (60% vs. 59%; rate ratio 1{middle dot}03; 95% CI 0{middle dot}97-1{middle dot}10; p=0{middle dot}29). Among those not on invasive mechanical ventilation at baseline, there was no difference in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (21% vs. 22%; risk ratio 0{middle dot}97; 95% CI 0{middle dot}89-1{middle dot}07; p=0{middle dot}54).\n\nInterpretationIn patients hospitalised with COVID-19, azithromycin did not provide any clinical benefit. Azithromycin use in patients hospitalised with COVID-19 should be restricted to patients where there is a clear antimicrobial indication.\n\nFundingUK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant ref: MC_PC_19056).", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.12.11.20247742", @@ -6859,6 +6957,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.12.08.20246231", + "date": "2020-12-11", + "link": "https://medrxiv.org/cgi/content/short/2020.12.08.20246231", + "title": "Artificial intelligence-enabled analysis of UK and US public attitudes on Facebook and Twitter towards COVID-19 vaccinations", + "authors": "Amir Hussain; Ahsen Tahir; Zain Hussain; Zakariya Sheikh; Mandar Gogate; Kia Dashtipour; Azhar Ali; Aziz Sheikh", + "affiliations": "Edinburgh Napier University, UK; Edinburgh Napier University, UK; Edinburgh Medical School, College of Medicine and Veterinary Medicine, University of Edinburgh, UK; Edinburgh Medical School, College of Medicine and Veterinary Medicine, University of Edinburgh, UK; Edinburgh Napier University, UK; Edinburgh Napier University, UK; NHS Forth Medical Group, UK & Harvard T.H. Chan School of Public Health, USA; Usher Institute, Edinburgh Medical School, University of Edinburgh, UK", + "abstract": "BackgroundGlobal efforts towards the development and deployment of a vaccine for SARS-CoV-2 are rapidly advancing. We developed and applied an artificial-intelligence (AI)-based approach to analyse social-media public sentiment in the UK and the US towards COVID-19 vaccinations, to understand public attitude and identify topics of concern.\n\nMethodsOver 300,000 social-media posts related to COVID-19 vaccinations were extracted, including 23,571 Facebook-posts from the UK and 144,864 from the US, along with 40,268 tweets from the UK and 98,385 from the US respectively, from 1st March - 22nd November 2020. We used natural language processing and deep learning based techniques to predict average sentiments, sentiment trends and topics of discussion. These were analysed longitudinally and geo-spatially, and a manual reading of randomly selected posts around points of interest helped identify underlying themes and validated insights from the analysis.\n\nResultsWe found overall averaged positive, negative and neutral sentiment in the UK to be 58%, 22% and 17%, compared to 56%, 24% and 18% in the US, respectively. Public optimism over vaccine development, effectiveness and trials as well as concerns over safety, economic viability and corporation control were identified. We compared our findings to national surveys in both countries and found them to correlate broadly.\n\nConclusionsAI-enabled social-media analysis should be considered for adoption by institutions and governments, alongside surveys and other conventional methods of assessing public attitude. This could enable real-time assessment, at scale, of public confidence and trust in COVID-19 vaccinations, help address concerns of vaccine-sceptics and develop more effective policies and communication strategies to maximise uptake.", + "category": "public and global health", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.12.03.20242941", @@ -6901,20 +7013,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.12.03.20243535", - "date": "2020-12-04", - "link": "https://medrxiv.org/cgi/content/short/2020.12.03.20243535", - "title": "OpenSAFELY: impact of national guidance on switching from warfarin to direct oral anticoagulants (DOACs) in early phase of COVID-19 pandemic in England", - "authors": "Helen J Curtis; Brian MacKenna; Alex J Walker; Richard Croker; Amir Mehrkar; Caroline E Morton; Seb Bacon; George Hickman; Peter Inglesby; Chris Bates; David Evans; Tom Ward; Jonathan Cockburn; Simon Davy; Krishnan Bhaskaran; Anna Schultze; Christopher T Rentsch; Elizabeth Williamson; William Hulme; Helen I McDonald; Laurie Tomlinson; Rohini Mathur; Henry Drysdale; Rosalind M Eggo; Kevin Wing; Angel Wong; Harriet Forbes; John Parry; Frank Hester; Sam Harper; Stephen JW Evans; Ian J Douglas; Liam Smeeth; Ben Goldacre", - "affiliations": "University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; University of Oxford; University of Oxford; TPP; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; TPP; TPP; TPP; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford", - "abstract": "BackgroundEarly in the COVID-19 pandemic the NHS recommended that appropriate patients anticoagulated with warfarin should be switched to direct acting oral anticoagulants (DOACs), requiring less frequent blood testing. Subsequently, a national safety alert was issued regarding patients being inappropriately co-prescribed two anticoagulants following a medication change, and associated monitoring.\n\nObjectiveTo describe which people were switched from warfarin to DOACs; identify potentially unsafe co-prescribing of anticoagulants; and assess whether abnormal clotting results have become more frequent during the pandemic.\n\nMethodsWorking on behalf of NHS England we conducted a population cohort based study using routine clinical data from >17 million adults in England.\n\nResults20,000 of 164,000 warfarin patients (12.2%) switched to DOACs between March and May 2020, most commonly to edoxaban and apixaban. Factors associated with switching included: older age, recent renal function test, higher number of recent INR tests recorded, atrial fibrillation diagnosis and care home residency. There was a sharp rise in co-prescribing of warfarin and DOACs from typically 50-100 per month to 246 in April 2020, 0.06% of all people receiving a DOAC or warfarin. INR testing fell by 14% to 506.8 patients tested per 1000 warfarin patients each month. We observed a very small increase in elevated INRs (n=470) during April compared with January (n=420).\n\nConclusionsIncreased switching of anticoagulants from warfarin to DOACs was observed at the outset of the COVID-19 pandemic in England following national guidance. There was a small but substantial number of people co-prescribed warfarin and DOACs during this period. Despite a national safety alert on the issue, a widespread rise in elevated INR test results was not found. Primary care has responded rapidly to changes in patient care during the COVID-19 pandemic.", - "category": "cardiovascular medicine", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.11.30.20240010", @@ -7055,6 +7153,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.11.18.20230649", + "date": "2020-11-20", + "link": "https://medrxiv.org/cgi/content/short/2020.11.18.20230649", + "title": "A network modelling approach to assess non-pharmaceutical disease controls in a worker population: An application to SARS-CoV-2", + "authors": "Edward M Hill; Benjamin D Atkins; Matt J Keeling; Louise Dyson; Michael J Tildesley", + "affiliations": "University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Warwick", + "abstract": "BackgroundAs part of a concerted pandemic response to protect public health, businesses can enact non-pharmaceutical controls to minimise exposure to pathogens in workplaces and premises open to the public. Amendments to working practices can lead to the amount, duration and/or proximity of interactions being changed, ultimately altering the dynamics of disease spread. These modifications could be specific to the type of business being operated.\n\nMethodsWe use a data-driven approach to parameterise an individual-based network model for transmission of SARS-CoV-2 amongst the working population, stratified into work sectors. The network is comprised of layered contacts to consider the risk of spread in multiple encounter settings (workplaces, households, social and other). We analyse several interventions targeted towards working practices: mandating a fraction of the population to work from home; using temporally asynchronous work patterns; and introducing measures to create COVID-secure workplaces. We also assess the general role of adherence to (or effectiveness of) isolation and test and trace measures and demonstrate the impact of all these interventions across a variety of relevant metrics.\n\nResultsThe progress of the epidemic can be significantly hindered by instructing a significant proportion of the workforce to work from home. Furthermore, if required to be present at the workplace, asynchronous work patterns can help to reduce infections when compared with scenarios where all workers work on the same days, particularly for longer working weeks. When assessing COVID-secure workplace measures, we found that smaller work teams and a greater reduction in transmission risk reduced the probability of large, prolonged outbreaks. Finally, following isolation guidance and engaging with contact tracing without other measures is an effective tool to curb transmission, but is highly sensitive to adherence levels.\n\nConclusionsIn the absence of sufficient adherence to non-pharmaceutical interventions, our results indicate a high likelihood of SARS-CoV-2 spreading widely throughout a worker population. Given the heterogeneity of demographic attributes across worker roles, in addition to the individual nature of controls such as contact tracing, we demonstrate the utility of a network model approach to investigate workplace-targeted intervention strategies and the role of test, trace and isolation in tackling disease spread.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.11.18.20225029", @@ -7363,6 +7475,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "bioRxiv", + "doi": "10.1101/2020.10.26.356014", + "date": "2020-10-28", + "link": "https://biorxiv.org/cgi/content/short/2020.10.26.356014", + "title": "COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms", + "authors": "Marek Ostaszewski; Anna Niarakis; Alexander Mazein; Inna Kuperstein; Robert Phair; Aurelio Orta-Resendiz; Vidisha Singh; Sara Sadat Aghamiri; Marcio Luis Acencio; Enrico Glaab; Andreas Ruepp; Gisela Fobo; Corinna Montrone; Barbara Brauner; Goar Frishman; Julia Somers; Matti Hoch; Shailendra Kumar Gupta; Julia Scheel; Hanna Borlinghaus; Tobias Czauderna; Falk Schreiber; Arnau Montagud; Miguel Ponce de Leon; Akira Funahashi; Yusuke Hiki; Noriko Hiroi; Takahiro G Yamada; Andreas Drager; Alina Renz; Muhammad Naveez; Zsolt Bocskei; Daniela Bornigen; Liam Fergusson; Marta Conti; Marius Rameil; Vanessa Nakonecnij; Jakob Vanhoefer; Leonard Schmiester; Muying Wang; Emily E Ackerman; Jason E Shoemaker; Jeremy Zucker; Kristie L Oxford; Jeremy Teuton; Ebru Kocakaya; Gokce Yagmur Summak; Kristina Hanspers; Martina Kutmon; Susan Coort; Lars Eijssen; Friederike Ehrhart; Rex D. A. B.; Denise Slenter; Marvin Martens; Nhung Pham; Robin Haw; Bijay Jassal; Lisa Matthews; Marija Orlic-Milacic; Andrea Senff-Ribeiro; Karen Rothfels; Veronica Shamovsky; Ralf Stephan; Cristoffer Sevilla; Thawfeek Mohamed Varusai; Jean-Marie Ravel; Vera Ortseifen; Silvia Marchesi; Piotr Gawron; Ewa Smula; Laurent Heirendt; Venkata Satagopam; Guanming Wu; Anders Riutta; Martin Golebiewski; Stuart Owen; Carole Goble; Xiaoming Hu; Rupert Overall; Dieter Maier; Angela Bauch; Benjamin M Gyori; John A Bachman; Carlos Vega; Valentin Groues; Miguel Vazquez; Pablo Porras; Luana Licata; Marta Iannuccelli; Francesca Sacco; Denes Turei; Augustin Luna; Ozgun Babur; Sylvain Soliman; Alberto Valdeolivas; Marina Esteban-Medina; Maria Pena-Chilet; Kinza Rian; Tomas Helikar; Bhanwar Lal Puniya; Anastasia Nesterova; Anton Yuryev; Anita de Waard; Dezso Modos; Agatha Treveil; Marton Laszlo Olbei; Bertrand De Meulder; Aurelien Naldi; Aurelien Dugourd; Laurence Calzone; Chris Sander; Emek Demir; Tamas Korcsmaros; Tom C Freeman; Franck Auge; Jacques S Beckmann; Jan Hasenauer; Olaf Wolkenhauer; Egon Willighagen; Alexander R Pico; Chris Evelo; Lincoln D Stein; Henning Hermjakob; Julio Saez-Rodriguez; Joaquin Dopazo; Alfonso Valencia; Hiroaki Kitano; Emmanuel Barillot; Charles Auffray; Rudi Balling; Reinhard Schneider; - the COVID-19 Disease Map Community", + "affiliations": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; Department of Biology, Univ. Evry, University of Paris-Saclay, GenHotel, Genopole, 91025, Evry, France; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; Institut Curie, PSL Research University, Paris, France.; Integrative Bioinformatics, Inc., 346 Paul Ave, Mountain View, CA, USA; Institut Pasteur, HIV, Inflammation and Persistence Unit, Paris, France; Laboratoire Europeen de Recherche pour la Polyarthrite Rhumatoide - Genhotel, Univ Evry, Universite Paris-Saclay, 2, rue Gaston Cremieux, 91057 EVRY-GENOPOLE ce; Inserm- Institut national de la sante et de la recherche medicale. Saint-Louis Hospital 1 avenue Claude Vellefaux Pavillon Bazin 75475 Paris; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; Institute of Experimental Genetics (IEG), Helmholtz Zentrum Munchen-German Research Center for Environmental Health (GmbH), Ingolstadter Landstrasse 1, D-85764 ; Institute of Experimental Genetics (IEG), Helmholtz Zentrum Munchen-German Research Center for Environmental Health (GmbH), Ingolstadter Landstrasse 1, D-85764 ; Institute of Experimental Genetics (IEG), Helmholtz Zentrum Munchen-German Research Center for Environmental Health (GmbH), Ingolstadter Landstrasse 1, D-85764 ; Institute of Experimental Genetics (IEG), Helmholtz Zentrum Munchen-German Research Center for Environmental Health (GmbH), Ingolstadter Landstrasse 1, D-85764 ; Institute of Experimental Genetics (IEG), Helmholtz Zentrum Munchen-German Research Center for Environmental Health (GmbH), Ingolstadter Landstrasse 1, D-85764 ; Oregong Health & Sciences Univerity; Department of Molecular and Medical Genetics; 3222 SW Research Drive, Portland, Oregon, U.S.A 97239; Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany; Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany; Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany; Department of Computer and Information Science, University of Konstanz, Konstanz, Germany; Monash University, Faculty of Information Technology, Department of Human-Centred Computing, Wellington Rd, Clayton VIC 3800, Australia; Department of Computer and Information Science, University of Konstanz, Konstanz, Germany; Barcelona Supercomputing Center (BSC), Barcelona, Spain; Barcelona Supercomputing Center (BSC), Barcelona, Spain; Keio University, Department of Biosciences and Informatics, 3-14-1 Hiyoshi Kouhoku-ku Yokohama Japan 223-8522; Keio University, Department of Biosciences and Informatics, 3-14-1 Hiyoshi Kouhoku-ku Yokohama Japan 223-8522; Sanyo-Onoda City University, Faculty of Pharmaceutical Sciences, University St.1-1-1, Yamaguchi, Japan 756-0884; Keio University, Department of Biosciences and Informatics, 3-14-1 Hiyoshi Kouhoku-ku Yokohama Japan 223-8522; Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tu; Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tu; Riga Technical University, Institute of Applied Computer Systems,1 Kalku Street, LV-1658 Riga, Latvia; Sanofi R&D Translational Sciences; Bioinformatics Core Facility, Universitaetsklinikum Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany; The University of Edinburgh, Royal (Dick) School of Veterinary Medicine, Easter Bush Campus, Midlothian, EH25 9RG; Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany; University of Bonn, Germany; Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany; Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany; Helmholtz Zentrum Munchen - German Research Center for Environmental Health, Institute of Computational Biology, 85764 Neuherberg, Germany; Department of Chemical Engineering, University of Pittsburgh; University of Pittsburgh, Department of Chemical and Petroleum Engineering; Dept. of Chemical & Petroleum Engineering, University of Pittsburgh; Pacific Northwest National Laboratory; Pacific Northwest National Laboratory; Pacific Northwest National Laboratory; Ankara University, Stem Cell Institute, Ceyhun Atif Kansu St. No: 169 06520 Cevizlidere/ANKARA/TURKEY; Ankara University, Stem Cell Institute, Ceyhun Atif Kansu St. No: 169 06520 Cevizlidere/ANKARA/TURKEY; Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands; Maastricht University, NUTRIM, Bioinformatics-BiGCaT, PO Box 616, 6200 MD, Maastricht, the Netherlands; Department of Bioninformatics-BiGCaT, NUTRIM, Maastricht University, Universiteitssingel 60, 6229 ER Maastricht, The Netherlands; Maastricht University, Department of Bioinformatics, NUTRIM, Universiteitssingel 60; 6229 ER Maastricht; The Netherlands; Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore 575018, India; Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands; Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, 6229 ER Maastricht, The Netherlands; Maastricht University, NUTRIM, Bioinformatics-BiGCaT, PO Box 616, 6200 MD, Maastricht, the Netherlands; Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3; Ontario Institute for Cancer Research (OICR), 661 University Ave Suite 510, Toronto, ON M5G 0A3, Canada; NYU Grossman School of Medicine, New York NY 10016 USA; Ontario Institute for Cancer Research, Department of Computational Biology, MaRS Centre, South Tower, 661 University Avenue, Suite 500, Toronto, Ontario, Canada; Ontario Institute for Cancer Research (OICR) (Canada); Ontario Institute for Cancer Research, Department of Computational Biology, MaRS Centre, South Tower, 661 University Avenue, Suite 500, Toronto, Ontario, Canada; NYU Langone Medical Center, New York, USA; Ontario Institute for Cancer Research, MaRS Centre, 661 University Ave, Suite 510, Toronto, Ontario, Canada; EMBL-EBI, Molecular Systems, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD; Reactome, EMBL-EBI, Cambridge, UK; University of Lorraine, INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, F-54000 Nancy, France.; Senior Research Group in Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitaetsstrasse 27, 33615 Bielefeld,; Uppsala University - Sweden; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239-3098, USA; Gladstone Institutes, Institute for Data Science and Biotechnology, 1650 Owens St., San Francisco, CA 94131, USA; Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg (Germany); The University of Manchester, Department of Computer Science, Oxford Road, Manchester, M13 9PL, UK; The University of Manchester, Department of Computer Science, Oxford Road, Manchester, M13 9PL, UK; Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg (Germany); German Center for Neurodegenerative Diseases (DZNE) Dresden, Tatzberg 41, 01307 Dresden, Germany.; Biomax Informatics AG, Robert-Koch-Str. 2, 82152 Planegg, Germany; Biomax Informatics AG, Robert-Koch-Str. 2, 82152 Planegg, Germany; Harvard Medical School, Laboratory of Systems Pharmacology, 200 Longwood Avenue, Boston, MA; Harvard Medical School, Laboratory of Systems Pharmacology, 200 Longwood Avenue, Boston, MA; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; Barcelona Supercomputing Center (BSC), Barcelona, Spain; EMBL-EBI, Molecular Systems, Wellcome Genome Campus, CB10 1SD, Hinxton, UK; University of Rome Tor Vergata, Department of Biology, Via della Ricerca Scientifica 1, 00133 Rome, Italy; University of Rome Tor Vergata, Department of Biology, Via della Ricerca Scientifica 1, 00133 Rome, Italy; University of Rome Tor Vergata, Department of Biology, Via della Ricerca Scientifica 1, 00133 Rome, Italy; Heidelberg Univarsity, Institute for Computational Biomedicine, BQ 0053, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany; cBio Center, Divisions of Biostatistics and Computational Biology, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.; University of Massachusetts Boston, Computer Science Department, 100 William T, Morrissey Blvd, Boston, MA 02125; Inria Saclay Ile-de-France; Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany; Clinical Bioinformatics Area. Fundacion Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain.; Clinical Bioinformatics Area. Fundacion Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain.; Clinical Bioinformatics Area. Fundacion Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain.; University of Nebraska-Lincoln, Department of Biochemistry, 1901 Vine St., Lincoln, NE, 68588, USA; University of Nebraska-Lincoln, Department of Biochemistry, 1901 Vine St., Lincoln, NE, 68588, USA; Elsevier, Life Science Department; Elsevier, Professional Services, 1600 John F Kennedy Blvd #1800, Philadelphia, PA 19103; Elsevier, Research Collaborations Unit, 71 Hanley Lane, Jericho, VT 05465; Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom; Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom; Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom; Association EISBM; Inria Saclay - Ile de France, Lifeware group, 91120 Palaiseau, France; Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany; Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, F-75005, Paris, France.; cBio Center, Divisions of Biostatistics and Computational Biology, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.; Oregon Health and Science University, Department of Molecular and Medical Genetics, 3222 SW Research Drive, Mail Code: L103, Portland, Oregon, U.S.A. 97239; Earlham Institute, Norwich Research Park, NR4 7UZ, Norwich, UK; The Roslin Institute, University of Edinburgh EH25 9RG; Sanofi R&D, Translational Sciences, 1 av Pierre Brossolette 91395 Chilly-Mazarin France; University of Lausanne, Lausanne, Switzerland; Interdisciplinary Research Unit Mathematics and Life Sciences, University of Bonn, Germany; University of Rostock, Dept of Systems Biology & Bioinformatics; Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands; Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA; Dept. Bioinformatics - BiGCaT, Maastricht University, The Netherlands; Ontario Institute for Cancer Research, Adaptive Oncology Theme, 661 University Ave, Toronto, ON M5G 1M1 Canada; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK; Institute for Computational Biomedicine Heidelberg University, Faculty of Medicine, Im Neuenheimer Feld 267, 69120 Heidelberg; Clinical Bioinformatics Area. Fundacion Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio. 41013. Sevilla. Spain.; Barcelona Supercomputing Center (BSC), Barcelona, Spain; Systems Biology Institute, Tokyo Japan; Institut Curie, PSL Research University, Paris, France.; European Institute for Systems Biology and Medicine (EISBM), Vourles, France; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg; -", + "abstract": "We describe a large-scale community effort to build an open-access, interoperable, and computable repository of COVID-19 molecular mechanisms - the COVID-19 Disease Map. We discuss the tools, platforms, and guidelines necessary for the distributed development of its contents by a multi-faceted community of biocurators, domain experts, bioinformaticians, and computational biologists. We highlight the role of relevant databases and text mining approaches in enrichment and validation of the curated mechanisms. We describe the contents of the Map and their relevance to the molecular pathophysiology of COVID-19 and the analytical and computational modelling approaches that can be applied for mechanistic data interpretation and predictions. We conclude by demonstrating concrete applications of our work through several use cases and highlight new testable hypotheses.", + "category": "systems biology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.10.25.20219048", @@ -8007,20 +8133,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.09.05.20188821", - "date": "2020-09-08", - "link": "https://medrxiv.org/cgi/content/short/2020.09.05.20188821", - "title": "Ethnicity and clinical outcomes in COVID-19A Systematic Review and Meta-analysis", - "authors": "Shirley Sze; Daniel Pan; Laura J Gray; Clareece R Nevill; Christopher A Martin; Joshua Nazareth; Jatinder S Minhas; Pip Divall; Kamlesh Khunti; Keith Abrams; Laura B Nellums; Manish Pareek", - "affiliations": "University of Leicester; University of Leicester; University of Leicester; University of Leicester; University of Leicester; University of Leicester; University of Leicester; University Hospitals of Leicester NHS Trust; University of Leicester; University of Leicester; University of Nottingham; University of Leicester", - "abstract": "ImportanceThe association of ethnicity with outcomes in patients with COVID-19 is unclear.\n\nObjectiveTo determine whether the risk of SARS-CoV-2 infection, COVID-19 intensive care unit (ICU) admission and mortality are associated with ethnicity.\n\nData SourcesWe searched all English language articles published 1st December 2019 - 30th June 2020 within MEDLINE, EMBASE, PROSPERO and the Cochrane library using indexing terms for COVID-19 and ethnicity, as well as manuscripts awaiting peer review on MedRxiv during the same period.\n\nStudy SelectionIncluded studies reported original clinical data, disaggregated by ethnicity, on patients with confirmed or suspected COVID-19. We excluded correspondence, area level, modelling and basic science articles. Two independent reviewers screened articles for inclusion. Of 926 identified articles, 35 were included in the meta-analyses.\n\nData Extraction and SynthesisThe review was conducted according to PRISMA guidelines. Reviewers independently extracted data using a piloted form on: (1) rates of infection, ICU admission and mortality by ethnicity; and (2) unadjusted and adjusted data comparing ethnic minority and White groups. Data were pooled using random effects models.\n\nMain Outcomes and MeasuresOutcomes were: (1) infection with SARS-CoV-2 confirmed on molecular testing; (2) ICU admission; and (3) mortality in COVID-19 confirmed and suspected cases.\n\nResults13,535,562 patients from 35 studies were included in the meta-analyses. Black, Asian and Hispanic individuals had a greater risk of infection compared to White individuals (Black: pooled adjusted RR: 2.06, 95% CI: 1.59-2.67; Asian: 1.35, 95%CI: 1.15-1.59; Hispanic: 1.77, 95% CI: 1.39-2.25). Black individuals were significantly more likely to be admitted to ICU than White individuals (pooled adjusted RR: 1.61, 95% CI: 1.02-2.55). Risk of mortality was similar across ethnicities among hospitalised patients, but increased among Asian and Mixed ethnic groups in the general population.\n\nConclusionsBlack, Asian and Hispanic ethnic groups are at increased risk of SARS-CoV-2 infection. Black individuals may be more likely to require ICU admission for COVID-19. There may also be disparities in risk of death from COVID-19 at a population level. Our findings are of critical public health importance and should inform policy on minimising SARS-CoV-2 exposure in ethnic minority groups.\n\nKEY POINTSO_ST_ABSQuestionC_ST_ABSIs ethnicity associated with vulnerability to, and outcomes from, coronavirus disease 2019 (COVID-19)?\n\nFindingsIn this systematic review and meta-analysis, rates of infection and outcomes from COVID-19 were compared between ethnic groups. Individuals from Black, Asian and Hispanic ethnicity were significantly more vulnerable to SARS-CoV-2 infection than those of White ethnicity. Black individuals were more likely to need intensive care unit (ICU) admission for COVID-19 than White individuals. Risk of mortality was similar across ethnicities among hospitalised patients, but increased among Asian and Mixed ethnic groups in the general population.\n\nMeaningThere is strong evidence for an increased risk of SARS-CoV-2 infection amongst ethnic minorities, and targeted public health policies are required to reduce this risk.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.09.02.20185892", @@ -8245,20 +8357,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.08.17.20175117", - "date": "2020-08-21", - "link": "https://medrxiv.org/cgi/content/short/2020.08.17.20175117", - "title": "Real-time spatial health surveillance: mapping the UK COVID-19 epidemic", - "authors": "Richard Fry; Joe Hollinghurst; Helen R Stagg; Daniel A Thompson; Claudio Fronterre; Chris Orton; Ronan A Lyons; David V Ford; Aziz Sheikh; Peter J Diggle", - "affiliations": "Swansea University; Swansea University; Edinburgh University; Swansea University; Lancaster University; Swansea University; Swansea University; Swansea University; Edinburgh University; Lancaster University", - "abstract": "The COVID-19 pandemic has highlighted the need for robust data linkage systems and methods for identifying outbreaks of disease in near real-time. Using self-reported app data and the Secure Anonymised Information Linkage (SAIL) Databank, we demonstrate the use of sophisticated spatial modelling for near-real-time prediction of COVID-19 prevalence at small-area resolution to inform strategic government policy areas. A pre-requisite to an effective control strategy is that predictions need to be accompanied by estimates of their precision, to guard against over-reaction to potentially spurious features of best guess predictions. In the UK, important emerging risk-factors such as social deprivation or ethnicity vary over small distances, hence risk needs to be modelled at fine spatial resolution to avoid aggregation bias. We demonstrate that existing geospatial statistical methods originally developed for global health applications are well-suited to this task and can be used in an anonymised databank environment, thus preserving the privacy of the individuals who contribute their data.", - "category": "public and global health", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.08.17.20161760", @@ -8287,6 +8385,20 @@ "author_similarity": 94, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.08.13.20174193", + "date": "2020-08-15", + "link": "https://medrxiv.org/cgi/content/short/2020.08.13.20174193", + "title": "CovidNudge: diagnostic accuracy of a novel lab-free point-of-care diagnostic for SARS-CoV-2", + "authors": "Malick M Gibani; Christofer Toumazou; Mohammadreza Sohbati; Rashmita Sahoo; Maria Karvela; Tsz-Kin Hon; Sara De Mateo; Alison Burdett; K Y Felice Leung; Jake Barnett; Arman Orbeladze; Song Luan; Stavros Pournias; Jiayang Sun; Barnaby Flower; Judith Bedzo-Nutakor; Maisarah Amran; Rachael Quinlan; Keira Skolimowska; Robert Klaber; Gary Davies; David Muir; Paul Randell; Derrick W M Crook; Graham P Taylor; Wendy Barclay; Nabeela Mughal; Luke S P Moore; Katie Jeffery; Graham S Cooke", + "affiliations": "Imperial College London; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; Department of Infectious Disease, Imperial College London, United Kingdom; DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London; Imperial College Healthcare NHS Trust, United Kingdom.; Department of Infectious Disease, Imperial College London, United Kingdom; Imperial College Healthcare NHS Trust, United Kingdom; Imperial College Healthcare NHS Trust, United Kingdom; Chelsea & Westminster NHS Foundation Trust, London; Imperial College Healthcare NHS Trust, United Kingdom; Imperial College Healthcare NHS Trust, United Kingdom; NIHR Oxford Biomedical Research Centre; Department of Infectious Disease, Imperial College London, United Kingdom; Department of Infectious Disease, Imperial College London, United Kingdom; Chelsea & Westminster NHS Foundation Trust, London; Chelsea & Westminster NHS Foundation Trust, London; Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; Department of Infectious Disease, Imperial College London, United Kingdom", + "abstract": "3.BackgroundAccess to rapid diagnosis is key to the control and management of SARS-CoV-2. Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) testing usually requires a centralised laboratory and significant infrastructure. We describe the development and diagnostic accuracy assessment of a novel, rapid point-of-care RT-PCR test, the DnaNudge(R) platform CovidNudge test, which requires no laboratory handling or sample pre-processing.\n\nMethodsNasopharyngeal swabs are inserted directly into a cartridge which contains all reagents and components required for RT-PCR reactions, including multiple technical replicates of seven SARS-CoV-2 gene targets (rdrp1, rdrp2, e-gene, n-gene, n1, n2 and n3) and human ribonuclease P (RNaseP) as positive control. Between April and May 2020, swab samples were tested in parallel using the CovidNudge direct-to-cartridge platform and standard laboratory RT-PCR using swabs in viral transport medium. Samples were collected from three groups: self-referred healthcare workers with suspected COVID-19 (Group 1, n=280/386; 73%); patients attending the emergency department with suspected COVID-19 (Group 2, n=15/386; 4%) and hospital inpatient admissions with or without suspected COVID-19 (Group 3, n=91/386; 23%).\n\nResultsOf 386 paired samples tested across all groups, 67 tested positive on the CovidNudge platform and 71 with standard laboratory RT-PCR. The sensitivity of the test varied by group (Group 1 93% [84-98%], Group 2 100% [48-100%] and Group 3 100% [29-100%], giving an average sensitivity of 94.4% (95% confidence interval 86-98%) and an overall specificity of 100% (95%CI 99-100%; Group 1 100% [98-100%]; Group 2 100% [69-100%] and Group 3 100% [96-100%]). Point of care testing performance was comparable during a period of high (25%) and low (3%) background prevalence. Amplification of the viral nucleocapsid (n1, n2, n3) targets were most sensitive for detection of SARS-CoV2, with the assay able to detect 1x104 viral particles in a single swab.\n\nConclusionsThe CovidNudge platform offers a sensitive, specific and rapid point of care test for the presence of SARS-CoV-2 without laboratory handling or sample pre-processing. The implementation of such a device could be used to enable rapid decisions for clinical care and testing programs.\n\n4. RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSThe WHO has highlighted the development of rapid, point-of-care diagnostics for detection of SARS-CoV-2 as a key priority to tackle COVID-19. The Foundation for Innovative Diagnostics (FIND) has identified over 90 point-of-care, near patient or mobile tests for viral detection of SARS-CoV-2. However, the most widely available rapid tests to date require some sample handling which limits their use at point-of-care. In addition, pressure on supply chains is restricting access to current diagnostics and alternatives are needed urgently.\n\nAdded value of this studyWe describe the development and clinical validation of COVID nudge, a novel point-of-care RT-PCR diagnostic, evaluated during the first wave of the SARS-CoV-2 epidemic. The platform is able to achieve high analytic sensitivity and specificity from dry swabs within a self-contained cartridge. The lack of downstream sample handling makes it suitable for use in a range of clinical settings, without need for a laboratory or specialized operator. Multiplexed assays within the cartridge allow inclusion of a positive human control, which reduces the false negative testing rate due to insufficient sampling.\n\nImplication of the available evidencePoint-of-care testing can relieve pressure on centralized laboratories and increase overall testing capacity, complementing existing approaches. These findings support a role for COVID Nudge as part of strategies to improve access to rapid diagnostics to SARS-CoV-2. Since May 2020, the system has been implemented in UK hospitals and is being rolled out nationwide.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 92, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.08.12.20173690", @@ -8301,6 +8413,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.08.13.20174227", + "date": "2020-08-14", + "link": "https://medrxiv.org/cgi/content/short/2020.08.13.20174227", + "title": "Long-Term Exposure to Outdoor Air Pollution and COVID-19 Mortality: an ecological analysis in England", + "authors": "Zhiqiang Feng; Mark Cherrie; Chris DIBBEN", + "affiliations": "University of Edinburgh; University of Edinburgh; University of Edinburgh", + "abstract": "There is an urgent need to examine what individual and environmental risk factors are associated with COVID-19 mortality. This objective of this study is to investigate the association between long term exposure to air pollution and COVID-19 mortality. We conducted a nationwide, ecological study using zero-inflated negative binomial models to estimate the association between long term (2014-2018) small area level exposure to NOx, PM2.5, PM10 and SO2 and COVID-19 mortality rates in England adjusting for socioeconomic factors and infection exposure. We found that all four pollutant concentrations were positively associated with COVID-19 mortality. The increase in mortality risk ratio per inter quarter range increase was for PM2.5:11%, 95%CIs 6%-17%), PM10 (5%; 95%CIs 1%-11%), NOx (11%, 95%CIs 6%-15%) and SO2 (7%, 95%CIs 3%-11%) were respectively in adjusted models. Public health intervention may need to protect people who are in highly polluted areas from COVID-19 infections.", + "category": "occupational and environmental health", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.08.12.20171405", @@ -8427,6 +8553,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.08.04.20163782", + "date": "2020-08-04", + "link": "https://medrxiv.org/cgi/content/short/2020.08.04.20163782", + "title": "Fitting models to the COVID-19 outbreak and estimating R", + "authors": "Matt J Keeling; Louise Dyson; Glen Guyver-Fletcher; Alex Holmes; Malcolm G Semple; - ISARIC4C Investigators; Michael J Tildesley; Edward M Hill", + "affiliations": "University of Warwick; University of Warwick; University of Warwick; University of Warwick; University of Liverpool; ; University of Warwick; University of Warwick", + "abstract": "The COVID-19 pandemic has brought to the fore the need for policy makers to receive timely and ongoing scientific guidance in response to this recently emerged human infectious disease. Fitting mathematical models of infectious disease transmission to the available epidemiological data provides a key statistical tool for understanding the many quantities of interest that are not explicit in the underlying epidemiological data streams. Of these, the effective reproduction number, R, has taken on special significance in terms of the general understanding of whether the epidemic is under control (R < 1). Unfortunately, none of the epidemiological data streams are designed for modelling, hence assimilating information from multiple (often changing) sources of data is a major challenge that is particularly stark in novel disease outbreaks.\n\nHere, focusing on the dynamics of the first-wave (March-June 2020), we present in some detail the inference scheme employed for calibrating the Warwick COVID-19 model to the available public health data streams, which span hospitalisations, critical care occupancy, mortality and serological testing. We then perform computational simulations, making use of the acquired parameter posterior distributions, to assess how the accuracy of short-term predictions varied over the timecourse of the outbreak. To conclude, we compare how refinements to data streams and model structure impact estimates of epidemiological measures, including the estimated growth rate and daily incidence.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.07.30.20165464", @@ -8679,20 +8819,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "medRxiv", - "doi": "10.1101/2020.07.13.20152793", - "date": "2020-07-14", - "link": "https://medrxiv.org/cgi/content/short/2020.07.13.20152793", - "title": "At what times during infection is SARS-CoV-2 detectable and no longer detectable using RT-PCR based tests?: A systematic review of individual participant data", - "authors": "Sue Mallett; Joy Allen; Sara Graziadio; Stuart A Taylor; Naomi S Sakai; Kile Green; Jana Suklan; Chris Hyde; Bethany Shinkins; Zhivko Zhelev; Jaime Peters; Philip Turner; Nia W Roberts; Lavinia Ferrante di Ruffano; Robert Wolff; Penny Whiting; Amanda Winter; Gauraang Bhatnagar; Brian D Nicholson; Steve Halligan", - "affiliations": "University College London, UK; Newcastle University, UK; Newcastle upon Tyne Hospitals NHS Foundation Trust, UK; University College London, UK; University College London, UK; Newcastle University, UK; Newcastle University, UK; University of Exeter, UK; University of Leeds, UK; University of Exeter, UK; University of Exeter, UK; University of Oxford, UK; University of Oxford, UK; University of Birmingham, UK; Kleijnen Systematic Reviews Ltd, UK; University of Bristol, UK; Newcastle University, UK; Frimley Health NHS Foundation Trust, UK; University of Oxford, UK; University College London, UK", - "abstract": "STRUCTURED SUMMARYO_ST_ABSBackgroundC_ST_ABSTests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral ribonucleic acid (RNA), using reverse transcription polymerase chain reaction (RT-PCR) are pivotal to detecting current coronavirus disease (COVID-19) and duration of detectable virus indicating potential for infectivity.\n\nMethodsWe conducted an individual participant data (IPD) systematic review of longitudinal studies of RT-PCR test results in symptomatic SARS-CoV-2. We searched PubMed, LitCOVID, medRxiv and COVID-19 Living Evidence databases. We assessed risk of bias using a QUADAS- 2 adaptation. Outcomes were the percentage of positive test results by time and the duration of detectable virus, by anatomical sampling sites.\n\nFindingsOf 5078 studies screened, we included 32 studies with 1023 SARS-CoV-2 infected participants and 1619 test results, from -6 to 66 days post-symptom onset and hospitalisation. The highest percentage virus detection was from nasopharyngeal sampling between 0 to 4 days post-symptom onset at 89% (95% confidence interval (CI) 83 to 93) dropping to 54% (95% CI 47 to 61) after 10 to 14 days. On average, duration of detectable virus was longer with lower respiratory tract (LRT) sampling than upper respiratory tract (URT). Duration of faecal and respiratory tract virus detection varied greatly within individual participants. In some participants, virus was still detectable at 46 days post- symptom onset.\n\nInterpretationRT-PCR misses detection of people with SARS-CoV-2 infection; early sampling minimises false negative diagnoses. Beyond ten days post-symptom onset, lower RT or faecal testing may be preferred sampling sites. The included studies are open to substantial risk of bias so the positivity rates are probably overestimated.\n\nPANEL: RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSThere are numerous reports of negative severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse transcription polymerase chain reaction (RT-PCR) test results in participants with known SARS-CoV-2 infection, and increasing awareness that the ability of RT-PCR tests to detect virus depends on the timing of sample retrieval and anatomical sampling site.\n\nIndividual studies suggest that positive test results from RT-PCR with nasopharyngeal sampling declines within a week of symptoms and that a positive test later in the disease course is more likely from sputum, bronchoalveolar lavage (BAL) or stool, but data are inconsistent.\n\nAdded value of this studyWe searched 5078 titles and abstracts for longitudinal studies reporting individual participant data (IPD) for RT-PCR for participants with COVID-19 linked to either time since symptom onset or time since hospitalisation. Search included SARS-CoV-2 and RT-PCR keywords and MeSH terms. Each included study was subject to careful assessment of risk of bias. This IPD systematic review (SR) addresses RT-PCR test detection rates at different times since symptom onset and hospitalisation for different sampling sites, and summarises the duration of detectable virus. To our knowledge, this is the first rapid SR addressing this topic. We identified 32 studies available as published articles or pre-prints between January 1st and April 24th 2020, including participants sampled at 11 different sampling sites and some participants sampled at more than one site. At earlier time points, nasopharyngeal sampling had the highest virus detection, but the duration of shedding was shorter compared to lower respiratory tract sampling. At 10 to 14 days post-symptom onset, the percentage of positive nasopharyngeal test results was 54% compared to 89% at day 0 to 4. Presence and duration of faecal detection varied by participant, and in nearly half duration was shorter than respiratory sample detection. Virus detection varies for participants and can continue to be detected up to 46 days post-symptom onset or hospitalisation. The included studies were open to substantial risk of bias, so the detection rates are probably overestimates. There was also poor reporting of sampling methods and sparse data on sampling methods that are becoming more widely implemented, such as self-sampling and short nasal swab sampling (anterior nares/mid turbinate).\n\nImplications of all the available evidenceResults from this IPD SR of SARS-CoV-2 testing at different time points and using different anatomical sample sites are important to inform strategies of testing. For prevention of ongoing transmission of SARS-CoV-2, samples for RT-PCR testing need to be taken as soon as possible post-symptom onset, as we confirm that RT-PCR misses more people with infection if sampling is delayed. The percentage of positive RT-PCR tests is also highly dependent on the anatomical site sampled in infected people. Sampling at more than one anatomical site may be advisable as there is variation between individuals in the sites that are infected, as well as the timing of SARS-CoV-2 virus detection at an anatomical site. Testing ten days after symptom onset will lead to a higher frequency of negative tests, particularly if using only upper respiratory tract sampling. However, our estimates may considerably understate the frequency of negative RT-PCR results in people with SARS-CoV- 2 infection. Further investment in this IPD approach is recommended as the amount data available was small given the scale of the pandemic and the importance of the question. More studies, learning from our observations about risk of bias and strengths of example studies (Box 1, Box 2) are urgently needed to inform the optimal sampling strategy by including self-collected samples such as saliva and short nasal swabs. Better reporting of anatomical sampling sites with a detailed methodology on sample collection is also urgently needed.", - "category": "infectious diseases", - "match_type": "fuzzy", - "author_similarity": 92, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.07.13.20152710", @@ -9771,6 +9897,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.05.06.20092999", + "date": "2020-05-07", + "link": "https://medrxiv.org/cgi/content/short/2020.05.06.20092999", + "title": "OpenSAFELY: factors associated with COVID-19-related hospital death in the linked electronic health records of 17 million adult NHS patients.", + "authors": "- The OpenSAFELY Collaborative; Elizabeth Williamson; Alex J Walker; Krishnan J Bhaskaran; Seb Bacon; Chris Bates; Caroline E Morton; Helen J Curtis; Amir Mehrkar; David Evans; Peter Inglesby; Jonathan Cockburn; Helen I Mcdonald; Brian MacKenna; Laurie Tomlinson; Ian J Douglas; Christopher T Rentsch; Rohini Mathur; Angel Wong; Richard Grieve; David Harrison; Harriet Forbes; Anna Schultze; Richard T Croker; John Parry; Frank Hester; Sam Harper; Rafael Perera; Stephen Evans; Liam Smeeth; Ben Goldacre", + "affiliations": "; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; University of Oxford; TPP; University of Oxford; University of Oxford; University of Oxford; University of Oxford; University of Oxford; TPP; London School of Hygiene and Tropical Medicine; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; ICNARC; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford; TPP; TPP; TPP; University of Oxford; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; University of Oxford", + "abstract": "BackgroundEstablishing who is at risk from a novel rapidly arising cause of death, and why, requires a new approach to epidemiological research with very large datasets and timely data. Working on behalf of NHS England we therefore set out to deliver a secure and pseudonymised analytics platform inside the data centre of a major primary care electronic health records vendor establishing coverage across detailed primary care records for a substantial proportion of all patients in England. The following results are preliminary.\n\nData sourcesPrimary care electronic health records managed by the electronic health record vendor TPP, pseudonymously linked to patient-level data from the COVID-19 Patient Notification System (CPNS) for death of hospital inpatients with confirmed COVID-19, using the new OpenSAFELY platform.\n\nPopulation17,425,445 adults.\n\nTime period1st Feb 2020 to 25th April 2020.\n\nPrimary outcomeDeath in hospital among people with confirmed COVID-19.\n\nMethodsCohort study analysed by Cox-regression to generate hazard ratios: age and sex adjusted, and multiply adjusted for co-variates selected prospectively on the basis of clinical interest and prior findings.\n\nResultsThere were 5683 deaths attributed to COVID-19. In summary after full adjustment, death from COVID-19 was strongly associated with: being male (hazard ratio 1.99, 95%CI 1.88-2.10); older age and deprivation (both with a strong gradient); uncontrolled diabetes (HR 2.36 95% CI 2.18-2.56); severe asthma (HR 1.25 CI 1.08-1.44); and various other prior medical conditions. Compared to people with ethnicity recorded as white, black people were at higher risk of death, with only partial attenuation in hazard ratios from the fully adjusted model (age-sex adjusted HR 2.17 95% CI 1.84-2.57; fully adjusted HR 1.71 95% CI 1.44-2.02); with similar findings for Asian people (age-sex adjusted HR 1.95 95% CI 1.73-2.18; fully adjusted HR 1.62 95% CI 1.431.82).\n\nConclusionsWe have quantified a range of clinical risk factors for death from COVID-19, some of which were not previously well characterised, in the largest cohort study conducted by any country to date. People from Asian and black groups are at markedly increased risk of in-hospital death from COVID-19, and contrary to some prior speculation this is only partially attributable to pre-existing clinical risk factors or deprivation; further research into the drivers of this association is therefore urgently required. Deprivation is also a major risk factor with, again, little of the excess risk explained by co-morbidity or other risk factors. The findings for clinical risk factors are concordant with policies in the UK for protecting those at highest risk. Our OpenSAFELY platform is rapidly adding further NHS patients records; we will update and extend these results regularly.", + "category": "epidemiology", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.05.02.20078642", @@ -9897,20 +10037,6 @@ "author_similarity": 100, "affiliation_similarity": 100 }, - { - "site": "bioRxiv", - "doi": "10.1101/2020.04.28.066977", - "date": "2020-04-29", - "link": "https://biorxiv.org/cgi/content/short/2020.04.28.066977", - "title": "Controlling the SARS-CoV-2 outbreak, insights from large scale whole genome sequences generated across the world", - "authors": "Jody Phelan; Wouter Deelder; Daniel Ward; Susana Campino; Martin L Hibberd; Taane G Clark", - "affiliations": "London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine; London School of Hygiene and Tropical Medicine", - "abstract": "BackgroundSARS-CoV-2 most likely evolved from a bat beta-coronavirus and started infecting humans in December 2019. Since then it has rapidly infected people around the world, with more than 4.5 million confirmed cases by the middle of May 2020. Early genome sequencing of the virus has enabled the development of molecular diagnostics and the commencement of therapy and vaccine development. The analysis of the early sequences showed relatively few evolutionary selection pressures. However, with the rapid worldwide expansion into diverse human populations, significant genetic variations are becoming increasingly likely. The current limitations on social movement between countries also offers the opportunity for these viral variants to become distinct strains with potential implications for diagnostics, therapies and vaccines.\n\nMethodsWe used the current sequencing archives (NCBI and GISAID) to investigate 15,487 whole genomes, looking for evidence of strain diversification and selective pressure.\n\nResultsWe used 6,294 SNPs to build a phylogenetic tree of SARS-CoV-2 diversity and noted strong evidence for the existence of two major clades and six sub-clades, unevenly distributed across the world. We also noted that convergent evolution has potentially occurred across several locations in the genome, showing selection pressures, including on the spike glycoprotein where we noted a potentially critical mutation that could affect its binding to the ACE2 receptor. We also report on mutations that could prevent current molecular diagnostics from detecting some of the sub-clades.\n\nConclusionThe worldwide whole genome sequencing effort is revealing the challenge of developing SARS-CoV-2 containment tools suitable for everyone and the need for data to be continually evaluated to ensure accuracy in outbreak estimations.", - "category": "genomics", - "match_type": "fuzzy", - "author_similarity": 100, - "affiliation_similarity": 100 - }, { "site": "medRxiv", "doi": "10.1101/2020.04.23.20076521", @@ -10107,6 +10233,20 @@ "author_similarity": 100, "affiliation_similarity": 100 }, + { + "site": "medRxiv", + "doi": "10.1101/2020.04.02.20051284", + "date": "2020-04-06", + "link": "https://medrxiv.org/cgi/content/short/2020.04.02.20051284", + "title": "Building an International Consortium for Tracking Coronavirus Health Status", + "authors": "Eran Segal; Feng Zhang; Xihong Lin; Gary King; Ophir Shalem; Smadar Shilo; William E. Allen; Yonatan H. Grad; Casey S. Greene; Faisal Alquaddoomi; Simon Anders; Ran Balicer; Tal Bauman; Ximena Bonilla; Gisel Booman; Andrew T. Chan; Ori Ori Cohen; Silvano Coletti; Natalie Davidson; Yuval Dor; David A. Drew; Olivier Elemento; Georgina Evans; Phil Ewels; Joshua Gale; Amir Gavrieli; Benjamin Geiger; Iman Hajirasouliha; Roman Jerala; Andre Kahles; Olli Kallioniemi; Ayya Keshet; Gregory Landua; Tomer Meir; Aline Muller; Long H. Nguyen; Matej Oresic; Svetlana Ovchinnikova; Hedi Peterson; Jay Rajagopal; Gunnar Ratsch; Hagai Rossman; Johan Rung; Andrea Sboner; Alexandros Sigaras; Tim Spector; Ron Steinherz; Irene Stevens; Jaak Vilo; Paul Wilmes; CCC (Coronavirus Census Collective)", + "affiliations": "Weizmann Institute of Science; Howard Hughes Medical Institute, Core Member, Broad Institute of MIT and Harvard, United States; Departments of Biostatistics and Statistics, Harvard T.H. Chan School of Public Health; Albert J. Weatherhead III University, Institute for Quantitative Social Science, Harvard University; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, United States; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Society of Fellows, Harvard University, United States; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, United States; Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, United States; ETH Zurich, NEXUS Personalized Health Technologies, Zurich, Switzerland; Center for Molecular Biology (ZMBH), University of Heidelberg, Germany; Clalit Research Institute, Clalit Health Services, Israel; Mapping and Geo-Information Engineering, Civil and Environmental Engineering Faculty, The Technion, Israel; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich, ; Regen Network, Argentina; Massachusetts General Hospital (MGH), United States; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Chelonia Applied Science, Switzerland; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich, ; School of Medicine-IMRIC-Developmental Biology and Cancer Research, The Hebrew University; Massachusetts General Hospital (MGH), United States; Englander Institute for Precision Medicine and Department of Physiology and Biophysics, Weill Cornell Medicine, USA; Institute for Quantitative Social Science, Harvard University; Science for Life Laboratory (SciLifeLab), Department of Biochemistry and Biophysics, Stockholm University, Sweden; symptometrics.org; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Department of immunology, Weizmann Institute of Science, Israel; Englander Institute for Precision Medicine and Department of Physiology and Biophysics, Weill Cornell Medicine, USA; Department of Synthetic biology and Immunology, National Institute of Chemistry, Slovenia; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich, ; Science for Life Laboratory (SciLifeLab), Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Regen Network, United States; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Luxembourg Institute of Socio-Economic Research and University of Luxembourg, Luxembourg; Massachusetts General Hospital (MGH), United States; School of Medical Sciences, Orebro University, Orebro, Sweden, and Turku Bioscience Centre, University of Turku and Abo Akademi University, Turku, Finland; Center for Molecular Biology (ZMBH), University of Heidelberg, Germany; Institute of Computer Science, University of Tartu, Estonia, Estonia; Internal Medicine, Harvard Medical School, Department of Pulmonary Medicine and Critical Care, Massachusetts General Hospital (MGH), United States; ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich a; Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel; Science for Life Laboratory (SciLifeLab), Department of Immunology, Genetics and Pathology, Uppsala university, Sweden; Englander Institute for Precision Medicine and Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, USA; Englander Institute for Precision Medicine and Department of Physiology and Biophysics, Weill Cornell Medicine, USA; Kings College, United Kingdom; Regen Network, United States; Science for Life Laboratory (SciLifeLab), Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Sweden; Institute of Computer Science, University of Tartu, Estonia, Estonia; Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg; ", + "abstract": "Information is the most potent protective weapon we have to combat a pandemic, at both the individual and global level. For individuals, information can help us make personal decisions and provide a sense of security. For the global community, information can inform policy decisions and offer critical insights into the epidemic of COVID-19 disease. Fully leveraging the power of information, however, requires large amounts of data and access to it. To achieve this, we are making steps to form an international consortium, Coronavirus Census Collective (CCC, coronaviruscensuscollective.org), that will serve as a hub for integrating information from multiple data sources that can be utilized to understand, monitor, predict, and combat global pandemics. These sources may include self-reported health status through surveys (including mobile apps), results of diagnostic laboratory tests, and other static and real-time geospatial data. This collective effort to track and share information will be invaluable in predicting hotspots of disease outbreak, identifying which factors control the rate of spreading, informing immediate policy decisions, evaluating the effectiveness of measures taken by health organizations on pandemic control, and providing critical insight on the etiology of COVID-19. It will also help individuals stay informed on this rapidly evolving situation and contribute to other global efforts to slow the spread of disease.\n\nIn the past few weeks, several initiatives across the globe have surfaced to use daily self-reported symptoms as a means to track disease spread, predict outbreak locations, guide population measures and help in the allocation of healthcare resources. The aim of this paper is to put out a call to standardize these efforts and spark a collaborative effort to maximize the global gain while protecting participant privacy.", + "category": "infectious diseases", + "match_type": "fuzzy", + "author_similarity": 100, + "affiliation_similarity": 100 + }, { "site": "medRxiv", "doi": "10.1101/2020.04.01.20049908", diff --git a/data/covid/raw-preprints.json b/data/covid/raw-preprints.json index b3124602..6e9c59f7 100644 --- a/data/covid/raw-preprints.json +++ b/data/covid/raw-preprints.json @@ -1,11 +1,924 @@ [ + { + "rel_doi": "10.1101/2024.03.20.24304410", + "rel_title": "Subjective and Objective Measures of Cognitive Function are Correlated in Persons with Post-COVID-19 Condition: A Secondary Analysis of a Randomized Controlled Trial", + "rel_date": "2024-03-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.03.20.24304410", + "rel_abs": "Background It remains unclear whether subjective and objective measures of cognitive function in Post COVID-19 Condition (PCC) are correlated. The extent of correlation has mechanistic and clinical implications. Methods This post-hoc analysis of a randomized, double-blind, placebo-controlled clinical trial contains baseline data of subjective and objective measures of cognition in a rigorously characterized cohort living with PCC. Herein, we evaluated the association between subjective and objective condition function, as measured by the Perceived Deficits Questionnaire, 20-item (PDQ-20) and the Digit Symbol Substitution Test (DSST) and Trails Making Test (TMT)-A/B, respectively. Results A total of 152 participants comprised the baseline sample. Due to missing data, our statistical analyses included 150 for self-reported PDQ-20, 147 individuals for combined DSST-measured cognitive function (composite z-score of the Pen/Paper plus Online CogState Version, NcombinedDSST), 71 for in-person DSST-measured cognitive function (Pen/Paper Version), 70 for TMT-A-measured cognitive function, and 70 for TMT-B-measured cognitive function. After adjusting for age, sex, and education, PDQ-20 was significantly correlated with pen-and-paper DSST ({beta} = -0.003, p = 0.002) and TMT-B ({beta} = 0.003, p = 0.008) scores, but not with TMT-A scores ({beta} = -0.001, p = 0.751). Conclusions Overall, a statistically significant correlation was observed between subjective and objective cognitive functions. Clinicians providing care for individuals with PCC who have subjective cognitive function complaints may consider taking a measurement-based approach to cognition at the point of care that focuses exclusively on patient-reported measures.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Angela T.H. Kwan", + "author_inst": "University of Ottawa Faculty of Medicine" + }, + { + "author_name": "Moiz Lakhani", + "author_inst": "University of Ottawa Faculty of Medicine" + }, + { + "author_name": "Gia Han Le", + "author_inst": "Brain and Cognition Discovery Foundation" + }, + { + "author_name": "Gurkaran Singh", + "author_inst": "University of British Columbia Faculty of Medicine" + }, + { + "author_name": "Kayla M. Teopiz", + "author_inst": "Brain and Cognition Discovery Foundation" + }, + { + "author_name": "Felicia Ceban", + "author_inst": "McMaster University, Michael G. DeGroote School of Medicine" + }, + { + "author_name": "Charnjit S. Nijjar", + "author_inst": "University of British Columbia Faculty of Medicine" + }, + { + "author_name": "Shakila Meshkat", + "author_inst": "Brain and Cognition Discovery Foundation" + }, + { + "author_name": "Sebastian Badulescu", + "author_inst": "Brain and Cognition Discovery Foundation" + }, + { + "author_name": "Roger Ho", + "author_inst": "Yong Loo Lin School of Medicine, Department of Psychological Medicine" + }, + { + "author_name": "Taeho Greg Rhee", + "author_inst": "Yale School of Medicine, Department of Psychiatry" + }, + { + "author_name": "Joshua Di Vincenzo", + "author_inst": "Brain and Cognition Discovery Foundation" + }, + { + "author_name": "Hartej Gill", + "author_inst": "Brain and Cognition Discovery Foundation" + }, + { + "author_name": "Roger S. McIntyre", + "author_inst": "Brain and Cognition Discovery Foundation" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, + { + "rel_doi": "10.1101/2024.03.18.24304509", + "rel_title": "Exploring the Psychological, Social, and Human Rights Dynamics and Consequences of COVID-19 Control Measures: A Systematic Review", + "rel_date": "2024-03-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.03.18.24304509", + "rel_abs": "This systematic review explores the social and psychological dynamics and consequences of COVID-19 control measures and their implications for human rights. Through a lens of social psychology, the review considers factors such as social influence, obedience, perceived control, social comparison, cognitive dissonance, propaganda, surveillance, fearmongering, incentives, coercion, persuasion, censorship, obfuscation, isolation, and rewards and punishment. By analyzing the influence of these factors on individuals and group responses to the pandemic and the manipulation of social and psychological dynamics by institutions to shape compliance, this review provides insights into the determinants that drive adherence to control measures and their negative consequences. The findings of the 13 selected studies contribute to understanding the multifaceted factors that influence compliance and inform the development of effective public health interventions to avoid consequences. The review emphasizes the importance of upholding human rights during the implementation of control measures, given the reported violations across the world. By providing insights to policymakers, politicians, health practitioners, and researchers, this review enables the formulation of strategies that promote public health while respecting human and individual rights and well-being. In conclusion, this study sheds light on the social and psychological dynamics, human rights, and implications of COVID-19 control measures, providing valuable insights for future interventions.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Djurdje Spasojevic", + "author_inst": "Bangkok Christian College" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, + { + "rel_doi": "10.1101/2024.03.20.24304332", + "rel_title": "Impact of COVID-19 Pandemic on Colonoscopy Wait Times by Procedure Indication", + "rel_date": "2024-03-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.03.20.24304332", + "rel_abs": "Background: Patients are referred for colonoscopy for symptom assessment, screening, and surveillance. Public health measures to mitigate the spread of the COVID-19 pandemic disrupted services and increased patient delays for colonoscopy services in Quebec. The differential impact of these interruptions by colonoscopy indication is largely unknown. Methods: Using 2018-2022 retrospective clinical data from two high-volume Montreal endoscopy centres and provincial administrative data, we characterized changes in colonoscopy wait times and the proportion of waitlisted patients who were delayed (wait time exceeded provincial guidelines) by procedure indication and demographics. We used regression to examine patient characteristics associated with delayed procedures during pre- and intra-COVID-19 periods. We used time series analysis to characterize trends in the proportion of waitlisted patients delayed. Results: The COVID-19-related public health measures resulted in record-high delays (median increase in wait times of 34-159% across indications). While older patients experienced longer wait times pre-pandemic, intra-COVID-19 wait times increased disproportionately for patients younger than 50. The proportion of waitlisted patients delayed peaked mid-2020 (56.9% for screening; 56.0% for symptom assessment patients). By early 2022, the proportion delayed had fallen to 37.3% for screening patients but remained at 53.8% for symptom assessment patients. Conclusions: In Quebec, intra-COVID-19 colonoscopy delays disproportionately impacted symptom assessment procedures and younger patients. Additional capacity or improved triaging may be needed to address persistent delays. Understanding the effects of the pandemic on colonoscopy services can help inform strategies to mitigate harms from on-going delays in Quebec.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Melina Thibault", + "author_inst": "McGill University" + }, + { + "author_name": "Alan Barkun", + "author_inst": "McGill University Health Centre" + }, + { + "author_name": "Myriam Martel", + "author_inst": "McGill University Health Centre" + }, + { + "author_name": "Alton W. Russell", + "author_inst": "McGill University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "gastroenterology" + }, + { + "rel_doi": "10.1101/2024.03.19.24304563", + "rel_title": "Navigating stroke care during the COVID-19 pandemic: A scoping review", + "rel_date": "2024-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.03.19.24304563", + "rel_abs": "Background: Previous viral outbreaks have highlighted implications for the management of complex health conditions. This study delves into the repercussions of the COVID-19 pandemic on stroke care, by examining evidence of shifts in healthcare utilization, the enduring effects on post-stroke recovery, and the overall quality of life experienced by stroke survivors. Methods: A scoping review was conducted following the Joanna Briggs Institute Methodology for Scoping Reviews. The search strategy encompassed electronic databases (APA PsycInfo, Embase, Medline, and CINAHL). English language articles published between December 2019 and January 2022 were included, focusing on individuals who experienced a stroke during the COVID-19 pandemic. Data extraction involved identifying study characteristics and significant findings, facilitating a qualitative and narrative synthesis of the gathered evidence. Results: Seven domain summaries were identified. They all described the aspects of systemic transformations in stroke care during the COVID-19 pandemic: (1) patient behavior and awareness; (2) telemedicine and remote care; (3) delays in treatment; (4) impact on healthcare resources; (5) quality of care; (6) changes in stroke severity; and (7) reduction in stroke admissions. Conclusions: This study underscored the critical need to encourage swift patient response to acute stroke symptoms, by finding new avenues for treatment, mitigating hospital-related infection fears, and advocating for the establishment of centralized stroke centers. These measures are integral to optimizing stroke care delivery and ensuring timely interventions, particularly in the challenging context of a pandemic.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Alixe M\u00e9nard", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Michelle Yang", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Samantha Oostlander", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Kanika Sarwal", + "author_inst": "University of Waterloo" + }, + { + "author_name": "Irfan Manji", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Tracey O'Sullivan", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Sarah Fraser", + "author_inst": "University of Ottawa" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, + { + "rel_doi": "10.1101/2024.03.19.24304557", + "rel_title": "\"She helped from the first minute to the last\" - experiences of respectful maternal and newborn care during the COVID-19 pandemic in Nampula Province, Mozambique", + "rel_date": "2024-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.03.19.24304557", + "rel_abs": "Pandemic-related health service adaptations raised concerns about provision of quality, respectful maternity care globally. Despite this, little research has focused on the experiences of those using intrapartum care during this time. This study aimed to elevate the voices and document the experiences of birthing people in Nampula Province, Mozambique during the COVID-19 pandemic. We conducted a longitudinal qualitative study from March-August 2021 and present an analysis of the 17 follow-up in-depth interviews conducted with participants who had a vaginal live birth. Interviews explored participants experience of labor and delivery care. They were conducted in Makua and Portuguese, audio-recorded, transcribed and translated. We applied thematic content analysis. Overall, participants did not express major concerns about COVID-19 or related service adaptations when describing their experiences of intrapartum care. Some noted its negative effects on elements of respectful care such as restricting birth companions. Overcrowding became more concerning due to the threat of infection. While unclear if affected by the pandemic, all participants who gave birth at a health facility reported experiencing at least one form of mistreatment, some recounting threats of cesarean delivery. Most explained that they and their newborns received care without their consent, especially regarding enemas and episiotomies. At the same time, respondents described a range of intrapartum experiences that included both respectful and disrespectful care. Most recalled positive verbal communication with their providers and many described receiving continuous attentive care. Participants explained that their satisfaction with childbirth services was tied to their birth outcome and their experience of respectful care. The findings indicate that steadfast commitments to quality care are critical to ensure families benefit from high-quality, respectful care at all times. The ramifications of the COVID-19 pandemic were limited but nonetheless signal a need for tighter connections between maternal health and emergency preparedness stakeholders.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Megan M Lydon", + "author_inst": "FHI 360" + }, + { + "author_name": "Joaquim Vilanculos", + "author_inst": "FHI 360" + }, + { + "author_name": "Carter Crew", + "author_inst": "FHI 360" + }, + { + "author_name": "Am\u00e9rico Barata", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Emily Keyes", + "author_inst": "FHI 360" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "obstetrics and gynecology" + }, + { + "rel_doi": "10.1101/2024.03.18.585599", + "rel_title": "Quantitating SARS-CoV-2 Neutralizing Antibodies from Human Dried Blood Spots", + "rel_date": "2024-03-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.03.18.585599", + "rel_abs": "Background: In the earliest days of COVID-19 pandemic, the collection of dried blood spots (DBS) enabled public health laboratories to undertake population-scale seroprevalence studies to estimate rates of SARS-CoV-2 exposure. With SARS-CoV-2 seropositivity levels now estimated to exceed 94% in the United States, attention has turned to using DBS to assess functional (neutralizing) antibodies within cohorts of interest. Methods: Contrived DBS eluates from convalescent, fully vaccinated and pre-COVID-19 serum samples were evaluated in SARS-CoV-2 plaque reduction neutralization titer (PRNT) assays, a SARS-CoV-2 specific 8-plex microsphere immunoassay, a cell-based pseudovirus assay, and two different spike-ACE2 inhibition assays. Results: DBS eluates from convalescent individuals were compatible with RBD-ACE2 inhibition assays, an in-house Luminex-based RBD-ACE2 inhibition assay, and commercial real-time PCR-based neutralization assay (NAB-Sure) but not cell-based pseudovirus assays or PRNT. The insensitivity of cell-based pseudovirus assays was overcome with DBS eluates from vaccinated individuals with high SARS-CoV-2 antibody titers. Conclusion: SARS-CoV-2 neutralizing titers can be derived with confidence from DBS eluates, thereby opening the door to the use of these biospecimens for the analysis of vulnerable populations and normally hard to reach communities.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Katherine Berman", + "author_inst": "Wadsworth Center, New York State Department of Health" + }, + { + "author_name": "Greta Van Slyke", + "author_inst": "Wadsworth Center" + }, + { + "author_name": "Haley Novak", + "author_inst": "Wadsworth Center" + }, + { + "author_name": "Jean Rock", + "author_inst": "Wadsworth Center" + }, + { + "author_name": "Rachel Bievenue", + "author_inst": "Wadsworth Center" + }, + { + "author_name": "Amanda Damjanovic", + "author_inst": "Wadsworth Center" + }, + { + "author_name": "Kate DeRosa", + "author_inst": "Wadsworth Center" + }, + { + "author_name": "Gianna Mirabile", + "author_inst": "Wadsworth Center" + }, + { + "author_name": "Roxie Giradin", + "author_inst": "Wadsworth Center" + }, + { + "author_name": "Alan Dupuis II", + "author_inst": "New York State Department of Health" + }, + { + "author_name": "Kathleen McDonough", + "author_inst": "Wadsworth Center, NYSDOH" + }, + { + "author_name": "Monica M Parker", + "author_inst": "Wadsworth Center, New York State Department of Health" + }, + { + "author_name": "Linda Styer", + "author_inst": "Wadsworth Center" + }, + { + "author_name": "Nicholas J MANTIS", + "author_inst": "Wadsworth Center, New York State Department of Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, + { + "rel_doi": "10.1101/2024.03.19.585194", + "rel_title": "Validation of RT-qPCR primers and probes for new and old variants of SARS-CoV-2 in a world scale", + "rel_date": "2024-03-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.03.19.585194", + "rel_abs": "Introduction: The demand for molecular diagnosis of pathogens has surged dramatically since the onset of the COVID-19 pandemic. In this context, different diagnostic tests have been developed to identify SARS-CoV-2 in patient samples. The emergence of new variants of SARS-CoV-2 raises questions about whether the molecular tests available for diagnosis continue to be effective in detecting the virus in biological samples. Objective: This study analyzed the viability of molecular targets directed to N, E and RdRp genes available against the new variants of SARS-CoV-2. Methodology: For this, we used bioinformatics tools to analyze SARS-CoV-2 genomic data of different variants deposited in GSAID and NCBI virus genomic databases to assess the accuracy of molecular tests available for the diagnosis of COVID-19. We also developed software for analyzing mutation frequencies in different molecular targets from the mutation database. Results: Mutation frequency analysis revealed a high rate of mutations in the N, E and RdRp genes and targets, although the target regions were more conserved. Only three SNPs were recurrent in the sequences of the variants identified in different continents and all in different targets. On the other hand, the registered mutations are not consistent and do not appear frequently in isolates of the same variant in all regions of the world. Conclusion: Our data suggest that the molecular targets designed for the first SARS-CoV-2 variants remain valid for the identification of new virus variants despite the large number of identified haplotypes. However, false negative test failures can be identified by using more than one molecular target for the same sample. Genomic regions that are under evolutive selective pressure should be avoided in the use of the diagnostic, once the emergence of new variants may affect the efficiency of molecular testing on a global scale.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Alderrosy Fragoso Rodrigues Almeida", + "author_inst": "Nucleo de Estudos de Agentes Infecciosos e Vetores, Centro das Ciencias Biologicas e da Saude, Universidade Federal do Oeste da Bahia, Barreiras, Bahia, Brasil" + }, + { + "author_name": "Weriskiney Araujo Almeida", + "author_inst": "Centro das Ciencias Exatas e das Tecnologias, Universidade Federal do Oeste da Bahia (UFOB), Barreiras, Bahia, Brasil" + }, + { + "author_name": "Wvelton Mendes Pereira", + "author_inst": "Nucleo de Estudos de Agentes Infecciosos e Vetores, Centro das Ciencias Biologicas e da Saude, Universidade Federal do Oeste da Bahia, Barreiras, Bahia, Brasil" + }, + { + "author_name": "Renato de Santana Silva", + "author_inst": "Nucleo de Estudos de Agentes Infecciosos e Vetores, Centro das Ciencias Biologicas e da Saude, Universidade Federal do Oeste da Bahia, Barreiras, Bahia, Brasil" + }, + { + "author_name": "Larissa Paola Rodrigues Venancio", + "author_inst": "Nucleo de Estudos de Agentes Infecciosos e Vetores, Centro das Ciencias Biologicas e da Saude, Universidade Federal do Oeste da Bahia, Barreiras, Bahia, Brasil" + }, + { + "author_name": "Mary Hellen Fabres-Klein", + "author_inst": "Nucleo de Estudos de Agentes Infecciosos e Vetores, Centro das Ciencias Biologicas e da Saude, Universidade Federal do Oeste da Bahia, Barreiras, Bahia, Brasil" + }, + { + "author_name": "Jonilson Berlink Lima", + "author_inst": "Nucleo de Estudos de Agentes Infecciosos e Vetores, Centro das Ciencias Biologicas e da Saude, Universidade Federal do Oeste da Bahia, Barreiras, Bahia, Brasil" + }, + { + "author_name": "Raphael Contelli Klein", + "author_inst": "Nucleo de Estudos de Agentes Infecciosos e Vetores, Centro das Ciencias Biologicas e da Saude, Universidade Federal do Oeste da Bahia, Barreiras, Bahia, Brasil" + }, + { + "author_name": "Theo Araujo-Santos", + "author_inst": "Nucleo de Estudos de Agentes Infecciosos e Vetores, Centro das Ciencias Biologicas e da Saude, Universidade Federal do Oeste da Bahia, Barreiras, Bahia, Brasil" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, + { + "rel_doi": "10.1101/2024.03.18.24304517", + "rel_title": "High transferability of neutralizing antibodies against SARS-CoV-2 to umbilical cord blood in pregnant women with BNT162b2 XBB.1.5 vaccine - a retrospective cohort study", + "rel_date": "2024-03-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.03.18.24304517", + "rel_abs": "Coronavirus disease 2019 (COVID-19), when contracted by pregnant women, can lead to severe respiratory illness, rapid disease progression, and higher rates of intensive care unit admission. COVID-19 infection during pregnancy is associated with an increased risk of preterm delivery, cesarean section, fetal dysfunction, preeclampsia, and perinatal death. Additionally, vertical transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from pregnant women to their fetuses has been observed. While severe infections in neonates and infants are rare, newborns can experience serious consequences from COVID-19, despite their suboptimal humoral immune system protection. The amino acids in the structural proteins of SARS-CoV-2 are subjected to constant mutation. Since around January 2023, COVID-19, caused by infection with omicron-type SARS-CoV-2 variants, has been prevalent globally. Omicron-type SARS-CoV-2 variants can evade the immune response triggered by traditional mRNA-based COVID-19 vaccines, such as BNT162b2. Therefore, vaccination with a vaccine (BNT162b2 XBB.1.5) that can provide protection against omicron-type SARS-CoV-2 variants is recommended. Therefore, we examined the titers of anti-spike glycoprotein of SARS-CoV-2 IgG and IgA in the blood and umbilical cord blood obtained from pregnant women vaccinated with BNT162b2 XBB.1.5. The results showed that anti-spike glycoprotein of SARS-CoV-2 IgG and IgA titers were highest in the blood and cord blood obtained from pregnant women vaccinated with BNT162b2 XBB.1.5 at late gestational age (28-34 weeks). No serious side effects or adverse events caused by vaccination of pregnant women with BNT162b2 XBB.1.5 were observed in either pregnant women or newborns. In the future, to validate our findings, large cohort clinical studies involving numerous pregnant women must be conducted.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Takuma Hayashi", + "author_inst": "National Hospital Organization Kyoto Medical Center" + }, + { + "author_name": "Kenji Sano", + "author_inst": "Shinshu University Hospital" + }, + { + "author_name": "Ikuo Konishi", + "author_inst": "National Hospital Organization Kyoto Medical Center/Kyoto University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, + { + "rel_doi": "10.1101/2024.03.18.24304375", + "rel_title": "The Impact of Cognitive Function on Health-Related Quality of Life in Persons with Post-COVID-19 Condition: A Randomized Controlled Trial on Vortioxetine", + "rel_date": "2024-03-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.03.18.24304375", + "rel_abs": "Background Post-Covid-19 Condition (PCC) manifests in persistent, debilitating symptoms that affect multiple cognitive domains. These symptoms can negatively impact an affected individual's health-related quality of life (HRQoL). Herein, we investigate the effects of cognitive function on HRQoL in persons with PCC. Secondarily, we determine whether vortioxetine modulates cognitive function on HRQoL. Methods Participants aged 18-65 years were randomized to receive vortioxetine or placebo for 8 weeks. HRQoL was measured using the World Health organization Wellbeing Scale 5-item, cognition was measured using the Digit Symbol Substitution Test and the Trail-Making Test A/B. Generalized estimating equations were used to model the relationship of cognition to HRQoL for each treatment group. Results 147 participants, 75.5% of which were female, were included in the analysis. At baseline, there was a statistically significant positive association between WHO-5 scores and combined DSST z-scores (beta; = 0.090, 95% CI [0.051, 0.129], p < 0.001), and a statistically significant negative association with TMT-A (beta; = -0.007, 95% CI [-0.011, -0.003], p < 0.001) and -B (beta; = -0.002, 95% CI [-0.003, 0.000], p = 0.024) scores, respectively. A significant treatment, time, and combined DSST z-score interaction on changes in overall WHO-5 total score (x2 = 15.481, p = 0.004) was reported. After adjusting for the type of cognitive test, there was a significant between-group difference (mean change = 1.77, SEM = 0.868, p = 0.042) favoring vortioxetine. Conclusion Cognitive function is significantly associated with HRQoL in persons with PCC where enhanced cognitive functioning is associated with a better HRQoL. Vortioxetine is effective in improving HRQoL through enhancing cognitive function. Cognitive function in persons with PCC provides the impetus for future therapeutic targets for persons with PCC. Future studies should aim to investigate pro-cognitive therapeutic strategies.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Angela T.H. Kwan", + "author_inst": "University of Ottawa Faculty of Medicine" + }, + { + "author_name": "Moiz Lakhani", + "author_inst": "University of Ottawa, Faculty of Medicine" + }, + { + "author_name": "Gia Han Le", + "author_inst": "Brain and Cognition Discovery Foundation" + }, + { + "author_name": "Gurkaran Singh", + "author_inst": "University of British Colombia Faculty of Medicine" + }, + { + "author_name": "Kayla M. Teopiz", + "author_inst": "Brain and Cognition Discovery Foundation" + }, + { + "author_name": "Ziji Guo", + "author_inst": "Brain and Cognition Discovery Foundation" + }, + { + "author_name": "Arshpreet Singh Manku", + "author_inst": "University of British Colombia Faculty of Medicine" + }, + { + "author_name": "Joshua D. Rosenblat", + "author_inst": "Brain and Cognition Discovery Foundation" + }, + { + "author_name": "Roger S. McIntyre", + "author_inst": "Brain and Cognition Discovery Foundation" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, + { + "rel_doi": "10.1101/2024.03.19.24304303", + "rel_title": "The impact of wildtype SARS-CoV-2 on fatigue and quality of life: prevalence of post COVID-19 condition in a Dutch population-based serosurveillance cohort.", + "rel_date": "2024-03-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.03.19.24304303", + "rel_abs": "Background: Our aim was to assess the relationship between (time since) wild-type SARS-CoV-2 infection and health-related quality of life (HRQoL) and fatigue as endpoints linked to Post COVID-19 condition (PCC). Methods: Participants [≥]15 years were selected from the February 2021 round of the population-based PIENTER Corona study. We investigated the association between (time since) SARS-COV-2 infection and health outcomes: HRQoL (health utility (SF-6D); physical health and mental health (both SF-12)) and fatigue (CIS-fatigue) using multivariable logistic regression analyses adjusted for age, sex, educational level, number of comorbidities, COVID-19 vaccination status, and the intensity of restrictions. For each outcome, multivariable logistic regression models were fitted at cut-off points selected based on the cumulative distribution of those uninfected. Results: Results shown correspond to the cut-off point related to the worst off 15% of each outcome. Significant differences between those uninfected (n=4,614) and cases infected [≤]4 months ago (n=368) were observed for health utility (OR [95%CI]: 1.6 [1.2-2.2]), physical health (OR [95%CI]: 1.7 [1.3-2.3]) and fatigue (OR [95%CI]: 1.6 [1.2-2.0]), but not for mental health. There were no significant differences between uninfected and cases infected >4 months ago (n=345) for all outcomes. Conclusions: In a Dutch population-based cohort of seroconverted individuals, those infected with wild-type SARS-CoV-2 [≤]4 months ago more often reported poor health utility and physical health and were more often severely fatigued compared to those uninfected (at the 15% cut-off). HRQoL and fatigue remained below the detection limit for those infected >4 months ago, suggesting a relatively low prevalence of PCC.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Elizabeth N. Mutubuki", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Cheyenne C.E. van Hagen", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Eric R.A. Vos", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Gerco den Hartog", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Fiona R.M. van der Klis", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Cees C. van den Wijngaard", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Hester E. de Melker", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Albert Jan van Hoek", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, + { + "rel_doi": "10.1101/2024.03.18.24304157", + "rel_title": "COVID-19-associated acute renal failure in critically ill patients correlates with microthrombosis and renal loss of thrombomodulin", + "rel_date": "2024-03-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.03.18.24304157", + "rel_abs": "Critically ill COVID-19 patients have a high degree of acute kidney injury which develops in up to 85% of patients. We have previously shown that circulating levels of angiopoietin-2 increased in critically ill COVID-19 patients correlated to kidney injury, coagulopathy, and mortality. Furthermore, our experiments showed a causal effect on coagulopathy from angiopoietin-2 binding and inhibition of thrombomodulin mediated anticoagulation. In the current study we hypothesize that renal microthrombi may be a mechanism for reduced renal function in critically ill COVID-19 patients, and that local dysregulation of thrombomodulin and angiopoietin-2 may be involved. To investigate our hypothesis, we utilized postmortem kidney tissue from seven COVID-19 patients treated at the intensive care unit. We evaluated kidney function, thrombosis, tubular injury, fibrosis, glomerulosclerosis, glomerular size as well as renal expression of thrombomodulin and angiopoietin-2. Proximity ligation assay was utilized to evaluate the presence of angiopoietin-2 binding to thrombomodulin. Normal kidney tissue came from the healthy part of six nephrectomies due to cancer. Our experiments show renal thrombosis in 6/7 COVID-19 patients, on average 14.7 (6.9-22.5) thrombi per mm2. Most COVID-19 kidneys had extensive kidney injury, especially tubular necrosis, but also glomerular enlargement, glomerulosclerosis, and tubulointerstitial fibrosis which in some cases most likely resulted from underlying disease. Thrombomodulin expression was reduced in glomeruli and peritubular capillaries in kidneys from COVID-19 patients, whereas no change was found for angiopoietin-2. In summary, our study describes a high degree of acute renal failure, renal microthrombosis, and loss of thrombomodulin in postmortem tissue from critically ill COVID-19 patients.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Matilda Koskinen", + "author_inst": "Department of Medicin Huddinge, Karolinska Institutet" + }, + { + "author_name": "Elisabet Englund", + "author_inst": "Department of Clinical Sciences, Lund University" + }, + { + "author_name": "G\u00fcl Gizem Korkut", + "author_inst": "Department of Laboratory Medicine, Karolinska Institutet" + }, + { + "author_name": "Angelina Schwarz", + "author_inst": "Department of Clinical Science, Karolinska Institutet" + }, + { + "author_name": "Marie Jeansson", + "author_inst": "Department of Medicine Huddinge, Karolinska Institutet" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, + { + "rel_doi": "10.1101/2024.03.18.24304401", + "rel_title": "Integrated multiomics implicates dysregulation of ECM and cell adhesion pathways as drivers of severe COVID-associated kidney injury", + "rel_date": "2024-03-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.03.18.24304401", + "rel_abs": "COVID-19 has been a significant public health concern for the last four years; however, little is known about the mechanisms that lead to severe COVID-associated kidney injury. In this multicenter study, we combined quantitative deep urinary proteomics and machine learning to predict severe acute outcomes in hospitalized COVID-19 patients. Using a 10-fold cross-validated random forest algorithm, we identified a set of urinary proteins that demonstrated predictive power for both discovery and validation set with 87% and 79% accuracy, respectively. These predictive urinary biomarkers were recapitulated in non-COVID acute kidney injury revealing overlapping injury mechanisms. We further combined orthogonal multiomics datasets to understand the mechanisms that drive severe COVID-associated kidney injury. Functional overlap and network analysis of urinary proteomics, plasma proteomics and urine sediment single-cell RNA sequencing showed that extracellular matrix and autophagy-associated pathways were uniquely impacted in severe COVID-19. Differentially abundant proteins associated with these pathways exhibited high expression in cells in the juxtamedullary nephron, endothelial cells, and podocytes, indicating that these kidney cell types could be potential targets. Further, single-cell transcriptomic analysis of kidney organoids infected with SARS-CoV-2 revealed dysregulation of extracellular matrix organization in multiple nephron segments, recapitulating the clinically observed fibrotic response across multiomics datasets. Ligand-receptor interaction analysis of the podocyte and tubule organoid clusters showed significant reduction and loss of interaction between integrins and basement membrane receptors in the infected kidney organoids. Collectively, these data suggest that extracellular matrix degradation and adhesion-associated mechanisms could be a main driver of COVID-associated kidney injury and severe outcomes.", + "rel_num_authors": 38, + "rel_authors": [ + { + "author_name": "Nanditha Anandakrishnan", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Zhengzi Yi", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Zeguo Sun", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Tong Liu", + "author_inst": "Rutgers University, The State University of New Jersey" + }, + { + "author_name": "Jonathan Haydak", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sean Eddy", + "author_inst": "University of Michigan" + }, + { + "author_name": "Pushkala Jayaraman", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Stefanie Defronzo", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Aparna Saha", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Qian Sun", + "author_inst": "Rutgers, The State University of New Jersey" + }, + { + "author_name": "Yang Dai", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Anthony Mendoza", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Gohar Mosoyan", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Huei Hsun Wen", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jennifer A Schaub", + "author_inst": "University of Michigan" + }, + { + "author_name": "Jia Fu", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Thomas Kehrer", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Rajasree Menon", + "author_inst": "University of Michigan" + }, + { + "author_name": "Edgar A Otto", + "author_inst": "University of Michigan" + }, + { + "author_name": "Bradley Godfrey", + "author_inst": "University of Michigan" + }, + { + "author_name": "Mayte Suarezfarinas", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sean Lefferts", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Akosua Twumasi", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Kristin Meliambro", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Alexander Charney", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Adolfo Garcia-Sastre", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Kirk Campbell", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Luca G Gusella", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "John He", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Lisa Miorin", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Girish Nadkarni", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Juan P. Wisnivesky", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Hong Li", + "author_inst": "Rutgers, The State University of New Jersey" + }, + { + "author_name": "Matthias Kretzler", + "author_inst": "U Michigan" + }, + { + "author_name": "Steve Coca", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Lili Chan", + "author_inst": "ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI" + }, + { + "author_name": "Weijia Zhang", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Evren U Azeloglu", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, + { + "rel_doi": "10.1101/2024.03.18.24304464", + "rel_title": "COVID-19 Impact on Patients with Immune-Mediated Rheumatic Disease: A Comparative Study of Disease Activity and Psychological Well-Being Over Six Months", + "rel_date": "2024-03-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.03.18.24304464", + "rel_abs": "ObjectivesTo compare the impact of COVID-19 on clinical status and psychological condition in patients with immune-mediated rheumatic diseases (IMRD) infected by SARS-CoV-2 with IMRD controls not infected, during a 6-month follow-up.\n\nMethodsThe ReumaCoV Brasil is a longitudinal study designed to follow-up IMRD patients for 6 months after COVID-19 (cases) compared with IMRD patients no COVID-19 (controls). Clinical data, disease activity measurements and current treatment regarding IMRD, and COVID-19 outcomes were evaluated in all patients. Disease activity was assessed through validated tools at inclusion and at 3 and 6 months post-COVID-19. The FACIT-F (Functional Assessment of Chronic Illness Therapy) and DASS 21 (Depression, Anxiety and Stress Scale - 21 Items) questionnaires were also applied at 6 months after COVID-19 in both groups before large-scale vaccination. The significance level was set as p<0.05, with a 95% confidence interval.\n\nResultsA total of 601 patients were evaluated, being 321 cases (IMRD COVID-19+) and 280 controls (IMRD COVID-19 -), predominantly female with similar median age. No significant differences were noted in demographic data between the groups, including comorbidities, disease duration, and IMRD. Disease activity assessment over a 6-month follow-up showed no significant difference between cases and controls. While mean activity scores did not differ significantly, some patients reported worsened disease activity post-COVID-19, particularly in rheumatoid arthritis (RA) (32.2%) and systemic lupus erythematosus (SLE) (23.3%). Post-COVID-19 worsening in RA patients correlated with medical global assessment (MGA) and CDAI scores, with a moderate to large effect size. Diabetes mellitus showed a positive association (OR=7.15), while TNF inhibitors showed a protective effect (OR=0.51). Comparing SLEDAI pre- and post-COVID-19, a minority showed increased scores, with few requiring treatment changes. Fatigue, depression, anxiety, and stress were significantly higher in cases compared to controls. Worsening disease activity post-COVID correlated with worsened FACIT-F and DASS-21 stress scale in RA patients. No significant associations were found between COVID-19 outcomes and post-COVID-19 disease activity or psychological assessments.\n\nConclusionsPost-COVID-19 IMRD patients show significant psychological well-being deterioration despite similar disease activity scores. The variability in reports on IMRD flares and the potential trigger of SARS-CoV-2 for autoimmune manifestations underline the need for detailed clinical assessment and a comprehensive approach to managing them.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "CLAUDIA DINIZ LOPES MARQUES", + "author_inst": "HOSPITAL DAS CLINICAS, UNIVERSIDADE FEDERAL DE PERNAMBUCO" + }, + { + "author_name": "Marcelo Pinheiro", + "author_inst": "Department of Rheumatology, Escola Paulista de Medicina/ Universidade Federal de Sao Paulo (EPM/ UNIFESP), Sao Paulo, Brazil" + }, + { + "author_name": "Jeniffer Lopes", + "author_inst": "Postgraduate Program of Translacional Health. Universidade Federal de Pernambuco." + }, + { + "author_name": "Sandra Lucia Euzebio Ribeiro", + "author_inst": "Department of Rheumatology. Faculdade de Medicina da Universidade Federal do Amazonas." + }, + { + "author_name": "Mary Vania Marinho Castro", + "author_inst": "Department of Rheumatology. Faculdade de Medicina da Universidade Federal do Amazonas" + }, + { + "author_name": "Lilian David de Azevedo Valadares", + "author_inst": "Department of Internal Medicine. Hospital Getulio Vargas Recife. Pernambuco" + }, + { + "author_name": "Aline Ranzolin", + "author_inst": "Department of Internal Medicine. Hospital Getulio Vargas Recife. Pernambuco" + }, + { + "author_name": "Nicole Pamplona Bueno de Andrada", + "author_inst": "Department of Rheumatology. Hospital de Clinicas de Porto Alegre. Universidade Federal do Rio Grande do Sul." + }, + { + "author_name": "Rafaela Cavalheiro do Espirito Santo", + "author_inst": "Department of Rheumatology.Hospital de Clinicas de Porto Alegre. Universidade Federal do Rio Grande do Sul" + }, + { + "author_name": "Nafice Costa Araujo", + "author_inst": "Department of Rheumatology. Hospital do Servidor Publico Estadual de Sao Paulo. Instituto de Assistencia Medica ao Servidor Publico Estadual, Sao Paulo, Brazil" + }, + { + "author_name": "Cintya Martins Vieira", + "author_inst": "Department of Rheumatology. Hospital Universitario da Universidade Federal de Juiz de Fora. Minas Gerais" + }, + { + "author_name": "Valeria Valim", + "author_inst": "Department of Rheumatology. Universidade Federal de Sergipe" + }, + { + "author_name": "Flavia Santos", + "author_inst": "Department of Rheumatology, Hospital das Clinicas. Universidade Federal de Minas Gerais." + }, + { + "author_name": "Laurindo Ferreira da Rocha Junior", + "author_inst": "Instituto de Medicina Integral Professor Fernando Figueira. Recife. Pernambuco. Brazil" + }, + { + "author_name": "Adriana Maria Kakehasi", + "author_inst": "Department of Rheumatology. Hospital das Clinicas. Universidade Federal de Minas Gerais." + }, + { + "author_name": "Ana Paula Monteiro Gomides Reis", + "author_inst": "Centro Universitario de Brasilia" + }, + { + "author_name": "Edgard Torres Neto", + "author_inst": "Department of Rheumatology. Escola Paulista de Medicina. Universidade Federal de Sao Paulo." + }, + { + "author_name": "Gecilmara Pilegii", + "author_inst": "Department of Rheumatology. Escola Paulista de Medicina. Universidade Federal de Sao Paulo." + }, + { + "author_name": "Gilda Aparecida Ferreira", + "author_inst": "Department of Rheumatology. Hospital das Clinicas. Universidade Federal de Minas Gerais." + }, + { + "author_name": "Licia Mota", + "author_inst": "Department of Rheumatology. Universidade de Brasilia" + }, + { + "author_name": "Odirlei Monticielo", + "author_inst": "Department of Rheumatology. Hospital de Clinicas de Porto Alegre. Universidade Federal do Rio Grande do Sul." + }, + { + "author_name": "Ricardo Machado Xavier", + "author_inst": "Department of Rheumatology. Hospital de Clinicas de Porto Alegre. Universidade Federal do Rio Grande do Sul." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "rheumatology" + }, + { + "rel_doi": "10.1101/2024.03.15.24304071", + "rel_title": "H2 inhalation therapy in patients with moderate Covid 19 (H2 COVID) : a prospective ascending-dose phase 1 clinical trial", + "rel_date": "2024-03-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.03.15.24304071", + "rel_abs": "Introduction: The Covid-19 pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), has triggered a serious global health crisis, resulting in millions of reported deaths since its initial identification in China in November 2019. The global disparities in immunization access emphasize the urgent need for ongoing research into therapeutic interventions. This study focuses on the potential use of molecular dihydrogen (H2) inhalation as an adjunctive treatment for Covid-19. H2 therapy shows promise in inhibiting intracellular signaling pathways associated with inflammation, particularly when administered early in conjunction with nasal oxygen therapy. Methods: This Phase I study, characterized by an open-label, prospective, monocentric, and single ascending dose design, seeks to assess the safety and tolerability of the procedure in individuals with confirmed SARS-CoV-2 infection. Employing a 3+3 design, the study includes three exposure durations (target durations): 1 day (D1), 3 days (D2), and 6 days (D3). Results: We concluded that the Maximum Tolerated Duration is at least three days. Every patient showed clinical improvement and excellent tolerance to H2 therapy. Discussion/conclusion: To the best of our knowledge, this phase 1 clinical trial is the first to establish the safety of inhaling a mixture of H2 (3.6%) and N2 (96.4%) in hospitalized Covid-19 patients. The original device and method employed ensure the absence of explosion risk. The encouraging outcomes observed in the 12 patients included in the study justify further exploration through larger, controlled clinical trials.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Cordelia Salomez-Ihl", + "author_inst": "Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, CHU Grenoble Alpes, TIMC, UMR5525, 38000 Grenoble, France;Univ. Grenoble Alpes, CHU Grenoble Al" + }, + { + "author_name": "Joris Giai", + "author_inst": "Univ. Grenoble Alpes, Inserm, CHU Grenoble Alpes, CIC1406, 38000 Grenoble, France" + }, + { + "author_name": "Maud Barbado", + "author_inst": "Univ. Grenoble Alpes, Inserm, CHU Grenoble Alpes, CIC1406, 38000 Grenoble, France" + }, + { + "author_name": "Adeline Paris", + "author_inst": "Univ. Grenoble Alpes, Inserm, CHU Grenoble Alpes, CIC1406, 38000 Grenoble, France" + }, + { + "author_name": "Saber Touati", + "author_inst": "CHU Grenoble Alpes, Department of Infectious and Tropical Diseases, 38000 Grenoble, France" + }, + { + "author_name": "Jean-Pierre Alcaraz", + "author_inst": "Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, CHU Grenoble Alpes, TIMC, UMR5525, 38000 Grenoble, France" + }, + { + "author_name": "Stephane Tanguy", + "author_inst": "Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, CHU Grenoble Alpes, TIMC, UMR5525, 38000 Grenoble, France" + }, + { + "author_name": "Corentin Leroy", + "author_inst": "Univ. Grenoble Alpes, Inserm, CHU Grenoble Alpes, CIC1406, 38000 Grenoble, France" + }, + { + "author_name": "Audrey Lehmann", + "author_inst": "Univ. Grenoble Alpes, CHU Grenoble Alpes, Department of Pharmacy, 38000 Grenoble, France" + }, + { + "author_name": "Bruno Degano", + "author_inst": "CHU Grenoble Alpes, Department of Pneumology, 38000 Grenoble, France" + }, + { + "author_name": "Marylaure Gavard", + "author_inst": "CHU Grenoble Alpes, Delegation for Clinical Research and Innovation, 38000 Grenoble, France" + }, + { + "author_name": "Pierrick Bedouch", + "author_inst": "Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, CHU Grenoble Alpes, TIMC, UMR5525, 38000 Grenoble, France; Univ. Grenoble Alpes, CHU Grenoble A" + }, + { + "author_name": "Patricia Pavese", + "author_inst": "CHU Grenoble Alpes, Department of Infectious and Tropical Diseases, 38000 Grenoble, France" + }, + { + "author_name": "Alexandre Moreau-Gaudry", + "author_inst": "Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, CHU Grenoble Alpes, TIMC, UMR5525, 38000 Grenoble, France; Univ. Grenoble Alpes, Inserm, CHU Gr" + }, + { + "author_name": "Mathieu Roustit", + "author_inst": "Univ. Grenoble Alpes, Inserm, CHU Grenoble Alpes, CIC1406, 38000 Grenoble, France" + }, + { + "author_name": "Francois Boucher", + "author_inst": "Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, CHU Grenoble Alpes, TIMC, UMR5525, 38000 Grenoble, France" + }, + { + "author_name": "Philippe Cinquin", + "author_inst": "Univ. Grenoble Alpes, CNRS, UMR 5525, VetAgro Sup, Grenoble INP, CHU Grenoble Alpes, TIMC, UMR5525, 38000 Grenoble, France; Univ. Grenoble Alpes, Inserm, CHU Gr" + }, + { + "author_name": "Jean-Paul Brion", + "author_inst": "CHU Grenoble Alpes, Department of Infectious and Tropical Diseases, 38000 Grenoble, France" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, + { + "rel_doi": "10.1101/2024.03.12.24304127", + "rel_title": "Evaluation of Febrile Seizure Risk Following Ancestral Monovalent COVID-19 mRNA Vaccination Among U.S. Children Aged 2-5 Years", + "rel_date": "2024-03-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.03.12.24304127", + "rel_abs": "Importance The United States Food and Drug Administration noted a potential safety concern for seizure in children aged 2-5 years receiving the ancestral monovalent COVID-19 mRNA vaccines. Objective To evaluate febrile seizure risk following monovalent COVID-19 mRNA vaccination among children aged 2-5 years. Design, Setting, and Participants The primary analysis evaluated children who had a febrile seizure outcome in the 0-1 days following COVID-19 vaccination. A self-controlled case series analysis was performed in three commercial insurance databases to compare the risk of seizure in the risk interval (0-1 days) to a control interval (8-63 days). Exposure Receipt of dose 1 and/or dose 2 of monovalent COVID-19 mRNA vaccinations. Main Outcomes and Measures The primary outcome was febrile seizure (0-1 day risk interval). Analysis A conditional Poisson regression model was used to compare outcome rates in risk and control intervals and estimate incidence rate ratios (IRR) and 95% confidence intervals (CIs). Meta-analyses were used to pool results across databases. Results The primary meta-analysis found a statistically significant increased incidence of febrile seizure, in the 0-1 days following mRNA-1273 vaccination compared to the control interval (IRR: 2.52, 95% CI: 1.35 to 4.69, risk difference (RD)/100,000 doses = 3.22 (95%CI -0.31 to 6.75)). For the BNT162b2 vaccination, the IRR was elevated but not statistically significant (IRR: 1.41, 95%CI: 0.48 to 4.11, RD/100,000 doses = -0.25 (95%CI -2.75 to 2.24). Conclusions and Relevance Among children aged 2-5 years, the analysis showed a small elevated incidence rate ratio of febrile seizures in the 0-1 days following the mRNA-1273 vaccination. Based on the current body of scientific evidence, the safety profile of the monovalent mRNA vaccines remains favorable for use in young children.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Richard A Forshee", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Elizabeth R Smith", + "author_inst": "Acumen LLC" + }, + { + "author_name": "Zhiruo Wan", + "author_inst": "Acumen LLC" + }, + { + "author_name": "Kandace L Amend", + "author_inst": "Optum Epidemiology" + }, + { + "author_name": "Alex Secora", + "author_inst": "IQVIA" + }, + { + "author_name": "Djeneba Audrey Djibo", + "author_inst": "CVS Health" + }, + { + "author_name": "Kamran Kazemi", + "author_inst": "Acumen LLC" + }, + { + "author_name": "Jennifer Song", + "author_inst": "Optum Epidemiology" + }, + { + "author_name": "Lauren E Parlett", + "author_inst": "Carelon Research" + }, + { + "author_name": "John D Seeger", + "author_inst": "Optum Epidemiology" + }, + { + "author_name": "Nandini Selvam", + "author_inst": "IQVIA" + }, + { + "author_name": "Cheryl N McMahill-Walraven", + "author_inst": "CVS Health" + }, + { + "author_name": "Mao Hu", + "author_inst": "Acumen LLC" + }, + { + "author_name": "Yoganand Chillarige", + "author_inst": "Acumen LLC" + }, + { + "author_name": "Steven A Anderson", + "author_inst": "US Food and Drug Administration" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2024.03.14.585103", "rel_title": "Atomically accurate de novo design of single-domain antibodies", "rel_date": "2024-03-18", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2024.03.14.585103", - "rel_abs": "Despite the central role that antibodies play in modern medicine, there is currently no way to rationally design novel antibodies to bind a specific epitope on a target. Instead, antibody discovery currently involves time-consuming immunization of an animal or library screening approaches. Here we demonstrate that a fine-tuned RFdiffusion network is capable of designing de novo antibody variable heavy chains (VHH's) that bind user-specified epitopes. We experimentally confirm binders to four disease-relevant epitopes, and the cryo-EM structure of a designed VHH bound to influenza hemagglutinin is nearly identical to the design model both in the configuration of the CDR loops and the overall binding pose.", + "rel_abs": "Despite the central role that antibodies play in modern medicine, there is currently no way to rationally design novel antibodies to bind a specific epitope on a target. Instead, antibody discovery currently involves time-consuming immunization of an animal or library screening approaches. Here we demonstrate that a fine-tuned RFdiffusion network is capable of designing de novo antibody variable heavy chains (VHHs) that bind user-specified epitopes. We experimentally confirm binders to four disease-relevant epitopes, and the cryo-EM structure of a designed VHH bound to influenza hemagglutinin is nearly identical to the design model both in the configuration of the CDR loops and the overall binding pose.", "rel_num_authors": 21, "rel_authors": [ { @@ -104,7 +1017,7 @@ "rel_date": "2024-03-18", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2024.03.18.584627", - "rel_abs": "Background: During COVID-19 pandemic there emerged a need to efficiently monitor and process large volumes of scientific literature on the subject. Currently, as the pandemic is winding down, the clinicians encountered a novel syndrome - Post-acute Sequelae of COVID-19 (PASC) - that affects over 10% of those who contract SARS-CoV-2 and presents a significant and growing challenge in the medical field. The continuous influx of new research publications underscores a critical need for efficient tools for navigating the literature. Objectives: We aimed to develop an application which will allow monitoring and categorizing COVID-19-related literature through building publication networks and medical subject headings (MeSH) maps to be able to quickly identify key publications and publication networks. Methods: We introduce CORACLE (COVID-19 liteRAture CompiLEr), an innovative web application designed for the analysis of COVID-19-related scientific articles and the identification of research trends. CORACLE features three primary interfaces: The \"Search\" interface, which displays research trends and citation links; the \"Citation Map\" interface, allowing users to create tailored citation networks from PubMed Identifiers (PMIDs) to uncover common references among selected articles; and the \"MeSH\" interface, highlighting current MeSH trends and associations between MeSH terms. Results: Our web application, CORACLE, leverages regularly updated PubMed data to aggregate and categorize the extensive literature on COVID-19 and PASC, aiding in the identification of relevant research publication hubs. Using lung function in PASC patients as a search example, we demonstrate how to identify and visualize the interactions between the relevant publications. Conclusion: CORACLE proves to be an effective tool for the extraction and analysis of literature. Its functionalities, including the MeSH trends and customizable citation mapping, facilitate the discovery of relevant information and emerging trends in COVID-19 and PASC research.", + "rel_abs": "BackgroundDuring the COVID-19 pandemic there emerged a need to efficiently monitor and process large volumes of scientific literature on the subject. Currently, as the pandemic is winding down, the clinicians encountered a novel syndrome - Post-acute Sequelae of COVID- 19 (PASC) - that affects over 10% of those who contract SARS-CoV-2 and presents a significant and growing challenge in the medical field. The continuous influx of new research publications underscores a critical need for efficient tools for navigating the literature.\n\nObjectivesWe aimed to develop an application which will allow monitoring and categorizing COVID-19-related literature through building publication networks and medical subject headings (MeSH) maps to be able to quickly identify key publications and publication networks.\n\nMethodsWe introduce CORACLE (COVID-19 liteRAture CompiLEr), an innovative web application designed for the analysis of COVID-19-related scientific articles and the identification of research trends. CORACLE features three primary interfaces: The \"Search\" interface, which displays research trends and citation links; the \"Citation Map\" interface, allowing users to create tailored citation networks from PubMed Identifiers (PMIDs) to uncover common references among selected articles; and the \"MeSH\" interface, highlighting current MeSH trends and associations between MeSH terms.\n\nResultsOur web application, CORACLE, leverages regularly updated PubMed data to aggregate and categorize the extensive literature on COVID-19 and PASC, aiding in the identification of relevant research publication hubs. Using lung function in PASC patients as a search example, we demonstrate how to identify and visualize the interactions between the relevant publications.\n\nConclusionCORACLE proves to be an effective tool for the extraction and analysis of literature. Its functionalities, including the MeSH trends and customizable citation mapping, facilitate the discovery of relevant information and emerging trends in COVID-19 and PASC research.", "rel_num_authors": 8, "rel_authors": [ { @@ -151,7 +1064,7 @@ "rel_date": "2024-03-18", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2024.03.17.585388", - "rel_abs": "SARS-CoV-2 infection triggers strong antibody response toward Nucleocapsid-Protein (NP), suggesting extracellular presence beyond its intra-virion RNA binding. Interestingly, NP was found to decorate infected and proximal uninfected cell-surfaces. Here, we propose a new mechanism through which extracellular NP on uninfected cells contributes to COVID-19 pathogenicity. We show that NP binds to cell-surface sulfated linear-glycosaminoglycans by spatial rearrangement of its RNA-binding sites facilitated by the flexible, positively charged, linker. Coating of uninfected lung-derived cells with purified NP attracted anti-NP-IgG from lung fluids and sera collected from COVID-19 patients. The magnitude of this immune recognition was significantly elevated in moderate compared to mild COVID-19 cases. Importantly, binding of anti-NP-IgG present in sera generated clusters that triggered C3b deposition by the classical complement pathway. Heparin analog enoxaparin outcompeted NP-binding, rescuing cells from anti-NP IgG-mediated complement deposition. Our findings unveil how extracellular NP may exacerbate COVID-19 tissue damage, and suggest leads for preventative therapy.", + "rel_abs": "SARS-CoV-2 infection triggers strong antibody response toward Nucleocapsid-Protein (NP), suggesting extracellular presence beyond its intra-virion RNA binding. Interestingly, NP was found to decorate infected and proximal uninfected cell-surfaces. Here, we propose a new mechanism through which extracellular NP on uninfected cells contributes to COVID-19 pathogenicity. We show that NP binds to cell-surface sulfated linear-glycosaminoglycans by spatial rearrangement of its RNA-binding sites facilitated by the flexible, positively charged, linker. Coating of uninfected lung-derived cells with purified NP attracted anti-NP-IgG from lung fluids and sera collected from COVID-19 patients. The magnitude of this immune recognition was significantly elevated in moderate compared to mild COVID-19 cases. Importantly, binding of anti-NP-IgG present in sera generated clusters that triggered C3b deposition by the classical complement pathway. Heparin analog enoxaparin outcompeted NP-binding, rescuing cells from anti-NP IgG-mediated complement deposition. Our findings unveil how extracellular NP may exacerbate COVID-19 tissue damage, and suggest leads for preventative therapy.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC=\"FIGDIR/small/585388v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (31K):\norg.highwire.dtl.DTLVardef@1ed28eborg.highwire.dtl.DTLVardef@11973dborg.highwire.dtl.DTLVardef@545feorg.highwire.dtl.DTLVardef@3658f8_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIIgG from patients sera target NP-bound cells resulting in complement activation\nC_LIO_LIThe flexible linker allows NP to both bind linear sulfated GAGs and wrap around RNA\nC_LIO_LIHeparin analogs prevent NP surface binding and alleviate complement activation\nC_LIO_LICell-ELISA anti-NP IgG levels differ between mild and moderate COVID-19\nC_LI", "rel_num_authors": 20, "rel_authors": [ { @@ -246,7 +1159,7 @@ "rel_date": "2024-03-18", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2024.03.17.585378", - "rel_abs": "Motivation: With the advancement of structural biology techniques, the elucidation of increasingly large protein structures has become possible. However, the structural modeling of intrinsically disordered regions in proteins remains challenging. Particularly in the case of large protein complexes, it is difficult to rapidly construct models for all intrinsically disordered regions using existing methods. In the nuclear pore complex, a gigantic protein machine of interest, intrinsically disordered regions play a crucial role in the function of the nuclear pore complex. Therefore, there is a need to develop a modeling tool suitable for intrinsically disordered regions in large protein complexes. Results: We have developed a program named IDRWalker based on self-avoiding random walks, enabling convenient and rapid modeling of intrinsically disordered regions in large protein complexes. Using this program, modeling of all disordered regions within the nuclear pore complex can be completed in a matter of minutes. Furthermore, we have addressed issues related to peptide chain connectivity and knot that may arise during the application of random walks. Availability and implementation: IDRWalker is an open-source Python package. Its source code is publicly accessible on GitHub (https://github.com/zyzhangGroup/IDRWalker).", + "rel_abs": "MotivationWith the advancement of structural biology techniques, the elucidation of increasingly large protein structures has become possible. However, the structural modeling of intrinsically disordered regions in proteins remains challenging. Particularly in the case of large protein complexes, it is difficult to rapidly construct models for all intrinsically disordered regions using existing methods. In the nuclear pore complex, a gigantic protein machine of interest, intrinsically disordered regions play a crucial role in the function of the nuclear pore complex. Therefore, there is a need to develop a modeling tool suitable for intrinsically disordered regions in large protein complexes.\n\nResultsWe have developed a program named IDRWalker based on self-avoiding random walks, enabling convenient and rapid modeling of intrinsically disordered regions in large protein complexes. Using this program, modeling of all disordered regions within the nuclear pore complex can be completed in a matter of minutes. Furthermore, we have addressed issues related to peptide chain connectivity and knot that may arise during the application of random walks.\n\nAvailability and implementationIDRWalker is an open-source Python package. Its source code is publicly accessible on GitHub (https://github.com/zyzhangGroup/IDRWalker).", "rel_num_authors": 2, "rel_authors": [ { @@ -269,7 +1182,7 @@ "rel_date": "2024-03-18", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2024.03.15.585207", - "rel_abs": "The first step of SARS-CoV-2 infection involves the interaction between the trimeric viral spike protein () and the host angiotensin-converting enzyme 2 (2). The receptor binding domain () of adopts two conformations: open and closed, respectively, accessible and inaccessible to 2. Therefore, motions are suspected to affect 2 binding; yet a quantitative description of the underlying mechanism has been elusive. Here, using single-molecule approaches, we visualize opening and closing and probe the /2 interaction. Our results show that RBD dynamics affect 2 binding but not unbinding. The resulting modulation is quantitatively predicted by a conformational selection model in which each protomer behaves independently. Our work reveals a general molecular mechanism affecting binding affinity without altering binding strength, helping to understand coronavirus infection and immune evasion.", + "rel_abs": "The first step of SARS-CoV-2 infection involves the interaction between the trimeric viral spike protein (S) and the host angiotensin-converting enzyme 2 (ACE2). The receptor binding domain (RBD) of S adopts two conformations: open and closed, respectively, accessible and inaccessible to ACE2. Therefore, RBD motions are suspected to affect ACE2 binding; yet a quantitative description of the underlying mechanism has been elusive. Here, using single-molecule approaches, we visualize RBD opening and closing and probe the S/ACE2 interaction. Our results show that RBD dynamics affect ACE2 binding but not unbinding. The resulting modulation is quantitatively predicted by a conformational selection model in which each protomer behaves independently. Our work reveals a general molecular mechanism affecting binding affinity without altering binding strength, helping to understand coronavirus infection and immune evasion.", "rel_num_authors": 16, "rel_authors": [ { @@ -348,7 +1261,7 @@ "rel_date": "2024-03-18", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2024.03.16.585341", - "rel_abs": "In vitro screening of large libraries of compounds with automated High-throughput screening is expensive, time consuming and requires dedicated infrastructures. Conversely, the screening of DNA-encoded chemical libraries can be rapidly performed with basic equipment available in most laboratories. In this study we identified novel inhibitors of SARS-CoV-2 main protease (Mpro) through the affinity screening of the commercially available ''DELopen'' library, containing 4.2 billion compounds. The identified inhibitors were peptidomimetics compounds containing a C-terminal electrophilic group able to covalently bind to Mpro reactive Cys145 (confirmed by x-ray crystallography). Compound SLL11 had IC50 = 30nM and was found to be well optimized, proving that the rapid exploration of large chemical spaces, enabled by DECL technology, allows the direct identification of potent inhibitors avoiding several rounds of iterative medicinal chemistry. Compound MP6, a close analogue of SLL11, showed antiviral activity against SARS-CoV-2 in the low micromolar range when tested in Caco-2 and Calu-3 (EC50 = 2.3 M) cell lines. As peptidomimetics compounds can suffer from low cell permeability and metabolic stability, the cyclization of the compounds as well as the substitution of selected residues with D-enantiomers will be explored in the future to improve the antiviral activity of these novel compounds.", + "rel_abs": "In vitro screening of large libraries of compounds with automated High-throughput screening is expensive, time consuming and requires dedicated infrastructures. Conversely, the screening of DNA-encoded chemical libraries can be rapidly performed with basic equipment available in most laboratories. In this study we identified novel inhibitors of SARS-CoV-2 main protease (Mpro) through the affinity screening of the commercially available \"DELopen\" library, containing 4.2 billion compounds. The identified inhibitors were peptidomimetics compounds containing a C-terminal electrophilic group able to covalently bind to Mpro reactive Cys145 (confirmed by x-ray crystallography). Compound SLL11 had IC50 = 30nM and was found to be well optimized, proving that the rapid exploration of large chemical spaces, enabled by DECL technology, allows the direct identification of potent inhibitors avoiding several rounds of iterative medicinal chemistry. Compound MP6, a close analogue of SLL11, showed antiviral activity against SARS-CoV-2 in the low micromolar range when tested in Caco-2 and Calu-3 (EC50 = 2.3 {micro}M) cell lines. As peptidomimetics compounds can suffer from low cell permeability and metabolic stability, the cyclization of the compounds as well as the substitution of selected residues with D-enantiomers will be explored in the future to improve the antiviral activity of these novel compounds.", "rel_num_authors": 16, "rel_authors": [ { @@ -421,13 +1334,283 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2024.03.17.24304396", + "rel_title": "Mental Health Trends in India from 2020 to 2022: Association with Financial Stress, Food Insecurity, and COVID-19-related Illness Concerns", + "rel_date": "2024-03-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.03.17.24304396", + "rel_abs": "This study examines the impact of pandemic-related worries on mental health in the Indian general adult population from 2020 to 2022. Using data from the Global COVID-19 Trends and Impact Survey (N = 2,576,174 respondents aged[≥] 18 years in India; an average weekly sample size of around 25,000), it explores the associations between worry variables (namely financial stress, food insecurity, and COVID-19-related health worries) and self-reported symptoms of depression and nervousness. The statistical analysis was conducted using complete cases only (N = 747,996). Our analysis used survey-weighted models, focusing on the three pandemic-related worries as the exposures, while also adjusting for various other covariates, including demographics and calendar time. The study finds significant associations between these worries and mental health outcomes, with financial stress being the most significant factor affecting both depression (adjusted odds ratio: 2.36, 95% confidence interval: [2.27, 2.46]) and nervousness (adjusted odds ratio: 1.91, 95% confidence interval: [1.81, 2.01]) during the first phase of the study period (June 27, 2020, to May 19, 2021). The fully adjusted models also identify additional factors related to mental health, including age, gender, residential status, geographical region, occupation, and education. Moreover, the research highlights that males and urban residents had higher odds ratios for self-reported mental health problems regarding the worry variables than females and rural residents, respectively. Furthermore, the study reveals a rise in the prevalence of self-reported depression and nervousness and their association with COVID-19-related health worries during the lethal second wave of the pandemic in May 2021 compared to the onset of the pandemic. This study shows that social media platforms like Facebook can deploy surveys to a large number of participants globally and can be useful tools in capturing mental health trends and uncovering associations during a public health crisis.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Youqi Yang", + "author_inst": "University of Michigan" + }, + { + "author_name": "Anqi Sun", + "author_inst": "University of Michigan" + }, + { + "author_name": "Lauren Zimmermann", + "author_inst": "University of Michigan" + }, + { + "author_name": "Bhramar Mukherjee", + "author_inst": "University of Michigan" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, + { + "rel_doi": "10.1101/2024.03.17.24304386", + "rel_title": "Publication status of 95 clinical trials of 3 COVID-19 vaccines developed by Chinese companies: An observational cohort study", + "rel_date": "2024-03-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.03.17.24304386", + "rel_abs": "Transparency shortcomings can undermine confidence in the safety and efficacy of vaccines. This study assesses the publication status of 95 clinical trials of 3 COVID-19 vaccines developed by Chinese companies that received a World Health Organization Emergency Use Listing (EUL) and have been marketed globally. We searched trial registries and the scientific literature to assess current trial status and the public availability of results.\n\nAfter excluding 2 withdrawn trials, we found that at least 62/93 trials (67%) involving 307,933 patients had verifiably been completed or terminated. Only 44 of those 62 trials (71%) had published results in a peer-reviewed journal; none had tabular summary results available on a trial registry. The results of 18/62 (29%) verifiably completed or terminated trials remained unpublished. The trial status information stated in trial registries was often incorrect.\n\nOur findings reveal a substantial gap between the disclosure practices of the 3 Chinese companies and global best practice benchmarks. Transparency and global public trust in Chinese biopharmaceutical products could be improved by aligning Chinese legal disclosure requirements with those prevalent in more mature markets, or by the voluntary adoption of stronger transparency practices by Chinese companies.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Till Bruckner", + "author_inst": "UiT The Arctic University of Norway, Tromso, Norway; TranspariMED, Bristol, UK" + }, + { + "author_name": "Yixuan Chen", + "author_inst": "Independent Researcher, Jinhua, China" + }, + { + "author_name": "Carolina Cruz", + "author_inst": "University of Guadalajara, Guadalajara, Mexico" + }, + { + "author_name": "Christie Ebube Dike", + "author_inst": "Molecular and Genetics Unit, Institute of Child Health, College of Medicine, University of Ibadan, Ibadan, Nigeria" + }, + { + "author_name": "Belen Chavarria", + "author_inst": "National Autonomous University of Nicaragua at Leon" + }, + { + "author_name": "Shiyu Chen", + "author_inst": "Independent Researcher, London, UK" + }, + { + "author_name": "Ernest Dela Dzidzornu", + "author_inst": "Independent Researcher, Accra, Ghana" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, + { + "rel_doi": "10.1101/2024.03.17.24304409", + "rel_title": "Real-world Nuvaxovid COVID-19 vaccine safety profile after first 100,000 doses in Australia, 2022-2023", + "rel_date": "2024-03-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.03.17.24304409", + "rel_abs": "IntroductionNuvaxovid became available in Australia from February 2022, a year later than the first COVID-19 vaccines were released. It was a much-anticipated alternative vaccine for people that had either suffered an adverse event to-and/or were hesitant to receive-one of the mRNA or adenovirus-based COVID-19 vaccines. Although safety from clinical trials was reassuring, small trial population size, relatively low administration rates worldwide and limited post-licensure intelligence meant potential rare adverse events were underinformed.\n\nMethodsWe conducted a retrospective observational analysis of adverse events following immunisation (AEFI) spontaneously reported to SAFEVAC, the integrated vaccine safety surveillance system used by Victoria and Western Australia, Australia. Reports received from 14 Feb 2022 to 30 June 2023 were analysed by vaccinee demographics, reported reactions and COVID-19 vaccine dose received and compared as reporting rates (RR) per 100,000 doses administered.\n\nResults356 AEFI reports were received, following 102,946 Nuvaxovid doses administered. Rates were higher post dose 1 than dose 2 (rate ratio 1.5, p=0.0008); primary series than booster (rate ratio 2.4, p<0.0001); in females than males (rate ratio 1.4, p<0.01), especially those aged 30-49 years (RR=1.6, p=0.002).\n\nSerious AEFI included 76 chest pain (RR=73.8), two myocarditis (RR=1.9) and 20 pericarditis (RR=19.4). No cases of Guillain-Barre or thrombosis with thrombocytopaenia syndromes were reported and no deaths attributable to vaccination.\n\nConclusionThe shared SAFEVAC platform enables pooling of clinically reviewed data across jurisdictions, increasing the safety profile evidence-base of novel vaccines like Nuvaxovid and improving the odds for identification and description of rare events across all vaccines.\n\nO_TEXTBOXKey public health messageO_ST_ABSWhat did you want to address in this study and why?C_ST_ABSNuvaxovid is a protein-based vaccine for protection against COVID-19. Nuvaxovid received provisional licensure following clinical trials in which 30,058 participants received at least one dose of Nuvaxovid. Introduced following adenoviral vector and mRNA COVID-19 vaccines, some people had been waiting for this vaccine as an alternative to other brands that had risk of blood clots or heart inflammation. We wanted to inform on safety of Nuvaxovid following over 100,000 doses administered in real-world population-wide setting in two Australian states.\n\nWhat have we learnt from this study?Adverse events reported were mostly mild, transient symptoms and no deaths were attributed to Nuvaxovid immunisation. Reporting rate for heart inflammation was similar to the mRNA COVID-19 vaccines, but more likely to be milder pericarditis than myocarditis. For over 25,000 people Nuvaxovid was their first dose of a COVID-19 vaccine received, despite being more than a year since COVID-19 vaccines became available.\n\nWhat are the implications of your findings for public health?This first real-world population-wide evidence of Nuvaxovid vaccine safety provides reassurance on the risk-benefit of vaccination for protection from severe COVID-19 disease. We must continue to look hard, using real-world data, to not only ensure vaccines are safe, but also support confidence in immunisation.\n\nC_TEXTBOX", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Hazel J Clothier", + "author_inst": "Epi-Informatics Group and SAEFVIC Epidemiology, Surveillance and Signal Detection, Murdoch Childrens Research Institute, Melbourne, Australia" + }, + { + "author_name": "Claire Parker", + "author_inst": "Communicable Disease Control Directorate, Western Australia Department of Health, Perth, Australia" + }, + { + "author_name": "John H Mallard", + "author_inst": "Epi-Informatics Group and SAEFVIC Epidemiology, Surveillance and Signal Detection, Murdoch Childrens Research Institute, Melbourne, Australia" + }, + { + "author_name": "Paul Effler", + "author_inst": "Communicable Disease Control Directorate, Western Australia Department of Health, Perth, Australia" + }, + { + "author_name": "Lauren Bloomfield", + "author_inst": "Communicable Disease Control Directorate, Western Australia Department of Health, Perth, Australia" + }, + { + "author_name": "Dale Carcione", + "author_inst": "Communicable Disease Control Directorate, Western Australia Department of Health, Perth, Australia" + }, + { + "author_name": "Jim P Buttery", + "author_inst": "Epi-Informatics, Centre for Health Analytics, Melbourne Childrens Campus, Melbourne, Australia" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, + { + "rel_doi": "10.1101/2024.03.17.24304450", + "rel_title": "Exploring Machine Learning Strategies in COVID-19 Prognostic Modelling: A Systematic Analysis of Diagnosis, Classification and Outcome Prediction", + "rel_date": "2024-03-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.03.17.24304450", + "rel_abs": "BackgroundThe COVID-19 pandemic, which has impacted over 222 countries resulting in incalcu-lable losses, has necessitated innovative solutions via machine learning (ML) to tackle the problem of overburdened healthcare systems. This study consolidates research employing ML models for COVID-19 prognosis, evaluates prevalent models and performance, and provides an overview of suitable models and features while offering recommendations for experimental protocols, reproducibility and integration of ML algorithms in clinical settings.\n\nMethodsWe conducted a review following the PRISMA framework, examining ML utilisation for COVID-19 prediction. Five databases were searched for relevant studies up to 24 January 2023, resulting in 1,824 unique articles. Rigorous selection criteria led to 204 included studies. Top-performing features and models were extracted, with the area under the receiver operating characteristic curve (AUC) evaluation metric used for performance assessment.\n\nResultsThis systematic review investigated 204 studies on ML models for COVID-19 prognosis across automated diagnosis (18.1%), severity classification (31.9%), and outcome prediction (50%). We identified thirty-four unique features in five categories and twenty-one distinct ML models in six categories. The most prevalent features were chest CT, chest radiographs, and advanced age, while the most frequently employed models were CNN, XGB, and RF. Top-performing models included neural networks (ANN, MLP, DNN), distance-based methods (kNN), ensemble methods (XGB), and regression models (PLS-DA), all exhibiting high AUC values.\n\nConclusionMachine learning models have shown considerable promise in improving COVID-19 diagnostic accuracy, risk stratification, and outcome prediction. Advancements in ML techniques and their integration with complementary technologies will be essential for expediting decision-making and informing clinical decisions, with long-lasting implications for healthcare systems globally.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Reabal Najjar", + "author_inst": "Canberra Health Services" + }, + { + "author_name": "Md Zakir Hossain", + "author_inst": "Curtin University" + }, + { + "author_name": "Khandaker Asif Ahmed", + "author_inst": "Commonwealth Scientific and Industrial Research Organisation" + }, + { + "author_name": "Md Rakibul Hasan", + "author_inst": "Curtin University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, + { + "rel_doi": "10.1101/2024.03.14.24304224", + "rel_title": "Role of the complement system in Long COVID", + "rel_date": "2024-03-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.03.14.24304224", + "rel_abs": "Long COVID, or Post-Acute COVID Syndrome (PACS), may develop following SARS-CoV-2 infection, posing a substantial burden to society. Recently, PACS has been linked to a persistent activation of the complement system (CS), offering hope for both a diagnostic tool and targeted therapy. However, our findings indicate that, after adjusting proteomics data for age, body mass index and sex imbalances, the evidence of complement system activation disappears. Furthermore, proteomic analysis of two orthogonal cohorts--one addressing PACS following severe acute phase and another after a mild acute phase--fails to support the notion of persistent CS activation. Instead, we identify a proteomic signature indicative of either ongoing infections or sustained immune activation similar to that observed in acute COVID-19, particularly within the mild-PACS cohort.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Vadim Farztdinov", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Boris Zuehlke", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Franziska Sotzny", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Fridolin Steinbeis", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Martina Seifert", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Claudia Kedor", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Kirsten Wittke", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Pinkus Tober-Lau", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Kathrin Textoris-Taube", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Daniela Ludwig", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Clemens Dierks", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Dominik Bierbaum", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Leif Erik Sander", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Leif Gunnar Hanitsch", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Martin Witzenrath", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Florian Kurth", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Michael Muelleder", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Carmen Scheibenbogen", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Markus Ralser", + "author_inst": "Charite - Universitaetsmedizin Berlin" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, + { + "rel_doi": "10.1101/2024.03.15.24304383", + "rel_title": "Postpartum suicidal ideation in Austria and Germany during the COVID-19 pandemic", + "rel_date": "2024-03-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.03.15.24304383", + "rel_abs": "IntroductionPostpartum suicidal ideation is a significant concern, as it poses a risk for future suicide attempts, particularly in high income countries, where suicide ranks among the leading causes of death for postpartum mothers. The literature indicates a global average prevalence of postpartum suicidal ideation of approximately 7%, but for Austria and Germany there are few studies on this subject.\n\nMethodsIn a web-based survey for Austrian and German mothers of children born during the COVID-19 pandemic, several measures of mental health (depression, stress), social support and other parenting and pandemic-related questions were assessed in 1964 mothers. Based on the answers for the last item of the Edinburgh Postpartum Depression Scale, the suicidality risk and the presence or absence of suicidal ideation were computed. Furthermore, possible risk or protective factors for suicidality were investigated.\n\nResultsThe prevalence of suicidal ideation was 7.3%, which is in the range of the global prevalence reported in the literature, but two times higher than previous reports on German mothers. The three strongest risk factors for suicidal ideation were (i) high levels of stress (increased risk by 350%), (ii) a lack of perceived social support (increased risk by 265%), and (iii) a perceived negative effect of the pandemic on the relationship with the partner (increased risk by 223%). Not receiving help from family and friends, having a lower income, and feeling negatively impacted by the pandemic also significantly increased the risk of suicidal ideation.\n\nDiscussion and conclusionThe results indicate a higher prevalence of suicidality than previously reported in German mothers, and confirm the risk factors previously associated with depression and suicidality. These risk and protective factors could be targets of social and public health policies, while the first step should be a general screening program for suicidality in this population group.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Cristina Florea", + "author_inst": "Paris-Lodron University of Salzburg" + }, + { + "author_name": "Jasmin Preiss", + "author_inst": "Paris-Lodron University of Salzburg" + }, + { + "author_name": "Monika Angerer", + "author_inst": "University of Salzburg" + }, + { + "author_name": "Manuel Schabus", + "author_inst": "Paris-Lodron University of Salzburg" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2024.03.14.24304160", "rel_title": "Frequency of Depressive Symptoms and Suicidal Ideation Among University Students Before and After the COVID-19 Pandemic", "rel_date": "2024-03-16", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2024.03.14.24304160", - "rel_abs": "Background: The COVID-19 pandemic and lockdown have had negative effects on students mental health. However, little information is available regarding the frequencies of depressive symptoms and suicidal ideation during the post-pandemic period. We aimed to compare prevalence rates of depressive symptoms and suicidal ideation among university students, before versus after the COVID-19 pandemic. Methods: In this comparative study, 4464 students were recruited during the pre-COVID-19 pandemic period (2013-2020) and 1768 students, during the post-COVID-19 pandemic period (2022-2023). Standardized frequencies of depressive symptoms and suicidal ideation were compared between the two time periods. Adjusted logistic regression models were used to assess the association between the pandemic period (with the pre-COVID-19 period as reference) and depressive symptoms and suicidal ideation. Results: Compared to participants from the pre-pandemic sample, participants from the post-pandemic sample had higher standardized rates of depressive symptoms (40.6% vs 25.6%) and suicidal ideation (29.3% vs 21.1%). With adjustment for age, gender, university campus, scholarship, and past history of depression and suicide attempt, students in the post-pandemic period experienced more depressive symptoms (aOR, 1.89; 95% CI, 1.67-2.13) and suicidal ideation (aOR, 1.46; 95% CI, 1.28-1.67) compared to students in the pre-COVID-19 era. Limitations: The main limitations were self-selection bias and information bias due to potential over-reporting linked to media coverage, as well as measures of past history of depression and suicide attempt across the lifespan. Conclusions: These findings reveal an alarming deterioration of students mental health in the post-pandemic period compared to the pre-pandemic era. Pending replications in others countries, these results suggest that it is crucial to continue monitoring students mental health, strengthening communication on this topic, and reinforcing university mental healthcare systems.", + "rel_abs": "BackgroundThe COVID-19 pandemic and lockdown have had negative effects on students mental health. However, little information is available regarding the frequencies of depressive symptoms and suicidal ideation during the post-pandemic period. We aimed to compare prevalence rates of depressive symptoms and suicidal ideation among university students, before versus after the COVID-19 pandemic.\n\nMethodsIn this comparative study, 4464 students were recruited during the pre-COVID-19 pandemic period (2013-2020) and 1768 students, during the post-COVID-19 pandemic period (2022-2023). Standardized frequencies of depressive symptoms and suicidal ideation were compared between the two time periods. Adjusted logistic regression models were used to assess the association between the pandemic period (with the pre-COVID-19 period as reference) and depressive symptoms and suicidal ideation.\n\nResultsCompared to participants from the pre-pandemic sample, participants from the post-pandemic sample had higher standardized rates of depressive symptoms (40.6% vs 25.6%) and suicidal ideation (29.3% vs 21.1%). With adjustment for age, gender, university campus, scholarship, and past history of depression and suicide attempt, students in the post-pandemic period experienced more depressive symptoms (aOR, 1.89; 95% CI, 1.67-2.13) and suicidal ideation (aOR, 1.46; 95% CI, 1.28-1.67) compared to students in the pre-COVID-19 era.\n\nLimitationsThe main limitations were self-selection bias and information bias due to potential over-reporting linked to media coverage, as well as measures of past history of depression and suicide attempt across the lifespan.\n\nConclusionsThese findings reveal an alarming deterioration of students mental health in the post-pandemic period compared to the pre-pandemic era. Pending replications in others countries, these results suggest that it is crucial to continue monitoring students mental health, strengthening communication on this topic, and reinforcing university mental healthcare systems.", "rel_num_authors": 7, "rel_authors": [ { @@ -470,7 +1653,7 @@ "rel_date": "2024-03-16", "rel_site": "medRxiv", "rel_link": "https://medrxiv.org/cgi/content/short/2024.03.15.24304277", - "rel_abs": "Introduction The spring 2023 COVID-19 booster vaccination programme in England used both Pfizer BA.4-5 and Sanofi vaccines. All people aged 75 years or over and the clinically vulnerable were eligible to receive a booster dose. Direct comparisons of the effectiveness of these two vaccines in boosting protection against severe COVID-19 events have not been made in trials or observational data. Methods With the approval of NHS England, we used the OpenSAFELY-TPP database to compare effectiveness of the Pfizer BA.4-5 and Sanofi vaccines during the spring 2023 booster programme, between 1 April and 30 June 2023. We investigated two cohorts separately: those aged 75 or over (75+); and those aged 50 or over and clinically vulnerable (CV). In each cohort, vaccine recipients were matched on date of vaccination, COVID-19 vaccine history, age, and other characteristics. Effectiveness outcomes were COVID-19 hospital admission, COVID-19 critical care admission, and COVID-19 death up to 16 weeks after vaccination. Safety outcomes were pericarditis and myocarditis up to 4 weeks after vaccination. We report the cumulative incidence of each outcome, and compare safety and effectiveness using risk differences (RD), relative risks (RR), and incidence rate ratios (IRRs). Results 492,642 people were 1-1 matched in the CV cohort, and 673,926 in the 75+ cohort, contributing a total of 7,423,251 and 10,173,230 person-weeks of follow-up, respectively. The incidence of COVID-19 hospital admission was higher for Sanofi than for Pfizer BA.4-5. In the CV cohort, 16-week risks per 10,000 people were 22.3 (95%CI 20.4 to 24.3) for Pfizer BA.4-5 and 26.4 (24.4 to 28.7) for Sanofi, with an IRR of 1.19 (95%CI 1.06 to 1.34). In the 75+ cohort, these were 17.5 (16.1 to 19.1) for Pfizer BA.4-5 and 20.4 (18.9 to 22.1) for Sanofi, with an IRR of 1.18 (1.05-1.32). These findings were similar across all pre-specified subgroups. More severe COVID-19 related outcomes (critical care admission and death), and safety outcomes at 4 weeks, were rare in both vaccines so we could not reliably compare effectiveness of the two vaccines. Conclusion This observational study comparing effectiveness of Pfizer BA.4-5 and Sanofi vaccine during the spring 2023 programme in England in the two main eligible cohorts - people aged 75 and over and in clinically vulnerable people - found some evidence of superior effectiveness against COVID-19 hospital admission for Pfizer BA.4-5 compared with Sanofi within 16 weeks after vaccination.", + "rel_abs": "IntroductionThe spring 2023 COVID-19 booster vaccination programme in England used both Pfizer BA.4-5 and Sanofi vaccines. All people aged 75 years or over and the clinically vulnerable were eligible to receive a booster dose. Direct comparisons of the effectiveness of these two vaccines in boosting protection against severe COVID-19 events have not been made in trials or observational data.\n\nMethodsWith the approval of NHS England, we used the OpenSAFELY-TPP database to compare effectiveness of the Pfizer BA.4-5 and Sanofi vaccines during the spring 2023 booster programme, between 1 April and 30 June 2023. We investigated two cohorts separately: those aged 75 or over (75+); and those aged 50 or over and clinically vulnerable (CV). In each cohort, vaccine recipients were matched on date of vaccination, COVID-19 vaccine history, age, and other characteristics. Effectiveness outcomes were COVID-19 hospital admission, COVID-19 critical care admission, and COVID-19 death up to 16 weeks after vaccination. Safety outcomes were pericarditis and myocarditis up to 4 weeks after vaccination. We report the cumulative incidence of each outcome, and compare safety and effectiveness using risk differences (RD), relative risks (RR), and incidence rate ratios (IRRs).\n\nResults492,642 people were 1-1 matched in the CV cohort, and 673,926 in the 75+ cohort, contributing a total of 7,423,251 and 10,173,230 person-weeks of follow-up, respectively. The incidence of COVID-19 hospital admission was higher for Sanofi than for Pfizer BA.4-5. In the CV cohort, 16-week risks per 10,000 people were 22.3 (95%CI 20.4 to 24.3) for Pfizer BA.4-5 and 26.4 (24.4 to 28.7) for Sanofi, with an IRR of 1.19 (95%CI 1.06 to 1.34). In the 75+ cohort, these were 17.5 (16.1 to 19.1) for Pfizer BA.4-5 and 20.4 (18.9 to 22.1) for Sanofi, with an IRR of 1.18 (1.05-1.32). These findings were similar across all pre-specified subgroups. More severe COVID-19 related outcomes (critical care admission and death), and safety outcomes at 4 weeks, were rare in both vaccines so we could not reliably compare effectiveness of the two vaccines.\n\nConclusionThis observational study comparing effectiveness of Pfizer BA.4-5 and Sanofi vaccine during the spring 2023 programme in England in the two main eligible cohorts - people aged 75 and over and in clinically vulnerable people - found some evidence of superior effectiveness against COVID-19 hospital admission for Pfizer BA.4-5 compared with Sanofi within 16 weeks after vaccination.", "rel_num_authors": 20, "rel_authors": [ { @@ -586,85 +1769,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2024.03.15.24304168", - "rel_title": "Interventions for the management of post COVID-19 condition (long COVID): Protocol for a living systematic review & network meta-analysis", - "rel_date": "2024-03-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2024.03.15.24304168", - "rel_abs": "Background Up to 15% of survivors of COVID-19 infection experience long-term health effects, including fatigue, myalgia, and impaired cognitive function, termed post COVID-19 condition or long COVID. Several trials that study the benefits and harms of various interventions to manage long COVID have been published and hundreds more are planned or are ongoing. Trustworthy systematic reviews that clarify the benefits and harms of interventions are critical to promote evidence-based practice. Objective To create and maintain a living systematic review and network meta-analysis addressing the benefits and harms of pharmacologic and non-pharmacologic interventions for the treatment and management of long COVID. Methods Eligible trials will randomize adults with long COVID, to pharmacologic or non-pharmacologic interventions, placebo, sham, or usual care. We will identify eligible studies by searches of MEDLINE, EMBASE, CINAHL, PsycInfo, AMED, and CENTRAL, from inception, without language restrictions. Reviewers will work independently and in duplicate to screen search records, collect data from eligible trials, including trial and patient characteristics and outcomes of interest, and assess risk of bias. Our outcomes of interest will include fatigue, pain, post-exertional malaise, changes in education or employment status, cognitive function, mental health, dyspnea, quality of life, patient-reported physical function, recovery, and serious adverse events. For each outcome, when possible, we will perform a frequentist random-effects network meta-analysis. When there are compelling reasons to suspect that certain interventions are only applicable or effective for a subtype of long COVID, we will perform separate network meta-analyses. The GRADE approach will guide our assessment of the certainty of evidence. We will update our living review biannually, upon the publication of a seminal trial, or when new evidence emerges that may change clinical practice. Conclusion This living systematic review and network meta-analysis will provide comprehensive, trustworthy, and up-to-date summaries of the evidence addressing the benefits and harms of interventions for the treatment and management of long COVID. We will make our findings available publicly and work with guideline producing organizations to inform their recommendations.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Dena Zeraatkar", - "author_inst": "McMaster University" - }, - { - "author_name": "Michael Ling", - "author_inst": "McMaster University" - }, - { - "author_name": "Sarah Kirsh", - "author_inst": "McMaster University" - }, - { - "author_name": "Tanvir Jassal", - "author_inst": "McMaster University" - }, - { - "author_name": "Tyler Pitre", - "author_inst": "University of Toronto" - }, - { - "author_name": "Samantha Chakraborty", - "author_inst": "Monash University" - }, - { - "author_name": "Tari Turner", - "author_inst": "Monash University" - }, - { - "author_name": "Lyn Turkstra", - "author_inst": "McMaster University" - }, - { - "author_name": "Roger S McIntyre", - "author_inst": "University of Toronto" - }, - { - "author_name": "Ariel Izcovich", - "author_inst": "Hospital Aleman de Buenos Aires" - }, - { - "author_name": "Lawrence Mbuagbaw", - "author_inst": "McMaster University" - }, - { - "author_name": "Thomas Agoritsas", - "author_inst": "University Hospitals of Geneva" - }, - { - "author_name": "Signe Flottorp", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Paul Garner", - "author_inst": "Liverpool School of Tropical Medicine" - }, - { - "author_name": "Rachel Couban", - "author_inst": "McMaster University" - }, - { - "author_name": "Jason Busse", - "author_inst": "McMaster University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2024.03.14.583523", "rel_title": "de Novo Sequencing of Antibodies for Identification of Neutralizing Antibodies in Human Plasma Post SARS-CoV-2 Vaccination", @@ -1721,6 +2825,77 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2024.03.12.584682", + "rel_title": "Changes in the senescence profile and immune checkpoints in HIV-infected individuals after COVID-19", + "rel_date": "2024-03-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.03.12.584682", + "rel_abs": "BackgroundBoth SARS-CoV-2 and HIV infection exhibit alterations in the senescence profile and immune checkpoint (IC) molecules. However, the midterm impact of SARS-CoV-2 on these profiles in people with HIV (PWH) remains unclear. This study aimed to evaluate differences in plasma biomarker levels related to ICs, the senescence-associated secretory phenotype (SASP), and pro- and anti-inflammatory cytokines in PWH following recovery from SARS-CoV-2 infection.\n\nMethodsWe conducted a cross-sectional study of 95 PWH receiving antiretroviral therapy, stratified by SARS-CoV-2 infection status: a) 48 previously infected (HIV/SARS) and b) 47 controls without previous infection (HIV). Plasma biomarkers (n=44) were assessed using Procartaplex Multiplex Immunoassays. Differences were analyzed using a generalized linear model adjusted for sex and ethnicity and corrected for the false discovery rate. Significant values were defined as an adjusted arithmetic mean ratio [≥]1.2 or [≤]0.8 and a qvalue<0.1. Spearman correlation evaluated relationships between plasma biomarkers (significant correlations, rho[≥]0.3 and q value<0.1).\n\nResultsThe median age of the PWH was 45 years, and 80% were men. All SARS-CoV-2-infected PWH experienced symptomatic infection; 83.3% had mild symptomatic infection, and sample collection occurred at a median of 12 weeks postdiagnosis. The HIV/SARS group showed higher levels of ICs (CD80, PDCD1LG2, CD276, PDCD1, CD47, HAVCR2, TIMD4, TNFRSF9, TNFRSF18, and TNFRSF14), SASP (LTA, CXCL8, and IL13), and inflammatory plasma biomarkers (IL4, IL12B, IL17A, CCL3, CCL4, and INF1A) than did the HIV group.\n\nConclusionsSARS-CoV-2 infection in PWH causes significant midterm disruptions in plasma ICs and inflammatory cytokine levels, highlighting SASP-related factors, which could be risk factors for the emergence of complications in PWH.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Celia Crespo-Bermejo", + "author_inst": "National Center of Microbiology, Carlos III Health Institute. Madrid, Spain." + }, + { + "author_name": "Oscar Brochado-Kith", + "author_inst": "National Center of Microbiology, Carlos III Health Institute. Madrid, Spain." + }, + { + "author_name": "Sergio Grande-Garcia", + "author_inst": "National Center of Microbiology, Carlos III Health Institute. Madrid, Spain." + }, + { + "author_name": "Violeta Lara-Aguilar", + "author_inst": "National Center of Microbiology, Carlos III Health Institute. Madrid, Spain." + }, + { + "author_name": "Manuel Llamas-Adan", + "author_inst": "National Center of Microbiology, Carlos III Health Institute. Madrid, Spain." + }, + { + "author_name": "Sonia Arca-Lafuente", + "author_inst": "National Center of Microbiology, Carlos III Health Institute. Madrid, Spain." + }, + { + "author_name": "Luz Martin-Carbonero", + "author_inst": "Internal Medicine Department. Hospital Universitario La Paz (IdiPAZ). Madrid, Spain." + }, + { + "author_name": "Ignacio de los Santos", + "author_inst": "Internal Medicine-Infectious Diseases Department. Hospital Universitario de La Princesa. Madrid, Spain." + }, + { + "author_name": "M Angeles Jimenez Sousa", + "author_inst": "National Center of Microbiology, Carlos III Health Institute. Madrid, Spain." + }, + { + "author_name": "Salvador Resino", + "author_inst": "National Center of Microbiology, Carlos III Health Institute. Madrid, Spain." + }, + { + "author_name": "Juan Berenguer", + "author_inst": "Hospital General Universitario Gregorio Maranon, Madrid, Spain." + }, + { + "author_name": "Ricardo Madrid", + "author_inst": "Department of Genetics, Physiology and Microbiology. Faculty of Biological Sciences, Complutense University of Madrid. Madrid, Spain." + }, + { + "author_name": "Amanda Fernandez-Rodriguez", + "author_inst": "National Center of Microbiology, Carlos III Health Institute. Madrid, Spain." + }, + { + "author_name": "Veronica Briz", + "author_inst": "National Center of Microbiology, Carlos III Health Institute. Madrid, Spain." + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2024.03.13.583470", "rel_title": "SARS-CoV-2 methyltransferase nsp10-16 in complex with natural and drug-like purine analogs for guiding structure-based drug discovery", @@ -2234,53 +3409,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2024.03.11.584367", - "rel_title": "Exploring the therapeutic potential of defective interfering particles in reducing the replication of SARS-CoV-2", - "rel_date": "2024-03-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2024.03.11.584367", - "rel_abs": "SARS-CoV-2 still presents a global threat to human health due to the continued emergence of new strains and waning immunity amongst vaccinated populations. Therefore, it is still relevant to investigate potential therapeutics, such as therapeutic interfering particles (TIPs). Mathematical and computational modelling are valuable tools to study viral infection dynamics for predictive analysis. Here, we expand on the previous work by Grebennikov et al. (2021) on SARS-CoV-2 intra-cellular replication dynamics to include defective interfering particles (DIPs) as potential therapeutic agents. We formulate a deterministic model that describes the replication of wild-type (WT) SARS-CoV-2 virus in the presence of DIPs. Sensitivity analysis of parameters to several model outputs is employed to inform us on those parameters to be carefully calibrated from experimental data. We then study the effects of co-infection on WT replication and how DIP dose perturbs the release of WT viral particles. Furthermore, we provide a stochastic formulation of the model that is compared to the deterministic one. These models could be further developed into population-level models or used to guide the development and dose of TIPs.\n\nAuthor summarySARS-CoV-2 continues to evolve, with new strains or sub-strains being identified thanks to efforts to monitor the virus. Consequently, new strains threaten human health as current vaccinations may not adequately protect against future strains. It is therefore important to understand the roles that additional therapeutics could play in protecting against these future strains.\n\nTherapeutic interfering particles (TIPs), otherwise referred to as defective interfering particles (DIPs), could provide an additional treatment option against future strains. Previous models have examined the role of DIPs at the within-host level during co-infection with wild-type virus, but have paid little attention to intra-cellular dynamics. Here we extend the previous intra-cellular replication model of SARS-CoV-2 by Grebennikov et al. (2021) to include co-infection of WT virus with DIPs. We show that DIPs lead to a reduction in the WT virus in a dose-dependent manner, with higher doses leading to up to 10-fold reduction in total WT virus released from a cell depending on the multiplicity of infection (MOI). We find these results to be consistent for both deterministic and stochastic formulations of the model. Our approaches could be developed into a within-host model or population-level model, which could then be used to guide therapeutic DIP doses.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Macauley Locke", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Dmitry Grebennikov", - "author_inst": "Russian Academy of Sciences" - }, - { - "author_name": "Igor Sazonov", - "author_inst": "Swansea University" - }, - { - "author_name": "Martin Lopez-Garcia", - "author_inst": "University of Leeds School of Mathematics" - }, - { - "author_name": "Marina Loguinova", - "author_inst": "Ministry of Healthcare of the Russian Federation" - }, - { - "author_name": "Andreas Meyerhan", - "author_inst": "ICREA: Institucio Catalana de Recerca i Estudis Avancats" - }, - { - "author_name": "Gennady Bocharov", - "author_inst": "Marchuk Institute of Numerical Mathematics" - }, - { - "author_name": "Carmen Molina-Paris", - "author_inst": "University of Leeds" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2024.03.11.583978", "rel_title": "Distinct Patterns of SARS-CoV-2 BA.2.87.1 and JN.1 Variants in Immune Evasion, Antigenicity and Cell-Cell Fusion", @@ -3201,6 +4329,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2024.03.06.24303901", + "rel_title": "Understanding Food Insecurity in Kinshasa During the COVID-19 Pandemic", + "rel_date": "2024-03-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.03.06.24303901", + "rel_abs": "IntroductionFood insecurity is a vital issue, especially in places like Kinshasa. Additionally, food insecurity has been worsened by the COVID-19 pandemic, particularly in low- and middle-income countries. Thus, this study examined food insecurity in Kinshasa after the peak of the pandemic to understand food insecurity in post-pandemic recovery efforts and the possible implications for public health policies for future pandemics similar to COVID-19.\n\nMethodsThis study was conducted in Kinshasa with a representative sample of 2,160 households selected from 36 enumeration areas. We interviewed participants from different areas and used a questionnaire to ask them about their food situation. Interviews were conducted with the head of each household or their designated representative by 150 masters students using tablets powered by the SurveyCTO application. Household food security status was evaluated through the Household Food Insecurity Access Scale. A logistic regression model was developed to assess household risk factors associated with food insecurity.\n\nResultsMost people we talked to were over 40 years old, and many lived in households with fewer than six people. About a third of the households were overcrowded. Factors associated with food insecurity included being a household head aged over 50 years, insufficient living space, lower socioeconomic status, and residing in slum areas (AOR: 1.38; 95% CI: 1.06-1.79). In 2022, 12,627,424 individuals faced food insecurity in Kinshasa, including 8,829,820 individuals who experienced severe food insecurity.\n\nConclusionLiving conditions play a significant role in food insecurity. Governments need to do more to help people, especially those living in crowded areas. To combat economic restrictions that lead to food insecurity during crises, policymakers and implementing partners should enhance food assistance programs, such as cash transfers and food supply initiatives, focusing on overcrowded households and the informal job sector.\n\nKey MessagesO_ST_ABSWhat is already known on this topicC_ST_ABSThis study emphasizes the multifaceted nature of food security, defined as the continuous access to sufficient, safe, and nutritious food, comprising availability, accessibility, utilization, and stability. Food insecurity, resulting from unmet needs in any of these dimensions, correlates with poor health outcomes and increased mortality. The global COVID-19 pandemic exacerbated food insecurity, particularly in low- and middle-income countries, with rates exceeding 50%. Factors such as poverty, living conditions, low income, lack of livestock, large household size, and psychological factors contribute significantly.\n\nWhile prior studies in the Democratic Republic of the Congo exist, they are limited, often focusing on specific groups. This study aims to comprehensively assess household food security in Kinshasa during the post-COVID-19 period, identifying associated factors for a more nuanced understanding.\n\nWhat this study addsThis study adds to the existing literature by investigating the prevalence and determinants of food insecurity during a global health crisis, employing the Household Food Insecurity Access Scale for assessment. It contributes novel insights by examining the prevalence and severity of food insecurity in Kinshasa, the Democratic Republic of the Congo, offering a unique context for understanding the impact of a global health crisis on household food security.\n\nHow this study might affect research, practice, or policyThe study recommends implementing cash transfer strategies for vulnerable households, particularly those with informal jobs and young children, based on significant associations between lower socioeconomic status and food insecurity during the COVID-19 pandemic. Another recommendation is to expand food assistance programs for overcrowded households and the informal job sector, addressing the high prevalence of food insecurity in slum areas. Other social and structural determinants of food security, such as womens empowerment and access to water and electricity, should be further researched.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Pierre Akilimali", + "author_inst": "Kinshasa School of Public Health" + }, + { + "author_name": "Benito Kazenza", + "author_inst": "Kinshasa School of Public health" + }, + { + "author_name": "Francis Kabasubabo", + "author_inst": "Patrick Kayembe Reaserch Center" + }, + { + "author_name": "Landry Egbende", + "author_inst": "Kinshasa School of Public Health" + }, + { + "author_name": "Steve Botomba", + "author_inst": "Kinshasa School of Public Health" + }, + { + "author_name": "Dynah M. Kayembe", + "author_inst": "Patrick Kayembe Research Center" + }, + { + "author_name": "Branly K. Mbunga", + "author_inst": "Kinshasa School of Public Health" + }, + { + "author_name": "Nguyen T Tran", + "author_inst": "Faculty of Medicine, University of Geneva" + }, + { + "author_name": "Desire K Mashinda", + "author_inst": "Kinshasa School of Public Health" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2024.03.06.583815", "rel_title": "Learn!Bio - A time-limited cross-sectional study on biosciences students' pathway to resilience during and post the Covid-19 pandemic at an UK university from 2020-2023 and insights into future teaching approaches.", @@ -3564,61 +4743,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2024.03.05.24303828", - "rel_title": "COVID-19 Vaccination Booster Uptake Is Related to End of Pandemic Perception: Population-Based Survey in Four Provinces in Indonesia", - "rel_date": "2024-03-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2024.03.05.24303828", - "rel_abs": "Global COVID-19 booster vaccination uptake has been low, particularly in low-middle-income countries (LMICs). However, studies on the determinants of COVID-19 booster vaccination remain limited, especially in LMIC settings. This study aims to describe the determinants of COVID-19 booster vaccination uptake in an LMIC context. We analyzed data from a cross-sectional survey that was conducted in September 2022 in four provinces in Indonesia. Participants (n=2,223) were recruited using multiple-stage cluster sampling. Multivariable logistic regression analysis was used to identify factors associated with booster vaccination status. The proportion of COVID-19 booster vaccination among fully vaccinated adults was 29.5%, while fear of transmission (12.4%) and perceived risk of getting a COVID-19 infection (33.5%) were low. Multivariable analysis showed that people living on Java Island (aOR: 2.45, 95% CI: 1.87-3.24), living in the urban area (aOR: 2.04, 95% CI: 1.60-2.61), being an employee in the formal sector (aOR: 3.99, 95% CI: 1.93 - 8.58), experiencing a side effect from previous vaccination (aOR: 1.71, 95% CI: 1.40-2.09), having a history of SARS-COV2 infection (aOR: 2.10, 95%CI: 1.27-3.50), having perception on the upcoming new wave of COVID-19 (aOR: 1.37, 95% CI: 1.07 -1.76), and believing the pandemic has not ended (aOR: 1.29, 95% CI: 1.01, 1.64) were associated with booster shot uptake. Low educational level (aOR: 0.6, 95% CI: 0.39-0.93) inhibited booster vaccination uptake. Current booster dose coverage was considerably lower than the primary vaccination dosage. The low booster vaccination uptake in four provinces was associated with a belief the pandemic has no longer, which might hinder the catch up of wide-population target coverage and COVID-19 control for reduced disease severity and hospitalization. Thus, efforts need to be prioritized in reaching the COVID-19 vulnerable population, which includes elderly and those with comorbidities.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Ahmad Watsiq Maula", - "author_inst": "Faculty of Medicine Public Health and Nursing" - }, - { - "author_name": "citra indriani", - "author_inst": "Faculty of Medicine Public Health and Nursing Universitas Gadjah Mada" - }, - { - "author_name": "Risalia Reni Arisanti", - "author_inst": "Faculty of Medicine Public Health and Nursing Universitas Gadjah Mada" - }, - { - "author_name": "Vincentius Arca Testamenti", - "author_inst": "Facullty of Medicine Public Health and Nursing Universitas Gadjah Mada" - }, - { - "author_name": "Catharina Yekti Praptiningsih", - "author_inst": "U.S. Centers for Disease Control and Prevention, Jakarta, Indonesia" - }, - { - "author_name": "Rebecca Merril", - "author_inst": "U.S. Centers for Disease Control and Prevention, Jakarta, Indonesia" - }, - { - "author_name": "Ansariadi Ansariadi", - "author_inst": "Faculty of Public Health, Universitas Hasanuddin, Indonesia" - }, - { - "author_name": "Tri Yunis Miko Wahyono", - "author_inst": "Faculty of Public Health Universitas Indonesia Indonesia" - }, - { - "author_name": "Atik Choirul Hidajah", - "author_inst": "Faculty of Public Health, Universitas Airlangga, Indonesia" - }, - { - "author_name": "RIRIS ANDONO AHMAD", - "author_inst": "Faculty of Medicine, Public Health, Nursing Universitas Gadjah Mada" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2024.03.05.583578", "rel_title": "Regulation of virion production by the ORF8 signal peptide across SARS-CoV-2 variants", @@ -4991,6 +6115,109 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2024.03.01.582987", + "rel_title": "Newcastle Disease Virus Vector-Based SARS-CoV-2 Vaccine Candidate AVX/COVID-12 Activates T Cells and Is Recognized by Antibodies from COVID-19 Patients and Vaccinated", + "rel_date": "2024-03-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.03.01.582987", + "rel_abs": "Several effective vaccines for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been developed and implemented in the population. However, the current production capacity falls short of meeting global demand. Therefore, it is crucial to further develop novel vaccine platforms that can bridge the distribution gap. AVX/COVID-12 is a vector-based vaccine that utilizes the Newcastle Disease virus (NDV) to present the SARS-CoV-2 spike protein to the immune system. This study analyses the antigenicity of the vaccine candidate by examining antibody binding and T-cell activation in individuals infected with SARS-CoV-2 or variants of concern (VOCs), as well as in healthy volunteers who received coronavirus disease 2019 (COVID-19) vaccinations. Our findings indicate that the vaccine effectively binds antibodies and activates T-cells in individuals who received 2 or 3 doses of BNT162b2 or AZ/ChAdOx-1-S vaccines. Furthermore, the stimulation of T-cells from patients and vaccine recipients with AVX/COVID-12 resulted in their proliferation and secretion of interferon-gamma (IFN-{gamma}) in both CD4+ and CD8+ T-cells. In conclusion, the AVX/COVID-12 vectored vaccine candidate demonstrates the ability to stimulate robust cellular responses and is recognized by antibodies primed by the spike protein present in SARS-CoV-2 viruses that infected patients, as well as in the mRNA BNT162b2 and AZ/ChAdOx-1-S vaccines. These results support the inclusion of the AVX/COVID-12 vaccine as a booster in vaccination programs aimed at addressing COVID-19 caused by SARS-CoV-2 and its VOCs.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Alejandro Torres-Flores", + "author_inst": "Unidad de Investigaci\u00f3n M\u00e9dica en Inmunoqu\u00edmica, UMAE Hospital de Especialidades, Centro M\u00e9dico Nacional Siglo XXI, IMSS, Posgrado en Inmunolog\u00eda, ENCB, IPN, C" + }, + { + "author_name": "Luis Alberto Ontiveros-Padilla", + "author_inst": "Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Caroli" + }, + { + "author_name": "Ruth Lizzeth Madera-Sandoval", + "author_inst": "Departamento de Biolog\u00eda Molecular y Validaci\u00f3n de T\u00e9cnicas, Instituto de Diagn\u00f3stico y Referencia Epidemiol\u00f3gicos (InDRE) \"Dr, Manuel Mart\u00ednez B\u00e1ez\", Secretari" + }, + { + "author_name": "Araceli Tepale-Segura", + "author_inst": "Unidad de Investigaci\u00f3n M\u00e9dica en Inmunoqu\u00edmica, UMAE Hospital de Especialidades, Centro M\u00e9dico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad" + }, + { + "author_name": "Juli\u00e1n Gaj\u00f3n-Mart\u00ednez", + "author_inst": "Unidad de Investigaci\u00f3n M\u00e9dica en Inmunoqu\u00edmica, UMAE Hospital de Especialidades, Centro M\u00e9dico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad" + }, + { + "author_name": "Tania Rivera-Hern\u00e1ndez", + "author_inst": "Unidad de Investigaci\u00f3n M\u00e9dica en Inmunoqu\u00edmica, UMAE Hospital de Especialidades, Centro M\u00e9dico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, CONAHC" + }, + { + "author_name": "Eduardo Antonio Ferat-Osorio", + "author_inst": "Divisi\u00f3n de Investigaci\u00f3n en Salud, UMAE Hospital de Especialidades, Centro M\u00e9dico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de M\u00e9xico, M" + }, + { + "author_name": "Arturo C\u00e9rbulo-V\u00e1zquez", + "author_inst": "Servicio de Medicina Gen\u00f3mica. Hospital General de M\u00e9xico Dr. Eduardo Liceaga, Ciudad de M\u00e9xico, M\u00e9xico" + }, + { + "author_name": "Lourdes Andrea Arriaga-Pizano", + "author_inst": "Unidad de Investigaci\u00f3n M\u00e9dica en Inmunoqu\u00edmica, UMAE Hospital de Especialidades, Centro M\u00e9dico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad" + }, + { + "author_name": "Laura Bonifaz", + "author_inst": "Coordinaci\u00f3n de investigaci\u00f3n en salud, Centro M\u00e9dico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de M\u00e9xico, M\u00e9xico" + }, + { + "author_name": "Georgina Paz-De la Rosa", + "author_inst": "Laboratorio Avi-Mex S.A. de C.V., Ciudad de Mexico, Mexico." + }, + { + "author_name": "Oscar Rojas-Mart\u00ednez", + "author_inst": "Laboratorio Avi-Mex S.A. de C.V., Ciudad de M\u00e9xico, M\u00e9xico." + }, + { + "author_name": "Alejandro Su\u00e1rez-Mart\u00ednez", + "author_inst": "Laboratorio Avi-Mex S.A. de C.V., Ciudad de M\u00e9xico, M\u00e9xico." + }, + { + "author_name": "Gustavo Peralta-S\u00e1nchez", + "author_inst": "Laboratorio Avi-Mex S.A. de C.V., Ciudad de M\u00e9xico, M\u00e9xico." + }, + { + "author_name": "David Sarfati-Mizrahi", + "author_inst": "Laboratorio Avi-Mex S.A. de C.V., Ciudad de Mexico, Mexico." + }, + { + "author_name": "Weina Sun", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "H\u00e9ctor El\u00edas Chagoya-Cort\u00e9s", + "author_inst": "Consultora Mextrategy, S.A.S. de C.V., Ciudad de M\u00e9xico, M\u00e9xico." + }, + { + "author_name": "Peter Palese", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA." + }, + { + "author_name": "Florian Krammer", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Adolfo Garc\u00eda-Sastre", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Bernardo Lozano-Dubernard", + "author_inst": "Laboratorio Avi-Mex S.A. de C.V., Ciudad de M\u00e9xico, M\u00e9xico." + }, + { + "author_name": "Constantino L\u00f3pez-Mac\u00edas", + "author_inst": "Unidad de Investigaci\u00f3n M\u00e9dica en Inmunoqu\u00edmica, UMAE Hospital de Especialidades, Centro M\u00e9dico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad" + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2024.03.01.582176", "rel_title": "Physics-driven structural docking and protein language models accelerate antibody screening and design for broad-spectrum antiviral therapy", @@ -5778,29 +7005,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2024.03.04.24303713", - "rel_title": "Enhancing COVID-19 Case Forecasting in the United States: A Comparative Analysis of ARIMA, SARIMA, and RNN Models with Grid Search Optimization", - "rel_date": "2024-03-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2024.03.04.24303713", - "rel_abs": "The COVID-19 pandemic has resulted in a substantial number of fatalities in the United States since its onset in January 2020. In an effort to mitigate the spread of this highly infectious disease, a range of measures, including social distancing, mask-wearing, lockdowns, and vaccination campaigns, have been implemented. However, despite these extensive efforts, the persistent transmission of the virus can be attributed to a combination of vaccine hesitancy among certain individuals and the emergence of new viral strains. To effectively manage the ongoing pandemic, healthcare providers and government officials rely on infectious disease modeling to anticipate and secure the necessary resources. Accurate short-term case number forecasting is of paramount importance for healthcare systems.\n\nSince the beginning of the pandemic, numerous models have been employed to forecast the number of confirmed cases. In this study, we undertake a comparative analysis of six time-series techniques: Simple Moving Average (SMA), Exponentially Weighted Moving Average (EWMA), Holt-Winters Double Exponential Smoothing Additive (HWDESA), Autoregressive Integrated Moving Average (ARIMA), Seasonal Autoregressive Integrated Moving Average (SARIMA), and Recurrent Neural Network (RNN), with regard to their modeling and forecasting capabilities. SMA, EWMA, and HWDESA were employed for predictive modeling, while the ARIMA, SARIMA, and RNN models were utilized for case number forecasting. A comprehensive grid search was carried out to determine the optimal parameter combinations for both the ARIMA and SARIMA models. Our research findings demonstrate that the Holt-Winters Double Exponential model outperforms both the Exponentially Weighted Moving Average and Simple Moving Average in predicting the number of cases. On the other hand, the RNN model surpasses conventional time-series models such as ARIMA and SARIMA in terms of its forecasting accuracy. The finding of this study emphasizes the importance of accurately predicting the number of COVID-19 cases, given the substantial loss of lives caused by both the virus itself and the societal responses to it. Equipping healthcare managers with precise tools like Recurrent Neural Networks (RNNs) can enable them to forecast future cases more accurately and enhance their preparedness for effective response.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Saina Abolmaali", - "author_inst": "Auburn University" - }, - { - "author_name": "Samira Nichols", - "author_inst": "University of Central Arkansas" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2024.03.03.24303690", "rel_title": "Prospective Clinical Surveillance for Severe Acute Respiratory Illness in Kenyan Hospitals during the COVID-19 pandemic", @@ -7147,6 +8351,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2024.02.27.24303073", + "rel_title": "Implementing remote monitoring for COVID-19 patients in primary care", + "rel_date": "2024-02-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.27.24303073", + "rel_abs": "BackgroundIn Germany, most patients with coronavirus disease 2019 (COVID-19) are treated in an outpatient setting. To improve assessments of the health status of COVID-19 outpatients, various remote monitoring models have been developed. However, little information exists on experiences acquired with remote monitoring in an outpatient setting, particularly from a patient perspective. The aim of our COVID-19@home study was therefore to implement and evaluate an app-based remote monitoring concept for acute and post-acute COVID-19-patients in primary care. In this paper, we focus on the patients evaluation of our remote monitoring approach.\n\nMethodsPatients with acute COVID-19 measured heart rate, blood pressure, oxygen saturation, and body temperature daily for 28 days. Patients with post-acute COVID-19 determined the same parameters for 12 weeks, supplemented by lung parameters and daily step count. The data were documented using the SaniQ smartphone app. COVID-19 symptoms were assessed daily using an app-based questionnaire. Patients GPs could access the data on the SaniQ Praxis telemedicine platform. We used an app-based questionnaire consisting of 11 questions presented with a 4-point Likert scale to evaluate patient satisfaction. Data were analyzed descriptively.\n\nResultsOf the 51 patients aged 19-77 years that participated in the study, 42 completed the questionnaire. All patients rated home monitoring as very good or rather good and were able to integrate the measuring processes into their daily routines. Overall, 93% would recommend the app and the measuring devices to their family and friends. About 60% felt that their COVID-19 treatment had benefited from home monitoring. Only few patients were unsettled by the app and use of the measuring devices. During the course of the study, the implementation process was optimized.\n\nConclusionsThe use of remote monitoring in COVID-19 patients is feasible and was evaluated positively by most study patients. However, it is difficult to imagine how general practices could cope with monitoring patients with acute diseases without any further organizational support. Future research should address cost-effectiveness and changes in such clinical outcomes as hospitalization and mortality.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Susanne M. Koehler", + "author_inst": "Goethe University Frankfurt, Institute of General Practice, 60590 Frankfurt am Main, Germany" + }, + { + "author_name": "Svea Holtz", + "author_inst": "Goethe University Frankfurt, Institute of General Practice, 60590 Frankfurt am Main, Germany" + }, + { + "author_name": "Peter Jan Chabiera", + "author_inst": "Goethe University Frankfurt, Institute of General Practice, 60590 Frankfurt am Main, Germany" + }, + { + "author_name": "Nurlan Dauletbaev", + "author_inst": "Department of Internal, Respiratory and Critical Care Medicine, Philipps University of Marburg, 35043 Marburg, Germany" + }, + { + "author_name": "Kim Deutsch", + "author_inst": "Department of Digital Medicine, Medical Faculty OWL, Bielefeld University, 33615 Bielefeld, Germany" + }, + { + "author_name": "Zoe S. Oftring", + "author_inst": "Institute of Digital Medicine, Philipps University of Marburg, Germany" + }, + { + "author_name": "Dennis Lawin", + "author_inst": "Department of Cardiology and Intensive Care Medicine, University hospital OWL of Bielefeld University, Campus Klinikum Bielefeld, Bielefeld, Germany" + }, + { + "author_name": "Lukas Niekrenz", + "author_inst": "Department of Pneumology and Intensive Care Medicine, University Hospital Aachen, 52074 Aachen, Germany" + }, + { + "author_name": "Teresa Euler", + "author_inst": "Goethe University Frankfurt, University Hospital, Medical Clinic 1, Department of Respiratory Medicine, 60590 Frankfurt am Main, Germany" + }, + { + "author_name": "Rainer Gloeckl", + "author_inst": "Schoen Clinic Berchtesgadener Land, Institute for Pulmonary Rehabilitation Research, 83471 Schoenau am Koenigssee, Germany" + }, + { + "author_name": "Rembert Koczulla", + "author_inst": "Schoen Clinic Berchtesgadener Land, Institute for Pulmonary Rehabilitation Research, 83471 Schoenau am Koenigssee, Germany" + }, + { + "author_name": "Gernot Rohde", + "author_inst": "Goethe University Frankfurt, University Hospital, Medical Clinic 1, Department of Respiratory Medicine, 60590 Frankfurt am Main, Germany" + }, + { + "author_name": "Michael Dreher", + "author_inst": "Department of Pneumology and Intensive Care Medicine, University Hospital Aachen, 52074 Aachen, Germany" + }, + { + "author_name": "Claus F. Vogelmeier", + "author_inst": "Department of Internal, Respiratory and Critical Care Medicine, Philipps University of Marburg, 35043 Marburg, Germany" + }, + { + "author_name": "Sebastian Kuhn", + "author_inst": "Institute of Digital Medicine, Philipps University of Marburg, 35043 Marburg, Germany" + }, + { + "author_name": "Beate Sigrid Mueller", + "author_inst": "Institute of General Practice, University of Cologne, Faculty of Medicine and University Hospital Cologne, 50937 Cologne, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "primary care research" + }, { "rel_doi": "10.1101/2024.02.27.24303356", "rel_title": "Ineffectiveness of international travel restrictions to contain spread of the SARS-CoV-2 Omicron BA.1 variant: a continent-wide laboratory-based observational study from Africa", @@ -7906,69 +9189,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2024.02.27.582110", - "rel_title": "The effect of molnupiravir and nirmatrelvir on SARS-CoV-2 genome diversity in infected and immune suppressed mice", - "rel_date": "2024-02-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2024.02.27.582110", - "rel_abs": "SynopsisO_ST_ABSObjectivesC_ST_ABSImmunocompromised individuals are susceptible to severe COVID-19 and potentially contribute to the emergence of variants with altered pathogenicity due to persistent infection. This study investigated the impact of immunosuppression on SARS-CoV-2 infection in k18-hACE2 mice and the effectiveness of antiviral treatments in this context.\n\nMethodsMice were immunosuppressed using cyclophosphamide and infected with a B lineage of SARS-CoV-2. Molnupiravir and nirmatrelvir, alone and in combination, were administered and viral load and viral sequence diversity was assessed.\n\nResultsTreatment of infected but immune compromised mice with both compounds either singly or in combination resulted in decreased viral loads and pathological changes compared to untreated animals. Treatment also abrogated infection of neuronal tissue. However, no consistent changes in the viral consensus sequence were observed, except for the emergence of the S:H655Y mutation. Molnupiravir, but not nirmatrelvir or immunosuppression alone, increased the transition/transversion (Ts/Tv) ratio, representative of A>G and C>U mutations and this increase was not altered by the co-administration of nirmatrelvir with molnupiravir.\n\nNotably, immunosuppression itself did not appear to promote the emergence of mutational characteristic of variants of concern (VOCs).\n\nConclusionsFurther investigations are warranted to fully understand the role of immunocompromised individuals in VOC development and to inform optimised public health strategies. It is more likely that immunodeficiency promotes viral persistence but does not necessarily lead to substantial consensus-level changes in the absence of antiviral selection pressure. Consistent with mechanisms of action, molnupiravir showed a stronger mutagenic effect than nirmatrelvir in this model.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Rebekah Penrice-Randal", - "author_inst": "Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK." - }, - { - "author_name": "Eleanor G Bentley", - "author_inst": "Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK." - }, - { - "author_name": "Parul Sharma", - "author_inst": "Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK." - }, - { - "author_name": "Adam Kirby", - "author_inst": "Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK." - }, - { - "author_name": "I'ah Donovan-Banfield", - "author_inst": "Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK. NIHR Health Protection Research Unit in Emerging and Zoonotic Infection" - }, - { - "author_name": "Anja Kipar", - "author_inst": "Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK. Laboratory for Animal Model Pathology, Institute of Veterinary Patholog" - }, - { - "author_name": "Daniele F Mega", - "author_inst": "Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK." - }, - { - "author_name": "Chloe Bramwell", - "author_inst": "Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK. Department of Pharmacology and Therapeutics, University of Liverpool, U" - }, - { - "author_name": "Joanne Sharp", - "author_inst": "Department of Pharmacology and Therapeutics, University of Liverpool, UK." - }, - { - "author_name": "Andrew Owen", - "author_inst": "Department of Pharmacology and Therapeutics, University of Liverpool, UK. Centre of Excellence in Long-acting Therapeutics (CELT), University of Liverpool, UK." - }, - { - "author_name": "Julian A Hiscox", - "author_inst": "Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK. NIHR Health Protection Research Unit in Emerging and Zoonotic Infection" - }, - { - "author_name": "James P Stewart", - "author_inst": "Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK. Centre of Excellence in Long-acting Therapeutics (CELT), University of " - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2024.02.26.582219", "rel_title": "The S2 subunit of spike encodes diverse targets for functional antibody responses to SARS-CoV-2", @@ -9733,6 +10953,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2024.02.21.24303099", + "rel_title": "Modeling the relative influence of socio-demographic variables on post-acute COVID-19 quality of life: an application to settings in Europe, Asia, Africa, and South America", + "rel_date": "2024-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.21.24303099", + "rel_abs": "Long-term COVID-19 complications are a globally pervasive threat, but their plausible social drivers are often not prioritized. Here, we use data from a multinational consortium to quantify the relative contributions of social and clinical factors to differences in quality of life among participants experiencing long COVID and measure the extent to which social variables impacts can be attributed to clinical intermediates, across diverse contexts. In addition to age, neuropsychological and rheumatological comorbidities, educational attainment, employment status, and female sex were identified as important predictors of long COVID-associated quality of life days (long COVID QALDs). Furthermore, a great majority of their impacts on long COVID QALDs could not be tied to key long COVID-predicting comorbidities, such as asthma, diabetes, hypertension, psychological disorder, and obesity. In Norway, 90% (95% CI: 77%, 100%) of the effect of belonging to the highest versus lowest educational attainment quintile was not attributed to intermediate comorbidity impacts. The same was true for 86% (73%, 100%) of the protective effects of full-time employment versus all other employment status categories (excluding retirement) in the UK and 74% (46%,100%) of the protective effects of full-time employment versus all other employment status categories in a cohort of four middle-income countries (MIC). Of the effects of female sex on long COVID QALDs in Norway, UK, and the MIC cohort, 77% (46%,100%), 73% (52%, 94%), and 84% (62%, 100%) were unexplained by the clinical mediators, respectively. Our findings highlight that socio-economic proxies and sex may be as predictive of long COVID QALDs as commonly emphasized comorbidities and that broader structural determinants likely drive their impacts. Importantly, we outline a multi-method, adaptable causal machine learning approach for evaluating the isolated contributions of social disparities to long COVID quality of life experiences.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Tigist F Menkir", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Barbara Citarella", + "author_inst": "University of Oxford" + }, + { + "author_name": "Louise Sigfrid", + "author_inst": "University of Oxford" + }, + { + "author_name": "Yash Doshi", + "author_inst": "Terna Speciality Hospital & Research Centre" + }, + { + "author_name": "Luis Felipe Reyes", + "author_inst": "University of Oxford" + }, + { + "author_name": "Jose Andres Calvache", + "author_inst": "Universidad del Cauca" + }, + { + "author_name": "Anders Benjamin Kildal", + "author_inst": "University Hospital of North Norway" + }, + { + "author_name": "Anders B Nygaard", + "author_inst": "Oslo University Hospital" + }, + { + "author_name": "Jan Cato Holter", + "author_inst": "Oslo University Hospital" + }, + { + "author_name": "Prasan Kumar Panda", + "author_inst": "All India Institute of Medical Sciences" + }, + { + "author_name": "Waasila Jassat", + "author_inst": "South African National Institute for Communicable Diseases" + }, + { + "author_name": "Laura Merson", + "author_inst": "University of Oxford" + }, + { + "author_name": "Christl A. Donnelly", + "author_inst": "University of Oxford" + }, + { + "author_name": "Mauricio Santillana", + "author_inst": "Northeastern University" + }, + { + "author_name": "Caroline Buckee", + "author_inst": "Harvard School of Public Health" + }, + { + "author_name": "Stephane Verguet", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Nima S Hejazi", + "author_inst": "Harvard T.H. Chan School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2024.02.22.24303193", "rel_title": "Protection of natural infection against reinfection with SARS-CoV-2 JN.1 variant", @@ -10336,129 +11639,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2024.02.19.24302823", - "rel_title": "Real-world Effectiveness and Causal Mediation Study of BNT162b2 on Long COVID Risks in Children and Adolescents", - "rel_date": "2024-02-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.19.24302823", - "rel_abs": "BackgroundThe impact of pre-infection vaccination on the risk of long COVID remains unclear in the pediatric population. Further, it is unknown if such pre-infection vaccination can mitigate the risk of long COVID beyond its established protective benefits against SARS-CoV-2 infection.\n\nObjectiveTo assess the effectiveness of BNT162b2 on long COVID risks with various strains of the SARS-CoV-2 virus in children and adolescents, using comparative effectiveness methods. To disentangle the overall effectiveness of the vaccine on long COVID outcomes into its independent impact and indirect impact via prevention of SARS-CoV-2 infections, using causal mediation analysis.\n\nDesignReal-world vaccine effectiveness study and mediation analysis in three independent cohorts: adolescents (12 to 20 years) during the Delta phase, children (5 to 11 years) and adolescents (12 to 20 years) during the Omicron phase.\n\nSettingTwenty health systems in the RECOVER PCORnet electronic health record (EHR) Program.\n\nParticipants112,590 adolescents (88,811 vaccinated) in the Delta period, 188,894 children (101,277 vaccinated), and 84,735 adolescents (37,724 vaccinated) in the Omicron period.\n\nExposuresFirst dose of the BNT162b2 vaccine vs. no receipt of COVID-19 vaccine.\n\nMeasurementsOutcomes of interest include conclusive or probable diagnosis of long COVID following a documented SARS-CoV-2 infection, and body-system-specific condition clusters of post-acute sequelae of SARS-CoV-2 infection (PASC), such as cardiac, gastrointestinal, musculoskeletal, respiratory, and syndromic categories. The effectiveness was reported as (1-relative risk)*100 and mediating effects were reported as relative risks.\n\nResultsDuring the Delta period, the estimated effectiveness of the BNT162b2 vaccine against long COVID among adolescents was 95.4% (95% CI: 90.9% to 97.7%). During the Omicron phase, the estimated effectiveness against long COVID among children was 60.2% (95% CI: 40.3% to 73.5%) and 75.1% (95% CI: 50.4% to 87.5%) among adolescents. The direct effect of vaccination, defined as the effect beyond their impact on SARS-CoV-2 infections, was found to be statistically non-significant in all three study cohorts, with estimates of 1.08 (95% CI: 0.75 to 1.55) in the Delta study among adolescents, 1.24 (95% CI: 0.92 to 1.66) among children and 0.91 (95% CI: 0.69 to 1.19) among adolescents in the Omicron studies. Meanwhile, the estimated indirect effects, which are effects through protecting SARS-CoV-2 infections, were estimated as 0.04 (95% CI: 0.03 to 0.05) among adolescents during Delta phase, 0.31 (95% CI: 0.23 to 0.42) among children and 0.21 (95% CI: 0.16 to 0.27) among adolescents during the Omicron period.\n\nLimitationsObservational study design and potentially undocumented infection.\n\nConclusionsOur study suggests that BNT162b2 was effective in reducing risk of long COVID outcomes in children and adolescents during the Delta and Omicron periods. The mediation analysis indicates the vaccines effectiveness is primarily derived from its role in reducing the risk of SARS-CoV-2 infection.\n\nPrimary Funding SourceNational Institutes of Health.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Qiong Wu", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Bingyu Zhang", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Jiayi Tong", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "L. Charles Bailey", - "author_inst": "The Children's Hospital of Philadelphia" - }, - { - "author_name": "H. Timothy Bunnell", - "author_inst": "Nemours Children's Hospital" - }, - { - "author_name": "Jiajie Chen", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Elizabeth A. Chrischilles", - "author_inst": "University of Iowa" - }, - { - "author_name": "Dimitri A. Christakis", - "author_inst": "Seattle Children's Research Institute" - }, - { - "author_name": "Stephen M. Downs", - "author_inst": "Atrium Health Wake Forest Baptist" - }, - { - "author_name": "Kathryn Hirabayashi", - "author_inst": "Children's Hospital of Philadelphia" - }, - { - "author_name": "Ravi Jhaveri", - "author_inst": "Ann & Robert H. Lurie Children's Hospital of Chicago" - }, - { - "author_name": "Aaron D. Mishkin", - "author_inst": "Lewis Katz School of Medicine at Temple University" - }, - { - "author_name": "Abu S. M. Mosa", - "author_inst": "University of Missouri School of Medicine" - }, - { - "author_name": "Nathan M Pajor", - "author_inst": "Cincinnati Children's Hospital Medical Center" - }, - { - "author_name": "Suchitra Rao", - "author_inst": "University of Colorado School of Medicine" - }, - { - "author_name": "Hanieh Razzaghi", - "author_inst": "Children's Hospital of Philadelphia" - }, - { - "author_name": "Hayden T. Schwenk", - "author_inst": "Stanford School of Medicine" - }, - { - "author_name": "Marion R. Sills", - "author_inst": "University of Colorado School of Medicine" - }, - { - "author_name": "Huiyuan Wang", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Linbo Wang", - "author_inst": "University of Toronto" - }, - { - "author_name": "Yudong Wang", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Dazheng Zhang", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Ting Zhou", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Eric J. Tchetgen Tchetgen", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Jeffrey S. Morris", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Christopher B. Forrest", - "author_inst": "The Children's Hospital of Philadelphia" - }, - { - "author_name": "Yong Chen", - "author_inst": "University of Pennsylvania" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2024.02.17.24302708", "rel_title": "Private sector tuberculosis care quality during the COVID-19 pandemic: A repeated cross-sectional standardized patients study of adherence to national TB guidelines in urban Nigeria", @@ -11591,6 +12771,89 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2024.02.14.24302768", + "rel_title": "Differential associations between SARS-CoV-2 infection, perceived burden of the pandemic and mental health in the German population-based cohort for digital health research", + "rel_date": "2024-02-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.14.24302768", + "rel_abs": "IntroductionUnderstanding the potential adverse effects of the Covid-19-pandemic remains a challenge for public mental health. In this regard, the differentiation between potential consequences of actual infection with SARS-CoV-2 and the subjective burden of the pandemic due to measures and restrictions to daily life remains elusive.\n\nMethodsHere we investigated the differential association between infection with SARS-Cov-2 and subjective burden of the pandemic in a study cohort of 7601 participants from the German population-based cohort for digital health research (DigiHero), who were recruited between March 4th and April 25th 2022. Data was collected using the online survey tool LimeSurvey(R) between March and October 2022 in consecutive surveys, which included questionnaires on infection status and symptoms following COVID-19 as well as retrospective assessment of the subjective burden of the pandemic.\n\nResultsWe observed an association of a past SARS-CoV-2 infection on deteriorated mental health related symptoms, whereas no association or interaction with burden of the pandemic occurred. The association was driven by participants with persistent symptoms 12 weeks after acute infection. On a symptom specific level, neuropsychiatric symptoms such as exhaustion and fatigue, concentration deficits as well as problems with memory function were the primary drivers of the association.\n\nConclusionOur findings underscore the impact of SARS-CoV-2 infections on mental health in patients suffering from ongoing symptoms 12 weeks after infection. As the association between SARS-CoV-2 infection and mental health appeared more pronounced in populations with higher vulnerability for mental disorders, increased attention should be dedicated towards these subgroups regarding the prevention of infection.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Lavinia A. Steinmann", + "author_inst": "Department of Psychiatry and Psychotherapy, Jena University Hospital, Jena, Germany" + }, + { + "author_name": "Luise V. Claass", + "author_inst": "Department of Psychiatry and Psychotherapy, Jena University Hospital, Jena, Germany" + }, + { + "author_name": "Moritz Rau", + "author_inst": "Department of Psychiatry and Psychotherapy, Jena University Hospital, Jena, Germany" + }, + { + "author_name": "Janka Massag", + "author_inst": "Institute for Medical Epidemiology, Biometry and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther Univers" + }, + { + "author_name": "Sophie Diexer", + "author_inst": "Institute for Medical Epidemiology, Biometry and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther Univers" + }, + { + "author_name": "Bianca Klee", + "author_inst": "Institute for Medical Epidemiology, Biometry and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther Univers" + }, + { + "author_name": "Cornelia Gottschick", + "author_inst": "Institute for Medical Epidemiology, Biometry and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther Univers" + }, + { + "author_name": "Mascha Binder", + "author_inst": "Department of Internal Medicine IV, Oncology/Haematology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany" + }, + { + "author_name": "Daniel Sedding", + "author_inst": "Mid-German Heart Centre, Department of Cardiology and Intensive Care Medicine, University Hospital, Martin Luther University Halle-Wittenberg, Halle (Saale), Ge" + }, + { + "author_name": "Thomas Frese", + "author_inst": "Institute of General Practice and Family Medicine, Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther University Halle-Wittenber" + }, + { + "author_name": "Matthias Girndt", + "author_inst": "Department of Internal Medicine II, Martin Luther University Halle-Wittenberg, Germany" + }, + { + "author_name": "Jessica Hoell", + "author_inst": "Paediatric Haematology and Oncology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany" + }, + { + "author_name": "Irene Moor", + "author_inst": "Institute for Medical Sociology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany" + }, + { + "author_name": "Jonas Rosendahl", + "author_inst": "Department of Internal Medicine I, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany" + }, + { + "author_name": "Michael Gekle", + "author_inst": "Julius-Bernstein-Institute of Physiology, Medical Faculty of the Martin Luther University Halle-Wittenberg, Halle (Saale), Germany" + }, + { + "author_name": "Rafael Mikolajczyk", + "author_inst": "Institute for Medical Epidemiology, Biometry and Informatics (IMEBI), Interdisciplinary Centre for Health Sciences, Medical Faculty of the Martin Luther Univers" + }, + { + "author_name": "Nils Opel", + "author_inst": "Department of Psychiatry and Psychotherapy, Jena University Hospital, Jena, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2024.02.14.24302808", "rel_title": "COVID-19 VACCINATION-INFECTION STATUS AND IMMUNOLOGICAL PROFILE: IDENTIFICATION OF HIGH RISK POPULATION FOR TARGETED BOOSTER IMMUNIZATION IN INDIA", @@ -12134,69 +13397,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2024.02.13.24302781", - "rel_title": "Characteristics and Determinants of Pulmonary Long COVID", - "rel_date": "2024-02-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.13.24302781", - "rel_abs": "RATIONALEPersistent cough and dyspnea are prominent features of post-acute sequelae of SARS-CoV-2 (termed Long COVID); however, physiologic measures and clinical features associated with these pulmonary symptoms remain poorly defined.\n\nOBJECTIVESUsing longitudinal pulmonary function testing (PFTs) and CT imaging, this study aimed to identify the characteristics and determinants of pulmonary Long COVID.\n\nMETHODSThe University of Alabama at Birmingham Pulmonary Long COVID cohort was utilized to characterize lung defects in patients with persistent pulmonary symptoms after resolution primary COVID infection. Longitudinal PFTs including total lung capacity (TLC) and diffusion limitation of carbon monoxide (DLCO) were used to evaluate restriction and diffusion impairment over time in this cohort. Analysis of chest CT imaging was used to phenotype the pulmonary Long COVID pathology. Risk factors linked to development of pulmonary Long COVID were estimated using univariate and multivariate logistic regression models.\n\nMEASUREMENTS AND MAIN RESULTSLongitudinal evaluation 929 patients with post-COVID pulmonary symptoms revealed diffusion impairment (DLCO [≤]80%) and restriction (TLC [≤]80%) in 51% of the cohort (n=479). In multivariable logistic regression analysis (adjusted odds ratio; aOR, 95% confidence interval [CI]), invasive mechanical ventilation during primary infection conferred the greatest increased odds of developing pulmonary Long COVID with diffusion impaired restriction (aOR=10.9 [4.09-28.6]). Finally, a sub-analysis of CT imaging identified evidence of fibrosis in this population.\n\nCONCLUSIONSPersistent diffusion impaired restriction was identified as a key feature of pulmonary Long COVID. Subsequent clinical trials should leverage combined symptomatic and quantitative PFT measurements for more targeted enrollment of pulmonary Long COVID patients.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Michael John Patton", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Donald Benson", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Sarah W. Robison", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Raval Dhaval", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Morgan L. Locy", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Kinner Patel", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Scott Grumley", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Emily B. Levitan", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Peter Morris", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Matthew Might", - "author_inst": "University of Alabama At Birmingham" - }, - { - "author_name": "Amit Gaggar", - "author_inst": "University of Alabama at Birmingham" - }, - { - "author_name": "Nathaniel Erdmann", - "author_inst": "University of Alabama at Birmingham" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2024.02.11.24302530", "rel_title": "Phase II/III Double-Blind Study Evaluating Safety and Immunogenicity of a Single Intramuscular Booster Dose of the Recombinant SARS-CoV-2 Vaccine \"Patria\" (AVX/COVID-12) Using an Active Newcastle Disease Viral Vector (NDV) during the Omicron Outbreak in Healthy Adults with Elevated Baseline Antibody Titers from Prior COVID-19 and/or SARS-CoV-2 Vaccination", @@ -13609,6 +14809,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2024.02.08.24302520", + "rel_title": "Genome-wide association study reveals different T cell distributions in peripheral blood of healthy individuals at high genetic risk of type 1 diabetes and long COVID", + "rel_date": "2024-02-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.08.24302520", + "rel_abs": "The immune system plays a crucial role in many human diseases. In this context, genome-wide association studies (GWAS) offer valuable insights to elucidate the role of immunity in health and disease. The present multi-omics study aimed to identify genetic determinants of immune cell type distributions in the blood of healthy individuals and to assess whether the distributions of these cells may play a role for autoimmune and COVID-19 disease risk.\n\nTo this end, the frequencies of different immune cells in 483 healthy individuals from the Berlin Aging Study II were quantified using flow cytometry, and GWAS was performed for 92 immune cell phenotypes. Additionally, we performed linear regression analyses of immune cell distributions using polygenic risk scores (PRS) based on prior GWAS for five autoimmune diseases as well as for COVID-19 infection and post-COVID syndrome (\"long COVID\").\n\nWe validated seven previously described immune loci and identified 13 novel loci showing genome-wide significant (=5.00E-8) association with different immune cell phenotypes. The most significant novel signal was conferred by the SLC52A3 locus, encoding for a riboflavin transporter protein, which was associated with naive CD57+ CD8+ T cells (p=4.13E-17) and colocalized with SLC52A3 expression. Several novel loci contained immunologically plausible candidate genes, e.g., variants near TBATA and B3GAT1 representing genes associated with T cell phenotypes. The PRS of type 1 diabetes were significantly associated with CD8+ T cells at different differentiation states (p[≤]7.02E-4), and PRS of long COVID were associated with early-differentiated CD4+ T cells (p[≤]1.54E-4).\n\nIn conclusion, our extensive immune cell GWAS analyses highlight several novel genetic loci of likely relevance for immune system function. Furthermore, our PRS analyses point to a shared genetic basis between immune cell distributions in healthy adults and T1D (CD8+ T cells) as well as long COVID (CD4+ T cells).", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Laura Deecke", + "author_inst": "Institute of Epidemiology and Social Medicine, University of M\u00fcnster, M\u00fcnster, Germany" + }, + { + "author_name": "Jan Homann", + "author_inst": "Institute of Epidemiology and Social Medicine, University of M\u00fcnster, M\u00fcnster, Germany" + }, + { + "author_name": "David Goldeck", + "author_inst": "Department of Internal Medicine 2, University of T\u00fcbingen, T\u00fcbingen, Germany; Fairfax Centre, Kidlington, United Kingdom" + }, + { + "author_name": "Felix Luessi", + "author_inst": "Department of Neurology, Focus Program Translational Neuroscience (FTN), Rhine-Main Neuroscience Network (rmn2), University Medical Center of the Johannes Guten" + }, + { + "author_name": "Marijne Vandebergh", + "author_inst": "VIB Center for Molecular Neurology, University of Antwerp, 2610, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium; L" + }, + { + "author_name": "Olena Ohlei", + "author_inst": "L\u00fcbeck Interdisciplinary Platform for Genome Analytics (LIGA), University of L\u00fcbeck, L\u00fcbeck, Germany" + }, + { + "author_name": "Sarah Toepfer", + "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, Department of Endocrinology and Metabolic" + }, + { + "author_name": "Frauke Zipp", + "author_inst": "Department of Neurology, Focus Program Translational Neuroscience (FTN), Rhine-Main Neuroscience Network (rmn2), University Medical Center of the Johannes Guten" + }, + { + "author_name": "Ilja Demuth", + "author_inst": "Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin and Humboldt-Universit\u00e4t zu Berlin, Department of Endocrinology and Metabolic" + }, + { + "author_name": "Sarah L. Morgan", + "author_inst": "Department of Neuroscience, Sheffield Institute for Translational Neurosciences, University of Sheffield, Sheffield, UK" + }, + { + "author_name": "Lars Bertram", + "author_inst": "L\u00fcbeck Interdisciplinary Platform for Genome Analytics (LIGA), University of L\u00fcbeck, L\u00fcbeck, Germany" + }, + { + "author_name": "Graham Pawelec", + "author_inst": "Department of Immunology, University of T\u00fcbingen, T\u00fcbingen, Germany; Health Sciences North Research Institute of Canada, Sudbury, Ontario, Canada" + }, + { + "author_name": "Christina M. Lill", + "author_inst": "Institute of Epidemiology and Social Medicine, University of M\u00fcnster, M\u00fcnster, Germany; Ageing and Epidemiology Unit (AGE), School of Public Health, Imperial Co" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2024.02.09.579589", "rel_title": "SARS-COV-2 induces blood-brain barrier and choroid plexus barrier impairments and vascular inflammation in mice", @@ -14140,33 +15407,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2024.02.08.24302489", - "rel_title": "Impact of Shifting University Policies During the COVID-19 Pandemic on Self-Reported Employee Social Networks", - "rel_date": "2024-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.08.24302489", - "rel_abs": "ObjectivesTo ascertain if faculty and staff were the link between the two COVID-19 outbreaks in a rural university county, and if the local universitys COVID-19 policies affected contact rates of their employees across all its campuses.\n\nMethodsWe conducted two anonymous, voluntary online surveys for faculty and staff of a PAC-12 university on their contact patterns both within and outside the university during the COVID-19 pandemic. One was asked when classes were virtual, and another when classes were in-person but masking. Participants were asked about the individuals they encountered, the type and location of the interactions, what COVID-19 precautions were taken - if any, as well as general questions about their location and COVID-19.\n\nResultsWe received 271 responses from the first survey and 124 responses from the second. The first survey had a median of 3 contacts/respondent, with the second having 7 contacts/respondent (p<0.001). During the first survey, most contacts were family contacts (Spouse, Children), with the second survey period having Strangers and Students having the most contact (p<0.001). Over 50% of the first survey contacts happened at their home, while the second survey had 40% at work and 35% at home. Both respondents and contacts masked 42% and 46% of the time for the two surveys respectively (p<0.01).\n\nConclusionFor future pandemics, it would be wise to take employees into account when trying to plan for the safety of university students, employees, and surrounding communities. The main places to be aware of and potentially push infectious disease precautions would be on campus, especially confined spaces like offices or small classrooms, and the home, as these tend to be the largest areas of non-masked close contact.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Stephanie S Johnson", - "author_inst": "Washington State University" - }, - { - "author_name": "Katelin C. Jackson", - "author_inst": "Washington State University" - }, - { - "author_name": "Eric T Lofgren", - "author_inst": "Washington State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2024.02.08.24302486", "rel_title": "Bidirectional relationship between sleep problems and long COVID: a longitudinal analysis of data from the COVIDENCE UK study", @@ -15363,6 +16603,133 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2024.02.03.578771", + "rel_title": "XBB.1.5 monovalent booster improves antibody binding and neutralization against emerging SARS-CoV-2 Omicron variants", + "rel_date": "2024-02-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.02.03.578771", + "rel_abs": "The rapid emergence of divergent SARS-CoV-2 variants has led to an update of the COVID-19 booster vaccine to a monovalent version containing the XBB.1.5 spike. To determine the neutralization breadth following booster immunization, we collected blood samples from 24 individuals pre- and post-XBB.1.5 mRNA booster vaccination ([~]1 month). The XBB.1.5 booster improved both neutralizing activity against the ancestral SARS-CoV-2 strain (WA1) and the circulating Omicron variants, including EG.5.1, HK.3, HV.1, XBB.1.5 and JN.1. Relative to the pre-boost titers, the XBB.1.5 monovalent booster induced greater total IgG and IgG subclass binding, particular IgG4, to the XBB.1.5 spike as compared to the WA1 spike. We evaluated antigen-specific memory B cells (MBCs) using either spike or receptor binding domain (RBD) probes and found that the monovalent booster largely increases non-RBD cross-reactive MBCs. These data suggest that the XBB.1.5 monovalent booster induces cross-reactive antibodies that neutralize XBB.1.5 and related Omicron variants.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Shilpi Jain", + "author_inst": "Emory University" + }, + { + "author_name": "Sanjeev Kumar", + "author_inst": "Emory University" + }, + { + "author_name": "Lilin Lai", + "author_inst": "Emory University" + }, + { + "author_name": "Susanne Linderman", + "author_inst": "Emory University" + }, + { + "author_name": "Ansa A. Malik", + "author_inst": "Emory University" + }, + { + "author_name": "Madison L. Ellis", + "author_inst": "Emory University" + }, + { + "author_name": "Sucheta Godbole", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Daniel Solis", + "author_inst": "Stanford University" + }, + { + "author_name": "Malaya K. Sahoo", + "author_inst": "Stanford University" + }, + { + "author_name": "Kareem Bechnak", + "author_inst": "Emory University" + }, + { + "author_name": "Isabel Paredes", + "author_inst": "Emory University" + }, + { + "author_name": "Ralph Tanios", + "author_inst": "Emory University" + }, + { + "author_name": "Bahaa Kazzi", + "author_inst": "Emory University" + }, + { + "author_name": "Serena Maria Dib", + "author_inst": "Emory University" + }, + { + "author_name": "Matthew B. Litvack", + "author_inst": "Emory University" + }, + { + "author_name": "Sonia Tandon Wimalsena", + "author_inst": "Emory University" + }, + { + "author_name": "Carolina Ciric", + "author_inst": "Emory University" + }, + { + "author_name": "Christina Rostad", + "author_inst": "Emory University" + }, + { + "author_name": "Richard West", + "author_inst": "Emory University" + }, + { + "author_name": "I-Ting Teng", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Danyi Wang", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Peter D. Kwong", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Nadine Rouphael", + "author_inst": "Emory University" + }, + { + "author_name": "Benjamin A. Pinsky", + "author_inst": "Stanford University" + }, + { + "author_name": "Daniel C. Douek", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Jens Wrammert", + "author_inst": "Emory University" + }, + { + "author_name": "Alberto Moreno", + "author_inst": "Emory University" + }, + { + "author_name": "Mehul S Suthar", + "author_inst": "Emory University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2024.02.02.24302174", "rel_title": "Changes to an intensive care unit Acinetobacter baumannii population following COVID-19 disruptions and targeted infection prevention interventions.", @@ -15986,73 +17353,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2024.02.01.24302037", - "rel_title": "Treadmill Exercise Stress Echocardiography Exposes Impaired Left Ventricular Function in Patients Recovering from Hospitalization with COVID-19 Without Overt Myocarditis Versus Historical Controls", - "rel_date": "2024-02-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2024.02.01.24302037", - "rel_abs": "BackgroundUsual clinical testing rarely reveals cardiac abnormalities persisting after hospitalization for COVID-19. Such testing may overlook residual changes responsible for increased adverse cardiac events post-discharge.\n\nMethodsTo further elucidate long-term status, we performed exercise stress echocardiography (ESE) in 15 patients age 30-63 without myocarditis 3 to 31 months after hospital discharge. We compared patient outcomes to published data in healthy comparisons (HC) exercising according to the same protocol.\n\nResultsPatients treadmill exercise (Bruce protocol), averaging 8.2 min, was halted by dyspnea or fatigue. Pre-stress baselines in recovering patients (RP) matched HC except for higher heart rate: mean 81 bpm for RP and 63 for HC (p<0.0001). At peak stress, RP had significantly lower mean left ventricular (LV) ejection fraction (67% vs 73%, p<0.0017) and higher peak early mitral inflow velocity/early mitral annular velocity (E/e, 9.1 vs 6.6, p<0.006) compared with HC performing equal exercise (8.5 min). Thus, when stressed, patients without known cardiac impairment showed modest but consistently diminished systolic contractile function and diastolic LV compliance during recovery vs HC. Peak HR during stress was significantly elevated in RP vs HC; peak SBP also trended higher. Average pulmonary artery systolic pressures among RP remained normal.\n\nConclusionsOur measurements during ESE uniquely identified residual abnormality in cardiac contractile function not evident in the unstressed condition. This finding exposes a previously-unrecognized residual influence of COVID-19, possibly related to underlying autonomic dysfunction, microvascular disease, or diffuse interstitial changes after subclinical myocarditis; it may have long-term implications for clinical management and later prognosis.\n\nCLINICAL PERSPECTIVENew Findings (relative to a historical comparison group)\n\nO_LISymptom-limited treadmill exercise 3-31 months after hospitalization with COVID-19 without overt myocarditis elicited a lesser rise in left ventricular ejection fraction than seen in similar subjects with no exposure to COVID-19.\nC_LIO_LIThe same symptom-limited exercise in these patients revealed evidence of diminished left ventricular diastolic function relative to subjects with no exposure to COVID-19.\nC_LIO_LIThese distinctive differences in left ventricular function were observed although overall exercise capacity was the same as in the uninfected comparison group.\nC_LI\n\nClinical Implications\n\nO_LIPrior hospitalization with COVID-19 even in the absence of overt myocarditis was often associated with a modest but consistent decrement in left ventricular systolic contraction and diastolic relaxation; these functional abnormalities were evident after peak treadmill exercise stress despite lack of distinctive difference in contractile parameters at rest.\nC_LIO_LIPatients recovering after hospitalization with COVID-19 may benefit from sustained observation of their cardiovascular status and adjustment of their exercise requirements appropriate to individual cardiovascular capabilities.\nC_LIO_LITreadmill stress testing with echocardiography uniquely identifies potentially important differences in the cardiovascular function of patients recovering after hospitalization with COVID-19.\nC_LI", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Robert E. Goldstein", - "author_inst": "Uniformed Services University of the Health Sciences" - }, - { - "author_name": "Edward Hulten", - "author_inst": "US Army" - }, - { - "author_name": "Thomas B. Arnold", - "author_inst": "Uniformed Services University of the Health Sciences" - }, - { - "author_name": "Victoria M. Thomas", - "author_inst": "Uniformed Services University of the Health Sciences" - }, - { - "author_name": "Andrew Heroy", - "author_inst": "Uniformed Services University of the Health Sciences" - }, - { - "author_name": "Erika N. Walker", - "author_inst": "Walter Reed National Military Medical Center" - }, - { - "author_name": "Keiko Fox", - "author_inst": "Uniformed Services University of the Health Sciences" - }, - { - "author_name": "Hyun Lee", - "author_inst": "Uniformed Services University of the Health Sciences" - }, - { - "author_name": "Joya Libbus", - "author_inst": "Uniformed Services University of the Health Sciences" - }, - { - "author_name": "Bethelhem Marcos", - "author_inst": "Uniformed Services University of the Health Sciences" - }, - { - "author_name": "Maureen N Hood", - "author_inst": "Uniformed Services University of the Health Sciences" - }, - { - "author_name": "Travis E. Harrell", - "author_inst": "Walter Reed National Military Medical Center" - }, - { - "author_name": "Mark C. Haigney", - "author_inst": "Uniformed Services University of Health Sciences" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2024.01.31.24302105", "rel_title": "Socioeconomic correlates of urban mobility trends in two Australian cities during transitional periods of the COVID-19 pandemic", @@ -17429,6 +18729,29 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2024.01.29.577716", + "rel_title": "Mathematical model of replication-mutation dynamics in coronaviruses", + "rel_date": "2024-01-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.29.577716", + "rel_abs": "RNA viruses are known for their fascinating evolutionary dynamics, characterised by high mutation rates, fast replication, and ability to form quasispecies - clouds of genetically related mutants. Fast replication in RNA viruses is achieved by a very fast but error-prone RNA-dependent RNA polymerase (RdRP). High mutation rates are a double-edged sword: they provide RNA viruses with a mechanism of fast adaptation to a changing environment or host immune system, but at the same time they pose risk to virus survivability in terms of virus mutating beyond its error threshold. Coronaviruses, being a subset of RNA viruses, are unique in having a special enzyme, exoribonuclease (ExoN), responsible for proofreading and correcting errors induced by the RdRP. In this paper we consider replication dynamics of coronaviruses with account for mutations that can be neutral, deleterious or lethal, as well as ExoN. Special attention is paid to different virus replication modes that are known to be crucial for controlling the dynamics of virus populations. We analyse extinction, mutant-only and quasispecies steady states, and study their stability in terms of different parameters, identifying regimes of error catastrophe and lethal mutagenesis. With coronaviruses being responsible for some of the largest pandemics in the last twenty years, we also model the effects of antiviral treatment with various replication inhibitors and mutagenic drugs.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Konstantin B. Blyuss", + "author_inst": "University of Sussex" + }, + { + "author_name": "Yuliya N. Kyrychko", + "author_inst": "University of Sussex" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "systems biology" + }, { "rel_doi": "10.1101/2024.01.23.24301694", "rel_title": "Feasibility and preliminary efficacy of an online mindful walking intervention among COVID-19 long haulers: A mixed method study including daily diary surveys", @@ -17904,20 +19227,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2024.01.24.577015", - "rel_title": "Interferon-\u03b3 as a Potential Inhibitor of SARS-CoV-2 ORF6 Accessory Protein", - "rel_date": "2024-01-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.24.577015", - "rel_abs": "ORF6 protein of the SARS-CoV-2 virus plays a crucial role in blocking the innate immune response of the infected cells by inhibiting interferon pathways. Additionally, it binds and immobilises the RAE1 protein onto the cytoplasmic membranes, thereby blocking the transport of mRNA from the nucleus to the cytoplasm. In all these cases the host cell proteins are tethered by the flexible C-terminus of ORF6. A possible strategy to inhibit the biological activity of ORF6 is to bind its C-terminus with suitable ligands. Our in silico experiments suggest that hIFN{gamma} binds the ORF6 protein with high affinity, thus impairing its interactions with RAE1 and, consequently, its activity in viral invasion. The here reported in vitro studies reveal a shift of the localization of RAE1 in ORF6 overexpressing cells upon treatment with hIFN{gamma} from predominantly cytoplasmic to mainly nuclear, resulting in restoration of the export of mRNA from the nucleus. We also explored the expression of GFP in transfected with ORF6 cells by means of fluorescence microscopy and qRT-PCR, finding that treatment with hIFN{gamma} unblocks the mRNA trafficking and reinstates the GFP expression level. The ability of the cytokine to block ORF6 is also reflected in minimising its negative effects on DNA replication by reducing accumulated RNA-DNA hybrids. Our results, therefore, suggest hIFN{gamma} as a promising inhibitor of the most toxic SARS-CoV-2 protein.", - "rel_num_authors": 0, - "rel_authors": null, - "version": "1", - "license": "", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2024.01.24.576385", "rel_title": "Investigating Sensitivity, Specificity and Accuracy of Variant Calling Pipelines for Analyzing SARS-CoV-2 Data", @@ -19265,6 +20574,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2024.01.21.576083", + "rel_title": "Cytoarchitecture of SARS-CoV-2 infected hamster lungs by X-ray phase contrast tomography: imaging workflow and classification for drug testing", + "rel_date": "2024-01-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.21.576083", + "rel_abs": "X-ray Phase Contrast Tomography (XPCT) based on wavefield propagation has been established as a high resolution three-dimensional (3D) imaging modality, suitable to reconstruct the intricate structure of soft tissues, and the corresponding pathological alterations. However, for biomedical research, more is needed than 3D visualisation and rendering of the cytoarchitecture in a few selected cases. First, the throughput needs to be increased to cover a statistically relevant number of samples. Second, the cytoarchitecture has to be quantified in terms of morphometric parameters, independent of visual impression. Third, dimensionality reduction and classification are required for identification of effects and interpretation of results. In this work, we present a workflow implemented at a laboratory CT setup, using semi-automated data acquisition, reconstruction and statistical quantification of lung tissue in an early screen of Covid-19 drug candidates. Different drugs were tested in a hamster model after SARS-CoV-2 infection. To make full use of the recorded high-throughput XPCT data, we then used morphometric parameter determination followed by a dimensionality reduction and classification based on optimal transport. This approach allows efficient discrimination between physiological and pathological lung structure, thereby providing invaluable insights into the pathological progression and partial recovery due to drug treatment.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Jakob Reichmann", + "author_inst": "University of Goettingen" + }, + { + "author_name": "Clement Sarrazin", + "author_inst": "University of Goettingen" + }, + { + "author_name": "Sebastian Schmale", + "author_inst": "University of Goettingen" + }, + { + "author_name": "Claudia Blaurock", + "author_inst": "Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health" + }, + { + "author_name": "Anne Balkema-Buschmann", + "author_inst": "Friedrich-Loeffler-Institute" + }, + { + "author_name": "Bernhard Schmitzer", + "author_inst": "University of Goettingen" + }, + { + "author_name": "Tim Salditt", + "author_inst": "University of Goettingen" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2024.01.18.24301464", "rel_title": "Deaths induced by compassionate use of hydroxychloroquine during the first COVID-19 wave: the devil is in the details.", @@ -19744,193 +21096,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2024.01.16.24301337", - "rel_title": "Antiviral efficacy of fluoxetine in early symptomatic COVID-19: an open-label, randomised, controlled, adaptive platform trial (PLATCOV)", - "rel_date": "2024-01-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2024.01.16.24301337", - "rel_abs": "BackgroundThe selective serotonin reuptake inhibitors (SSRIs) fluoxetine and fluvoxamine were repurposed for the treatment of early COVID-19 based on their antiviral activity in vitro, and observational and clinical trial evidence suggesting they prevented progression to severe disease. However, these SSRIs have not been recommended in guidelines and their antiviral activity in vivo has not been characterised.\n\nMethodsPLATCOV is an open-label, multicentre, phase 2, randomised, controlled, adaptive pharmacometric platform trial running in Thailand, Brazil, Pakistan, and Laos. We recruited low-risk adult outpatients aged 18-50 with early symptomatic COVID-19 (symptoms <4 days). Patients were assigned using block randomisation to one of eleven treatment arms including oral fluoxetine (40mg/day for 7 days), or no study drug. Uniform randomisation ratios were applied across the active treatment groups while the no study drug group comprised [≥]20% of patients at all times.\n\nThe primary endpoint was the rate of oropharyngeal viral clearance assessed in a modified intention-to-treat population (>2 days follow-up). The viral clearance rate was estimated under a Bayesian hierarchical linear model fitted to the log10 viral densities in standardised duplicate oropharyngeal swab eluates taken daily over one week (18 measurements per patient). This ongoing trial is registered at ClinicalTrials.gov (NCT05041907).\n\nFindingsBetween 5 April 2022 and 8 May 2023 271 patients were concurrently randomised to either fluoxetine (n=120) or no study drug (n=151). Fluoxetine was well tolerated and accelerated the rate of viral clearance relative to the no study drug arm by 15% (95% credible interval (CrI): 2% to 34%). In a pooled meta-analysis including all unblinded patients the antiviral activity of fluoxetine was substantially less than ritonavir-boosted nirmatrelvir-85% increase in rate of viral clearance (95% CrI: 61 to 112%); and less than remdesivir 35% (14 to 59%), molnupiravir 37% (18 to 60%), and casirivimab/imdevimab 29% (10 to 48%).\n\nInterpretationFluoxetine has in vivo antiviral activity against SARS-CoV-2. Although the level of antiviral efficacy is substantially less than with other currently available antiviral drugs, fluoxetine might still be useful in prophylaxis where less antiviral effect is required.\n\nFundingWellcome Trust Grant ref: 223195/Z/21/Z through the COVID-19 Therapeutics Accelerator.\n\nEvidence before this studyThe SSRIs fluoxetine and fluvoxamine have been proposed as COVID-19 therapeutics based initially on observational, randomised trial and in vitro evidence. The observational reports suggested that patients taking SSRIs had a reduced probability of developing severe COVID-19 and dying. We searched PubMed and EMBASE for studies in English up until the 30th November 2023 using the search terms \"fluoxetine\", \"fluvoxamine\" and \"COVID-19\" with the search restricted to randomised controlled trials (RCTs). Eight outpatient fluvoxamine RCTs were identified. There were no fluoxetine RCTs in outpatients. A meta-analysis of available RCTs is compatible with a moderate reduction in hospitalisation and death in COVID-19 patients with an estimated risk ratio of 0.80 (95% CI: 0.62,1.01).\n\nAdded value of the studyWe showed that in early COVID-19 illness the SSRI fluoxetine has weak antiviral activity in vivo. This activity is substantially less than other available antivirals such as ritonavir-boosted nirmatrelvir and molnupiravir. The pharmacometric approach described here provides a quantitative measure of in vivo antiviral effects with tractable sample sizes.\n\nImplications of available evidenceFluoxetine has weak in vivo antiviral activity in early COVID-19. This is insufficient for treatment but, as less antiviral activity is required to prevent an infection, fluoxetine could still be beneficial in prophylaxis.", - "rel_num_authors": 43, - "rel_authors": [ - { - "author_name": "Podjanee Jittamala", - "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Simon Boyd", - "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "William Henry Keith Schilling", - "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "James Andrew Watson", - "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam" - }, - { - "author_name": "Thundon Ngamprasertchai", - "author_inst": "Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Tanaya Siripoon", - "author_inst": "Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Viravarn Luvira", - "author_inst": "Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Elizabeth M Batty", - "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Phrutsamon Wongnak", - "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Lisia M Esper", - "author_inst": "Clinical Research Unit, Center for Advanced and Innovative Therapies, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil" - }, - { - "author_name": "Pedro J Almeida", - "author_inst": "Clinical Research Unit, Center for Advanced and Innovative Therapies, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil" - }, - { - "author_name": "Cintia Cruz", - "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Fernando R Ascencao", - "author_inst": "Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil" - }, - { - "author_name": "Renato S Aguiar", - "author_inst": "Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil" - }, - { - "author_name": "Najia K Ghanchi", - "author_inst": "Aga Khan University, Karachi, Pakistan" - }, - { - "author_name": "James J Callery", - "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Shivani Singh", - "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Varaporn Kruabkontho", - "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Thatsanun Ngernseng", - "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Jaruwan Tubprasert", - "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Wanassanan Madmanee", - "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Kanokon Suwannasin", - "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Amornrat Promsongsil", - "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Borimas Hanboonkunupakarn", - "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Kittiyod Poovorawan", - "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Manus Potaporn", - "author_inst": "Department of Medical Services, Ministry of Public Health, Bangkok, Thailand" - }, - { - "author_name": "Attasit Srisubat", - "author_inst": "Department of Medical Services, Ministry of Public Health, Bangkok, Thailand" - }, - { - "author_name": "Bootsakorn Loharjun", - "author_inst": "Department of Medical Services, Ministry of Public Health, Bangkok, Thailand" - }, - { - "author_name": "Walter RJ Taylor", - "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Farah N Qamar", - "author_inst": "Aga Khan University, Karachi, Pakistan" - }, - { - "author_name": "Abdul Momin Kazi", - "author_inst": "Aga Khan University, Karachi, Pakistan" - }, - { - "author_name": "M Asim Beg", - "author_inst": "Aga Khan University, Karachi, Pakistan" - }, - { - "author_name": "Danoy Chommanam", - "author_inst": "Laos-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos P.D.R." - }, - { - "author_name": "Sisouphanh Vidhamaly", - "author_inst": "Pulmonology Department, Mahosot Hospital, Vientiane, Laos P.D.R." - }, - { - "author_name": "Kesinee Chotivanich", - "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Mallika Imwong", - "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Sasithon Pukrittayakamee", - "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Arjen M Dondorp", - "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Nicholas PJ Day", - "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Mauro M Teixeira", - "author_inst": "Clinical Research Unit, Center for Advanced and Innovative Therapies, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil" - }, - { - "author_name": "Watcharapong Piyaphanee", - "author_inst": "Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Weerapong Phumratanaprapin", - "author_inst": "Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Nicholas J White", - "author_inst": "Mahidol Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2024.01.17.24301374", "rel_title": "Altered IgG4 Antibody Response to Repeated mRNA versus Protein COVID Vaccines", @@ -21123,6 +22288,77 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2024.01.12.575122", + "rel_title": "mRNA-LNP COVID-19 vaccine lipids induce low level complement activation and production of proinflammatory cytokines: Mechanisms, effects of complement inhibitors, and relevance to adverse reactions", + "rel_date": "2024-01-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.12.575122", + "rel_abs": "Messenger RNA-containing lipid nanoparticles (mRNA-LNPs) enabled widespread COVID-19 vaccination with a small fraction of vaccine recipients displaying acute or sub-acute inflammatory symptoms. The molecular mechanism of these adverse events (AEs) remains undetermined. Here we report that the mRNA-LNP vaccine, Comirnaty, triggers low-level complement (C) activation and production of inflammatory cytokines, which may be key underlying processes of inflammatory AEs. In serum, Comirnaty and the control PEGylated liposome (Doxebo) caused different rises of C split products, C5a, sC5b-9, Bb and C4d, indicating stimulation of the classical pathway of C activation mainly by the liposomes, while a stronger stimulation of the alternative pathway was equal with the vaccine and the liposomes. Spikevax had similar C activation as Comirnaty, but viral or synthetic mRNAs had no such effect. In autologous serum-supplemented peripheral blood mononuclear cell (PBMC) cultures, Comirnaty caused increases in the levels of sC5b-9 and proinflammatory cytokines in the following order: IL-1 < IFN-{gamma} < IL-1{beta} < TNF- < IL-6 < IL-8, whereas heatinactivation of serum prevented the rises of IL-1, IL-1{beta}, and TNF-. Clinical C inhibitors, Soliris and Berinert, suppressed vaccine-induced C activation in serum but did not affect cytokine production when applied individually. These findings suggest that the PEGylated lipid coating of mRNA-LNP nanoparticles can trigger C activation mainly via the alternative pathway, which may be causally related to the induction of some, but not all inflammatory cytokines. While innate immune stimulation is essential for the vaccines efficacy, concurrent production of C- and PBMC-derived inflammatory mediators may contribute to some of the AEs. Pharmacological attenuation of harmful cytokine production using C inhibitors likely requires blocking the C cascade at multiple points.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Tamas Bakos", + "author_inst": "Nanomedicine Research and Education Center, Department of Translational Medicine, Semmelweis University, Budapest, Hungary" + }, + { + "author_name": "Tamas Meszaros", + "author_inst": "Nanomedicine Research and Education Center, Department of Translational Medicine, Semmelweis University, Budapest, Hungary" + }, + { + "author_name": "Gergely T. Kozma", + "author_inst": "Nanomedicine Research and Education Center, Department of Translational Medicine, Semmelweis University, Budapest, Hungary" + }, + { + "author_name": "Petra Berenyi", + "author_inst": "Nanomedicine Research and Education Center, Department of Translational Medicine, Semmelweis University, Budapest, Hungary" + }, + { + "author_name": "Reka Facsko", + "author_inst": "Nanomedicine Research and Education Center, Department of Translational Medicine, Semmelweis University, Budapest, Hungary" + }, + { + "author_name": "Henriette Farkas", + "author_inst": "Hungarian Center of Reference and Excellence, Department of Internal Medicine and Hematology, Semmelweis University, Budapest, Hungary" + }, + { + "author_name": "Laszlo Dezsi", + "author_inst": "Nanomedicine Research and Education Center, Department of Translational Medicine, Semmelweis University, Budapest, Hungary" + }, + { + "author_name": "Carlo Heirman", + "author_inst": "Etherna Biopharmaceuticals, Niel, Belgium" + }, + { + "author_name": "Stefaan de Koker", + "author_inst": "Etherna Biopharmaceuticals, Niel, Belgium" + }, + { + "author_name": "Raymond Schiffelers", + "author_inst": "Division of Laboratories and Pharmacy, University Medical Center Utrecht, Germany" + }, + { + "author_name": "Kathryn Anne Glatter", + "author_inst": "Gratz College, Philadelphia, PA, USA" + }, + { + "author_name": "Tamas Radovits", + "author_inst": "Heart and Vascular Center, Semmelweis University, Budapest, Hungary" + }, + { + "author_name": "Gabor Szenasi", + "author_inst": "Department of Translational Medicine, Semmelweis University, Budapest, Hungary" + }, + { + "author_name": "Janos Szebeni", + "author_inst": "Nanomedicine Research and Education Center, Department of Translational Medicine, Semmelweis University, Budapest, Hungary" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2024.01.11.575201", "rel_title": "The relationship between gut and nasopharyngeal microbiome composition can predict the severity of COVID-19", @@ -21966,57 +23202,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2024.01.10.575114", - "rel_title": "SARS-CoV-2 papain-like protease activates nociceptors to drive sneeze and pain", - "rel_date": "2024-01-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.10.575114", - "rel_abs": "SARS-CoV-2, the virus responsible for COVID-19, triggers symptoms such as sneezing, aches and pain.1 These symptoms are mediated by a subset of sensory neurons, known as nociceptors, that detect noxious stimuli, densely innervate the airway epithelium, and interact with airway resident epithelial and immune cells.2-6 However, the mechanisms by which viral infection activates these neurons to trigger pain and airway reflexes are unknown. Here, we show that the coronavirus papain-like protease (PLpro) directly activates airway-innervating trigeminal and vagal nociceptors in mice and human iPSC-derived nociceptors. PLpro elicits sneezing and acute pain in mice and triggers the release of neuropeptide calcitonin gene-related peptide (CGRP) from airway afferents. We find that PLpro-induced sneeze and pain requires the host TRPA1 ion channel that has been previously demonstrated to mediate pain, cough, and airway inflammation.7-9 Our findings are the first demonstration of a viral product that directly activates sensory neurons to trigger pain and airway reflexes and highlight a new role for PLpro and nociceptors in COVID-19.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Sonali S Mali", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Ricardo Silva", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Zhongyan Gong", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Michael Cronce", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Uyen Vo", - "author_inst": "HHMI/UC Berkeley" - }, - { - "author_name": "Cliff Vuong", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Yalda Moayedi", - "author_inst": "New York University College of Dentistry" - }, - { - "author_name": "Jeffery S Cox", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Diana M Bautista", - "author_inst": "HHMI/University of California, Berkeley" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "neuroscience" - }, { "rel_doi": "10.1101/2024.01.11.575161", "rel_title": "APNet, an explainable sparse deep learning model to discover differentially active drivers of severe COVID-19", @@ -23361,6 +24546,77 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2024.01.05.574280", + "rel_title": "Innate Immune Activation and Mitochondrial ROS Invoke Persistent Cardiac Conduction System Dysfunction after COVID-19", + "rel_date": "2024-01-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.05.574280", + "rel_abs": "BackgroundCardiac risk rises during acute SARS-CoV-2 infection and in long COVID syndrome in humans, but the mechanisms behind COVID-19-linked arrhythmias are unknown. This study explores the acute and long term effects of SARS-CoV-2 on the cardiac conduction system (CCS) in a hamster model of COVID-19.\n\nMethodsRadiotelemetry in conscious animals was used to non-invasively record electrocardiograms and subpleural pressures after intranasal SARS-CoV-2 infection. Cardiac cytokines, interferon-stimulated gene expression, and macrophage infiltration of the CCS, were assessed at 4 days and 4 weeks post-infection. A double-stranded RNA mimetic, polyinosinic:polycytidylic acid (PIC), was used in vivo and in vitro to activate viral pattern recognition receptors in the absence of SARS-CoV-2 infection.\n\nResultsCOVID-19 induced pronounced tachypnea and severe cardiac conduction system (CCS) dysfunction, spanning from bradycardia to persistent atrioventricular block, although no viral protein expression was detected in the heart. Arrhythmias developed rapidly, partially reversed, and then redeveloped after the pulmonary infection was resolved, indicating persistent CCS injury. Increased cardiac cytokines, interferon-stimulated gene expression, and macrophage remodeling in the CCS accompanied the electrophysiological abnormalities. Interestingly, the arrhythmia phenotype was reproduced by cardiac injection of PIC in the absence of virus, indicating that innate immune activation was sufficient to drive the response. PIC also strongly induced cytokine secretion and robust interferon signaling in hearts, human iPSC-derived cardiomyocytes (hiPSC-CMs), and engineered heart tissues, accompanied by alterations in electrical and Ca2+ handling properties. Importantly, the pulmonary and cardiac effects of COVID-19 were blunted by in vivo inhibition of JAK/STAT signaling or by a mitochondrially-targeted antioxidant.\n\nConclusionsThe findings indicate that long term dysfunction and immune cell remodeling of the CCS is induced by COVID-19, arising indirectly from oxidative stress and excessive activation of cardiac innate immune responses during infection, with implications for long COVID Syndrome.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Deepthi Ashok", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Ting Liu", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Joseph Criscione", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Meghana Prakash", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Byunggik Kim", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Julian Chow", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Morgan Craney", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Kyriakos Papanicolaou", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Agnieszka Sidor", + "author_inst": "The Johns Hopkins University School of Medicine" + }, + { + "author_name": "D. Brian Foster", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Andrew Pekosz", + "author_inst": "Johns Hopkins School of Public Health" + }, + { + "author_name": "Jason Villano", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Deok-Ho Kim", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Brian O'Rourke", + "author_inst": "Johns Hopkins University School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2024.01.06.574128", "rel_title": "GENOMIC PROFILING OF SARS-COV-2 STRAINS CIRCULATING IN SOUTH EASTERN REGION OF INDIA DURING THREE WAVES OF PANDEMIC", @@ -23948,49 +25204,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2024.01.04.574272", - "rel_title": "Antigen-display exosomes provide adjuvant-free protection against SARS-CoV-2 disease at nanogram levels of spike protein", - "rel_date": "2024-01-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2024.01.04.574272", - "rel_abs": "As the only bionormal nanovesicle, exosomes have high potential as a nanovesicle for delivering vaccines and therapeutics. We show here that the loading of type-1 membrane proteins into the exosome membrane is induced by exosome membrane anchor domains, EMADs, that maximize protein delivery to the plasma membrane, minimize protein sorting to other compartments, and direct proteins into exosome membranes. Using SARS-CoV-2 spike as an example and EMAD13 as our most effective exosome membrane anchor, we show that cells expressing a spike-EMAD13 fusion protein produced exosomes that carry dense arrays of spike trimers on 50% of all exosomes. Moreover, we find that immunization with spike-EMAD13 exosomes induced strong neutralizing antibody responses and protected hamsters against SARS-CoV-2 disease at doses of just 0.5-5 ng of spike protein, without adjuvant, demonstrating that antigen-display exosomes are particularly immunogenic, with important implications for both structural and expression-dependent vaccines.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Chenxu Guo", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Jaiprasath Sachithanandham", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "William Zhong", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Morgan Craney", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Jason Villano", - "author_inst": "Johns Hopkins School of Medicine" - }, - { - "author_name": "Andrew Pekosz", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Stephen Gould", - "author_inst": "Johns Hopkins University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2024.01.04.24300847", "rel_title": "Time to publication in medical education journals: An analysis of publication timelines during COVID-19 (2019-2022)", @@ -25131,6 +26344,89 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.12.30.573713", + "rel_title": "Major role of S-glycoprotein in providing immunogenicity and protective immunity in mRNA lipid nanoparticle vaccines based on SARS-CoV-2 structural proteins", + "rel_date": "2024-01-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.12.30.573713", + "rel_abs": "Recently we have developed an mRNA lipid nanoparticle (mRNA-LNP) platform providing efficient long-term expression of an encoded gene in vivo after both intramuscular and intravenous application. Based on this platform, we have generated mRNA-LNP coding SARS-CoV-2 structural proteins M, N, S from different virus variants and studied their immunogenicity separately or in combinations in vivo. As a result, all candidate vaccine compositions coding S and N proteins induced excellent anti-RBD and N titers of binding antibodies. T cell responses mainly represented specific CD4+ T cell lymphocyte producing IL-2 and TNF-. mRNA-LNP coding M protein did not show high immunogenicity. High neutralizing activity was detected in sera of mice vaccinated with mRNA-LNP coding S protein (alone or in combinations) against closely related strains but was not detectable or significantly lower against an evolutionarily distant variant. Our data showed that the addition of mRNAs encoding S and M antigens to the mRNA-N in the vaccine composition enhanced immunogenicity of mRNA-N inducing more robust immune response to the N protein. Based on our results, we suggested that the S protein plays a key role in enhancement of immune response to the N protein in the mRNA-LNP vaccine.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Evgeniia N. Bykonia", + "author_inst": "National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya of the Ministry of Health of the Russian Federation, Mo" + }, + { + "author_name": "Denis A Kleymenov", + "author_inst": "National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya of the Ministry of Health of the Russian Federation, Mo" + }, + { + "author_name": "Vladimir A. Gushchin", + "author_inst": "National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya of the Ministry of Health of the Russian Federation, Mo" + }, + { + "author_name": "Andrey E. Sinyavin", + "author_inst": "National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya of the Ministry of Health of the Russian Federation, Mo" + }, + { + "author_name": "Elena P. Mazunina", + "author_inst": "National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya of the Ministry of Health of the Russian Federation, Mo" + }, + { + "author_name": "Nadezhda Kuznetsova", + "author_inst": "National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya of the Ministry of Health of the Russian Federation, Mo" + }, + { + "author_name": "Sofia R. Kozlova", + "author_inst": "National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya of the Ministry of Health of the Russian Federation, Mo" + }, + { + "author_name": "Anastasia N. Zolotar", + "author_inst": "National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya of the Ministry of Health of the Russian Federation, Mo" + }, + { + "author_name": "Elena V Shidlovskaya", + "author_inst": "National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya of the Ministry of Health of the Russian Federation, Mo" + }, + { + "author_name": "Evgeny V. Usachev", + "author_inst": "National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya of the Ministry of Health of the Russian Federation, Mo" + }, + { + "author_name": "Andrei A. Pochtovyi", + "author_inst": "National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya of the Ministry of Health of the Russian Federation, Mo" + }, + { + "author_name": "Daria D Kustova", + "author_inst": "National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya of the Ministry of Health of the Russian Federation, Mo" + }, + { + "author_name": "Igor A. Ivanov", + "author_inst": "National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya of the Ministry of Health of the Russian Federation, Mo" + }, + { + "author_name": "Sergey E Dmitriev", + "author_inst": "Moscow State University" + }, + { + "author_name": "Roman A. Ivanov", + "author_inst": "Sirius University of Science and Technology, Sochi, Russian Federation" + }, + { + "author_name": "Denis Y. Logunov", + "author_inst": "National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya of the Ministry of Health of the Russian Federation, Mo" + }, + { + "author_name": "Alexander L. Gintsburg", + "author_inst": "National Research Centre for Epidemiology and Microbiology named after Honorary Academician N F Gamaleya of the Ministry of Health of the Russian Federation, Mo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.12.27.23299358", "rel_title": "Metformin mitigates insulin signaling variations induced by COVID-19 vaccine boosters in type 2 diabetes", @@ -25678,49 +26974,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.12.28.23300622", - "rel_title": "Changes in the medical admissions and mortality amongst children in four South African hospitals following the COVID -19 pandemic: A five-year review.", - "rel_date": "2023-12-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.12.28.23300622", - "rel_abs": "BackgroundVulnerable children from poor communities with high HIV and Tuberculosis(TB) burdens were impacted by COVID-19 lockdowns. Concern was raised about the extent of this impact and anticipated post-pandemic surges in mortality.\n\nMethodsInterrupted time series segmented regression analyses were done using routinely collected facility-level data of children admitted for medical conditions at four South African referral hospitals. Monthly admission and mortality data over a 60-month period from 01 April 2018 to 31 January 2023 was analysed using models which included dummy lockdown level variables, a dummy post-COVID period variable, Fourier terms to account for seasonality, and excess mortality as a proxy for healthcare burden.\n\nResultsOf the 45 015 admissions analysed, 1237(2{middle dot}75%) demised with significant decreases in admissions during all the lockdown levels, with the most significant mean monthly decrease of 450(95%, CI=657{middle dot}3, -244{middle dot}3) p<0{middle dot}001 in level 5 (the most severe) lockdown. There was evidence of loss of seasonality on a six-month scale during the COVID periods for all admissions (p=0{middle dot}002), including under-one-year-olds (p=0{middle dot}034) and under-five-year-olds (p=0{middle dot}004). No decreases in mortality accompanied decreased admissions. Post-pandemic surges in admissions or mortality were not identified in children with acute gastroenteritis, acute pneumonia and severe acute malnutrition.\n\nConclusionDuring the COVID-19 pandemic, paediatric admissions in 4 hospitals serving communities with high levels of HIV, TB and poverty decreased similar to global experiences however there was no change in in-hospital mortality. No post-pandemic surge in admissions or mortality were documented. Differences in the impact of pandemic control measures on transmission of childhood infections and access to health care may account for differing outcomes seen in our setting compared to the global experiences. Further studies are needed to understand the impact of pandemic control measures on healthcare provision and transmission dynamics and to better inform future responses amongst vulnerable child populations.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Kimesh Loganathan Naidoo", - "author_inst": "University of KwaZulu-Natal Nelson R Mandela School of Medicine: University of KwaZulu-Natal College of Health Sciences" - }, - { - "author_name": "Jienchi Dorwood", - "author_inst": "University of Oxford Nuffield Department of Clinical Medicine: University of Oxford Nuffield Department of Medicine" - }, - { - "author_name": "Kogielambal Chinniah", - "author_inst": "University of KwaZulu-Natal Nelson R Mandela School of Medicine: University of KwaZulu-Natal College of Health Sciences" - }, - { - "author_name": "Melissa Lawler", - "author_inst": "University of KwaZulu-Natal Nelson R Mandela School of Medicine: University of KwaZulu-Natal College of Health Sciences" - }, - { - "author_name": "Yugendhree Nattar", - "author_inst": "University of KwaZulu-Natal Nelson R Mandela School of Medicine: University of KwaZulu-Natal College of Health Sciences" - }, - { - "author_name": "Christian Bottomley", - "author_inst": "London School of Hygiene & Tropical Medicine Centre of Global Change and Health: London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Moherndran Archary", - "author_inst": "University of KwaZulu-Natal Nelson R Mandela School of Medicine: University of KwaZulu-Natal College of Health Sciences" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2023.12.27.23300589", "rel_title": "Investigating the spatial accessibility and coverage of the pediatric COVID-19 vaccine: an ecologic study of regional health data", @@ -26893,6 +28146,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.12.22.572975", + "rel_title": "Genomic analysis of Staphylococcus aureus isolates from bacteremia reveals genetic features associated with the COVID-19 pandemic", + "rel_date": "2023-12-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.12.22.572975", + "rel_abs": "Genomic analyses of bacterial isolates are necessary to monitor the prevalence of antibiotic resistance genes and virulence determinants. Herein, we provide a comprehensive genomic description of a collection of 339 Staphylococcus aureus strains isolated from patients with bacteremia between 2014 and 2022. Nosocomial acquisition accounted for 56.6% of episodes, with vascular catheters being the predominant source of infection (31.8%). Cases of fatality (27.4%), persistent bacteremia (19.5%) and diagnosis of septic emboli (24.2%) were documented. During the COVID-19 pandemic, we observed a 140% increase of the episodes of S. aureus bacteremia per year, with a concomitant increase of the cases from nosocomial origin. This prompted us to investigate the existence of genetic features associated with S. aureus isolates from the COVID-19 pandemic. While genes conferring resistance to {beta}-lactams (blaI-blaR-blaZ), macrolides (ermA, ermC, ermT, mphC, msrA) and aminoglycosides (ant(4)-Ia, ant(9)-Ia, aph(3)-IIIa, aph(2)-Ih) were prevalent in our collection, detection of the msrA and mphC genes increased significantly in pandemic S. aureus isolates. Similarly, we observed a higher prevalence of isolates carrying the genes encoding the Clumping Factors A and B, involved in fibrinogen binding. Of note, macrolides were extensively used as accessory therapy for COVID-19 and fibrinogen levels were usually elevated upon SARS-CoV-2 infection. Therefore, our results reveal a remarkable adaptation of the S. aureus isolates to the COVID-19 pandemic context and demonstrates the potential of whole-genome sequencing to conduct molecular epidemiology studies.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Miquel Sanchez-Osuna", + "author_inst": "Hospital Universitari Parc Tauli, Institut d'Investigacio i Innovacio Parc Tauli" + }, + { + "author_name": "Marc Pedrosa", + "author_inst": "Hospital Universitari Parc Tauli, Institut d'Investigacio i Innovacio Parc Tauli" + }, + { + "author_name": "Paula Bierge", + "author_inst": "Hospital Universitari Parc Tauli, Institut d'Investigacio i Innovacio Parc Tauli" + }, + { + "author_name": "Inmaculada Gomez-Sanchez", + "author_inst": "Hospital Universitari Parc Tauli, Institut d'Investigacio i Innovacio Parc Tauli" + }, + { + "author_name": "Marina Alguacil-Guillen", + "author_inst": "Hospital Universitari Parc Tauli, Institut d'Investigacio i Innovacio Parc Tauli" + }, + { + "author_name": "Mateu Espasa", + "author_inst": "Hospital Universitari Parc Tauli, Institut d'Investigacio i Innovacio Parc Tauli" + }, + { + "author_name": "Ivan Erill", + "author_inst": "Department of Biological Sciences, University of Maryland Baltimore County" + }, + { + "author_name": "Oriol Gasch", + "author_inst": "Hospital Universitari Parc Tauli, Institut d'Investigacio i Innovacio Parc Tauli" + }, + { + "author_name": "Oscar Q Pich", + "author_inst": "Hospital Universitari Parc Tauli, Institut d'Investigacio i Innovacio Parc Tauli" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2023.12.20.23300304", "rel_title": "Cohort Profile of the Chilean COVID-19 Biorepository: a Multicentric initiative for multi-omics research on COVID-19 and LONG-COVID in a Latin American population.", @@ -27436,157 +28740,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2023.12.20.572426", - "rel_title": "Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data", - "rel_date": "2023-12-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.12.20.572426", - "rel_abs": "Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region. WBS gained widespread adoption globally during the SARS-CoV-2 pandemic for estimating community infection levels by qPCR. Sequencing pathogen genes or genomes from wastewater adds information about pathogen genetic diversity which can be used to identify viral lineages (including variants of concern) that are circulating in a local population. Capturing the genetic diversity by WBS sequencing is not trivial, as wastewater samples often contain a diverse mixture of viral lineages with real mutations and sequencing errors, which must be deconvoluted computationally from short sequencing reads. In this study we assess nine different computational tools that have recently been developed to address this challenge. We simulated 100 wastewater sequence samples consisting of SARS-CoV-2 BA.1, BA.2, and Delta lineages, in various mixtures, as well as a Delta-Omicron recombinant and a synthetic \"novel\" lineage. Most tools performed well in identifying the true lineages present and estimating their relative abundances, and were generally robust to variation in sequencing depth and read length. While many tools identified lineages present down to 1% frequency, results were more reliable above a 5% threshold. The presence of an unknown synthetic lineage, which represents an unclassified SARS-CoV-2 lineage, increases the error in relative abundance estimates of other lineages, but the magnitude of this effect was small for most tools. The tools also varied in how they labelled novel synthetic lineages and recombinants. While our simulated dataset represents just one of many possible use cases for these methods, we hope it helps users understand potential sources of noise or bias in wastewater sequencing data and to appreciate the commonalities and differences across methods.", - "rel_num_authors": 34, - "rel_authors": [ - { - "author_name": "Steven G Sutcliffe", - "author_inst": "Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada" - }, - { - "author_name": "Susanne A Kraemer", - "author_inst": "Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada" - }, - { - "author_name": "Isaac Ellmen", - "author_inst": "Department of Biology, University of Waterloo, Waterloo, ON, Canada" - }, - { - "author_name": "Jennifer J Knapp", - "author_inst": "Department of Biology, University of Waterloo, Waterloo, ON, Canada" - }, - { - "author_name": "Alyssa K Overton", - "author_inst": "Department of Biology, University of Waterloo, Waterloo, ON, Canada" - }, - { - "author_name": "Delaney Nash", - "author_inst": "Department of Biology, University of Waterloo, Waterloo, ON, Canada" - }, - { - "author_name": "Jozef I Nissimov", - "author_inst": "Department of Biology, University of Waterloo, Waterloo, ON, Canada" - }, - { - "author_name": "Trevor C Charles", - "author_inst": "Department of Biology, University of Waterloo, Waterloo, ON, Canada" - }, - { - "author_name": "David Dreifuss", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland" - }, - { - "author_name": "Ivan Topolsky", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland" - }, - { - "author_name": "Pelin I Baykal", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland" - }, - { - "author_name": "Lara Fuhrmann", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland" - }, - { - "author_name": "Kim P Jablonski", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland" - }, - { - "author_name": "Niko Beerenwinkel", - "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland" - }, - { - "author_name": "Joshua I Levy", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Abayomi S Olabode", - "author_inst": "Department of Pathology, Western University, London, ON, Canada" - }, - { - "author_name": "Devan G Becker", - "author_inst": "Department of Pathology, Western University, London, ON, Canada" - }, - { - "author_name": "Gopi Gugan", - "author_inst": "Department of Pathology, Western University, London, ON, Canada" - }, - { - "author_name": "Erin Britnell", - "author_inst": "Department of Pathology, Western University, London, ON, Canada" - }, - { - "author_name": "Art F.Y Poon", - "author_inst": "Department of Pathology, Western University, London, ON, Canada" - }, - { - "author_name": "Renan Valieris", - "author_inst": "Computational Biology, A.C. Camargo Cancer Center, Sao Paulo, SP, Brazil" - }, - { - "author_name": "Rodrigo D Drummond", - "author_inst": "Computational Biology, A.C. Camargo Cancer Center, Sao Paulo, SP, Brazil" - }, - { - "author_name": "Alexandre Defelicibus", - "author_inst": "Computational Biology, A.C. Camargo Cancer Center, Sao Paulo, SP, Brazil" - }, - { - "author_name": "Emmanuel Dias-Neto", - "author_inst": "Rutgers University, New Brunswick, NJ, USA" - }, - { - "author_name": "Rafael A Rosales", - "author_inst": "Universidade de Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Israel Tojal da Silva", - "author_inst": "Computational Biology, A.C. Camargo Cancer Center, Sao Paulo, SP, Brazil" - }, - { - "author_name": "Aspasia Orfanou", - "author_inst": "Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001 Thessaloniki, Greece" - }, - { - "author_name": "Fotis Psomopoulos", - "author_inst": "Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001 Thessaloniki, Greece" - }, - { - "author_name": "Nikolaos Pechlivanis", - "author_inst": "Institute of Applied Biosciences, Centre of Research and Technology Hellas, Thermi, 57001 Thessaloniki, Greece" - }, - { - "author_name": "Lenore Pipes", - "author_inst": "Department of Integrative Biology, University of California, Berkeley, CA, USA" - }, - { - "author_name": "Zihao Chen", - "author_inst": "School of Mathematical Sciences, Peking University, Beijing, BJ, China" - }, - { - "author_name": "Jasmijn A Baaijens", - "author_inst": "Delft University of Technology, Delft, ZH, Netherlands; Department of Systems Biology, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Michael Baym", - "author_inst": "Department of Systems Biology, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "B. Jesse Shapiro", - "author_inst": "Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2023.12.21.572736", "rel_title": "Analysing the distribution of SARS-CoV-2 infections in schools: integrating model predictions with real world observations", @@ -28839,6 +29992,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2023.12.18.23300176", + "rel_title": "The magnitude and cross reactivity of SARS-CoV-2 specific antibody responses in vaccinated and unvaccinated Sri Lankan children and association with nutrition status", + "rel_date": "2023-12-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.12.18.23300176", + "rel_abs": "BackgroundWe investigated the seropositivity rates of Sri Lankan children in a large island wide serosurvey, to determine the magnitude and breadth of antibody responses to SARS-CoV-2 variants and the association with the vaccination and nutritional status to understand the likely impact of newer variants in Sri Lanka.\n\nMethodsUsing the WHO UNITY protocol, we recruited 5207 children, aged 10 to 20 years, representative of the 9 provinces of Sri Lanka, and assessed seropositive rates, ACE2 blocking antibodies and antibodies to BA.2.75 and XBB.1.5, in vaccinated and unvaccinated children. Anthropometric measurements were taken to determine the association between nutrition status and antibody levels.\n\nResults3111/3119 (99.7%) vaccinated and 2008/2088 (96.2%) of unvaccinated children, were seropositive for SARS-CoV-2. 2984/3111 (95.9%) of vaccinated children had ACE2 blocking antibodies above the cut-off threshold, compared to 1346/2008 (67.0%) of unvaccinated children. 27.2 % unvaccinated children had positive antibody responses to BA.2.75 and 30.7% to XBB.1.5, while 64.3% of vaccinated had a positive response to BA.2.75 and 43.1% to XBB.1.5. Vaccinated children had significantly higher titres of total antibodies, ACE2 blocking antibodies and antibodies to XBB.1.5 and BA.2.75 than unvaccinated children. However, the vaccinated had significantly higher responses to BA.2.75 (p<0.0001), than XBB.1.5. Unvaccinated children, with <3rd BMI centile had significantly lower ACE2 blocking antibodies than other groups.\n\nDiscussionThe high seropositivity rates and antibody titres to SARS-CoV-2 variants in unvaccinated children, suggests that they are likely to have been infected more than once with SARS-CoV-2. The implications of lower antibody levels in undernourished children should be further investigated.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Chandima Jeewandara", + "author_inst": "University of Sri Jayewardenepura" + }, + { + "author_name": "Maneshka V Karunananda", + "author_inst": "University of Sri Jayewardenepura" + }, + { + "author_name": "Suranga Fernando", + "author_inst": "Ministry of Health Sri Lanka" + }, + { + "author_name": "Saubhagya Danasekara", + "author_inst": "University of Sri Jayewardenepura" + }, + { + "author_name": "Gamini Jayakody", + "author_inst": "Ministry of Health Sri Lanka" + }, + { + "author_name": "S Arulkumaran", + "author_inst": "Ministry of Health Sri Lanka" + }, + { + "author_name": "Nayana Y Samaraweera", + "author_inst": "Ministry of Health Sri Lanka" + }, + { + "author_name": "Sarathchandra Kumarawansha", + "author_inst": "Ministry of Health Sri Lanka" + }, + { + "author_name": "Subramaniyam Sivaganesh", + "author_inst": "Ministry of Health Sri Lanka" + }, + { + "author_name": "P G Amarasinghe", + "author_inst": "Ministry of Health Sri Lanka" + }, + { + "author_name": "Chintha Jayasinghe", + "author_inst": "Ministry of Health Sri Lanka" + }, + { + "author_name": "Dilini Wijesekara", + "author_inst": "Ministry of Health Sri Lanka" + }, + { + "author_name": "Manonath B Marasinghe", + "author_inst": "Ministry of Health Sri Lanka" + }, + { + "author_name": "Udari Mambulage", + "author_inst": "Ministry of Health Sri Lanka" + }, + { + "author_name": "Helanka Wijayatilaka", + "author_inst": "Ministry of Health Sri Lanka" + }, + { + "author_name": "Kasun Seneviratne", + "author_inst": "Ministry of Health Sri Lanka" + }, + { + "author_name": "A D P Bandara", + "author_inst": "Ministry of Health Sri Lanka" + }, + { + "author_name": "C P Gallage", + "author_inst": "Ministry of Health Sri Lanka" + }, + { + "author_name": "N R Colambage", + "author_inst": "Ministry of Health Sri Lanka" + }, + { + "author_name": "Tilak T Udayasiri", + "author_inst": "Ministry of Health Sri Lanka" + }, + { + "author_name": "Tharaka Lokumarambage", + "author_inst": "Ministry of Health Sri Lanka" + }, + { + "author_name": "Y Upasena", + "author_inst": "Ministry of Health Sri Lanka" + }, + { + "author_name": "W P K P Weerasooriya", + "author_inst": "Ministry of Health Sri Lanka" + }, + { + "author_name": "- Seroprevalence Study Group", + "author_inst": "-" + }, + { + "author_name": "Tion Kit Tang", + "author_inst": "University of Oxford" + }, + { + "author_name": "Alain Townsend", + "author_inst": "University of Oxford" + }, + { + "author_name": "Graham S Ogg", + "author_inst": "University of Oxford" + }, + { + "author_name": "Gathsaurie Neelika Malavige", + "author_inst": "University of Sri Jayewardenepura" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.12.18.23300150", "rel_title": "Clinical, laboratory, and imaging findings of stage 3-5 chronic kidney disease patients suffering from COVID-19 in Bangladesh: a prospective cross-sectional study", @@ -29406,81 +30686,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.12.15.23298521", - "rel_title": "Adiposity and Sex Influence on SARS-CoV-2 Antibody Response in University Students. An ESFUERSO cross-sectional study.", - "rel_date": "2023-12-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.12.15.23298521", - "rel_abs": "IntroductionPrior studies have identified various determinants of differential immune responses to COVID-19. This investigation delves into the Ig-G anti-RBD marker, scrutinizing its potential correlations with sex, vaccine type, body fat percentage, metabolic risk, perceived stress, and previous COVID-19 exposure.\n\nMethodsIn this study, data were obtained from 116 participants from the ESFUERSO cohort, who completed questionnaires detailing their COVID-19 experiences and stress levels assessed through the SISCO scale. Quantification of Ig-G anti-RBD concentrations was executed using an ELISA assay developed by UNAM. Multiple regression analysis was adeptly employed to control for covariates, including sex, age, body fat percentage, BMI, and perceived stress.\n\nResultsThis sample comprised young individuals (average age of 21.4 years), primarily consisting of females (70%), with a substantial proportion reporting a family history of diabetes, hypertension, or obesity. Most students had received the Moderna or Pfizer vaccines, and 91% displayed a positive anti-RBD response.\n\nA noteworthy finding was the interaction between body fat percentage and sex. In males, increased adiposity was associated with a decrease in Ig-G anti-RBD concentration, while in females, the response increased. Importantly, this trend was consistent regardless of the vaccine received. No significant associations were observed for variables such as dietary habits or perceived stress.\n\nConclusionsIn summation, this research reports the impact of both sex and body fat percentage on the immune response through Ig-G anti-RBD levels to COVID-19 vaccines. The implications of these findings offers a foundation for educational initiatives and the formulation of preventive policies aimed at mitigating health disparities.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Adriana L. Perales-Torres", - "author_inst": "Universidad Aut\u00f3noma de Tamaulipas: Universidad Autonoma de Tamaulipas" - }, - { - "author_name": "Lucia M. Perez-Navaro", - "author_inst": "Hospital General de Mexico Dr Eduardo Liceaga" - }, - { - "author_name": "Esperanza M. Garcia-Oropesa", - "author_inst": "Universidad Autonoma de Tamaulipas" - }, - { - "author_name": "Alvaro Diaz-Badillo", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Yoscelina Estrella Martinez-Lopez", - "author_inst": "The University of Texas Health Science Center at Houston" - }, - { - "author_name": "Marisol Rosas", - "author_inst": "Universidad Autonoma de Tamaulipas" - }, - { - "author_name": "Octelina Castillo", - "author_inst": "Universidad Autonoma de Tamaulipas" - }, - { - "author_name": "Laura Ramirez-Quintanilla", - "author_inst": "Universidad Autonoma de Tamaulipas" - }, - { - "author_name": "Jacquelynne Cervantes", - "author_inst": "Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Edda Sciutto", - "author_inst": "Universidad Nacional Autonoma de Mexico" - }, - { - "author_name": "Claudia X. Munguia Cisneros", - "author_inst": "Universidad Mexico Americana del Norte" - }, - { - "author_name": "Carlos Ramirez-Pfeifer", - "author_inst": "Universidad Mexico Americana del Norte" - }, - { - "author_name": "Leonel Vela", - "author_inst": "The University of Texas Rio Grande Valley" - }, - { - "author_name": "Beatriz Tapia", - "author_inst": "The University of Texas Rio Grande Valley" - }, - { - "author_name": "Juan C. Lopez-Alvarenga", - "author_inst": "University of Texas Rio Grande Valley" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.12.15.23300043", "rel_title": "Self-perception of mental health, COVID-19 and associated sociodemographic-contextual factors in Latin American", @@ -30649,6 +31854,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.12.12.23299855", + "rel_title": "Early COVID-19 vaccine effectiveness of XBB.1.5 vaccine against hospitalization and ICU admission, the Netherlands, 9 October - 5 December 2023", + "rel_date": "2023-12-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.12.12.23299855", + "rel_abs": "We present early vaccine effectiveness (VE) estimates of the 2023 seasonal COVID-19 vaccination campaign using XBB.1.5 vaccine against COVID-19 hospitalization and ICU admission in previously vaccinated adults [≥]60 years old in the Netherlands. We compared vaccination status of 2050 hospitalizations including 92 ICU admissions with age group-, sex-, region- and date-specific population vaccination coverage between 9 October and 5 December 2023. VE against hospitalization was 70.7% (95% CI: 66.6; 74.3), VE against ICU admission was 73.3% (95% CI: 42.2; 87.6).", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Henri van Werkhoven", + "author_inst": "RIVM, UMCU" + }, + { + "author_name": "Anne-Wil Valk", + "author_inst": "RIVM" + }, + { + "author_name": "Bente Smagge", + "author_inst": "RIVM" + }, + { + "author_name": "Hester E de Melker", + "author_inst": "RIVM" + }, + { + "author_name": "Mirjam J Knol", + "author_inst": "RIVM" + }, + { + "author_name": "Susan Hahne", + "author_inst": "RIVM" + }, + { + "author_name": "Susan van den Hof", + "author_inst": "RIVM" + }, + { + "author_name": "Brechje de Gier", + "author_inst": "RIVM" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.12.12.23299862", "rel_title": "The availability, use and impact of workplace mental health supports during the COVID-19 pandemic in a Canadian prospective cohort of healthcare workers.", @@ -31060,69 +32312,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.12.11.23299052", - "rel_title": "Changes in internalizing and externalizing problems in Dutch children and adolescents receiving youth care before and during the COVID-19 pandemic", - "rel_date": "2023-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.12.11.23299052", - "rel_abs": "BackgroundThe COVID-19 pandemic had serious effects on the mental health of children and adolescents. However, it is unclear how the pandemic may have affected treatment effects and outcomes in youth care. We investigated if treatment effects and externalizing and internalizing problems of children and adolescents receiving youth care were affected by the COVID-19 pandemic.\n\nMethodsWe used data from children and adolescents in youth care (N = 1,090, Mage = 12.85 (SD = 2.83; range = 8-18 years)). Internalizing and externalizing problems were assessed at the start and end of treatment using the Child Behavior Checklist. We inspected change in internalizing and externalizing problems and clinical status at the end of treatment to investigate treatment effects, and the level of problems at the start and end of treatment. Outcomes were compared between three groups: children treated entirely before the COVID-19 pandemic, children who experienced the transition into COVID-19 measures during treatment, and children treated entirely during the pandemic.\n\nResultsWe did not find evidence that the pandemic affected treatment effectiveness. However, fewer children who were treated during the pandemic recovered from externalizing problems compared to children treated before the pandemic. Children who received treatment entirely during the pandemic also showed more internalizing and externalizing problems at both the start and end of their treatment, and children who experienced the transition into the pandemic showed elevated externalizing problems at both timepoints.\n\nConclusionsAlthough the change in internalizing and externalizing problems from start to end of treatment was not affected by the pandemic, our findings that children are entering and leaving care with more problems suggest that child mental health has deteriorated since the pandemic.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Emma M. Broek", - "author_inst": "LUMC Curium" - }, - { - "author_name": "Ronald De Meyer", - "author_inst": "Praktikon" - }, - { - "author_name": "Rachel van der Rijken", - "author_inst": "Praktikon" - }, - { - "author_name": "Josjan Zijlmans", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Hedy A van Oers", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Michiel Luijten", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Hekmat Alrouh", - "author_inst": "Vrije Universiteit Amsterdam" - }, - { - "author_name": "Arne Popma", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Meike Bartels", - "author_inst": "Vrije Universiteit Amsterdam" - }, - { - "author_name": "Robert RJM Vermeiren", - "author_inst": "LUMC Curium" - }, - { - "author_name": "Tinca JC Polderman", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Jacintha M Tieskens", - "author_inst": "LUMC Curium" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2023.12.11.23299663", "rel_title": "Effectiveness and durability of mRNA-1273 BA.4/BA.5 bivalent vaccine (mRNA-1273.222) against SARS-CoV-2 BA.4/BA.5 and XBB sublineages", @@ -32507,6 +33696,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.12.05.23299493", + "rel_title": "The role of veterinary diagnostic laboratories during COVID-19 response in the United States", + "rel_date": "2023-12-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.12.05.23299493", + "rel_abs": "Robust testing capacity was necessary for public health agencies to respond to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during the coronavirus disease 19 (COVID-19) pandemic. As the nation faced the need for robust testing capacity, it became necessary to use all possible resources. In many cases, veterinary diagnostic laboratories rose to meet this demand because these facilities routinely perform high throughput diagnostic testing of large animal populations and are typically familiar with pathogens of high pandemic concern. In this study, we evaluated the impact of veterinary diagnostic laboratories in the United States on SARS-CoV-2 testing. Results of surveys, semi-structured interviews, and analysis of publicly available information showed that veterinary diagnostic laboratories had a substantial impact on human health through population-level testing in the COVID-19 response, supporting timely and informed public health interventions. This success was not without significant hurdles, as many participating veterinary diagnostic laboratories experienced restriction in their response due to difficulties obtaining the Clinical Laboratory Improvement Amendments (CLIA) certification required to conduct human diagnostic testing. Our results point out the importance of reducing hurdles before the next major public health emergency to enhance access to testing resources overall and to ultimately improve population health.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Nia Clements", + "author_inst": "Cornell University" + }, + { + "author_name": "Diego G Diel", + "author_inst": "Cornell University" + }, + { + "author_name": "Fran\u00e7ois Elvinger", + "author_inst": "Cornell University" + }, + { + "author_name": "Gary Koretzky", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Julie Siler", + "author_inst": "Cornell University" + }, + { + "author_name": "Lorin Dean Warnick", + "author_inst": "Cornell University College of Veterinary Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.12.05.23299499", "rel_title": "Feasibility characteristics of wrist-worn fitness trackers in health status monitoring for post-COVID patients in remote and rural areas", @@ -32946,33 +34174,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.12.05.23299475", - "rel_title": "COVID-19 vaccination uptake among healthcare workers in Ghana: A comprehensive analysis of knowledge, attitude, perceived vaccine effectiveness, and health belief model constructs", - "rel_date": "2023-12-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.12.05.23299475", - "rel_abs": "The novel Coronavirus Disease 19 (COVID-19) caused devastating effects globally, and healthcare workers were among the most affected by the pandemic. To mitigate this impact, healthcare workers were prioritized in COVID-19 vaccination globally and in Ghana. However, hesitancy by healthcare workers to receive the vaccination resulted in delayed control of the pandemic. In Ghana, vaccine acceptance rate among healthcare workers was estimated to be 39.3% in the pre-vaccine rollout period. Consequently, this study assessed uptake of COVID-19 vaccination and associated factors among healthcare workers in Ghana in the post-vaccine roll-out period.\n\nThis was an analytical cross-sectional study that used a semi-structured questionnaire to collect data on COVID-19 vaccination uptake and influencing factors from randomly selected 256 healthcare workers in Ayawaso West Municipality, Ghana. Bivariable and Multivariable logistic regression was performed using IBM SPSS version 22 to identify predictors of vaccine uptake and a statistical significance was declared at p<0.05.\n\nMore than three-fourths of participants 220 (85.9%) had received at least one dose of the COVID-19 vaccination, while 36 (14.9%) were hesitant. More than half 139 (54.3%) had adequate knowledge about COVID-19 vaccination and the majority 188 (73.4%) had positive perceptions about its effectiveness. Moreover, 218 (85.2%) of HCWs had a positive attitude towards COVID-19 vaccination. Positive attitude towards COVID-19 vaccination (AOR = 4.3; 95% CI: 1.4, 13.0) and high cues to action (AOR = 5.7; 95% CI: 2.2, 14.8) were the factors that significantly predicted uptake of COVID-19 vaccination among healthcare workers.\n\nCOVID-19 vaccination among HCWs in Ghana is promising. However, hesitancy to receive the vaccination among a significant proportion of HCWs raises concerns. To ensure vaccination of all healthcare workers, interventions to promote vaccination should target key determinants of vaccination uptake, such as attitude towards the vaccination and cues to action.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Whiteson Mbele", - "author_inst": "University of Ghana School of Public Health" - }, - { - "author_name": "Phyllis Dako-Gyeke", - "author_inst": "University of Ghana School of Public Health" - }, - { - "author_name": "Andreas Ndapewa Frans", - "author_inst": "University of Ghana School of Public Health" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.12.04.23299409", "rel_title": "Immune profiling of COVID-19 vaccine responses in people with multiple sclerosis on B cell-depleting therapy", @@ -34084,6 +35285,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.11.30.23299238", + "rel_title": "Knowledge mobilisation of rapid evidence reviews to inform health and social care policy and practice in a public health emergency: appraisal of the Wales COVID-19 Evidence Centre processes and impact, 2021-23.", + "rel_date": "2023-12-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.30.23299238", + "rel_abs": "The Wales COVID-19 Evidence Centre (WCEC) was established from 2021-23 to ensure that the latest coronavirus (COVID-19) relevant research evidence was readily available to inform health and social care policy and practice decision-makers. Although decisions need to be evidence-based, ensuring that accessible and relevant research evidence is available to decision-makers is challenging, especially in a rapidly evolving pandemic environment when timeframes for decision-making are days or weeks rather than months or years. We set up knowledge mobilisation processes to bridge the gap between evidence review and informing decisions, making sure that the right information reaches the right people at the right time.\n\nAims and objectivesTo describe the knowledge mobilisation processes used by the WCEC, evaluate the impact of the WCEC rapid evidence reviews, and share lessons learned.\n\nMethodsOur knowledge mobilisation methods were flexible and tailored to meet stakeholders needs. They included stakeholder co-production in our rapid evidence review processes, stakeholder-informed and participatory knowledge mobilisation, wider dissemination of outputs and associated activities including public engagement, capacity building and sharing of methodologies. Feedback on processes and evidence of impact was collected via stakeholder engagement and a stakeholder survey.\n\nResultsFindings indicate that WCEC knowledge mobilisation processes successfully supported co-production and use of rapid evidence review findings by scientific advisors and policy and practice decision-makers during the COVID-19 pandemic. Identified barriers and facilitators are of potential relevance to wider evidence initiatives. Knowledge mobilisation require sustained development to continue building stakeholder links, embed co-production and sustain knowledge mobilisation as we move to support evidence-based policy and practice decision-making beyond the pandemic.\n\nDiscussion and ConclusionThe WCEC knowledge mobilisation processes successfully supported co-production and use of rapid evidence review findings by scientific advisors and policy and practice decision-makers during the COVID-19 pandemic. Identified barriers and facilitators are of potential relevance to wider evidence initiatives. Knowledge mobilisation require sustained development to continue building stakeholder links, embed co-production and sustain knowledge mobilisation as we move to support evidence-based policy and practice decision-making beyond the pandemic.\n\nFunding statementThe Wales COVID-19 Evidence Centre was funded for this work by Health and Care Research Wales on behalf of Welsh Government.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Micaela Gal", + "author_inst": "Health and Care Research Wales Evidence Centre, Cardiff University, United Kingdom" + }, + { + "author_name": "Alison Cooper", + "author_inst": "Health and Care Research Wales Evidence Centre, Cardiff University, United Kingdom" + }, + { + "author_name": "Natalie Joseph-Williams", + "author_inst": "Health and Care Research Wales Evidence Centre, and the Division of Population Medicine, Cardiff University, United Kingdom" + }, + { + "author_name": "Elizabeth C Doe", + "author_inst": "Health and Care Research Wales Evidence Centre, Cardiff University, United Kingdom" + }, + { + "author_name": "Ruth Lewis", + "author_inst": "Health and Care Research Wales Evidence Centre, Bangor University, United Kingdom" + }, + { + "author_name": "Rebecca-Jane Law", + "author_inst": "Science Team, Health and Social Services Division, Welsh Government, United Kingdom" + }, + { + "author_name": "Sally Anstey", + "author_inst": "Health and Care Research Wales Evidence Centre, Cardiff University, United Kingdom" + }, + { + "author_name": "Nathan Davies", + "author_inst": "Health and Care Research Wales Evidence Centre, Cardiff University, United Kingdom" + }, + { + "author_name": "Amy Walters", + "author_inst": "Health and Care Research Wales, United Kingdom" + }, + { + "author_name": "Robert Orford", + "author_inst": "Science Evidence Advice Division, Welsh Government, United Kingdom" + }, + { + "author_name": "Brendan Collins", + "author_inst": "Science Evidence Advice Division, Welsh Government, United Kingdom" + }, + { + "author_name": "Lisa Trigg", + "author_inst": "Social Care Wales, United Kingdom" + }, + { + "author_name": "Chris Roberts", + "author_inst": "Knowledge Analytical Services, Welsh Government, United Kingdom" + }, + { + "author_name": "Sarah Meredith", + "author_inst": "Science Evidence Advice Division, Welsh Government, United Kingdom" + }, + { + "author_name": "Steven Macey", + "author_inst": "Equality, Poverty and Childrens Evidence and Support Division, Welsh Government, United Kingdom" + }, + { + "author_name": "Andrew P Carson-Stevens", + "author_inst": "Division of Population Medicine, Cardiff University, United Kingdom" + }, + { + "author_name": "Jane Greenwell", + "author_inst": "Information Technology, Cardiff University, United Kingdom" + }, + { + "author_name": "Ffion Coomber", + "author_inst": "Division of Population Medicine, Cardiff University, United Kingdom" + }, + { + "author_name": "Adrian G Edwards", + "author_inst": "Health and Care Research Wales Evidence Centre, and the Division of Population medicine, Cardiff University, United Kingdom" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2023.11.30.23299229", "rel_title": "Population age as a key factor in the COVID-19 pandemic dynamics", @@ -34611,61 +35903,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2023.11.28.569052", - "rel_title": "copepodTCR: Identification of Antigen-Specific T Cell Receptors with combinatorial peptide pooling", - "rel_date": "2023-11-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.28.569052", - "rel_abs": "T cell receptor (TCR) repertoire diversity enables the orchestration of antigen-specific immune responses against the vast space of possible pathogens. Identifying TCR/antigen binding pairs from the large TCR repertoire and antigen space is crucial for biomedical research. Here, we introduce copepodTCR, an open-access tool for the design and interpretation of high-throughput experimental assays to determine TCR specificity. copepodTCR implements a combinatorial peptide pooling scheme for efficient experimental testing of T cell responses against large overlapping peptide libraries, useful for \"deorphaning\" TCRs of unknown specificity. The scheme detects experimental errors and, coupled with a hierarchical Bayesian model for unbiased results interpretation, identifies the response-eliciting peptide for a TCR of interest out of hundreds of peptides tested using a simple experimental set-up. We experimentally validated our approach on a library of 253 overlapping peptides covering the SARS-CoV-2 spike protein. We provide experimental guides for efficient design of larger screens covering thousands of peptides which will be crucial for the identification of antigen-specific T cells and their targets from limited clinical material.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Vasilisa A Kovaleva", - "author_inst": "Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA" - }, - { - "author_name": "David J Pattinson", - "author_inst": "Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI 53711, USA" - }, - { - "author_name": "Carl Barton", - "author_inst": "Birkbeck, University of London, WC1E 7HX London, UK" - }, - { - "author_name": "Sarah R Chapin", - "author_inst": "Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA" - }, - { - "author_name": "Anastasia A Minervina", - "author_inst": "Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA" - }, - { - "author_name": "Katherine A Richards", - "author_inst": "David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642" - }, - { - "author_name": "Andrea J Sant", - "author_inst": "David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY 14642" - }, - { - "author_name": "Paul G Thomas", - "author_inst": "Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA" - }, - { - "author_name": "Mikhail V Pogorelyy", - "author_inst": "Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA" - }, - { - "author_name": "Hannah V Meyer", - "author_inst": "Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.11.28.569051", "rel_title": "Functional and antigenic characterization of SARS-CoV-2 spike fusion peptide by deep mutational scanning", @@ -35822,6 +37059,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.11.24.23298841", + "rel_title": "Characteristics of SARS-CoV-2 reinfection with Omicron BA.2.75 subvariants in Thai Adults.", + "rel_date": "2023-11-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.24.23298841", + "rel_abs": "Omicron subvariants of SARS-CoV-2 may resist vaccine- or infection-induced immunity thereby increasing the risk of reinfections in previously infected persons. This study aimed to investigate the clinical severity and the average time to the onset of Omicron reinfection. This survey study collected clinical data on Omicron reinfection. Information on time of infection, reinfection interval, overall clinical presentation, and severity of infection was reported. The total prevalence of symptoms among 201 participants was significantly higher in the first infection (risk difference (RD), 9.86%; 95% CI, 7.54-12.19]) compared to the second infection, and the hospitalization rate among all participants was significantly lower for the second infection than the primary infection (odds ratio (OR), 6.25; 95% CI, 2.158-24.71). The prevalence of symptoms compared with the first infection with pre-Omicron variants was similar to that of the first infection with the Omicron variant (RD, 2.56%; 95% CI, -6.14-1.01). However, the hospitalization rate for pre-Omicron primary infection was significantly higher (OR, 6.76; 95% CI, 2.87-15.87]) than that observed with Omicron variants. The severity of the primary infection and of a pre-Omicron variant was greater than that of a secondary infection or with an Omicron variant.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Suvichada Assawakosri", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Natthinee Sudhinaraset", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Jira Chansaenroj", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Nungruthai Suntronwong", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Sitthichai Kanokudom", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Natach Nalinpakorn", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Napat Tantipraphat", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Amica Sethabutra", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + }, + { + "author_name": "Sittisak Honsawek", + "author_inst": "Center of Excellence in Osteoarthritis and Musculoskeleton, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross " + }, + { + "author_name": "Yong Poovorawan", + "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.11.24.23299005", "rel_title": "Early warning system using primary healthcare data in the post-COVID-19-pandemic era: Brazil nationwide case-study", @@ -36437,93 +37729,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2023.11.24.23296021", - "rel_title": "Severe acute myositis and myocarditis upon initiation of six-weekly Pembrolizumab post-COVID-19 mRNA vaccination", - "rel_date": "2023-11-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.24.23296021", - "rel_abs": "We describe three cases of critical acute myositis with myocarditis occurring within 22 days of each other at a single institution, all within one month of receiving the initial cycle of the anti-PD-1 drug Pembrolizumab. Analysis of T cell receptor repertoires from peripheral blood and tissues revealed a high degree of clonal expansion and public clones between cases, with several T cell clones expanded within the skeletal muscle putatively recognising viral epitopes. All patients had recently received a COVID-19 mRNA booster vaccine prior to treatment and were positive for SARS-CoV2 Spike antibody. In conclusion, we report a series of unusually severe myositis and myocarditis following PD-1 blockade and the COVID-19 mRNA vaccination.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Robert Aerwyn Watson", - "author_inst": "University of Oxford" - }, - { - "author_name": "Weiyu Ye", - "author_inst": "University of Oxford" - }, - { - "author_name": "Chelsea Alice Taylor", - "author_inst": "University of Oxford" - }, - { - "author_name": "Rosalin Anisha Cooper", - "author_inst": "University of Oxford" - }, - { - "author_name": "Orion Tong", - "author_inst": "University of Oxford" - }, - { - "author_name": "Tim James", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Brian Shine", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Monika Hofer", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Damian Jenkins", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Robert Pell", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Eleni Ieremia", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Stephanie Jones", - "author_inst": "University of Oxford" - }, - { - "author_name": "David Maldonado-Perez", - "author_inst": "University of Oxford" - }, - { - "author_name": "Ian Roberts", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Nicholas Coupe", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Mark Ross Middleton", - "author_inst": "University of Oxford" - }, - { - "author_name": "Miranda Jane Payne", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Benjamin Peter Fairfax", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "oncology" - }, { "rel_doi": "10.1101/2023.11.24.568532", "rel_title": "Isogenic iPSC-derived proximal and distal lung-on-chip models: Tissue- and virus-specific immune responses in human lungs", @@ -37540,6 +38745,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "otolaryngology" }, + { + "rel_doi": "10.1101/2023.11.21.23298818", + "rel_title": "Using the Public Health and Social Measures Severity Index for analysing government responses during the COVID-19 pandemic in the WHO European Region", + "rel_date": "2023-11-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.21.23298818", + "rel_abs": "Public health and social measures (PHSM), such as adaptions to the operation of schools, businesses and workplaces, international travel measures and restrictions on gatherings and peoples movements, as well as individual preventive measures such as physical distancing, have been a vital set of tools utilized by many countries to mitigate the spread of SARS-CoV-2 virus throughout the COVID-19 pandemic. In January 2020, the WHO Regional Office for Europe started to systematically monitor, collect and categorize data on response measures taken by its Member States. In order to visualize and analyse the collected data, WHO developed a methodology for quantifying the response measures into an index, capturing the severity of these policy measures in terms of six key indicators. The aim of this article is to describe the methodology underlying the index, including data collection, categorization and calculation, in order to provide researchers and policy-makers with a better understanding of its application. Furthermore, it provides an overview and examples of possible applications of the index, as well as serve as a reference for subsequent research on the effectiveness of PHSM, including empirical studies and models that can help to guide health policies, their timing and severity.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Christoph Wippel", + "author_inst": "World Health Organization" + }, + { + "author_name": "Lisa Owen", + "author_inst": "World Health Organization" + }, + { + "author_name": "Dominic Cocciolone", + "author_inst": "World Health Organization" + }, + { + "author_name": "Jussi Sane", + "author_inst": "World Health Organization" + }, + { + "author_name": "Jennifer Addo", + "author_inst": "World Health Organization" + }, + { + "author_name": "Christian Gapp", + "author_inst": "World Health Organization" + }, + { + "author_name": "Aimee Lee Latta", + "author_inst": "World Health Organization" + }, + { + "author_name": "Sandra Lindmark", + "author_inst": "World Health Organization" + }, + { + "author_name": "Ihor Perehinets", + "author_inst": "World Health Organization" + }, + { + "author_name": "Catherine Smallwood", + "author_inst": "World Health Organization" + }, + { + "author_name": "Tanja Schmidt", + "author_inst": "World Health Organization" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.11.22.567930", "rel_title": "Durable immunity to SARS-CoV-2 in both lower and upper airways achieved with a gorilla adenovirus (GRAd) S-2P vaccine in non-human primates", @@ -38239,45 +39503,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2023.11.18.567697", - "rel_title": "Accurate Characterization of Conformational Ensembles and Binding Mechanisms of the SARS-CoV-2 Omicron BA.2 and BA.2.86 Spike Protein with the Host Receptor and Distinct Classes of Antibodies Using AlphaFold2-Augmented Integrative Computational Modeling", - "rel_date": "2023-11-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.18.567697", - "rel_abs": "The latest wave SARS-CoV-2 Omicron variants displayed a growth advantage and the increased viral fitness through convergent evolution of functional hotspots that work synchronously to balance fitness requirements for productive receptor binding and efficient immune evasion. In this study, we combined AlphaFold2-based structural modeling approaches with all-atom MD simulations and mutational profiling of binding energetics and stability for prediction and comprehensive analysis of the structure, dynamics, and binding of the SARS-CoV-2 Omicron BA.2.86 spike variant with ACE2 host receptor and distinct classes of antibodies. We adapted several AlphaFold2 approaches to predict both structure and conformational ensembles of the Omicron BA.2.86 spike protein in the complex with the host receptor. The results showed that AlphaFold2-predicted conformational ensemble of the BA.2.86 spike protein complex can accurately capture the main dynamics signatures obtained from microscond molecular dynamics simulations. The ensemble-based dynamic mutational scanning of the receptor binding domain residues in the BA.2 and BA.2.86 spike complexes with ACE2 dissected the role of the BA.2 and BA.2.86 backgrounds in modulating binding free energy changes revealing a group of conserved hydrophobic hotspots and critical variant-specific contributions of the BA.2.86 mutational sites R403K, F486P and R493Q. To examine immune evasion properties of BA.2.86 in atomistic detail, we performed large scale structure-based mutational profiling of the S protein binding interfaces with distinct classes of antibodies that displayed significantly reduced neutralization against BA.2.86 variant. The results quantified specific function of the BA.2.86 mutations to ensure broad resistance against different classes of RBD antibodies. This study revealed the molecular basis of compensatory functional effects of the binding hotspots, showing that BA.2.86 lineage may have primarily evolved to improve immune escape while modulating binding affinity with ACE2 through cooperative effect of R403K, F486P and R493Q mutations. The study supports a hypothesis that the impact of the increased ACE2 binding affinity on viral fitness is more universal and is mediated through cross-talk between convergent mutational hotspots, while the effect of immune evasion could be more variant-dependent.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Nishank Raisinghani", - "author_inst": "Chapman University" - }, - { - "author_name": "Mohammed Alshahrani", - "author_inst": "Chapman University" - }, - { - "author_name": "Grace Gupta", - "author_inst": "Chapman University" - }, - { - "author_name": "Sian Xiao", - "author_inst": "Southern Methodist University" - }, - { - "author_name": "Peng Tao", - "author_inst": "Southern Methodist University" - }, - { - "author_name": "Gennady Verkhivker", - "author_inst": "Chapman University School of Pharmacy" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2023.11.20.23298760", "rel_title": "Affect and post-COVID-19 symptoms in daily life: An exploratory experience sampling study", @@ -39538,6 +40763,117 @@ "type": "new results", "category": "scientific communication and education" }, + { + "rel_doi": "10.1101/2023.11.15.567132", + "rel_title": "The Impact of SIV-Induced Immunodeficiency on Clinical Manifestation, Immune Response, and Viral Dynamics in SARS-CoV-2 Coinfection", + "rel_date": "2023-11-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.15.567132", + "rel_abs": "Persistent and uncontrolled SARS-CoV-2 replication in immunocompromised individuals has been observed and may be a contributing source of novel viral variants that continue to drive the pandemic. Importantly, the effects of immunodeficiency associated with chronic HIV infection on COVID-19 disease and viral persistence have not been directly addressed in a controlled setting. Here we conducted a pilot study wherein two pigtail macaques (PTM) chronically infected with SIVmac239 were exposed to SARS-CoV-2 and monitored for six weeks for clinical disease, viral replication, and viral evolution, and compared to our previously published cohort of SIV-naive PTM infected with SARS-CoV-2. At the time of SARS-CoV-2 infection, one PTM had minimal to no detectable CD4+ T cells in gut, blood, or bronchoalveolar lavage (BAL), while the other PTM harbored a small population of CD4+ T cells in all compartments. Clinical signs were not observed in either PTM; however, the more immunocompromised PTM exhibited a progressive increase in pulmonary infiltrating monocytes throughout SARS-CoV-2 infection. Single-cell RNA sequencing (scRNAseq) of the infiltrating monocytes revealed a less activated/inert phenotype. Neither SIV-infected PTM mounted detectable anti-SARS-CoV-2 T cell responses in blood or BAL, nor anti-SARS-CoV-2 neutralizing antibodies. Interestingly, despite the diminished cellular and humoral immune responses, SARS-CoV-2 viral kinetics and evolution were indistinguishable from SIV-naive PTM in all sampled mucosal sites (nasal, oral, and rectal), with clearance of virus by 3-4 weeks post infection. SIV-induced immunodeficiency significantly impacted immune responses to SARS-CoV-2 but did not alter disease progression, viral kinetics or evolution in the PTM model. SIV-induced immunodeficiency alone may not be sufficient to drive the emergence of novel viral variants.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Alexandra Melton", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Lori A Rowe", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Toni Penney", + "author_inst": "Tulane University" + }, + { + "author_name": "Clara Krzykwa", + "author_inst": "Tulane University" + }, + { + "author_name": "Kelly Goff", + "author_inst": "Tulane University" + }, + { + "author_name": "Sarah E Scheuermann", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Hunter J Melton", + "author_inst": "Florida State University" + }, + { + "author_name": "Kelsey Williams", + "author_inst": "Tulane University" + }, + { + "author_name": "Nadia Golden", + "author_inst": "Tulane University" + }, + { + "author_name": "Kristyn Moore Green", + "author_inst": "Tulane University" + }, + { + "author_name": "Brandon Smith", + "author_inst": "Tulane University" + }, + { + "author_name": "Kasi Russell-Lodrigue", + "author_inst": "Tulane University" + }, + { + "author_name": "Jason P Dufour", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Lara A Doyle-Meyers", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Faith Schiro", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Pyone Pyone Aye", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Jeffrey D. Lifson", + "author_inst": "AIDS and Cancer Viruses Program, Frederick National Laboratory" + }, + { + "author_name": "Brandon J Beddingfield", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Robert V Blair", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Rudolf P Bohm", + "author_inst": "Oregon National Primate Research Center" + }, + { + "author_name": "Jay K Kolls", + "author_inst": "Tulane University" + }, + { + "author_name": "Jay Rappaport", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "James A Hoxie", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Nicholas J Maness", + "author_inst": "Tulane National Primate Research Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.11.13.566859", "rel_title": "Evolutionary arms race between SARS-CoV-2 and interferon signaling via dynamic interaction with autophagy.", @@ -40073,49 +41409,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.11.14.566998", - "rel_title": "COVID-19-related research data availability and quality according to the FAIR principles: A meta-research study", - "rel_date": "2023-11-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.14.566998", - "rel_abs": "BackgroundAs per the FAIR principles (Findable, Accessible, Interoperable, and Reusable), scientific research data should be findable, accessible, interoperable, and reusable. The COVID-19 pandemic has led to massive research activities and an unprecedented number of topical publications in a short time. There has not been any evaluation to assess if this COVID-19-related research data complied with FAIR principles (or FAIRness) so far.\n\nObjectiveOur objective was to investigate the availability of open data in COVID-19-related research and to assess compliance with FAIRness.\n\nMethodsWe conducted a comprehensive search and retrieved all open-access articles related to COVID-19 from journals indexed in PubMed, available in the Europe PubMed Central database, published from January 2020 through June 2023, using the metareadr package. Using rtransparent, a validated automated tool, we identified articles that included a link to their raw data hosted in a public repository. We then screened the link and included those repositories which included data specifically for their pertaining paper. Subsequently, we automatically assessed the adherence of the repositories to the FAIR principles using FAIRsFAIR Research Data Object Assessment Service (F-UJI) and rfuji package. The FAIR scores ranged from 1-22 and had four components. We reported descriptive analysis for each article type, journal category and repository. We used linear regression models to find the most influential factors on the FAIRness of data.\n\nResults5,700 URLs were included in the final analysis, sharing their data in a general-purpose repository. The mean (standard deviation, SD) level of compliance with FAIR metrics was 9.4 (4.88). The percentages of moderate or advanced compliance were as follows: Findability: 100.0%, Accessibility: 21.5%, Interoperability: 46.7%, and Reusability: 61.3%. The overall and component-wise monthly trends were consistent over the follow-up. Reviews (9.80, SD=5.06, n=160), and articles in dental journals (13.67, SD=3.51, n=3) and Harvard Dataverse (15.79, SD=3.65, n=244) had the highest mean FAIRness scores, whereas letters (7.83, SD=4.30, n=55), articles in neuroscience journals (8.16, SD=3.73, n=63), and those deposited in GitHub (4.50, SD=0.13, n=2,152) showed the lowest scores. Regression models showed that the most influential factor on FAIRness scores was the repository (R2=0.809).\n\nConclusionThis paper underscored the potential for improvement across all facets of FAIR principles, with a specific emphasis on enhancing Interoperability and Reusability in the data shared within general repositories during the COVID-19 pandemic.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ahmad Sofi-Mahmudi", - "author_inst": "McMaster University" - }, - { - "author_name": "Eero Raittio", - "author_inst": "University of Eastern Finland - Kuopio Campus: Ita-Suomen yliopisto - Kuopion kampus" - }, - { - "author_name": "Yeganeh Khazaei", - "author_inst": "LMU M\u00fcnchen: Ludwig-Maximilians-Universitat Munchen" - }, - { - "author_name": "Javed Ashraf", - "author_inst": "University of Eastern Finland: Ita-Suomen yliopisto" - }, - { - "author_name": "Falk Schwendicke", - "author_inst": "Charite Universitatsmedizin Berlin Campus Charite Mitte: Charite Universitatsmedizin Berlin" - }, - { - "author_name": "Sergio E. Uribe", - "author_inst": "Riga Stradins University: Rigas Stradina Universitate" - }, - { - "author_name": "David Moher", - "author_inst": "Ottawa Hospital Research Institute" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2023.11.14.567145", "rel_title": "CCR5/CXCR3 antagonist TAK-779 prevents diffuse alveolar damage of the lung in murine model of the SARS-CoV-2-related acute respiratory distress syndrome", @@ -41456,6 +42749,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.11.10.23298350", + "rel_title": "Effectiveness of non-pharmaceutical interventions on SARS-CoV-2 transmission during the period January 2021 until May 2022: A systematic literature review", + "rel_date": "2023-11-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.10.23298350", + "rel_abs": "ObjectivesIn response to the COVID-19 pandemic, countries implemented various non-pharmaceutical interventions(NPIs). With this systematic review, we investigated the effectiveness of NPIs in mitigating SARS-CoV-2 transmission by assessing empirical evidence and data obtained through modelling studies.\n\nDesignWe searched Medline(OVID) and EMBASE until 26 May 2022. The PICO framework was used to determine the eligibility of the studies. Populations were restricted to studies on humans, and there was no geographical limitation. The included articles assessed NPIs at the regional or national level as mitigation measures against SARS-CoV-2 transmission for human population without geographical limitation. Unmitigated SARS-CoV-2 transmission or the period before the implementation of the assessed NPI were used as the comparator.\n\nMain outcome measuresOutcome indicators were extracted and included COVID-19 cases, incidence and peaks, reproduction rate, growth rate, case mortality, and hospital and Intensive Care Unit admissions. Due to the heterogeneity between studies, statistical analysis was not possible and hence the results were presented narratively.\n\nResults49 studies were included; 21 based on empirical evidence and 28 modelling studies. Among the latter, the effectiveness of facemasks was evaluated in 11 studies, five assessed stay-at-home orders and five school closures. Regarding face mask use, the majority of studies presented a beneficial effect when appropriate social distancing measures could not be maintained. Restrictions on mass gatherings, stay-at-home-orders and lockdown measures were found to be effective in reducing SARS-CoV-2 transmission when timely and properly implemented. The results related to school closures were inconclusive.\n\nConclusionsThis systematic review assesses the effectiveness of NPIs in reducing SARS-CoV-2 transmission from January 2021 until May 2022. It suggests the importance of timely implementation and the optimised impact when implementing multiple NPIs in parallel. Continuous monitoring of the effectiveness of NPIs is required to determine the most suitable nature, time, and duration of the implemented NPIs.\n\nWhat is already known on this topicPrior to this study, it was recognised that in response to the COVID-19 pandemic, various non-pharmaceutical interventions (NPIs) such as hygiene measures, face mask usage, travel restrictions, social distancing, and contact tracing were implemented worldwide. The scientific community has been assessing the effectiveness of these NPIs in mitigating the pandemics impact on public health and the economy.\n\nWhat this study addsThis systematic review contributes by presenting updated and comprehensive evidence regarding the effectiveness of NPIs as a means of mitigating SARS-CoV-2 transmission, using both real-world evidence and data obtained through modelling studies. The study affirms that the timely application of NPIs, including the use of face masks, stay-at-home orders, restrictions on mass gatherings, and school closures, substantially reduced COVID-19 cases and fatalities. It underscores the significance of employing multiple NPIs in tandem for heightened effectiveness within future respiratory pandemics. The review emphasises the necessity for ongoing assessment of NPI efficacy, taking into account factors such as public compliance, vaccination rates, and the prevalence of virus variants.\n\nHow this study might affect research, practice, or policyThe findings of this study carry various implications. Firstly, they inform policymakers about the critical importance of promptly implementing NPIs and employing them in combination to manage respiratory pandemics. Secondly, the results underscore the enduring relevance of NPIs even as pandemic vaccination campaigns progress. Thirdly, the study highlights the need for standardized methodologies for evaluating the effectiveness of NPIs. Lastly, this review can guide future public health strategies by offering valuable insights into the impact of different interventions on pandemic control.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Constantine I. Vardavas", + "author_inst": "School of Medicine, University of Crete, Greece" + }, + { + "author_name": "Katerina Nikitara", + "author_inst": "School of Medicine, University of Crete, Greece" + }, + { + "author_name": "Katerina Aslanoglou", + "author_inst": "School of Medicine, University of Crete, Greece" + }, + { + "author_name": "Valia Marou", + "author_inst": "School of Medicine, University of Crete, Greece" + }, + { + "author_name": "Zinovia Plyta", + "author_inst": "School of Medicine, University of Crete, Greece" + }, + { + "author_name": "Revati Phalkey", + "author_inst": "Centre for Evidence Based Healthcare, Division of Epidemiology and Public Health, School of Medicine, University of Nottingham, UK" + }, + { + "author_name": "Jo Leonardi Bee", + "author_inst": "Centre for Evidence Based Healthcare, Division of Epidemiology and Public Health, School of Medicine, University of Nottingham, UK" + }, + { + "author_name": "Orla Condell", + "author_inst": "European Centre for Disease Prevention and Control, Solna, Sweden" + }, + { + "author_name": "Favelle Lamb", + "author_inst": "European Centre for Disease Prevention and Control, Solna, Sweden" + }, + { + "author_name": "Jonathan E. Suk", + "author_inst": "European Centre for Disease Prevention and Control, Solna, Sweden" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.11.08.566276", "rel_title": "Generation and characterization of a multi-functional panel of monoclonal antibodies for SARS-CoV-2 research and treatment", @@ -41899,53 +43247,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.11.07.566110", - "rel_title": "Nanoscale cellular organization of viral RNA and proteins in SARS-CoV-2 replication organelles", - "rel_date": "2023-11-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.07.566110", - "rel_abs": "The SARS-CoV-2 viral infection transforms host cells and produces special organelles in many ways, and we focus on the replication organelle where the replication of viral genomic RNA (vgRNA) occurs. To date, the precise cellular localization of key RNA molecules and replication intermediates has been elusive in electron microscopy studies. We use super-resolution fluorescence microscopy and specific labeling to reveal the nanoscopic organization of replication organelles that contain vgRNA clusters along with viral double-stranded RNA (dsRNA) clusters and the replication enzyme, encapsulated by membranes derived from the host endoplasmic reticulum (ER). We show that the replication organelles are organized differently at early and late stages of infection. Surprisingly, vgRNA accumulates into distinct globular clusters in the cytoplasmic perinuclear region, which grow and accommodate more vgRNA molecules as infection time increases. The localization of ER labels and nsp3 (a component of the double-membrane vesicle, DMV) at the periphery of the vgRNA clusters suggests that replication organelles are enclosed by DMVs at early infection stages which then merge into vesicle packets as infection progresses. Precise co-imaging of the nanoscale cellular organization of vgRNA, dsRNA, and viral proteins in replication organelles of SARS-CoV-2 may inform therapeutic approaches that target viral replication and associated processes.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Leonid Andronov", - "author_inst": "Department of Chemistry, Stanford University" - }, - { - "author_name": "Mengting Han", - "author_inst": "Department of Bioengineering, Stanford University" - }, - { - "author_name": "Yanyu Zhu", - "author_inst": "Department of Bioengineering, Stanford University" - }, - { - "author_name": "Anish R. Roy", - "author_inst": "Department of Chemistry, Stanford University" - }, - { - "author_name": "Andrew E. S. Barentine", - "author_inst": "Department of Chemistry, Stanford University" - }, - { - "author_name": "Jaishree Garhyan", - "author_inst": "In Vitro Biosafety Level 3 (BSL-3) Service Center, School of Medicine, Stanford University" - }, - { - "author_name": "Lei S. Qi", - "author_inst": "Department of Bioengineering & Sarafan ChEM-H, Stanford University" - }, - { - "author_name": "W.E. Moerner", - "author_inst": "Department of Bioengineering & Sarafan ChEM-H, Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.11.08.23297633", "rel_title": "Standardization and Comparison of Emergency Use Authorized COVID-19 Assays and Testing Laboratories", @@ -43338,6 +44639,61 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2023.11.03.564190", + "rel_title": "Blood transcriptomics analysis offers insights into variant-specific immune response to SARS-CoV-2", + "rel_date": "2023-11-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.11.03.564190", + "rel_abs": "Bulk RNA sequencing (RNA-seq) of blood is typically used for gene expression analysis in biomedical research but is still rarely used in clinical practice. In this study, we argue that RNA-seq should be considered a routine diagnostic tool, as it offers not only insights into aberrant gene expression and splicing but also delivers additional readouts on immune cell type composition as well as B-cell and T-cell receptor (BCR/TCR) repertoires. We demonstrate that RNA-seq offers vital insights into a patients immune status via integrative analysis of RNA-seq data from patients infected with various SARS-CoV-2 variants (in total 240 samples with up to 200 million reads sequencing depth). We compare the results of computational cell-type deconvolution methods (e.g., MCP-counter, xCell, EPIC, quanTIseq) to complete blood count data, the current gold standard in clinical practice. We observe varying levels of lymphocyte depletion and significant differences in neutrophil levels between SARS-CoV-2 variants. Additionally, we identify B and T cell receptor (BCR/TCR) sequences using the tools MiXCR and TRUST4 to show that - combined with sequence alignments and pBLAST - they could be used to classify a patients disease. Finally, we investigated the sequencing depth required for such analyses and concluded that 10 million reads per sample is sufficient. In conclusion, our study reveals that computational cell-type deconvolution and BCR/TCR methods using bulk RNA-seq analyses can supplement missing CBC data and offer insights into immune responses, disease severity, and pathogen-specific immunity, all achievable with a sequencing depth of 10 million reads per sample.\n\nKey PointsO_LIComputational deconvolution of transcriptomes can estimate immune cell abundances in SARS-CoV-2 patients, supplementing missing CBC data.\nC_LIO_LI10 million RNA sequencing reads per sample suffice for analyzing immune responses and disease severity, including BCR/TCR identification.\nC_LI", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Markus Hoffmann", + "author_inst": "NIDDK, NIH" + }, + { + "author_name": "Lina-Liv Willruth", + "author_inst": "Technical University Munich" + }, + { + "author_name": "Alexander Dietrich", + "author_inst": "Technical University Munich" + }, + { + "author_name": "Hye Kyung Lee", + "author_inst": "NIDDK, NIH" + }, + { + "author_name": "Ludwig Knabl", + "author_inst": "TyrolPath Obrist Brunhuber GMBH, Zams, Austria" + }, + { + "author_name": "Nico Trummer", + "author_inst": "Technical University Munich" + }, + { + "author_name": "Jan Baumbach", + "author_inst": "University of Hamburg: Universitat Hamburg" + }, + { + "author_name": "Priscilla A Furth", + "author_inst": "Georgetown University" + }, + { + "author_name": "Lothar Hennighausen", + "author_inst": "NIDDK, NIH" + }, + { + "author_name": "Markus List", + "author_inst": "Technical University Munich" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2023.11.02.565391", "rel_title": "Global Biogeography of the Soil Virosphere", @@ -43909,29 +45265,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2023.11.01.23297908", - "rel_title": "Gods Lockdown: the effect of the April 2022 Colorado low blizzard on SARS-Cov-2 transmission in the midwest United States", - "rel_date": "2023-11-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.11.01.23297908", - "rel_abs": "BackgroundLockdowns have been used as a primary non-pharmaceutical intervention to stop transmission of COVID19. There are many issues with interpreting the causal effects of most of these intentional, policy driven interventions. We leverage a natural experiment to avoid many of these issues to better understand the direct effects of lockdown like conditions on COVID19 transmission.\n\nMethodsWe exploit a blizzard that interrupted activity across several midwestern states in April 2022. This blizzard broke records for snowfall and caused economic disruption. We leverage this to create control and treatment counties that were more or less affected by the snowfall. We demonstrate effects using event studies comparing these treatment and control counties.\n\nResultsWe find that mobility within treatment counties was severely curtailed as a result of the blizzard relative to control counties. We find cumulative declines in the number of COVID19 cases per country by 400 and cumulative declines in COVID19 deaths by 1 per county over the 30 days after the storm. We find declines in by one per hospitalization due to COVID19.\n\nConclusionsThe April 2022 blizzard caused disruption in activity across the midwest United States akin to a lockdown. It reduced the number of COVID19 cases, deaths, and hospitalizations in treatment counties relative to control counties suggesting that similar policies do limit transmissions of SARS-Cov-2.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Stephenson Strobel", - "author_inst": "Weill Cornell Medical College" - }, - { - "author_name": "Michael Daly", - "author_inst": "Brooks School of Public Policy, Cornell University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.11.01.565087", "rel_title": "Phylogenetic meta-analysis of chronic SARS-CoV-2 infections in immunocompromised patients shows no evidence of elevated evolutionary rates", @@ -45036,6 +46369,37 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2023.10.28.564530", + "rel_title": "Deciphering the code of viral-host adaptation through maximum entropy models", + "rel_date": "2023-10-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.28.564530", + "rel_abs": "Understanding how the genome of a virus evolves depending on the host it infects is an important question that challenges our knowledge about several mechanisms of host-pathogen interactions, including mutational signatures, innate immunity, and codon optimization. A key facet of this general topic is the study of viral genome evolution after a host-jumping event, a topic which has experienced a surge in interest due to the fight against emerging pathogens such as SARS-CoV-2. In this work, we tackle this question by introducing a new method to learn Maximum Entropy Nucleotide Bias models (MENB) reflecting single, di- and tri-nucleotide usage, which can be trained from viral sequences that infect a given host. We show that both the viral family and the host leave a fingerprint in nucleotide usages which MENB models decode. When the task is to classify both the host and the viral family for a sequence of unknown viral origin MENB models outperform state of the art methods based on deep neural networks. We further demonstrate the generative properties of the proposed framework, presenting an example where we change the nucleotide composition of the 1918 H1N1 Influenza A sequence without changing its protein sequence, while manipulating the nucleotide usage, by diminishing its CpG content. Finally we consider two well-known cases of zoonotic jumps, for the H1N1 Influenza A and for the SARS-CoV-2 viruses, and show that our method can be used to track the adaptation to the new host and to shed light on the more relevant selective pressures which have acted on motif usage during this process. Our work has wide-ranging applications, including integration into metagenomic studies to identify hosts for diverse viruses, surveillance of emerging pathogens, prediction of synonymous mutations that effect immunogenicity during viral evolution in a new host, and the estimation of putative evolutionary ages for viral sequences in similar scenarios. Additionally, the computational frame-work introduced here can be used to assist vaccine design by tuning motif usage with fine-grained control.\n\nAuthor summaryIn our research, we delved into the fascinating world of viruses and their genetic changes when they jump from one host to another, a critical topic in the study of emerging pathogens. We developed a novel computational method to capture how viruses change the nucleotide usage of their genes when they infect different hosts. We found that viruses from various families have unique strategies for tuning their nucleotide usage when they infect the same host. Our model could accurately pinpoint which host a viral sequence came from, even when the sequence was vastly different from the ones we trained on. We demonstrated the power of our method by altering the nucleotide usage of an RNA sequence without affecting the protein it encodes, providing a proof-of-concept of a method that can be used to design better RNA vaccines or to fine-tune other nucleic acid-based therapies. Moreover the framework we introduce can help tracking emerging pathogens, predicting synonymous mutations in the adaptation to a new host and estimating how long viral sequences have been evolving in it. Overall, our work sheds light on the intricate interactions between viruses and their hosts.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Andrea Di Gioacchino", + "author_inst": "Ecole Normale Superieure" + }, + { + "author_name": "Benjamin D Greenbaum", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Remi Monasson", + "author_inst": "Ecole Normale Superieure" + }, + { + "author_name": "Simona Cocco", + "author_inst": "Ecole Normale Superieure" + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2023.10.27.564435", "rel_title": "Colloidal aggregation confounds cell-based Covid-19 antiviral screens", @@ -45447,105 +46811,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, - { - "rel_doi": "10.1101/2023.10.26.23297608", - "rel_title": "Understanding COVID-19 testing behaviour in England through a sociodemographic lens", - "rel_date": "2023-10-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.26.23297608", - "rel_abs": "BackgroundUnderstanding underlying mechanisms of heterogeneity in test-seeking and reporting behaviour can help to protect the vulnerable and guide equity-driven interventions. Using COVID-19 testing data for England and data from community prevalence surveillance surveys (REACT-1 and ONS-CIS) from October 2020 to March 2022, we investigated the relationship between sociodemographic factors and testing behaviours in England.\n\nMethodsWe used mass testing data for lateral flow device (LFD; data for 290 million tests performed and reported) and polymerase chain reaction (PCR) (data for 107 million tests performed and returned from the laboratory) tests made available for the general public, provided by date, self-reported age and ethnicity at lower tier local authority (LTLA) level. Using a mechanistic causal model to debias the PCR testing data, we obtained estimates of weekly SARS-CoV-2 prevalence by self-reported ethnic groups and age groups for LTLAs in England. This approach to debiasing the PCR (or LFD) testing data also estimated a testing bias parameter defined as the odds of testing in infected versus not infected individuals, which would be close to zero if the likelihood of test seeking (or seeking and reporting) was the same regardless of infection status. Using confirmatory PCR data, we estimated false positivity rates, sensitivity, specificity, and the rate of decline in detection probability by PCR by sociodemographic groups. We also estimated the daily incidence allowing us to determine the fraction of cases captured by the testing programme.\n\nFindingsFrom March 2021 onwards, individuals in the most deprived regions reported approximately half as many LFD tests per-capita than those in the least deprived areas (Median ratio [Inter quartile range, IQR]: 0{middle dot}50 [0{middle dot}44, 0{middle dot}54]). During October 2020 - June 2021, PCR testing patterns were in the opposite direction (Median ratio [IQR]: 1{middle dot}8 [1{middle dot}7, 1{middle dot}9]). Infection prevalences in Asian or Asian British communities were considerably higher than those of other ethnic groups during the Alpha and Omicron BA.1 waves. Our estimates indicate that the England COVID-19 testing program detected 26% - 40% of all cases (including asymptomatic cases) over the study period with no consistent differences by deprivation levels or ethnic groups.\n\nPCR testing biases were generally higher than for LFDs, which was in line with the general policy of symptomatic and asymptomatic use of these tests. During the invasion phases of the Delta and Omicron variants of concern, the PCR testing bias in the most deprived populations was roughly double (ratio: 2{middle dot}2 and 2{middle dot}7 respectively) that in the least. We also determined that ethnic minorities and older individuals were less likely to use confirmatory PCR tests through most of the pandemic and that there was possibly a longer delay in reporting a positive LFD test in the Black populations.\n\nInterpretationDifferences in testing behaviours across sociodemographic groups may be reflective of the relatively higher costs of self-isolation to vulnerable populations, differences in test accessibility, digital literacy, and differing perception about the utility of tests and risks posed by infection. Our work shows how mass testing data can be used in conjunction with surveillance surveys to identify gaps in the uptake of public health interventions at fine scale levels and by sociodemographic groups. It provides a framework for monitoring local interventions and yields valuable lessons for policy makers in ensuring an equitable response to future pandemics.\n\nFundingUK Health Security Agency.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Sumali Bajaj", - "author_inst": "University of Oxford" - }, - { - "author_name": "Siyu Chen", - "author_inst": "University of Oxford" - }, - { - "author_name": "Richard Creswell", - "author_inst": "University of Oxford" - }, - { - "author_name": "Reshania Naidoo", - "author_inst": "University of Oxford, Ernst & Young (EY) UKI Health Sciences and Wellness" - }, - { - "author_name": "Joseph L.-H. Tsui", - "author_inst": "University of Oxford" - }, - { - "author_name": "Olumide Kolade", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "George Nicholson", - "author_inst": "University of Oxford, The Alan Turing Institute and Royal Statistical Society Health Data Lab" - }, - { - "author_name": "Brieuc Lehmann", - "author_inst": "University College London, The Alan Turing Institute and Royal Statistical Society Health Data Lab" - }, - { - "author_name": "James A. Hay", - "author_inst": "University of Oxford" - }, - { - "author_name": "Moritz U.G. Kraemer", - "author_inst": "University of Oxford" - }, - { - "author_name": "Ricardo Aguas", - "author_inst": "University of Oxford" - }, - { - "author_name": "Christl A. Donnelly", - "author_inst": "University of Oxford, Imperial College London" - }, - { - "author_name": "Tom Fowler", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Susan Hopkins", - "author_inst": "UK Health Security Agency" - }, - { - "author_name": "Liberty Cantrell", - "author_inst": "University of Oxford" - }, - { - "author_name": "Prabin Dahal", - "author_inst": "University of Oxford" - }, - { - "author_name": "Lisa J. White", - "author_inst": "University of Oxford" - }, - { - "author_name": "Kasia Stepniewska", - "author_inst": "University of Oxford" - }, - { - "author_name": "Merryn Voysey", - "author_inst": "University of Oxford" - }, - { - "author_name": "Ben Lambert", - "author_inst": "University of Oxford, University of Exeter" - }, - { - "author_name": "- EY-Oxford Health Analytics Consortium", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.10.26.23297597", "rel_title": "Complement dysregulation is a predictive and therapeutically amenable feature of long COVID", @@ -46962,6 +48227,81 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.10.24.563841", + "rel_title": "Simulation-Driven Design of Stabilized SARS-CoV-2 Spike S2 Immunogens", + "rel_date": "2023-10-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.24.563841", + "rel_abs": "The full-length prefusion-stabilized SARS-CoV-2 spike (S) is the principal antigen of COVID-19 vaccines. Vaccine efficacy has been impacted by emerging variants of concern that accumulate most of the sequence modifications in the immunodominant S1 subunit. S2, in contrast, is the most evolutionarily conserved region of the spike and can elicit broadly neutralizing and protective antibodies. Yet, S2s usage as an alternative vaccine strategy is hampered by its general instability. Here, we use a simulation-driven approach to design S2-only immunogens stabilized in a closed prefusion conformation. Molecular simulations provide a mechanistic characterization of the S2 trimers opening, informing the design of tryptophan substitutions that impart kinetic and thermodynamic stabilization. Structural characterization via cryo-EM shows the molecular basis of S2 stabilization in the closed prefusion conformation. Informed by molecular simulations and corroborated by experiments, we report an engineered S2 immunogen that exhibits increased protein expression, superior thermostability, and preserved immunogenicity against sarbecoviruses.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Xandra Nuqui", + "author_inst": "UC San Diego" + }, + { + "author_name": "Lorenzo Casalino", + "author_inst": "UC San Diego" + }, + { + "author_name": "Ling Zhou", + "author_inst": "UT Austin" + }, + { + "author_name": "Mohamed Shehata", + "author_inst": "UC San Diego" + }, + { + "author_name": "Albert Wang", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Alexandra L. Tse", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Anupam Ojha", + "author_inst": "UC San Diego" + }, + { + "author_name": "Fiona L. Kearns", + "author_inst": "UC San Diego" + }, + { + "author_name": "Mia A. Rosenfeld", + "author_inst": "UC San Diego / NIH" + }, + { + "author_name": "Emily Happy Miller", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Cory M. Acreman", + "author_inst": "UT Austin" + }, + { + "author_name": "Surl-Hee Ahn", + "author_inst": "UC Davis" + }, + { + "author_name": "Kartik Chandran", + "author_inst": "Albert Einstein College of Medicine" + }, + { + "author_name": "Jason S. McLellan", + "author_inst": "UT Austin" + }, + { + "author_name": "Rommie E Amaro", + "author_inst": "University of California, San Diego" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2023.10.24.563866", "rel_title": "Cross-platform comparison of highly-sensitive immunoassays for inflammatory markers in a COVID-19 cohort", @@ -47625,61 +48965,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.10.24.23297192", - "rel_title": "COVID-19 vaccination-induced antibody responses and waning by age and comorbidity status in a large population-based prospective cohort study", - "rel_date": "2023-10-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.24.23297192", - "rel_abs": "BackgroundInformation on the magnitude and duration of antibody levels after COVID-19 vaccination in different groups may be useful for prioritizing of additional vaccinations.\n\nMethodsSerum samples were collected every six months in a prospective cohort study among adults in the Netherlands. Geometric mean concentrations (GMCs) of antibodies against the receptor binding domain of the SARS-CoV-2 spike protein were calculated after the primary series, first, and second booster vaccinations. Effects of age (18-59 vs 60-85 years) and medical risk conditions on GMC 2-6 weeks and 21-25 weeks after each vaccination, and on waning during 3-25 weeks after each vaccination, were estimated by linear regression.\n\nResultsWe included 20,816, 16,820 and 5,879 samples collected after primary, first and second booster vaccination, respectively. GMCs at 2-6 and 21-25 weeks after primary series were lower in participants with older age or medical risk conditions. After the first booster, older age was associated with lower GMC at 2-6 weeks, higher GMC at 21-25 weeks, and slower waning. GMCs or waning after the first and second boosters (only 60-85) were not associated with medical risk conditions.\n\nConclusionsSince antibody differences by age and medical risk groups have become small with increasing number of doses, other factors such as disease severity rather than antibody levels are useful for prioritization of additional vaccinations.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Christina E Hoeve", - "author_inst": "National Institute for Public Health and Environment" - }, - { - "author_name": "Anne J. Huiberts", - "author_inst": "National Institute for Public Health and Environment" - }, - { - "author_name": "Brechje de Gier", - "author_inst": "National Institute for Public Health and Environment" - }, - { - "author_name": "Stijn P Andeweg", - "author_inst": "National Institute for Public Health and Environment" - }, - { - "author_name": "Gerco den Hartog", - "author_inst": "National Institute for Public Health and Environment" - }, - { - "author_name": "Hester E de Melker", - "author_inst": "National Institute for Public Health and Environment" - }, - { - "author_name": "Susan JM Hahne", - "author_inst": "National Institute for Public Health and Environment" - }, - { - "author_name": "Janneke HHM van de Wijgert", - "author_inst": "National Institute for Public Health and Environment" - }, - { - "author_name": "Susan van den Hof", - "author_inst": "National Institute for Public Health and Environment" - }, - { - "author_name": "Mirjam Knol", - "author_inst": "National Institute for Public Health and the Environment" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.10.24.23297475", "rel_title": "Projections of the incidence of COVID-19 in Japan and the potential impact of a Fall 2023 COVID-19 Vaccine", @@ -48924,6 +50209,89 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.10.20.23297306", + "rel_title": "Assessment of Sociodemographic Factors Associated with Time to Self-reported COVID-19 Infection Among a Large Multi-Center Prospective Cohort Population in the Southeastern United States", + "rel_date": "2023-10-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.20.23297306", + "rel_abs": "ObjectiveWe aimed to investigate sociodemographic factors associated with self-reported COVID-19 infection.\n\nMethodsThe study population is a multicenter prospective cohort of adult volunteers recruited from healthcare systems located in the mid-Atlantic and southern United States. Between April 2020 and October 2021 participants completed daily online questionnaires about symptoms, exposures, and risk behaviors related to COVID-19, including self-reports of positive SARS CoV-2 detection tests and COVID-19 vaccination. Analysis of time from study enrollment to self-reported COVID-19 infection used a time-varying mixed effects Cox-proportional hazards framework.\n\nResultsOverall, 1,603 of 27,214 study participants (5.9%) reported a positive COVID-19 test during the study period. The adjusted hazard ratio demonstrated lower risk for women, those with a graduate level degree, and smokers. A higher risk was observed for healthcare workers, those aged 18-34, those in rural areas, those from households where a member attends school or interacts with the public, and those who visited a health provider in the last year.\n\nConclusionsIncreased risk of self-reported COVID-19 was associated with specific demographic characteristics, which may help to inform targeted interventions for future pandemics.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Andrew J Beron", + "author_inst": "Tulane University School of Public Health and Tropical Medicine" + }, + { + "author_name": "Joshua O. Yukich", + "author_inst": "Tulane University School of Public Health and Tropical Medicine" + }, + { + "author_name": "Andrea A. Berry", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Adolfo Correa", + "author_inst": "University of Mississippi University Hospital: The University of Mississippi Medical Center" + }, + { + "author_name": "Joseph Keating", + "author_inst": "Tulane University School of Public Health and Tropical Medicine" + }, + { + "author_name": "Matthew Bott", + "author_inst": "George Washington University School of Public Health and Health Services: The George Washington University Milken Institute of Public Health" + }, + { + "author_name": "Thomas F Wierzba", + "author_inst": "Wake Forest School of Medicine: Wake Forest University School of Medicine" + }, + { + "author_name": "William S Weintraub", + "author_inst": "MedStar Research Institute: MedStar Health Research Institute" + }, + { + "author_name": "Deanna J Friedman-Klabanoff", + "author_inst": "University of Maryland Medical System Corporation: University of Maryland Medical System" + }, + { + "author_name": "Morgana Mongraw-Chaffin", + "author_inst": "Wake Forest School of Medicine: Wake Forest University School of Medicine" + }, + { + "author_name": "Michael A. Gibbs", + "author_inst": "Atrium Health" + }, + { + "author_name": "Yhenneko J. Taylor", + "author_inst": "Atrium Health" + }, + { + "author_name": "Patricia J. Kissinger", + "author_inst": "Tulane University School of Public Health and Tropical Medicine" + }, + { + "author_name": "Devin V. Hayes", + "author_inst": "Vysnova Partners" + }, + { + "author_name": "John S. Schieffelin", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Brian Burke", + "author_inst": "George Washington University School of Public Health and Health Services: The George Washington University Milken Institute of Public Health" + }, + { + "author_name": "Richard A Oberhelman", + "author_inst": "Tulane University School of Public Health and Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.10.20.23297317", "rel_title": "Reduced risk of SARS-CoV-2 infection among household contacts with recent vaccination and past COVID-19 infection: results from two multi-site case-ascertained household transmission studies", @@ -49547,29 +50915,6 @@ "type": "confirmatory results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2023.10.19.563184", - "rel_title": "Divergent spike mutations impact the activation of the fusion core in Delta and Omicronvariants of SARS-CoV-2", - "rel_date": "2023-10-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.19.563184", - "rel_abs": "SARS-CoV-2 infects host cells by binding the receptor-binding domain (RBD) of its spike protein to the receptor, ACE2. A subset of highly effective spike mutations plays critical roles in altering the conformational dynamics of spike protein. Here, we use molecular dynamics simulations to investigate how spike mutations affect the conformational dynamics of spike/ACE2 complex in the D614G, Delta (B.1.617.2) and Omicron (B.1.1.529) SARS-CoV-2 variants. We observe that the increased positive-charged mutations in the Omicron spike amplify its structural rigidity and reduce its structural flexibility. The mutations (P681R in Delta and P681H in Omicron) at the S1/S2 junction facilitate S1/S2 cleavage and aid the activation of the fusion core. We report that high structural flexibility in Delta lowers the barrier for the activation of the S2 core; however, high structural rigidity in Omicron enhances the barrier for the same. Our results also explain why Omicron requires the presence of a higher number of ACE2 to activate its fusion core than Delta.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Mandira Dutta", - "author_inst": "The University of Chicago" - }, - { - "author_name": "Gregory A Voth", - "author_inst": "University of Chicago" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2023.10.20.23297300", "rel_title": "Relative vaccine effectiveness of a CoronaVac booster dose in preventing symptomatic SARS-CoV-2 infection among healthcare workers during an Omicron period in Azerbaijan, January-August 2022", @@ -50470,6 +51815,181 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2023.10.15.23295628", + "rel_title": "Omicron COVID-19 Immune Correlates Analysis of a Third Dose of mRNA-1273 in the COVE Trial", + "rel_date": "2023-10-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.15.23295628", + "rel_abs": "In the coronavirus efficacy (COVE) phase 3 efficacy trial of the mRNA-1273 vaccine, IgG binding antibody (bAb) concentration against Spike (BA.1 strain) and neutralizing antibody (nAb) titer against Spike (BA.1 strain) pseudovirus were assessed as correlates of risk of Omicron COVID-19 and as correlates of relative boost efficacy in per-protocol recipients of a third (booster) dose. Markers were measured on the day of the boost (BD1) and 28 days later (BD29). For SARS-CoV-2 naive individuals, BD29 Spike IgG-BA.1 strain bAbs and BD29 BA.1-strain nAbs inversely correlated with Omicron COVID-19: hazard ratio (HR) per 10-fold marker increase [95% confidence interval (CI)] = 0.16 (0.03, 0.79); P=0.024 and 0.31 (0.10, 0.96); P = 0.042, respectively. These markers also inversely correlated with Omicron COVID-19 in non-naive individuals: HR = 0.15 (0.04, 0.63); P = 0.009 and 0.28 (0.07, 1.08); P = 0.06, trend. Fold-rise in markers from BD1 to BD29 had similarly strong inverse correlations. For SARS-CoV-2 naive individuals, overall booster relative (three-dose vs two-dose) efficacy was 46% (95% CI: 20%, 64%) and correlated with BA.1 strain nAb titer at exposure. At 56, 251, and 891 arbitrary units (AU)/ml (10th, 50th, and 90th percentile), the booster relative efficacies were -8% (95% CI: -126%, 48%), 50% (25%, 67%), and 74% (49%, 87%), respectively. Similar relationships were observed for Spike IgG-BA.1 strain bAbs and for the markers measured at BD29. The performance of bAb and nAb markers as correlates of protection against Omicron COVID-19 supports their continued use as surrogate endpoints for mRNA vaccination against Omicron COVID-19.", + "rel_num_authors": 40, + "rel_authors": [ + { + "author_name": "Bo Zhang", + "author_inst": "Fred Hutchinson Cancer Center" + }, + { + "author_name": "Youyi Fong", + "author_inst": "Fred Hutchinson Cancer Center" + }, + { + "author_name": "Jonathan Fintzi", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Eric Chu", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Holly E. Janes", + "author_inst": "Fred Hutchinson Cancer Center" + }, + { + "author_name": "Lindsay N. Carpp", + "author_inst": "Fred Hutchinson Cancer Center" + }, + { + "author_name": "Avi Kenny", + "author_inst": "University of Washington" + }, + { + "author_name": "Marco Carone", + "author_inst": "University of Washington" + }, + { + "author_name": "David Benkeser", + "author_inst": "Emory University" + }, + { + "author_name": "Lars W. P. van der Laan", + "author_inst": "University of Washington" + }, + { + "author_name": "Weiping Deng", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Honghong Zhou", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Xiaowei Wang", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Yiwen Lu", + "author_inst": "Fred Hutchinson Cancer Center" + }, + { + "author_name": "Chenchen Yu", + "author_inst": "Fred Hutchinson Cancer Center" + }, + { + "author_name": "Bhavesh Borate", + "author_inst": "Fred Hutchinson Cancer Center" + }, + { + "author_name": "Christopher R. Houchens", + "author_inst": "Biomedical Advanced Research and Development Authority" + }, + { + "author_name": "Karen Martins", + "author_inst": "Biomedical Advanced Research and Development Authority" + }, + { + "author_name": "Lakshmi Jayashankar", + "author_inst": "Biomedical Advanced Research and Development Authority" + }, + { + "author_name": "Chuong Huynh", + "author_inst": "Biomedical Advanced Research and Development Authority" + }, + { + "author_name": "Carl J. Fichtenbaum", + "author_inst": "University of Cincinnati" + }, + { + "author_name": "Spyros Kalams", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Cynthia L. Gay", + "author_inst": "University of Carolina at Chapel Hill School of Medicine" + }, + { + "author_name": "Michele P. Andrasik", + "author_inst": "Fred Hutchinson Cancer Center" + }, + { + "author_name": "James G. Kublin", + "author_inst": "Fred Hutchinson Cancer Center" + }, + { + "author_name": "Lawrence Corey", + "author_inst": "Fred Hutchinson Cancer Center" + }, + { + "author_name": "Kathleen M. Neuzil", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Frances Priddy", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Rituparna Das", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Bethany Girard", + "author_inst": "Moderna, Inc." + }, + { + "author_name": "Hana M. El Sahly", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Lindsey R. Baden", + "author_inst": "Brigham and Womens Hospital" + }, + { + "author_name": "Ruben O. Donis", + "author_inst": "Biomedical Advanced Research and Development Authority" + }, + { + "author_name": "Richard A. Koup", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Peter B. Gilbert", + "author_inst": "Fred Hutchinson Cancer Center" + }, + { + "author_name": "Dean Follmann", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "- United States Government (USG) COVID-19 Immune Assays Team", + "author_inst": "-" + }, + { + "author_name": "- Moderna, Inc. Team", + "author_inst": "-" + }, + { + "author_name": "- Coronavirus Vaccine Prevention Network (CoVPN)/Coronavirus Efficacy (COVE) Team", + "author_inst": "-" + }, + { + "author_name": "- USG/CoVPN Biostatistics Team", + "author_inst": "-" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.10.14.23296666", "rel_title": "Surveillance and Stability of SARS-CoV-2 Wastewater Samples in Minnesota", @@ -51024,7 +52544,7 @@ "rel_date": "2023-10-14", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.10.12.561935", - "rel_abs": "Genetic innovation is fundamental to the ability of viruses to adapt in the face of host immunity. Coronaviruses exhibit many mechanisms of innovation given flexibility in genomic composition relative to most RNA virus families1-5. Examples include the acquisition of unique accessory genes that can originate by capture of cellular genes or through duplication and divergence of existing viral genes6,7. Accessory genes may be influential in dictating viral host range and cellular tropism, but little is known about how selection acts on these variable regions of virus genomes. We used experimental evolution of mouse hepatitis virus (MHV) with an inactive native phosphodiesterase, NS2, that encodes a complementing cellular AKAP7 gene9, to simulate the capture of a host gene and found hidden patterns of constraint that determine the fate of coronavirus accessory genes. After courses of serial infection, AKAP7 was retained under strong selection but rapidly lost under relaxed selection. In contrast, the gene encoding inactive NS2, ORF2, remained intact, suggesting it is under cryptic evolutionary constraint. Guided by the retention of ORF2 and hints of similar patterns in related betacoronaviruses, we analyzed the evolution of SARS-CoV-2 ORF8, which arose via gene duplication6 and contains premature stop codons in several globally successful lineages. As with MHV ORF2, the coding-defective SARS- CoV-2 ORF8 gene remains largely intact, mirroring patterns observed during MHV experimental evolution and extending these findings to viruses currently adapting to humans. Retention of inactive genes challenges assumptions on the dynamics of gene loss in virus genomes and can help guide evolutionary analysis of emerging and pandemic coronaviruses.", + "rel_abs": "Coronaviruses exhibit many mechanisms of genetic innovation (1-5), including the acquisition of accessory genes that originate by capture of cellular genes or through duplication of existing viral genes (6,7). Accessory genes influence viral host range and cellular tropism, but little is known about how selection acts on these variable regions of virus genomes. We used experimental evolution of mouse hepatitis virus (MHV) encoding a cellular AKAP7 phosphodiesterase and an inactive native phosphodiesterase, NS2 (ref 8) to simulate the capture of a host gene and analyze its evolution. After courses of serial infection, the gene encoding inactive NS2, ORF2, unexpectedly remained intact, suggesting it is under cryptic constraint uncoupled from the function of NS2. In contrast, AKAP7 was retained under strong selection but rapidly lost under relaxed selection. Guided by the retention of ORF2 and similar patterns in related betacoronaviruses, we analyzed ORF8 of SARS-CoV-2, which arose via gene duplication6 and contains premature stop codons in several globally successful lineages. As with MHV ORF2, the coding-defective SARS-CoV-2 ORF8 gene remains largely intact, mirroring patterns observed during MHV experimental evolution, challenging assumptions on the dynamics of gene loss in virus genomes and extending these findings to viruses currently adapting to humans.", "rel_num_authors": 7, "rel_authors": [ { @@ -51061,109 +52581,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2023.10.12.23296928", - "rel_title": "Evolution of SARS-CoV-2 in the RhineNeckar/Heidelberg Region 01/2021 07/2023", - "rel_date": "2023-10-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.12.23296928", - "rel_abs": "At the beginning of 2021 the monitoring of the circulating variants of SARS-CoV-2 was established in Germany in accordance with the Corona Surveillance Act (discontinued after July 2023) to allow a better containment of the pandemic, because certain amino acid exchanges (especially) in the spike protein lead to higher transmission as well as a reduced vaccination efficacy.\n\nTherefore, our group performed whole genome sequencing applying the ARTIC protocol (currently V4) on Illuminas NextSeq 500 platform (and starting in May 2023 on the MiSeq DX platform) for SARS-CoV-2 positive specimen from patients of the Heidelberg University Hospital (and associated hospitals) as well as the Public health office in Rhine-Neckar/Heidelberg region.\n\nOur group sequenced a total of 26,795 SARS-CoV-2-positive samples between January 2021 and July 2023 - valid sequences, according to the requirements for sequence upload to the German electronic sequencing data hub (DESH) operated by the Robert Koch Institute (RKI), could be determined for 24,852 samples, while the lineage/clade could be identified for 25,912 samples.\n\nWhile the year 2021 was very dynamic and changing regarding the circulating variants in the Rhine-Neckar/Heidelberg region with the initial non-variant of concerns, followed by A.27.RN and the rise of B.1.1.7 in winter/spring and its displacement by B.1.617.2 in spring/summer, which remained almost exclusive until the beginning of December and the first B.1.1.529 incidences, which rose to a proportion of 40 percent by the end of 2021 (and superseded B.1.617.2 by January 2022 with a proportion of over 90 percent). The years 2022 and 2023 were then dominated by B.1.1.529 and its numerous sublineages, especially BA.5 and BA.2, and more recently by the rise of recombinant variants, such as XBB.1.5. By the end of July 2023 (and since calendar week 20) the proportion of the recombinant variants amounted to 100 percent of all circulating variants in the Rhine-Neckar/Heidelberg region.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Christian Bundschuh", - "author_inst": "Medical University Heidelberg" - }, - { - "author_name": "Niklas Weidner", - "author_inst": "Heidelberg University Medical Faculty Heidelberg" - }, - { - "author_name": "Julian Klein", - "author_inst": "Heidelberg University Medical Faculty Heidelberg" - }, - { - "author_name": "Tobias Rausch", - "author_inst": "EMBL Heidelberg Genomics Core Facility" - }, - { - "author_name": "Nayara Azevedo", - "author_inst": "EMBL Heidelberg Genomics Core Facility" - }, - { - "author_name": "Anja Telzerow", - "author_inst": "Heidelberg University Medical Faculty Heidelberg" - }, - { - "author_name": "Jan-Philipp Mallm", - "author_inst": "German Cancer Research Center" - }, - { - "author_name": "Heeyoung Kim", - "author_inst": "Heidelberg University Medical Faculty Heidelberg" - }, - { - "author_name": "Simon Steiger", - "author_inst": "German Cancer Research Center" - }, - { - "author_name": "Isabella Seufert", - "author_inst": "German Cancer Research Center" - }, - { - "author_name": "Kathleen Boerner", - "author_inst": "Heidelberg University Medical Faculty Heidelberg" - }, - { - "author_name": "Katharina Bauer", - "author_inst": "German Cancer Research Center" - }, - { - "author_name": "Daniel Huebschmann", - "author_inst": "German Cancer Research Center" - }, - { - "author_name": "Katharina Laurence Jost", - "author_inst": "Heidelberg University Medical Faculty Heidelberg" - }, - { - "author_name": "Sylvia Parthe", - "author_inst": "Heidelberg University Medical Faculty Heidelberg" - }, - { - "author_name": "Paul Schnitzler", - "author_inst": "Heidelberg University Medical Faculty Heidelberg" - }, - { - "author_name": "Michael Boutros", - "author_inst": "German Cancer Research Center" - }, - { - "author_name": "Karsten Rippe", - "author_inst": "German Cancer Research Center" - }, - { - "author_name": "Barbara Mueller", - "author_inst": "Heidelberg University Medical Faculty Heidelberg" - }, - { - "author_name": "Ralf Bartenschlager", - "author_inst": "Heidelberg University Medical Faculty Heidelberg" - }, - { - "author_name": "Hans-Georg Kraeusslich", - "author_inst": "Heidelberg University Medical Faculty Heidelberg" - }, - { - "author_name": "Vladimir Benes", - "author_inst": "EMBL Heidelberg Genomics Core Facility" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.10.12.23296888", "rel_title": "Mathematical modeling of SARS-CoV-2 variant substitutions in European countries: Transmission dynamics and epidemiological insights", @@ -52412,6 +53829,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "addiction medicine" }, + { + "rel_doi": "10.1101/2023.10.10.23296807", + "rel_title": "Scaling COVID-19 rates with population size in the United States", + "rel_date": "2023-10-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.10.23296807", + "rel_abs": "We assessed Urban Scaling Theory using time-series data by quantifying allometric scaling relationships of coronavirus disease (COVID-19) cases, deaths, and demographic cohorts within and across three major variant waves of the pandemic (first, delta, omicron). Results indicate that with county-level population size in the United States, the burden of cases disproportionately impacted larger-sized counties. In contrast, the burden of deaths disproportionately impacted smaller counties, which may be partially due to a higher proportion of older adults who live in smaller counties. Future infectious disease burden across populations might be attenuated by applying Urban Scaling Theory to epidemiological efforts through identifying disease allometry and concomitant allocation of medical interventions.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Austin R. Cruz", + "author_inst": "University of Arizona" + }, + { + "author_name": "Brian J. Enquist", + "author_inst": "University of Arizona" + }, + { + "author_name": "Joseph R. Burger", + "author_inst": "University of Kentucky" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.10.10.23296792", "rel_title": "Surrogate virus neutralisation test based on nanoluciferase-tagged antigens to quantify inhibitory antibodies against SARS-CoV-2 and characterise Omicron-specific reactivity", @@ -53135,57 +54579,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.10.09.23296728", - "rel_title": "Impact of sampling site on diagnostic test accuracy of RT-PCR in diagnosing Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection since the emergence of omicron: a systematic review and meta-analysis", - "rel_date": "2023-10-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.09.23296728", - "rel_abs": "Nasopharyngeal sampling (NP) is the routine standard for SASR-CoV-2 detection using reverse transcription polymerase chain reaction (RT-PCR). In this systematic review, we assessed diagnostic test accuracy of alternative sampling sites compared to NP for RT-PCR testing of Omicron (sub)-variants.\n\nWe systematically searched for studies from January 2022 until February 2023 investigating any type of respiratory sample for RT-PCR in people with suspected, known, or known absence of SARS-CoV-2 Omicron infection. Data were pooled for each comparison using the bivariate model, sensitivity and specificity was estimated with 95% confidence intervals (CIs). Risk of bias was assessed with QUADAS-2 tool, certainty of evidence with GRADE.\n\nWe included three cohort-type cross-sectional studies (1,003 participants). Saliva versus NP sampling in three studies showed a sensitivity of 92% (95% CI 87% to 96%) and a specificity of 94% (95% CI 83% to 98%). AN versus NP sampling in one study showed a sensitivity of 90% (95% CI 82% to 95%) and a specificity of 99% (95% CI 95% to 100%). Certainty of evidence for sensitivity and specificity of both comparisons was low to very low.\n\nBased on the current very low- to low-certainty evidence, we are uncertain about accuracy of different sampling sites for RT-PCR.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Lena Saal-Bauernschubert", - "author_inst": "University Hospital Wuerzburg" - }, - { - "author_name": "Carina Wagner", - "author_inst": "University of Cologne" - }, - { - "author_name": "Alexey Fomenko", - "author_inst": "Technical University of Munich" - }, - { - "author_name": "Theo Daehne", - "author_inst": "University of Freiburg" - }, - { - "author_name": "Ana-Mihaela Bora", - "author_inst": "University of Cologne" - }, - { - "author_name": "Heidrun Janka", - "author_inst": "Heinrich-Heine-University Duesseldorf" - }, - { - "author_name": "Stephanie Stangl", - "author_inst": "University Hospital Wuerzburg" - }, - { - "author_name": "Nicole Skoetz", - "author_inst": "University of Cologne" - }, - { - "author_name": "Stephanie Weibel", - "author_inst": "University Hospital of Wuerzburg" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.10.08.23296718", "rel_title": "Effects of COVID-19 mRNA vaccination on HIV viremia and reservoir size", @@ -54502,6 +55895,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.10.03.23296513", + "rel_title": "Behavioural and Social Predictors of COVID-19 Vaccine Uptake among Persons with Disabilities in Kenya.", + "rel_date": "2023-10-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.10.03.23296513", + "rel_abs": "The uptake of the COVID-19 vaccine by persons with disabilities remains largely unknown in low-and middle-income countries. This evidence gap necessitates disability-focused research to inform improvements in access and inclusion in the last mile of COVID-19 vaccination programs and to support future programs for other vaccine-preventable diseases. We aimed to identify behavioural and social predictors of COVID-19 uptake among persons with disabilities in Kenya. This was a convergent parallel mixed method study that involved questionnaires (792), key informants interviews, and focus group discussions among persons with disabilities and key stakeholders (government actors and professional associations). Data were analysed using STATA statistical analysis software (version 14). Chi-square (X2) and Fishers exact tests were used to test for differences in categorical variables; multivariate regression analysis was employed to ascertain the factors that influence uptake of COVID-19 among persons with disabilities (PWDs) in Kenya. Approximately 59% of persons with disabilities reported to be fully vaccinated, with significant disparities noted among those with cognition (34.2%) and self-care (36.6%) impairments. Confidence in vaccine benefits (Adjusted odds ration [OR]; 11.3, 95% CI; 5.2-24.2), health worker recommendation (OR; 2.6, 95% CI; 1.8-3.7), employment (OR; 2.1, 95% CI; 1.4-3.1), perceived risk (OR; 2.0, 95% CI; 1.3-3.1), age and area of residence were statistically significant predictors of vaccine uptake among PWDs. The primary reasons for low uptake included perceived negative vaccine effects and lack of adequate information. No association was found between having a primary caregiver and/or assistive device, with COVID-19 vaccine uptake. Subsequent vaccination deployments should map and reach PWDs through relevant institutions of PWDs, and localized vaccination campaigns. Related communication strategies should leverage on behaviour change techniques that inspire confidence in vaccines, and on the credibility and trust in health workers to improve vaccine uptake.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Martin Josphat", + "author_inst": "AMREF: Amref Health Africa" + }, + { + "author_name": "Rogers Moraro", + "author_inst": "AMREF: Amref Health Africa" + }, + { + "author_name": "Jarim Oduor Omogi", + "author_inst": "Amref International University" + }, + { + "author_name": "Abrar Alasmari", + "author_inst": "Saudi Arabia Ministry of Health" + }, + { + "author_name": "Lennah Kanyangi", + "author_inst": "AMREF: Amref Health Africa" + }, + { + "author_name": "Rehema Mwema", + "author_inst": "AMREF: Amref Health Africa" + }, + { + "author_name": "Sheillah Simiyu", + "author_inst": "APHRC: African Population and Health Research Center" + }, + { + "author_name": "Sarah Kosgei", + "author_inst": "AMREF: Amref Health Africa" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.10.03.23296502", "rel_title": "United States Marijuana Legalization and Opioid Mortality Trends Before and During the First Year of the COVID-19 Pandemic", @@ -54965,41 +56405,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2023.09.30.23296175", - "rel_title": "Simulation of COVID-19 Epidemic from Potential Viral Loads in Saudi Arabian Wastewater Treatment Plants", - "rel_date": "2023-10-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.30.23296175", - "rel_abs": "SARS-CoV-2 is a contagious respiratory virus that has been discovered in sewage, human waste, and wastewater treatment facilities. Wastewater surveillance has been considered one of the lowest-cost means of testing for tracking the COVID-19 outbreak in communities. This paper highlights the dynamics of the viruss infection, persistence, and occurrence in wastewater treatment plants. Our aim is to develop and implement a mathematical model to infer the epidemic dynamics from the possible density of SARS-CoV-2 viral load in wastewater. We present a log-normal model and fractional order of susceptible-exposed-infected-recovery (SEIR) epidemic model for predicting the spread of the COVID-19 disease from the wastewater data. We study the dynamic properties of the fractional order SEIR model with respect to the fractional ordered values. The model is used to comprehend how the coronavirus spreads through wastewater treatment plants in Saudi Arabia. Our modeling approach can help with wastewater surveillance for early prediction and cost-effective monitoring of the epidemic outbreak in a situation of low testing capacity.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Mutum Zico Meetei", - "author_inst": "Department of Mathematics, College of Science, Jazan University, Jazan 45142, Saudi Arabia" - }, - { - "author_name": "Ahmed H. Msmali", - "author_inst": "Department of Mathematics, College of Science, Jazan University, Jazan 45142, Saudi Arabia" - }, - { - "author_name": "Abdullah Ali H. Ahmadini", - "author_inst": "Department of Mathematics, College of Science, Jazan University, Jazan 45142, Saudi Arabia" - }, - { - "author_name": "Shokrya Saleh A Alshqaq", - "author_inst": "Department of Mathematics, College of Science, Jazan University, Jazan 45142, Saudi Arabia" - }, - { - "author_name": "Hassien M Alnashiri", - "author_inst": "Department of Biology, College of Science, Jazan University, Jazan 45142, Saudi Arabia" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.09.29.23296354", "rel_title": "Suppressed IgG4 class switching in dupilumab- and TNF inhibitor-treated patients after repeated SARS-CoV-2 mRNA vaccination", @@ -55913,7 +57318,7 @@ "rel_date": "2023-09-29", "rel_site": "bioRxiv", "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.28.560070", - "rel_abs": "Turmeric extract (TE) with curcumin as its main active ingredient has been studied as a potential COVID-19 therapeutic. Curcumin has been studied in silico and in vitro against a naive SARS-CoV-2 virus, yet little is known about TEs impact on SARS-CoV-2 infection. Moreover, no study reveals the potential of both curcumin and TE on the inhibition of SARS-CoV-2 cell-to-cell transmission. Here, we investigated the effects of both curcumin and TE on inhibiting SARS-CoV-2 entry and cell-to-cell transmission using pseudovirus (PSV) and syncytia models. We performed a PSV entry assay in 293T or 293 cells expressing hACE2. The cells were pretreated with curcumin or TE and then treated with PSV with or without the test samples. Next, we carried out syncytia assay by co-transfecting 293T cells with plasmids encoding spike, hACE2, and TMPRSS2 to be treated with the test samples. The results showed that in PSV entry assay on 293T/hACE/TMPRSS2 cells, both curcumin and TE inhibited PSV entry at concentrations of 1 {micro}M and 10 {micro}M for curcumin and 1 {micro}g/ml and 10 {micro}g/ml for TE. Moreover, both curcumin and TE reduced syncytia formation compared to control cells. Our study shows that TE and curcumin are potential inhibitors of SARS-CoV-2 infection at entry points, either by direct or indirect infection models.\n\nGRAPHICAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=164 SRC=\"FIGDIR/small/560070v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (29K):\norg.highwire.dtl.DTLVardef@8d893aorg.highwire.dtl.DTLVardef@2c4339org.highwire.dtl.DTLVardef@1f15552org.highwire.dtl.DTLVardef@118b6fc_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_abs": "Turmeric extract (TE) with curcumin as its main active ingredient has been studied as a potential COVID-19 therapeutic. Curcumin has been studied in silico and in vitro against a naive SARS-CoV-2 virus, yet little is known about TEs impact on SARS-CoV-2 infection. Moreover, no study reveals the potential of both curcumin and TE on the inhibition of SARS-CoV-2 cell-to-cell transmission. Here, we investigated the effects of both curcumin and TE on inhibiting SARS-CoV-2 entry and cell-to-cell transmission using pseudovirus (PSV) and syncytia models. We performed a PSV entry assay in 293T or 293 cells expressing hACE2. The cells were pretreated with curcumin or TE and then treated with PSV with or without the test samples. Next, we carried out syncytia assay by co-transfecting 293T cells with plasmids encoding spike, hACE2, and TMPRSS2 to be treated with the test samples. The results showed that in PSV entry assay on 293T/hACE/TMPRSS2 cells, both curcumin and TE inhibited PSV entry at concentrations of 1 {micro}M and 10 {micro}M for curcumin and 1 {micro}g/ml and 10 {micro}g/ml for TE. Moreover, both curcumin and TE reduced syncytia formation compared to control cells. Our study shows that TE and curcumin are potential inhibitors of SARS-CoV-2 infection at entry points, either by direct or indirect infection models.\n\nGRAPHICAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=164 SRC=\"FIGDIR/small/560070v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (29K):\norg.highwire.dtl.DTLVardef@7c0f8dorg.highwire.dtl.DTLVardef@e11935org.highwire.dtl.DTLVardef@3e1a50org.highwire.dtl.DTLVardef@131b6d5_HPS_FORMAT_FIGEXP M_FIG C_FIG", "rel_num_authors": 8, "rel_authors": [ { @@ -56004,6 +57409,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.09.29.23296222", + "rel_title": "Influence of age, sex, body habitus, vaccine type and anti-S serostatus on cellular and humoral responses to SARS-CoV-2 vaccination", + "rel_date": "2023-09-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.29.23296222", + "rel_abs": "Vaccine development targeting SARS-CoV-2 in 2020 was of critical importance in reducing COVID-19 severity and mortality. In the U.K. during the initial roll-out most individuals either received two doses of Pfizer COVID-19 vaccine (BNT162b2) or the adenovirus-based vaccine from Oxford/AstraZeneca (ChAdOx1-nCoV-19). There are conflicting data as to the impact of age, sex and body habitus on cellular and humoral responses to vaccination, and most studies in this area have focused on determinants of mRNA vaccine immunogenicity. Here we studied a cohort of participants in a population-based longitudinal study (COVIDENCE UK) to determine the influence of age, sex, body mass index (BMI) and pre- vaccination anti-Spike (anti-S) antibody status on vaccine-induced humoral and cellular immune responses to two doses of BNT162b2 or ChAdOx-n-CoV-19 vaccination.\n\nYounger age and pre-vaccination anti-S seropositivity were both associated with stronger antibody responses to vaccination. BNT162b2 generated higher neutralising and anti-S antibody titres to vaccination than ChAdOx1-nCoV-19, but cellular responses to the two vaccines were no different. Irrespective of vaccine type, increasing age was also associated with decreased frequency of cytokine double-positive CD4+ T cells. Increasing BMI was associated with reduced frequency of SARS-CoV-2-specific TNF+ CD8% T cells for both vaccines.\n\nTogether, our findings demonstrate that increasing age and BMI associate with attenuated cellular and humoral responses to SARS-CoV-2 vaccination. Whilst both vaccines induced T cell responses, BNT162b2 induced significantly elevated humoral immune response as compared to ChAdOx-n-CoV-19.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Emma S Chambers", + "author_inst": "Queen Mary University of London" + }, + { + "author_name": "Weigang Cai", + "author_inst": "Queen Mary University of London" + }, + { + "author_name": "Giulia Vivaldi", + "author_inst": "Queen Mary University of London" + }, + { + "author_name": "David A Jolliffe", + "author_inst": "Queen Mary University of London" + }, + { + "author_name": "Natalia Perdek", + "author_inst": "Queen Mary University of London" + }, + { + "author_name": "Wenhao Li", + "author_inst": "Queen Mary University of London" + }, + { + "author_name": "Sian E Faustini", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Joseph M Gibbons", + "author_inst": "Queen Mary University of London" + }, + { + "author_name": "Corinna Pade", + "author_inst": "Queen Mary University of London" + }, + { + "author_name": "Alex G Richter", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Anna K Cousens", + "author_inst": "Walter and Eliza Hall Institute of Medical Research" + }, + { + "author_name": "Adrian R Martineau", + "author_inst": "Queen Mary University of London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2023.09.26.23296186", "rel_title": "The more symptoms the better? Covid-19 vaccine side effects and long-term neutralizing antibody response", @@ -56435,29 +57903,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.09.26.559599", - "rel_title": "survInTime - Exploring surveillance methods and data analysis on Brazilian respiratory syndrome dataset and community mobility changes", - "rel_date": "2023-09-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.26.559599", - "rel_abs": "BackgroundThe covid-19 pandemic brought negative impacts in almost every country in the world. These impacts were observed mainly in the public health sphere, with a rapid raise and spread of the disease and failed attempts to restrain it while there was no treatment. However, in developing countries, the impacts were severe in other aspects such as the intensification of social inequality, poverty and food insecurity. Specifically in Brazil, the miscommunication among the government layers conducted the control measures to a complete chaos in a country of continental dimensions. Brazil made an effort to register granular informative data about the case reports and their outcomes, while this data is available and can be consumed freely, there are issues concerning the integrity and inconsistencies between the real number of cases and the number of notifications in this dataset.\n\nResultsWe projected and implemented four types of analysis to explore the Brazilian public dataset of Severe Acute Respiratory Syndrome (srag dataset) notifications and the google dataset of community mobility change (mobility dataset). These analysis provides some diagnosis of data integration issues and strategies to integrate data and experimentation of surveillance analysis. The first type of analysis aims at describing and exploring the data contained in both datasets, starting by assessing the data quality concerning missing data, then summarizing the patterns found in this datasets. The Second type concerns an statistical experiment to estimate the cases from mobility patterns organized in periods of time. We also developed, as the third analysis type, an algorithm to help the understanding of the disease waves by detecting them and compare the time periods across the cities. Lastly, we build time series datasets considering deaths, overall cases and residential mobility change in regular time periods and used as features to group cities with similar behavior.\n\nConclusionThe exploratory data analysis showed the under representation of covid-19 cases in many small cities in Brazil that were absent in the srag dataset or with a number of cases very low than real projections. We also assessed the availability of data for the Brazilian cities in the mobility dataset in each state, finding out that not all the states were represented and the best coverage occurred in Rio de Janeiro state. We compared the capacity of place categories mobility change combination on estimating the number of cases measuring the errors and identifying the best components in mobility that could affect the cases. In order to target specific strategies for groups of cities, we compared strategies to cluster cities that obtained similar outcomes behavior along the time, highlighting the divergence on handling the disease.\n\nAvailabilityhttps://github.com/YasCoMa/dashboard-srag-mobility", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Yasmmin Cortes Martins", - "author_inst": "None at the moment" - }, - { - "author_name": "Ronaldo da Silva Francisco Jr.", - "author_inst": "Stanford" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2023.09.27.559660", "rel_title": "p38-MAPK is prerequisite for the synthesis of SARS-CoV-2 protein", @@ -57794,6 +59239,117 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2023.09.22.559019", + "rel_title": "Immune Correlates of Hyperglycemia and Vaccination in a Non-human Primate Model of Long-COVID", + "rel_date": "2023-09-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.22.559019", + "rel_abs": "Hyperglycemia, and exacerbation of pre-existing deficits in glucose metabolism, are major manifestations of the post-acute sequelae of SARS-CoV-2 (PASC). Our understanding of lasting glucometabolic disruptions after acute COVID-19 remains unclear due to the lack of animal models for metabolic PASC. Here, we report a non-human primate model of metabolic PASC using SARS-CoV-2 infected African green monkeys (AGMs). Using this model, we have identified a dysregulated chemokine signature and hypersensitive T cell population during acute COVID-19 that correlates with elevated and persistent hyperglycemia four months post-infection. This persistent hyperglycemia correlates with elevated hepatic glycogen, but there was no evidence of long-term SARS-CoV-2 replication in the liver and pancreas. Finally, we report a favorable glycemic effect of the SARS-CoV-2 mRNA vaccine, administered on day 4 post-infection. Together, these data suggest that the AGM metabolic PASC model exhibits important similarities to human metabolic PASC and can be utilized to assess therapeutic candidates to combat this syndrome.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Clovis S Palmer", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Chrysostomos Perdios", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Mohamed Abdel-Mohsen", + "author_inst": "The Wistar Institute" + }, + { + "author_name": "Joseph Mudd", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Prasun Datta", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Nicholas Maness", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Gabrielle Lehmicke", + "author_inst": "1Tulane National Primate Research Center" + }, + { + "author_name": "Nadia Golden", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Lihn Hellmer", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Carol Coyne", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Kristyn Moore Green", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Cecily Midkiff", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Kelsey Williams", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Rafael Tiburcio", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Marissa Fahlberg", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Kyndal Boykin", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Carys Kenway", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Kasi Russell-Lodrigue", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Rudolf Bohm", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Robert V Blair", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Jason Dufour", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Tracy Fischer", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Ahmed Saied", + "author_inst": "Tulane National Primate Research Center" + }, + { + "author_name": "Jay Rappaport", + "author_inst": "Tulane National Primate Research Center" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.09.22.558628", "rel_title": "A comprehensive study of SARS-CoV-2 main protease (Mpro) inhibitor-resistant mutants selected in a VSV-based system", @@ -58273,85 +59829,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.09.21.23295919", - "rel_title": "Anti-SARS-CoV-2 Antibody Levels Associated with COVID-19 Protection in Outpatients Tested for SARS-CoV-2, US Flu VE Network, October 2021 to June 2022", - "rel_date": "2023-09-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.21.23295919", - "rel_abs": "BackgroundWe assessed the association between antibody concentration [≤]5 days of symptom onset and COVID-19 illness among patients enrolled in a test-negative study\n\nMethodsFrom October 2021[boxh]June 2022, study sites in seven states enrolled and tested respiratory specimens from patients of all ages presenting with acute respiratory illness for SARS-CoV-2 infection using rRT-PCR. In blood specimens, we measured concentration of anti- SARS-CoV-2 antibodies against the ancestral strain spike protein receptor binding domain (RBD) and nucleocapsid (N) antigens in standardized binding antibody units (BAU/mL). Percent reduction in odds of symptomatic COVID-19 by anti-RBD antibody was estimated using logistic regression modeled as (1-adjusted odds ratio of COVID-19)x100, adjusting for COVID-19 vaccination status, age, site, and high-risk exposure.\n\nResultsA total of 662 (33%) of 2,018 symptomatic patients tested positive for acute SARS- CoV-2 infection. During the Omicron-predominant period, geometric mean anti-RBD binding antibody concentrations measured 823 BAU/mL (95%CI:690[boxh]981) among COVID-19 case- patients versus 1,189 BAU/mL (95%CI:1,050[boxh]1,347) among SARS-CoV-2 test-negative patients. In the adjusted logistic regression, increasing levels of anti-RBD antibodies were associated with reduced odds of COVID-19 for both Delta and Omicron infections.\n\nConclusionHigher anti-RBD antibodies in patients were associated with protection against symptomatic COVID-19 during emergence of SARS-CoV-2 Delta and Omicron variants.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Kelsey M Sumner", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Ruchi Yadav", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Emma K Noble", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Ryan Sandford", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Devyani J Joshi", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Sara Y Tartof", - "author_inst": "Kaiser Permanente Southern California" - }, - { - "author_name": "Karen J Wernli", - "author_inst": "Kaiser Permanente Bernard J. Tyson School of Medicine" - }, - { - "author_name": "Emily Toth Martin", - "author_inst": "University of Michigan-Ann Arbor" - }, - { - "author_name": "Manjusha Gaglani", - "author_inst": "Baylor Scott & White Health" - }, - { - "author_name": "Richard Zimmerman", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "H. Keipp Talbot", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Carlos G Grijalva", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Jessie Chung", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Brendan M Flannery", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Melissa M Coughlin", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Eric Rogier", - "author_inst": "Centers for Disease Control and Prevention" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.09.22.23295850", "rel_title": "Group A streptococcal cases and treatments during the COVID-19 pandemic and 2022 outbreak: a retrospective cohort study in England using OpenSAFELY-TPP", @@ -59636,6 +61113,29 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.09.18.23295630", + "rel_title": "Adherence Behaviors to Prevent COVID: The Role of Anxiety and Prosocial Behaviors", + "rel_date": "2023-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.18.23295630", + "rel_abs": "ObjectiveIn situations of acute stress, individuals may engage in prosocial behaviors or alternatively, individuals may engage in risk taking self-oriented behaviors. The COVID-19 pandemic created large stress-promoting conditions that impacted individuals decisions to adhere to COVID-19 preventative behaviors. The aim of this study is to examine the relationship between anxiety during the pandemic and adherence behaviors to prevent the spread of COVID-19, and the moderating influence prosocial behaviors.\n\nMethod54 undergraduate students completed online questionnaires during the second wave of the pandemic: prosocial behaviors, anxiety, and COVID-19 preventive behaviors. Moderation analyses were conducted using Process in SPSS.\n\nResultsResults demonstrated a statistically significant interaction of public prosocial behavior with state anxiety ({beta} = -.17, p=.01) predicting engagement in COVID-19 preventative behaviors. At low levels of anxiety, low levels of prosocial public behaviors were associated with higher engagement in COVID-19 preventative behaviors. In contrast, high levels of public prosocial behavior were associated with lower engagement in COVID-19 preventative behaviors at low levels of anxiety.\n\nConclusionResults provide information that can aid at in the creation of anxiety reducing interventions that could increase adherence to COVID-19 preventative behaviors.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Silvia Corbera", + "author_inst": "Central Connecticut State University" + }, + { + "author_name": "Amanda M Marin-Chollom", + "author_inst": "Central Connecticut State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2023.09.18.23295709", "rel_title": "Can we start to ignore the SARS-CoV-2 disease?", @@ -60243,37 +61743,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.09.15.557899", - "rel_title": "The SARS-CoV-2 nucleoprotein associates with anionic lipid membranes", - "rel_date": "2023-09-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.15.557899", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a lipid-enveloped virus that acquires its lipid bilayer from the host cell it infects. SARS-CoV-2 can spread from cell to cell or from patient to patient by undergoing assembly and budding to form new virions. The assembly and budding of SARS-CoV-2 is mediated by several structural proteins known as envelope (E), membrane (M), nucleoprotein (N) and spike (S), which can form virus-like particles (VLPs) when co-expressed in mammalian cells. Assembly and budding of SARS-CoV-2 from the host ER-Golgi intermediate compartment is a critical step in the virus acquiring its lipid bilayer. To date, little information is available on how SARS-CoV-2 assembles and forms new viral particles from host membranes. In this study, we find the N protein can strongly associate with anionic lipids including phosphoinositides and phosphatidylserine. Moreover, lipid binding is shown to occur in the N protein C-terminal domain, which is supported by extensive in silico analysis. Anionic lipid binding occurs for both the free and N oligomeric forms suggesting N can associate with membranes in the nucleocapsid form. Herein we present a lipid-dependent model based on in vitro, cellular and in silico data for the recruitment of N to M assembly sites in the lifecycle of SARS-CoV-2.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Mandira Dutta", - "author_inst": "University of Chicago" - }, - { - "author_name": "Yuan Su", - "author_inst": "Purdue University" - }, - { - "author_name": "Gregory A Voth", - "author_inst": "University of Chicago" - }, - { - "author_name": "Robert V Stahelin", - "author_inst": "Purdue University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.09.14.557399", "rel_title": "Cooperativity and induced oligomerisation control the interaction of SARS- CoV-2 with its cellular receptor and patient-derived antibodies", @@ -61322,6 +62791,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2023.09.13.23295484", + "rel_title": "Changes in stillbirths and child and youth mortality in 2020 and 2021 during the Covid-19 pandemic", + "rel_date": "2023-09-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.13.23295484", + "rel_abs": "BackgroundThe COVID-19 pandemics impact on mortality, especially among the elderly, has been extensively studied. While COVID-19 rarely causes direct mortality in children and youth, the pandemics indirect effects might harm these age groups. Yet, its influence on stillbirths and mortality rates in neonates, infants, children, and youth remains poorly understood. This study examines disruptions in such trends across 95 countries in 2020 and 72 in 2021, providing the inaugural comprehensive analysis of COVID-19s effect on young mortality and stillbirths.\n\nMethodsWe estimate expected mortality levels in a non-pandemic setting and calculate relative mortality changes (p-scores) by applying generalized linear models to data from civil registers and vital statistics systems (CRSV) and from the Health Management Information System (HMIS). We then use these estimates to analyze, for each age group, the distribution of country-specific mortality changes and the proportion of countries experiencing mortality deficits, no changes, and excess.\n\nResultsFor most countries and territories, stillbirths and mortality at ages under 25 did not differ from expected levels in 2020 and 2021. However, when focusing on the countries that did show changes, more countries experienced mortality deficits than excess. The exception was stillbirths in both years and mortality among neonates and those aged 10-24 in 2021, where more countries had an excess rather than a deficit. Overall, a quarter of the countries examined experienced increases in stillbirths and young adult mortality (20-24).\n\nConclusionDespite global disruptions to essential services, stillbirths and youth mortality were as expected in most countries, defying expectations. However, this doesnt dismiss hypotheses suggesting delayed adverse effects on the youngest that may require more time to be noticeable at the population level. Close and long-term monitoring of health and deaths among children and youth, particularly in low-income and lower-middle-income countries, is required to fully understand the lasting impacts of the COVID-19 pandemic.\n\nKey messagesO_LIThis study aims to assess the global impact of the COVID-19 pandemic on stillbirths and child and youth mortality during the years 2020 and 2021.\nC_LIO_LIWe found that despite the pandemic severity and the related socioeconomic disruptions worldwide, most of the 95 countries and territories under analysis experienced no changes in stillbirths and under-25 mortality.\nC_LIO_LIThese findings are important because the impact of the pandemic on the youngest ages remains poorly understood; it contributes essential information for conceiving tailored interventions that can effectively mitigate the adverse consequences of the pandemic on children and youth; and highlight the urgency of strengthen surveillance systems for monitoring health and deaths among children and youth, particularly in low-income and lower-middle-income countries.\nC_LI", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Enrique Acosta", + "author_inst": "Centre for Demographic Studies" + }, + { + "author_name": "Lucia Hug", + "author_inst": "Division of Data, Analytics, Planning and Monitoring, UNICEF" + }, + { + "author_name": "Helena Cruz-Castanheira", + "author_inst": "CELADE - Population Division of ECLAC" + }, + { + "author_name": "David Sharrow", + "author_inst": "Division of Data, Analytics, Planning and Monitoring, UNICEF" + }, + { + "author_name": "Jose Henrique Monteiro da Silva", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Danzhen You", + "author_inst": "Division of Data, Analytics, Planning and Monitoring, UNICEF" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.09.12.23295464", "rel_title": "Circulation of SARS-CoV-2 and co-infection with Plasmodium falciparum in Equatorial Guinea", @@ -61701,69 +63209,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.09.11.557190", - "rel_title": "Compartmentalized SARS-CoV-2 replication in upper versus lower respiratory tract after intranasal inoculation or aerosol exposure", - "rel_date": "2023-09-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.11.557190", - "rel_abs": "Non-human primate models are essential for the development of vaccines and antivirals against infectious diseases. Rhesus macaques are a widely utilized infection model for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We compared cellular tropism and virus replication in rhesus macaques inoculated with SARS-CoV-2 via the intranasal route, or via exposure to aerosols. Intranasal inoculation results in replication in the upper respiratory tract and limited lower respiratory tract involvement, whereas exposure to aerosols results in infection throughout the respiratory tract. In comparison to multi-route inoculation, the intranasal and aerosol inoculation routes result in reduced SARS-CoV-2 replication in the respiratory tract.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Robert Fischer", - "author_inst": "NIAID, NIH" - }, - { - "author_name": "Trenton Bushmaker", - "author_inst": "NIAID, NIH" - }, - { - "author_name": "Brandi N Williamson", - "author_inst": "NIAID, NIH" - }, - { - "author_name": "Lizzette Perez-Perez", - "author_inst": "NIAID, NIH" - }, - { - "author_name": "Friederike Feldmann", - "author_inst": "NIAID, NIH" - }, - { - "author_name": "Jamie Lovaglio", - "author_inst": "NIAID, NIH" - }, - { - "author_name": "Dana Scott", - "author_inst": "NIAID, NIH" - }, - { - "author_name": "Greg Saturday", - "author_inst": "NIAID, NIH" - }, - { - "author_name": "Heinz Feldmann", - "author_inst": "NIAID, NIH" - }, - { - "author_name": "Vincent J Munster", - "author_inst": "NIAID, NIH" - }, - { - "author_name": "Emmie de Wit", - "author_inst": "NIAID, NIH" - }, - { - "author_name": "Neeltje van Doremalen", - "author_inst": "NIAID, NIH" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.09.11.557206", "rel_title": "Immune Evasion, Infectivity, and Fusogenicity of SARS-CoV-2 Omicron BA.2.86 and FLip Variants", @@ -63052,6 +64497,81 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.09.10.557067", + "rel_title": "Protocol for primary human lung organoid-derived air-liquid interface in vitro model to study response to SARS-CoV-2", + "rel_date": "2023-09-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.09.10.557067", + "rel_abs": "This article presents a comprehensive protocol for establishing primary human lung organoid-derived air-liquid interface (ALI) cultures from cryopreserved human lung tissue. These cultures serve as a physiologically relevant model to study human airway epithelium in vitro. The protocol encompasses lung tissue cryostorage, tissue dissociation, lung epithelial organoid generation, and ALI culture differentiation. It also demonstrates SARS-CoV-2 infection in these cultures as an example of their utility. Quality control steps, ALI characterization, and technical readouts for monitoring virus response are included in the study.\n\nFor additional details on the use and execution of this protocol, please refer to Diana Cadena Castaneda et al (https://doi.org/10.1016/j.isci.2023.107374).\n\nHighlightsO_LIHuman lung tissue dissection, embedding in OCT blocks, and tissue cryopreservation.\nC_LIO_LIThawing & lung tissue dissociation for lung epithelium organoid generation.\nC_LIO_LIOrganoid-derived air-liquid-interface cultures for the study of viral infection.\nC_LIO_LIBulk RNA-Seq, flow cytometry, viral titer, and imaging to follow response to virus.\nC_LI\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC=\"FIGDIR/small/557067v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (52K):\norg.highwire.dtl.DTLVardef@b47fbdorg.highwire.dtl.DTLVardef@2e6e60org.highwire.dtl.DTLVardef@508ac6org.highwire.dtl.DTLVardef@1c701a4_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Diana Cadena Castaneda", + "author_inst": "The Jackson Laboratory for Genomic Medicine" + }, + { + "author_name": "Sonia Jangra", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Marina Yurieva", + "author_inst": "The Jackson Laboratory for Genomic Medicine, Farmington" + }, + { + "author_name": "Jan Martinek", + "author_inst": "The Jackson Laboratory for Genomic Medicine" + }, + { + "author_name": "Megan Callender", + "author_inst": "The Jackson Laboratory for Genomic Medicine" + }, + { + "author_name": "Matthew Coxe", + "author_inst": "The Jackson Laboratory for Genomic Medicine" + }, + { + "author_name": "Angela Choi", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Juan Garcia-Bernalt Diego", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Te-Chia Wu", + "author_inst": "The Jackson Laboratory for Genomic Medicine" + }, + { + "author_name": "Florentina Marches", + "author_inst": "The Jackson Laboratory for Genomic Medicine" + }, + { + "author_name": "Damien Chaussabel", + "author_inst": "The Jackson Laboratory for Genomic Medicine" + }, + { + "author_name": "Adolfo Garcia-Sastre", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Michael Schotsaert", + "author_inst": "Department of Microbiology, Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Adam Williams", + "author_inst": "The Jackson Laboratory for Genomic Medicine" + }, + { + "author_name": "Karolina Palucka", + "author_inst": "The Jackson Laboratory For Genomic Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.09.10.557088", "rel_title": "Enhanced Omicron subvariant cross-neutralization efficacy of a monovalent SARS-CoV-2 BA.4/5 mRNA vaccine encoding a noncleaved, nonfusogenic spike antigen", @@ -63591,61 +65111,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.09.08.23295267", - "rel_title": "Prevalence and predictors of self-medication for COVID-19 among slum dwellers in Jinja City, Uganda", - "rel_date": "2023-09-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.08.23295267", - "rel_abs": "IntroductionSelf-medication is a serious public health concern globally and is more prevalent in underserved populations, especially in resource limited settings. The lack of effective treatment for COVID-19 and poor access to healthcare were drivers of self-medication. We investigated the prevalence and associated factors with self-medication for COVID-19 among slum dwellers in a Ugandan slum.\n\nMethods and materialsWe conducted a cross-sectional study using randomly selected respondents from slums in Jinja city, Uganda. Households were proportionately selected from the slums and one participant with confirmed or self-reported COVID-19 during 2021 was recruited. Poisson regression with robust standard errors was used to determine the crude (CPR) and adjusted prevalence ratios (APR) (95% CI) of factors associated with self-medication. Variables were selected apriori and backward elimination approach used to fit the final multivariate model in which variables with a P[≤] 0.05 were included.\n\nResultsOverall, 517 respondents were recruited, median age (years) was 31 (26-40), and 59% were male. The prevalence of self-medication for COVID-19 was 87.23% (451/517), 95% CI: [84.00%-90.00%] and 56% knew that self-medication was dangerous. Age[≥]50 years, compared to 20-29 years [APR: 1.12, 95% CI:1.05, 1.20], being female [APR: 1.07, 95% CI: 1.02, 1.13], minor [APR: 1.62, 95% CI: 1.25, 2.11], and severe symptoms [APR: 1.51, 95% CI: 1.16, 1.96], access to internet [APR: 1.13, 95% CI: 1.07, 1.20]. Having medical insurance [APR: 0.63, 95% CI: 0.46, 0.87] and awareness about laws against self-medication [APR: 0.89, 95% CI: 0.81, 0.97] were associated with a lower risk of self-medication.\n\nConclusionThe prevalence of self-medication in slum dwellers in Uganda was high despite high awareness about its dangers. Self-medication was common in those with severe symptoms and those access to internet. There is need to control infodemia and improve health insurance cover in informal settlements within Uganda.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Prossy Nakito", - "author_inst": "Makerere University CHS: Makerere University College of Health Sciences" - }, - { - "author_name": "Angela Nakanwagi Kisakye", - "author_inst": "Makerere University CHS: Makerere University College of Health Sciences" - }, - { - "author_name": "Abel Wilson Walekhwa", - "author_inst": "University of Cambridge Department of Veterinary Medicine" - }, - { - "author_name": "Gloria Tumukunde", - "author_inst": "Makerere University CHS: Makerere University College of Health Sciences" - }, - { - "author_name": "Charity Mutesi", - "author_inst": "Makerere University CHS: Makerere University College of Health Sciences" - }, - { - "author_name": "Nicholas Muhumuza", - "author_inst": "Makerere University CHS: Makerere University College of Health Sciences" - }, - { - "author_name": "Carolyne Nyamor", - "author_inst": "Makerere University CHS: Makerere University College of Health Sciences" - }, - { - "author_name": "David Musoke", - "author_inst": "Makerere University CHS: Makerere University College of Health Sciences" - }, - { - "author_name": "Geofrey Musinguzi", - "author_inst": "Makerere University CHS: Makerere University College of Health Sciences" - }, - { - "author_name": "Dathan Mirembe Byonanebye", - "author_inst": "Makerere University CHS: Makerere University College of Health Sciences" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.09.07.554570", "rel_title": "Stereotypic persistent B cell receptor clonotypes in Alzheimer's Disease", @@ -65078,6 +66543,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, + { + "rel_doi": "10.1101/2023.09.05.23295073", + "rel_title": "Serological outcomes of SARS-CoV-2 infection by vaccination status and variant in England", + "rel_date": "2023-09-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.09.05.23295073", + "rel_abs": "BackgroundThroughout the SARS-CoV-2 pandemic, several vaccines have been rolled out and distinct variants with different severity and immune profiles emerged in England. Using data from enhanced surveillance of COVID-19 in vaccine eligible individuals we investigated the antibody response following SARS-CoV-2 infection according to vaccination status and variant.\n\nMethodsPCR-positive eligible individuals were identified from community PCR testing data in England between February 2021 and April 2022 and contacted by nurses to complete questionnaires at recruitment and 21 days post recruitment. Individuals were sent self-sampling kits and self-sampled nasal/oropharyngeal swabs were taken day 1, day 3 and day 7 post-recruitment as well as acute (day 1), convalescent (follow-up) serum and oral fluid samples. Regression analyses were used to investigate how N antibody seroconversion differs by vaccine status, and to investigate how N and S antibody levels differ by vaccine status overall and stratified by variants. Interval-censored analyses and regression analyses were used to investigate the effect of acute S antibody levels on the duration of positivity, the cycle threshold values, the self-reported symptom severity and the number of symptoms reported.\n\nResultsA total of 1,497 PCR positive individuals were included. A total of 369 (24.7%) individuals were unvaccinated, 359 (24.0%) participants were infected with Alpha, 762 (50.9%) with Delta and 376 (25.2%) with Omicron. The median age of participants was 49 years old (IQR 39-57). Convalescent anti-N antibody levels were lower in vaccinated individuals and convalescent anti-S antibody levels were higher in vaccinated individuals and increased with the number of doses received. Acute anti-S antibody level increased with the number of doses received. Higher acute anti-S antibody levels were associated with a shorter duration of positivity (overall and for the Delta variant). Higher acute anti-S antibody levels were also associated with higher Ct values (overall and for the Alpha and Delta variants). There was no association between the acute anti-S antibody level and self-reported symptom severity. Individuals with higher acute anti-S antibody level were less likely to report six or more symptoms (overall and for Delta variant).\n\nConclusionUnderstanding the characteristics of the antibody response, its dynamics over time and the immunity it confers is important to inform future vaccination strategies and policies. Our findings suggest that vaccination is associated with high acute anti-S antibody level but reduced convalescent anti-N antibody level. High anti-S antibody level is associated with reduced duration of infection, reduced infectiousness and may also be associated with reduced symptoms severity and number of symptoms.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Catherine Quinot", + "author_inst": "UKHSA" + }, + { + "author_name": "Rachel Lunt", + "author_inst": "UKHSA" + }, + { + "author_name": "Freja Kirsebom", + "author_inst": "UKHSA" + }, + { + "author_name": "Nick Andrews", + "author_inst": "UKHSA" + }, + { + "author_name": "Heather Whitaker", + "author_inst": "UKHSA" + }, + { + "author_name": "Catriona Skarnes", + "author_inst": "UKHSA" + }, + { + "author_name": "Louise Letley", + "author_inst": "UKHSA" + }, + { + "author_name": "Donna Haskins", + "author_inst": "UKHSA" + }, + { + "author_name": "Catriona Angel", + "author_inst": "UKHSA" + }, + { + "author_name": "Skye Firminger", + "author_inst": "UKHSA" + }, + { + "author_name": "Kay Ratcliffe", + "author_inst": "UKHSA" + }, + { + "author_name": "Angela Sheridan", + "author_inst": "UKHSA" + }, + { + "author_name": "Shelina Rajan", + "author_inst": "UKHSA" + }, + { + "author_name": "Lola Akindele", + "author_inst": "UKHSA" + }, + { + "author_name": "Samreen Ijaz", + "author_inst": "UKHSA" + }, + { + "author_name": "Maria Zambon", + "author_inst": "UKHSA" + }, + { + "author_name": "Kevin Brown", + "author_inst": "UKHSA" + }, + { + "author_name": "Mary Ramsay", + "author_inst": "UKHSA" + }, + { + "author_name": "Jamie Lopez Bernal", + "author_inst": "UKHSA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.09.04.23294493", "rel_title": "Safety and immunogenicity of VLPCOV-02, a SARS-CoV-2 self-amplifying RNA vaccine with a modified base, 5-methylcytosine, in healthy individuals", @@ -65537,33 +67093,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.08.30.23294845", - "rel_title": "A Literature Review and Meta-Analysis of the Effects of Lockdowns on COVID-19 Mortality - II", - "rel_date": "2023-09-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.30.23294845", - "rel_abs": "The purpose of this systematic review and meta-analysis is to determine the effect of lockdowns on COVID-19 mortality based on available empirical evidence. Lockdowns are defined as the imposition of at least one compulsory, non-pharmaceutical intervention (NPI). We employ a systematic search and screening procedure in which 19,646 studies are identified that could potentially address the purpose of our study. After three levels of screening, 32 studies qualified. Of those, estimates from 22 studies could be converted to standardized measures for inclusion in the meta-analysis. They are separated into three groups: lockdown stringency index studies, shelter-in-place-order (SIPO) studies, and specific NPI studies. Stringency index studies find that the average lockdown in Europe and the United States in the spring of 2020 only reduced COVID-19 mortality by 3.2%. This translates into approximately 6,000 avoided deaths in Europe and 4,000 in the United States. SIPOs were also relatively ineffective in the spring of 2020, only reducing COVID-19 mortality by 2.0%. This translates into approximately 4,000 avoided deaths in Europe and 3,000 in the United States. Based on specific NPIs, we estimate that the average lockdown in Europe and the United States in the spring of 2020 reduced COVID-19 mortality by 10.7%. This translates into approximately 23,000 avoided deaths in Europe and 16,000 in the United States. In comparison, there are approximately 72,000 flu deaths in Europe and 38,000 flu deaths in the United States each year. When checked for potential biases, our results are robust. Our results are also supported by the natural experiments we have been able to identify. The results of our meta-analysis support the conclusion that lockdowns in the spring of 2020 had little to no effect on COVID-19 mortality. This result is consistent with the view that voluntary changes in behavior, such as social distancing, did play an important role in mitigating the pandemic.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Jonas Herby", - "author_inst": "CEPOS" - }, - { - "author_name": "Lars Jonung", - "author_inst": "Lund University" - }, - { - "author_name": "Steve Hanke", - "author_inst": "Johns Hopkins University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2023.09.03.23294798", "rel_title": "SARS-CoV-2 quarantine mandated by contact tracing: burden and infection rate among close contacts in Zurich, Switzerland, 2020-2021", @@ -66664,6 +68193,101 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.08.31.555819", + "rel_title": "Characterization of an EG.5.1 clinical isolate in vitro and in vivo", + "rel_date": "2023-09-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.31.555819", + "rel_abs": "EG.5.1 is a subvariant of the SARS-CoV-2 Omicron XBB variant that is rapidly increasing in prevalence worldwide. EG.5.1 has additional substitutions in its spike protein (namely, Q52H and F456L) compared with XBB.1.5. However, the pathogenicity, transmissibility, and immune evasion properties of clinical isolates of EG.5.1 are largely unknown.\n\nIn this study, we used wild-type Syrian hamsters to investigate the replicative ability, pathogenicity, and transmissibility of a clinical EG.5.1 isolate. Our data show that there are no obvious differences in growth ability and pathogenicity between EG.5.1 and XBB.1.5, and both EG.5.1 and XBB.1.5 are attenuated compared to a Delta variant isolate.\n\nWe also found that EG.5.1 is transmitted more efficiently between hamsters compared with XBB.1.5. In addition, unlike XBB.1.5, we detected EG.5.1 virus in the lungs of four of six exposed hamsters, suggesting that the virus tropism of EG.5.1 is different from that of XBB.1.5 after airborne transmission.\n\nFinally, we assessed the neutralizing ability of plasma from convalescent individuals and found that the neutralizing activity against EG.5.1 was slightly, but significantly, lower than that against XBB.1.5 or XBB.1.9.2. This suggests that EG.5.1 effectively evades humoral immunity and that the amino acid differences in the S protein of EG.5.1 compared with that of XBB.1.5 or XBB.1.9.2 (i.e., Q52H, R158G, and F456L) alter the antigenicity of EG.5.1.\n\nOur data suggest that the increased transmissibility and altered antigenicity of EG.5.1 may be driving its increasing prevalence over XBB.1.5 in the human population.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Ryuta Uraki", + "author_inst": "Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan." + }, + { + "author_name": "Maki Kiso", + "author_inst": "Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan." + }, + { + "author_name": "Kiyoko Iwatsuki-Horimoto", + "author_inst": "Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan." + }, + { + "author_name": "Seiya Yamayoshi", + "author_inst": "Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan." + }, + { + "author_name": "Mutsumi Ito", + "author_inst": "Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan." + }, + { + "author_name": "Shiho Chiba", + "author_inst": "Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan." + }, + { + "author_name": "Yuko Sakai-Tagawa", + "author_inst": "Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan." + }, + { + "author_name": "Masaki Imai", + "author_inst": "Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan." + }, + { + "author_name": "Yukie Kashima", + "author_inst": "Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan." + }, + { + "author_name": "Michiko Koga", + "author_inst": "Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo, Japan." + }, + { + "author_name": "Noriko Fuwa", + "author_inst": "Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, Tokyo, Japan" + }, + { + "author_name": "Nobumasa Okumura", + "author_inst": "Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, Tokyo, Japan" + }, + { + "author_name": "Masayuki Hojo", + "author_inst": "Department of Respiratory Medicine, National Center for Global Health and Medicine Hospital, Tokyo, Japan" + }, + { + "author_name": "Noriko Iwamoto", + "author_inst": "Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, Tokyo, Japan" + }, + { + "author_name": "Hideaki Kato", + "author_inst": "Department of Hematology and Clinical Immunology, Yokohama City University School of Medicine, Yokohama, Japan" + }, + { + "author_name": "Hideaki Nakajima", + "author_inst": "Department of Stem Cell and Immune Regulation, Yokohama City University Graduate School of Medicine, Kanagawa, Japan" + }, + { + "author_name": "Norio Ohmagari", + "author_inst": "Disease Control and Prevention Center, National Center for Global Health and Medicine Hospital, Tokyo, Japan" + }, + { + "author_name": "Hiroshi Yotsuyanagi", + "author_inst": "Department of Infectious Diseases and Applied Immunology, IMSUT Hospital of The Institute of Medical Science, University of Tokyo, Tokyo, Japan." + }, + { + "author_name": "Yutaka Suzuki", + "author_inst": "Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan." + }, + { + "author_name": "Yoshihiro Kawaoka", + "author_inst": "Division of Virology, Institute of Medical Science, University of Tokyo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.08.31.555772", "rel_title": "Sequential early-life viral infections modulate the microbiota and adaptive immune responses to systemic and mucosal vaccination", @@ -67171,37 +68795,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.08.30.555506", - "rel_title": "Explainable machine learning for the identification of proteome states via the data processing kitchen sink", - "rel_date": "2023-08-31", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.30.555506", - "rel_abs": "The application of machine learning algorithms to facilitate the understanding of changes in proteome states has emerged as a promising methodology in proteomics research. Unfortunately, these methods can prove difficult to interpret, as it may not be immediately obvious how models reach their predictions. We present the data processing kitchen sink (DPKS) which provides reproducible access to classic statistical methods and advanced explainable machine learning algorithms to build highly accurate and fully interpretable predictive models. In DPKS, explainable machine learning methods are used to calculate the importance of each protein towards the prediction of a model for a particular proteome state. The calculated importance of each protein can enable the identification of proteins that drive phenotypic change in a data-driven manner while classic techniques rely on arbitrary cutoffs that may exclude important features from consideration. DPKS is a free and open source Python package available at https://github.com/InfectionMedicineProteomics/DPKS.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Aaron Michael Scott", - "author_inst": "Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden" - }, - { - "author_name": "Erik Hartman", - "author_inst": "Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden" - }, - { - "author_name": "Johan Malmstroem", - "author_inst": "Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden" - }, - { - "author_name": "Lars Malmstroem", - "author_inst": "Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2023.08.30.555211", "rel_title": "Convergent evolution of SARS-CoV-2 XBB lineages on receptor-binding domain 455-456 enhances antibody evasion and ACE2 binding", @@ -68482,6 +70075,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2023.08.29.23294767", + "rel_title": "Social contact patterns following the COVID-19 pandemic: a snapshot of post-pandemic behaviour from the CoMix study", + "rel_date": "2023-08-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.29.23294767", + "rel_abs": "BackgroundThe COVID-19 pandemic led to unprecedented changes in behaviour. To estimate if these persisted a final new round of the CoMix survey was conducted in four countries at a time when all societal restrictions had been lifted for several months.\n\nMethodsWe conducted a survey on a nationally representative sample in the UK, Netherlands (NL), Belgium (BE), and Switzerland (CH). Participants were asked about their contacts and behaviours on the previous day. We calculated contact matrices and compared the contact levels to a pre-pandemic baseline to estimate R0.\n\nResultsData collection occurred from 17 November to 7 December 2022. 7,477 participants were recruited. Some were asked to undertake the survey on behalf of their children. Only 14.4% of all participants reported wearing a facemask on the previous day, varying between 6.7% in NL to 17.8% in CH. Self-reported vaccination rates in adults were similar for each country at around 86%. Trimmed mean recorded contacts were highest in NL with 9.9 (95% confidence interval [CI] 9.0 to 10.8) contacts per person per day and lowest in CH at 6.0 (95% CI 5.4 to 6.6). The number of contacts at home were similar between the countries. Contacts at work were lowest in the UK (1.4 contacts per person per day) and highest in NL at 2.8 contacts per person per day. Other contacts were also lower in the UK at 1.6 per person per day (95% CI 1.4 to 1.9) and highest in NL at 3.4 recorded per person per day (95% CI 4.0 to 4.0). Using the next-generation approach suggests that R0 for a close-contact disease would be roughly half pre-pandemic levels in the UK, 80% in NL and intermediate in the other two countries.\n\nConclusionsThe pandemic appears to have resulted in lasting changes in contact patterns that would be expected to have an impact on the epidemiology of many different pathogens. Further post-pandemic surveys are necessary to confirm this finding.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Christopher I Jarvis", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Pietro Coletti", + "author_inst": "Hasselt University" + }, + { + "author_name": "Jantien A Backer", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "James D Munday", + "author_inst": "Department of Biosystems Science and Engineering, ETH Zurich, Switzerland" + }, + { + "author_name": "Christel Faes", + "author_inst": "Hasselt University" + }, + { + "author_name": "Philippe Beutels", + "author_inst": "University of Antwerp" + }, + { + "author_name": "Christian L Althaus", + "author_inst": "University of Bern" + }, + { + "author_name": "Nicola Low", + "author_inst": "University of Bern" + }, + { + "author_name": "Jacco Wallinga", + "author_inst": "National Institute for Public Health and the Environment, Leiden University Medical Center" + }, + { + "author_name": "Niel Hens", + "author_inst": "Hasselt University, University of Antwerp" + }, + { + "author_name": "W John Edmunds", + "author_inst": "London School of Hygiene and Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.08.29.23293775", "rel_title": "Estimating seroprevalence of SARS-CoV-2 infection after highly contagious Omicron outbreak: A cross sectional study in a university setting", @@ -69161,69 +70813,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.08.28.23294549", - "rel_title": "Environmental surveillance for SARS-CoV-2 for outbreak detection in hospital: A single centre prospective study", - "rel_date": "2023-08-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.28.23294549", - "rel_abs": "Identifying COVID-19 outbreaks in hospitals at an early stage requires active surveillance. Our objective was to assess whether floor swabs correlated with COVID-19 outbreak status in hospital. We swabbed the floors of an inpatient ward at Mount Sinai Hospital for 32 weeks, from October 31, 2022 to June 15, 2023 and RT-qPCR analysis provided a quantification cycle of detection for each positive swab. 182 swabs were processed for SARS CoV-2, of which 98.4% were positive. Two COVID-19 outbreaks were declared during the study period. The median viral copy number was 210 (IQR, 49 to 1018) during non-outbreak periods and 653 (IQR, 300 to 1754) during outbreak periods. Analyzing the number of viral copies of SARS-CoV-2, instead of percentage positivity, gave a clearer view of changes in outbreak status over time, thereby illustrating the benefits of this approach to monitor pathogen load in hospital settings.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Prachi Ray", - "author_inst": "Department of Medicine, Sinai Health System, Toronto, ON, Canada" - }, - { - "author_name": "Bryant Lim", - "author_inst": "Department of Medicine, University of Toronto, Toronto, ON, Canada" - }, - { - "author_name": "Katarina Zorcic", - "author_inst": "Department of Medicine, Sinai Health System, Toronto, ON, Canada" - }, - { - "author_name": "Jennie Johnstone", - "author_inst": "Infection Prevention and Control, Sinai Health System, Toronto, ON, Canada" - }, - { - "author_name": "Aaron Hinz", - "author_inst": "Department of Biology, University of Ottawa, Ottawa, ON, Canada" - }, - { - "author_name": "Alexandra M.A. Hicks", - "author_inst": "Department of Biology, University of Ottawa, Ottawa, ON, Canada" - }, - { - "author_name": "Alex Wong", - "author_inst": "Department of Biology, Carleton University, Ottawa, ON, Canada" - }, - { - "author_name": "Derek R. MacFadden", - "author_inst": "The Ottawa Hospital Research Institute, Ottawa, ON, Canada" - }, - { - "author_name": "Caroline Nott", - "author_inst": "The Ottawa Hospital Research Institute, Ottawa, ON, Canada" - }, - { - "author_name": "Lucas Castellani", - "author_inst": "Division of Clinical Sciences, NOSM University, Sudbury, ON, Canada" - }, - { - "author_name": "Rees Kassen", - "author_inst": "Department of Biology, University of Ottawa, Ottawa, ON, Canada" - }, - { - "author_name": "Mike Fralick", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.08.27.23294704", "rel_title": "Improvement of immune dysregulation and health-related quality of life in individuals with long COVID at 24-months following SARS-CoV-2 infection", @@ -70264,6 +71853,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.08.22.23294416", + "rel_title": "SARS-CoV-2 shedding and evolution in immunocompromised hosts during the Omicron period: a multicenter prospective analysis", + "rel_date": "2023-08-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.22.23294416", + "rel_abs": "BackgroundProlonged SARS-CoV-2 infections in immunocompromised hosts may predict or source the emergence of highly mutated variants. The types of immunosuppression placing patients at highest risk for prolonged infection and associated intrahost viral evolution remain unclear.\n\nMethodsAdults aged [≥]18 years were enrolled at 5 hospitals and followed from 4/11/2022 - 2/1/2023. Eligible patients were SARS-CoV-2-positive in the previous 14 days and had a moderate or severely immunocompromising condition or treatment. Nasal specimens were tested by rRT-PCR every 2-4 weeks until negative in consecutive specimens. Positive specimens underwent viral culture and whole genome sequencing. A Cox proportional hazards model was used to assess factors associated with duration of infection.\n\nResultsWe enrolled 150 patients with: B cell malignancy or anti-B cell therapy (n=18), solid organ or hematopoietic stem cell transplant (SOT/HSCT) (n=59), AIDS (n=5), non-B cell malignancy (n=23), and autoimmune/autoinflammatory conditions (n=45). Thirty-eight (25%) were rRT-PCR-positive and 12 (8%) were culture-positive [≥]21 days after initial SARS-CoV-2 detection or illness onset. Patients with B cell dysfunction had longer duration of rRT-PCR- positivity compared to those with autoimmune/autoinflammatory conditions (aHR 0.32, 95% CI 0.15-0.64). Consensus (>50% frequency) spike mutations were identified in 5 individuals who were rRT-PCR-positive >56 days; 61% were in the receptor-binding domain (RBD). Mutations shared by multiple individuals were rare (<5%) in global circulation.\n\nConclusionsIn this cohort, prolonged replication-competent Omicron SARS-CoV-2 infections were uncommon. Within-host evolutionary rates were similar across patients, but individuals with infections lasting >56 days accumulated spike mutations, which were distinct from those seen globally.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Zoe Raglow", + "author_inst": "Department of Internal Medicine, University of Michigan" + }, + { + "author_name": "Diya Surie", + "author_inst": "National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention" + }, + { + "author_name": "James D. Chappell", + "author_inst": "Department of Pediatrics, Vanderbilt University Medical Center" + }, + { + "author_name": "Yuwei Zhu", + "author_inst": "Department of Biostatistics, Vanderbilt University Medical Center" + }, + { + "author_name": "Emily Toth Martin", + "author_inst": "School of Public Health, University of Michigan" + }, + { + "author_name": "Jennie H. Kwon", + "author_inst": "Department of Medicine, Washington University" + }, + { + "author_name": "Anne E. Frosch", + "author_inst": "Department of Medicine, Hennepin County Medical Center" + }, + { + "author_name": "Amira Mohamed", + "author_inst": "Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine" + }, + { + "author_name": "Julie Gilbert", + "author_inst": "Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan" + }, + { + "author_name": "Emily E. Bendall", + "author_inst": "Department of Internal Medicine, University of Michigan" + }, + { + "author_name": "Auden Bahr", + "author_inst": "Computational Medicine and Bioinformatics, University of Michigan" + }, + { + "author_name": "Natasha Halasa", + "author_inst": "Department of Pediatrics, Vanderbilt University Medical Center" + }, + { + "author_name": "H. Keipp Talbot", + "author_inst": "Departments of Medicine and Health Policy, Vanderbilt University Medical Center" + }, + { + "author_name": "Carlos G. Grijalva", + "author_inst": "Department of Health Policy, Vanderbilt University Medical Center" + }, + { + "author_name": "Adrienne Baughman", + "author_inst": "Department of Emergency Medicine, Vanderbilt University Medical Center" + }, + { + "author_name": "Kelsey N. Womack", + "author_inst": "Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center" + }, + { + "author_name": "Cassandra Johnson", + "author_inst": "Department of Biostatistics, Vanderbilt University Medical Center" + }, + { + "author_name": "Sydney A. Swan", + "author_inst": "Department of Biostatistics, Vanderbilt University Medical Center" + }, + { + "author_name": "Emilia Koumans", + "author_inst": "Division of STD Prevention, Centers for Disease Control and Prevention" + }, + { + "author_name": "Meredith L. McMorrow", + "author_inst": "National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention" + }, + { + "author_name": "Jennifer L. Harcourt", + "author_inst": "National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention" + }, + { + "author_name": "Lydia J. Atherton", + "author_inst": "National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention" + }, + { + "author_name": "Ashley Burroughs", + "author_inst": "National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention" + }, + { + "author_name": "Natalie J. Thornburg", + "author_inst": "National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention" + }, + { + "author_name": "Wesley H. Self", + "author_inst": "Vanderbilt Institute for Clinical and Translational Research and Department of Emergency Medicine and, Vanderbilt University Medical Center" + }, + { + "author_name": "Adam S. Lauring", + "author_inst": "Departments of Internal Medicine and Microbiology and Immunology, University of Michigan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.08.23.23294509", "rel_title": "COVID-19 Symptoms and Immunotherapy in People with Multiple Sclerosis: An Analysis of the COVID-19 in MS Global Data Sharing Initiative Dataset", @@ -70655,45 +72363,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.08.23.23294474", - "rel_title": "COVID-19 self-testing: Countries accelerating policies ahead of WHO guidelines during pandemics: A Global Survey.", - "rel_date": "2023-08-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.23.23294474", - "rel_abs": "IntroductionThe widespread use of antigen-detection rapid diagnostic tests (Ag-RDTs) has revolutionized SARS-CoV-2 (COVID-19) testing, particularly through the option of self-testing. The full extent of Ag-RDT utilization for self-testing, however, remains largely unexplored. To inform the development of WHO guidance on COVID-19 self-testing, we conducted a cross-sectional survey to gather the views and experiences of policy makers, researchers, and implementers worldwide.\n\nMethodsThe survey was shared through professional networks via email and social media, encouraging onward sharing. We used closed and open-ended questions related to policy and program information concerning the regulation, availability, target population, indications, implementation, benefits, and challenges of COVID-19 self-testing (C19ST). We defined self-testing as tests performed and interpreted by an untrained individual, often at home. Descriptive summaries, cross-tabulations, and proportions were used to calculate outcomes at the global level and by WHO region and World Bank income classifications.\n\nResultsBetween 01 and 11 February 2022, 844 individuals from 139 countries responded to the survey, with 45% reporting affiliation with governments and 47% operating at the national level. 504 respondents from 101 countries reported policies supporting C19ST for a range of use cases, including symptomatic and asymptomatic populations. More respondents from low-and-middle-income countries (LMICs) than high-income countries (HICs) reported a lack of an C19ST policy (61 vs 11 countries) and low population-level reach of C19ST. Respondents with C19ST experience perceived that the tests were mostly acceptable to target populations, provided significant benefits, and highlighted several key challenges to be addressed for increased success. Reported costs varied widely, ranging from specific programmes enabling free access to certain users and others with high costs via the private sector.\n\nConclusionBased on the survey responses, systems for the regulatory review, policy development and implementation of C19STappeared to be much more common in HIC when compared to LIC in early 2022, though most respondents indicated self-testing was available to some extent (101 out of 139 countries) in their country. Addressing such global inequities is critical for ensuring access to innovative and impactful interventions in the context of a public health emergency of international concern. The challenges and opportunities highlighted by survey respondents could be valuable to consider as future testing strategies are being set for outbreak-prone diseases.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Melody Sakala", - "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research Programme" - }, - { - "author_name": "Cherly Johnson", - "author_inst": "World Health Organization" - }, - { - "author_name": "James Chirombo", - "author_inst": "Malawi-Liverpool-Wellcome Trust Clinical Research Programme" - }, - { - "author_name": "Jilian A Sacks", - "author_inst": "World Health Organization" - }, - { - "author_name": "Rachel Baggaley", - "author_inst": "World Health Organization" - }, - { - "author_name": "Titus Divala", - "author_inst": "Kamuzu University of Health Sciences: University of Malawi College of Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.08.22.23294419", "rel_title": "Prediction of COVID-19 infection risk using personal mobile location data only", @@ -71858,6 +73527,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.08.18.23294172", + "rel_title": "Cohort Profile: Prospective Cohort to Study the COVID-19 Immune Response in Retail Workers in Quebec, Canada (CISACOV)", + "rel_date": "2023-08-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.18.23294172", + "rel_abs": "PurposeRetail workers are an understudied occupational group that may have been at increased risk of contracting SARS-CoV-2 during the COVID-19 pandemic. Therefore, we set up a longitudinal cohort of participants working in this sector to better document the incidence of SARS-CoV-2 infection and the immune response to infection and/or vaccination in this group.\n\nParticipantsA total of 304 participants were recruited between April 20, 2021 and October 22, 2021. They were invited to attend three visits (each separated by [~]12 weeks) during which they provided blood samples and information on participant characteristics, COVID-19 symptoms, and vaccination. An extension phase of two additional visits was carried out between March 15th, 2022 and October 3rd, 2022 to document the impact of the Omicron variant among the 198 participants who were still eligible for recruitment. Participants were aged 18 to 75 and worked in grocery stores, hardware stores, bars or restaurants within the Quebec City metropolitan area (Canada). Findings to date: This article describes participants demographic, socioeconomic, behavioral, clinical and occupational characteristics, and their COVID-19 symptoms (where applicable). It also describes SARS-CoV-2 vaccination status and any SARS-CoV-2 diagnostic test (i.e., PCR or rapid antigen) performed from the beginning of the pandemic until the last visit.\n\nFuture plansThe incidence of SARS-CoV-2 infections will be assessed. The immune response (innate and acquired) to SARS-CoV-2 infection or vaccination will be studied using a variety of techniques, including reference and experimental enzyme-linked immunosorbent assays, microneutralization assays with live viruses, experimental pseudoneutralization with an angiotensin-converting enzyme 2-spike assay, peripheral blood mononuclear cells and neutrophil stimulation, and a proliferation assay based on carboxyfluorescein diacetate succinimidyl ester.\n\nRegistrationNot applicable.\n\nStrengths and limitationsO_LIThis cohort offers a comprehensive dataset to study the immune response to SARS-CoV-2 infection or vaccination (alone), or hybrid immunity, as participants provided information on a wide range of demographic, socioeconomic, behavioral, clinical, and occupational variables. However, the low proportion of racial minorities (i.e., 3.0%) limits the use of this cohort to study racial determinants of immunity to SARS-CoV-2.\nC_LIO_LIThis cohort focuses on workers in the food and retail service sector, an understudied population at high risk of occupational exposure to infectious agents.\nC_LIO_LIThis study covered seven pandemic waves and thus captured a large number of confirmed infections from different variants.\nC_LIO_LISample collection was initiated immediately prior to COVID-19 vaccine availability for this population and thus captured successive vaccination campaigns over 17 months.\nC_LIO_LIIn keeping with the study design, none of the participants had severe COVID-19 disease requiring hospitalization at baseline, and none of the COVID-19 illnesses that occurred during the study required hospitalization; this cohort may not, therefore, be used to study the immune response leading to severe health outcomes, but is appropriate to study the immune response to mild SARS-CoV-2 infections.\nC_LIO_LINearly 1300 blood samples were collected; furthermore, only 13 out of 304 (4.3%) participants withdrew before attending all three initial visits, and 4 out of 198 (2.0%) participants who remained eligible in the extension phase withdrew before attending the fifth visit. A series of at least 5 blood samples drawn over 48 weeks is therefore available for most participants.\nC_LI", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Kim Santerre", + "author_inst": "Centre de recherche du CHU de Qu\u00e9bec - Universit\u00e9 Laval" + }, + { + "author_name": "Mathieu Th\u00e9riault", + "author_inst": "Centre de recherche du CHU de Qu\u00e9bec - Universit\u00e9 Laval" + }, + { + "author_name": "Nicholas Brousseau", + "author_inst": "Institut national de sant\u00e9 publique du Qu\u00e9bec" + }, + { + "author_name": "Samuel Rochette", + "author_inst": "SR Scientific Writing Services" + }, + { + "author_name": "Joelle Pelletier", + "author_inst": "Universit\u00e9 de Montr\u00e9al" + }, + { + "author_name": "Caroline Gilbert", + "author_inst": "Centre de recherche du CHU de Qu\u00e9bec - Universit\u00e9 Laval" + }, + { + "author_name": "Jean-Francois Masson", + "author_inst": "Universit\u00e9 de Montr\u00e9al" + }, + { + "author_name": "Mariana Baz", + "author_inst": "Centre de recherche du CHU de Qu\u00e9bec - Universit\u00e9 Laval" + }, + { + "author_name": "Denis Boudreau", + "author_inst": "Universit\u00e9 Laval" + }, + { + "author_name": "Sylvie Trottier", + "author_inst": "Centre de recherche du CHU de Qu\u00e9bec - Universit\u00e9 Laval" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.08.16.23294170", "rel_title": "Offspring cardiometabolic outcomes and postnatal growth trajectories after exposure to maternal SARS-CoV-2 infection", @@ -72401,125 +74125,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.08.18.23293746", - "rel_title": "Emergence of neutralizing antibodies associates with clearance of SARS-CoV-2 during HIV-mediated immunosuppression", - "rel_date": "2023-08-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.18.23293746", - "rel_abs": "To design effective vaccines and other immune interventions against a pathogen, it is necessary to know which aspect of immunity associates with protection. We investigated whether neutralizing antibodies associate with infection clearance in long-term SARS-CoV-2 infection during HIV-mediated immunosuppression. We monitored neutralizing antibody activity against SARS-CoV-2 over 1 to 2 years in five participants with advanced HIV disease and delayed control of HIV viremia. These participants had persistent SARS-CoV-2 infection ranging from 110 to 289 days which was associated with low or undetectable neutralizing antibody responses. SARS-CoV-2 clearance was associated with the emergence of neutralizing antibodies and occurred in two participants before suppression of HIV viremia, but after some CD4 T cell reconstitution. Vaccination only further increased neutralizing antibody levels in the advanced HIV disease participants who achieved HIV suppression pre-vaccination. During the prolonged SARS-CoV-2 infection we observed widespread evolution which was particularly pronounced in one Delta variant infection. This resulted in high-level escape from Delta-elicited neutralizing antibodies and a virus antigenically distinct from both ancestral SARS-CoV-2 and Omicron XBB in hamster experimental infections. The results offer new evidence that neutralizing antibodies associate with SARS-CoV-2 clearance and argue that successful management of HIV may be necessary to curtail long-term infection and evolution of co-infecting pathogens.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Farina Karim", - "author_inst": "Africa Health Research Institute, Durban, South Africa; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal" - }, - { - "author_name": "Mallory Bernstein", - "author_inst": "Africa Health Research Institute, Durban, South Africa" - }, - { - "author_name": "Zesuliwe Zesuliwe", - "author_inst": "Africa Health Research Institute, Durban, South Africa" - }, - { - "author_name": "Gil Lustig", - "author_inst": "Centre for the AIDS Programme of Research in South Africa, Durban, South Africa." - }, - { - "author_name": "Janine-Lee Upton", - "author_inst": "Africa Health Research Institute, Durban, South Africa" - }, - { - "author_name": "Yashica Ganga", - "author_inst": "Africa Health Research Institute, Durban, South Africa" - }, - { - "author_name": "Khadija Khan", - "author_inst": "Africa Health Research Institute, Durban, South Africa; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal" - }, - { - "author_name": "Kajal Reedoy", - "author_inst": "Africa Health Research Institute, Durban, South Africa" - }, - { - "author_name": "Matilda Mazibuko", - "author_inst": "Africa Health Research Institute, Durban, South Africa" - }, - { - "author_name": "Katya Govender", - "author_inst": "Africa Health Research Institute, Durban, South Africa" - }, - { - "author_name": "Kershnee Thambu", - "author_inst": "Africa Health Research Institute, Durban, South Africa" - }, - { - "author_name": "Nokuthula Ngcobo", - "author_inst": "Africa Health Research Institute, Durban, South Africa" - }, - { - "author_name": "Elizabeth Venter", - "author_inst": "SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. 5National I" - }, - { - "author_name": "Zanele Makhado", - "author_inst": "SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. 5National I" - }, - { - "author_name": "Willem Hanekom", - "author_inst": "Africa Health Research Institute; Division of Infection and Immunity, University College London" - }, - { - "author_name": "Anne von Gottberg", - "author_inst": "Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Afri" - }, - { - "author_name": "Quarraisha Abdool Karim", - "author_inst": "Centre for the AIDS Programme of Research in South Africa, Durban, South Africa.Department of Epidemiology, Mailman School of Public Health, Columbia University" - }, - { - "author_name": "Salim S. Adbool Karim", - "author_inst": "Centre for the AIDS Programme of Research in South Africa, Durban, South Africa.Department of Epidemiology, Mailman School of Public Health, Columbia University" - }, - { - "author_name": "Nithendra Manickchund", - "author_inst": "Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa" - }, - { - "author_name": "Nombulelo Magula", - "author_inst": "Department of Internal Medicine, Nelson R. Mandela School of Medicine. Univeristy of Kwa-Zulu Natal" - }, - { - "author_name": "Bernadett Gosnell", - "author_inst": "Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal" - }, - { - "author_name": "Penny L Moore", - "author_inst": "National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa. SA MRC Antibody Immunity Research Unit, Scho" - }, - { - "author_name": "Richard Lessells", - "author_inst": "KwaZulu-Natal Research Innovation & Sequencing Platform" - }, - { - "author_name": "Tulio de Oliveira", - "author_inst": "KwaZulu-Natal Research Innovation & Sequencing Platform, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; " - }, - { - "author_name": "Yunus Moosa", - "author_inst": "Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal" - }, - { - "author_name": "Alex Sigal", - "author_inst": "Africa Health Research Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.08.20.23294345", "rel_title": "SARS-CoV-2 antibody response among COVID-19 patients is not affected by parasite co-infection", @@ -73552,6 +75157,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.08.12.23294016", + "rel_title": "Association of polypharmacy and burden of comorbidities on COVID-19 adverse outcomes in people with type 1 or type 2 diabetes", + "rel_date": "2023-08-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.12.23294016", + "rel_abs": "AimTo investigate whether polypharmacy and comorbidities conveyed more risk of adverse health outcomes following COVID-19 infection in people with type 1 diabetes (T1DM) or type 2 diabetes (T2DM).\n\nMaterials and methodsThe Greater Manchester Care Record (GMCR) is an integrated database of electronic health records containing data collected from 433 general practices in Greater Manchester. Baseline demographic information (age, BMI, gender, ethnicity, smoking status, deprivation index), hospital admission or death within 28 days of infection were extracted for adults (18+) diagnosed with either T1DM or T2DM.\n\nResultsFor T2DM, 16 to 20 medications (p=0.01; OR [95% CI]=2.37 [1.31 to 4.32]) and > 20 medications (p=0; OR [95% CI]=3.14 [1.75 to 5.62]) were associated with increased risk of death following COVID-19 infection. Increased risk of hospital admissions in T2DM individuals was determined for 11 to 15 medications (p=0.01; OR [95% CI]=1.34 [1.06 to 1.69]) and above. This was independent of comorbidities, metabolic and demographic factors. For T1DM there was no association of polypharmacy with hospital admission. Respiratory, cardiovascular/cerebrovascular and gastrointestinal conditions were associated with increased risk of hospital admissions and deaths in T2DM (p>0.001).\n\nConclusionWe have shown in T2DM an independent association of number of medications taken from 11 upwards with adverse health consequences following COVID-19 infection. We also found that individuals with diabetes develop comorbidities that were common across both T1DM and T2DM. This study has laid the foundation for future investigations into the way that complex pharmacological interactions may influence clinical outcomes in people with T2DM.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Juhi K Gupta", + "author_inst": "University of Manchester" + }, + { + "author_name": "Rathi Ravindrarajah", + "author_inst": "University of Manchester" + }, + { + "author_name": "George Tilston", + "author_inst": "University of Manchester" + }, + { + "author_name": "William Ollier", + "author_inst": "Manchester Metropolitan University" + }, + { + "author_name": "Darren M Ashcroft", + "author_inst": "University of Manchester" + }, + { + "author_name": "Adrian H Heald", + "author_inst": "Salford Royal NHS Foundation Trust" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "endocrinology" + }, { "rel_doi": "10.1101/2023.08.11.23293983", "rel_title": "Reproduction Number EXCEL Model of COVID-19 for predictive calculation of nearby trend up to the end of infection", @@ -74031,65 +75675,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.08.10.23293869", - "rel_title": "A Single-Tube Colorimetric Loop-Mediated Isothermal Amplification for Rapid Detection of SARS-CoV-2 RNA", - "rel_date": "2023-08-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.10.23293869", - "rel_abs": "Since SARS-CoV-2 is a highly transmissible virus, a rapid and accurate diagnostic method is necessary to prevent virus spread. We aimed to develop and evaluate a new rapid colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for SARS-CoV-2 detection in a single closed-tube. Nasopharyngeal and throat swabs collected from at-risk individuals testing for SARS-CoV-2 were used to assess the sensitivity and specificity of a new RT-LAMP assay against a commercial qRT-PCR assay. Total RNA extracts were submitted to the RT-LAMP reaction under optimal conditions and amplified at 65{degrees}C for 30 minutes using three sets of specific primers targeting the nucleocapsid gene. The reaction was detected using two different indicator dyes, hydroxynaphthol blue (HNB) and cresol red. A total of 82 samples were used for detection with HNB and 94 samples with cresol red, and results were compared with the qRT-PCR assay. The sensitivity of the RT-LAMP-based HNB assay was 92.1% and the specificity was 93.2%. The sensitivity of the RT-LAMP-based cresol red assay was 80.3%, and the specificity was 97%. This colorimetric feature makes this assay highly accessible, low-cost, and user-friendly, which can be deployed for massive scale-up and rapid diagnosis of SARS-CoV-2 infection, particularly in low-resource settings.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Sayamon Hongjaisee", - "author_inst": "Chiang Mai University" - }, - { - "author_name": "Nang Kham-Kjing", - "author_inst": "Chiang Mai University" - }, - { - "author_name": "Piyagorn Musikul", - "author_inst": "Chiang Mai University" - }, - { - "author_name": "Wannaporn Daengkaokhew", - "author_inst": "Chiang Mai University" - }, - { - "author_name": "Nuntita Kongson", - "author_inst": "Chiang Mai University" - }, - { - "author_name": "Ratchadakorn Guntala", - "author_inst": "University of Phayao" - }, - { - "author_name": "Nitipoom Jaiyapan", - "author_inst": "Chiang Mai University" - }, - { - "author_name": "Enos C Kline", - "author_inst": "University of Washington" - }, - { - "author_name": "Nuttada Panpradist", - "author_inst": "University of Washington" - }, - { - "author_name": "Nicole Ngo-Giang-Huong", - "author_inst": "LUCENT International Collaboration" - }, - { - "author_name": "Woottichai Khamduang", - "author_inst": "Chiang Mai University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.08.10.23293924", "rel_title": "Published benefits of ivermectin use in Itajai, Brazil for COVID-19 infection, hospitalisation, and mortality are entirely explained by statistical artefacts", @@ -74994,6 +76579,45 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.08.09.552685", + "rel_title": "Open-source milligram-scale, four channel, automated protein purification system", + "rel_date": "2023-08-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.09.552685", + "rel_abs": "Liquid chromatography purification of multiple recombinant proteins, in parallel, could catalyze research and discovery if the processes are fast and approach the robustness of traditional, \"one-protein-at-a-time\" purification. Here, we report an automated, four channel chromatography platform that we have designed and validated for parallelized protein purification at milligram scales. The device can purify up to four proteins (each with its own single column), has inputs for up to eight buffers or solvents that can be directed to any of the four columns via a network of software-driven valves, and includes an automated fraction collector with ten positions for 1.5 or 5.0 mL collection tubes and four positions for 50 mL collection tubes for each column output. The control software can be accessed either via Python scripting, giving users full access to all steps of the purification process, or via a simple-to-navigate touch screen graphical user interface that does not require knowledge of the command line or any programming language. Using our instrument, we report milligram-scale, parallelized, single-column purification of a panel of mammalian cell expressed coronavirus (SARS-CoV-2, HCoV-229E, HCoV-OC43, HCoV-229E) trimeric Spike and monomeric Receptor Binding Domain (RBD) antigens, and monoclonal antibodies targeting SARS-CoV-2 Spike (S) and Influenza Hemagglutinin (HA). We include a detailed hardware build guide, and have made the controlling software open source, to allow others to build and customize their own protein purifier systems.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Robert R. Puccinelli", + "author_inst": "Chan Zuckerberg Biohub - San Francisco" + }, + { + "author_name": "Samia S. Sama", + "author_inst": "Chan Zuckerberg Biohub - San Francisco" + }, + { + "author_name": "Caroline M. Worthington", + "author_inst": "Chan Zuckerberg Biohub - San Francisco" + }, + { + "author_name": "Andreas S. Puschnik", + "author_inst": "Chan Zuckerberg Biohub - San Francisco" + }, + { + "author_name": "John E. Pak", + "author_inst": "Chan Zuckerberg Biohub - San Francisco" + }, + { + "author_name": "Rafael Gomez-Sjoberg", + "author_inst": "Chan Zuckerberg Biohub - San Francisco" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2023.08.08.552470", "rel_title": "Development and Analytical Evaluation of a Point-of-Care Electrochemical Biosensor for Rapid and Accurate SARS-CoV-2 Detection", @@ -75361,41 +76985,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.08.05.23293566", - "rel_title": "SARS-CoV-2 Pandemic Non-Pharmacologic Interventions Temporally Associated with Reduced Pediatric Infections Due to Mycoplasma pneumoniae and Co-Infecting Respiratory Viruses in Arkansas", - "rel_date": "2023-08-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.05.23293566", - "rel_abs": "IntroductionNon-pharmacologic interventions (NPIs), such as universal masking, implemented during the SARS-CoV-2 pandemic have reduced respiratory infections among children. This study focuses on evaluating the impact of NPIs on Mycoplasma pneumoniae infections in children, analyzing data from two hospitals in Arkansas, and examining age-related differences and coinfections with other viruses.\n\nMethodsThe study was approved by the Institutional Review Board and included patients aged [≤]18 years with upper respiratory tract symptoms. Data from the FilmArray(R) Respiratory Panel (FARP) were collected and divided into pre-NPI and NPI periods for analysis. Total test positivity rate and interval change in the positivity rate were evaluated. Statistical differences were determined by Chi-square ({chi}2-independence) analysis.\n\nResultsA total of 68,949 tests were performed with a statistical increase in testing during the NPI period. The overall test positivity rate for M. pneumoniae decreased by 74% (0.86% to 0.03%) during the NPI period, and the preschool age group had the highest number of positive tests in the pre- and NPI periods (Pre-NPI: n=40, NPI: n=12 positive tests, p=<0.001). The reduction in M. pneumoniae infections was consistent across age groups. Coinfections with other respiratory viruses, particularly human rhinovirus/enterovirus, were observed at much lower levels.\n\nConclusionsNPIs effectively reduced M. pneumoniae in pediatric patients in Arkansas, and coinfections with specific viruses still occurred, albeit at lower levels during the SARS-CoV-2 pandemic. As NPIs are relaxed and the pandemic ends, we expect M. pneumoniae infections to return to pre-pandemic levels within the next 1-2 years.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Bobby L Boyanton Jr.", - "author_inst": "Arkansas Children's Hospital" - }, - { - "author_name": "Rachel A Frenner", - "author_inst": "Arkansas Children's Hospital" - }, - { - "author_name": "Ashton Ingold", - "author_inst": "Arkansas Children's Research Institute" - }, - { - "author_name": "Lilliam Ambroggio", - "author_inst": "Children's Hospital of Colorado" - }, - { - "author_name": "Joshua L Kennedy", - "author_inst": "University of Arkansas for Medical Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.08.05.23293695", "rel_title": "Prevalence of Long COVID19 among paediatric age group in Duhok Kurdistan region, Iraq", @@ -76424,6 +78013,53 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.08.06.552160", + "rel_title": "SARS-CoV-2 infection of human pluripotent stem cell-derived vascular cells reveals smooth muscle cells as key mediators of vascular pathology during infection", + "rel_date": "2023-08-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.06.552160", + "rel_abs": "Although respiratory symptoms are the most prevalent disease manifestation of infection by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), nearly 20% of hospitalized patients are at risk for thromboembolic events1. This prothrombotic state is considered a key factor in the increased risk of stroke, which has been observed clinically during both acute infection and long after symptoms have cleared2. Here we developed a model of SARS-CoV-2 infection using human-induced pluripotent stem cell-derived endothelial cells, pericytes, and smooth muscle cells to recapitulate the vascular pathology associated with SARS-CoV-2 exposure. Our results demonstrate that perivascular cells, particularly smooth muscle cells (SMCs), are a specifically susceptible vascular target for SARS-CoV-2 infection. Utilizing RNA sequencing, we characterized the transcriptomic changes accompanying SARS-CoV-2 infection of SMCs, and endothelial cells (ECs). We observed that infected human SMCs shift to a pro-inflammatory state and increase the expression of key mediators of the coagulation cascade. Further, we showed human ECs exposed to the secretome of infected SMCs produce hemostatic factors that can contribute to vascular dysfunction, despite not being susceptible to direct infection. The findings here recapitulate observations from patient sera in human COVID-19 patients and provide mechanistic insight into the unique vascular implications of SARS-CoV-2 infection at a cellular level.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Alexsia Richards", + "author_inst": "Whitehead Institute for Biomedical Reseach" + }, + { + "author_name": "Andrew Khalil", + "author_inst": "Whitehead Institute for Biomedical Research" + }, + { + "author_name": "Max Friesen", + "author_inst": "Whitehead Institute for Biomedical Research" + }, + { + "author_name": "Troy Whitfield", + "author_inst": "Whitehead Institute for Biomedical Reseach" + }, + { + "author_name": "Tenzin Lungjangwa", + "author_inst": "Whitehead Institute for Biomedical Research" + }, + { + "author_name": "Lee Gehrke", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "David Mooney", + "author_inst": "Harvard University" + }, + { + "author_name": "Rudolph Jaenisch", + "author_inst": "Whitehead Institute for Biomedical Research" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.08.04.551973", "rel_title": "Recombinant SARS-CoV-2 lacking initiating and internal methionine codons within ORF10 is attenuated in vivo", @@ -76935,41 +78571,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.08.01.23293449", - "rel_title": "Impact of Adjustment for Differential Testing by Age and Sex on Apparent Epidemiology of SARS-CoV-2 Infection in Ontario, Canada", - "rel_date": "2023-08-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.08.01.23293449", - "rel_abs": "BackgroundSurveillance of communicable diseases typically relies on case counts for estimates of risk, and counts can be strongly influenced by testing rates. In the Canadian province of Ontario, testing rates varied markedly by age, sex, geography and time over the course of the SARS-CoV-2 pandemic. We applied a standardization-based approach to test-adjustment to better understand pandemic dynamics from 2020 to 2022, and to better understand when test-adjustment is necessary for accurate estimation of risk.\n\nMethodsSARS-CoV-2 case counts by age, sex, public health unit and week were obtained from Ontarios Case and Contact Management system (CCM), which includes all SARS-CoV-2 cases from March 2020 to August 2022. Complete data on testing volumes was obtained from the Ontario Laboratory Information System (OLIS). Case counts were adjusted for under-testing using a previously published standardization-based approach that estimates case numbers that would have been expected if the entire population was tested at the same rate as most-tested age and sex groups. Logistic regression was used to identify threshold testing rates beyond which test-adjustment was unnecessary.\n\nResultsTesting rates varied markedly by age, sex, public health unit and pandemic wave. After adjustment for under-testing, overall case counts increased threefold. Adjusted epidemic curves suggested, in contrast to reported case counts, that the first two pandemic waves were equivalent in size, and that there were three distinct pandemic waves in 2022, due to the emergence of Omicron variants. Under-reporting was greatest in children and young males, and varied significantly across public health units, with variation explained partly by testing rates and prevalence of multigenerational households. Test adjustment resulted in little change in the epidemic curve during pandemic waves when testing rates were highest; we found that test-adjustment did not increase case counts once weekly per capita testing rates exceeded 6.3%.\n\nConclusionsStandardization-based adjustment for differential testing by age and sex, and for dynamic changes in testing over time, results in a different picture of infection risk during the SARS-CoV-2 pandemic in Ontario; test-adjusted epidemic curves are concordant with observed patterns of mortality during the pandemic and have face validity. This methodology offers an alternative to sero-epidemiology for identification of true burden of infection when reinfection, sero-reversion, and non-specificity of serological assays make sero-epidemiology challenging.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Savana Bosco", - "author_inst": "University of Toronto" - }, - { - "author_name": "Amy Peng", - "author_inst": "University of Toronto" - }, - { - "author_name": "Alison E. Simmons", - "author_inst": "University of Toronto" - }, - { - "author_name": "Ashleigh Tuite", - "author_inst": "University of Toronto" - }, - { - "author_name": "David Fisman", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.08.01.23293521", "rel_title": "Diagnostic performance of LumiraDx SARS-CoV-2 rapid antigen test compared to PCR for diagnosis of COVID-19 in Liberia", @@ -77982,6 +79583,61 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.08.02.551424", + "rel_title": "Neutralizing antibody responses and cellular responses against severe acute respiratory syndrome coronavirus 2 omicron subvariant BA.5 after an mRNA severe acute respiratory syndrome coronavirus 2 vaccine dose in kidney transplant recipients", + "rel_date": "2023-08-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.08.02.551424", + "rel_abs": "We examined the anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein IgG antibody and neutralizing antibody titers and cellular immunity in 73 uninfected recipients and 17 uninfected healthy controls who received three doses of a coronavirus 2019 mRNA vaccine. Neutralizing antibody titers were evaluated using GFP-carrying recombinant SARS-CoV-2 with spike protein of B.1.1, omicron BA.1, or BA.5. For cellular immunity, peripheral blood mononuclear cells were stimulated with peptides corresponding to spike protein antigens of B.1.1, BA.1, and BA.5; spike-specific CD4/CD8 memory T cells were evaluated using intracellular cytokine staining. The median IgG antibody titers were 7.8 AU/mL in recipients and 143.0 AU/mL in healthy controls (p < 0.0001). Neutralizing antibody titers against all three viral variants were significantly lower in recipients (p < 0.0001). The number of spike-specific CD8 + memory T cells significantly decreased in recipients (p < 0.0001). Twenty recipients and seven healthy controls additionally received a bivalent omicron-containing booster vaccine, and IgG antibody and neutralizing antibody titers increased in both groups; however, the increase was significantly lower in recipients. Recipients did not gain sufficient immunity with a third dose of vaccine, suggesting a need to explore methods other than vaccines.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Keita Kawashiro", + "author_inst": "Hokkaido University Hospital" + }, + { + "author_name": "Rigel Suzuki", + "author_inst": "Hokkaido university" + }, + { + "author_name": "Takuto Nogimori", + "author_inst": "National Institutes of Biomedical Innovation, Health and Nutrition" + }, + { + "author_name": "Naoya Iwahara", + "author_inst": "Hokkaido University Hospital" + }, + { + "author_name": "Takayuki Hirose", + "author_inst": "Hokkaido University Hospital" + }, + { + "author_name": "Kazufumi Okada", + "author_inst": "Hokkaido University Hospital" + }, + { + "author_name": "Takuya Yamamoto", + "author_inst": "National Institutes of Biomedical Innovation, Health and Nutrition" + }, + { + "author_name": "Takasuke Fukuhara", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Kiyohiko Hotta", + "author_inst": "Hokkaido University Hospital" + }, + { + "author_name": "Nobuo Shinohara", + "author_inst": "Hokkaido University Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.08.01.551423", "rel_title": "Gonadal androgens are associated with decreased type I interferon production by pDCs and increased IgG titres to BNT162b2 following co-vaccination with live attenuated influenza vaccine in adolescents", @@ -78549,61 +80205,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.07.27.23293244", - "rel_title": "Prevalence of long-term symptoms varies by using different post-COVID-19 definitions in positively and negatively tested adults: the PRIME post-COVID study", - "rel_date": "2023-08-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.27.23293244", - "rel_abs": "BackgroundLong-term symptoms after a SARS-CoV-2 infection (i.e., post-COVID-19 condition or long COVID), constitute a substantial public health problem. Yet, the prevalence remains currently unclear as different case definitions are used, and negatively tested controls are lacking. We aimed to estimate post-COVID-19 condition prevalence using six definitions.\n\nMethodsThe Prevalence, Risk factors, and Impact Evaluation (PRIME) post-COVID-19 condition study is a population-based sample of COVID-19 tested adults. End 2021, 61,655 adults were invited to complete an online questionnaire, including 44 symptoms plus a severity score (0-10) per symptom. The prevalence was calculated in both positively and negatively tested adults, stratified by time since their COVID-19 test (3-5, 6-11 or [≥]12 months ago).\n\nResultsIn positives (n=7,405; 75.6%), the prevalence of long-term symptoms was between 26.9% and 64.1% using the six definitions, while in negatives (n=2,392; 24.4%) the prevalence varied between 11.4% and 32.5%. The prevalence of long-term symptoms potentially accountable to COVID-19 ranged from 17.9% to 26.3%.\n\nConclusionThere is a (substantial) variation in prevalence estimates by using different definitions as is current practice, showing limited overlap between definitions, indicating that the essential post-COVID-19 condition criteria are still unclear. Including negatives is important to determine long-term symptoms accountable to COVID-19.\n\nTrial registration ClinicalTrials.gov Identifier: NCT05128695.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Demi ME Pagen", - "author_inst": "Public Health Service South Limburg" - }, - { - "author_name": "Celine JA van Bilsen", - "author_inst": "Public Health Service South Limburg" - }, - { - "author_name": "Stephanie Brinkhues", - "author_inst": "Public Health Service South Limburg" - }, - { - "author_name": "Maarten Van Herck", - "author_inst": "Ciro" - }, - { - "author_name": "Kevin Konings", - "author_inst": "Public Health Service South Limburg" - }, - { - "author_name": "Casper DJ den Heijer", - "author_inst": "Public Health Service South Limburg" - }, - { - "author_name": "Henriette LG ter Waarbeek", - "author_inst": "Public Health Service South Limburg" - }, - { - "author_name": "Martijn A Spruit", - "author_inst": "Ciro" - }, - { - "author_name": "Christian JPA Hoebe", - "author_inst": "South Limburg Public Health Service" - }, - { - "author_name": "Nicole HTM Dukers-Muijrers", - "author_inst": "Maastricht University/Public Health Service" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.07.30.23292881", "rel_title": "Loss of severe respiratory syncytial virus infection-associated antibody function during the peak of the COVID-19 pandemic mitigation measures", @@ -80096,6 +81697,25 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2023.07.27.550841", + "rel_title": "Mapping immunological and host receptor binding determinants of SARS-CoV spike protein utilizing the Qubevirus platform", + "rel_date": "2023-07-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.27.550841", + "rel_abs": "The motifs involved in tropism and immunological interactions of SARS-CoV spike (S) protein were investigated utilizing the Qubevirus platform. We showed that separately, 14 overlapping peptide fragments representing the S protein (F1-14 of 100 residues each) could be inserted into the C-terminus of A1 on recombinant Qubevirus without affecting its viability. Additionally, recombinant phage expression resulted in the surface exposure of different engineered fragments in an accessible manner. The F6 from S425-525, was found to contain the binding determinant of the recombinant human angiotensin converting enzyme 2 (rhACE2), with the shortest active binding motif situated between residues S437-492. Upstream, another fragment, F7, containing an overlapping portion of F6 would not bind to rhACE2, confirming not just only that residues were linear but equally also the appropriate structural orientation of F6 upon the Qubevirus. The F6 (S441-460) and other inserts, including F7/F8 (S601-620) and F10 (S781-800), were demonstrated to contain important immunological determinants through recognition and binding of S protein specific (anti-S) antibodies. An engineered chimeric insert bearing the fusion of all three anti-S reactive epitopes, improved substantially the recognition and binding to their cognate antibodies. These results provide insights into humoral immune relevant epitopes and tropism characteristics of the S protein with implications for the development of subunit vaccines or other biologics against SARS-CoV.\n\nSignificanceMapping epitopes within the receptor binding domains of viruses which are essential for viral tropism is critical for developing antiviral agents and subunit vaccines. In this study we have engineered the surface of Qubevirus to display a peptide library derived from the SARS-CoV S protein. In biopanning with S protein antibodies, we have identified three peptide fragments (EP1, EP2 and EP3) which reacted selectively with antibodies specific to the S protein. We demonstrated that all recombinant phage displayed peptide fragments both individually and as chimera exposed important immunological epitopes to their cognate antibodies. A peptide fragment F6 situated at S425-525, was found containing the binding determinant of the recombinant human angiotensin converting enzyme 2 (rhACE2), with the shortest active binding motif situated between residues S437-492. The platform is rapidly to identify epitopes and receptor binding sites within viral receptors found in target host cell. Thus, this platform holds great significance.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Alain Bopda Waffo", + "author_inst": "Indiana University School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "synthetic biology" + }, { "rel_doi": "10.1101/2023.07.27.550811", "rel_title": "Butyrate Protects against SARS-CoV-2-induced Tissue Damage in Golden Hamsters.", @@ -80623,33 +82243,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2023.07.24.23293101", - "rel_title": "WEIRD or not: A Cross-Cultural Behavioral Economic Assessment of Demand for HIV and COVID-19 Vaccines", - "rel_date": "2023-07-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.24.23293101", - "rel_abs": "BackgroundDespite empirical evidence supporting vaccine effectiveness, vaccine hesitancy continues to thrive. Demand as a behavioral economic process provides useful indices for evaluating vaccine acceptance likelihood in individuals and groups. Using this framework, our study investigates the dynamics governing vaccine acceptance in two culturally dissimilar countries.\n\nMethodsHypothetical purchase tasks (HPTs) assessed how Nigerian and US participants varied vaccine acceptance as a function of hospitalization risks due to vaccination (N = 109). Aggregate and individual demand indices (Q0 and Pmax) were computed with nonlinear regressions. Secondary analyses were conducted using repeated measures ANOVAs with vaccine type (COVID-19 and HIV) as the within-subject factor; country, age, and socioeconomic status as between-subjects factors; demand indices served as dependent variables.\n\nResultsDemand indices varied significantly as a function of vaccine type (F (1, 57) = 17.609, p < .001, [Formula]). Demand for HIV vaccines was higher relative to COVID19 vaccines. Interactions between vaccine type and country of origin (F (1, 56) = 4.001, p = .05, [Formula]) were also significant with demand for HIV vaccines among Nigerian respondents higher than that of COVID-19 vaccines. This was reversed for US participants. Interactions between vaccine type, country of origin and age were also significant (F (2, 51) = 3.506, p < .05, [Formula]).\n\nConclusionsThese findings provide evidence that vaccine type can influence demand. The relationship between demand and vaccine type also varies as a function of country of origin and age. Significance, limitations, and future directions are also discussed.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Promise Tewogbola", - "author_inst": "Southern Illinois University" - }, - { - "author_name": "Eric A. Jacobs", - "author_inst": "Southern Illinois University" - }, - { - "author_name": "Justin T. McDaniel", - "author_inst": "Southern Illinois University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.07.24.23293091", "rel_title": "Age- and sex-specific differences in immune responses to BNT162b2 COVID-19 and live-attenuated influenza vaccines in UK adolescents", @@ -81814,6 +83407,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2023.07.23.23293040", + "rel_title": "Impact of Emerging COVID-19 variants on psychosocial health: A Systematic Review", + "rel_date": "2023-07-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.23.23293040", + "rel_abs": "BackgroundThe COVID-19 pandemic has had significant psychological effects on individuals and communities around the world. Studies have found that the prevalence of anxiety and depression symptoms increased significantly during the pandemic. The goal of the study is to understand how the emerging new virus variants keep the world in a state of fear and the ways in which mental health measures can be implemented and adopted to alleviate anxiety.\n\nMethodsA broad search for observational studies were carried out in Pubmed, Google Scholar, Clinical Key, and World Medical Library. Studies that reported and/or related the existence of anxiety generated by suffering or not from diseases caused by the new emerging Covid-19 viruses and that for which the full text of the article was accessible were included in the study while systematic review and meta-analysis and studies in groups were excluded.\n\nResults22 studies were included in the review. The deleterious psychosocial effects were the restructuring of life, establishment of unhealthy habits, emergence of \"corona phobia\", fear and stigma of being afflicted with the disease and spreading it to loved ones, and lack of contact with others. Increased rates of depression and anxiety were also seen. The circulating variants responsible for these main psychosocial repercussions were: Epsilon, Zeta, Eta, Iota, Kappa, Alpha, Beta, Gamma, and Delta. Social support was found to be protective.\n\nConclusionHence interventions targeted at promoting mental health should be considered a public health priority.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Pratyush Kumar", + "author_inst": "Dr Baba Saheb Ambedkar Medical College and Hospital, Delhi, India" + }, + { + "author_name": "Manali Sarkar", + "author_inst": "MGM MEDICAL COLLEGE NAVI MUMBAI" + }, + { + "author_name": "Morales Femenias Yurkina", + "author_inst": "Logopedia and Phoniatrics Department. Provincial General Teaching Hospital Dr. Antonio Luaces Iraola." + }, + { + "author_name": "Ramya Gnanaraj", + "author_inst": "Madras Medical College, Chennai, India" + }, + { + "author_name": "Daniel Jesus Garcia Martinez", + "author_inst": "Francisco De Vitoria University, Madrid, Spain" + }, + { + "author_name": "Yhojar A. Pisfil-Farronay", + "author_inst": "Emerge, Unidad de Investigacion en Enfermedades Emergentes y Cambio Climatico, Facultad de Salud Publica y Administracion, Universidad Peruana Cayetano Heredia," + }, + { + "author_name": "Laxmi Chaudhary", + "author_inst": "Casualty Medical Officer (CMO), Dr. Baba Saheb Ambedkar Medical College & Hospital, Delhi, India" + }, + { + "author_name": "Poonam Agrawal", + "author_inst": "Dr Baba Saheb Ambedkar Medical College and Hospital, Delhi, India" + }, + { + "author_name": "G P Kaushal", + "author_inst": "Dr Baba Saheb Ambedkar Medical College and Hospital, Delhi, India" + }, + { + "author_name": "Matthew Mbwogge", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Kumar Abhishek", + "author_inst": "Dr Baba Saheb Ambedkar Medical College and Hospital, Delhi, India" + }, + { + "author_name": "Muhannad Alnaasan", + "author_inst": "University of Aleppo faculty of medicine" + }, + { + "author_name": "Maximiliano Ezequiel Arlettaz", + "author_inst": "National University of Entre Rios, Argentina" + }, + { + "author_name": "Reem Kozum", + "author_inst": "Aleppo University Hospital" + }, + { + "author_name": "Miguel Fernando Juarez Moyron", + "author_inst": "National Autonomous University of Mexico" + }, + { + "author_name": "Suhrud Panchawagh", + "author_inst": "Smt. Kashibai Navale Medical College & General Hospital, Pune" + }, + { + "author_name": "Asmitha P Reddy", + "author_inst": "Father Muller Medical College, Mangalore, India" + }, + { + "author_name": "Vishnu B Unnithan", + "author_inst": "Seth GS Medical College and KEM Hospital, Mumbai, India." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2023.07.24.23293059", "rel_title": "Temporal changes in the positivity rate of common enteric viruses among paediatric admissions in coastal Kenya, in the period spanning the COVID-19 pandemic, 2019-2022", @@ -82221,33 +83901,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2023.07.24.550379", - "rel_title": "The Role of the Tyrosine-Based Sorting Signals of the ORF3a Protein of SARS-CoV-2 on Intracellular Trafficking, Autophagy, and Apoptosis", - "rel_date": "2023-07-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.24.550379", - "rel_abs": "The open reading frame 3a (ORF3a) is an accessory transmembrane protein that is important to the pathogenicity of SARS-CoV-2. The cytoplasmic domain of ORF3a has three canonical tyrosine-based sorting signals (Yxx{Phi}; where x is any amino acid and {Phi} is a hydrophobic amino acid with a bulky -R group). They have been implicated in the trafficking of membrane proteins to the cell plasma membrane and to intracellular organelles. Previous studies have indicated that mutation of the 160YSNV163 motif abrogated plasma membrane expression and inhibited ORF3a-induced apoptosis. However, two additional canonical tyrosine-based sorting motifs (211YYQL213, 233YNKI236) exist in the cytoplasmic domain of ORF3a that have not been assessed. We removed all three potential tyrosine-based motifs and systematically restored them to assess the importance of each motif or combination of motifs that restored efficient trafficking to the cell surface and lysosomes. Our results indicate that the Yxx{Phi} motif at position 160 was insufficient for the trafficking of ORF3a to the cell surface. Our studies also showed that ORF3a proteins with an intact Yxx{Phi} at position 211 or at 160 and 211 were most important. We found that ORF3a cell surface expression correlated with the co-localization of ORF3a with LAMP-1 near the cell surface. These results suggest that Yxx{Phi} motifs within the cytoplasmic domain may act cooperatively in ORF3a transport to the plasma membrane and endocytosis to lysosomes. Further, our results indicate that certain tyrosine mutants failed to activate caspase 3 and did not correlate with autophagy functions associated with this protein.\n\nIMPORTANCEOpen reading frame 3a (ORF3a) encodes for the largest of the SARS-CoV-2 accessory proteins. While deletion of the ORF3a gene from SARS-CoV-2 results in a virus that replicates slightly less efficiently in cell culture, deletion also results in a virus that is less pathogenic in mouse models of SARS-CoV-2 infections. The ORF3a has been reported to be a viroporin, induces apoptosis and incomplete autophagy in cells. Thus, determining the domains involved in these functions will further our understanding of how this protein influences virus assembly and pathogenesis. Here, we investigated the role of the three potential tyrosine-based sorting signals in the cytoplasmic domain of the ORF3a on intracellular protein trafficking, apoptosis, and in the initiation of autophagy. Our results indicate that more than one Yxx{Phi} motif is required for efficient transport of ORF3a, ORF3a expression resulted in minimal apoptosis, and cell surface expression was not required for autophagy.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Edward Brice Stephens", - "author_inst": "The University of Kansas Medical Center" - }, - { - "author_name": "Wyatt Henke", - "author_inst": "University of Kansas Medical Center" - }, - { - "author_name": "Maria Kalamvoki", - "author_inst": "University of Kansas Medical Center Continuing Education and Professional Development" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2023.07.20.23292951", "rel_title": "Factors influencing COVID-19 vaccination decision-making among African American and Hispanic pregnant and postpartum women in Deep South", @@ -83308,6 +84961,53 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2023.07.20.549891", + "rel_title": "No evidence for the association between COVID-19 and neuroinflammation: A diffusion basis spectrum imaging study.", + "rel_date": "2023-07-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.20.549891", + "rel_abs": "COVID-19 remains a significant international public health concern. Yet, the mechanisms through which symptomatology emerges remain poorly understood. While SARS-CoV-2 infection may induce prolonged inflammation within the central nervous system, the evidence primarily stems from limited small-scale case investigations. To address this gap, our study capitalized on longitudinal UK Biobank neuroimaging data acquired prior to and following COVID-19 testing (N=416 including n=224 COVID-19 cases; Mage=58.6). Putative neuroinflammation was assessed in gray matter structures and white matter tracts using non-invasive Diffusion Basis Spectrum Imaging (DBSI), which estimates inflammation-related cellularity (DBSI-restricted fraction; DBSI-RF) and vasogenic edema (DBSI-hindered fraction; DBSI-HF).We hypothesized that COVID-19 case status would be associated with increases in DBSI markers after accounting for potential confound (age, sex, race, body mass index, smoking frequency, and data acquisition interval) and multiple testing.\n\nCOVID-19 case status was not significantly associated with DBSI-RF (|{beta}|s<0.28, pFDR >0.05), but with greater DBSI-HF in left pre- and post-central gyri and right middle frontal gyrus ({beta}s>0.3, all pFDR=0.03). Intriguingly, the brain areas exhibiting increased putative vasogenic edema had previously been linked to COVID-19-related functional and structural alterations, whereas brain regions displaying subtle differences in cellularity between COVID-19 cases and controls included regions within or functionally connected to the olfactory network, which has been implicated in COVID-19 psychopathology.\n\nNevertheless, our study might not have captured acute and transitory neuroinflammatory effects linked to SARS-CoV-2 infection, possibly due to symptom resolution before the imaging scan. Future research is warranted to explore the potential time- and symptom-dependent neuroinflammatory relationship with COVID-19.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Wei Zhang", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Aaron J Gorelik", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Qing Wang", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Sara A Norton", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Tamara Hershey", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Arpana Agrawal", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Janine D Bijsterbosch", + "author_inst": "Washington University in St Louis" + }, + { + "author_name": "Ryan Bogdan", + "author_inst": "Washington University in St. Louis" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "neuroscience" + }, { "rel_doi": "10.1101/2023.07.19.549731", "rel_title": "Complete Protection from SARS-CoV-2 Lung Infection in Mice Through Combined Intranasal Delivery of PIKfyve Kinase and TMPRSS2 Protease Inhibitors", @@ -83883,41 +85583,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.07.17.23292714", - "rel_title": "The impact of frailty on the outcomes of COVID-19 patients with persistent critical illness: A population-based cohort study.", - "rel_date": "2023-07-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.17.23292714", - "rel_abs": "ObjectivesPersistent critical illness (PerCI, [≥]10 days in Intensive Care Unit [ICU]) is defined as the time from ICU admission when patients antecedent characteristics define their mortality rather than the admission aetiology. Patients with frailty and without COVID-19 have a higher risk of developing and dying from PerCI. We aimed to investigate the impact of frailty on critically ill patients with COVID-19 experiencing PerCI.\n\nMethodsWe conducted a retrospective multicentre cohort study including 103 Australian and New Zealand ICUs over two years, investigating the impact of frailty, measured with Clinical Frailty Scale (CFS), in patients with COVID-19, between patients with and without PerCI.\n\nResultsThe prevalence of PerCI was similar between patients with and without frailty (25.4% vs. 27.9%; p=0.44). Hospital mortality was higher in patients with PerCI than without (28.8% vs. 9.3%; p<0.001), with mortality rising with increasing CFS (p<0.001). Frailty independently predicted hospital mortality, but when adjusted for ANZROD and sex, its impact was no different in patients with and without PerCI (odds ratio [OR]=1.30 [95%-CI: 1.14-1.49] vs. OR=1.46 [95%-CI: 1.29-1.64]).\n\nConclusionsThe presence of frailty independently predicted hospital mortality in patients with PerCI, but frailty did not have a different impact on patients with and without PerCI.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "William Bonavia", - "author_inst": "Alfred Health" - }, - { - "author_name": "Ravindranath Tiruvoipati", - "author_inst": "Peninsula Health" - }, - { - "author_name": "Mallikarjuna reddy Ponnapareddy", - "author_inst": "Calvary Public Hospital" - }, - { - "author_name": "David Pilcher", - "author_inst": "Alfred Health" - }, - { - "author_name": "ashwin subramaniam", - "author_inst": "Peninsula Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2023.07.16.23292747", "rel_title": "Effects of nutritional supplements on antibody levels in pregnant women vaccinated with inactivated SARS-CoV-2 vaccines", @@ -85006,6 +86671,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.07.14.549077", + "rel_title": "Absence of SARS-CoV-2 in Wildlife of Northeastern Minnesota and Isle Royale National Park", + "rel_date": "2023-07-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.14.549077", + "rel_abs": "We investigated the presence of SARS-CoV-2 in free-ranging wildlife populations in Northeastern Minnesota on the Grand Portage Indian Reservation and Isle Royale National Park. 120 nasal samples were collected from white-tailed deer, moose, gray wolves, and black bears monitored for conservation efforts during 2022-2023. Samples were tested for viral RNA by RT-qPCR using the CDC N1/N2 primer set. Our data indicate that no wildlife samples were positive for SARS-CoV-2 RNA. Continued surveillance is therefore crucial to better understand the changing landscape of zoonotic SARS-CoV-2 in the Upper Midwest.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "David Castaneda", + "author_inst": "University of Minnesota, Twin Cities" + }, + { + "author_name": "Edmund J Isaac", + "author_inst": "Grand Portage Band of Lake Superior Chippewa Biology and Environment" + }, + { + "author_name": "Todd Kautz", + "author_inst": "Grand Portage Band of Lake Superior Chippewa Biology and Environment" + }, + { + "author_name": "Mark C Romanski", + "author_inst": "Isle Royale National Park" + }, + { + "author_name": "Seth A Moore", + "author_inst": "Grand Portage Band of Lake Superior Chippewa Biology and Environment" + }, + { + "author_name": "Matthew Aliota", + "author_inst": "University of Minnesota Twin Cities" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.07.14.549076", "rel_title": "Oral immunization with rVSV bivalent vaccine elicits protective immune responses, including ADCC, against both SARS-CoV-2 and Influenza A viruses", @@ -85469,81 +87173,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.07.12.23292576", - "rel_title": "Comparative Effectiveness of the Bivalent (Original/Omicron BA.4/BA.5) mRNA COVID-19 Vaccines mRNA-1273.222 and BNT162b2 Bivalent in Adults in the United States", - "rel_date": "2023-07-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.07.12.23292576", - "rel_abs": "BackgroundThe emergence of Omicron variants coincided with declining vaccine-induced protection against SARS-CoV-2 infection and other COVID-19-related outcomes. Two bivalent mRNA vaccines, mRNA-1273.222 (Moderna) and BNT162b2 Bivalent (Pfizer-BioNTech) were developed to provide greater protection against the predominate circulating variants by including the mRNA that encodes both the ancestral (original) strain and BA.4/BA.5. We estimated their relative vaccine effectiveness (rVE) in preventing COVID-19-related outcomes in the US.\n\nMethodsWe conducted a retrospective cohort study using a US nationwide dataset linking primary care electronic health records (EHR) and pharmacy/medical claims data. The adult study population (aged [≥]18 years) received either mRNA-1273.222 or BNT162b2 Bivalent vaccination between August 31, 2022, and February 28, 2023. We used a propensity score weighting based on the inverse probability of treatment to adjust for the baseline differences in age, sex, race, ethnicity, geographic region, vaccination week, and health status between groups. Outcomes evaluated were rVE of the two bivalent mRNA vaccines against COVID-19-related hospitalizations (primary outcome) and outpatient visits (secondary). We weighted the vaccine groups prior to analysis and estimated adjusted hazard ratios (HR) using multivariable Cox regression models. We calculated rVE as (1-HR) x 100.\n\nResultsWe evaluated outcomes for 1,034,538 mRNA-1273.222 and 1,670,666 BNT162b2 Bivalent vaccine recipients. The adjusted rVE of mRNA-1273.222 versus BNT162b2 Bivalent vaccines against COVID-19-related hospitalization was 9.8% (95% confidence interval: 2.6%-16.4%). The adjusted rVE against COVID-19-related outpatient visits was 5.1% (95% CI: 3.2%-6.9%). When evaluated by age group, the incremental relative effectiveness was greater. Among adults [≥] 65, rVE against COVID-19-related hospitalizations and outpatient visits was 13.5% (95% CI: 5.5%-20.8%) and 10.7% (8.2%-13.1%), respectively.\n\nConclusionWe found greater effectiveness of mRNA-1273.222 compared with the BNT162b2 Bivalent vaccine in preventing COVID-19-related hospitalizations and outpatient visits, with increased benefits in older adults.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Hagit Kopel", - "author_inst": "Moderna" - }, - { - "author_name": "Van Hung Nguyen", - "author_inst": "VHN Consulting" - }, - { - "author_name": "Catherine Boileau", - "author_inst": "VHN consulting" - }, - { - "author_name": "Alina Bogdanov", - "author_inst": "Veradigm" - }, - { - "author_name": "Isabelle Winer", - "author_inst": "Veradigm" - }, - { - "author_name": "Thierry Ducruet", - "author_inst": "VHN consulting" - }, - { - "author_name": "Ni Zeng", - "author_inst": "Veradigm" - }, - { - "author_name": "Mac Bonafede", - "author_inst": "Veradigm" - }, - { - "author_name": "Daina Esposito", - "author_inst": "Moderna" - }, - { - "author_name": "David Martin", - "author_inst": "Moderna" - }, - { - "author_name": "Andrew Rosen", - "author_inst": "Moderna" - }, - { - "author_name": "Nicolas Van de Velde", - "author_inst": "Moderna" - }, - { - "author_name": "Sten Vermund", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Stefan Gravenstein", - "author_inst": "Brown University" - }, - { - "author_name": "James A. Mansi", - "author_inst": "Moderna, Inc." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.07.12.23292582", "rel_title": "A Population Level Study on the Determinants of COVID-19 Vaccine Hesitancy at the U.S. County Level", @@ -86548,6 +88177,133 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.07.10.548424", + "rel_title": "An ACE2 decamer viral trap as a durable intervention solution for current and future SARS-CoV", + "rel_date": "2023-07-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.10.548424", + "rel_abs": "The capacity of SARS-CoV-2 to evolve poses challenges to conventional prevention and treatment options such as vaccination and monoclonal antibodies, as they rely on viral receptor binding domain (RBD) sequences from previous strains. Additionally, animal CoVs, especially those of the SARS family, are now appreciated as a constant pandemic threat. We present here a new antiviral approach featuring inhalation delivery of a recombinant viral trap composed of ten copies of angiotensin-converting enzyme 2 (ACE2) fused to the IgM Fc. This ACE2 decamer viral trap is designed to inhibit SARS-CoV-2 entry function, regardless of viral RBD sequence variations as shown by its high neutralization potency against all known SARS-CoV-2 variants, including Omicron BQ.1, BQ.1.1, XBB.1 and XBB.1.5. In addition, it demonstrates potency against SARS-CoV-1, human NL63, as well as bat and pangolin CoVs. The multivalent trap is effective in both prophylactic and therapeutic settings since a single intranasal dosing confers protection in human ACE2 transgenic mice against viral challenges. Lastly, this molecule is stable at ambient temperature for more than twelve weeks and can sustain physical stress from aerosolization. These results demonstrate the potential of a decameric ACE2 viral trap as an inhalation solution for ACE2-dependent coronaviruses of current and future pandemic concerns.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Hailong Guo", + "author_inst": "IGM Biosciences" + }, + { + "author_name": "Bomsoo Cho", + "author_inst": "IGM Biosciences" + }, + { + "author_name": "Paul R Hinton", + "author_inst": "IGM Biosciences" + }, + { + "author_name": "Sijia He", + "author_inst": "IGM Biosciences" + }, + { + "author_name": "Yongjun Yu", + "author_inst": "IGM Biosciences" + }, + { + "author_name": "Ashwin Kumar Ramesh", + "author_inst": "Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston" + }, + { + "author_name": "Jwala Priyadarsini Sivaccumar", + "author_inst": "Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston" + }, + { + "author_name": "Zhiqiang Ku", + "author_inst": "Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston" + }, + { + "author_name": "Kristen Campo", + "author_inst": "IGM Biosciences" + }, + { + "author_name": "Sarah Holland", + "author_inst": "IGM Biosciences" + }, + { + "author_name": "Sameer Sachdeva", + "author_inst": "IGM Biosciences" + }, + { + "author_name": "Christopher Mensch", + "author_inst": "IGM Biosciences" + }, + { + "author_name": "Mohamed Dawod", + "author_inst": "IGM Biosciences" + }, + { + "author_name": "Annalis Whitaker", + "author_inst": "University of Vermont" + }, + { + "author_name": "Philip Eisenhauer", + "author_inst": "University of Vermont" + }, + { + "author_name": "Allison Falcone", + "author_inst": "University of Vermont" + }, + { + "author_name": "Rebekah Honce", + "author_inst": "University of Vermont" + }, + { + "author_name": "Jason W. Botten", + "author_inst": "University of Vermont" + }, + { + "author_name": "Stephen F Carroll", + "author_inst": "IGM Biosciences" + }, + { + "author_name": "Bruce A Keyt", + "author_inst": "IGM Biosciences" + }, + { + "author_name": "Andrew W Womack", + "author_inst": "IGM Biosciences" + }, + { + "author_name": "William R Strohl", + "author_inst": "IGM Biosciences" + }, + { + "author_name": "Kai Xu", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Zhiqiang An", + "author_inst": "Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston" + }, + { + "author_name": "Ningyan Zhang", + "author_inst": "Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston" + }, + { + "author_name": "Sha Ha", + "author_inst": "IGM Biosciences" + }, + { + "author_name": "John W Shiver", + "author_inst": "IGM Biosciences" + }, + { + "author_name": "Tong-Ming Fu", + "author_inst": "IGM Biosciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.07.10.548464", "rel_title": "Genomic Surveillance of SARS-CoV-2 Using Long-Range PCR Primers", @@ -87003,81 +88759,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.07.06.547945", - "rel_title": "In vitro broad-spectrum antiviral activity of MIT-001, a mitochondria-targeted reactive oxygen species scavenger, against severe acute respiratory syndrome coronavirus 2 and multiple zoonotic viruses", - "rel_date": "2023-07-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.07.06.547945", - "rel_abs": "The COVID-19 pandemic caused by SARS-CoV-2 becomes a serious threat to global health and requires the development of effective antiviral therapies. Current therapies that target viral proteins have limited efficacy with side effects. In this study, we investigated the antiviral activity of MIT-001, a small molecule reactive oxygen species (ROS) scavenger targeting mitochondria, against SARS-CoV-2 and other zoonotic viruses in vitro. The antiviral activity of MIT-001 was quantified by RT-qPCR and plaque assay. We also evaluated the functional analysis of MIT-001 by JC-1 staining to measure mitochondrial depolarization, total RNA sequencing to investigate gene expression changes, and immunoblot to quantify protein expression levels. The results showed that MIT-001 effectively inhibited the replication of B.1.617.2 and BA.1 strains, Zika virus, Seoul virus, and Vaccinia virus. Treatment with MIT-001 restored the expression of heme oxygenase-1 (HMOX1) and NAD(P)H: quinone oxidoreductase 1 (NqO1) genes, anti-oxidant enzymes reduced by SARS-CoV-2, to normal levels. The presence of MIT-001 also alleviated mitochondrial depolarization caused by SARS-CoV-2 infection. These findings highlight the potential of MIT-001 as a broad-spectrum antiviral compound that targets for zoonotic RNA and DNA viruses, providing a promising therapeutic approach to combat viral infection.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Taehun Lim", - "author_inst": "Hallym University Graduated school of Medicine" - }, - { - "author_name": "Shivani Rajoriya", - "author_inst": "Hallym University Graduated School of Medicine" - }, - { - "author_name": "Bohyeon Kim", - "author_inst": "Hallym University Graduated School of Medicine" - }, - { - "author_name": "Sara p Prayitno", - "author_inst": "Hallym University Graduated School of Medicine" - }, - { - "author_name": "Augustine Natasha", - "author_inst": "Hallym University Graduated School of Medicine" - }, - { - "author_name": "Jieun Park", - "author_inst": "Hallym University Graduated School of Medicine" - }, - { - "author_name": "Na Yeon Jang", - "author_inst": "Hallym University College of Medicine" - }, - { - "author_name": "Hyeonjoo Im", - "author_inst": "Stand up therapeutics Inc." - }, - { - "author_name": "Hyun Soo Shim", - "author_inst": "Stand up therapeutics Inc." - }, - { - "author_name": "Junsang Yoo", - "author_inst": "Stand up Therapeutics Inc." - }, - { - "author_name": "Jong Woo Kim", - "author_inst": "Korea Research Institute of Bioscience and Biotechnology" - }, - { - "author_name": "Eun-Woo Lee", - "author_inst": "Korea Research Institute of Bioscience and Biotechnology" - }, - { - "author_name": "Hye Jin Shin", - "author_inst": "Chungnam National University School of Medicine" - }, - { - "author_name": "Soon Ha Kim", - "author_inst": "Mitoimmune Therapeutics Inc." - }, - { - "author_name": "Won-Keun Kim", - "author_inst": "Hallym University College of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.07.06.547955", "rel_title": "Single cell susceptibility to SARS-CoV-2 infection is driven by variable cell states", @@ -88278,6 +89959,357 @@ "type": "new results", "category": "ecology" }, + { + "rel_doi": "10.1101/2023.06.28.23291998", + "rel_title": "Informing pandemic response in the face of uncertainty. An evaluation of the U.S. COVID-19 Scenario Modeling Hub", + "rel_date": "2023-07-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.28.23291998", + "rel_abs": "Our ability to forecast epidemics more than a few weeks into the future is constrained by the complexity of disease systems, our limited ability to measure the current state of an epidemic, and uncertainties in how human action will affect transmission. Realistic longer-term projections (spanning more than a few weeks) may, however, be possible under defined scenarios that specify the future state of critical epidemic drivers, with the additional benefit that such scenarios can be used to anticipate the comparative effect of control measures. Since December 2020, the U.S. COVID-19 Scenario Modeling Hub (SMH) has convened multiple modeling teams to make 6-month ahead projections of the number of SARS-CoV-2 cases, hospitalizations and deaths. The SMH released nearly 1.8 million national and state-level projections between February 2021 and November 2022. SMH performance varied widely as a function of both scenario validity and model calibration. Scenario assumptions were periodically invalidated by the arrival of unanticipated SARS-CoV-2 variants, but SMH still provided projections on average 22 weeks before changes in assumptions (such as virus transmissibility) invalidated scenarios and their corresponding projections. During these periods, before emergence of a novel variant, a linear opinion pool ensemble of contributed models was consistently more reliable than any single model, and projection interval coverage was near target levels for the most plausible scenarios (e.g., 79% coverage for 95% projection interval). SMH projections were used operationally to guide planning and policy at different stages of the pandemic, illustrating the value of the hub approach for long-term scenario projections.", + "rel_num_authors": 84, + "rel_authors": [ + { + "author_name": "Emily Howerton", + "author_inst": "The Pennsylvania State University" + }, + { + "author_name": "Lucie Contamin", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Luke C Mullany", + "author_inst": "Johns Hopkins University Applied Physics Lab" + }, + { + "author_name": "Michelle M Qin", + "author_inst": "Harvard University" + }, + { + "author_name": "Nicholas G Reich", + "author_inst": "University of Massachusetts Amherst" + }, + { + "author_name": "Samantha J Bents", + "author_inst": "National Institutes of Health Fogarty International Center" + }, + { + "author_name": "Rebecca K Borchering", + "author_inst": "The Pennsylvania State University, Centers for Disease Control and Prevention" + }, + { + "author_name": "Sung-mok Jung", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Sara L Loo", + "author_inst": "Johns Hopkins University Infectious Disease Dynamics" + }, + { + "author_name": "Claire P Smith", + "author_inst": "Johns Hopkins University Infectious Disease Dynamics" + }, + { + "author_name": "John Levander", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Jessica Kerr", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "J. Espino", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Willem G van Panhuis", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Harry Hochheiser", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Marta Galanti", + "author_inst": "Columbia University" + }, + { + "author_name": "Teresa K Yamana", + "author_inst": "Columbia University" + }, + { + "author_name": "Sen Pei", + "author_inst": "Columbia University" + }, + { + "author_name": "Jeffrey Shaman", + "author_inst": "Columbia University" + }, + { + "author_name": "Kaitlin Rainwater-Lovett", + "author_inst": "Johns Hopkins University Applied Physics Lab" + }, + { + "author_name": "Matt Kinsey", + "author_inst": "Johns Hopkins University Applied Physics Lab" + }, + { + "author_name": "Kate Tallaksen", + "author_inst": "Johns Hopkins University Applied Physics Lab" + }, + { + "author_name": "Shelby Wilson", + "author_inst": "Johns Hopkins University Applied Physics Lab" + }, + { + "author_name": "Lauren Shin", + "author_inst": "Johns Hopkins University Applied Physics Lab" + }, + { + "author_name": "Joseph C Lemaitre", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Joshua Kaminsky", + "author_inst": "Johns Hopkins University Infectious Disease Dynamics" + }, + { + "author_name": "Juan Dent Hulse", + "author_inst": "Johns Hopkins University Infectious Disease Dynamics" + }, + { + "author_name": "Elizabeth C Lee", + "author_inst": "Johns Hopkins University Infectious Disease Dynamics" + }, + { + "author_name": "Clifton D McKee", + "author_inst": "Johns Hopkins University Infectious Disease Dynamics" + }, + { + "author_name": "Alison Hill", + "author_inst": "Johns Hopkins University Infectious Disease Dynamics" + }, + { + "author_name": "Dean Karlen", + "author_inst": "University of Victoria" + }, + { + "author_name": "Matteo Chinazzi", + "author_inst": "Northeastern University" + }, + { + "author_name": "Jessica T Davis", + "author_inst": "Northeastern University" + }, + { + "author_name": "Kunpeng Mu", + "author_inst": "Northeastern University" + }, + { + "author_name": "Xinyue Xiong", + "author_inst": "Northeastern University" + }, + { + "author_name": "Ana Pastore Piontti", + "author_inst": "Northeastern University" + }, + { + "author_name": "Alessandro Vespignani", + "author_inst": "Northeastern University" + }, + { + "author_name": "Erik T Rosenstrom", + "author_inst": "North Carolina State University" + }, + { + "author_name": "Julie S Ivy", + "author_inst": "North Carolina State University" + }, + { + "author_name": "Maria E Mayorga", + "author_inst": "North Carolina State University" + }, + { + "author_name": "Julie L Swann", + "author_inst": "North Carolina State University" + }, + { + "author_name": "Guido Espana", + "author_inst": "University of Notre Dame" + }, + { + "author_name": "Sean Cavany", + "author_inst": "University of Notre Dame" + }, + { + "author_name": "Sean M Moore", + "author_inst": "University of Notre Dame" + }, + { + "author_name": "Alex Perkins", + "author_inst": "University of Notre Dame" + }, + { + "author_name": "Thomas Hladish", + "author_inst": "University of Florida" + }, + { + "author_name": "Alexander Pillai", + "author_inst": "University of Florida" + }, + { + "author_name": "Kok Ben Toh", + "author_inst": "Northwestern University" + }, + { + "author_name": "Ira Longini Jr.", + "author_inst": "University of Florida" + }, + { + "author_name": "Shi Chen", + "author_inst": "University of North Carolina at Charlotte" + }, + { + "author_name": "Rajib Paul", + "author_inst": "University of North Carolina at Charlotte" + }, + { + "author_name": "Daniel Janies", + "author_inst": "University of North Carolina at Charlotte" + }, + { + "author_name": "Jean-Claude Thill", + "author_inst": "University of North Carolina at Charlotte" + }, + { + "author_name": "Anass Bouchnita", + "author_inst": "University of Texas at El Paso" + }, + { + "author_name": "Kaiming Bi", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "Michael Lachmann", + "author_inst": "Santa Fe Institute" + }, + { + "author_name": "Spencer J Fox", + "author_inst": "University of Georgia" + }, + { + "author_name": "Lauren A Meyers", + "author_inst": "University of Texas at Austin" + }, + { + "author_name": "- UT COVID-19 Modeling Consortium", + "author_inst": "-" + }, + { + "author_name": "Ajitesh Srivastava", + "author_inst": "University of Southern California" + }, + { + "author_name": "Przemyslaw Porebski", + "author_inst": "University of Virginia" + }, + { + "author_name": "Srinivasan Venkatramanan", + "author_inst": "University of Virginia" + }, + { + "author_name": "Aniruddha Adiga", + "author_inst": "University of Virginia" + }, + { + "author_name": "Bryan Lewis", + "author_inst": "University of Virginia" + }, + { + "author_name": "Brian Klahn", + "author_inst": "University of Virginia" + }, + { + "author_name": "Joseph Outten", + "author_inst": "University of Virginia" + }, + { + "author_name": "Benjamin Hurt", + "author_inst": "University of Virginia" + }, + { + "author_name": "Jiangzhuo Chen", + "author_inst": "University of Virginia" + }, + { + "author_name": "Henning Mortveit", + "author_inst": "University of Virginia" + }, + { + "author_name": "Amanda Wilson", + "author_inst": "University of Virginia" + }, + { + "author_name": "Madhav Marathe", + "author_inst": "University of Virginia" + }, + { + "author_name": "Stefan Hoops", + "author_inst": "University of Virginia" + }, + { + "author_name": "Parantapa Bhattacharya", + "author_inst": "University of Virginia" + }, + { + "author_name": "Dustin Machi", + "author_inst": "University of Virginia" + }, + { + "author_name": "Betsy L Gunnels", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Jessica M Healy", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Rachel B Slayton", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Michael A Johansson", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Matthew Biggerstaff", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Shaun Truelove", + "author_inst": "Johns Hopkins University Infectious Disease Dynamics" + }, + { + "author_name": "Michael C Runge", + "author_inst": "U.S. Geological Survey Eastern Ecological Science Center" + }, + { + "author_name": "Katriona Shea", + "author_inst": "The Pennsylvania State University" + }, + { + "author_name": "Cecile Viboud", + "author_inst": "National Institutes of Health Fogarty International Center" + }, + { + "author_name": "Justin Lessler", + "author_inst": "University of North Carolina at Chapel Hill" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.07.03.23292158", "rel_title": "A new Omicron lineage with Spike Y451H mutation that dominated a new COVID-19 wave in Kilifi, Coastal Kenya: March-May 2023", @@ -88741,49 +90773,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.06.29.23292061", - "rel_title": "Intention to be vaccinated against COVID-19 in Benin and Senegal: a structural equation modelling (SEM)", - "rel_date": "2023-07-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.29.23292061", - "rel_abs": "IntroductionVaccination is considered one of the solutions to the COVID-19 pandemic. However, a small proportion of the population was fully vaccinated in Benin (20.9%) and Senegal (7.6%) by December 2022. This study explores the determinants of intent to vaccinate.\n\nMethodsThis was a cross-sectional, descriptive, and analytical study of 865 Beninese and 607 Senegalese aged 18 years and older. Marginal quota sampling by age, gender and region was adopted. Data collection, using a survey instrument based on the Random Digit Dialing (RDD) method, was conducted from December 24, 2020, to January 16, 2021, in Senegal and from March 29 to May 14, 2021, in Benin. The questionnaire used the Theory of Planned Behavior (TPB) and the Health Belief Model (HBM). The influence of factors was tested using a structural equation model. All analyses were conducted in R.\n\nResultsResults show that a good perception of the benefits of vaccination ({beta}sen =0.33***; {beta}Ben=0.12***), a positive attitude ({beta}sen=0.22***; {beta}Ben=0.20***), and sensitivity to subjective norms ({beta}sen=0.19***; {beta}Ben=0.32***) positively influence the intention to vaccinate. Low trust in health care providers ({beta}sen=-0.40***; {beta}Ben=-0.36***) amplifies the perceived risk of vaccination ({beta}sen=-0.14***; {beta}Ben=-0.25***), which negatively impacts intention to vaccinate. Perceived vaccine efficacy was affected by perceived risk ({beta}sen=-0.12***; {beta}Ben=-0.05***) of the disease and improved by good apprehension of the benefits of vaccination ({beta}sen=0.60***; {beta}Ben=0.13***). Aspects related to behavioral control, vaccine information seeking, efficacy, or fairness did not appear as correlates of vaccine intention (P>0.05).\n\nConclusionBeninese and Senegalese public health authorities could develop additional intervention strategies to improve immunization coverage by considering these influencing factors, the basis of which could be better understood through subsequent qualitative studies.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ibrahima GAYE", - "author_inst": "Universit\u00e9 Cheikh Anta Diop Facult\u00e9 de M\u00e9decined de Pharmacie et d'Odontologie: Universite Cheikh Anta Diop Faculte de Medecine de Pharmacie et d'Odontologie" - }, - { - "author_name": "Val\u00e9ry Ridde", - "author_inst": "Institut de recherche pour le d\u00e9veloppement: Institut de recherche pour le developpement" - }, - { - "author_name": "El\u00edas Avahoundjea", - "author_inst": "CERRHUD" - }, - { - "author_name": "Mouhamadou Faly BA", - "author_inst": "Cheikh Anta Diop University Faculty of Medicine Pharmacy and Dentistry: Universite Cheikh Anta Diop Faculte de Medecine de Pharmacie et d'Odontologie" - }, - { - "author_name": "Jean paul DOSSOU", - "author_inst": "CERRHUD" - }, - { - "author_name": "Amadou Ibra Diallo", - "author_inst": "Cheikh Anta Diop University Faculty of Medicine Pharmacy and Dentistry: Universite Cheikh Anta Diop Faculte de Medecine de Pharmacie et d'Odontologie" - }, - { - "author_name": "Adama FAYE", - "author_inst": "Cheikh Anta Diop University Faculty of Medicine Pharmacy and Dentistry: Universite Cheikh Anta Diop Faculte de Medecine de Pharmacie et d'Odontologie" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.06.29.23292037", "rel_title": "Clinical Profile, Comorbidities, and Outcome of the Unvaccinated and Hospitalized for COVID-19 in Northern Brazil: Retrospective Cohort", @@ -90416,6 +92405,161 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.06.23.23291827", + "rel_title": "Increased circulating fibronectin, depletion of natural IgM and heightened EBV, HSV-1 reactivation in ME/CFS and long COVID", + "rel_date": "2023-06-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.23.23291827", + "rel_abs": "Myalgic Encephalomyelitis/ Chronic Fatigue syndrome (ME/CFS) is a complex, debilitating, long-term illness without a diagnostic biomarker. ME/CFS patients share overlapping symptoms with long COVID patients, an observation which has strengthened the infectious origin hypothesis of ME/CFS. However, the exact sequence of events leading to disease development is largely unknown for both clinical conditions. Here we show antibody response to herpesvirus dUTPases, particularly to that of Epstein-Barr virus (EBV) and HSV-1, increased circulating fibronectin (FN1) levels in serum and depletion of natural IgM against fibronectin ((n)IgM-FN1) are common factors for both severe ME/CFS and long COVID. We provide evidence for herpesvirus dUTPases-mediated alterations in host cell cytoskeleton, mitochondrial dysfunction and OXPHOS. Our data show altered active immune complexes, immunoglobulin-mediated mitochondrial fragmentation as well as adaptive IgM production in ME/CFS patients. Our findings provide mechanistic insight into both ME/CFS and long COVID development. Finding of increased circulating FN1 and depletion of (n)IgM-FN1 as a biomarker for the severity of both ME/CFS and long COVID has an immediate implication in diagnostics and development of treatment modalities.", + "rel_num_authors": 35, + "rel_authors": [ + { + "author_name": "Zheng Liu", + "author_inst": "Institute for Virology and Immunobiology, Julius-Maximilians-University of Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Claudia Hollmann", + "author_inst": "Institute for Virology and Immunobiology, Julius-Maximilians-University of Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Sharada Kalanidhi", + "author_inst": "Stanford Genome Technology Center, Stanford University School of Medicine, Stanford, CA, USA" + }, + { + "author_name": "Arnhild Grothey", + "author_inst": "Institute for Virology and Immunobiology, Julius-Maximilians-University of Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Samuel Keating", + "author_inst": "Institute for Virology and Immunobiology, Julius-Maximilians-University of Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Irene Mena-Palomo", + "author_inst": "Institute for Behavioral Medicine Research (IBMR), The Ohio State University, Columbus, Ohio, USA" + }, + { + "author_name": "Stephanie Lamer", + "author_inst": "Rudolf Virchow Center, Center for Translational Bioimaging, Julius-Maximilians-University of Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Andreas Schlosser", + "author_inst": "Rudolf Virchow Center, Center for Translational Bioimaging, Julius-Maximilians-University of Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Agnes Kaiping", + "author_inst": "Institute for Virology and Immunobiology, Julius-Maximilians-University of Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Carsten Scheller", + "author_inst": "Institute for Virology and Immunobiology, Julius-Maximilians-University of Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Franziska Sotzny", + "author_inst": "Institute for Medical Immunology, Charite-Universitaetsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Anna Horn", + "author_inst": "Institute of Clinical Epidemiology and Biometry, Julius-Maximilians-University of Wuerzburg, Wuerzburg, Germany." + }, + { + "author_name": "Carolin Nuernberger", + "author_inst": "Institute of Clinical Epidemiology and Biometry, Julius-Maximilians-University of Wuerzburg, Wuerzburg, Germany." + }, + { + "author_name": "Vladimir Cejka", + "author_inst": "Department of Clinical Research & Epidemiology, Comprehensive Heart Failure Center and Department of Medicine I, University Hospital Wuerzburg, Wuerzburg, Germa" + }, + { + "author_name": "Boshra Afshar", + "author_inst": "Institute for Virology and Immunobiology, Julius Maximilian University of Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Thomas Bahmer", + "author_inst": "Internal Medicine Department I, University Hospital Schleswig-Holstein UKSH - Campus Kiel, Kiel, Germany" + }, + { + "author_name": "Stefan Schreiber", + "author_inst": "Internal Medicine Department I, University Hospital Schleswig-Holstein UKSH - Campus Kiel, Kiel, Germany" + }, + { + "author_name": "Joerg Janne Vehreschild", + "author_inst": "University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn Cologn" + }, + { + "author_name": "Olga Milljukov", + "author_inst": "Institute of Clinical Epidemiology and Biometry, Julius Maximilian University of Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Christian Schaefer", + "author_inst": "University Medicine Greifswald, Institute of Clinical Chemistry and Laboratory Medicine, Greifswald, Germany" + }, + { + "author_name": "Luzie Kretzler", + "author_inst": "Charite - Universitaetsmedizin Berlin and Berlin Institute of Health (BIH), Berlin, Germany" + }, + { + "author_name": "Thomas Keil", + "author_inst": "Charite - Universitaetsmedizin Berlin and Berlin Institute of Health (BIH), Berlin, Germany" + }, + { + "author_name": "Jens-Peter Reese", + "author_inst": "Institute of Clinical Epidemiology and Biometry, Julius Maximilian University of Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Felizitas A Eichner", + "author_inst": "Institute of Clinical Epidemiology and Biometry, Julius-Maximilians-University of Wuerzburg, Wuerzburg, Germany." + }, + { + "author_name": "Lena Schmidbauer", + "author_inst": "Institute of Clinical Epidemiology and Biometry, Julius-Maximilians-University of Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Peter U Heuschmann", + "author_inst": "Institute of Clinical Epidemiology and Biometry, Julius-Maximilians-University of Wuerzburg, Wuerzburg, Germany." + }, + { + "author_name": "Stefan Stoerk", + "author_inst": "Comprehensive Heart Failure Center and Department of Medicine I, University Hospital Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Caroline Morbach", + "author_inst": "Department of Clinical Research & Epidemiology, Comprehensive Heart Failure Center and Department of Medicine I, University Hospital Wuerzburg, Wuerzburg, Germa" + }, + { + "author_name": "Gabriela Riemekasten", + "author_inst": "Klinik fuer Rheumatologie, Universitaetsklinikum Schleswig-Holstein, Luebeck, Germany" + }, + { + "author_name": "Niklas Beyersdorf", + "author_inst": "Institute for Virology and Immunobiology, Julius-Maximilians-University of Wuerzburg, Wuerzburg, Germany" + }, + { + "author_name": "Carmen Scheibenbogen", + "author_inst": "Institute for Medical Immunology, Charite-Universitaetsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Robert K Naviaux", + "author_inst": "Departments of Medicine, Pediatrics, and Pathology, University of California, San Diego School of Medicine, San Diego, USA" + }, + { + "author_name": "Marshall Williams", + "author_inst": "Institute for Behavioral Medicine Research (IBMR), The Ohio State University, Columbus, Ohio, USA" + }, + { + "author_name": "Maria E Ariza", + "author_inst": "Institute for Behavioral Medicine Research (IBMR), The Ohio State University, Columbus, Ohio, USA" + }, + { + "author_name": "Bhupesh Kumar Prusty", + "author_inst": "Institute for Virology and Immunobiology, Julius-Maximilians-University of Wuerzburg, Wuerzburg, Germany." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.06.26.23291883", "rel_title": "Long-term outcomes of hospitalized SARS-CoV-2/COVID-19 patients with and without neurological involvement: 3-year follow-up assessment", @@ -90999,57 +93143,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.06.26.23291891", - "rel_title": "SARS-CoV-2 testing in the Slovak Republic from March 2020 to September 2022 - summary of the pandemic trends", - "rel_date": "2023-06-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.26.23291891", - "rel_abs": "The COVID-19 pandemic has been part of Slovakia since March 2020. Intensive laboratory testing ended in October 2022, when the number of tests dropped significantly, but the state of the pandemic continues to this day. For the management of COVID-19, it is important to find an indicator that can predict pandemic changes in the community. The average daily/weekly Ct value with a certain time delay can predict changes in the number of cases of SARS-CoV-2 infection, which can be a useful indicator for the healthcare system. The study analyzed the results of 1,420,572 RT-qPCR tests provided by one accredited laboratory during the ongoing pandemic in Slovakia from March 2020 to September 2022. The total positivity of the analyzed tests was 24.64%. The average Ct values found were the highest in the age group of 3-5 years, equal to the number 30.75; the lowest were in the age group > 65 years, equal to the number 27. The average weekly Ct values ranged from 22.33 (pandemic wave week) to 30.12 (summer week). We have summarized the results of SARS-CoV-2 diagnostic testing in Slovakia with the scope defined by the rate and positivity of tests carried out at Medirex a.s. laboratories.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Nikola Janostiakova", - "author_inst": "Comenius University in Bratislava Faculty of Medicine, Department of Clinical Biology, Genetics and Clinical Genetics, Bratislava, Slovakia" - }, - { - "author_name": "Andrej Gnip", - "author_inst": "Medirex Inc." - }, - { - "author_name": "Dominik Kodada", - "author_inst": "Comenius University in Bratislava Faculty of Medicine, Department of Clinical Biology, Genetics and Clinical Genetics, Bratislava, Slovakia" - }, - { - "author_name": "Rami Saade", - "author_inst": "Comenius University in Bratislava Faculty of Medicine, Department of Clinical Biology, Genetics and Clinical Genetics, Bratislava, Slovakia" - }, - { - "author_name": "Gabriela Blandova", - "author_inst": "Comenius University in Bratislava Faculty of Medicine, Department of Clinical Biology, Genetics and Clinical Genetics, Bratislava, Slovakia" - }, - { - "author_name": "Emilia Mikova", - "author_inst": "Medirex, a.s., Pezinok, Slovakia" - }, - { - "author_name": "Elena Tibenska", - "author_inst": "Medirex, a.s., Pezinok, Slovakia" - }, - { - "author_name": "Vanda Repiska", - "author_inst": "Comenius University in Bratislava Faculty of Medicine, Department of Clinical Biology, Genetics and Clinical Genetics, Bratislava, Slovakia" - }, - { - "author_name": "Gabriel Minarik", - "author_inst": "Medirex Group Academy n.p.o., Nitra, Slovakia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.06.22.23291610", "rel_title": "COVID-19 Impact in Crohn Disease Patients Underwent Autologous Hematopoietic Stem Cell Transplantation", @@ -92026,6 +94119,53 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2023.06.26.546492", + "rel_title": "Oligomeric state of \u03b2-coronavirus non-structural protein 10 stimulators studied by OmniSEC and Small Angle X-ray Scattering", + "rel_date": "2023-06-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.26.546492", + "rel_abs": "Members of the {beta}-coronavirus family such as SARS-CoV-2, SARS, and MERS have caused pandemics over the last 20 years. Future pandemics are likely and studying the coronavirus family members is necessary for their understanding and treatment. Coronaviruses possess 16 non-structural proteins, many of which are involved in viral replication and other vital functions. Non-structural protein 10 (nsp10) is an essential stimulator of nsp14 and nsp16, modulating RNA proofreading and viral RNA cap formation. Studying nsp10 of pathogenic coronaviruses is central to understanding its multifunctional role. We report the biochemical and biophysical characterisation of full-length nsp10 from MERS, SARS and SARS-CoV-2. Proteins were subjected to a combination of OmniSEC and SEC-MALS to characterise their oligomeric state. Full-length nsp10s were predominantly monomeric in solution, while truncated versions of nsp10 have a higher tendency to oligomerise. Small angle X-ray scattering (SAXS) experiments reveal a globular shape of nsp10 which is conserved in all three coronaviruses, including MERS nsp10, which diverges most from SARS and SARS-CoV-2 nsp10s. In conclusion, unbound nsp10 proteins from SARS, MERS, and SARS-CoV-2 are globular and predominantly monomeric in solution. Additionally, we describe for the first time a functional role of the C-terminus of nsp10 for tight binding to nsp14.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Wolfgang Knecht", + "author_inst": "Lund University" + }, + { + "author_name": "Zoe Fisher", + "author_inst": "European Spallation Source" + }, + { + "author_name": "Jiaqi Lou", + "author_inst": "University College London" + }, + { + "author_name": "Celeste Sele", + "author_inst": "Lund University" + }, + { + "author_name": "Shumeng Ma", + "author_inst": "University College London" + }, + { + "author_name": "Anna Andersson Rasmussen", + "author_inst": "Lund University" + }, + { + "author_name": "Nikos Nikos Pinotsis", + "author_inst": "Birkbeck College" + }, + { + "author_name": "Frank Gerhard Kozielski", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2023.06.22.546100", "rel_title": "Classification of patients with COVID-19 by blood RNA endotype: A prospective cohort study", @@ -92405,45 +94545,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.06.18.545480", - "rel_title": "Identification of a novel HKU4-related coronavirus in single-cell datasets and clade viral host analysis", - "rel_date": "2023-06-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.18.545480", - "rel_abs": "HKU4-related coronaviruses (CoVs) are merbecoviruses related to Middle Eastern Respiratory Syndrome coronavirus (MERS-CoV). In 2022 and 2023, two HKU4-related CoV strains were discovered in Manis javanica (Malayan pangolin) metagenomic datasets derived from organ samples: HKU4-P251T and MjHKU4r-CoV-1. Together with the Tylonycteris robustula bat CoV 162275, which was discovered in 2022, pangolin CoVs HKU4-P251T and MjHKU4r-CoV-1 form a novel phylogenetic clade distinct from all previously documented HKU4-related CoVs. In this study, we identified a novel HKU4-related CoV in a pangolin single-cell sequencing dataset generated by BGI-Shenzhen in Shenzhen, Guangdong, China in 2020. The CoV phylogenetically belongs to the same newly identified clade. The single cell datasets were reported as generated from organ samples of a single pangolin that died of natural causes. 98% of the HKU4-related CoV reads were found in only one of the seven single cell datasets -- a large intestine cell dataset, cells of which exhibit low expression of DPP4. Bacterial contamination was found to be moderately correlated with HKU4-related CoV presence. We further identified with high confidence that the RNA-Seq dataset supporting one of four near identical variants of MjHKU4r-CoV-1 is a Sus scrofa (wild pig) metagenomic dataset, with only a trace level of Manis javanica genomic content. The presence of HKU4-related CoV reads in the dataset are almost certainly laboratory research-related and not from a premortal pangolin or pig infection. Our findings raise concerns about the provenance of the novel HKU4-related CoV we identify here, MjHKU4r-CoV-1 and its four near-identical variants.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Adrian Jones", - "author_inst": "Independent Bioinformatics Researcher" - }, - { - "author_name": "Steven E. Massey", - "author_inst": "Department of Biology, University of Puerto Rico - Rio Piedras, San Juan, PR 00931, USA" - }, - { - "author_name": "Louis R Nemzer", - "author_inst": "Nova Southeastern University" - }, - { - "author_name": "Daoyu Zhang", - "author_inst": "Independent Genetics Researcher" - }, - { - "author_name": "Yuri Deigin", - "author_inst": "Youthereum Genetics Inc." - }, - { - "author_name": "Steven C. Quay", - "author_inst": "Atossa Therapeutics, Inc., Seattle, WA USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2023.06.20.545832", "rel_title": "Combination therapy with oral antiviral and anti-inflammatory drugs improves the efficacy of delayed treatment in severe COVID-19", @@ -93732,6 +95833,53 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.06.19.545534", + "rel_title": "SARS-CoV-2 variants of concern exhibit differential gastro-intestinal tropism and pathogenesis in the Syrian golden hamster model.", + "rel_date": "2023-06-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.19.545534", + "rel_abs": "The Coronavirus Disease 2019 (COVID-19) pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has taken its toll on worldwide public health infrastructure. SARS-CoV-2 is reported to exhibit wide tissue tropism, contributing to its severe pathogenicity that often culminates in multiple-organ failure. The onslaught of this disease has intensified due to the emergence of variants of concern (VOC), such as Delta and Omicron. These variants have been linked to gastrointestinal (GI) symptoms, suggesting a potential fecal-oral route of viral transmission. Here we compared the broad tissue tropism of ancestral Hong-Kong SARS-CoV-2 (SARS-CoV-2 HK) against Delta and Omicron VOCs in aa hamster model by analyzing tissue samples collected from the upper and lower respiratory system and the GI tract. We observed an overall increase in vRNA load and pro- inflammatory cytokines, especially in GI tracts of animals infected with Delta virus, indicating selective virus tropism and pathology in these tissues. However, no apparent spike in Delta viral load was observed in the large intestine and fecal matter. Overall, our research investigates the wide range of tissues that various SARS-CoV-2 strains can infect in hamsters and presents evidence supporting the increased preference of Delta VOCs for infecting the GI tract.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Santhosh K Nagraj", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Christy M Joy", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Rohan Narayan", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Rishad Shiraz", + "author_inst": "Indian Institute Of Science" + }, + { + "author_name": "Sumandeep Kaur", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Oyahida Khatun", + "author_inst": "Indian Institute Of Science" + }, + { + "author_name": "Sagar Dubey", + "author_inst": "Indian Institute of Science" + }, + { + "author_name": "Shashank Tripathi", + "author_inst": "Indian Institute of Science" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2023.06.18.545507", "rel_title": "Dysregulated Platelet Function and Thrombosis in Patients with Post-Acute Sequelae of COVID-19", @@ -94379,41 +96527,6 @@ "type": "new results", "category": "ecology" }, - { - "rel_doi": "10.1101/2023.06.16.545251", - "rel_title": "High-confidence placement of difficult-to-fit fragments into electron density by using anomalous signals - a case study using hits targeting SARS-CoV-2 non-structural protein 1", - "rel_date": "2023-06-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.16.545251", - "rel_abs": "The identification of multiple simultaneous orientations of small molecule inhibitors binding to a protein target is a common challenge. It has recently been reported that the conformational heterogeneity of ligands is widely underreported in the Protein Data Bank, which is likely to impede optimal exploitation to improve affinity of these ligands1. Significantly less is even known about multiple binding orientations for fragments (< 300 Da) although this information would be essential for subsequent fragment optimisation using growing, linking or merging and rational structure-based design. Here we use recently reported fragment hits for the SARS-CoV-2 non-structural protein 1 (nsp1) N-terminal domain to propose a general procedure for unambiguously identifying binding orientations of 2-dimensional fragments containing either sulphur or chloro substituents within the wavelength range of most tunable beamlines. By measuring datasets at two energies, using a tuneable beamline operating in vacuum and optimised for data collection at very low X-ray energies, we show that the anomalous signal can be used to identify multiple orientations in small fragments containing sulphur and/or chloro substituents or to verify recently reported conformations. Although in this specific case we identified the positions of sulphur and chlorine in fragments bound to their protein target, we are confident that this work can be further expanded to additional atoms or ions which often occur in fragments. Finally, our improvements in the understanding of binding orientations will also serve to advance the rational optimisation of SARS-CoV-2 nsp1 targeting fragment hits.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Frank Gerhard Kozielski", - "author_inst": "University College London" - }, - { - "author_name": "Shumeng Ma", - "author_inst": "University College London (UCL)" - }, - { - "author_name": "Matthew W Bowler", - "author_inst": "European Molecular Biology Laboratory" - }, - { - "author_name": "Vitaliy Mykhaylyk", - "author_inst": "Diamond Light Source" - }, - { - "author_name": "Nikos Pinotsis", - "author_inst": "Birkbeck College" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2023.06.15.545129", "rel_title": "Repurposing Remdesivir for COVID-19: Computational Drug Design Targeting SARS-CoV-2 RNA Polymerase and Main Protease using Molecular Dynamics Approach", @@ -95670,6 +97783,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2023.06.08.23291154", + "rel_title": "Neurodivergence as a risk factor for Post-Covid-19 Syndrome", + "rel_date": "2023-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.08.23291154", + "rel_abs": "Neurodivergent (ND) individuals (e.g., Autistic people) are more likely to experience health problems that are characterised by central sensitisation . Recent research suggests that a so-called Long-COVID syndrome might also be explained by a heightened response to internal physiological stimuli, much like in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Using a standardised assessment tool, we examined whether traits associated with Autism would predict long-term COVID-19 symptoms in 267 Healthcare Workers (HCW).. Higher autistic traits predicted COVID-19 symptoms that lasting more than 12 weeks regardless of formal autism diagnosis. A personality measure also showed that negative affect was associated with experiencing COVID-19 symptoms for 4-12 weeks, though the direction of causality in this case is uncertain. Limitations of the present study are 1) the retrospective nature of COVID-19 symptom reporting; 2) likely self-selection bias given the high number of HCWs who reported long-term COVID-19 symptoms; and 3) the gender-bias towards females in our sample.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Rachael Kathleen Raw", + "author_inst": "Newcastle University" + }, + { + "author_name": "Jon Rees", + "author_inst": "University of Sunderland" + }, + { + "author_name": "Amy Pearson", + "author_inst": "University of Sunderland" + }, + { + "author_name": "David Chadwick", + "author_inst": "James Cook University Hospital" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.06.07.23291077", "rel_title": "Large scale phenotyping of long COVID inflammation reveals mechanistic subtypes of disease", @@ -96221,33 +98365,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.06.08.23291183", - "rel_title": "Assessment of the relationship between Google Trend search data on clinical symptoms and cases reported during the first wave of the COVID-19 outbreak in India.", - "rel_date": "2023-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.08.23291183", - "rel_abs": "Infodemiology and infoveillance approaches have been extensively used in recent years to support traditional epidemiology and disease surveillance. Hence, the present study aimed to explore the association between Google Trends (GTs) search of clinical symptoms and cases reported during the first wave of COVID-19. The GT data from January 30, 2020, to September 30, 2020, and daily COVID-19 cases in India and a few selected states were collected from the Ministry of Health and Family Welfare, Government of India. Correlation analysis was performed between the GT index values and the number of confirmed cases. Followed by, the COVID-19 cases were predicted using Bayesian regression and classical linear regression models. A strong association was observed between the search index of clinical symptoms and reported COVID-19 cases (cold: R=0.41, headache: R=0.46, fever: R=0.66, loss of taste: R=0.78, loss of smell R=0.86) across India. Similarly, lagged correlations were also observed (loss of smell, loss of taste, loss of taste and loss of smell, fever and headache show 3, 9, 1, 9, and 13 days lag periods respectively). Besides this, the Bayesian regression model was outperformed (MAE: 0.331164, RMSE: 0.411087) for predicting the COVID-19 cases in India and regionally than the frequentist linear regression (MAE: 0.33134, RMSE: 0.411316). The study helps health authorities better prepare and planning of health care facility timely to avoid adverse impacts.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Srinivasa Rao Mutheneni", - "author_inst": "CSIR-Indian Institute of Chemical Technology, Uppal road, Tarnaka, Hyderabad - 500007, India. Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- " - }, - { - "author_name": "Hariprasad Vavilala", - "author_inst": "CSIR-Indian Institute of Chemical Technology, Uppal road, Tarnaka, Hyderabad - 500007, India. Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- " - }, - { - "author_name": "Rajasekhar Mopuri", - "author_inst": "CSIR-Indian Institute of Chemical Technology, Uppal road, Tarnaka, Hyderabad - 500007, India." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.06.08.23291159", "rel_title": "Poor immunogenicity upon SARS-CoV-2 mRNA vaccinations in autoimmune SLE patients is associated with pronounced EF-mediated responses and anti-BAFF/Belimumab treatment.", @@ -97340,6 +99457,57 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2023.06.08.544212", + "rel_title": "Towards Pandemic-Scale Ancestral Recombination Graphs of SARS-CoV-2", + "rel_date": "2023-06-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.06.08.544212", + "rel_abs": "Recombination is an ongoing and increasingly important feature of circulating lineages of SARS-CoV-2, challenging how we represent the evolutionary history of this virus and giving rise to new variants of potential public health concern by combining transmission and immune evasion properties of different lineages. Detection of new recombinant strains is challenging, with most methods looking for breaks between sets of mutations that characterise distinct lineages. In addition, many basic approaches fundamental to the study of viral evolution assume that recombination is negligible, in that a single phylogenetic tree can represent the genetic ancestry of the circulating strains. Here we present an initial version of sc2ts, a method to automatically detect recombinants in real time and to cohesively integrate them into a genealogy in the form of an ancestral recombination graph (ARG), which jointly records mutation, recombination and genetic inheritance. We infer two ARGs under different sampling strategies, and study their properties. One contains 1.27 million sequences sampled up to June 30, 2021, and the second is more sparsely sampled, consisting of 657K sequences sampled up to June 30, 2022. We find that both ARGs are highly consistent with known features of SARS-CoV-2 evolution, recovering the basic backbone phylogeny, mutational spectra, and recapitulating details on the majority of known recombinant lineages. Using the well-established and feature-rich tskit library, the ARGs can also be stored concisely and processed efficiently using standard Python tools. For example, the ARG for 1.27 million sequences--encoding the inferred reticulate ancestry, genetic variation, and extensive metadata--requires 58MB of storage, and loads in less than a second. The ability to fully integrate the effects of recombination into downstream analyses, to quickly and automatically detect new recombinants, and to utilise an efficient and convenient platform for computation based on well-engineered technologies makes sc2ts a promising approach.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Shing H Zhan", + "author_inst": "University of Oxford" + }, + { + "author_name": "Anastasia Ignatieva", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Yan Wong", + "author_inst": "University of Oxford" + }, + { + "author_name": "Katherine Eaton", + "author_inst": "National Microbiology Laboratory, Public Health Agency of Canada, Canada" + }, + { + "author_name": "Benjamin Jeffery", + "author_inst": "University of Oxford" + }, + { + "author_name": "Duncan S Palmer", + "author_inst": "University of Oxford" + }, + { + "author_name": "Carmen Lia Murall", + "author_inst": "National Microbiology Laboratory, Public Health Agency of Canada, Canada" + }, + { + "author_name": "Sarah Otto", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Jerome Kelleher", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2023.06.06.543529", "rel_title": "Early acquisition of S-specific Tfh clonotypes after SARS-CoV-2 vaccination is associated with the longevity of anti-S antibodies", @@ -97847,49 +100015,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.06.06.23291015", - "rel_title": "Impact of CoronaVac on Covid-19 outcomes of elderly adults in a large and socially unequal Brazilian city: A target trial emulation study", - "rel_date": "2023-06-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.06.23291015", - "rel_abs": "BackgroundAlthough CoronaVac was the only Covid-19 vaccine adopted in the first months of the Brazilian vaccination campaign, randomized clinical trials to evaluate its efficacy in elderly adults were limited. In this study, we use routinely collected surveillance and SARS-CoV-2 vaccination and testing data comprising the population of the fifth largest city of Brazil to evaluate the effectiveness of CoronaVac in adults 60+ years old against severe outcomes.\n\nMethodsUsing large observational databases on vaccination and surveillance data from the city of Fortaleza, Brazil, we defined a retrospective cohort including 324,302 eligible adults aged [≥] 60 years to evaluate the effectiveness of the CoronaVac vaccine. The cohort included individuals vaccinated between January 21, 2021, and August 31, 2021, who were matched with unvaccinated persons at the time of rollout following a 1:1 ratio according to baseline covariates of age, sex, and Human Development Index of the neighborhood of residence. Only Covid-19-related severe outcomes were included in the analysis: hospitalization, ICU admission, and death. Vaccine effectiveness for each outcome was calculated by using the risk ratio between the two groups, with the risk obtained by the Kaplan-Meier estimator.\n\nResultsWe obtained 62,643 matched pairs for assessing the effectiveness of the two-dose regimen of CoronaVac. The demographic profile of the matched population was statistically representative of the population of Fortaleza. Using the cumulative incidence as the risk associated with each group, starting at day 14 since the receipt of the second dose, we found an 82.3% (95% CI 66.3 - 93.9) effectiveness against Covid-19-related death, 68.4% (95% CI 42.3 - 86.4) against ICU admission, and 55.8% (95% CI 42.7 - 68.3) against hospital admission.\n\nConclusionsOur results show that, despite critical delays in vaccine delivery and limited evidence in efficacy trial estimates, CoronaVac contributed to preventing deaths and severe morbidity due to Covid-19 in elderly adults.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Higor da Silva Monteiro", - "author_inst": "Universidade Federal do Cear\u00e1" - }, - { - "author_name": "Antonio Silva Lima Neto", - "author_inst": "Universidade de Fortaleza" - }, - { - "author_name": "Rebecca Kahn", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Geziel Sousa Santos", - "author_inst": "Secretaria Municipal da Sa\u00fade de Fortaleza" - }, - { - "author_name": "Humberto Andrade Carmona", - "author_inst": "Universidade Federal do Cear\u00e1" - }, - { - "author_name": "Jos\u00e9 Soares de Andrade Jr.", - "author_inst": "Universidade Federal do Cear\u00e1" - }, - { - "author_name": "Marcia C. Castro", - "author_inst": "Harvard TH Chan School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.06.06.23290989", "rel_title": "Metformin reduces SARS-CoV-2 in a Phase 3 Randomized Placebo Controlled Clinical Trial", @@ -98966,6 +101091,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.06.02.23290879", + "rel_title": "Estimation of introduction and transmission rates of SARS-CoV-2 in a prospective household study", + "rel_date": "2023-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.06.02.23290879", + "rel_abs": "Household studies provide an efficient means to study transmission of infectious diseases, enabling estimation of individual susceptibility and infectivity. A main inclusion criterion in such studies is often the presence of an infected person. This precludes estimation of the hazards of pathogen introduction into the household. Here we use data from a prospective household-based study to estimate SARS-CoV-2 age- and time-dependent household introduction hazards together with within household transmission rates in the Netherlands from August 2020 to August 2021. Introduction hazards and within-household transmission rates are estimated with penalized splines and stochastic epidemic models, respectively. The estimated hazard of introduction of SARS-CoV-2 in the households was lower for children (0-12 years) than for adults (relative hazard: 0.62; 95%CrI: 0.34-1.0). Estimated introduction hazards peaked in mid October 2020, mid December 2020, and mid April 2021, preceding peaks in hospital admissions by 1-2 weeks. The best fitting transmission models include increased infectivity of children relative to adults and adolescents, such that the estimated child-to-child transmission probability (0.62; 95%CrI: 0.40-0.81) was considerably higher than the adult-to-adult transmission probability (0.12; 95%CrI: 0.057-0.19). Scenario analyses show that vaccination of adults could have strongly reduced infection attack rates in households and that adding adolescent vaccination would have offered limited added benefit.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Michiel van Boven", + "author_inst": "Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands" + }, + { + "author_name": "Christiaan H. van Dorp", + "author_inst": "Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, United States" + }, + { + "author_name": "Ilse Westerhof", + "author_inst": "Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands" + }, + { + "author_name": "Vincent Jaddoe", + "author_inst": "Erasmus Medical Center, Rotterdam, the Netherlands" + }, + { + "author_name": "Valerie Heuvelman", + "author_inst": "Erasmus Medical Center, Rotterdam, the Netherlands" + }, + { + "author_name": "Liesbeth Duijts", + "author_inst": "Erasmus Medical Center, Rotterdam, the Netherlands" + }, + { + "author_name": "Elandri Fourie", + "author_inst": "Spaarne Gasthuis, Hoofddorp, the Netherlands" + }, + { + "author_name": "Judith Sluiter-Post", + "author_inst": "Spaarne Gasthuis, Hoofddorp, the Netherlands" + }, + { + "author_name": "Marlies A. van Houten", + "author_inst": "Spaarne Gasthuis, Hoofddorp, the Netherlands" + }, + { + "author_name": "Paul Badoux", + "author_inst": "Regional Public Health Laboratory Kennemerland, Haarlem, the Netherlands" + }, + { + "author_name": "Sjoerd Euser", + "author_inst": "Regional Public Health Laboratory Kennemerland, Haarlem, the Netherlands" + }, + { + "author_name": "Bjorn Herpers", + "author_inst": "Regional Public Health Laboratory Kennemerland, Haarlem, the Netherlands" + }, + { + "author_name": "Dirk Eggink", + "author_inst": "National Institute for Public Health and the Environment, Bilthoven, the Netherlands" + }, + { + "author_name": "Trisja Boom", + "author_inst": "Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands" + }, + { + "author_name": "Joanne Wildenbeest", + "author_inst": "Department of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's hospital, University Medical Center Utrecht, the Netherlands" + }, + { + "author_name": "Louis Bont", + "author_inst": "Department of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's hospital, University Medical Center Utrecht, the Netherlands" + }, + { + "author_name": "Ganna Rozhnova", + "author_inst": "Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands" + }, + { + "author_name": "Marc J. Bonten", + "author_inst": "Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands" + }, + { + "author_name": "Mirjam E. Kretzschmar", + "author_inst": "Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands" + }, + { + "author_name": "Patricia Bruijning-Verhagen", + "author_inst": "Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.06.04.23290948", "rel_title": "Mental health issues among medical students: Exploring predictors of mental health in Dhaka during COVID-19 pandemic", @@ -100001,73 +102221,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.05.31.23290613", - "rel_title": "A non-enzymatic test for SARS-CoV-2 RNA using DNA nanoswitches", - "rel_date": "2023-06-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.31.23290613", - "rel_abs": "The emergence of a highly contagious novel coronavirus in 2019 led to an unprecedented need for large scale diagnostic testing. The associated challenges including reagent shortages, cost, deployment delays, and turnaround time have all highlighted the need for an alternative suite of low-cost tests. Here, we demonstrate a diagnostic test for SARS-CoV-2 RNA that provides direct detection of viral RNA and eliminates the need for costly enzymes. We employ DNA nanoswitches that respond to segments of the viral RNA by a change in shape that is readable by gel electrophoresis. A new multi-targeting approach samples 120 different viral regions to improve the limit of detection and provide robust detection of viral variants. We apply our approach to a cohort of clinical samples, positively identifying a subset of samples with high viral loads. Since our method directly detects multiple regions of viral RNA without amplification, it eliminates the risk of amplicon contamination and renders the method less susceptible to false positives. This new tool can benefit the COVID-19 pandemic and future emerging outbreaks, providing a third option between amplification-based RNA detection and protein antigen detection. Ultimately, we believe this tool can be adapted both for low-resource onsite testing as well as for monitoring viral loads in recovering patients.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Javier Vilcapoma", - "author_inst": "University at Albany" - }, - { - "author_name": "Asmer Aliyeva", - "author_inst": "University at Albany" - }, - { - "author_name": "Andrew Hayden", - "author_inst": "University at Albany" - }, - { - "author_name": "Arun Richard Chandrasekaran", - "author_inst": "University at Albany" - }, - { - "author_name": "Lifeng Zhou", - "author_inst": "University at Albany" - }, - { - "author_name": "Jibin Abraham Punnoose", - "author_inst": "University at Albany" - }, - { - "author_name": "Darren Yang", - "author_inst": "Boston Children's Hospital" - }, - { - "author_name": "Clinton Hansen", - "author_inst": "Boston Children's Hospital" - }, - { - "author_name": "Simon Chi-Chin Shiu", - "author_inst": "University at Albany" - }, - { - "author_name": "Alexis Russell", - "author_inst": "Wadsworth Center, NYS Department of Health" - }, - { - "author_name": "Kirsten St. George", - "author_inst": "Wadsworth Center - NYSDOH" - }, - { - "author_name": "Wesley Wong", - "author_inst": "Harvard University and Boston Children's Hospital" - }, - { - "author_name": "Ken Halvorsen", - "author_inst": "University at Albany" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.05.29.23290677", "rel_title": "Social inequalities in the misbelief of chloroquines protective effect against COVID-19: results from the EPICOVID-19 study in Brazil", @@ -101292,6 +103445,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.05.25.23290402", + "rel_title": "Infection by SARS-CoV-2 with alternate frequencies of mRNA vaccine boosting for patients undergoing antineoplastic treatment for cancer", + "rel_date": "2023-05-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.25.23290402", + "rel_abs": "Patients undergoing antineoplastic therapies often exhibit reduced immune response to COVID-19 vaccination, necessitating assessment of alternate boosting frequencies for these patients. However, data on reinfection risks to guide clinical decision-making is limited. We quantified reinfection risks of SARS-CoV-2 at different mRNA boosting frequencies of patients on antineoplastic therapies. Antibody levels following Pfizer-BioNTech BNT162b2 vaccination were analyzed for patients without cancer, with cancer undergoing various treatments, and treated with different antineoplastic therapeutics. Using long-term antibody data from other coronaviruses in an evolutionary framework, we estimated infection probabilities based on antibody levels and projected waning. We calculated cumulative probabilities of breakthrough infection for alternate booster schedules over two years. Annual boosting reduced risks for targeted or hormonal treatments, immunotherapy, and chemotherapy-immunotherapy combinations similarly to the general population. Patients receiving no treatment or chemotherapy exhibited higher risks, suggesting that accelerated vaccination schedules should be considered. Patients treated with rituximab therapy posed the highest infection risk, suggesting that a combination of frequent boosting and additional interventions may be warranted for mitigating SARS-CoV-2 infection in these patients.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jeffrey P. Townsend", + "author_inst": "Yale University" + }, + { + "author_name": "Hayley Hassler", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Brinda Emu", + "author_inst": "Yale University" + }, + { + "author_name": "Alex Dornburg", + "author_inst": "University of North Carolina Charlotte" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.05.29.542720", "rel_title": "Development of a SARS-COV-2 monoclonal antibody panel and its applicability as a reagent in high-throughput fluorescence reduction neutralization and immunohistochemistry assays", @@ -101795,61 +103979,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.05.24.23290470", - "rel_title": "Missing data and missed infections: Investigating racial and ethnic disparities in SARS-CoV-2 testing and infection rates in Holyoke, Massachusetts", - "rel_date": "2023-05-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.24.23290470", - "rel_abs": "Routinely collected testing data has been a vital resource for public health response during the COVID-19 pandemic and has revealed the extent to which Black and Hispanic persons have borne a disproportionate burden of SARS-CoV-2 infections and hospitalizations in the United States. However, missing race and ethnicity data and missed infections due to testing disparities limit the interpretation of testing data and obscure the true toll of the pandemic. We investigated potential bias arising from these two types of missing data through a case study in Holyoke, Massachusetts during the pre-vaccination phase of the pandemic. First, we estimated SARS-CoV-2 testing and case rates by race/ethnicity, imputing missing data using a joint modelling approach. We then investigated disparities in SARS-CoV-2 reported case rates and missed infections by comparing case rate estimates to estimates derived from a COVID-19 seroprevalence survey. Compared to the non-Hispanic white population, we found that the Hispanic population had similar testing rates (476 vs. 480 tested per 1,000) but twice the case rate (8.1% vs. 3.7%). We found evidence of inequitable testing, with a higher rate of missed infections in the Hispanic population compared to the non-Hispanic white population (77 vs. 58 infections missed per 1,000).", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Sara M Sauer", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Isabel R Fulcher", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Wilfredo R Matias", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Ryan Paxton", - "author_inst": "Holyoke Board of Health" - }, - { - "author_name": "Ahmed Elnaiem", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Sean Gonsalves", - "author_inst": "Holyoke Board of Health" - }, - { - "author_name": "Jack Zhu", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Yodeline Guillaume", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Molly F Franke", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Louise C Ivers", - "author_inst": "Massachusetts General Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.05.26.23290475", "rel_title": "Researching COVID to enhance recovery (RECOVER) adult study protocol: Rationale, objectives and design", @@ -103870,6 +105999,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2023.05.23.23289798", + "rel_title": "Primary Care Post-COVID syndrome Diagnosis and Referral Coding", + "rel_date": "2023-05-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.23.23289798", + "rel_abs": "IntroductionGuidelines for diagnosing and managing Post-COVID syndrome have been rapidly developed. Consistency of the application of these guidelines in primary care is unknown. Electronic health records provide an opportunity to review the use of codes relating to Post-COVID syndrome. This paper explores the use of primary care records as a surrogate uptake measure for NICEs rapid guideline \"managing the long-term effects of COVID-19\" by measuring the use of Post-COVID syndrome diagnosis and referral codes in the pathway.\n\nMethodWith the approval of NHS England we used routine clinical data from the OpenSafely-EMIS/-TPP platforms. Counts of Post-COVID syndrome diagnosis and referral codes were generated from a cohort of all adults, establishing numbers of diagnoses and referrals following diagnosis. The relationship between Post-COVID syndrome diagnosis and referral codes was explored with reference to NICEs rapid guideline.\n\nResultsOf over 45 million patients, 69,220 (0.15%) had a Post-COVID syndrome diagnostic code, and 67,741 (0.15%) had a referral code. 78% of referral codes did not have an associated diagnosis code. 79% of diagnosis codes had no subsequent referral code. Only 18,633 (0.04%) had both. There were higher rates of both diagnosis and referral in those who were more deprived, female and some ethnic groups.\n\nDiscussionThis study demonstrates variation in diagnosis and referral coding rates for Post-COVID syndrome across different patient groups. The results, with limited crossover of referral and diagnostic codes, suggest only one type of code is usually recorded. Recording one code limits the use of routine data for monitoring Post-COVID syndrome diagnosis and management, but suggests several areas for improvement in coding. Post-COVID syndrome coding, particularly diagnosis coding, needs to improve before administrators and researchers can use it to evaluate care pathways.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Robert Willans", + "author_inst": "National Institute of Health and Care Excellence" + }, + { + "author_name": "Gail Allsopp", + "author_inst": "Royal College of General Practitioners" + }, + { + "author_name": "Pall Jonsson", + "author_inst": "National Institute of Health and Care Excellence" + }, + { + "author_name": "Fiona Glen", + "author_inst": "National Institute of Health and Care Excellence" + }, + { + "author_name": "Felix Greaves", + "author_inst": "National Institute of Health and Care Excellence" + }, + { + "author_name": "John Macleod", + "author_inst": "University of Bristol" + }, + { + "author_name": "Yinghui Wei", + "author_inst": "University of Plymouth" + }, + { + "author_name": "Sebastian Bacon", + "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford" + }, + { + "author_name": "Amir Mehrkar", + "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford" + }, + { + "author_name": "Alex Walker", + "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford" + }, + { + "author_name": "Brian MacKenna", + "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford" + }, + { + "author_name": "Louis Fisher", + "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford" + }, + { + "author_name": "Ben Goldacre", + "author_inst": "Bennett Institute for Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford" + }, + { + "author_name": "- The OpenSAFELY Collaborative", + "author_inst": "" + }, + { + "author_name": "- The CONVALESCENCE Collaborative", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.05.23.23290387", "rel_title": "Spatiotemporal Variations of \"Triple-demic\" Outbreaks of Respiratory Infections in the United States in the Post-COVID-19 Era", @@ -104449,113 +106653,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.05.16.23290059", - "rel_title": "Distinct T cell functional profiles in SARS-CoV-2 seropositive and seronegative children associated with endemic human coronavirus cross-reactivity", - "rel_date": "2023-05-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.16.23290059", - "rel_abs": "SARS-CoV-2 infection in children typically results in asymptomatic or mild disease. There is a paucity of studies on antiviral immunity in African children. We investigated SARS-CoV-2-specific T cell responses in 71 unvaccinated asymptomatic South African children who were seropositive or seronegative for SARS-CoV-2. SARS-CoV-2-specific CD4+ T cell responses were detectable in 83% of seropositive and 60% of seronegative children. Although the magnitude of the CD4+ T cell response did not differ significantly between the two groups, their functional profiles were distinct, with SARS-CoV-2 seropositive children exhibiting a higher proportion of polyfunctional T cells compared to their seronegative counterparts. The frequency of SARS-CoV-2-specific CD4+ T cells in seronegative children was associated with the endemic human coronavirus (HCoV) HKU1 IgG response. Overall, the presence of SARS-CoV-2-responding T cells in seronegative children may result from cross-reactivity to endemic coronaviruses and could contribute to the relative protection from disease observed in SARS-CoV-2-infected children.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Ntombi S.B. Benede", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Marius B Tincho", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Avril Walters", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Vennesa Subbiah", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Amkele Ngomti", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Richard Baguma", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Claire Butters", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Mathilda Mennen", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Sango Skelem", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Marguerite Adriaanse", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Strauss van Graan", - "author_inst": "NICD" - }, - { - "author_name": "Sashkia R. Balla", - "author_inst": "NICD" - }, - { - "author_name": "Thandeka Moyo-Gwete", - "author_inst": "NICD" - }, - { - "author_name": "Penny L. Moore", - "author_inst": "NICD" - }, - { - "author_name": "Maresa Botha", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Lesley Workman", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Heather J. Zar", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Ntobeko A. B. Ntusi", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Liesl Z\u00fchlke", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Kate Webb", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Catherine Riou", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Wendy A Burgers", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Roanne S Keeton", - "author_inst": "University of Cape Town" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.05.19.541479", "rel_title": "The COVID-19 mRNA vaccine Comirnaty induces anaphylactic shock in an anti-PEG hyperimmune large animal model: Role of complement in cardiovascular, hematological, and inflammatory mediator changes", @@ -105664,6 +107761,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, + { + "rel_doi": "10.1101/2023.05.17.541098", + "rel_title": "SARS-CoV-2 infection leads to Tau pathological signature in neurons", + "rel_date": "2023-05-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.05.17.541098", + "rel_abs": "BackgroundThe coronavirus disease 19 (COVID-19) has represented an issue for global health since its outbreak in March 2020. It is now evident that the SARS-CoV-2 infection results in a wide range of long-term neurological symptoms and is worryingly associated with the aggravation of Alzheimers disease. Little is known about the molecular basis of these manifestations.\n\nMethodsSeveral SARS-CoV-2 strain variants were used to infect SH-SY5Y neuroblastoma cells and K18-hACE C57BL/6J mice. The Tau phosphorylation profile and aggregation propensity upon infection were investigated using immunoblot and immunofluorescence on cellular extracts, subcellular fractions, and brain tissue. The viral proteins Spike, Nucleocapsid, and Membrane were overexpressed in SH-SY5Y cells and the direct effect on Tau phosphorylation was checked using immunoblot experiments.\n\nResultsUpon infection, Tau is phosphorylated at several pathological epitopes associated with Alzheimers disease and other tauopathies. Moreover, this event increases Taus propensity to form insoluble aggregates and alters its subcellular localization.\n\nConclusionsOur data support the evidence that SARS-CoV-2 infection in the Central Nervous System triggers downstream effects altering Tau function, eventually leading to the impairment of neuronal function.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Cristina Di Primio", + "author_inst": "Istituto di Neuroscienze" + }, + { + "author_name": "Paola Quaranta", + "author_inst": "Retrovirus Center, Virology Section, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa." + }, + { + "author_name": "Marianna Mignanelli", + "author_inst": "Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, Pisa, 56126, Italy" + }, + { + "author_name": "Giacomo Siano", + "author_inst": "BIO@SNS" + }, + { + "author_name": "Matteo Bimbati", + "author_inst": "Institute of Neuroscience, Italian National Research Council (CNR), Via Moruzzi, 1, Pisa 56124, Italy. Department of Biotechnology, University of Verona, 37134," + }, + { + "author_name": "Carmen Rita Piazza", + "author_inst": "Retrovirus Center, Virology Section, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa. Department of Medica" + }, + { + "author_name": "Piero Giorgio Spezia", + "author_inst": "Retrovirus Center, Virology Section, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa." + }, + { + "author_name": "Paola Perrera", + "author_inst": "Retrovirus Center, Virology Section, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa." + }, + { + "author_name": "Fulvio Basolo", + "author_inst": "Department of Surgical, Medical and Molecular Pathology, University Hospital of Pisa, Via Paradisa 2, 56124 Pisa, Italy" + }, + { + "author_name": "Anello Marcello Poma", + "author_inst": "Department of Surgical, Medical and Molecular Pathology, University Hospital of Pisa, Via Paradisa 2, 56124 Pisa, Italy" + }, + { + "author_name": "Mario Costa", + "author_inst": "Institute of Neuroscience, Italian National Research Council (CNR), Via Moruzzi, 1, Pisa 56124, Italy" + }, + { + "author_name": "Mauro Pistello", + "author_inst": "Retrovirus Center, Virology Section, Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa. Virology Unit, Pisa " + }, + { + "author_name": "Antonino Cattaneo", + "author_inst": "Laboratorio di Biologia Bio@SNS, Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, Pisa, 56126, Italy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "neuroscience" + }, { "rel_doi": "10.1101/2023.05.16.541033", "rel_title": "Longitudinal analysis of memory T follicular helper cells and antibody response following CoronaVac vaccination", @@ -106295,57 +108459,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.05.11.23289882", - "rel_title": "Understanding COVID-19 Vaccine Uptake and Hesitancy Among People With HIV in Freetown, Sierra Leone: A Cross-sectional Study", - "rel_date": "2023-05-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.11.23289882", - "rel_abs": "ObjectivesPeople living with HIV (PWH) are at increased risk of COVID-19 related morbidity and mortality, yet less is known about COVID-19 vaccination uptake and hesitancy, especially in sub-Saharan Africa. We aimed to evaluate COVID-19 vaccine uptake and hesitancy among PWH in Sierra Leone.\n\nMethodsWe conducted a cross-sectional study in a convenience sample of PWH in routine care at Connaught Hospital in Freetown, Sierra Leone from April through June 2022. We collected sociodemographic and health-related data. We used the VAX Scale, a validated instrument to assess attitudes towards COVID-19 vaccination. From the responses, we constructed hesitancy (VAX) scores, with higher scores implying negative attitudes towards vaccination. We used generalized linear models to identify factors associated with vaccine hesitancy.\n\nResultsA total of 490 PWH were enrolled (71.4% female, median age 38 years, median CD4 count 412 cells/mm3, 83.9% virologically suppressed). About 17.3% had received at least one dose of a COVID-19 vaccine. The mean VAX score was 43.14 {+/-} 7.05, corresponding to 59.9% participants classified as vaccine hesitant. Preference for natural immunity (65.8%) and concerns about commercial profiteering (64.4%) were the commonest reasons for hesitancy, followed by mistrust of vaccine benefits (61.4%) and worries about future side effects (48.0%). In adjusted regression analysis, being Muslim ({beta} = 2.563, p < 0.001) and residence in urban areas ({beta} = 1.709, p = 0.010) were associated with greater vaccine hesitancy, while having tested ever for COVID-19 was associated with lesser vaccine hesitancy ({beta} = -3.417, p = 0.027).\n\nConclusionWe observed a low COVID-19 vaccine uptake and high hesitancy among PWH in Sierra Leone. Our findings underscore the need to address vaccine hesitancy as a critical element of efforts to boost COVID-19 vaccine uptake among this population in Sierra Leone.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Peterlyn E Cummings", - "author_inst": "University of Sierra Leone" - }, - { - "author_name": "Sulaiman Lakoh", - "author_inst": "University of Sierra Leone" - }, - { - "author_name": "Sahr A Yendewa", - "author_inst": "Ministry of Health and Sanitation, Sierra Leone" - }, - { - "author_name": "Samuel P E Massaquoi", - "author_inst": "Ministry of Health and Sanitation" - }, - { - "author_name": "Peter B James", - "author_inst": "Southern Cross University" - }, - { - "author_name": "Foday Sahr", - "author_inst": "University of Sierra Leone" - }, - { - "author_name": "Gibrilla F Deen", - "author_inst": "COMAHS: University of Sierra Leone College of Medicine and Allied Health Sciences" - }, - { - "author_name": "Pelema Gevao", - "author_inst": "University of Sierra Leone" - }, - { - "author_name": "George A Yendewa", - "author_inst": "Case Western Reserve University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.05.12.23289900", "rel_title": "Absolute and relative excess mortality across demographic and clinical subgroups during the COVID-19 pandemic: an individual-level cohort study from a nationwide healthcare system of US Veterans", @@ -107242,6 +109355,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.05.08.23289661", + "rel_title": "COVID-19 in meat plants: activation of a Target Prevention Plan, in Italy", + "rel_date": "2023-05-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.08.23289661", + "rel_abs": "During the COVID-19 pandemics, several outbreaks have been recorded all other the world in industrial slaughterhouses and meat processing plants. Occupational preventive medicine in such non-healthcare frontline essential services accounts for combined different environmental, social, and economic factors, to reduce the burden of COVID-19 in the workplaces and in the connected residential settings. In Italy, during the first year of the pandemics, an advocacy action has been activated, targeted on meat plant managers and related food business operators. A risk-oriented control plan was agreed by competent Italian Health Authorities at Region/Province level. A questionnaire focused on the inventoried risk factors reported in the literature in such working places have been developped as supporting tool, and administered on voluntary basis to the interested stakeholders. In addition, an outbreak questionnaire was proposed to the Prevention Depts of the Local Health Units. In the 2021 - 2022 years timeframe, we collected 333 advocacy and 24 outbreak questionnaires, respectively, on 4,765 inventoried plants at national level. Responses came mainly from those districts that locally activated the risk-oriented control plan. The lack of awareness to update the Risk Assessment Document of the meat plant for COVID-19, non instrumental body Temperature checks of workers at the entrance, working force from different subcontractors, poor hygiene in the shared places and insufficient ventilation represented the main critical points recorded. The cross-checks between the results from the advocacy and from the outbreak questionnaires are feeding an after-action review for such food-chain related essential work settings within a One Health approach.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Giorgio Di Leone", + "author_inst": "ASL Bari, Dipartimento di prevenzione, Servizio Prevenzione e Sicurezza degli Ambienti di Lavoro (SPESAL), Via Giorgio de Chirico, 7 - 70056 Molfetta - Italy" + }, + { + "author_name": "Luigi Bertinato", + "author_inst": "Istituto Superiore di Sanita', Segreteria Scientifica Del Presidente, Viale Regina Elena, 299 I-00161 Rome, Italy" + }, + { + "author_name": "Gianfranco Brambilla", + "author_inst": "Istituto Superiore di Sanita', Dipartimento Alimentazione, Nutrizione e Sanita' Pubblica Veterinaria, Viale Regina Elena, 299 I-00161 Rome, Italy" + }, + { + "author_name": "Valerio Manno", + "author_inst": "Istituto Superiore di Sanita', Servizio di Statistica, Viale Regina Elena, 299 I-00161 Rome, Italy" + }, + { + "author_name": "Flavio Napolano", + "author_inst": "ASL Bari, Dipartimento di prevenzione, Servizio Prevenzione e Sicurezza degli Ambienti di Lavoro (SPESAL), Via Giorgio de Chirico, 7 - 70056 Molfetta - Italy" + }, + { + "author_name": "Simona Savi", + "author_inst": "ATS Citta' metropolitana di Milano, Servizio Prevenzione e Sicurezza Ambienti di Lavoro (SPESAL), sede di Lodi, Piazza ospitale 10, I- 26900 Lodi, Italy" + }, + { + "author_name": "Gaetano Settimo", + "author_inst": "Istituto Superiore di Sanita', Dipartimento Ambiente e Salute, Viale Regina Elena, 299 I-00161 Rome, Italy" + }, + { + "author_name": "Domenico Lagravinese", + "author_inst": "ASL Bari, Dipartimento di prevenzione, Direzione, Lungomare Starita, 6, I-70100 Bari, Italy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2023.05.11.23289783", "rel_title": "SARS-CoV-2 introductions to the island of Ireland", @@ -107901,85 +110061,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2023.05.10.23289557", - "rel_title": "Healthcare resource utilisation and costs of hospitalisation and primary care among adults with COVID-19 in England: a population-based cohort study", - "rel_date": "2023-05-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.10.23289557", - "rel_abs": "ObjectivesTo quantify healthcare resource utilisation (HCRU) and costs to the National Health Service (NHS) associated with acute COVID-19 in adults in England.\n\nDesignPopulation-based retrospective cohort study, using Clinical Practice Research Datalink (CPRD) Aurum primary care electronic medical records linked when available to Hospital Episode Statistics (HES) secondary care administrative data.\n\nSettingPatients registered to primary care practices in England.\n\nPopulation1,706,368 adults with a positive SARS-CoV-2 PCR or antigen test from August 2020 to January 2022 were included; 13,105 within the hospitalised cohort indexed between August 2020 and March 2021, and 1,693,263 within the primary care cohort indexed between August 2020 and January 2022.\n\nMain outcome measuresPrimary and secondary care HCRU and associated costs during the acute phase of COVID-19 ([≤]4 weeks following positive test), stratified by age group, risk of severe COVID-19 and immunocompromised status.\n\nResultsAmong the hospitalised cohort, average total length of stay, as well as in critical care wards, was longer in older adults. Median healthcare cost per hospitalisation was higher in those aged 75 - 84 ({pound}8,942) and [greater double equals]85 years ({pound}8,835) than in those aged <50 years ({pound}7,703). Whilst few (6.0%) patients in critical care required mechanical ventilation, its use was higher in older adults (50 - 74 years: 8.3%; <50 years: 4.3%). HCRU and associated costs were often greater in those at higher risk of severe COVID-19 when compared to the overall cohort, although minimal differences in HCRU were found across the three different high-risk definitions implemented. Among the primary care cohort, GP or nurse consultations were more frequent among older adults and the immunocompromised.\n\nConclusionsCOVID-19 related hospitalisations in older adults, particularly critical care admissions, were the primary drivers of high resource use of COVID-19 in England. These findings may inform health policy decisions and resource allocation in the prevention and management of COVID-19.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Jingyan Yang", - "author_inst": "Pfizer Inc; Colombia University" - }, - { - "author_name": "Kathleen M Andersen", - "author_inst": "Pfizer Inc" - }, - { - "author_name": "Kiran K Rai", - "author_inst": "Adelphi Real World" - }, - { - "author_name": "Theo Tritton", - "author_inst": "Adelphi Real World" - }, - { - "author_name": "Tendai Mugwagwa", - "author_inst": "Pfizer Inc" - }, - { - "author_name": "Maya Reimbaeva", - "author_inst": "Pfizer Inc" - }, - { - "author_name": "Carmen Tsang", - "author_inst": "Pfizer Ltd" - }, - { - "author_name": "Leah McGrath", - "author_inst": "Pfizer Inc" - }, - { - "author_name": "Poppy Payne", - "author_inst": "Adelphi Real World" - }, - { - "author_name": "Bethany Emma Backhouse", - "author_inst": "Adelphi Real World" - }, - { - "author_name": "Diana Mendes", - "author_inst": "Pfizer Ltd" - }, - { - "author_name": "Rebecca Butfield", - "author_inst": "Pfizer Ltd" - }, - { - "author_name": "Kevin Naicker", - "author_inst": "Pfizer Ltd" - }, - { - "author_name": "Mary Araghi", - "author_inst": "Pfizer Ltd" - }, - { - "author_name": "Robert Wood", - "author_inst": "Adelphi Real World" - }, - { - "author_name": "Jennifer Nguyen", - "author_inst": "Pfizer Inc" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.05.08.23289517", "rel_title": "Persistent humoral immunity in children and adolescents throughout the COVID-19 pandemic (June 2020 to July 2022): a prospective school-based cohort study (Ciao Corona) in Switzerland", @@ -109080,6 +111161,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.05.08.23289653", + "rel_title": "A global meta-analysis of effects of green infrastructure on COVID-19 infection and mortality rates", + "rel_date": "2023-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.08.23289653", + "rel_abs": "Evidence of the benefits of greenspaces or greenness to human wellbeing in the context of COVID-19 is fragmented and sometimes contradictory. This calls for a meta-analysis of existing studies to clarify the matter. Here, we identified 621 studies across the world, which were then filtered down to 13 relevant studies covering Africa, Asia, Europe, and USA. These studies were meta-analysed, with the impacts of greenspaces on COVID-19 infection rate quantified using regression estimates whereas impacts on mortality was measured using mortality rate ratios. We found evidence of significant negative correlations between greenness and both COVID-19 infection and mortality rates. We further found that the impacts on COVID-19 infection and mortality are moderated by year of publication, greenness metrics, sample size, health and political covariates. This clarification has far-reaching implications on policy development towards the establishment and management of green infrastructure for the benefits of human wellbeing.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Bopaki Phogole Sr.", + "author_inst": "University of Johannesburg" + }, + { + "author_name": "Kowiyou Yessoufou", + "author_inst": "University of Johannesburg" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2023.05.06.23289604", "rel_title": "Association of Seizure with COVID-19 Vaccines in Persons with Epilepsy: A Systematic Review and Meta-analysis", @@ -109515,77 +111619,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2023.05.03.23289488", - "rel_title": "COVID-19 Infection Is Associated with Poor Outcomes in Patients with Intracerebral Hemorrhage", - "rel_date": "2023-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.03.23289488", - "rel_abs": "BackgroundPatients with ischemic stroke and concomitant coronavirus 2019 (COVID-19) infection have worse outcomes than those without this infection. However, research on the impact of COVID-19 infection on outcomes following hemorrhagic stroke remains limited. We aim to study whether concomitant COVID-19 infection leads to worse outcomes in spontaneous intracerebral hemorrhage (ICH).\n\nDesignWe conducted an observational study using data from Get With The Guidelines(R) Stroke, an ongoing, multi-center, nationwide quality assurance registry.\n\nMethodsWe implemented a two-stage design: first, we compared outcomes of ICH patients with and without COVID-19 infection admitted during the pandemic (from March 2020 to February 2021). Second, we compared the same outcomes between ICH patients admitted before (March 2019 to February 2020) and during (March 2020 and February 2021) the pandemic. Main outcomes were poor functional outcome (defined as a modified Rankin Scale of 4 to 6 [mRS] at discharge), mortality and discharge to skilled nursing facility (SNF) or hospice.\n\nResultsThe first stage included 60,091 COVID-19-negative and 1,326 COVID-19-positive ICH patients. In multivariable analyses, ICH patients with versus without COVID-19 infection had 68% higher odds of poor outcome (OR 1.68, 95%CI 1.41-2.01), 51% higher odds of mortality (OR 1.51, CI 1.33-1.71) and 66% higher odds of being discharged to a SNF/hospice (OR 1.66, 95%CI 1.43-1.93). The second stage included 62,743 pre-pandemic and 64,681 intra-pandemic ICH cases. In multivariable analyses, ICH patients admitted during versus before the COVID-19 pandemic had a 10% higher odds of poor outcome (OR 1.10, 95%CI 1.07-1.14), 5% higher mortality (OR 1.05, 95%CI 1.02-1.08) and no significant difference in the risk of being discharged to SNF/hospice (OR 0.93, 95%CI 0.90-0.95).\n\nConclusionsThe pathophysiology of the COVID-19 infection and changes in healthcare delivery during the pandemic played a role in worsening outcomes in this patient population. Further research is needed to identify these factors and understand their effect on the long-term outcome.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Daniela Brenda Renedo", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Audrey C. Leasure", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Rebecca Young", - "author_inst": "The Duke Clinical Research Institute" - }, - { - "author_name": "Cyprien Rivier", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Brooke Alhanti", - "author_inst": "DCRI" - }, - { - "author_name": "Brian Mac Grory", - "author_inst": "Duke University School of Medicine" - }, - { - "author_name": "Steven R. Mess\u00e9", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Mathew J Reeves", - "author_inst": "Michigan State University" - }, - { - "author_name": "Ameer E. Hassan", - "author_inst": "UTRGV" - }, - { - "author_name": "Lee H. Schwamm", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Adam de Havenon", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Charles Christian Matouk", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Kevin N Sheth", - "author_inst": "Yale University School of Medicine" - }, - { - "author_name": "Guido J. Falcone", - "author_inst": "Yale University School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2023.05.03.23289456", "rel_title": "The plasma metabolome of long COVID-19 patients two years after infection", @@ -110962,6 +112995,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2023.05.02.23289410", + "rel_title": "UDCA May Promote COVID-19 Recovery: A Cohort Study with AI-Aided Analysis", + "rel_date": "2023-05-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.02.23289410", + "rel_abs": "To investigate the impact of ursodeoxycholic acid (UDCA) treatment on the clinical outcome of mild and moderate COVID-19 cases, a retrospective analysis was conducted to evaluate the efficacy of UDCA on patients diagnosed with COVID-19 during the peak of the Omicron outbreak in China. This study presents promising results, demonstrating that UDCA significantly reduced the time to Body Temperature Recovery after admission and a higher daily dose seems to be associated with a better outcome without observed safety concerns. We also introduced VirtualBody, a physiologically plausible artificial neural network model, to generate an accurate depiction of the drug concentration-time curve individually, which represented the absorption, distribution, metabolism, and excretion of UDCA in each patient. It exhibits exceptional performance in modeling the complex PK-PD profile of UDCA, characterized by its endogenous and enterohepatic cycling properties, and further validates the effectiveness of UDCA as a treatment option from the drug exposure-response perspective. Our work highlights the potential of UDCA as a novel treatment option for periodic outbreaks of COVID-19 and introduces a new paradigm for PK-PD analysis in retrospective studies to provide evidence for optimal dosing strategies.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Yang Yu", + "author_inst": "Nanjing University" + }, + { + "author_name": "Guo Yu", + "author_inst": "China Pharmaceutical University" + }, + { + "author_name": "Lu-Yao Han", + "author_inst": "China Pharmaceutical University" + }, + { + "author_name": "Jian Li", + "author_inst": "Nanjing University" + }, + { + "author_name": "Zhi-Long Zhang", + "author_inst": "Nanjing University" + }, + { + "author_name": "Tian-Shuo Liu", + "author_inst": "Nanjing University" + }, + { + "author_name": "Ming-Feng Li", + "author_inst": "China Pharmaceutical University" + }, + { + "author_name": "De-Chuan Zhan", + "author_inst": "Nanjing University" + }, + { + "author_name": "Shao-Qiu Tang", + "author_inst": "Nanjing University" + }, + { + "author_name": "Zhi-Hua Zhou", + "author_inst": "Nanjing University" + }, + { + "author_name": "Guang-Ji Wang", + "author_inst": "China Pharmaceutical University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.05.02.539139", "rel_title": "Chronic alcohol consumption dysregulates innate immune response to SARS-CoV-2 in the lung", @@ -111493,81 +113585,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "addiction medicine" }, - { - "rel_doi": "10.1101/2023.05.01.23289163", - "rel_title": "COVID AMP: An Open Access Database of COVID-19 Response Policies", - "rel_date": "2023-05-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.05.01.23289163", - "rel_abs": "As the COVID-19 pandemic unfolded in the spring of 2020, governments around the world began to implement policies to mitigate and manage the outbreak. Significant research efforts were deployed to track and analyse these policies in real-time to better inform the response. While much of the policy analysis focused narrowly on social distancing measures designed to slow the spread of disease, here, we present a dataset focused on capturing the breadth of policy types implemented by jurisdictions globally across the whole-of-government. COVID Analysis and Mapping of Policies (COVID AMP) includes nearly 50,000 policy measures from 150 countries, 124 intermediate areas, and 235 local areas between January 2020 and June 2022. With up to 40 structured and unstructured characteristics encoded per policy, as well as the original source and policy text, this dataset provides a uniquely broad capture of the governance strategies for pandemic response, serving as a critical data source for future work in legal epidemiology and political science.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Rebecca Katz", - "author_inst": "Georgetown University" - }, - { - "author_name": "Kate Toole", - "author_inst": "Georgetown University" - }, - { - "author_name": "Hailey Robertson", - "author_inst": "Georgetown University" - }, - { - "author_name": "Alaina Case", - "author_inst": "Talus Analytics" - }, - { - "author_name": "Justin Kerr", - "author_inst": "Talus Analytics" - }, - { - "author_name": "Siobhan Robinson-Marshall", - "author_inst": "Georgetown University" - }, - { - "author_name": "Jordan Schermerhorn", - "author_inst": "Georgetown University" - }, - { - "author_name": "Sarah Orsborn", - "author_inst": "Talus Analytics" - }, - { - "author_name": "Michael Van Maele", - "author_inst": "Talus Analytics" - }, - { - "author_name": "Ryan Zimmerman", - "author_inst": "Georgetown University" - }, - { - "author_name": "Tess Stevens", - "author_inst": "Georgetown University" - }, - { - "author_name": "- COVID AMP Coding Team", - "author_inst": "" - }, - { - "author_name": "Alexandra Phelan", - "author_inst": "Georgetown University" - }, - { - "author_name": "Colin J. Carlson", - "author_inst": "Georgetown University" - }, - { - "author_name": "Ellie Graeden", - "author_inst": "Georgetown University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2023.05.02.23289398", "rel_title": "Did knowledge, attitudes, and practices matter during the second wave of COVID-19 pandemic in Bangladesh? Results from a web-based cross-sectional study", @@ -113356,6 +115373,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2023.04.27.23289199", + "rel_title": "Evaluation of the Pilot Wastewater Surveillance for SARS-CoV-2 in Norway, June 2022 - March 2023", + "rel_date": "2023-04-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.27.23289199", + "rel_abs": "BackgroundDuring the COVID-19 pandemic, wastewater-based surveillance gained great international interest as an additional tool to monitor SARS-CoV-2. In autumn 2021, the Norwegian Institute of Public Health decided to pilot a national wastewater surveillance (WS) system for SARS-CoV-2 and its variants between June 2022 and March 2023. We evaluated the system to assess if it met its objectives and its attribute-based performance.\n\nMethodsWe adapted the available guidelines for evaluation of surveillance systems. The evaluation was carried out as a descriptive analysis and consisted of the following three steps: (i) description of the WS system, (ii) identification of users and stakeholders, and (iii) analysis of the systems attributes and performance including sensitivity, specificity, timeliness, usefulness, representativeness, simplicity, flexibility, stability, and communication. Cross-correlation analysis was performed to assess the systems ability to provide early warning signal of new wave of infections.\n\nResultsThe pilot WS system was a national surveillance system using existing wastewater infrastructures from the largest Norwegian municipalities. We found that the system was sensitive, timely, useful, representative, simple, flexible, acceptable, and stable to follow the general trend of infection. Preliminary results indicate that the system could provide an early signal of changes in variant distribution. However, challenges may arise with: (i) specificity due to temporary fluctuations of RNA levels in wastewater, (ii) representativeness when downscaling, and (iii) flexibility and acceptability when upscaling the system due to limited resources and/or capacity.\n\nConclusionsOur results showed that the pilot WS system met most of its surveillance objectives. The system was able to provide an early warning signal of 1-2 weeks, and the system was useful to monitor infections at population level and complement routine surveillance when individual testing activity was low. However, temporary fluctuations of WS values need to be carefully interpreted. To improve quality and efficiency, we recommend to standardise and validate methods for assessing trends of new waves of infection and variants, evaluate the WS system using a longer operational period particularly for new variants, and conduct prevalence studies in the population to calibrate the system and improve data interpretation.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Ettore Amato", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Susanne Hyllestad", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Petter Heradstveit", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Petter Langlete", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Line Victoria Moen", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Andreas Rohringer", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Joao Pires", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Jose Antonio Baz Lomba", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Karoline Bragstad", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Siri Laura Feruglio", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Preben Aavitsland", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Elisabeth Henie Madslien", + "author_inst": "Norwegian Institute of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.04.26.23289095", "rel_title": "Inequalities in Healthcare Use during the COVID-19 Pandemic", @@ -114139,25 +116219,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.04.25.538336", - "rel_title": "Association between SARS-CoV-2 and metagenomic content of samples from the Huanan Seafood Market", - "rel_date": "2023-04-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.04.25.538336", - "rel_abs": "The role of the Huanan Seafood Market in the early SARS-CoV-2 outbreak remains unclear. Recently the Chinese CDC released data from deep sequencing of environmental samples collected from the market after it was closed on January-1-2020 (Liu et al. 2023a). Prior to this release, Crits-Christoph et al. (2023) analyzed data from a subset of the samples. Both studies concurred that the samples contained genetic material from a variety of species, including some like raccoon dogs that are susceptible to SARS-CoV-2. However, neither study systematically analyzed the relationship between the amount of genetic material from SARS-CoV-2 and different animal species. Here I implement a fully reproducible computational pipeline that jointly analyzes the number of reads mapping to SARS-CoV-2 and the mitochondrial genomes of chordate species across the full set of samples. I validate the presence of genetic material from numerous species, and calculate mammalian mitochondrial compositions similar to those reported by Crits-Christoph et al. (2023). However, the number of SARS-CoV-2 reads is not consistently correlated with reads mapping to non-human susceptible species. For instance, 14 samples have >20% of their chordate mitochondrial material from raccoon dogs, but only one of these samples contains any SARS-CoV-2 reads, and that sample only has 1 of[~] 200,000,000 reads mapping to SARS-CoV-2. Instead, SARS-CoV-2 reads are most correlated with reads mapping to various fish, such as catfish and largemouth bass. These results suggest that while metagenomic analysis of the environmental samples is useful for identifying animals or animal products sold at the market, co-mingling of animal and viral genetic material is unlikely to reliably indicate whether any animals were infected by SARS-CoV-2.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.04.26.23289142", "rel_title": "A systematic review of the prevalence of persistent gastrointestinal symptoms and incidence of new gastrointestinal illness after acute SARS-CoV-2 infection", @@ -115258,6 +117319,53 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2023.04.23.537985", + "rel_title": "Mechanism of the Covalent Inhibition of Human Transmembrane Protease Serine 2 as an Original Antiviral Strategy", + "rel_date": "2023-04-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.04.23.537985", + "rel_abs": "The Transmembrane Protease Serine 2 (TMPRSS2) is a human enzyme which is involved in the maturation and post-translation of different proteins. In addition of being overexpressed in cancer cells, TMPRSS2 plays a further fundamental role in favoring viral infections by allowing the fusion of the virus envelope and the cellular membrane, notably in SARS-CoV-2. In this contribution we resort to multiscale molecular modeling to unravel the structural and dynamical features of TMPRSS2 and its interaction with a model lipid bilayer. Furthermore, we shed light into the mechanism of action of a potential inhibitor (Nafamostat), determining the free-energy profile associated with the inhibition reaction, and showing the facile poisoning of the enzyme. Our study, while providing the first atomistically resolved mechanism of TMPRSS2 inhibition, is also fundamental in furnishing a solid framework for further rational design targeting transmembrane proteases in a host-directed antiviral strategy.\n\nTOC GRAPHICS\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=193 SRC=\"FIGDIR/small/537985v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (108K):\norg.highwire.dtl.DTLVardef@19dd8c9org.highwire.dtl.DTLVardef@394c0org.highwire.dtl.DTLVardef@11ad383org.highwire.dtl.DTLVardef@347a8c_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Angelo Spinello", + "author_inst": "Universita di Palermo" + }, + { + "author_name": "Emmanuelle Bignon", + "author_inst": "Universite de Lorraine" + }, + { + "author_name": "Tom Miclot", + "author_inst": "Universita di Palermo" + }, + { + "author_name": "Stephanie Grandemange", + "author_inst": "Universite de Lorraine" + }, + { + "author_name": "Alessio Terenzi", + "author_inst": "Universita di Palermo" + }, + { + "author_name": "Giampaolo Barone", + "author_inst": "Universita di Palermo" + }, + { + "author_name": "Florent Barbault", + "author_inst": "Universite Paris Cite" + }, + { + "author_name": "Antonio MONARI", + "author_inst": "Universite Paris Cite" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2023.04.24.23289025", "rel_title": "Researching COVID to enhance recovery (RECOVER) pregnancy study protocol: Rationale, objectives, and design", @@ -115933,77 +118041,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.04.20.537738", - "rel_title": "An in vitro experimental pipeline to characterize the binding specificity of SARS-CoV-2 neutralizing antibodies", - "rel_date": "2023-04-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.04.20.537738", - "rel_abs": "The coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has led to over 760 million cases and >6.8 million deaths worldwide. We developed a panel of human neutralizing monoclonal antibodies (mAbs) targeting the SARS-CoV-2 Spike protein using Harbour H2L2 transgenic mice immunized with Spike receptor binding domain (RBD) (1). Representative antibodies from genetically-distinct families were evaluated for inhibition of replication-competent VSV expressing SARS-CoV-2 Spike (rcVSV-S) in place of VSV-G. One mAb (denoted FG-10A3) inhibited infection of all rcVSV-S variants; its therapeutically-modified version, STI-9167, inhibited infection of all tested SARS-CoV-2 variants, including Omicron BA.1 and BA.2, and limited virus proliferation in vivo (1). To characterize the binding specificity and epitope of FG-10A3, we generated mAb-resistant rcVSV-S virions and performed structural analysis of the antibody/antigen complex using cryo-EM. FG-10A3/STI-9167 is a Class 1 antibody that prevents Spike-ACE2 binding by engaging a region within the Spike receptor binding motif (RBM). Sequencing of mAb-resistant rcVSV-S virions identified F486 as a critical residue for mAb neutralization, with structural analysis revealing that both the variable heavy and light chains of STI-9167 bound the disulfide-stabilized 470-490 loop at the Spike RBD tip. Interestingly, substitutions at position 486 were later observed in emerging variants of concern BA.2.75.2 and XBB. This work provides a predictive modeling strategy to define the neutralizing capacity and limitations of mAb therapeutics against emerging SARS-CoV-2 variants.\n\nImportanceThe COVID-19 pandemic remains a significant public health concern for the global population; development and characterization of therapeutics, especially ones that are broadly effective, will continue to be essential as SARS-CoV-2 variants emerge. Neutralizing monoclonal antibodies remain an effective therapeutic strategy to prevent virus infection and spread with the caveat that they interact with the circulating variants. The epitope and binding specificity of a broadly neutralizing anti-SARS-CoV-2 Spike RBD antibody clone against many SARS-CoV-2 VOC was characterized by generating antibody-resistant virions coupled with cryo-EM structural analysis. This workflow can serve to predict the efficacy of antibody therapeutics against emerging variants and inform the design of therapeutics and vaccines.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Kristina E Atanasoff", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Luca Brambilla", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Daniel Cole Adelsberg", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Shreyas S Kowdle", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Christian S Stevens", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Chuan-tien Hung", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Yanwen Fu", - "author_inst": "Sorrento, Inc" - }, - { - "author_name": "Reyna Lim", - "author_inst": "Sorrento, Inc" - }, - { - "author_name": "Linh Tran", - "author_inst": "Sorrento, Inc" - }, - { - "author_name": "Robert Allen", - "author_inst": "Sorrento, Inc" - }, - { - "author_name": "J Andrew Duty", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Goran Bajic", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Benhur Lee", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Domenico Tortorella", - "author_inst": "Icahn School of Medicine at Mount Sinai" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2023.04.18.23288060", "rel_title": "Evaluation of coronavirus decay in French coastal water and application to SARS-CoV-2 risk evaluation using Porcine Epidemic Diarrhea Virus as surrogate.", @@ -117712,6 +119749,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.04.18.537104", + "rel_title": "A single inactivating amino acid change in the SARS-CoV-2 NSP3 Mac1 domain attenuates viral replication and pathogenesis in vivo", + "rel_date": "2023-04-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.04.18.537104", + "rel_abs": "Despite unprecedented efforts, our therapeutic arsenal against SARS-CoV-2 remains limited. The conserved macrodomain 1 (Mac1) in NSP3 is an enzyme exhibiting ADP-ribosylhydrolase activity and a possible drug target. To determine the therapeutic potential of Mac1 inhibition, we generated recombinant viruses and replicons encoding a catalytically inactive NSP3 Mac1 domain by mutating a critical asparagine in the active site. While substitution to alanine (N40A) reduced catalytic activity by [~]10-fold, mutations to aspartic acid (N40D) reduced activity by [~]100-fold relative to wildtype. Importantly, the N40A mutation rendered Mac1 unstable in vitro and lowered expression levels in bacterial and mammalian cells. When incorporated into SARS-CoV-2 molecular clones, the N40D mutant only modestly affected viral fitness in immortalized cell lines, but reduced viral replication in human airway organoids by 10-fold. In mice, N40D replicated at >1000-fold lower levels compared to the wildtype virus while inducing a robust interferon response; all animals infected with the mutant virus survived infection and showed no signs of lung pathology. Our data validate the SARS-CoV-2 NSP3 Mac1 domain as a critical viral pathogenesis factor and a promising target to develop antivirals.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Taha Y Taha", + "author_inst": "Gladstone Institutes" + }, + { + "author_name": "Rahul K Suryawanshi", + "author_inst": "Gladstone Institutes, San Francisco, CA" + }, + { + "author_name": "Irene P Chen", + "author_inst": "Gladstone Institutes, San Francisco, CA; Department of Medicine, University of California, San Francisco, CA" + }, + { + "author_name": "Galen J Correy", + "author_inst": "University of California, San Francisco, CA" + }, + { + "author_name": "Patrick C O'Leary", + "author_inst": "University of California, San Francisco, CA" + }, + { + "author_name": "Manasi P Jogalekar", + "author_inst": "University of California, San Francisco, CA" + }, + { + "author_name": "Maria McCavitt-Malvido", + "author_inst": "Gladstone Institutes, San Francisco, CA" + }, + { + "author_name": "Morgan Diolaiti", + "author_inst": "University of California, San Francisco, CA" + }, + { + "author_name": "Gabriella R Kimmerly", + "author_inst": "Gladstone Institutes, San Francisco, CA" + }, + { + "author_name": "Chia-Lin Tsou", + "author_inst": "Gladstone Institutes, San Francisco, CA" + }, + { + "author_name": "Luis Martinez-Sobrido", + "author_inst": "Texas Biomedical Research Institute, San Antonio, TX" + }, + { + "author_name": "Nevan J Krogan", + "author_inst": "University of California, San Francisco, CA" + }, + { + "author_name": "Alan Ashworth", + "author_inst": "University of California, San Francisco, CA" + }, + { + "author_name": "James S Fraser", + "author_inst": "University of California, San Francisco, CA" + }, + { + "author_name": "Melanie Ott", + "author_inst": "Gladstone Institutes" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.04.17.536926", "rel_title": "Loss-of-function mutation in Omicron variants reduces spike protein expression and attenuates SARS-CoV-2 infection", @@ -118223,73 +120335,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2023.04.15.536998", - "rel_title": "Human airway ex vivo models: new tools to study the airway epithelial cell response to SARS-CoV-2 infection", - "rel_date": "2023-04-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.04.15.536998", - "rel_abs": "Airway-liquid interface cultures of primary epithelial cells and of induced pluripotent stem cell-derived airway epithelial cells (ALI and iALI, respectively) are physiologically relevant models for respiratory virus infection studies because they can mimic the in vivo human bronchial epithelium. Here, we investigated gene expression profiles in human airway cultures (ALI and iALI models) infected or not with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using publicly available and our own bulk and single-cell transcriptome datasets. SARS-CoV-2 infection significantly increased the expression of interferon-stimulated genes (IFI44, IFIT1, IFIT3, IFI35, IRF9, MX1, OAS1, OAS3 and ISG15) and inflammatory genes (NFKBIA, CSF1, FOSL1, IL32 and CXCL10) at day 4 post-infection, indicating activation of the interferon and immune responses to the virus. Extracellular matrix genes (ITGB6, ITGB1 and GJA1) also were altered in infected cells. Single-cell RNA sequencing data revealed that SARS-CoV-2 infection damaged the respiratory epithelium, particularly mature ciliated cells. The expression of genes encoding intercellular communication and adhesion proteins also was deregulated, suggesting a mechanism to promote shedding of infected epithelial cells. These data demonstrate that ALI/iALI models help to understand the airway epithelium response to SARS-CoV-2 infection and are a key tool for developing COVID-19 treatments.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Said Assou", - "author_inst": "UNIVERSITY OF MONTPELLIER" - }, - { - "author_name": "Engi Ahmed", - "author_inst": "CHU Montpellier" - }, - { - "author_name": "Lisa Morichon", - "author_inst": "CNRS" - }, - { - "author_name": "Amel Nasri", - "author_inst": "UNIVERSITY OF MONTPELLIER" - }, - { - "author_name": "Florent Foisset", - "author_inst": "UNIVERSITY OF MONTPELLIER" - }, - { - "author_name": "Carine Bourdais", - "author_inst": "UNIVERSITY OF MONTPELLIER" - }, - { - "author_name": "Nathalie Gros", - "author_inst": "CNRS" - }, - { - "author_name": "Sonia Wong", - "author_inst": "UNIVERSITY OF MONTPELLIER" - }, - { - "author_name": "Aurelie Fort Petit", - "author_inst": "CHU Montpellier" - }, - { - "author_name": "Isabelle Vachier", - "author_inst": "CHU Montpellier" - }, - { - "author_name": "Delphine Muriaux", - "author_inst": "CNRS" - }, - { - "author_name": "Arnaud Bourdin", - "author_inst": "UNIVERSITY OF MONTPELLIER" - }, - { - "author_name": "John De Vos", - "author_inst": "UNIVERSITY OF MONTPELLIER" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2023.04.14.533542", "rel_title": "SARS-CoV-2 occurrence in white-tailed deer throughout their range in the conterminous United States", @@ -119242,6 +121287,185 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2023.04.12.534029", + "rel_title": "Analysis of SARS-CoV-2 Recombinant Lineages XBC and XBC.1 in the Philippines and Evidence for Delta-Omicron Co-infection as a Potential Origin", + "rel_date": "2023-04-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.04.12.534029", + "rel_abs": "We report the sequencing and analysis of 60 XBC and 114 XBC.1 SARS-CoV-2 lineages detected in the Philippines from August to September 2022, which are regarded as recombinant lineages of the BA.2 Omicron and B.1.617.2 Delta (21I Clade) variants. The sequences described here place the Philippines as the country with the earliest and highest number of XBC and XBC.1 cases within the included period. Majority of the detected cases were sampled from the adjacent Davao and Soccskargen regions in southern Philippines, but have also been observed at lower proportions in other regions of the country. Time-scaled phylogenetic analysis with global samples from GISAID reaffirms the supposed root of XBC-like cases from the Philippines. Furthermore, the apparent clustering of some foreign cases separate from those collected in the country suggests several occurrences of cross-border transmissions resulting in the spread of XBC-like lineages within and among those countries. The consensus mutation profile shows regions harboring mutations specific to either the Omicron BA.2 or Delta B.1.617.2 lineages, supporting the recombinant nature of XBC. Finally, alternative allele fraction pattern and intrahost mutation analysis revealed that a relatively early case of XBC collected in March 2022 is likely to be an active co-infection event. This suggests that co-infection of Omicron and Delta was already occurring in the Philippines early in 2022, facilitating the generation of recombinants that may have further evolved and gained additional mutations enabling its spread across certain local populations at a later time.\n\nAuthor summaryMore recently, various lineages of the SARS-CoV-2 virus, the causative agent COVID-19 pandemic, have been observed to form recombinant lineages, further expanding the ways by which the virus can evolve and adapt to human interventions. Therefore, a large part of biosurveillance efforts is dedicated to detecting and observing new lineages, including recombinants, for early and effective control. In this paper, we present an analysis of 174 XBC and XBC.1 cases detected in the Philippines between August and September of 2022 which contextualize these cases as some of the earliest reported cases of this hybrid lineage. We show that when compared to cases from other countries collected at a similar time, the earliest cases of the XBC lineage are from the Philippines. Additionally, when samples were reclassified following an update of Pangolin, a tool for assigning SARS-CoV-2 lineages to samples, we found two samples of interest reclassified as XBC pointing to a potential origin via co-infection events occurring as early as March of 2022.", + "rel_num_authors": 41, + "rel_authors": [ + { + "author_name": "Elcid Aaron R. Pangilinan", + "author_inst": "Core Facility for Bioinformatics, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "John Michael C. Egana", + "author_inst": "Core Facility for Bioinformatics, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Renato Jacinto Q. Mantaring", + "author_inst": "Core Facility for Bioinformatics, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Alyssa Joyce E. Telles", + "author_inst": "Core Facility for Bioinformatics, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Francis A. Tablizo", + "author_inst": "Core Facility for Bioinformatics, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Carlo M. Lapid", + "author_inst": "Core Facility for Bioinformatics, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Maria Sofia L. Yangzon", + "author_inst": "Core Facility for Bioinformatics, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Joshua Jose S. Endozo", + "author_inst": "Core Facility for Bioinformatics, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Karol Sophia Agape R. Padilla", + "author_inst": "Science Education Institute, Department of Science and Technology; DNA Sequencing Core Facility, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Jarvin E. Nipales", + "author_inst": "DNA Sequencing Core Facility, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Lindsay Clare D.L. Carandang", + "author_inst": "DNA Sequencing Core Facility, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Zipporah Mariebelle R. Enriquez", + "author_inst": "DNA Sequencing Core Facility, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Tricia Anne U. Barot", + "author_inst": "DNA Sequencing Core Facility, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Romano A. Manlimos", + "author_inst": "DNA Sequencing Core Facility, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Kelly Nicole P. Mangonon", + "author_inst": "DNA Sequencing Core Facility, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Ma. Exanil L. Plantig", + "author_inst": "DNA Sequencing Core Facility, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Shiela Mae M. Araiza", + "author_inst": "DNA Sequencing Core Facility, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Jo-Hannah S. Llames", + "author_inst": "DNA Sequencing Core Facility, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Kris P. Punayan", + "author_inst": "DNA Sequencing Core Facility, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Rachelle P. Serrano", + "author_inst": "Clinical Multi-Omics Laboratory, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Anne M. Drueco", + "author_inst": "Clinical Multi-Omics Laboratory, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Honeylett T. Lagnas", + "author_inst": "Clinical Multi-Omics Laboratory, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Philip A. Bistayan", + "author_inst": "Clinical Multi-Omics Laboratory, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Aristio C. Aguilar", + "author_inst": "Clinical Multi-Omics Laboratory, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Joie G. Charisse Apo", + "author_inst": "Clinical Multi-Omics Laboratory, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Yvonne Valerie D. Austria", + "author_inst": "Clinical Multi-Omics Laboratory, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Ni\u00f1a Francesca M. Bustamante", + "author_inst": "Clinical Multi-Omics Laboratory, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Alyssa Jamila R. Caelian", + "author_inst": "Clinical Multi-Omics Laboratory, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Rudy E. Fernandez", + "author_inst": "Clinical Multi-Omics Laboratory, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Xerxanne A. Galilea", + "author_inst": "Clinical Multi-Omics Laboratory, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Marielle M. Gamboa", + "author_inst": "Clinical Multi-Omics Laboratory, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Clarence Jane A. Gervacio", + "author_inst": "Clinical Multi-Omics Laboratory, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Zyrel V. Mollejon", + "author_inst": "Clinical Multi-Omics Laboratory, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Joshua Paul N. Pineda", + "author_inst": "Clinical Multi-Omics Laboratory, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Kristel B. Rico", + "author_inst": "Clinical Multi-Omics Laboratory, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Jan Michael C. Yap", + "author_inst": "Core Facility for Bioinformatics, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Ma. Celeste S. Abad", + "author_inst": "DNA Sequencing Core Facility, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Benedict A. Maralit", + "author_inst": "DNA Sequencing Core Facility, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Marc Edsel C. Ayes", + "author_inst": "Clinical Multi-Omics Laboratory, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Eva Maria Cutiongco-de la Paz", + "author_inst": "Health Research Program, Philippine Genome Center, University of the Philippines System" + }, + { + "author_name": "Cynthia P. Saloma", + "author_inst": "Philippine Genome Center, University of the Philippines System" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genetics" + }, { "rel_doi": "10.1101/2023.04.11.536467", "rel_title": "An Azapeptide Platform in Conjunction with Covalent Warheads to Uncover High-Potency Inhibitors for SARS-CoV-2 Main Protease", @@ -119744,61 +121968,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.04.05.23288177", - "rel_title": "The Impact Of COVID-19 on Health Financing in Kenya", - "rel_date": "2023-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.05.23288177", - "rel_abs": "BackgroundSudden shocks to health systems, such as the COVID-19 pandemic may disrupt health system functions. Health system functions may also influence the health systems ability to deliver in the face of sudden shocks such as the COVID-19 pandemic. We examined the impact of COVID-19 on the health financing function in Kenya, and how specific health financing arrangements influenced the health systems capacity to deliver services during the COVID-19 pandemic.\n\nMethodsWe conducted a cross-sectional study in three purposively selected counties in Kenya using a qualitative approach. We collected data using in-depth interviews (n = 56) and relevant document reviews. We interviewed national level health financing stakeholders, county department of health managers, health facility managers and COVID-19 healthcare workers. We analysed data using a framework approach.\n\nResultsPurchasing arrangements: COVID-19 services were partially subsidized by the national government, exposing individuals to out-of-pocket costs given the high costs of these services. The National Health Insurance Fund (NHIF) adapted its enhanced schemes benefit package targeting formal sector groups to include COVID-19 services but did not make any adaptations to its general scheme targeting the less well-off in society. This had potential equity implications. Public Finance Management (PFM) systems: Nationally, PFM processes were adaptable and partly flexible allowing shorter timelines for budget and procurement processes. At county level, PFM systems were partially flexible with some resource reallocation but maintained centralized purchasing arrangements. The flow of funds to counties and health facilities was delayed and the procurement processes were lengthy. Reproductive and child health services: Domestic and donor funds were reallocated towards the pandemic response resulting in postponement of program activities and affected family planning service delivery. Universal Health Coverage (UHC) plans: Prioritization of UHC related activities was negatively impacted due the shift of focus to the pandemic response. Contrarily the strategic investments in the health sector were found to be a beneficial approach in strengthening the health system.\n\nConclusionsStrengthening health systems to improve their resilience to cope with public health emergencies requires substantial investment of financial and non-financial resources. Health financing arrangements are integral in determining the extent of adaptability, flexibility, and responsiveness of health system to COVID-19 and future pandemics.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Angela Kairu", - "author_inst": "KEMRI-Wellcome Trust Research Programme Nairobi" - }, - { - "author_name": "Stacey Orangi", - "author_inst": "KEMRI-Wellcome Trust Research Programme Nairobi" - }, - { - "author_name": "Boniface Mbuthia", - "author_inst": "Thinkwell Kenya" - }, - { - "author_name": "Brian Arwah", - "author_inst": "KEMRI-Wellcome Trust Research Programme Nairobi" - }, - { - "author_name": "Fatuma Guleid", - "author_inst": "KEMRI-Wellcome Trust Research Programme Nairobi" - }, - { - "author_name": "Janet Keru", - "author_inst": "ThinkWell Kenya" - }, - { - "author_name": "Ileana Vilcu", - "author_inst": "ThinkWell Global" - }, - { - "author_name": "Anne Musuva", - "author_inst": "ThinkWell Kenya" - }, - { - "author_name": "Nirmala Ravishankar", - "author_inst": "ThinkWell Global" - }, - { - "author_name": "Edwine Barasa", - "author_inst": "KEMRI-Wellcome Trust Research Programme Nairobi" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2023.04.07.536037", "rel_title": "SARS-CoV-2's evolutionary capacity is mostly driven by host antiviral molecules", @@ -121195,6 +123364,141 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2023.04.04.535604", + "rel_title": "SARS-CoV-2 Spike Protein Accumulation in the Skull-Meninges-Brain Axis: Potential Implications for Long-Term Neurological Complications in post-COVID-19", + "rel_date": "2023-04-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.04.04.535604", + "rel_abs": "Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), has been associated mainly with a range of neurological symptoms, including brain fog and brain tissue loss, raising concerns about the viruss acute and potential chronic impact on the central nervous system. In this study, we utilized mouse models and human post-mortem tissues to investigate the presence and distribution of the SARS-CoV-2 spike protein in the skull-meninges-brain axis. Our results revealed the accumulation of the spike protein in the skull marrow, brain meninges, and brain parenchyma. The injection of the spike protein alone caused cell death in the brain, highlighting a direct effect on brain tissue. Furthermore, we observed the presence of spike protein in the skull of deceased long after their COVID-19 infection, suggesting that the spikes persistence may contribute to long-term neurological symptoms. The spike protein was associated with neutrophil-related pathways and dysregulation of the proteins involved in the PI3K-AKT as well as complement and coagulation pathway. Overall, our findings suggest that SARS-CoV-2 spike protein trafficking from CNS borders into the brain parenchyma and identified differentially regulated pathways may present insights into mechanisms underlying immediate and long-term consequences of SARS-CoV-2 and present diagnostic and therapeutic opportunities.\n\nGraphical Summary\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC=\"FIGDIR/small/535604v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (32K):\norg.highwire.dtl.DTLVardef@b223eforg.highwire.dtl.DTLVardef@15539e9org.highwire.dtl.DTLVardef@4d17a9org.highwire.dtl.DTLVardef@14c63af_HPS_FORMAT_FIGEXP M_FIG C_FIG Short SummaryThe accumulation of SARS-CoV-2 spike protein in the skull-meninges-brain axis presents potential molecular mechanisms and therapeutic targets for neurological complications in long-COVID-19 patients.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Zhouyi Rong", + "author_inst": "Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center Munich, Neuherberg, Germany." + }, + { + "author_name": "Hongcheng Mai", + "author_inst": "Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center Munich, Neuherberg, Germany." + }, + { + "author_name": "Saketh Kapoor", + "author_inst": "Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center Munich, Neuherberg, Germany." + }, + { + "author_name": "Victor Puelles", + "author_inst": "III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany." + }, + { + "author_name": "Jan Czogalla", + "author_inst": "III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany." + }, + { + "author_name": "Julia Schaedler", + "author_inst": "Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany." + }, + { + "author_name": "Jessica Vering", + "author_inst": "Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany." + }, + { + "author_name": "Claire Delbridge", + "author_inst": "Institute of Pathology, Division of Neuropathology, School of Medicine, Technical University Munich, Munich, Germany." + }, + { + "author_name": "Hanno Steinke", + "author_inst": "Institute of Anatomy, University of Leipzig, Leipzig, Germany." + }, + { + "author_name": "Hannah Frenzel", + "author_inst": "Institute of Anatomy, University of Leipzig, Leipzig, Germany." + }, + { + "author_name": "Katja Schmidt", + "author_inst": "Institute of Anatomy, University of Leipzig, Leipzig, Germany." + }, + { + "author_name": "Oezuem Sehnaz Caliskan", + "author_inst": "Institute for Diabetes and Obesity, Helmholtz Center Munich, Neuherberg, Germany." + }, + { + "author_name": "Jochen Martin Wettengel", + "author_inst": "Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany." + }, + { + "author_name": "Fatma Cherif", + "author_inst": "German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany." + }, + { + "author_name": "Mayar Ali", + "author_inst": "Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center Munich, Neuherberg, Germany." + }, + { + "author_name": "Zeynep Ilgin Kolabas", + "author_inst": "Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center Munich, Neuherberg, Germany." + }, + { + "author_name": "Selin Ulukaya", + "author_inst": "Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center Munich, Neuherberg, Germany." + }, + { + "author_name": "Izabela Horvath", + "author_inst": "Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center Munich, Neuherberg, Germany." + }, + { + "author_name": "Shan Zhao", + "author_inst": "Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center Munich, Neuherberg, Germany." + }, + { + "author_name": "Natalie Krahmer", + "author_inst": "Institute for Diabetes and Obesity, Helmholtz Center Munich, Neuherberg, Germany." + }, + { + "author_name": "Sabina Tahirovic", + "author_inst": "German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany." + }, + { + "author_name": "Ali Oender Yildirim", + "author_inst": "Institute of Lung Health and Immunity (LHI), Comprehensive Pneumology Center (CPC), Helmholtz Munich, Member of the German Center for Lung Research (DZL), Munic" + }, + { + "author_name": "Tobias Huber", + "author_inst": "III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany." + }, + { + "author_name": "Benjamin Ondruschka", + "author_inst": "III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany." + }, + { + "author_name": "Ingo Bechmann", + "author_inst": "Institute of Anatomy, University of Leipzig, Leipzig, Germany." + }, + { + "author_name": "Gregor Ebert", + "author_inst": "Institute of Virology, Technical University of Munich/Helmholtz Center Munich, Munich, Germany." + }, + { + "author_name": "Ulrike Protzer", + "author_inst": "Institute of Virology, School of Medicine, Technical University of Munich, Munich, Germany." + }, + { + "author_name": "Harsharan Singh Bhatia", + "author_inst": "Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center Munich, Neuherberg, Germany." + }, + { + "author_name": "Farida Hellal", + "author_inst": "Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center Munich, Neuherberg, Germany." + }, + { + "author_name": "Ali Erturk", + "author_inst": "Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Center Munich, Neuherberg, Germany." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "neuroscience" + }, { "rel_doi": "10.1101/2023.04.05.531513", "rel_title": "The purinergic receptor P2X7 and the NLRP3 inflammasome are druggable host factors required for SARS-CoV-2 infection", @@ -121694,89 +123998,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.04.03.23287649", - "rel_title": "Early Treatment with Hydroxychloroquine and Azithromycin: A Real-Life Monocentric Retrospective Cohort Study of 30,423 COVID-19 Patients", - "rel_date": "2023-04-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.04.03.23287649", - "rel_abs": "The authors have withdrawn this manuscript because analytic strategies for this project have changed. Therefore, the authors do not wish this work to be cited as reference for the project.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Matthieu Million", - "author_inst": "Aix Marseille University IHU Mediterranee Infection" - }, - { - "author_name": "Sebastien Cortaredona", - "author_inst": "Aix Marseille University IHU Mediterranee Infection IRD" - }, - { - "author_name": "Lea Delorme", - "author_inst": "Assistance Publique-Hopitaux de Marseille- IHU Mediterranee Infection-" - }, - { - "author_name": "Philippe Colson", - "author_inst": "Aix-Marseille university" - }, - { - "author_name": "Anthony LEVASSEUR", - "author_inst": "Aix-Marseille University" - }, - { - "author_name": "Herve Tissot-Dupont", - "author_inst": "Assistance publique Hopitaux de Marseille - IHU Mediterranee Infection" - }, - { - "author_name": "Karim bendamardji", - "author_inst": "Assistance Publique Hopitaux de Marseille - IHU Mediterranee Infection" - }, - { - "author_name": "Salima Lahouel", - "author_inst": "Assistance Publique Hopitaux de Marseille - IHU Mediterranee Infection" - }, - { - "author_name": "Bernard LA SCOLA", - "author_inst": "Aix Marseille University" - }, - { - "author_name": "Laurence Camoin", - "author_inst": "Aix Marseille University" - }, - { - "author_name": "Florence Fenollar", - "author_inst": "University Aix-Marseille" - }, - { - "author_name": "Philippe Gautret", - "author_inst": "Assistance Publique Hopitaux de Marseille - IHU Mediterranee Infection" - }, - { - "author_name": "Philippe Parola", - "author_inst": "Aix Marseille University - IHU Mediterranee Infection" - }, - { - "author_name": "Jean-Christophe Lagier", - "author_inst": "Aix Marseille University - IHU Mediterranee Infection" - }, - { - "author_name": "Stephanie Gentile", - "author_inst": "Aix Marseille Universite - Assistance des Hopitaux de Marseille" - }, - { - "author_name": "Philippe BROUQUI", - "author_inst": "Aix Marseille Universite -IHU Mediterranee Infection" - }, - { - "author_name": "Didier Raoult", - "author_inst": "Aix Marseille Universite IHU Mediterranee Infection" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.04.03.23287902", "rel_title": "Para-infectious brain injury in COVID-19 persists at follow-up despite attenuated cytokine and autoantibody responses", @@ -123025,6 +125246,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.03.31.535059", + "rel_title": "Determinants of species-specific utilization of ACE2 by human and animal coronaviruses", + "rel_date": "2023-03-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.31.535059", + "rel_abs": "Utilization of human ACE2 allowed several bat coronaviruses (CoVs), including the causative agent of COVID-19, to infect humans either directly or via intermediate hosts. Here, we analyzed the ability of Spike proteins from 24 human or animal CoVs to use ACE2 receptors across nine reservoir, potential intermediate and human hosts. We show that overall SARS-CoV-2 Omicron variants evolved more efficient ACE2 usage but mutation of R493Q in BA.5 Spike disrupts utilization of ACE2 from Greater horseshoe bats. Spikes from most CoVs showed species-specific differences in ACE2 usage, partly due to variations in ACE2 residues 31, 41 or 354. Mutation of T403R allowed the RaTG13 bat CoV Spike to use all ACE2 orthologs analysed for viral entry. Sera from COVID-19 vaccinated individuals neutralized the Spike proteins of a range of bat Sarbecoviruses. Our results define determinants of ACE2 receptor usage of diverse CoVs and suggest that COVID-19 vaccination may protect against future zoonoses of SARS-CoV-related bat viruses.\n\nHighlightsO_LIMutation of R493Q in BA.5 Spike disrupts utilization of ACE2 from Greater horseshoe bats\nC_LIO_LIVariations in ACE2 residues 31, 41 or 354 affect utilization by coronavirus Spike proteins\nC_LIO_LIResidue R403 in the Spike protein of bat coronavirus allow broad and effective ACE2 usage\nC_LIO_LISera from COVID-19 vaccinated individuals neutralize Spike proteins of bat Sarbecoviruses\nC_LI", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Qingxing Wang", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany" + }, + { + "author_name": "Sabrina Noettger", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany" + }, + { + "author_name": "Qinya Xie", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany" + }, + { + "author_name": "Chiara Pastorio", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany" + }, + { + "author_name": "Alina Seidel", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany" + }, + { + "author_name": "Janis A. Mueller", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany" + }, + { + "author_name": "Christoph Jung", + "author_inst": "Institute of Electrochemistry, Ulm University, 89081 Ulm, Germany" + }, + { + "author_name": "Timo Jacob", + "author_inst": "Institute of Electrochemistry, Ulm University, 89081 Ulm, Germany" + }, + { + "author_name": "Konstantin M.J. Sparrer", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany" + }, + { + "author_name": "Fabian Zech", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany" + }, + { + "author_name": "Frank Kirchhoff", + "author_inst": "Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2023.03.31.535057", "rel_title": "miRNA binding pressure channels evolution of SARS-CoV-2 genomes", @@ -123572,65 +125852,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2023.03.29.23287924", - "rel_title": "Younger and Rural Children are More Likely to be Hospitalized for SARS-CoV-2 Infections.", - "rel_date": "2023-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.29.23287924", - "rel_abs": "PurposeTo identify characteristics of SARS-CoV-2 infection that are associated with hospitalization in children initially evaluated in a Pediatric Emergency Department (ED).\n\nMethodsWe identified cases of SARS-CoV-2 positive patients seen in the Arkansas Childrens Hospital (ACH) ED or hospitalized between May 27, 2020, and April 28, 2022 using ICD-10 codes within the Pediatric Hospital Information System (PHIS) Database. We compared infection waves for differences in patient characteristics, and used logistic regressions to examine which characteristics led to a higher chance of hospitalization.\n\nFindingsWe included 681 pre-Delta cases, 673 Delta cases, and 970 Omicron cases. Almost 17% of patients were admitted to the hospital. Compared to Omicron infected children, pre-Delta and Delta infected children were twice as likely to be hospitalized (OR=2.2 and 2.0, respectively; p<0.0001). Infants less than 1 year of age were >3 times as likely to be hospitalized than children ages 5-14 years regardless of wave (OR=3.42; 95%CI=2.36-4.94). Rural children were almost 3 times as likely than urban children to be hospitalized across all waves (OR=2.73; 95%CI=1.97-3.78). Finally, those with a complex condition had nearly a 15-fold increase in odds of admission (OR=14.6; 95%CI=10.6-20.0).\n\nConclusionsChildren diagnosed during the pre-Delta or Delta waves were more likely to be hospitalized than those diagnosed during the Omicron wave. Younger and rural patients were more likely to be hospitalized regardless of wave. We suspect lower vaccination rates and larger distances from medical care influenced higher hospitalization rates.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Rebecca Cantu", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Sara C Sanders", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Grace A Turner", - "author_inst": "Arkansas Children's Research Institute" - }, - { - "author_name": "Jessica Snowden", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Ashton K Ingold", - "author_inst": "Arkansas Children's Research Institute" - }, - { - "author_name": "Susanna L Hartzell", - "author_inst": "Arkansas Children's Research Institute" - }, - { - "author_name": "Suzanne House", - "author_inst": "Arkansas Children's Research Institute" - }, - { - "author_name": "Dana Frederick", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Uday K Chalwadi", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Eric R Siegel", - "author_inst": "University of Arkansas for Medical Sciences" - }, - { - "author_name": "Joshua L Kennedy", - "author_inst": "University of Arkansas for Medical Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.03.29.534838", "rel_title": "Improving mRNA vaccine safety and efficiency with cationized lipid nanoparticle formula", @@ -124690,6 +126911,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.03.28.23287759", + "rel_title": "Single-cell analysis of bronchoalveolar cells in inflammatory and fibrotic post-COVID lung disease", + "rel_date": "2023-03-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.28.23287759", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSBackgroundC_ST_ABSPersistent radiological lung abnormalities are evident in many survivors of acute coronavirus disease 2019 (COVID-19). Consolidation and ground glass opacities are interpreted to indicate subacute inflammation whereas reticulation is thought to reflect fibrosis. We sought to identify differences at molecular and cellular level, in the local immunopathology of post-COVID inflammation and fibrosis.\n\nMethodsWe compared single-cell transcriptomic profiles and T cell receptor (TCR) repertoires of bronchoalveolar cells obtained from convalescent individuals with each radiological pattern, targeting lung segments affected by the predominant abnormality.\n\nResultsSingle-cell transcriptomes of inflammatory and fibrotic post-COVID lung disease closely resembled each other across all cell types. However, CD4 central memory T cells and CD8 effector memory T cells were significantly more abundant in those with inflammatory radiology. Clustering of similar TCRs from multiple donors was a striking feature of both phenotypes, consistent with tissue localised antigen-specific immune responses. There was no enrichment for known SARS-CoV-2-reactive TCRs, raising the possibility of T cell-mediated immunopathology driven by failure in immune self-tolerance.\n\nConclusionsWe found no evidence that post-COVID radiographic inflammation and fibrosis are associated with differential immmunopathological pathways. Both show evidence of shared antigen-specific T cell responses, suggesting a role for therapies targeting T cells in limiting post-COVID lung damage.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Puja Mehta", + "author_inst": "UCL Respiratory, University College London, London, UK" + }, + { + "author_name": "Blanca Sanz-Magallon Duque de Estrada", + "author_inst": "Division of Infection and Immunity, University College London, London, UK" + }, + { + "author_name": "Emma K Denneny", + "author_inst": "UCL Respiratory, University College London, London, UK" + }, + { + "author_name": "Kane Foster", + "author_inst": "UCL Cancer Institute, University College London, London, UK" + }, + { + "author_name": "Carolin T Turner", + "author_inst": "Division of Infection and Immunity, University College London, London, UK" + }, + { + "author_name": "Andreas Mayer", + "author_inst": "Division of Infection and Immunity, University College London, London, UK" + }, + { + "author_name": "Martina Milighetti", + "author_inst": "Division of Infection and Immunity, University College London, London, UK" + }, + { + "author_name": "Manuela Plate", + "author_inst": "UCL Respiratory, University College London, London, UK" + }, + { + "author_name": "Kaylee B Worlock", + "author_inst": "UCL Respiratory, University College London, London, UK" + }, + { + "author_name": "Masahiro Yoshida", + "author_inst": "UCL Respiratory, University College London, London, UK" + }, + { + "author_name": "Jeremy S Brown", + "author_inst": "UCL Respiratory, University College London, London, UK" + }, + { + "author_name": "Marko Z Nikolic", + "author_inst": "UCL Respiratory, University College London, London, UK" + }, + { + "author_name": "Benjamin M Chain", + "author_inst": "Division of Infection and Immunity, University College London, London, UK" + }, + { + "author_name": "Mahdad Noursadeghi", + "author_inst": "Division of Infection and Immunity, University College London, London, UK" + }, + { + "author_name": "Rachel C Chambers", + "author_inst": "UCL Respiratory, University College London, London, UK" + }, + { + "author_name": "Joanna C Porter", + "author_inst": "UCL Respiratory, University College London, London, UK" + }, + { + "author_name": "Gillian S Tomlinson", + "author_inst": "Division of Infection and Immunity, University College London, London, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2023.03.29.23287906", "rel_title": "Impact of vaccinations, boosters and lockdowns on COVID-19 waves in French Polynesia", @@ -125017,61 +127321,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.03.22.23287571", - "rel_title": "Trends in STI testing, diagnoses, and use of online chlamydia self-sampling services among young people during the first year of the COVID-19 pandemic in England", - "rel_date": "2023-03-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.22.23287571", - "rel_abs": "PurposeMeasures to control COVID-19 reduced face-to-face appointments and walk-ins at sexual health services (SHSs). Remote access to SHSs through online self-sampling for STIs was increased. This analysis assesses how these changes affected service use and STI testing among young people in England.\n\nMethodsData on all chlamydia, gonorrhoea and syphilis tests from 2019-2020 amongst English-resident 15-24 year olds (hereafter referred to as young people) were obtained from national STI surveillance datasets. We calculated proportional differences in tests and diagnoses for each STI, by demographic characteristics including age and socioeconomic deprivation, between 2019 and 2020. Among those tested for chlamydia, we used binary logistic regression to determine crude and adjusted odds ratios (OR) between demographic characteristics and being tested for chlamydia by an online service.\n\nResultsCompared to 2019, there were declines in testing (30% for chlamydia, 26% for gonorrhoea, 36% for syphilis) and diagnoses (31% for chlamydia, 25% for gonorrhoea and 23% for syphilis) among young people in 2020. These reductions were greater amongst 15-19 year-olds (vs. 20-24 year-olds). Among young people tested for chlamydia, those living in the least deprived areas were more likely to be tested using an online self-sampling kit compared to those living in the most deprived areas (males; OR=1.24[1.22-1.26], females; OR=1.28[1.27-1.30]).\n\nConclusionThe first year of the COVID-19 pandemic in England saw declines in STI testing and diagnoses in young people and disparities in the use of online chlamydia self-sampling which risk widening existing health inequalities.\n\nImplications and contributionsThere was a decrease in STI testing of young people during the first year of the COVID-19 pandemic in England with larger reductions among teenagers. There was an increase in use of online STI self-sampling services but with inequalities in provision which risk widening existing inequalities in sexual health.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Tamilore Sonubi", - "author_inst": "UKHSA" - }, - { - "author_name": "Dahir Sheik-Mohamud", - "author_inst": "UKHSA" - }, - { - "author_name": "Natasha Ratna", - "author_inst": "UKHSA" - }, - { - "author_name": "James Bell", - "author_inst": "UKHSA" - }, - { - "author_name": "Alireza Talebi", - "author_inst": "UKHSA" - }, - { - "author_name": "Catherine Heather Mercer", - "author_inst": "UCL" - }, - { - "author_name": "Katy Sinka", - "author_inst": "UKHSA" - }, - { - "author_name": "Stephanie J Migchelsen", - "author_inst": "UKHSA" - }, - { - "author_name": "Kate Folkard", - "author_inst": "UKHSA" - }, - { - "author_name": "Hamish Mohammed", - "author_inst": "UKHSA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "sexual and reproductive health" - }, { "rel_doi": "10.1101/2023.03.25.23287718", "rel_title": "Sequential viral introductions and spread of BA.1 drove the Omicron wave across Pakistani provinces", @@ -126380,6 +128629,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.03.21.23287524", + "rel_title": "Employment outcomes of people with Long Covid symptoms: community-based cohort study", + "rel_date": "2023-03-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.21.23287524", + "rel_abs": "BackgroundEvidence on the long-term employment consequences of SARS-CoV-2 infection is lacking. We used data from a large, community-based sample in the UK to estimate associations between Long Covid and subsequent employment outcomes.\n\nMethodsThis was an observational, longitudinal study using a pre-post design. We included survey participants from 3 February 2021 to 30 September 2022 when they were aged 16 to 64 years and not in full-time education. Using conditional logit modelling, we explored the time-varying relationship between Long Covid status [≥]12 weeks after a first test-confirmed SARS-CoV-2 infection (reference: pre-infection) and labour market inactivity (neither working nor looking for work) or workplace absence lasting [≥]4 weeks.\n\nResultsOf 206,299 included participants (mean age 45 years, 54% female, 92% white), 15% were ever inactive in the labour market and 10% were ever long-term absent during follow-up. Compared with pre-infection, inactivity was higher in participants reporting Long Covid 30 to <40 weeks (adjusted odds ratio (aOR): 1.45; 95% CI: 1.17 to 1.81) or 40 to <52 weeks (1.34; 1.05 to 1.72) post-infection. Combining with official statistics on Long Covid prevalence, our estimates translate to 27,000 (95% CI: 6,000 to 47,000) working-age adults in the UK being inactive because of Long Covid in July 2022.\n\nConclusionsLong Covid is likely to have contributed to reduced levels of participation in the UK labour market, though it is unlikely to be the sole driver. Further research is required to quantify the contribution of other factors, such as indirect health effects of the pandemic.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Daniel Ayoubkhani", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Francesco Zaccardi", + "author_inst": "University of Leicester" + }, + { + "author_name": "Koen B Pouwels", + "author_inst": "University of Oxford" + }, + { + "author_name": "Ann Sarah Walker", + "author_inst": "University of Oxford" + }, + { + "author_name": "Donald Houston", + "author_inst": "University of Portsmouth" + }, + { + "author_name": "Nisreen A Alwan", + "author_inst": "University of Southampton" + }, + { + "author_name": "Josh Martin", + "author_inst": "Bank of England" + }, + { + "author_name": "Kamlesh Khunti", + "author_inst": "University of Leicester" + }, + { + "author_name": "Vahe Nafilyan", + "author_inst": "Office for National Statistics" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.03.17.23287415", "rel_title": "Persons Diagnosed with COVID in England in the Clinical Practice Research Datalink (CPRD): A Cohort Description", @@ -126767,29 +129067,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.03.22.23287566", - "rel_title": "COVID-19 Genome Surveillance: A Geographical Landscape and Mutational Mapping of SARS-CoV-2 Variants in Central India over Two Years", - "rel_date": "2023-03-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.22.23287566", - "rel_abs": "Reading the viral genome through whole genome sequencing enables the detection of changes in the viral genome. The rapid changes in the SARS-CoV-2 viral genome may cause immune escape leading to an increase in the pathogenicity or infectivity. Monitoring mutations through genomic surveillance helps understand the amino acid changes resulting from the mutation. These amino acid changes, especially in the spike glycoprotein, may have implications on the pathogenicity of the virus by rendering it immune-escape. The region of Vidarbha in Maharashtra represents 31.6% of the total area and 21.3% of the total population of the state. In total, 7457 SARS-CoV-2 positive samples belonging to 16 Indian States were included in the study, out of which 3002 samples passed the sequencing quality control criteria. The metadata of 7457 SARS-CoV-2 positive samples included in the study was sourced from the Integrated Health Information Platform. The metadata of 3002 sequenced samples, including the FASTA sequence, was submitted to the Global initiative on sharing Avian Influenza Data and the Indian biological data centre. This study identified 104 different SARS-CoV-2 pango-lineages classified into 19 clades. We have also analysed the mutation profiles of the variants found in the study, which showed eight mutations of interest, including L18F, K417N, K417T, L452R, S477N, N501Y, P681H, P681R, and mutation of concern E484K in the spike glycoprotein region. The study was from November 2020 to December 2022, making this study the most comprehensive genomic surveillance of SARS-CoV-2 conducted for the region.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Krishna Khairnar", - "author_inst": "Council of Scientific and Industrial Research-National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur, India." - }, - { - "author_name": "Siddharth Singh Tomar", - "author_inst": "Council of Scientific and Industrial Research-National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur, India." - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.03.22.533805", "rel_title": "Evolving antibody evasion and receptor affinity of the Omicron BA.2.75 sublineage of SARS-CoV-2", @@ -127942,6 +130219,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.03.20.23287479", + "rel_title": "Childhood Adversity and COVID-19 Outcomes: Findings from the UK Biobank", + "rel_date": "2023-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.20.23287479", + "rel_abs": "ObjectivesTo investigate the association between childhood adversity and COVID-19-related hospitalization and COVID-19-related mortality in the UK Biobank.\n\nDesignCohort study.\n\nSettingUnited Kingdom.\n\nParticipants151,200 participants in the UK Biobank cohort who had completed the Childhood Trauma Screen, were alive at the start of the COVID-19 pandemic (01-10-2021), and were still active in the UK Biobank when hospitalization and mortality data were most recently updated (11-2021).\n\nMain outcome measuresCOVID-19-related hospitalization and COVID-19-related mortality.\n\nResultsHigher self-reports of childhood adversity were related to greater likelihood of COVID-19-related hospitalization in all statistical models. In models adjusted for age, ethnicity, and sex, childhood adversity was associated with an OR of 1.227 of hospitalization (95% CI=1.153 to 1.306, Childhood Adversity z=6.49, p<0.005) and an OR of 1.25 of a COVID-19 related death (95% CI=1.11 to 1.424, Childhood Adversity z=3.5, p<0.005). Adjustment for potential confounds attenuated these associations, although associations remained statistically significant.\n\nConclusionsChildhood adversity was significantly associated with COVID-19-related hospitalization and COVID-19-related mortality after adjusting for sociodemographic and health confounders. Further research is needed to clarify the biological and psychosocial processes underlying these associations to inform public health intervention and prevention strategies to minimize COVID-19 disparities.\n\nTrial registrationWork Completed under UK Biobank Project ID 92699 (\"Associations between COVID-19 Symptoms & Stressful Life Experiences\").\n\nSummary PromptsO_ST_ABSWhat is already known on this topicC_ST_ABSO_LIDisparities in COVID-19 outcomes are driven by numerous health and sociodemographic risk factors\nC_LIO_LIChildhood adversity is associated with lifelong physical health disparities and early mortality\nC_LIO_LINo known studies to date have examined the association between childhood adversity and COVID-19 mortality and morbidity\nC_LI\n\nWhat the study addsO_LIIn the UK Biobank, childhood adversity was significantly associated with COVID-19-related hospitalization and COVID-19-related mortality.\nC_LIO_LIFor both morbidity and mortality, these links were seen in statistical models adjusted for important sociodemographic and physical health confounders.\nC_LI\n\nHow this study might affect research, practice or policyO_LIModifiable and more proximal psychosocial factors may impact adult health outcomes, including COVID-19-related mortality and hospitalization\nC_LIO_LIAdversity may relate to depression, self-concept, or self-regulation, cascading from childhood experiences to the outcomes that we investigated here.\nC_LIO_LIPinpointing these processes may allow for policy and interventions to lessen the negative impact of COVID-19 in those that have suffered childhood adversity.\nC_LI", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jamie L Hanson", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Kristen A O'Connor", + "author_inst": "Saint Vincent College" + }, + { + "author_name": "Dorthea J Adkins", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Isabella Kahhale", + "author_inst": "University of Pittsburgh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.03.13.23287177", "rel_title": "New Approach to the SIR Inversion Problem: From the 1905-1906 Plague Outbreak in the Isle of Bombay to the 2021-2022 Omicron Surges in New York City and Los Angeles County", @@ -128788,41 +131096,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.03.17.23287413", - "rel_title": "Trends in Pediatric Firearm-Related Encounters during the COVID-19 Pandemic by Age Group, Race/Ethnicity, and Schooling Mode in Tennessee", - "rel_date": "2023-03-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.17.23287413", - "rel_abs": "PurposeIncreases in pediatric firearm-related injuries during the COVID-19 pandemic may be due to changes in where children and adolescents spent their time. This paper examines changes in the frequency of pediatric firearm-related encounters as a function of schooling mode overall and by race/ethnicity and age group at a large trauma center through 2021.\n\nMethodsWe use data from a large pediatric and adult trauma center in Tennessee from January 2018 to December 2021 (N=211 encounters) and geographically linked schooling mode data. We use Poisson regressions to estimate smoothed monthly pediatric firearm-related encounters as a function of schooling mode overall and stratified by race and age.\n\nResultsCompared to pre-pandemic, we find a 42% increase in pediatric encounters per month during March 2020 to August 2020, when schools were closed, and a 23% increase in encounters after schools returned to in-person instruction. Effects of schooling mode are heterogeneous by race. Encounters increased among non-Hispanic Black children and adolescents across all periods relative to pre-pandemic. Among non-Hispanic white children and adolescents, encounters increased during the closure period and decreased on return to in-person instruction. Effects of schooling mode are also heterogeneous by age. Relative to pre-pandemic, pediatric firearm-related encounters increased 205% for children aged 5 to 11 and 69% for adolescents aged 12 to 15 during the school closure period.\n\nConclusionCOVID-19-related changes to school instruction mode in 2020 and 2021 are associated with changes in the frequency and composition of pediatric firearm-related encounters at a major trauma center in Tennessee.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Tara McKay", - "author_inst": "Vanderbilt University" - }, - { - "author_name": "Kelsey Gastineau", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Jesse O. Wrenn", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Jin H. Han", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Alan B. Storrow", - "author_inst": "Vanderbilt University Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2023.03.15.23287287", "rel_title": "Effect of Andrographis paniculata treatment for patients with early-stage COVID-19 on the prevention of pneumonia: A retrospective cohort study", @@ -130143,6 +132416,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.03.11.23287148", + "rel_title": "Increased vaccine sensitivity of an emerging SARS-CoV-2 variant", + "rel_date": "2023-03-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.11.23287148", + "rel_abs": "Host immune responses are a key source of selective pressure driving pathogen evolution. Emergence of many SARS-CoV-2 lineages has been associated with improvements in their ability to evade population immunity resulting from both vaccination and infection. Here we show diverging trends of escape from vaccine-derived and infection-derived immunity for the emerging XBB/XBB.1.5 Omicron lineage. Among 31,739 patients tested in ambulatory settings in Southern California from December, 2022 to February, 2023, adjusted odds of prior receipt of 2, 3, 4, and [≥]5 COVID-19 vaccine doses were 10% (95% confidence interval: 1-18%), 11% (3-19%), 13% (3-21%), and 25% (15-34%) lower, respectively, among cases infected with XBB/XBB.1.5 than among cases infected with other co-circulating lineages. Similarly, prior vaccination was associated with greater protection against progression to hospitalization among cases with XBB/XBB.1.5 than among non-XBB/XBB.1.5 cases (70% [30-87%] and 48% [7-71%], respectively, for recipients of [≥]4 doses). In contrast, cases infected with XBB/XBB.1.5 had 17% (11-24%) and 40% (19-65%) higher adjusted odds of having experienced 1 and [≥]2 prior documented infections, respectively, including with pre-Omicron variants. As immunity acquired from SARS-CoV-2 infection becomes increasingly widespread, fitness costs associated with enhanced vaccine sensitivity in XBB/XBB.1.5 may be offset by increased ability to evade infection-derived host responses.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Joseph A Lewnard", + "author_inst": "University of California Berkeley" + }, + { + "author_name": "Vennis Hong", + "author_inst": "Kaiser Permanente Southern California" + }, + { + "author_name": "Jeniffer S Kim", + "author_inst": "Kaiser Permanente Southern California" + }, + { + "author_name": "Sally F Shaw", + "author_inst": "Kaiser Permanente Southern California" + }, + { + "author_name": "Bruno Lewin", + "author_inst": "Kaiser Permanente Southern California" + }, + { + "author_name": "Harpreet Takhar", + "author_inst": "Kaiser Permanente Southern California" + }, + { + "author_name": "Marc Lipsitch", + "author_inst": "US Centers for Disease Control & Prevention" + }, + { + "author_name": "Sara Y Tartof", + "author_inst": "Kaiser Permanente Southern California" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.03.11.23287141", "rel_title": "Predicting COVID-19 pandemic waves with biologically and behaviorally informed universal differential equations", @@ -130694,57 +133014,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2023.03.15.23287298", - "rel_title": "Post-COVID-19 syndrome and related dysautonomia affect patients life and work productivity", - "rel_date": "2023-03-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.15.23287298", - "rel_abs": "BackgroundA significant percentage of COVID-19 patients experience post-COVID-19 symptoms and signs. Post-COVID-19 syndrome affects physical and mental health of patients in several ways.\n\nAimTo investigate the impact of post-COVID-19 syndrome and related dysautonomia on patients life and work productivity.\n\nMethodsWe conducted a cross-sectional study in Greece using an online questionnaire. Study population included 108 workers over 18 years old that have been diagnosed with post-COVID-19 syndrome. Patients were recruited from the Long COVID Greece patients society. We measured demographic and clinical characteristics of patients, resilience, and social support.\n\nResultsAmong patients, 68.5% stated that post-COVID-19 syndrome affected their daily life to a great extent, 25% to a moderate level, and 6.5% to a small extent. Moreover, 56.5% stated that post-COVID-19 syndrome affected their work productivity to a great extent, 27.8% to a moderate level, and 15.7% to a small extent. Multivariable analysis identified that females and patients with post-COVID-19 dysautonomia had more problems in their daily life. Moreover, increased duration of COVID-19 symptoms was associated with increased daily problems. Increased resilience was related with fewer problems in daily life. Also, we found that patients with post-COVID-19 dysautonomia had less work productivity. Moreover, increased duration of COVID-19 symptoms was associated with more problems in work. Resilience was related with increased work productivity.\n\nConclusionsPost-COVID-19 syndrome and related dysautonomia affect significantly patients daily and work life. Also, resilience is an important preventive factor improving patients life. Policy makers should develop and implement educational programs to improve patients life. Healthcare professionals should be aware of the post-COVID-19 syndrome and its consequences in order to understand post-COVID-19 patients and their problems.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Petros A Galanis", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Aglaia Katsiroumpa", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Irene Vraka", - "author_inst": "P. & A. Kyriakou Children Hospital" - }, - { - "author_name": "Katerina Kosiara", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Olga Siskou", - "author_inst": "University of Piraeus" - }, - { - "author_name": "Olympia Konstantakopoulou", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Theodoros Katsoulas", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Parisis Gallos", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Daphne Kaitelidou", - "author_inst": "National and Kapodistrian University of Athens" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.03.15.23287285", "rel_title": "Modeling COVID-19 vaccination strategies in LMICs considering uncertainty in viral evolution and immunity", @@ -131781,6 +134050,29 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.03.13.532357", + "rel_title": "Inhibition of SARS-CoV-2 3CLpro in vitro by chemically modified tyrosinase from Agaricus bisporus", + "rel_date": "2023-03-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.03.13.532357", + "rel_abs": "Antiviral compounds are crucial to controlling the SARS-CoV-2 pandemic. Approved drugs have been tested for their efficacy against COVID-19, and new pharmaceuticals are being developed as a complementary tool to vaccines However, there are not any effective treatment against this disease yet. In this work, a cheap and fast purification method of natural tyrosinase from Agaricus bisporus fresh mushrooms was developed in order to evaluate the potential of this enzyme as a therapeutic protein by the inhibition of SARS-CoV-2 3CLpro protease activity in vitro. Tyrosinase showed a mild inhibition of 3CLpro of around 15%. Thus, different variants of this protein were synthesized through chemical modifications, covalently binding different tailor-made glycans and peptides to the amino terminal groups of the protein. These new tyrosinase conjugates were purified and characterized by circular dichroism and fluorescence spectroscopy analyses, and their stability under different conditions. Then all these tyrosinase conjugates were tested in 3CLpro protease inhibition. From them, the conjugate between tyrosinase and dextran-aspartic acid (6kDa) polymer showed the highest inhibition, with an IC50 of 2.5 g/ml and IC90 of 5 g/ml, results that highlight the potential use of modified tyrosinase as a therapeutic protein and opens the possibility of developing this and other enzymes as pharmaceutical drugs against diseases.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "David Aguilera", + "author_inst": "CSIC" + }, + { + "author_name": "Jose M. Palomo", + "author_inst": "Institute of Catalysis-CSIC" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2023.03.13.532385", "rel_title": "SARS-CoV-2 N-protein induces the formation of composite \u03b1-synuclein/N-protein fibrils that transform into a strain of \u03b1-synuclein fibrils", @@ -132244,53 +134536,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.03.09.23286797", - "rel_title": "Molecular pathology of acute respiratory distress syndrome, mechanical ventilation and abnormal coagulation in severe COVID-19", - "rel_date": "2023-03-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.09.23286797", - "rel_abs": "Systemic inflammation in critically ill patients can lead to serious consequences such as acute respiratory distress syndrome (ARDS), a condition characterized by the presence of lung inflammation, edema, and impaired gas exchange, associated with poor survival. Understanding molecular pathobiology is essential to improve critical care of these patients. To this end, we use multimodal profiles of SARS-CoV-2 infected hospitalized participants to the Biobanque Quebecoise de la COVID-19 (BQC-19) to characterize endophenotypes associated with different degrees of disease severity. Proteomic, metabolomic, and genomic characterization supported a role for neutrophil-associated procoagulant activity in severe COVID-19 ARDS that is inversely correlated with sphinghosine-1 phosphate plasma levels. Fibroblast Growth Factor Receptor (FGFR) and SH2-containing transforming protein 4 (SHC4) signaling were identified as molecular features associated with endophenotype 6 (EP6). Mechanical ventilation in EP6 was associated with alterations in lipoprotein metabolism. These findings help define the molecular mechanisms related to specific severe outcomes, that can be used to identify early unfavorable clinical trajectories and treatable traits to improve the survival of critically ill patients.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Antione Soule", - "author_inst": "McGill University" - }, - { - "author_name": "William R Ma", - "author_inst": "McGill University" - }, - { - "author_name": "Katelyn Yixiu Liu", - "author_inst": "McGill University" - }, - { - "author_name": "Catherine Allard", - "author_inst": "Centre de recherche du Centre hospitalier universitaire de Sherbrooke" - }, - { - "author_name": "Salman Qureshi", - "author_inst": "McGill University" - }, - { - "author_name": "Karine Tremblay", - "author_inst": "Universit\u00e9 de Sherbrooke" - }, - { - "author_name": "Amin Emad", - "author_inst": "McGill University" - }, - { - "author_name": "Simon Rousseau", - "author_inst": "McGill University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2023.03.09.531948", "rel_title": "Impaired potency of neutralizing antibodies against cell-cell fusion mediated by SARS-CoV-2", @@ -133751,6 +135996,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.03.06.23286886", + "rel_title": "Archetypal analysis of COVID-19 in Montana, USA, March 13, 2020 to April 26, 2022", + "rel_date": "2023-03-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.06.23286886", + "rel_abs": "Given the potential consequences of infectious diseases, it is important to understand how broad scale incidence variability influences the probability of localized outbreaks. Often, these infectious disease data can involve complex spatial patterns intermixed with temporal trends. Archetypal Analysis is a method to mine complex spatiotemporal epidemiological data, and can be used to discover the dynamics of spatial patterns. The application of Archetypal Analysis to epistemological data is relatively new, and here we present one of the first applications using COVID-19 data from March 13, 2020 to April 26, 2022, in the counties of Montana, USA. We present three views of the data set with Archetypal Analysis. First, we evaluate the entire 56 county data set. Second, we compute mutual information of the 56 counties time series to remove counties whose dynamics are mainly independent from most of the other counties. We choose the top 17 counties ranked in terms of increasing total mutual information. Finally, to compare how population size might influence results, we conducted an analysis with 10 of the largest counties. Using the Archetypal Analysis results, we analyze the disease outbreaks across Montana, comparing and contrasting the three different cases and showing how certain counties can be found in distinct sets of archetypes. Using the reconstruction time series, we show how each outbreak had a unique trajectory across the state in terms of the archetypes.\n\nAuthor summaryArchetypal Analysis provides an additional tool for the study of spatio-temporal epidemiological data. We apply Archetypal Analysis to COVID-19 data and reveal how this approach can be used to analyse the dynamics of each COVID-19 outbreak across the state.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Emily Stone", + "author_inst": "University of Montana" + }, + { + "author_name": "Erin Landguth", + "author_inst": "UM: University of Montana" + }, + { + "author_name": "Sebastian Coombs", + "author_inst": "University of Montana" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.03.07.23286899", "rel_title": "Covid-19 impact on food insecurity in Uganda: a dynamic analysis", @@ -134098,49 +136370,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.03.03.23286284", - "rel_title": "Trends in Antibody Titers after SARS-CoV-2 Vaccination - Insights from a Self-Paid Tests at a General Internal Medicine Clinic", - "rel_date": "2023-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.03.23286284", - "rel_abs": "BackgroundThe rise in antibody titers against the novel coronavirus (SARS-CoV-2), and its duration is considered an important indicator for confirming the efficacy of the COVID-19 vaccine, and self-paid tests of antibody titer are conducted at many facilities nationwide.\n\nMethodsThe relationship between the number of days after the second and third dose of vaccines, age, and antibody titer was determined from the medical records of general internal medicine clinics that conducted self-paid testing of SARS-CoV-2 antibody titer using Elecsys Anti-SARS-CoV-2 S (Roche Diagnostics), as well as the relationship between the number of days after two or more dose of vaccines and antibody titer. We also examined antibody titers in cases of spontaneous infection with SARS-CoV-2 after two or more doses of the vaccine.\n\nResultsAge and antibody titer were negatively correlated in 86 subjects whose antibody titer was measured within 1 month after the second vaccination with the COVID-19 vaccine. In 31 subjects whose antibody titer was measured within one month after the third dose of vaccine, age and antibody titer showed a negative correlation (p<0.01). The mean antibody titer after the third vaccination was 20704.9{+/-}16820.7 U/mL, more than 10 times the mean antibody titer after the second dose of vaccine of 1601.9{+/-}1297.9 U/mL. There were also cases of infection after the third or fourth dose of vaccine, with antibody titers in the tens of thousands after infection, but they still received further booster vaccinations after infection.\n\nDiscussionSARS-CoV-2 antibody titers measured within 1 month of the second or third dose of vaccine showed a negative correlation with age, and antibody titers also showed a negative correlation trend with the number of days after the second dose of vaccine. It is considered that many people in Japan received further booster vaccinations after spontaneous infection, even though they already had antibody titers in the tens of thousands U/mL by \"hybrid immunity\" after spontaneous infection following two or more dose of vaccine.\n\nConclusionAfter measuring SARS-CoV-2 antibody titers, booster vaccination of those with low antibody titers should be done on a priority basis.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Hiroshi Kusunoki", - "author_inst": "Department of Internal Medicine, Osaka Dental University, Hirakata, Osaka, Japan." - }, - { - "author_name": "Kazumi Ekawa", - "author_inst": "Department of Environmental and Preventive Medicine, Hyogo Medical University" - }, - { - "author_name": "Masakazu Ekawa", - "author_inst": "Ekawa Medical Clinic" - }, - { - "author_name": "Nozomi Kato", - "author_inst": "Department of Internal Medicine, Osaka Dental University" - }, - { - "author_name": "Keita Yamasaki", - "author_inst": "Department of Health and Sports Sciences Graduate School of Medicine, Osaka University" - }, - { - "author_name": "Masaharu Motone", - "author_inst": "Faculty of Health Sciences, Osaka Dental University" - }, - { - "author_name": "Hideo Shimizu", - "author_inst": "Department of Internal Medicine, Osaka Dental University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.03.07.23286963", "rel_title": "Myocardial Infarction across COVID-19 Pandemic Phases: Insights from the Veterans Health Affairs System", @@ -135365,6 +137594,61 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2023.03.05.23286509", + "rel_title": "COVID-19 vaccination coverage and linkages with public willingness to receive vaccination prior to vaccine roll-out: Evidence from Rwanda", + "rel_date": "2023-03-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.05.23286509", + "rel_abs": "The rapid development of multiple SARS-CoV-2 vaccines within one year of the viruss emergence is unprecedented and redefines the timeline for vaccine approval and rollout. Consequently, over 13 billion COVID-19 vaccine doses have been administered worldwide, accounting for [~]70% of the global population. Despite this steadfast scientific achievement, many inequalities exist in vaccine distribution and procurement, particularly in low- and middle-income countries such as those in Africa. This stems from the cost of COVID-19 vaccines, storage and cold-chain challenges, distribution to remote areas, proper personnel training, and so on. In addition to logistical challenges, many developed nations rapidly procured available vaccines, administering second and third doses and leaving many developing nations without the first dose. In this paper, we explore the level of reception to COVID-19 vaccines prior to their availability in Rwanda using a survey-based approach. While several countries reported spikes in vaccine hesitancy generally coinciding with new information, new policies, or newly reported vaccine risks, Rwanda functions as an exemplar for controlling disease burden and educating locals regarding the benefits of vaccination. We show that, even before COVID-19 vaccines were available, many Rwandans (97%) recognized the importance of COVID-19 vaccination and (93%) were willing to receive a COVID-19 vaccine following vaccine availability. Our results underscore the level of preparedness in Rwanda, which rivals and outcompetes many developed nations in terms of vaccination rate (nearing 80% in Rwanda), vaccine acceptance, and local knowledge relating to vaccination. Furthermore, in addition to the whole-of-government coordination as well as tailored delivery approach, previously developed practices relating to vaccination and communication surrounding the Ebola Virus Disease may have compounded the COVID-19 vaccine program in Rwanda, prior to its implementation.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Pacifique Ndishimye", + "author_inst": "Laboratory of Emerging Infectious Diseases, Department of Microbiology and Immunology, Faculty of Medicine, Canadian Centre for Vaccinology CCfV, Dalhousie Univ" + }, + { + "author_name": "Gustavo Sganzerla-Martinez", + "author_inst": "Laboratory of Emerging Infectious Diseases, Department of Microbiology and Immunology, Faculty of Medicine, Canadian Centre for Vaccinology CCfV, Dalhousie Univ" + }, + { + "author_name": "Benjamin Hewins", + "author_inst": "Laboratory of Emerging Infectious Diseases, Department of Microbiology and Immunology, Faculty of Medicine, Canadian Centre for Vaccinology CCfV, Dalhousie Univ" + }, + { + "author_name": "Ali Toloue Ostadgavahi", + "author_inst": "Laboratory of Emerging Infectious Diseases, Department of Microbiology and Immunology, Faculty of Medicine, Canadian Centre for Vaccinology CCfV, Dalhousie Univ" + }, + { + "author_name": "Anuj Kumar", + "author_inst": "Laboratory of Emerging Infectious Diseases, Department of Microbiology and Immunology, Faculty of Medicine, Canadian Centre for Vaccinology CCfV, Dalhousie Univ" + }, + { + "author_name": "Mansi Sharma", + "author_inst": "Laboratory of Emerging Infectious Diseases, Department of Microbiology and Immunology, Faculty of Medicine, Canadian Centre for Vaccinology CCfV, Dalhousie Univ" + }, + { + "author_name": "Janvier Karuhije", + "author_inst": "Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda" + }, + { + "author_name": "Menelas Nkeshimana", + "author_inst": "University Teaching Hospital of Kigali, Kigali, Rwanda" + }, + { + "author_name": "Sabin Nsanzimana", + "author_inst": "Ministry of Health, Kigali, Rwanda" + }, + { + "author_name": "David Kelvin", + "author_inst": "Laboratory of Emerging Infectious Diseases, Department of Microbiology and Immunology, Faculty of Medicine, Canadian Centre for Vaccinology CCfV, Dalhousie Univ" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.03.05.531143", "rel_title": "Mutations in S2 subunit of SARS-CoV-2 Omicron spike strongly influence its conformation, fusogenicity and neutralization sensitivity", @@ -135812,49 +138096,6 @@ "type": "new results", "category": "scientific communication and education" }, - { - "rel_doi": "10.1101/2023.03.03.23286122", - "rel_title": "Phenome-wide association study to explore the long-term symptoms after infection with novel coronavirus in the UK Biobank", - "rel_date": "2023-03-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.03.23286122", - "rel_abs": "BackgroundObservational research studies have shown that even after the acute phase, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can affect patients, and increase the risk of cardiovascular, mental, metabolic, and other disorders. However, the spectrum of diseases for individuals with a genetic predisposition to COVID-19 remains unclear.\n\nMethodsWe leveraged individual-level data from UK Biobank to implement a phenome-wide association study to explore the relationships between COVID-19 and 1061 diseases. Then, the inverse-variance weighted (IVW) method was adopted with summary-level data from global consortiums as sensitivity analyses combined with other MR methods with different model assumptions to identify robust associations.\n\nFindingsThe PheWAS found severe respiratory, hospitalized, and susceptibility COVID-19 had detrimental effects on 36, 37, and 51 kinds of diseases, separately. The IVW test found severe respiratory COVID-19 had detrimental effects on breast cancer [OR 95% CI: 1.065 (1.000-1.133)], pan-cancer [OR 95% CI: 1.002 (1.000-1.004)], and Alzheimers disease [OR 95% CI: 1.042 (1.005-1.081)], etc. Hospitalized COVID-19 had detrimental effects on ischemic stroke (IS) [OR 95%CI: 1.049 (1.001-1.100)], breast cancer [OR 95%CI: 1.139 (1.011-1.283)], and pan-cancer [OR 95%CI: 1.003 (1.000-1.006)], etc. Susceptibility COVID-19 had detrimental effects on deep vein thrombosis (DVT) of lower extremities [OR 95%CI: 2.392 (1.167-4.902)], venous thromboembolism [OR 95%CI: 1.962 (1.115-3.453)], pulmonary heart disease/diseases of pulmonary circulation [OR 95%CI: 1.767 (1.142-2.733)], IS (large artery atherosclerosis) [OR 95%CI: 1.405 (1.025-1.927)], myocardial infarction [OR 95%CI: 1.235 (1.012-1.509)], heart failure [OR 95%CI: 1.140 (1.009-1.287)], etc.\n\nInterpretationThis study describes the extensive link between genetically determined COVID-19 and a broad range of diseases, especially those of the circulatory system, neuropsychiatric system, neoplasms, immune system, and digestive systems. Early detection and management of post-COVID-19 conditions could be tremendously beneficial to public health.\n\nFundingThis work was supported by the National Natural Science Foundation of China (81773547 and 82173625) and the National Key Research and Development Program (2020YFC2003500).", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Kai Zhang", - "author_inst": "1. Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, P.R. China.3. National Institute of He" - }, - { - "author_name": "Xiaowen Liu", - "author_inst": "1. Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, P.R. China. 3. National Institute of H" - }, - { - "author_name": "Ping Fu", - "author_inst": "1. Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, P.R. China. 3. National Institute of H" - }, - { - "author_name": "Yingqi Zhao", - "author_inst": "1. Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, P.R. China. 3. National Institute of " - }, - { - "author_name": "Qingqing Yu", - "author_inst": "1. Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, P.R. China. 3. National Institute of " - }, - { - "author_name": "Shuling Liu", - "author_inst": "1. Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, P.R. China. 3. National Institute of H" - }, - { - "author_name": "Fuzhong Xue", - "author_inst": "1. Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, P.R. China. 2. Institute for Medical D" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.03.03.23286745", "rel_title": "Decline in prevalence of tuberculosis following an intensive case-finding campaign and the COVID-19 pandemic in an urban Ugandan community", @@ -137039,6 +139280,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.03.02.23286677", + "rel_title": "Analysis of SARS-CoV-2 mutations associated with resistance to therapeutic monoclonal antibodies that emerge after treatment.", + "rel_date": "2023-03-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.03.02.23286677", + "rel_abs": "The mutation rate of the Omicron sublineage has led to baseline resistance against all previously authorized anti-Spike monoclonal antibodies (mAbs). Nevertheless, in case more antiviral mAbs will be authorized in the future, it is relevant to understand how frequently treatment-emergent resistance has emerged so far, under different combinations and in different patient subgroups. We report the results of a systematic review of the medical literature for case reports and case series for treatment-emergent immune escape, which is defined as emergence of a resistance-driving mutation in at least 20% of sequences in a given host at a given timepoint. We identified 31 publications detailing 201 cases that included different variants of concern (VOC) and found that the incidence of treatment emergent-resistance ranged from 10% to 50%. Most of the treatment-emergent resistance events occurred in immunocompromised patients. Interestingly, resistance also emerged against cocktails of two mAbs, albeit at lower frequencies. The heterogenous therapeutic management of those cases doesnt allow inferences about the clinical outcome in patients with treatment-emergent resistance. Furthermore, we noted a temporal correlation between the introduction of mAb therapies and a subsequent increase in SARS-CoV-2 sequences across the globe carrying mutations conferring resistance to that mAb, raising concern as to whether these had originated in mAb-treated individuals. Our findings confirm that treatment-emergent immune escape to anti-Spike mAbs represents a frequent and concerning phenomenon and suggests that these are associated with mAb use in immunosuppressed hosts.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Daniele Focosi", + "author_inst": "Pisa University Hospital" + }, + { + "author_name": "Scott McConnell", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "David J Sullivan", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Arturo Casadevall", + "author_inst": "Johns Hopkins School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.03.01.530717", "rel_title": "Assessment of neutralization susceptibility of Omicron subvariants XBB.1.5 and BQ.1.1 against broad-spectrum neutralizing antibodies through epitopes mapping", @@ -137526,65 +139798,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.02.27.23286454", - "rel_title": "Mixed methods approach to examining the implementation experience of a phone-based health research survey investigating risk factors for SARS-CoV-2 infection in California", - "rel_date": "2023-03-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.27.23286454", - "rel_abs": "ObjectiveTo describe the implementation of a test-negative design case-control study in California during the Coronavirus Disease 2019 (COVID-19) pandemic.\n\nMethodsBetween February 24, 2021 - February 24, 2022, 34 interviewers called 38,470 SARS-CoV-2-tested Californians to enroll 1,885 cases and 1,871 controls in a 20-minute telephone survey. We estimated adjusted odds ratios for answering the phone and consenting to participate using mixed effects logistic regression. We used a web-based anonymous survey to compile interviewer experiences.\n\nResultsCases had 1.29-fold (95% CI: 1.24-1.35) higher adjusted odds of answering the phone and 1.69-fold (1.56-1.83) higher adjusted odds of consenting to participate compared to controls. Calls placed from 4pm to 6pm had the highest adjusted odds of being answered. Interviewers who faced participants with dire need for social services or harassment experienced poor mental health.\n\nConclusionsWe suggest calling during afternoons and allocating more effort towards enrolling controls when designing a case-control study. Remaining adaptive to the dynamic needs of the team is critical to a successful study, especially in a pandemic setting.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Nozomi Fukui", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Sophia Suk Li", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Jennifer DeGuzman", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Jennifer Myers", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "John Openshaw", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Anjali Sharma", - "author_inst": "Center for Infectious Disease Research in Zambia" - }, - { - "author_name": "James Watt", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Joseph Lewnard", - "author_inst": "University of California Berkeley" - }, - { - "author_name": "Seema Jain", - "author_inst": "California Department of Public Health" - }, - { - "author_name": "Kristin Andrejko", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Jake M Pry", - "author_inst": "University of California" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.02.28.23286559", "rel_title": "Elevated symptoms of depression and anxiety among family members and friends of critically ill COVID-19 patients - An observational study of five cohorts across four countries", @@ -138809,6 +141022,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2023.02.23.23286326", + "rel_title": "Quantifying the impact of SARS-CoV-2 temporal vaccination trends and disparities on disease control", + "rel_date": "2023-02-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.23.23286326", + "rel_abs": "SARS-CoV-2 vaccines were developed and distributed during a global crisis at unprecedented speed. Still, little is known about trends in vaccine uptake over time, their association with socioeconomic inequality, and the impact of these temporal trends on disease control. By analyzing data from dozens of countries, we examined vaccination rates across high and low socioeconomic (SES) groups, showing that socioeconomic disparities in the fraction of the population vaccinated exist at both national and sub-national levels. We also identified two distinct vaccination trends: one characterized by rapid initial roll-out, quickly reaching a plateau; and another trend that is sigmoidal and slow to begin. Informed by these patterns, we implemented an SES-stratified mechanistic model, finding profound differences across the two vaccination types in the burden of infections and deaths. The timing of initial roll-out has a more significant effect on transmission and deaths than the eventual level of coverage or the degree of SES disparity. Surprisingly, the speed of the roll-out is not associated with wealth inequality or GDP per capita of countries. While socioeconomic disparity should be addressed, accelerating the initial roll-out for all groups is a broadly accessible intervention and has the potential to minimize the burden of infections and deaths across socioeconomic groups.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Sophie L Larsen", + "author_inst": "University of Illinois at Urbana-Champaign" + }, + { + "author_name": "Ikgyu Shin", + "author_inst": "University of Illinois at Urbana Champaign" + }, + { + "author_name": "Jefrin Joseph", + "author_inst": "University of Illinois at Urbana Champaign" + }, + { + "author_name": "Haylee West", + "author_inst": "University of Illinois at Urbana Champaign" + }, + { + "author_name": "Rafael Anorga", + "author_inst": "University of Illinois at Urbana Champaign" + }, + { + "author_name": "Gonzalo E Mena", + "author_inst": "University of Oxford" + }, + { + "author_name": "Ayesha Mahmud", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Pamela P. Martinez", + "author_inst": "University of Illinois at Urbana Champaign" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.02.22.23286167", "rel_title": "A Snapshot of COVID-19 Incidence, Hospitalizations, and Mortality from Indirect Survey Data in China in January 2023", @@ -139308,173 +141568,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, - { - "rel_doi": "10.1101/2023.02.21.23286239", - "rel_title": "Performance of Rapid Antigen Tests Based on Symptom Onset and Close Contact Exposure: A secondary analysis from the Test Us At Home prospective cohort study", - "rel_date": "2023-02-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.21.23286239", - "rel_abs": "BackgroundThe performance of rapid antigen tests for SARS-CoV-2 (Ag-RDT) in temporal relation to symptom onset or exposure is unknown, as is the impact of vaccination on this relationship.\n\nObjectiveTo evaluate the performance of Ag-RDT compared with RT-PCR based on day after symptom onset or exposure in order to decide on when to test.\n\nDesign, Setting, and ParticipantsThe Test Us at Home study was a longitudinal cohort study that enrolled participants over 2 years old across the United States between October 18, 2021 and February 4, 2022. All participants were asked to conduct Ag-RDT and RT-PCR testing every 48 hours over a 15-day period. Participants with one or more symptoms during the study period were included in the Day Post Symptom Onset (DPSO) analyses, while those who reported a COVID-19 exposure were included in the Day Post Exposure (DPE) analysis.\n\nExposureParticipants were asked to self-report any symptoms or known exposures to SARS-CoV-2 every 48-hours, immediately prior to conducting Ag-RDT and RT-PCR testing. The first day a participant reported one or more symptoms was termed DPSO 0, and the day of exposure was DPE 0. Vaccination status was self-reported.\n\nMain Outcome and MeasuresResults of Ag-RDT were self-reported (positive, negative, or invalid) and RT-PCR results were analyzed by a central laboratory. Percent positivity of SARS-CoV-2 and sensitivity of Ag-RDT and RT-PCR by DPSO and DPE were stratified by vaccination status and calculated with 95% confidence intervals.\n\nResultsA total of 7,361 participants enrolled in the study. Among them, 2,086 (28.3%) and 546 (7.4%) participants were eligible for the DPSO and DPE analyses, respectively. Unvaccinated participants were nearly twice as likely to test positive for SARS-CoV-2 than vaccinated participants in event of symptoms (PCR+: 27.6% vs 10.1%) or exposure (PCR+: 43.8% vs. 22.2%). The highest proportion of vaccinated and unvaccinated individuals tested positive on DPSO 2 and DPE 5-8. Performance of RT-PCR and Ag-RDT did not differ by vaccination status. Ag-RDT detected 78.0% (95% Confidence Interval: 72.56-82.61) of PCR-confirmed infections by DPSO 4. For exposed participants, Ag-RDT detected 84.9% (95% CI: 75.0-91.4) of PCR-confirmed infections by day five post-exposure (DPE 5).\n\nConclusions and RelevancePerformance of Ag-RDT and RT-PCR was highest on DPSO 0-2 and DPE 5 and did not differ by vaccination status. These data suggests that serial testing remains integral to enhancing the performance of Ag-RDT.", - "rel_num_authors": 38, - "rel_authors": [ - { - "author_name": "Carly Herbert", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Biqi Wang", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Honghuang Lin", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Nathaniel Hafer", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Caitlin Pretz", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Pamela Stamegna", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Seanan Tarrant", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Paul Hartin", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Julia Ferranto", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Stephanie Behar", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Colton Wright", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Taylor Orwig", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Thejas Suvarna", - "author_inst": "CareEvolution, LLC" - }, - { - "author_name": "Emma Harman", - "author_inst": "CareEvolution, LLC" - }, - { - "author_name": "Summer Schrader", - "author_inst": "CareEvolution, LLC" - }, - { - "author_name": "Chris Nowak", - "author_inst": "CareEvolution, LLC" - }, - { - "author_name": "Vik Kheterpal", - "author_inst": "CareEvolution, LLC" - }, - { - "author_name": "Elizabeth Orvek", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Steven Wong", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Adrian Zai", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Bruce Barton", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Ben Gerber", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Stephenie C Lemon", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Andreas Filippaios", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Kylie D'Amore", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Laura Gibson", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Sharone Greene", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Sakeina Howard Wilson", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Andres Colubri", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Chad Achenbach", - "author_inst": "Northwestern University" - }, - { - "author_name": "Robert Murphy", - "author_inst": "Northwestern University" - }, - { - "author_name": "Bill Heetderks", - "author_inst": "National Institute of Biomedical Imaging and Bioengineering" - }, - { - "author_name": "Yukari C Manabe", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Nisha Fahey", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Katherine L Luzuriaga", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "John Broach", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "David D McManus", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Apurv Soni", - "author_inst": "University of Massachusetts Chan Medical School" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.02.21.23286222", "rel_title": "Genomic surveillance reveals early detection and transition of Delta to Omicron Lineages of SARS-CoV-2 Variants in wastewater treatment plants of Pune, India", @@ -140767,6 +142860,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.02.15.23286011", + "rel_title": "Underlying Pressures that Black Mothers and Their Children Face: A Qualitative Assessment on the Effects of Racism/Discrimination and the COVID-19 Pandemic", + "rel_date": "2023-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.15.23286011", + "rel_abs": "BackgroundPoverty, racism, discrimination, inadequate access to healthcare, and personal, everyday stressors lead to poor health outcomes, especially in African American families in the south. There is limited data on how these stressors are absorbed between the mother and child dyad.\n\nObjectiveTo assess the effects of racism, everyday stressors (i.e. motherhood), and the COVID pandemic on African American/Black mothers and their children.\n\nMethodsUtilizing the Health Belief Model, a survey was developed to assess mother-child stressors relating to three different constructs: racism/discrimination, pandemic/covid-19, and parenting. We interviewed seven black mothers and their children (aged 4-10yo). The families were recruited from a pediatric office in the rural city of Alexander City, Alabama. Interviews took place in an intimate setting and lasted for 1.5-2 hours. Medical students conducted, recorded, and transcribed each interview. The interview assessed the association between the COVID-19 pandemic, personal traumatic events, and racism and discrimination in their everyday lives.\n\nResultsThrough qualitative analysis; racism, daily activities, and the COVID-19 pandemic were demonstrated to be significant stressors for the mothers. Knowledge, school/work, actions, emotions, and seriousness/susceptibility displayed stressors not only in the mom as one would expect, but in the children as well. Using the resilience model, we assessed adversity, coping strategies, and self-efficacy. As one might expect, each situation caused a different level of anxiety; however, the coping strategies varied. Some moms took to smoking to cope with it while others chose suppression. The childrens coping ranged from inconsolable crying and using outlets such as phones to cope.\n\nConclusionUltimately, our qualitative approach saw an association between the pandemic and discrimination. Mothers often felt the need to shield children from the emotions attached to discrimination, and ultimately were unable to. There is a need to explore resilience and assess these stressors and changes in perception over time.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Denisia Nesha Thomas", + "author_inst": "Edward Via College of Osteopathic Medicine - Auburn Campus" + }, + { + "author_name": "Mayra Rodriguez", + "author_inst": "Edward Via College of Osteopathic Medicine - Auburn Campus" + }, + { + "author_name": "Ashley Rizzieri", + "author_inst": "Edward Via College of Osteopathic Medicine - Auburn Campus" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.02.19.23286148", "rel_title": "Impact of Pulmonary and Sleep Disorders on COVID-19 Infection Severity in a Large Clinical Biobank", @@ -141150,101 +143270,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.02.17.23286059", - "rel_title": "A unique cytotoxic CD4+ T cells signature defines critical COVID-19", - "rel_date": "2023-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.17.23286059", - "rel_abs": "Background and objectivesSARS-CoV-2 infection causes a spectrum of clinical disease presentation, ranging from asymptomatic to fatal. While neutralising antibody (NAb) responses correlate with protection against symptomatic and severe infection, the contribution of the T cell response to the resolution or progression of disease is still unclear. Optimal protective immunity may require activation of distinct immune pathways. As such, defining the contribution of individual T cell subsets to disease outcome is imperative to inform the development of next-generation COVID-19 vaccines. To address this, we performed immunophenotyping of T cell responses in unvaccinated individuals, representing the full spectrum of COVID-19 clinical presentation.\n\nMethodsSpectral cytometry was performed on peripheral blood mononuclear cell samples from patients with PCR-confirmed SARS-CoV-2 infection. Computational and manual analyses were used to identify T cell populations associated with distinct disease states through unbiased clustering, principal component analysis and discriminant analysis.\n\nResultsCritical SARS-CoV-2 infection was characterised by an increase in activated and cytotoxic CD4+ (CTL) cells of a T follicular helper (TFH) or effector memory re-expressing CD45RA (TEMRA) phenotype. These CD4+ CTLs were largely absent in those with less severe disease. In contrast, those with asymptomatic or mild disease were associated with high proportions of naive T cells and reduced expression of activation markers.\n\nConclusionHighly activated and cytotoxic CD4+ T cell responses may contribute to cell-mediated host tissue damage and progression of COVID-19. Potential for induction of these detrimental T cell responses should be considered when developing and implementing effective COVID-19 control strategies.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Sarah Baird", - "author_inst": "The University of Sydney" - }, - { - "author_name": "Caroline L Ashley", - "author_inst": "The University of Sydney" - }, - { - "author_name": "Felix Marsh-Wakefield", - "author_inst": "The University of Sydney" - }, - { - "author_name": "Sibel Alca", - "author_inst": "The University of Sydney" - }, - { - "author_name": "Thomas M Ashhurst", - "author_inst": "The University of Sydney" - }, - { - "author_name": "Angela L Ferguson", - "author_inst": "The University of Sydney" - }, - { - "author_name": "Hannah Lukeman", - "author_inst": "The University of Sydney" - }, - { - "author_name": "Claudio Counoupas", - "author_inst": "Centenary Institute" - }, - { - "author_name": "Jeffrey J Post", - "author_inst": "Prince of Wales Clinical School" - }, - { - "author_name": "Pamela Konecny", - "author_inst": "St George Hospital" - }, - { - "author_name": "Adam Bartlett", - "author_inst": "The Kirby Institute" - }, - { - "author_name": "Marianne Martinello", - "author_inst": "The Kirby Institute" - }, - { - "author_name": "Rowena A Bull", - "author_inst": "The Kirby Institute" - }, - { - "author_name": "Andrew Lloyd", - "author_inst": "The Kirby Institute" - }, - { - "author_name": "Alice Grey", - "author_inst": "RPA Virtual Hospital" - }, - { - "author_name": "Owen Hutchings", - "author_inst": "RPA Virtual Hospital" - }, - { - "author_name": "Umaimainthan Palendira", - "author_inst": "The University of Sydney" - }, - { - "author_name": "Warwick J Britton", - "author_inst": "Centenary Institute" - }, - { - "author_name": "Megan Steain", - "author_inst": "The University of Sydney" - }, - { - "author_name": "James A Triccas", - "author_inst": "The University of Sydney" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.02.22.23286197", "rel_title": "Peruvian National Survey of Mental Health and Service Utilization in the third year of the COVID-19 pandemic: Protocol for a nationally representative multistage survey", @@ -142353,6 +144378,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.02.12.528210", + "rel_title": "Discovery of a novel merbecovirus cDNA clone contaminating agricultural rice sequencing datasets from Wuhan, China", + "rel_date": "2023-02-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.12.528210", + "rel_abs": "HKU4-related coronaviruses are a group of betacoronaviruses belonging to the same merbecovirus subgenus as Middle Eastern Respiratory Syndrome coronavirus (MERS-CoV), which causes severe respiratory illness in humans with a mortality rate of over 30%. The high genetic similarity between HKU4-related coronaviruses and MERS-CoV makes them an attractive subject of research for modeling potential zoonotic spillover scenarios. In this study, we identify a novel coronavirus contaminating agricultural rice RNA sequencing datasets from Wuhan, China. The datasets were generated by the Huazhong Agricultural University in early 2020. We were able to assemble the complete viral genome sequence, which revealed that it is a novel HKU4-related merbecovirus. The assembled genome is 98.38% identical to the closest known full genome sequence, Tylonycteris pachypus bat isolate BtTp-GX2012. Using in silico modeling, we identified that the novel HKU4-related coronavirus spike protein likely binds to human dipeptidyl peptidase 4 (DPP4), the receptor used by MERS-CoV. We further identified that the novel HKU4-related coronavirus genome has been inserted into a bacterial artificial chromosome in a format consistent with previously published coronavirus infectious clones. Additionally, we have found a near complete read coverage of the spike gene of the MERS-CoV reference strain HCoV-EMC/2012, and identify the likely presence of a HKU4-related-MERS chimera in the datasets. Our findings contribute to the knowledge of HKU4-related coronaviruses and document the use of a previously unpublished HKU4 reverse genetics system in apparent MERS-CoV related gain-of-function research. Our study also emphasizes the importance of improved biosafety protocols in sequencing centers and coronavirus research facilities.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Adrian Jones", + "author_inst": "Independent bioinformatics researcher" + }, + { + "author_name": "Daoyu Zhang", + "author_inst": "Independent genetics researcher" + }, + { + "author_name": "Steven E. Massey", + "author_inst": "Department of Biology, University of Puerto Rico - Rio Piedras" + }, + { + "author_name": "Yuri Deigin", + "author_inst": "Youthereum Genetics Inc." + }, + { + "author_name": "Louis R Nemzer", + "author_inst": "Nova Southeastern University" + }, + { + "author_name": "Steven Carl Quay", + "author_inst": "Atossa Therapeutics, Inc." + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2023.02.20.529234", "rel_title": "Bovine milk glycoproteins inhibit SARS-CoV-2 and influenza virus co-infection", @@ -142920,53 +144984,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2023.02.18.23286126", - "rel_title": "Mental health symptoms in Latin America during the first year of COVID-19 pandemic: a meta-analysis of prevalence and potential moderator variables", - "rel_date": "2023-02-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.18.23286126", - "rel_abs": "This meta-analysis examines the impacts of the COVID-19 pandemic on mental health in Latin America during its first year, using data from 71 studies with 231,441 participants. To address knowledge gaps in the existent literature we considered the type of study design, country of origin, effects of lockdown, and several potential moderating factors. We found prevalence rates of 31% for depression symptoms and 36% for anxiety symptoms. These estimates were higher than those observed in studies from the northern hemisphere. Longitudinal studies showed that depressive symptoms persisted over time, and lockdowns were associated with mildly increased anxiety levels. Female gender was associated with higher rates of depressive symptoms. Our analyses revealed high statistical heterogeneity, and moderating factors such as pandemic duration, COVID-19 cases and deaths, and lockdown stringency did not explain observed mental health symptoms. Methodological limitations include an overreliance on cross-sectional studies and a lack of pre-pandemic parameters that may lead to an overestimation of mental health symptom rates. Overall, this study provides valuable insights into mental health symptoms in Latin America during the first year of the COVID-19 pandemic, highlighting the need for improved epidemiological research and mental health support in the region.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Fernando Torrente", - "author_inst": "Institute of Cognitive and Translational Neurosciences (CONICET-INECO Foundation-Favaloro University)" - }, - { - "author_name": "Delfina Ailan", - "author_inst": "Institute of Cognitive and Translational Neurosciences (CONICET-INECO Foundation-Favaloro University)" - }, - { - "author_name": "Emilia Del Cerro", - "author_inst": "Institute of Cognitive and Translational Neurosciences (CONICET-INECO Foundation-Favaloro University)" - }, - { - "author_name": "Julieta Del Negro", - "author_inst": "Institute of Cognitive and Translational Neurosciences (CONICET-INECO Foundation-Favaloro University)" - }, - { - "author_name": "Barbara Gorodetzky", - "author_inst": "Institute of Cognitive and Translational Neurosciences (CONICET-INECO Foundation-Favaloro University)" - }, - { - "author_name": "Delfina Slonimschik", - "author_inst": "Institute of Cognitive and Translational Neurosciences (CONICET-INECO Foundation-Favaloro University)" - }, - { - "author_name": "Marcelo Cetkovich-Bakmas", - "author_inst": "Institute of Cognitive and Translational Neurosciences (CONICET-INECO Foundation-Favaloro University)" - }, - { - "author_name": "Pablo Lopez", - "author_inst": "Institute of Cognitive and Translational Neurosciences (CONICET-INECO Foundation-Favaloro University)" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2023.02.13.23285842", "rel_title": "Mortality by cause of death in Brazil: effects of the COVID-19 pandemic and contribution to changes in life expectancy at birth", @@ -143995,6 +146012,193 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.02.13.23285855", + "rel_title": "Early Treatment, Inflammation and Post-COVID Conditions", + "rel_date": "2023-02-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.13.23285855", + "rel_abs": "BackgroundPost-COVID conditions (PCC) are common and have significant morbidity. Risk factors for PCC include advancing age, female sex, obesity, and diabetes mellitus. Little is known about early treatment, inflammation, and PCC.\n\nMethodsAmong 883 individuals with confirmed SARS-CoV-2 infection participating in a randomized trial of CCP vs. control plasma with available biospecimens and symptom data, the association between early COVID treatment, cytokine levels and PCC was evaluated. Cytokine and chemokine levels were assessed at baseline, day 14 and day 90 using a multiplexed sandwich immuosassay (Mesoscale Discovery). Presence of any self-reported PCC symptoms was assessed at day 90. Associations between COVID treatment, cytokine levels and PCC were examined using multivariate logistic regression models.\n\nResultsOne-third of the 882 participants had day 90 PCC symptoms, with fatigue (14.5%) and loss of smell (14.5%) being most common. Cytokine levels decreased from baseline to day 90. In a multivariable analysis including diabetes, body mass index, race, and vaccine status, female sex (adjusted odds ratio[AOR]=2.70[1.93-3.81]), older age (AOR=1.32[1.17-1.50]), and elevated baseline levels of IL-6 (AOR=1.59[1.02-2.47]) were associated with development of PCC. There was a trend for decreased PCC in those with early CCP treatment (<5 days after symptom onset) compared to late CCP treatment.\n\nConclusionIncreased IL-6 levels were associated with the development of PCC and there was a trend for decreased PCC with early CCP treatment in this predominately unvaccinated population. Future treatment studies should evaluate the effect of early treatment and anti-IL-6 therapies on PCC development.\n\nSummaryIncreased IL-6 levels were associated with the development of Post-COVID Conditions (PCC) and there was a trend for decreased PCC with early COVID convalescent plasma treatment in this predominately unvaccinated population.", + "rel_num_authors": 43, + "rel_authors": [ + { + "author_name": "Kelly A. Gebo", + "author_inst": "Department of Medicine, Division of Infectious Diseases" + }, + { + "author_name": "Sonya L. Heath", + "author_inst": "Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL" + }, + { + "author_name": "Yuriko Fukuta", + "author_inst": "Department of Medicine, Section of Infectious Diseases, Baylor College of Medicine, Houston, TX" + }, + { + "author_name": "Xianming Zhu", + "author_inst": "Johns Hopkins School of Medicine, Department of Pathology" + }, + { + "author_name": "Sheriza Baksh", + "author_inst": "Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD; Department of Medicine, Division of Infectious Diseases" + }, + { + "author_name": "Alison G. Abraham", + "author_inst": "Department of Medicine, Department of Neurology, Brain Injury Outcomes Division" + }, + { + "author_name": "Feben Habtehyimer", + "author_inst": "The Department of Medicine, Division of Infectious Diseases" + }, + { + "author_name": "David J.D Shade", + "author_inst": "Departments of Molecular Microbiology and Immunology International Health and Epidemiology" + }, + { + "author_name": "Jessica Ruff", + "author_inst": "The Department of Medicine, Division of Infectious Diseases, Department of Pathology" + }, + { + "author_name": "Malathi Ram", + "author_inst": "The Departments of Molecular Microbiology and Immunology" + }, + { + "author_name": "Oliver Laeyendecker", + "author_inst": "Division of Intramural Research, National Institute of Allergy and Infectious Diseases, NIH" + }, + { + "author_name": "Reinaldo E. Fernandez", + "author_inst": "Department of Medicine, Division of Infectious Diseases" + }, + { + "author_name": "Eshan U. Patel", + "author_inst": "Departments of Molecular Microbiology and Immunology, International Health and Epidemiology" + }, + { + "author_name": "Owen R. Baker", + "author_inst": "The Department of Medicine, Division of Infectious Diseases" + }, + { + "author_name": "Shmuel Shoham", + "author_inst": "The Department of Medicine, Division of Infectious Diseases" + }, + { + "author_name": "Edward R. Cachay", + "author_inst": "Department of Medicine, Division of Infectious Diseases, University of California, San Diego, San Diego, CA" + }, + { + "author_name": "Judith S. Currier", + "author_inst": "Department of Medicine, Division of Infectious Diseases, University of California, Los Angeles, Los Angeles, CA" + }, + { + "author_name": "Jonathan M. Gerber", + "author_inst": "Department of Medicine, Division of Hematology and Oncology, University of Massachusetts, Worchester, MA" + }, + { + "author_name": "Barry Meisenberg", + "author_inst": "Luminis Health, Annapolis, MD" + }, + { + "author_name": "Donald N. Forthal", + "author_inst": "Department of Medicine, Division of Infectious Diseases, University of California, Irvine, Irvine, CA" + }, + { + "author_name": "Laura L. Hammit", + "author_inst": "The Departments of Molecular Microbiology and Immunology, International Health" + }, + { + "author_name": "Moises A. Huaman", + "author_inst": "Department of Medicine, Division of Infectious Diseases University of Cincinnati, Cincinnati, OH" + }, + { + "author_name": "Adam Levine", + "author_inst": "Department of Emergency Medicine, Rhode Island Hospital Warren Alpert Medical School of Brown University, Providence, RI" + }, + { + "author_name": "Giselle S. Mosnaim", + "author_inst": "Division of Allergy and Immunology, Department of Medicine" + }, + { + "author_name": "Bela Patel", + "author_inst": "Northshore University Health System, Evanston, IL; Department of Medicine, Divisions of Pulmonary and Critical Care Medicine, University of Texas Health Science" + }, + { + "author_name": "James H. Paxton", + "author_inst": "Department of Emergency Medicine, Wayne State University, Detroit, MI" + }, + { + "author_name": "Jay S. Raval", + "author_inst": "Department of Pathology, University of New Mexico, Albuquerque, NM" + }, + { + "author_name": "Catherine G. Sutcliffe", + "author_inst": "The Departments of Molecular Microbiology and Immunology, International Health" + }, + { + "author_name": "Sweta Anjan", + "author_inst": "Department of Medicine, Department of Medicine, Division of Infectious Diseases, University of Miami, Miller School of Medicine, Miami, FL" + }, + { + "author_name": "Thomas Gniadek", + "author_inst": "Division of Allergy and Immunology, Department of Medicine and Department of Pathology" + }, + { + "author_name": "Seble Kassaye", + "author_inst": "Departments of Molecular Microbiology and Immunology" + }, + { + "author_name": "Janis E. Blair", + "author_inst": "Department of Medicine, Division of Infectious Diseases, Mayo Clinic Hospital, Phoenix, AZ" + }, + { + "author_name": "Karen Lane", + "author_inst": "Department of Neurology, Brain Injury Outcomes Division" + }, + { + "author_name": "Nichol A. McBee", + "author_inst": "Department of Neurology, Brain Injury Outcomes Division" + }, + { + "author_name": "Amy L. Gawad", + "author_inst": "Department of Neurology, Brain Injury Outcomes Division" + }, + { + "author_name": "Piyali Das", + "author_inst": "Department of Neurology, Brain Injury Outcomes Division" + }, + { + "author_name": "Sabra L. Klein", + "author_inst": "The Departments of Molecular Microbiology and Immunology" + }, + { + "author_name": "Andrew Pekosz", + "author_inst": "The Departments of Molecular Microbiology and Immunology" + }, + { + "author_name": "Arturo Casadevall", + "author_inst": "The Departments of Molecular Microbiology and Immunology" + }, + { + "author_name": "Evan M. Bloch", + "author_inst": "The Department of Medicine, Department of Pathology" + }, + { + "author_name": "Daniel Hanley", + "author_inst": "Department of Neurology, Brain Injury Outcomes Division" + }, + { + "author_name": "Aaron AR Tobian", + "author_inst": "Johns Hopkins Hospital" + }, + { + "author_name": "David J. Sullivan", + "author_inst": "The Departments of Molecular Microbiology and Immunology International Health and Epidemiology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.02.15.23285584", "rel_title": "Post-COVID syndrome is associated with capillary alterations, macrophage infiltration and distinct transcriptomic signatures in skeletal muscles", @@ -144658,57 +146862,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.02.15.23285994", - "rel_title": "Characteristics and outcomes of 7620 Multiple Sclerosis patients admitted with COVID-19 in the United States", - "rel_date": "2023-02-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.15.23285994", - "rel_abs": "BackgroundAt the start of the COVID-19 pandemic, several experts raised concerns about its impact on Multiple Sclerosis (MS) patients. Several small sample studies were published throughout the pandemic highlighting certain risk factors and outcomes. This study aims to provide a perspective using the biggest inpatient database from the United States.\n\nMethodWe screened for COVID-19 cases between April to December 2020, via the 2020 National Inpatient Sample (NIS). Characteristics of COVID-19 patients with and without MS were studied. The odds of mortality, mechanical ventilation and non-invasive ventilation were also analyzed. Finally, we investigated the risk factors of various outcomes among MS patients.\n\nResultsWe identified 1,628,110 hospitalizations with COVID-19, including 7620 (0.5%) MS patients. 68.6% of MS cases were Whites, and 63.3% were covered by Medicare. Compared to non-MS patients, MS patients with COVID-19 were mostly Females, had depression, peripheral vascular disease, and smoked. However, MS patients had lower cases of alcohol abuse, obesity, hyperlipidemia, diabetes, hypertension, CKD, or maintenance dialysis. MS patients with COVID-19 were also younger (mean age 60.65 years vs. 62.60 years, p<0.01). 8.9% of MS patients with COVID-19 did not survive their hospitalization, and it was lower than non-MS cases (12.9%, aOR 0.783, 95% CI 0.721-0.852, p<0.01). Less MS patients with COVID-19 needed non-invasive ventilation (4.5% vs. 6.4%, aOR 0.790, 95% CI 0.706-0.883, p<0.01) and mechanical ventilation (9.0% vs. 11.2%, aOR 1.017, 95% CI 0.937-1.104, p=0.687).\n\nFurthermore, MS patients with COVID-19 reported higher odds of non-invasive ventilation if they were of ages 60 and above (aOR 2.124, p<0.01), had chronic pulmonary disease (aOR 1.691, p<0.01), obesity (aOR 1.69, p<0.01), and diabetes (aOR 1.573, p<0.01). Private insurance beneficiaries showed reduced risk compared to Medicare (aOR 0.523, p<0.01). Similarly, for mechanical ventilation, those ages 60 and above (aOR 1.404, p<0.01), alcohol abuse (aOR 6.404, p<0.01), obesity (aOR 1.417, p<0.01), diabetes (aOR 1.992, p<0.01), hypertension (aOR 1.269, p=0.016), or dialysis (aOR 3.003, p<0.01) had higher odds, while females (aOR 0.700, p<0.01), smokers (aOR 0.588, p<0.01), and those with depression (aOR 0.698, p<0.01) or hyperlipidemia (aOR 0.711, p<0.01) showed reduced odds.\n\nOur study further found higher odds of mortality among those of age 60 and above (aOR 3.813, p<0.01), chronic pulmonary disease (aOR 1.739, p<0.01), obesity (aOR 1.425, p<0.01), CKD (aOR 1.982, p<0.01), or a history of old MI (aOR 1.864, p<0.01) while females (aOR 0.610, p<0.01), smokers (aOR 0.770, p<0.01), as well as those with depression (aOR 0.695, p<0.01), and hyperlipidemia (aOR 0.769, p<0.01) showed better outcomes. Blacks had lower odds of dying (aOR 0.636, p<0.01), whereas Hispanics had higher odds of dying (aOR 1.674, p<0.01), compared to Whites. Medicaid and Privately insured patients had lower odds of dying compared to Medicare i.e. (aOR 0.435, p<0.01), and (aOR 0.488, p<0.01), respectively.\n\nConclusionWe found several differences in patient characteristics among MS and non-MS patients with COVID-19. MS patients were also less likely to die or require non-invasive ventilation than non-MS patients. Further risk factors influencing the different outcomes among MS patients were also identified.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Kamleshun Ramphul", - "author_inst": "Independent Researcher, Mauritius" - }, - { - "author_name": "Shaheen Sombans", - "author_inst": "Department of Neurology, Bharati Vidyapeeth Univ Med College and Hosp, Hyderabad, India" - }, - { - "author_name": "Renuka Verma", - "author_inst": "Department of Neurology, Raj Multispecialty Hospital, Punjab, India" - }, - { - "author_name": "Petras Lohana", - "author_inst": "Department of Nephrology, Jacobi Medical Centre, Bronx, New York" - }, - { - "author_name": "Balkiranjit Kaur Dhillon", - "author_inst": "Independent Researcher, Canada" - }, - { - "author_name": "Stephanie Gonzalez Mejias", - "author_inst": "Independent Researcher, Santo Domingo, Dominican Republic" - }, - { - "author_name": "Sailaja Sanikommu", - "author_inst": "Department of Neurology, Sri Manakula Vinayagar Med College and Hosp, Puducherry, India" - }, - { - "author_name": "Yogeshwaree Ramphul", - "author_inst": "Department of Medicine, Sir Seewoosagur Ramgoolam National Hospital, Mauritius" - }, - { - "author_name": "Prince Kwabla Pekyi-Boateng", - "author_inst": "Greater Accra Regional Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2023.02.14.23285921", "rel_title": "Optimal Delivery Management for the Prevention of Early Neonatal SARS-CoV-2 Infection: Systematic review and Meta-analysis", @@ -145997,6 +148150,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.02.09.527884", + "rel_title": "Nuclear export inhibitor Selinexor targeting XPO1 enhances coronavirus replication.", + "rel_date": "2023-02-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.09.527884", + "rel_abs": "Nucleocytoplasmic transport of proteins using XPO1 (exportin 1) plays a vital role in cell proliferation and survival. Many viruses also exploit this pathway to promote infection and replication. Thus, inhibiting XPO1-mediated nuclear export with selective inhibitors activates multiple antiviral and anti-inflammatory pathways. The XPO1 inhibitor, Selinexor, is an FDA-approved anticancer drug predicted to have antiviral function against many viruses, including SARS-CoV-2. Unexpectedly, we observed that pretreatment of cultured human cells with Selinexor actually enhanced protein expression and replication of coronaviruses, including SARS-CoV-2. Knockdown of cellular XPO1 protein expression significantly enhanced the replication of coronaviruses in human cells. We further demonstrate that Selinexor treatment reduced the formation of unique cytoplasmic antiviral granules that include RNA helicase DHX9 in the virus-infected cells. These results, for the first time, show that the anti-cancer drug Selinexor enhances the replication of coronaviruses in human cells in vitro and thus should be further explored in vivo for the potential impact on the dual use for anticancer and antiviral therapy.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Masmudur M. Rahman", + "author_inst": "Biodesign Institute, Arizona State University" + }, + { + "author_name": "Bereket Estifanos", + "author_inst": "Biodesign Institute, Arizona State University" + }, + { + "author_name": "Honor L. Glenn", + "author_inst": "Biodesign Institute, Arizona State University" + }, + { + "author_name": "Karen V Kibler", + "author_inst": "Biodesign Institute, Arizona State University" + }, + { + "author_name": "Yize Li", + "author_inst": "Biodesign Institute, Arizona State University" + }, + { + "author_name": "Bertram L Jacobs", + "author_inst": "Biodesign Institute, Arizona State University" + }, + { + "author_name": "Grant McFadden", + "author_inst": "Biodesign Institute, Arizona State University" + }, + { + "author_name": "Brenda G. Hogue", + "author_inst": "Biodesign Institute, Arizona State University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2023.02.10.527147", "rel_title": "Proteolytic cleavage and inactivation of the TRMT1 tRNA modification enzyme by SARS-CoV-2 main protease", @@ -146500,25 +148700,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.02.07.23285380", - "rel_title": "Summaries, Analysis and Simulations of Recent COVID-19 Epidemic in Mainland China During December 31 2021-December 6 2022", - "rel_date": "2023-02-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.07.23285380", - "rel_abs": "BackgroundThe recent COVID-19 epidemic in mainland China is an important issue for studying the prevention and disease control measures and the spread of the COVID-19 epidemic. Following our previous study for the mainland China epidemic during December 31 2021 to 30 April 2022, this paper studies and compares the the mainland China epidemic during December 31 2021 to December 6, 2022.\n\nMethodsUsing differential equations and real word data (both domestic and foreign input infected individuals) modelings and simulates COVID-19 epidemic in mainland China during May 1 2022 to December 6 2022, estimates the transmission rates, the recovery rates, the blocking rates to the symptomatic and the asymptomatic infections, and the died rate of the symptomatic infected individuals. The transmission rates and the recovery rates of the foreign input COVID-19 infected individuals in mainland China have also been studied. Using virtual simulations predict the outcomes of the epidemics.\n\nResultsThe simulation results were in good agreement with the real word data.\n\nO_LIThe average input transmission rate of the foreign input symptomatic infection individuals was much lower than the average transmission rates of the symptomatic infection causing by the mainland symptomatic and asymptomatic individuals.\nC_LIO_LIThe average input transmission rate of the foreign input asymptomatic infection individuals was was much lower than the average transmission rate of the asymptomatic infection causing by the mainland symptomatic individuals.\nC_LIO_LIThe average recovery rates of the foreign input COVID-19 symptomatic and asymptomatic infected individuals were much higher than the average recovery rates of the mainland symptomatic and asymptomatic infected individuals.\nC_LI\n\nFor the mainland epidemic simulations:\n\nO_LIIf kept the transmission rates, the recovery rates, the death rate and the blocking rates on day 181 (June 30, 2022), the numbers of the current symptomatic and asymptomatic individuals would reduce to about one on day 270 (September 27, 2022).\nC_LIO_LIIf kept the transmission rates, the recovery rates, the death rate and the blocking rates on day 340 (December 6, 2022) until day 380 (January 15, 2023), the numbers of the current symptomatic and the asymptomatic infected individuals would increase to 37 999 and 224 945, respectively, the cumulative death individuals would increase from 599 to 616.\nC_LIO_LIIf kept the transmission rates, the recovery rates on day 340, but decreased the blocking rates to 34% and select the death rate to equal to the average death rate during days 104-150, then the simulation showed that on day 380, the numbers of current symptomatic and the asymptomatic infected individuals would increase to about 323 559 095 and 481 270 717, respectively, and the cumulative death individuals would reach about 1 055 607.\nC_LI\n\nFor the foreign input epidemic simulations:\n\nO_LIIf kept the transmission rates, the recovery rates, and the blocking rates day 242 (August 30, 2022), until day 340, the numbers of the current symptomatic and the asymptomatic infected individuals would decrease to 13 and 430, respectively.\nC_LIO_LIIf kept the transmission rates, the recovery rates, and the blocking rates on day 340 until day 380 (January 15, 2023), the numbers of the current symptomatic and the asymptomatic infected individuals would decrease and increase to 168 and 1952, respectively.\nC_LIO_LIRecommendations on COVID-19 epidemic base on WHOs technic guidelines and HBV infection experiment in Chimpanzees are provided.\nC_LI\n\nConclusionsO_LIFor the mainland individuals epidemic, keeping the blocking rates of over 86% and 93% to the symptomatic and asymptomatic infections, and the recovery rates of over 0.119 and 0.112 to the symptomatic and asymptomatic individuals may make the numbers of the current symptomatic and asymptomatic infected individuals to decrease to very low levels in three months.\nC_LIO_LIFor the foreign input individuals epidemic, keeping the transmission rates of under 0.07 to the symptomatic and asymptomatic infections, and the recovery rates of over 0.125 and 0.099 to the symptomatic and asymptomatic individuals may make the numbers of the current symptomatic and asymptomatic infected individuals to decrease to very low levels in four months.\nC_LIO_LIAfter December 6 2022, decreasing the blocking rates of under 34% to the symptomatic and asymptomatic infections may cause over 1100 millions individuals COVID-19 infections and over one million COVID-19 infected individuals death.\nC_LIO_LIIt is necessary that administrations implement strict prevent and control strategies to prevent the spread of new COVID-19 variants.\nC_LI", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Lequan Min", - "author_inst": "University of Science and Technology Beijing" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.02.08.527785", "rel_title": "Functional comparisons of the virus sensor RIG-I from humans, the microbat Myotis daubentonii, and the megabat Rousettus aegyptiacus, and their response to SARS-CoV-2 infection", @@ -147691,6 +149872,69 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2023.02.10.527437", + "rel_title": "Antagonistic pleiotropy plays an important role in governing the evolution and genetic diversity of SARS-CoV-2", + "rel_date": "2023-02-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.02.10.527437", + "rel_abs": "Analyses of the genomic diversity of SARS-CoV-2 found that some sites across the genome appear to have mutated independently multiple times with frequency significantly higher than four-fold sites, which can be either due to mutational bias, i.e., elevated mutation rate in some sites of the genome, or selection of the variants due to antagonistic pleiotropy, a condition where mutations increase some components of fitness at a cost to others. To examine how different forces shaped evolution of SARS-CoV-2 in 2020-2021, we analyzed a large set of genome sequences (~ 2 million). Here we show that while evolution of SARS-CoV-2 during the pandemic was largely mutation-driven, a group of nonsynonymous changes is probably maintained by antagonistic pleiotropy. To test this hypothesis, we studied the function of one such mutation, spike M1237I. Spike I1237 increases viral assembly and secretion, but decreases efficiency of transmission in vitro. Therefore, while the frequency of spike M1237I may increase within hosts, viruses carrying this mutation would be outcompeted at the population level. We also discuss how the antagonistic pleiotropy might facilitate positive epistasis to promote virus adaptation and reconcile discordant estimates of SARS-CoV-2 transmission bottleneck sizes in previous studies.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Ding-Chin Lee", + "author_inst": "National Taiwan University College of Medicine" + }, + { + "author_name": "Jui-Hung Tai", + "author_inst": "National Taiwan University College of Medicine" + }, + { + "author_name": "Hsin-Fu Lin", + "author_inst": "National Taiwan University College of Medicine" + }, + { + "author_name": "Tai-Ling Chao", + "author_inst": "National Taiwan University College of Medicine" + }, + { + "author_name": "Yongsen Ruan", + "author_inst": "Sun Yat-sen University School of Life Science" + }, + { + "author_name": "Ya-Wen Cheng", + "author_inst": "National Taiwan University College of Medicine" + }, + { + "author_name": "Yu-Chi Chou", + "author_inst": "Academia Sinica" + }, + { + "author_name": "You-Yu Lin", + "author_inst": "National Taiwan University College of Medicine" + }, + { + "author_name": "Sui-Yuan Chang", + "author_inst": "National Taiwan University College of Medicine" + }, + { + "author_name": "Pei-Jer Chen", + "author_inst": "National Taiwan University College of Medicine" + }, + { + "author_name": "Shiou-Hwei Yeh", + "author_inst": "National Taiwan University College of Medicine" + }, + { + "author_name": "Hurng-Yi Wang", + "author_inst": "National Taiwan University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2023.02.10.528014", "rel_title": "Effect of the SARS-CoV-2 Delta-associated G15U mutation on the s2m element dimerization and its interactions with miR-1307-3p", @@ -148126,33 +150370,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2023.02.07.23285570", - "rel_title": "Who Wears the Face Mask? Preventive Measures Against COVID-19 in Latin America Before Vaccination", - "rel_date": "2023-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.07.23285570", - "rel_abs": "The COVID-19 pandemic outbreak imposed the use of the sanitary mask as a protective measure to reduce the spread of the pandemic, recommended by the World Health Organization. However, the use of the face mask has been uneven and determined by individual, regional, cultural, and political factors. Based on data from the Latinobarometer, we aim to understand the profile of people who used a mask in the context of the COVID-19 pandemic in 18 countries of Latin America, between October and November 2020, right before the mass vaccination campaigns. Results show that women, older people, those with higher education, being employed and not working in temporarily jobs, retirees, students, people with a centrist political ideology, and Catholics, had a higher chance of using a face mask on a regular basis. People living in Venezuela, Chile, Costa Rica and Brazil were the most likely to use face masks. These results call attention to the need to understand social forces behind the willingness to adopt non-pharmacological preventive measures in order to make them more effective in health crisis emergencies.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Elisenda Renter\u00eda", - "author_inst": "Centre d'Estudis Demogr\u00e0fics" - }, - { - "author_name": "Amalia G\u00f3mez-Casillas", - "author_inst": "Centre d'Estudis Demogr\u00e0fics" - }, - { - "author_name": "Pilar Zueras", - "author_inst": "Centre d'Estudis Demogr\u00e0fics; University of Essex" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.02.06.23285436", "rel_title": "Mental distress among Norwegian adults during the Covid-19 pandemic: predictors of initial response and subsequent trajectories", @@ -149297,6 +151514,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.02.05.23285494", + "rel_title": "Serosurvey of SARS-COV-2 at a large public university", + "rel_date": "2023-02-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.05.23285494", + "rel_abs": "Arizona State University (ASU) is one the largest universities in the United States, with more than 79,000 students attending in-person classes. We conducted a seroprevalence study from September 13-17, 2021 to estimate the number of people in our community with SARS-CoV-2-specific antibodies due to previous exposure to SARS-CoV-2 and/or vaccination. Participants provided their age, gender, race, status (student or employee), and general COVID-19 health-related information like previous exposure and vaccination status. The seroprevalence of the anti-receptor binding domain (RBD) antibody was 90% by a lateral flow assay and 88% by a semi-quantitative chemiluminescent immunoassay. The seroprevalence for anti-nucleocapsid (NC) was 20%. In addition, individuals with previous natural COVID infection plus vaccination had higher anti-RBD antibody levels compared to those who had vaccination only or infection only. Individuals who had a breakthrough infection had the highest anti-RBD antibody levels.\n\nAccurate estimates of the cumulative incidence of SARS-CoV-2 infection can inform the development of university risk mitigation protocols such as encouraging booster shots, extending mask mandates, or reverting to online classes. It could help us to have clear guidance to take action at the first sign of the next surge as well, especially since there is a surge of COVID subvariant infections.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Ching-Wen Hou", + "author_inst": "ASU" + }, + { + "author_name": "Stacy Williams", + "author_inst": "ASU" + }, + { + "author_name": "Kylee Taylor", + "author_inst": "ASU" + }, + { + "author_name": "Veronica Boyle", + "author_inst": "ASU" + }, + { + "author_name": "Bradley Bobbett", + "author_inst": "ASU" + }, + { + "author_name": "Joseph Kouvetakis", + "author_inst": "ASU" + }, + { + "author_name": "Keana Nguyen", + "author_inst": "ASU" + }, + { + "author_name": "Aaron McDonald", + "author_inst": "ASU" + }, + { + "author_name": "Valerie Harris", + "author_inst": "ASU" + }, + { + "author_name": "Benjamin Nussle", + "author_inst": "ASU" + }, + { + "author_name": "Phillip Scharf", + "author_inst": "ASU" + }, + { + "author_name": "Megan Jehn", + "author_inst": "ASU" + }, + { + "author_name": "Timothy Lant", + "author_inst": "ASU" + }, + { + "author_name": "Mitch Magee", + "author_inst": "ASU" + }, + { + "author_name": "Yunro Chung", + "author_inst": "ASU" + }, + { + "author_name": "Joshua Labaer", + "author_inst": "ASU" + }, + { + "author_name": "Vel Murugan", + "author_inst": "ASU" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.02.07.527419", "rel_title": "Dogs and cats are less susceptible to the omicron variant of concern of SARS-CoV-2 - a field study", @@ -149756,45 +152056,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.02.02.23285377", - "rel_title": "Disease severity of unvaccinated SARS-CoV-2 positive adults less than 65 years old without comorbidity, in the Omicron period and pre-Omicron periods", - "rel_date": "2023-02-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.02.23285377", - "rel_abs": "BackgroundThe reduced severity and burden of COVID-19 in 2022 can largely be attributable to vaccination and a shift to Omicron predominance. However, millions of individuals remain unvaccinated. In the present study, we aimed to study disease severity in unvaccinated individuals without risk factors during the Omicron period, compared to pre-Omicron periods.\n\nMethodsThis register-based study included all unvaccinated individuals in Sweden aged 18-64 years without comorbidity or care dependency who were SARS-CoV-2 positive between week 45 of 2020 and week 5 of 2022. Variant of concern (VOC) periods were periods with certain VOCs identified in [≥]92% of sequenced cases nationwide. Outcomes were hospitalization with a main discharge code of COVID-19; severe illness, defined as high-flow nasal oxygen treatment or intensive care unit admission; and death with COVID-19 as the underlying cause of death on the death certificate.\n\nResultsAmong 788,895 individuals in the overall SARS-CoV-2 positive cohort, both hospitalization and death increased stepwise from the pre-VOC period to the Alpha and Delta periods, and decreased in the Omicron period. Among 15,179 patients hospitalized for COVID-19, the proportions with severe illness and death increased to the Delta period, but in the Omicron period, these outcomes returned to the level of the pre-VOC period.\n\nConclusionIn the Omicron period, compared to pre-Omicron periods, unvaccinated SARS-CoV-2 positive adults <65 years old without comorbidity had reduced proportions of hospitalization and death overall, but similar proportion of severe illness among patients hospitalized for COVID-19. These results support continuous efforts to prevent hospitalizations for COVID-19.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Erik Wahlstrom", - "author_inst": "National Board of Health and Welfare" - }, - { - "author_name": "Daniel Bruce", - "author_inst": "National Board of Health and Welfare" - }, - { - "author_name": "Anna M Bennet-Bark", - "author_inst": "National Board of Health and Welfare" - }, - { - "author_name": "Sten Walther", - "author_inst": "Swedish Intensive Care Registry" - }, - { - "author_name": "Hakan Hanberger", - "author_inst": "Faculty of Medicine" - }, - { - "author_name": "Kristoffer Stralin", - "author_inst": "Karolinska Institutet" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2023.02.05.527215", "rel_title": "Prior vaccination enhances immune responses during SARS-CoV-2 breakthrough infection with early activation of memory T cells followed by production of potent neutralizing antibodies", @@ -151191,6 +153452,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.02.01.23285134", + "rel_title": "Covid-19 Vaccination in India: An Exploratory Analysis", + "rel_date": "2023-02-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.02.01.23285134", + "rel_abs": "Our study is designed to explore the patterns in covid vaccination coverage in India at the district level. We use data from the first six months of covid vaccination drive in India that we combine with several other administrative data to create a unique data set that facilitates heterogeneity analysis across different vaccination phases and districts. We find evidence of past reported infection rates positively correlated with higher first dose covid vaccination outcomes. Higher Deaths as a proportion of district population is associated with lower vaccination uptake but as a percentage of reported infection was positively correlated with first dose covid vaccination. Districts that on average had higher population burden per health centre also had lower covid vaccination rates. Vaccination rates were lower in rural areas relative to urban areas whereas the association with literacy rate was positive. A higher vaccination rate among the population with higher blood pressure and hypertension (one of the comorbidities with covid infection) was observed while vaccination rates were lower among pregnant women and breastfeeding mothers. Districts with higher percentage of children with complete immunisation were associated with higher covid vaccination rates whereas low vaccination rates were observed in districts that reported relatively higher percentage of wasted children.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Sandip Kumar Agarwal", + "author_inst": "Indian Institute of Science Education and Research Bhopal" + }, + { + "author_name": "Maharnab Naha", + "author_inst": "Indian Institute of Science Education and Research Bhopal" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.02.01.23285349", "rel_title": "Minimal mRNA uptake and inflammatory response to COVID-19 mRNA vaccine exposure in human placental explants", @@ -151710,77 +153994,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.01.31.23285233", - "rel_title": "Sociodemographic and socioeconomic disparities in COVID-19 vaccine uptake - A nationwide record linkage study", - "rel_date": "2023-02-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.31.23285233", - "rel_abs": "BackgroundRecent studies have identified important social inequalities in SARS-CoV-2 infection and related COVID-19 outcomes in the Belgian population. The aim of our study was to investigate the sociodemographic and socioeconomic characteristics associated with the uptake of COVID-19 vaccine in Belgium.\n\nMethodsWe conducted a cross-sectional analysis of the uptake of a first COVID-19 vaccine dose among 5,342,110 adults ([≥]18 years) in Belgium from December 28th 2020 (official starting date of the vaccination campaign) until August 31st 2021. We integrated data from four national data sources: the Belgian vaccine register (vaccination status), COVID-19 Healthdata (laboratory test results), DEMOBEL (sociodemographic/socioeconomic data), and the Common Base Registry for HealthCare Actors (individuals licensed to practice a healthcare profession in Belgium). We used multivariable logistic regression analysis for identifying characteristics associated with not having obtained a first COVID-19 vaccine dose in Belgium and for each of its three regions (Flanders, Brussels, and Wallonia).\n\nResultsDuring the study period, 10% (536,716/5,342,110) of the Belgian adult population included in our study sample was not vaccinated with a first COVID-19 vaccine dose. A lower COVID-19 vaccine uptake was found among young individuals, men, migrants, single parents, one-person households, and disadvantaged socioeconomic groups (with lower levels of income and education, unemployed). Overall, the sociodemographic and socioeconomic disparities were comparable for all regions.\n\nConclusionsThe identification of sociodemographic and socioeconomic disparities in COVID-19 vaccination uptake is critical to develop strategies guaranteeing a more equitable vaccination coverage of the Belgian adult population.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Lisa Cavillot", - "author_inst": "Sciensano, Catholic university of Louvain" - }, - { - "author_name": "Joris A.F van Loenhout", - "author_inst": "Sciensano" - }, - { - "author_name": "Brecht Devleesschauwer", - "author_inst": "Sciensano, Ghent university" - }, - { - "author_name": "Chloe Whyndham-Thomas", - "author_inst": "Sciensano" - }, - { - "author_name": "Herman Van Oyen", - "author_inst": "Sciensano" - }, - { - "author_name": "Jinane Ghattas", - "author_inst": "Catholic university of Louvain" - }, - { - "author_name": "Koen Blot", - "author_inst": "Sciensano" - }, - { - "author_name": "Laura Van den Borre", - "author_inst": "Sciensano, Vrije universiteit of Brussels" - }, - { - "author_name": "Matthieu Billuart", - "author_inst": "Sciensano" - }, - { - "author_name": "Niko Speybroeck", - "author_inst": "Catholic university of Louvain" - }, - { - "author_name": "Robby De Pauw", - "author_inst": "Sciensano, Ghent university" - }, - { - "author_name": "Veerle Stouten", - "author_inst": "Sciensano" - }, - { - "author_name": "Lucy Catteau", - "author_inst": "Sciensano" - }, - { - "author_name": "Pierre Hubin", - "author_inst": "Sciensano" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2023.01.30.23285170", "rel_title": "Older age, lack of vaccination and infection with variants other than Omicron associated with severity of COVID-19 and in-hospital mortality in Pakistan", @@ -152997,6 +155210,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, + { + "rel_doi": "10.1101/2023.01.28.525917", + "rel_title": "SARS-CoV-2 Mpro protease variants of concern display altered viral and host target processing but retain potency towards antivirals", + "rel_date": "2023-01-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.28.525917", + "rel_abs": "Main protease of SARS-CoV-2 (Mpro) is the most promising drug target against coronaviruses due to its essential role in virus replication. With newly emerging variants there is a concern that mutations in Mpro may alter structural and functional properties of protease and subsequently the potency of existing and potential antivirals. We explored the effect of 31 mutations belonging to 5 variants of concern (VOC) on catalytic parameters and substrate specificity, which revealed changes in substrate binding and rate of cleavage of a viral peptide. Crystal structures of 11 Mpro mutants provided structural insight into their altered functionality. Additionally, we show Mpro mutations influence proteolysis of an immunomodulatory host protein Galectin-8 (Gal-8) and subsequent significant decrease in cytokine secretion, providing evidence for alterations in escape of host-antiviral mechanisms. Accordingly, mutations associated with the highly virulent Delta VOC resulted in significant increase in Gal-8 cleavage. Importantly, IC50s of nirmatrelvir (Pfizer) and our irreversible inhibitor AVI-8053 demonstrated no changes in potency for both drugs for all mutants, suggesting Mpro will remain a high-priority antiviral drug candidate as SARS-CoV-2 evolves.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Sizhu Amelia Chen", + "author_inst": "University of Alberta" + }, + { + "author_name": "Elena Arutyunova", + "author_inst": "Department of Biochemistry, Li Ka Shing Institute of Virology, University of Alberta" + }, + { + "author_name": "Jimmy Lu", + "author_inst": "Department of Biochemistry, Li Ka Shing Institute of Virology, University of Alberta" + }, + { + "author_name": "Muhammad Bashir Khan", + "author_inst": "Department of Biochemistry, University of Alberta" + }, + { + "author_name": "Wioletta Rut", + "author_inst": "Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology" + }, + { + "author_name": "Mikolaj Zmudzinski", + "author_inst": "Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology" + }, + { + "author_name": "Shima Shahbaz", + "author_inst": "Department of Dentistry & Dental Hygiene, University of Alberta" + }, + { + "author_name": "Jegan Iyyathurai", + "author_inst": "Department of Biochemistry, Li Ka Shing Institute of Virology, University of Alberta" + }, + { + "author_name": "Eman Moussa", + "author_inst": "Department of Biochemistry, University of Alberta" + }, + { + "author_name": "Zoe Turner", + "author_inst": "Department of Biochemistry, University of Alberta" + }, + { + "author_name": "Bing Bai", + "author_inst": "Li Ka Shing Applied Virology Institute, Department of Medical Microbiology and Immunology, University of Alberta" + }, + { + "author_name": "Tess Lamer", + "author_inst": "Department of Chemistry, University of Alberta" + }, + { + "author_name": "James A. Nieman", + "author_inst": "Li Ka Shing Applied Virology Institute, Department of Medical Microbiology and Immunology, University of Alberta" + }, + { + "author_name": "John C. Vederas", + "author_inst": "Department of Chemistry, University of Alberta" + }, + { + "author_name": "Olivier Julien", + "author_inst": "Department of Biochemistry, University of Alberta" + }, + { + "author_name": "Marcin Drag", + "author_inst": "Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology" + }, + { + "author_name": "Shokrollah Elahi", + "author_inst": "Department of Dentistry & Dental Hygiene, University of Alberta" + }, + { + "author_name": "Howard S. Young", + "author_inst": "Department of Biochemistry, University of Alberta" + }, + { + "author_name": "M. Joanne Lemieux", + "author_inst": "Department of Biochemistry, Li Ka Shing Institute of Virology, University of Alberta" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2023.01.27.525936", "rel_title": "Motifs in SARS-CoV-2 evolution", @@ -153604,77 +155908,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2023.01.24.23284959", - "rel_title": "Effectiveness of a chatbot in improving the mental wellbeing of health workers in Malawi during the COVID-19 pandemic: A randomized, controlled trial", - "rel_date": "2023-01-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.24.23284959", - "rel_abs": "We conducted a randomized, controlled trial (RCT) to investigate our hypothesis that the interactive chatbot, Vitalk, is more effective in improving mental wellbeing and resilience outcomes of health workers in Malawi than the passive use of Internet resources.\n\nFor our 2-arm, 8-week, parallel RCT (ISRCTN Registry: trial ID ISRCTN16378480), we recruited participants from 8 professional cadres from public and private healthcare facilities. The treatment arm used Vitalk; the control arm received links to Internet resources. The research team was blinded to the assignment. Of 1,584 participants randomly assigned to the treatment and control arms, 215 participants in the treatment and 296 in the control group completed baseline and endline anxiety assessments. Six assessments provided outcome measures for: anxiety (GAD-7); depression (PHQ-9); burnout (OLBI); loneliness (ULCA); resilience (RS-14); and resilience-building activities. We analyzed effectiveness using mixed-effects linear models, effect size estimates, and reliable change in risk levels.\n\nResults support our hypothesis. Difference-in-differences estimators showed that Vitalk reduced: depression (-0.68 [95% CI -1.15 to -0.21]); anxiety (-0.44 [95% CI -0.88 to 0.01]); and burnout (-0.58 [95% CI -1.32 to 0.15]). Changes in resilience (1.47 [95% CI 0.05 to 2.88]) and resilience-building activities (1.22 [95% CI 0.56 to 1.87]) were significantly greater in the treatment group. Our RCT produced a medium effect size for the treatment and a small effect size for the control group.\n\nThis is the first RCT of a mental health app for healthcare workers during the COVID-19 pandemic in Southern Africa combining multiple mental wellbeing outcomes and measuring resilience and resilience-building activities. A substantial number of participants could have benefited from mental health support (1 in 8 reported anxiety and depression; 3 in 4 suffered burnout; and 1 in 4 had low resilience). Such help is not readily available in Malawi. Vitalk has the potential to fill this gap.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Eckhard Kleinau", - "author_inst": "University Research Co. (URC)" - }, - { - "author_name": "Tilinao Lamba", - "author_inst": "Dept. of Psychology, University of Malawi, Chancellor College, Zomba, Malawi" - }, - { - "author_name": "Wanda Jaskiewicz", - "author_inst": "Global Health Division, Chemonics International, Washington, District of Columbia, United States of America" - }, - { - "author_name": "Katy Gorentz", - "author_inst": "Global Health Division, Chemonics International, Washington, District of Columbia, United States of America" - }, - { - "author_name": "Ines Hungerbuehler", - "author_inst": "Clinical Division, Vitalk, Sao Paulo, Brazil" - }, - { - "author_name": "Donya Rahimi", - "author_inst": "Global Health Division, Chemonics International, Washington, District of Columbia, United States of America" - }, - { - "author_name": "Demoubly Kokota", - "author_inst": "Dept. of Psychology, University of Malawi, Chancellor College, Zomba, Malawi" - }, - { - "author_name": "Limbika Maliwichi", - "author_inst": "Dept. of Psychology, University of Malawi, Chancellor College, Zomba, Malawi" - }, - { - "author_name": "Edister Jamu", - "author_inst": "Dept. of Psychology, University of Malawi, Chancellor College, Zomba, Malawi" - }, - { - "author_name": "Alex Zumazuma", - "author_inst": "Department of Mental Health, Kamuzu University of Health Sciences (KUHES), Blantyre, Malawi" - }, - { - "author_name": "Mariana Negrao", - "author_inst": "Clinical Division, Vitalk, Sao Paulo, Brazil" - }, - { - "author_name": "Raphael Mota", - "author_inst": "Clinical Division, Vitalk, Sao Paulo, Brazil" - }, - { - "author_name": "Yasmine Khouri", - "author_inst": "Clinical Division, Vitalk, Sao Paulo, Brazil" - }, - { - "author_name": "Michael Kapps", - "author_inst": "Clinical Division, Vitalk, Sao Paulo, Brazil" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2023.01.24.23284913", "rel_title": "Longitudinal home self-collection of capillary blood using homeRNA correlates interferon and innate viral defense pathways with SARS-CoV-2 viral clearance", @@ -154911,6 +157144,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.01.25.23285015", + "rel_title": "HPV and HBV vaccine hesitancy, intention and uptake in the era of social media and COVID-19: A review", + "rel_date": "2023-01-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.25.23285015", + "rel_abs": "Prior to the COVID-19 pandemic, the World Health Organization named vaccine hesitancy as one of the top 10 threats to global health. The impact of hesitancy on uptake of human papillomavirus (HPV) vaccines was of particular concern, given the markedly lower uptake compared to other adolescent vaccines in some countries, notably the United States. With the recent approval of COVID-19 vaccines coupled with the widespread use of social media, concerns regarding vaccine hesitancy have grown. However, the association between COVID-related vaccine hesitancy and cancer vaccines such as HPV is unclear. To examine the potential association, we performed two reviews using Ovid Medline and APA PsychInfo. Our aim was to answer two questions: (1) Is COVID-19 vaccine hesitancy, intention, or uptake associated with HPV or HBV vaccine hesitancy, intention, or uptake? and (2) Is exposure to COVID-19 vaccine misinformation on social media associated with HPV or HBV vaccine hesitancy, intention, or uptake? Our review identified few published empirical studies that addressed these questions. Our results highlight the urgent need for studies that can shift through the vast quantities of social media data to better understand the link between COVID-19 vaccine misinformation and disinformation and its impact on uptake of cancer vaccines.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Emily K Vraga", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Sonya S Brady", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Chloe Gansen", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Euna Mehnaz Khan", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Sarah L Bennis", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Madalyn Nones", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Rongwei Tang", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Jaideep Srivastava", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Shalini Kulasingam", + "author_inst": "University of Minnesota" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.01.25.23285014", "rel_title": "Incident autoimmune diseases in association with a SARS-CoV-2 infection: A matched cohort study", @@ -155502,53 +157786,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.01.24.525413", - "rel_title": "RAMEN identifies effective indicators for severe COVID and Long COVID patients", - "rel_date": "2023-01-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.24.525413", - "rel_abs": "The COVID-19 pandemic has significantly altered global socioeconomic structures and individual lives. Understanding the disease mechanisms and facilitating diagnosis requires comprehending the complex interplay among clinical factors like demographics, symptoms, comorbidities, treatments, lab results, complications, and other metrics, and their relation to outcomes such as disease severity and long term outcomes (e.g., post-COVID-19 condition/long COVID). Conventional correlational methods struggle with indirect and directional connections among these factors, while standard graphical methods like Bayesian networks are computationally demanding for extensive clinical variables. In response, we introduced RAMEN, a methodology that integrates Genetic Algorithms with random walks for efficient Bayesian network inference, designed to map the intricate relationships among clinical variables. Applying RAMEN to the Biobanque quebecoise de la COVID-19 (BQC19) dataset, we identified critical markers for long COVID and varying disease severity. The Bayesian Network, corroborated by existing literature and supported through multi-omics analyses, highlights significant clinical variables linked to COVID-19 outcomes. RAMENs ability to accurately map these connections contributes substantially to developing early and effective diagnostics for severe COVID-19 and long COVID.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Yiwei Xiong", - "author_inst": "Meakins-Christie Laboratories, Research Institute of McGill Health Centre, Montreal, QC, Canada" - }, - { - "author_name": "Jingtao Wang", - "author_inst": "Meakins-Christie Laboratories, Research Institute of McGill Health Centre, Montreal, QC, Canada" - }, - { - "author_name": "Xiaoxiao Shang", - "author_inst": "Meakins-Christie Laboratories, Research Institute of McGill Health Centre, Montreal, QC, Canada" - }, - { - "author_name": "Tingting Chen", - "author_inst": "Meakins-Christie Laboratories, Research Institute of McGill Health Centre, Montreal, QC, Canada" - }, - { - "author_name": "Douglas D. Fraser", - "author_inst": "Lawson Health Research Institute" - }, - { - "author_name": "Gregory Fonseca", - "author_inst": "Meakins-Christie Laboratories, Research Institute of McGill Health Centre, Montreal, QC, Canada" - }, - { - "author_name": "Simon Rousseau", - "author_inst": "Meakins-Christie Laboratories, Research Institute of McGill Health Centre, Montreal, QC, Canada" - }, - { - "author_name": "Jun Ding", - "author_inst": "Meakins-Christie Laboratories, Research Institute of McGill Health Centre, Montreal, QC, Canada" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2023.01.23.23284902", "rel_title": "COVID-19 in Pakistan: A national analysis of five pandemic waves", @@ -156769,6 +159006,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.01.23.525130", + "rel_title": "Prediction of SARS-CoV-2 spike protein mutations using Sequence-to-Sequence and Transformer models", + "rel_date": "2023-01-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.23.525130", + "rel_abs": "In the study of viral epidemics, having information about the structural evolution of the virus can be very helpful in controlling the disease and making vaccines. Various deep learning and natural language processing techniques (NLP) can be used to analyze genetic structure of viruses, namely to predict their mutations. In this paper, by using Sequence-to-Sequence (Seq2Seq) model with Long Short-Term Memory (LSTM) cell and Transformer model with the attention mechanism, we investigate the spike protein mutations of SARS-CoV-2 virus. We make time-series datasets of the spike protein sequences of this virus and generate upcoming spike protein sequences. We also determine the mutations of the generated spike protein sequences, by comparing these sequences with the Wuhan spike protein sequence. We train the models to make predictions in December 2021, February 2022, and October 2022. Furthermore, we find that some of our generated spike protein sequences have been reported in December 2021 and February 2022, which belong to Delta and Omicron variants. The results obtained in the present study could be useful for prediction of future mutations of SARS-CoV-2 and other viruses.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Hamed Ahmadi", + "author_inst": "Iran University of Science and Technology" + }, + { + "author_name": "Vahid Nikoofard", + "author_inst": "Rio de Janeiro State University: Universidade do Estado do Rio de Janeiro" + }, + { + "author_name": "Hossein Nikoofard", + "author_inst": "Iran University of Science and Technology" + }, + { + "author_name": "Ruhollah Abdolvahab", + "author_inst": "Iran University of Science and Technology" + }, + { + "author_name": "Narges Nikoofard", + "author_inst": "University of Kashan" + }, + { + "author_name": "Mahdi Esmaeilzadeh", + "author_inst": "Iran University of Science and Technology" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2023.01.23.23284899", "rel_title": "Real-world effectiveness of Azvudine in hospitalized patients with COVID-19: a retrospective cohort study", @@ -157260,129 +159536,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.01.20.524893", - "rel_title": "Whole transcriptome profiling of placental pathobiology in SARS-CoV-2 pregnancies identifies a preeclampsia-like gene signature", - "rel_date": "2023-01-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.20.524893", - "rel_abs": "ObjectivesSevere Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus infection in pregnancy is associated with higher incidence of placental dysfunction, referred to by a few studies as a \"preeclampsia-like syndrome\". However, the mechanisms underpinning SARS-CoV-2-induced placental malfunction are still unclear. Here, we investigated whether the transcriptional architecture of the placenta is altered in response to SARS-CoV-2 infection.\n\nMethodsWe utilized whole-transcriptome, digital spatial profiling, to examine gene expression patterns in placental tissues from participants who contracted SARS-CoV-2 in the third trimester of their pregnancy (n=7) and those collected prior to the start of the coronavirus disease 2019 (COVID-19) pandemic (n=9).\n\nResultsThrough comprehensive spatial transcriptomic analyses of the trophoblast and villous core stromal cell subpopulations in the placenta, we identified signatures associated with hypoxia and placental dysfunction during SARS-CoV-2 infection in pregnancy. Notably, genes associated with vasodilation (NOS3), oxidative stress (GDF15, CRH), and preeclampsia (FLT1, EGFR, KISS1, PAPPA2), were enriched with SARS-CoV-2. Pathways related to increased nutrient uptake, vascular tension, hypertension, and inflammation, were also enriched in SARS-CoV-2 samples compared to uninfected controls.\n\nConclusionsOur findings demonstrate the utility of spatially resolved transcriptomic analysis in defining the underlying pathogenic mechanisms of SARS-CoV-2 in pregnancy, particularly its role in placental dysfunction. Furthermore, this study highlights the significance of digital spatial profiling in mapping the intricate crosstalk between trophoblasts and villous core stromal cells, thus shedding light on pathways associated with placental dysfunction in pregnancies with SARS-CoV-2 infection.\n\nGraphical abstractIn this study, using spatial digital profiling transcriptomic approaches, we demonstrate that SARS-CoV-2 infection in pregnancy disrupts optimal placental function by altering the genomic architecture of trophoblasts and villous core stromal cells.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Nataly Stylianou", - "author_inst": "Queensland University of Technology" - }, - { - "author_name": "Ismail Sebina", - "author_inst": "QIMR Berghofer Medical Research Institute" - }, - { - "author_name": "Nicholas Matigian", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Hadeel Deohler", - "author_inst": "Queensland University of Technology" - }, - { - "author_name": "James Monkman", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Joan Rohl", - "author_inst": "Bond University" - }, - { - "author_name": "Mark Allenby", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Andy Nam", - "author_inst": "Nanostring Technologies" - }, - { - "author_name": "Liuliu Pan", - "author_inst": "Nanostring Technologies" - }, - { - "author_name": "Anja Rockstroh", - "author_inst": "Queensland University of Technology" - }, - { - "author_name": "Habib Sadeghirad", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Kimberly Chung", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Thais Sobanski", - "author_inst": "Queensland University of Technology" - }, - { - "author_name": "Kenneth O'Byrne", - "author_inst": "Queensland University of Technology" - }, - { - "author_name": "Particia Zadorosnei Rebutini", - "author_inst": "Postgraduate Program of Health Sciences, School of Medicine, Pontif\u00edcia Universidade Cat\u00f3lica do Paran\u00e1 -PUCPR" - }, - { - "author_name": "Cleber Machado-Souza", - "author_inst": "Instituto de Pesquisa Pel\u00e9 Pequeno pr\u00edncipe" - }, - { - "author_name": "Emanuele Therezinha Schueda Stonoga", - "author_inst": "Universidade Federal do Paran\u00e1 -UFPR" - }, - { - "author_name": "Majid E. Warkiani", - "author_inst": "Sydney Informatics Hub, Core Research Facilities, University of Sydney, NSW, Australia" - }, - { - "author_name": "Carlos Salomon", - "author_inst": "Centre for Clinical Research, University of Queensland" - }, - { - "author_name": "Kirsty Renfree Short", - "author_inst": "University of Queensland" - }, - { - "author_name": "Lana McClements", - "author_inst": "University of Technology Sydney" - }, - { - "author_name": "Lucia de Noronha", - "author_inst": "Pontifical Catholic University of Parana" - }, - { - "author_name": "Ruby Yun-Ju Huang", - "author_inst": "National Taiwan University" - }, - { - "author_name": "Gabrielle Belz", - "author_inst": "The University of Queensland" - }, - { - "author_name": "Fernando Guimaraes", - "author_inst": "Diamantina Institute" - }, - { - "author_name": "Vicki Clifton", - "author_inst": "Mater Medical Research Institute" - }, - { - "author_name": "Arutha Kulasinghe", - "author_inst": "The University of Queensland" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "developmental biology" - }, { "rel_doi": "10.1101/2023.01.19.23284772", "rel_title": "Estimating The Uncertain Effect of the COVID Pandemic on Drug Overdoses", @@ -158491,6 +160644,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2023.01.13.23284501", + "rel_title": "The impact on mental health of young Asian Americans due to acts of discrimination and hate crimes during COVID-19", + "rel_date": "2023-01-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.13.23284501", + "rel_abs": "This article is an examination of the acts of discriminiation and hate crimes against the Asian American community and how their mental health has been impacted. The historical examination of acts against the Asian American community stem from acts against the Asian American community during both the yellow peril and the Roosevelt Era. Alongside current day institutionalized policies that are propagated by the media, the resurrection of historical tropes further act to seclude Asian Americans from mainstream society. These acts of seclusion further drive mental health inequality in Asian American society that include, but are not limited to: anxiety, depression, and psychological stress. These mental health inequalities are further subdivided into different ethnic groups that worsen as data is collected from older generations. More recently, COVID-19 has brought forth an upsurge in hate crimes that has only worsened the ability of Asian American youth to fully develop a racial identity; the upsurge in hate crimes is also coupled with invalidation of interethnic differences and invalidation of their discriminatory experiences. The synthesis of current day research will aid in the understanding of the mental health inequality in the Asian American community and aid in further studies that can address these plights.\n\nPurpose StatementThe purpose of this paper is to investigate how acts of discrimination and hate crimes against the Asian community have impacted the mental health of young Asian Americans. This review seeks to explore the many effects of race-based discrimiation specifically for Asian Americans during and after the COVID-19 (coronavirus pandemic) such as: general feelings of inclusivity, physiological responses as a result of increasing racist encounters, and incidences of mental health experiences. Overall, the paper highlights how these characteristics manifest within the Asian American population and what measures and interventions can be done to protect Asian American from the negative consequences of hate.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ahmed Gawash", + "author_inst": "Rowan University School of Osteopathic Medicine" + }, + { + "author_name": "David Lo", + "author_inst": "APSEA" + }, + { + "author_name": "Brianna Nghiem", + "author_inst": "Rowan School of Osteopathic Medicine" + }, + { + "author_name": "Priscilla Rofail", + "author_inst": "Rowan School of Osteopathic Medicine" + }, + { + "author_name": "Sayan Basu", + "author_inst": "Rowan School of Osteopathic Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2023.01.15.23284579", "rel_title": "Extensive SARS-CoV-2 testing reveals BA.1/BA.2 asymptomatic rates and underreporting in school children", @@ -159190,57 +161378,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2023.01.16.23284633", - "rel_title": "Differences Between Reported COVID-19 Deaths and Estimated Excess Deaths in Counties Across the United States, March 2020 to February 2022", - "rel_date": "2023-01-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.16.23284633", - "rel_abs": "Accurate and timely tracking of COVID-19 deaths is essential to a well-functioning public health surveillance system. The extent to which official COVID-19 death tallies have captured the true toll of the pandemic in the United States is unknown. In the current study, we develop a Bayesian hierarchical model to estimate monthly excess mortality in each county over the first two years of the pandemic and compare these estimates to the number of deaths officially attributed to Covid-19 on death certificates. Overall, we estimated that 268,176 excess deaths were not reported as Covid-19 deaths during the first two years of the Covid-19 pandemic, which represented 23.7% of all excess deaths that occurred. Differences between excess deaths and reported COVID-19 deaths were substantial in both the first and second year of the pandemic. Excess deaths were less likely to be reported as COVID-19 deaths in the Mountain division, in the South, and in nonmetro counties. The number of excess deaths exceeded COVID-19 deaths in all Census divisions except for the New England and Middle Atlantic divisions where there were more COVID-19 deaths than excess deaths in large metro areas and medium or small metro areas. Increases in excess deaths not assigned to COVID-19 followed similar patterns over time to increases in reported COVID-19 deaths and typically preceded or occurred concurrently with increases in reported COVID-19 deaths. Estimates from this study can be used to inform targeting of resources to areas in which the true toll of the COVID-19 pandemic has been underestimated.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Eugenio Paglino", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Dielle J. Lundberg", - "author_inst": "University of Washington" - }, - { - "author_name": "Zhenwei Zhou", - "author_inst": "Boston University School of Public Health" - }, - { - "author_name": "Joe A. Wasserman", - "author_inst": "RTI International" - }, - { - "author_name": "Rafeya Raquib", - "author_inst": "Boston University School of Public Health" - }, - { - "author_name": "Katherine Hempstead", - "author_inst": "Robert Wood Johnson Foundation" - }, - { - "author_name": "Samuel H. Preston", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Irma T. Elo", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Andrew C. Stokes", - "author_inst": "Boston University School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.01.17.23284684", "rel_title": "Who is most at risk of dying if infected with SARS-CoV-2? A mortality risk factor analysis using machine learning of COVID-19 patients over time in a large Mexican population.", @@ -160509,6 +162646,57 @@ "type": "new results", "category": "neuroscience" }, + { + "rel_doi": "10.1101/2023.01.13.524025", + "rel_title": "Redistribution and activation of CD16brightCD56dim NK cell subset to fight against Omicron subvariant BA.2 after COVID-19 vaccination", + "rel_date": "2023-01-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.13.524025", + "rel_abs": "With the alarming surge in COVID-19 cases globally, vaccination must be prioritised to achieve herd immunity. Immune dysfunction is detected in the majority of patients with COVID-19; however, it remains unclear whether the immune responses elicited by COVID-19 vaccination function against the Omicron subvariant BA.2. Of the 508 Omicron BA.2-infected patients enrolled, 102 were unvaccinated controls and 406 were vaccinated. Despite the presence of clinical symptoms in both groups, vaccination led to a significant decline in nausea or vomiting, abdominal pain, headache, pulmonary infection, overall clinical symptoms, and a moderate rise in body temperature. Omicron BA.2-infected individuals were also characterised by a mild increase in both serum pro- and anti-inflammatory cytokine levels after vaccination. There were no significant differences or trend changes between T and B lymphocyte subsets; however, a significant expansion of NK lymphocytes in COVID-19-vaccinated patients was observed. Moreover, the most effective CD16brightCD56dim subsets of NK cells showed increased functional capacities, as evidenced by a significantly greater IFN-{gamma} secretion and stronger cytotoxic potential in Omicron BA.2-infected patients after vaccination. Collectively, these results suggest that COVID-19 vaccination interventions promote the redistribution and activation of CD16brightCD56dim NK cell subsets against viral infections, and could facilitate the clinical management of Omicron BA.2-infected patients.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Yang Liu", + "author_inst": "First Affiliated Hospital of Nanchang University" + }, + { + "author_name": "Huiyun Peng", + "author_inst": "Nanchang University" + }, + { + "author_name": "Tianxin Xiang", + "author_inst": "Medical Center for Major Public Health Events in Jiangxi Province, the First Affiliated Hospital of Nanchang University" + }, + { + "author_name": "Fei Xu", + "author_inst": "The First Affiliated Hospital of Nanchang University" + }, + { + "author_name": "Yuhuan Jiang", + "author_inst": "The First Affiliated Hospital of Nanchang University" + }, + { + "author_name": "Lipeng Zhong", + "author_inst": "The First Affiliated Hospital of Nanchang University" + }, + { + "author_name": "Yanqi Peng", + "author_inst": "The First Affiliated Hospital of Nanchang University" + }, + { + "author_name": "Aiping Le", + "author_inst": "The First Affiliated Hospital of Nanchang University" + }, + { + "author_name": "Wei Zhang", + "author_inst": "Department of Respiratory Medicine, First Affiliated Hospital of Nanchang University, Nanchang" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2023.01.13.523998", "rel_title": "Maintained imbalance of triglycerides, apolipoproteins, energy metabolites and cytokines in long-term COVID-19 syndrome (LTCS) patients", @@ -161088,101 +163276,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.01.13.23284507", - "rel_title": "SARS-CoV-2 VARIANT PREVALENCE ESTIMATION USING WASTEWATER SAMPLES", - "rel_date": "2023-01-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.13.23284507", - "rel_abs": "The present work describes a statistical model to account for sequencing information of SARS-CoV-2 variants in wastewater samples. The model expresses the joint probability distribution of the number of genomic reads corresponding to mutations and non-mutations in every locus in terms of the variant proportions and the joint mutation distribution within every variant. Since the variant joint mutation distribution can be estimated using GISAID data, the only unknown parameters in the model are the variant proportions. These are estimated using maximum likelihood. The method is applied to monitor the evolution of variant proportions using genomic data coming from wastewater samples collected in A Coruna (NW Spain) in the period May 2021 - March 2022. Although the procedure is applied assuming independence among the number of reads along the genome, it is also extended to account for Markovian dependence of counts along loci in the aggregated information coming from wastewater samples.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Ignacio Lopez-de-Ullibarri", - "author_inst": "Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruna (UDC)" - }, - { - "author_name": "Laura Tomas", - "author_inst": "CINBIO, Universidade de Vigo. Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO" - }, - { - "author_name": "Noelia Trigo-Tasende", - "author_inst": "Microbiology Research Group: meiGAbiome-Biomedical Research Institute (INIBIC)-Center for Advanced Research (CICA)-University of A Coruna (UDC)-CIBER of Infecti" - }, - { - "author_name": "Borja Freire", - "author_inst": "University of A Coruna (UDC), Research Center for Information and Communication Technologies (CITIC), Database Laboratory" - }, - { - "author_name": "Manuel Vaamonde", - "author_inst": "Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruna (UDC)" - }, - { - "author_name": "Pilar Gallego-Garcia", - "author_inst": "CINBIO, Universidade de Vigo. Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO" - }, - { - "author_name": "Ines Barbeito", - "author_inst": "Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruna (UDC)" - }, - { - "author_name": "Juan A. Vallejo", - "author_inst": "Microbiology Research Group: meiGAbiome-Biomedical Research Institute (INIBIC)-Center for Advanced Research (CICA)-University of A Coruna (UDC)-CIBER of Infecti" - }, - { - "author_name": "Javier Tarrio-Saavedra", - "author_inst": "Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruna (UDC)" - }, - { - "author_name": "Pilar Alvarino", - "author_inst": "Universidade de Vigo" - }, - { - "author_name": "Elena Beade", - "author_inst": "Evolutionary Biology Research Group, University of A Coruna" - }, - { - "author_name": "Nuria Estevez", - "author_inst": "CINBIO, Universidade de Vigo" - }, - { - "author_name": "Soraya Rumbo-Feal", - "author_inst": "Microbiology Research Group: meiGAbiome-Biomedical Research Institute (INIBIC)-Center for Advanced Research (CICA)-University of A Coruna (UDC)-CIBER of Infecti" - }, - { - "author_name": "Kelly Conde-Perez", - "author_inst": "Microbiology Research Group: meiGAbiome-Biomedical Research Institute (INIBIC)-Center for Advanced Research (CICA)-University of A Coruna (UDC)-CIBER of Infecti" - }, - { - "author_name": "Loretta De Chiara", - "author_inst": "CINBIO, Universidade de Vigo" - }, - { - "author_name": "Iago Iglesias-Corras", - "author_inst": "University of A Coruna (UDC), Research Center for Information and Communication Technologies (CITIC), Database Laboratory" - }, - { - "author_name": "Margarita Poza", - "author_inst": "Microbiology Research Group: meiGAbiome-Biomedical Research Institute (INIBIC)-Center for Advanced Research (CICA)-University of A Coruna (UDC)-CIBER of Infecti" - }, - { - "author_name": "Susana Ladra", - "author_inst": "University of A Coruna (UDC), Research Center for Information and Communication Technologies (CITIC), Database Laboratory" - }, - { - "author_name": "David Posada", - "author_inst": "CINBIO, Universidade de Vigo. Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO. Department of Biochemistry, Genetics, and Immunology, Unive" - }, - { - "author_name": "Ricardo Cao", - "author_inst": "Research Group MODES, Research Center for Information and Communication Technologies (CITIC), University of A Coruna (UDC)" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.01.13.22274536", "rel_title": "Occupational Determinants of COVID-19 Cumulative Incidence and Vaccination Rate in the United States", @@ -162307,6 +164400,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2023.01.12.23284479", + "rel_title": "Comparison of different isolation periods for preventing the spread of COVID-19: a rapid systematic review and a modelling study", + "rel_date": "2023-01-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.12.23284479", + "rel_abs": "BackgroundThe optimal isolation duration for COVID-19 patients remains unclear. To support an update of WHO Living Clinical management guidelines for COVID-19 (https://www.who.int/publications/i/item/WHO-2019-nCoV-clinical-2022.2), this rapid systematic review and modelling study addresses the effects of different isolation periods for preventing onward transmission leading to hospitalization and death among secondary cases.\n\nMethodsWe searched World Health Organization (WHO) COVID-19 database for clinical studies evaluating the impact of isolation periods for COVID-19 patients up to July 28, 2022. We performed random-effects meta-analyses to summarize testing rates of persistent test positivity rates after COVID-19 infection. We developed a model to compare the effects of the five-day isolation and removal of isolation based on a negative antigen test with ten-day isolation on onward transmission leading to hospitalization and death. We assumed that patients with a positive test are infectious and those with a negative test are not. If the test becomes negative, patients will stay negative. The model included estimates of test positivity rates, effective reproduction number, and hospitalization rate or case fatality rate.\n\nFindingsTwelve studies addressing persistent test positivity rates including 2799 patients proved eligible. Asymptomatic patients (27.1%, 95% CI: 15.8% to 40.0%) had a significantly lower rapid antigen test (RAT) positive rate than symptomatic patients (68.1%, 95% CI: 40.6% to 90.3%) on day 5. The RAT positive rate was 21.5% (95% CI: 0 to 64.1%; moderate certainty) on day 10. Our modelling study suggested that the risk difference (RD) for asymptomatic patients between five-day isolation and ten-day isolation in hospitalization (2 more hospitalizations of secondary cases per 1000 patients isolated, 95% uncertainty interval (UI) 2 more to 3 more) and mortality (1 more per 1000 patients, 95% UI 0 to 1 more) of secondary cases proved very small (very low certainty). For symptomatic patients, the potential impact of five- versus ten-day isolation was much greater in hospitalizations (RD 19 more per 1000 patients, 95% UI 14 more to 24 more; very low certainty) and mortality (RD 5 more per 1000 patients, 95% UI 4 more to 6 more; very low certainty). There may be no difference between removing isolation based on a negative antigen test and ten-day isolation in the onward transmission leading to hospitalization or death, but the average isolation period (mean difference -3 days) will be shorter for the removal of isolation based on a negative antigen test (moderate certainty).\n\nInterpretationFive versus 10 days of isolation in asymptomatic patients may result in a small amount of onward transmission and negligible hospitalization and mortality, but in symptomatic patients concerning transmission and resulting hospitalization and mortality. The evidence is, however, very uncertain.\n\nFundingWHO.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSIsolating infected patients and quarantining individuals with a high risk of recent infection remain widely used strategies to prevent the spread of SARS-CoV-2. There are no prior systematic reviews to evaluate effects relevant to decisions regarding protocols for ending COVID-19 isolation. Many modelling studies have, however, evaluated impact of five days of isolation or alternative strategies (e.g. 7 days and 10 days) with or without one negative lateral flow device on secondary infections or additional transmission risk. However, none has focused on the most patient-important outcomes - onward transmission leading to hospitalization or death. The optimal isolation duration for COVID-19 patients remains unclear. We searched WHO COVID-19 database for clinical studies evaluating the impact of isolation periods for COVID-19 patients up to July 28, 2022. We performed random-effects meta-analyses to summarize testing rates of persistent test positivity rates after COVID-19 infection. We used a model to compare the effects of the five-day isolation and removal of isolation based on a negative antigen test with ten-day isolation on onward transmission leading to hospitalization and death.\n\nAdded value of this studyTo our knowledge, this is the first systematic review and modelling study to compare effects of the five-day isolation and removal of isolation based on a negative antigen test with ten-day isolation on most patient-important outcomes - onward transmission leading to hospitalization or death. This study demonstrates that for symptomatic patients the five-day isolation may increase onward transmission and thus hospitalization and mortality of secondary cases compared with the ten-day isolation by a magnitude most would consider important. For asymptomatic patients, the increase in hospitalizations and death may be small enough to be considered unimportant. Removal of isolation based on a negative antigen test will probably shorten the average isolation period compared with isolating all patients for 10 days.\n\nImplications of all the available evidenceOur study provides evidence that 5 versus 10 days of isolation in asymptomatic patients may result in a small amount of onward transmission and negligible hospitalization and mortality, but in symptomatic patients concerning transmission and resulting hospitalization and mortality.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Ya Gao", + "author_inst": "1. Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China; 2. Department of Health Research Methods, Evidence, and" + }, + { + "author_name": "Yunli Zhao", + "author_inst": "1. National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China; 2. Department of Health Research Methods, Evidence" + }, + { + "author_name": "Xi Zhang", + "author_inst": "Department of Mathematics and Statistics, McMaster University, Hamilton, ON, Canada" + }, + { + "author_name": "Jinhui Tian", + "author_inst": "Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou, China" + }, + { + "author_name": "Gordon Guyatt", + "author_inst": "1. Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada; 2. Department of Medicine, McMaster University, Hamil" + }, + { + "author_name": "Qiukui Hao", + "author_inst": "1. School of Rehabilitation Science, McMaster University, Hamilton, ON, Canada; 2. Department of Health Research Methods, Evidence, and Impact, McMaster Univers" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2023.01.12.23284434", "rel_title": "The role of SARS-CoV-2 variants of concern in children and adolescents with COVID-19: a systematic review", @@ -162762,73 +164894,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2023.01.10.23284397", - "rel_title": "Prior SARS-CoV-2 Infection and COVID-19 Vaccine Effectiveness against Outpatient Illness during Widespread Circulation of SARS-CoV-2 Omicron Variant, US Flu VE Network", - "rel_date": "2023-01-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.10.23284397", - "rel_abs": "BackgroundWe estimated combined protection conferred by prior SARS-CoV-2 infection and COVID-19 vaccination against COVID-19-associated acute respiratory illness (ARI).\n\nMethodsDuring SARS-CoV-2 Delta (B.1.617.2) and Omicron (B.1.1.529) variant circulation between October 2021 and April 2022, prospectively enrolled adult patients with outpatient ARI had respiratory and filter paper blood specimens collected for SARS-CoV-2 molecular testing and serology. Dried blood spots were tested for immunoglobulin-G antibodies against SARS-CoV-2 nucleocapsid (NP) and spike protein receptor binding domain antigen using a validated multiplex bead assay. Evidence of prior SARS-CoV-2 infection also included documented or self-reported laboratory-confirmed COVID-19. We used documented COVID-19 vaccination status to estimate vaccine effectiveness (VE) by multivariable logistic regression by prior infection status.\n\nResults455 (29%) of 1577 participants tested positive for SARS-CoV-2 infection at enrollment; 209 (46%) case-patients and 637 (57%) test-negative patients were NP seropositive, had documented previous laboratory-confirmed COVID-19, or self-reported prior infection. Among previously uninfected patients, three-dose VE was 97% (95% confidence interval [CI], 60%- 99%) against Delta, but not statistically significant against Omicron. Among previously infected patients, three-dose VE was 57% (CI, 20%-76%) against Omicron; VE against Delta could not be estimated.\n\nConclusionsThree mRNA COVID-19 vaccine doses provided additional protection against SARS-CoV-2 Omicron variant-associated illness among previously infected participants.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Sara Y Tartof", - "author_inst": "Kaiser Permanente Southern California" - }, - { - "author_name": "Fagen Xie", - "author_inst": "Kaiser Permanente Southern California" - }, - { - "author_name": "Ruchi Yadav", - "author_inst": "US Centers for Disease Control and Prevention" - }, - { - "author_name": "Karen J Wernli", - "author_inst": "Kaiser Permanente Washington Health Research Institute" - }, - { - "author_name": "Emily Toth Martin", - "author_inst": "University of Michigan-Ann Arbor" - }, - { - "author_name": "Edward A Belongia", - "author_inst": "Marshfield Clinic Research Institute" - }, - { - "author_name": "Manjusha Gaglani", - "author_inst": "Baylor Scott & White Health" - }, - { - "author_name": "Richard Zimmerman", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "H. Keipp Talbot", - "author_inst": "Vanderbilt University" - }, - { - "author_name": "Natalie Thornburg", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Brendan Flannery", - "author_inst": "US Centers for Disease Control and Prevention" - }, - { - "author_name": "- US Flu VE Network Investigators", - "author_inst": "-" - }, - { - "author_name": "Jessie Chung", - "author_inst": "US Centers for Disease Control and Prevention" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2023.01.11.23284424", "rel_title": "Country Learning on Maintaining Quality Essential Health Services (EHS) during COVID-19 in Timor-Leste: A mixed methods qualitative analysis", @@ -163797,6 +165862,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2023.01.09.23284361", + "rel_title": "Research on the mental health status of frontline medical staff during the normalization of the COVID-19 pandemic", + "rel_date": "2023-01-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.09.23284361", + "rel_abs": "ObjectiveThis study aimed to investigate the relationship between personality characteristics and psychological health of hospitals frontline medical staff and provide a basis and reference for targeted psychological health education for frontline medical staff and for the staff of related departments to formulate relevant policies.\n\nMethodsThe self-evaluation scale of symptoms (SCL-90) was used to investigate the mental health status of 150 first-line medical staff in Zhejiang Province in response to the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia.\n\nResultsThe average scores of SCL-90 and somatization, obsessive-compulsive, depression, anxiety, hostility, terror, and psychotic factors were significantly higher than those of the normal sample in the first-aid medical staff of Aihu Hubei. The degree of influence on the mental health status of the frontline medical staff in service in Hubei is as follows, from high to low: the degree of suspicion that they may have been infected when new coronavirus pneumonia-related symptoms occur, the degree of fear of being infected and thus bring the infection to their families, and whether they have received a medical check-up recently, as well as a high level of education (both P<0.05).\n\nConclusionThe psychological health level of the frontline medical staff is lower than the national norm. In the context of the increasing number of confirmed cases and the new type of coronavirus pneumonia in the absence of any specific curative treatments, the frontline medical staff is under great psychological pressure. It is necessary to institute targeted mental health promotion to relieve the psychological pressure endured by the frontline medical staff, promote their physical and mental health, and better respond to the pandemic in China.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "ning sun", + "author_inst": "ningbo college of health sciences" + }, + { + "author_name": "Laiyou Li", + "author_inst": "Ningbo College of Health Sciences" + }, + { + "author_name": "Jinmei Xu", + "author_inst": "Ningbo College of Health Sciences" + }, + { + "author_name": "shuping Zhou", + "author_inst": "Ningbo College of Health Sciences" + }, + { + "author_name": "Hongyu Li", + "author_inst": "Ningbo College of Health Sciences" + }, + { + "author_name": "shuang Yang", + "author_inst": "Ningbo College of Health Sciences" + }, + { + "author_name": "Chaoyan Fan", + "author_inst": "The Affiliated People's Hospital of Ningbo University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2023.01.09.23284337", "rel_title": "SARS-CoV-2 molecular testing and whole genome sequencing following RNA recovery from used BinaxNOW COVID-19 Antigen Self Tests", @@ -164472,65 +166580,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2023.01.07.523115", - "rel_title": "The Ecology of Viruses in Urban Rodents with a Focus on SARS-CoV-2", - "rel_date": "2023-01-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.07.523115", - "rel_abs": "Wild animals are naturally infected with a range of viruses, some of which may be zoonotic for humans. During the human COIVD pandemic there was also the possibility of rodents acquiring SARS-CoV-2 from people, so-called reverse zoonoses. To investigate this we have sampled rats (Rattus norvegicus) and mice (Apodemus sylvaticus) from urban environments in 2020 during the human COVID-19 pandemic. We metagenomically sequenced lung and gut tissue and faeces for viruses, PCR screened for SARS-CoV-2, and serologically surveyed for anti-SARS-CoV-2 Spike antibodies. We describe the range of viruses that we found in these two rodent species. We found no molecular evidence of SARS-CoV-2 infection, though in rats we found lung antibody responses and evidence of neutralisation ability, that are consistent with rats being exposed to SARS-CoV-2 and / or exposed to other viruses that result in cross-reactive antibodies.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Adam Fisher", - "author_inst": "Queen Mary University of London," - }, - { - "author_name": "George Airey", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Yuchen Liu", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Matthew Gemmell", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Jordan Thomas", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Eleanor Bentley", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Mark Whitehead", - "author_inst": "University of Liverpool" - }, - { - "author_name": "William Paxton", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Georgios Pollakis", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Steve Paterson", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Mark Viney", - "author_inst": "University of Liverpool" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "ecology" - }, { "rel_doi": "10.1101/2023.01.09.523246", "rel_title": "Unique amino acid substitution in RBD region of SARS-CoV-2 Omicron XAY.2", @@ -165651,6 +167700,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.01.03.23284127", + "rel_title": "The Defense of Shangri-La: A Thought Experiment of Periodic Community-wide Screening in the Future Pandemic", + "rel_date": "2023-01-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.03.23284127", + "rel_abs": "ObjectivesIn a dangerous future pandemic without effective vaccines and medicines, a reliable screening-and-isolation strategy can be the last opportunity to keep critical facilities and communities running and avoid a complete shutdown.\n\nMethodsIn this study, we introduced an epidemiological model that included essential parameters of infection transmission and screening. With varying parameters, we studied the dynamics of viral infection in the semi-isolated communities.\n\nResultsIn the scenario with a periodic infection screening once per 3 days and a viral basic reproduction number 3.0, more than 85% of the infection waves have a duration less than 7 days and the infection size in each of the waves is generally less than 4 individuals when the efficiency of infection discovery is 0.9 in the screening. When the period of screening was elongated to once per 7 days, the cases of infection dramatically increased to 5 folds of that mentioned previously. Further, with a weak discovery efficiency of 0.7 and the aforementioned low screening frequency, the spread of infection would be out of control.\n\nConclusionsOur study suggests that frequent periodic screening is capable of controlling a future epidemic in a semi-isolated community without vaccines and medicines.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Anqi Duan", + "author_inst": "Fudan University" + }, + { + "author_name": "Jian Li", + "author_inst": "Fudan University" + }, + { + "author_name": "Zhen Yang", + "author_inst": "Fudan University" + }, + { + "author_name": "YUNGANG HE", + "author_inst": "Fudan University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2023.01.04.23284173", "rel_title": "Mechanistic view on the influence of fluctuations in outdoor temperature on the worsening of the course of the disease and hospitalizations associated with the SARS-CoV-2 Omicron wave in 2022 in the Tomsk region, Russia", @@ -166674,41 +168754,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.01.05.522845", - "rel_title": "Poor neutralizing antibody responses against SARS-CoV-2 Omicron BQ.1.1 and XBB in Norway in October 2022", - "rel_date": "2023-01-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.05.522845", - "rel_abs": "New sub-lineages of the SARS-CoV-2 omicron variants with enhanced ability to evade existing antibody responses continue to evolve. A better understanding how susceptible emerging virus variants are to immunity induced by vaccination or infection could help predict which strains will become dominant going forward. Here we evaluate neutralizing antibodies against several clinical isolates of omicron variants including BQ.1.1 and XBB in sera from 3x mRNA vaccinated individuals and individuals with breakthrough infections with early (BA.1 or 2) or late (BA.5) omicron variants. In addition, we evaluate neutralizing antibodies in serum samples harvested from 32 individuals from the middle of October 2022, to provide a more recent estimate of immunity. As expected, serum samples harvested after breakthrough infections were more efficient at neutralizing all the omicron variants, compared to sera from non-infected individuals. While neutralization remained high against variants such as BA.2.75.2, BR.1 and BF.7, there was a marked reduction in neutralizing titers against BQ.1.1 and XBB. Similarly, most serum samples harvested in October 2022 had very low neutralizing antibodies against BQ.1.1 and XBB, suggesting that these variants and their descendants will dominate infection waves in Norway this winter season.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Elisabeth Lea Vikse", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Even Fossum", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Magnhild Sekse Erdal", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Olav Hungnes", - "author_inst": "Norwegian Insitute of Public Health" - }, - { - "author_name": "Karoline Bragstad", - "author_inst": "Norwegian Institute of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.01.05.522853", "rel_title": "The SARS-CoV-2 Spike protein induces long-term transcriptional perturbations of mitochondrial metabolic genes, causes cardiac fibrosis, and reduces myocardial contractile in obese mice", @@ -168097,6 +170142,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2023.01.01.22283267", + "rel_title": "Usability and performance of the MicroGEM Sal6830, an RT-PCR saliva-based point-of-care platform to detect SARS-CoV-2 in primary healthcare settings with non-laboratory trained operators.", + "rel_date": "2023-01-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2023.01.01.22283267", + "rel_abs": "The beginning of the COVID-19 pandemic demonstrated how few point-of-care diagnostic tools were available that could be safely and easily operated by healthcare workers with no laboratory training. The gold-standard test, and initially the only test, used RT-PCR with nasal pharyngeal swabs (NPS). Two issues quickly emerged: 1) RT-PCR required central laboratory processing leading to significant time delays and 2) NPS collection causes discomfort, is inappropriate for ongoing repeat sampling of individuals (e.g., frontline healthcare workers) and poses difficulty when obtaining samples from some sections of the population (e.g. some elderly and young children). The Sal6830 platform is a fully self-contained, RT-PCR point-of-care device for detecting SARS-CoV-2 from saliva that takes less than thirty minutes to complete. In this study we tested the usability of the Sal6830 platform by healthcare workers unfamiliar with the instrument at two community clinics: Care 4 U Community Health Center (Miami, Florida, USA) and St. Marys Health Wagon (Wise, Virginia, USA). Staff participated in three tests: 1) determining SARS-CoV-2 status from blinded positive and negative saliva samples, 2) a clinical study comparing SARS-CoV-2 detection with a comparator point-of-care technology from the same patient and 3) completing a survey designed to measure comfort and confidence using the Sal6830 point-of-care device having received no training. Participants overwhelming found the Sal6830 platform easy and intuitive to use, successfully called SARS-CoV-2 status of contrived, blinded samples and measured a 93.3% overall percent agreement when comparing patient samples across two point-of-care technologies.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Vanessa Mills", + "author_inst": "Care 4 U Community Health Centre, Miami, Florida, USA" + }, + { + "author_name": "Teresa Owen Tyson", + "author_inst": "St. Marys Health Wagon, Wise, Virginia, USA." + }, + { + "author_name": "Rachel Helton", + "author_inst": "St. Marys Health Wagon, Wise, Virginia, USA." + }, + { + "author_name": "Paula Hill-Collins", + "author_inst": "St. Marys Health Wagon, Wise, Virginia, USA." + }, + { + "author_name": "Sarah Hubbard", + "author_inst": "St. Marys Health Wagon, Wise, Virginia, USA." + }, + { + "author_name": "Anchi Scott", + "author_inst": "MicroGEM, Charlottesville, Virginia, United States of America" + }, + { + "author_name": "Jeff Hickey", + "author_inst": "MicroGEM, Charlottesville, Virginia, United States of America" + }, + { + "author_name": "Brian E Root", + "author_inst": "MicroGEM, Charlottesville, Virginia, United States of America" + }, + { + "author_name": "Rory O'Brien", + "author_inst": "MicroGEM, Charlottesville, Virginia, United States of America" + }, + { + "author_name": "Jillian Conte", + "author_inst": "MicroGEM, Charlottesville, Virginia, United States of America" + }, + { + "author_name": "Jo-Ann L Stanton", + "author_inst": "MicroGEM, Charlottesville, Virginia, United States of America" + }, + { + "author_name": "Jeff D Chapman", + "author_inst": "MicroGEM, Charlottesville, Virginia, United States of America" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.12.28.22283666", "rel_title": "Post-Exposure Prophylaxis with SA58 (anti-COVID-19 monoclonal antibody) Nasal Spray for the prevention of symptomatic Coronavirus Disease 2019 in healthy adult workers: A randomized, single-blind, placebo-controlled clinical study", @@ -168684,61 +170792,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2023.01.03.522427", - "rel_title": "Enhanced transmissibility of XBB.1.5 is contributed by both strong ACE2 binding and antibody evasion", - "rel_date": "2023-01-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2023.01.03.522427", - "rel_abs": "SARS-CoV-2 recombinant subvariant XBB.1.5 is growing rapidly in the United States, carrying an additional Ser486Pro substitution compared to XBB.1 and outcompeting BQ.1.1 and other XBB sublineages. The underlying mechanism for such high transmissibility remains unclear. Here we show that XBB.1.5 exhibits a substantially higher hACE2-binding affinity compared to BQ.1.1 and XBB/XBB.1. Convalescent plasma samples from BA.1, BA.5, and BF.7 breakthrough infection are significantly evaded by both XBB.1 and XBB.1.5, with XBB.1.5 displaying slightly weaker immune evasion capability than XBB.1. Evusheld and Bebtelovimab could not neutralize XBB.1/XBB.1.5, while Sotrovimab remains weakly reactive and notably, SA55 is still highly effective. The fact that XBB.1 and XBB.1.5 showed comparable antibody evasion but distinct transmissibility suggests enhanced receptor-binding affinity would indeed lead to higher growth advantages. The strong hACE2 binding of XBB.1.5 could also enable its tolerance of further immune escape mutations, which should be closely monitored.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Can Yue", - "author_inst": "CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences" - }, - { - "author_name": "Weiliang Song", - "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University" - }, - { - "author_name": "Lei Wang", - "author_inst": "CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences" - }, - { - "author_name": "Fanchong Jian", - "author_inst": "College of Chemistry and Molecular Engineering, Peking University" - }, - { - "author_name": "Xiaosu Chen", - "author_inst": "Frontier Research Center for Cell Response, Institute of Immunology, College of Life Sciences, Nankai University" - }, - { - "author_name": "Fei Gao", - "author_inst": "Department of Pulmonary and Critical Care Medicine, The Fourth Hospital of Inner Mongolia" - }, - { - "author_name": "Zhongyang Shen", - "author_inst": "Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University" - }, - { - "author_name": "Youchun Wang", - "author_inst": "National Institutes for Food and Drug Control" - }, - { - "author_name": "Xiangxi Wang", - "author_inst": "CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences" - }, - { - "author_name": "Yunlong Richard Cao", - "author_inst": "Peking University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2023.01.01.522435", "rel_title": "L-shape distribution of the relative substitution rate (c micro) observed for SARS-COV-2 genome, inconsistent with the selectionist theory, the neutral theory and the nearly neutral theory but a near-neutral balanced selection theory: implication on neutralist-selectionist debate", @@ -169919,6 +171972,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.12.27.22283962", + "rel_title": "New compartment model for COVID-19", + "rel_date": "2022-12-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.27.22283962", + "rel_abs": "Population is separated into five compartments for COVID-19; susceptible individuals (S), pre-symptomatic patients (P), asymptomatic patients (A), quarantined patients (Q) and recovered and/or dead patients (R). The time evolution of each compartment is described by a set of ordinary differential equations. Numerical solution to the set of differential equations shows that quarantining pre-symptomatic and asymptomatic patients is effective in controlling the pandemic. It is also shown that the ratio of non-symptomatic patients to the daily confirmed new cases can be as large as 20 and that the fraction of untraceable cases in new cases can be as large as 80%, depending on the policies for social distancing and PCR test.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Takashi Odagaki", + "author_inst": "Research Institute for Science Education Inc." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.12.29.522182", "rel_title": "A robust deep learning platform to predict CD8+ T-cell epitopes", @@ -170334,61 +172406,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.12.26.521940", - "rel_title": "ESCRT recruitment to mRNA-encoded SARS-CoV-2 spike induces virus-like particles and enhanced antibody responses", - "rel_date": "2022-12-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.26.521940", - "rel_abs": "Prime-boost regimens for COVID-19 vaccines elicit poor antibody responses against Omicron-based variants and employ frequent boosters to maintain antibody levels. We present a natural infection-mimicking technology that combines features of mRNA- and protein nanoparticle-based vaccines through encoding self-assembling enveloped virus-like particles (eVLPs). eVLP assembly is achieved by inserting an ESCRT- and ALIX-binding region (EABR) into the SARS-CoV-2 spike cytoplasmic tail, which recruits ESCRT proteins to induce eVLP budding from cells. Purified spike-EABR eVLPs presented densely-arrayed spikes and elicited potent antibody responses in mice. Two immunizations with mRNA-LNP encoding spike-EABR elicited potent CD8+ T-cell responses and superior neutralizing antibody responses against original and variant SARS-CoV-2 compared to conventional spike-encoding mRNA-LNP and purified spike-EABR eVLPs, improving neutralizing titers >10-fold against Omicron-based variants for three months post-boost. Thus, EABR technology enhances potency and breadth of vaccine-induced responses through antigen presentation on cell surfaces and eVLPs, enabling longer-lasting protection against SARS-CoV-2 and other viruses.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Magnus AG Hoffmann", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Zhi Yang", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Kathryn E Huey-Tubman", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Alexander A Cohen", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Priyanthi NP Gnanapragasam", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Leesa M Nakatomi", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Kaya N Storm", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Woohyun J Moon", - "author_inst": "Acuitas Therapeutics" - }, - { - "author_name": "Paulo JC Lin", - "author_inst": "Acuitas Therapeutics" - }, - { - "author_name": "Pamela J Bjorkman", - "author_inst": "California Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.12.27.521990", "rel_title": "An alpaca-derived nanobody neutralizes the SARS-CoV-2 omicron variant", @@ -171781,6 +173798,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.12.22.22283855", + "rel_title": "Comparison of multiple whole-genome and Spike-only sequencing protocols for estimating variant frequencies via wastewater-based epidemiology", + "rel_date": "2022-12-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.22.22283855", + "rel_abs": "Sequencing of SARS-CoV-2 in wastewater provides a key opportunity to monitor the prevalence of variants spatiotemporally, potentially facilitating their detection simultaneously with, or even prior to, observation through clinical testing. However, there are multiple sequencing methodologies available. This study aimed to evaluate the performance of alternative protocols for detecting SARS-CoV-2 variants. We tested the detection of two synthetic RNA SARS-CoV-2 genomes in a wide range of ratios and at two concentrations representative of those found in wastewater using whole-genome and Spike-gene-only protocols utilising Illumina and Oxford Nanopore platforms. We developed a Bayesian hierarchical model to determine the predicted frequencies of variants and the error surrounding our predictions. We found that most of the sequencing protocols detected polymorphic nucleotide frequencies at a level that would allow accurate determination of the variants present at higher concentrations. Most methodologies, including the Spike-only approach, could also predict variant frequencies with a degree of accuracy in low-concentration samples but, as expected, with higher error around the estimates. All methods were additionally confirmed to detect the same prevalent variants in a set of wastewater samples. Our results provide the first quantitative statistical comparison of a range of alternative methods that can be used successfully in the surveillance of SARS-CoV-2 variant frequencies from wastewater.\n\nImpactGenetic sequencing of SARS-CoV-2 in wastewater provides an ideal system for monitoring variant frequencies in the general population. The advantages over clinical data are that it is more cost efficient and has the potential to identify new variants before clinical testing. However, to date, there has been no direct comparison to determine which sequencing methodologies perform best at identifying the presence and prevalence of variants. Our study compares seven sequencing methods to determine which performs best. We also develop a Bayesian statistical methodology to estimate the confidence around variant frequency estimates. Our results will help monitor SARS-CoV-2 variants in wastewater, and the methodology could be adapted for other disease monitoring, including future pandemics.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Lucy A Winder", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Paul Parsons", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Gavin Horsburgh", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Kathryn Maher", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Helen Hipperson", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Claudia Wierzbicki", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Aaron R Jeffries", + "author_inst": "University of Exeter" + }, + { + "author_name": "Mathew R Brown", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Aine Fairbrother-Browne", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Hubert Denise", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Mohammad S Khalifa", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Irene Bassano", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Ronny van Aerle", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Rachel Williams", + "author_inst": "Bangor University" + }, + { + "author_name": "Kata Farcas", + "author_inst": "Bangor University" + }, + { + "author_name": "Steve Paterson", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Paul G Blackwell", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Terry Burke", + "author_inst": "The University of Sheffield" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.12.23.22283921", "rel_title": "EFFECTIVENESS OF CASIRIVIMAB-IMDEVIMAB AND SOTROVIMAB MONOCLONAL ANTIBODY TREATMENT AMONG HIGH-RISK PATIENTS WITH SARS-CoV-2 INFECTION: A REAL-WORLD EXPERIENCE", @@ -172452,141 +174556,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.12.21.22283753", - "rel_title": "Outpatient treatment of Covid-19 with metformin, ivermectin, and fluvoxamine and the development of Long Covid over 10-month follow-up.", - "rel_date": "2022-12-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.21.22283753", - "rel_abs": "BackgroundLong Covid is an emerging chronic illness potentially affecting millions, sometimes preventing the ability to work or participate in normal daily activities. COVID-OUT was an investigator-initiated, multi-site, phase 3, randomized, quadruple-blinded placebo-controlled clinical trial (NCT04510194). The design simultaneously assessed three oral medications (metformin, ivermectin, fluvoxamine) using two by three parallel treatment factorial assignment to efficiently share placebo controls and assessed Long Covid outcomes for 10 months to understand whether early outpatient treatment of SARS-CoV-2 with metformin, ivermectin, or fluvoxamine prevents Long Covid.\n\nMethodsThis was a decentralized, remotely delivered trial in the US of 1,125 adults age 30 to 85 with overweight or obesity, fewer than 7 days of symptoms, and enrolled within three days of a documented SARS-CoV-2 infection. Immediate release metformin titrated over 6 days to 1,500mg per day 14 days total; ivermectin 430mcg/kg/day for 3 days; fluvoxamine, 50mg on day one then 50mg twice daily through 14 days. Medical-provider diagnosis of Long Covid, reported by participant by day 300 after randomization was a pre-specified secondary outcome; the primary outcome of the trial was severe Covid by day 14.\n\nResultThe median age was 45 years (IQR 37 to 54), 56% female of whom 7% were pregnant. Two percent identified as Native American; 3.7% as Asian; 7.4% as Black/African American; 82.8% as white; and 12.7% as Hispanic/Latino. The median BMI was 29.8 kg/m2 (IQR 27 to 34); 51% had a BMI >30kg/m2. Overall, 8.4% reported having received a diagnosis of Long Covid from a medical provider: 6.3% in the metformin group and 10.6% in the metformin control; 8.0% in the ivermectin group and 8.1% in the ivermectin control; and 10.1% in the fluvoxamine group and 7.5% in the fluvoxamine control. The Hazard Ratio (HR) for Long Covid in the metformin group versus control was 0.58 (95% CI 0.38 to 0.88); 0.99 (95% CI 0.592 to 1.643) in the ivermectin group; and 1.36 in the fluvoxamine group (95% CI 0.785 to 2.385).\n\nConclusionsThere was a 42% relative decrease in the incidence of Long Covid in the metformin group compared to its blinded control in a secondary outcome of this randomized phase 3 trial.\n\nTrial registrationNCT04510194.\n\nIND152439", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "Carolyn T Bramante", - "author_inst": "University of Minnesota" - }, - { - "author_name": "John B Buse", - "author_inst": "University of North Carolina" - }, - { - "author_name": "David Liebovitz", - "author_inst": "Northwestern University" - }, - { - "author_name": "Jacinda Nicklas", - "author_inst": "University of Colorado" - }, - { - "author_name": "Michael A Puskarich", - "author_inst": "Hennepin Healthcare" - }, - { - "author_name": "Ken Cohen", - "author_inst": "Optum" - }, - { - "author_name": "Hrishikesh Belani", - "author_inst": "Olive View - UCLA Medical Center" - }, - { - "author_name": "Blake Anderson", - "author_inst": "Emory School of Medicine" - }, - { - "author_name": "Jared D Huling", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Christopher Tignanelli", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Jennifer Thompson", - "author_inst": "Vanderbilt University" - }, - { - "author_name": "Matthew Pullen", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Lianne Siegel", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Jennifer Proper", - "author_inst": "University of Minnesota" - }, - { - "author_name": "David J Odde", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Nichole Klatt", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Nancy Sherwood", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Sarah Lindberg", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Esteban Lemus Wirtz", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Amy Krager", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Kenny Beckman", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Spencer Erickson", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Sarah Fenno", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Katrina Hartman", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Michael Rose", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Barkha Patel", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Gwendolyn Griffiths", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Neeta Bhat", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Thomas A Murray", - "author_inst": "University of Minnesota" - }, - { - "author_name": "David R Boulware", - "author_inst": "University of Minnesota" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.12.22.521646", "rel_title": "Glyco-engineered pentameric SARS-CoV-2 IgMs show superior activities compared to IgG1 orthologues", @@ -173587,6 +175556,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.12.22.22283816", + "rel_title": "SARS-CoV-2 RNA and viable virus contamination of hospital emergency department surfaces and association with patient COVID-19 status and aerosol generating procedures", + "rel_date": "2022-12-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.22.22283816", + "rel_abs": "BackgroundInfectious aerosols and droplets generated by SARS-CoV-2-positive patient aerosol generating procedures (AGPs), coughing, or exhalation could potentially contaminate surfaces, leading to indirect SARS-CoV-2 spread via fomites. Our objective was to determine SARS-CoV-2 surface contamination frequency in Emergency Department (ED) patient rooms with respect to patient SARS-CoV-2 status and AGP receipt.\n\nMethodsSwabs were collected from fixed surfaces or equipment in the rooms of patients under investigation for COVID-19 or known to be SARS-CoV-2-positive. Environmental swabs were tested for SARS-CoV-2 RNA by RT-qPCR; RNA-positive samples were cultured in Vero E6 cells. Room contamination was also evaluated by clinical severity of COVID-19 and time since symptom onset.\n\nResultsIn total, 202 rooms were sampled: 42 SARS-CoV-2-positive AGP patient rooms, 45 non-AGP SARS-CoV-2-positive patient rooms, and 115 SARS-CoV-2-negative AGP patient rooms. SARS-CoV-2 RNA was detected on 36 (3.6%) surfaces from 29 (14.4%) rooms. RNA contamination was detected more frequently in rooms occupied by non-AGP SARS-CoV-2- positive patients than SARS-CoV-2-positive AGP patients (28.9% vs 14.3%, p=0.078). Infectious virus was cultured from one non-AGP SARS-CoV-2-positive patient room. There was no significant difference in room positivity according to COVID-19 severity or time since symptom onset.\n\nConclusionSARS-CoV-2 RNA contamination of ED room surfaces was highest and most frequent in rooms occupied by SARS-CoV-2-positive patients who did not undergo an AGP, which may be attributable to disease stage and viral shedding; however, there was no difference in room contamination according to COVID-19 severity or time since symptom onset.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Scott C. Roberts", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Elliana S. Barbell", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Doug Barber", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Suzanne Dahlberg", + "author_inst": "Yale New Haven Hospital" + }, + { + "author_name": "Robert Heimer", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Karen Jubanyik", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Vivek Parwani", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Melinda M. Pettigrew", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Jason M. Tanner", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Andrew Ulrich", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Martina Wade", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Anne L. Wyllie", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Devyn Yolda-Carr", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Richard A. Martinello", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Windy D Tanner", + "author_inst": "Yale School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.12.21.22283785", "rel_title": "Quantitative multi-organ proteomics of fatal COVID-19 uncovers tissue-specific effects beyond inflammation", @@ -174070,101 +176114,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2022.12.20.521247", - "rel_title": "Identification of new drugs to counteract anti-spike IgG-induced hyperinflammation in severe COVID-19", - "rel_date": "2022-12-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.20.521247", - "rel_abs": "Previously, we and others have shown that SARS-CoV-2 spike-specific IgG antibodies play a major role in disease severity in COVID-19 by triggering macrophage hyperactivation, disrupting endothelial barrier integrity, and inducing thrombus formation. This hyper-inflammation is dependent on high levels of anti-spike IgG with aberrant Fc tail glycosylation, leading to Fc{gamma} receptor hyper-activation. For development of immune-regulatory therapeutics, drug specificity is crucial to counteract excessive inflammation while simultaneously minimizing inhibition of antiviral immunity. We here developed an in vitro activation assay to screen for small molecule drugs that specifically counteract antibody-induced pathology. We identified that anti-spike induced inflammation is specifically blocked by small molecule inhibitors against SYK and PI3K. We identified SYK inhibitor entospletinib as the most promising candidate drug, which also counteracted anti-spike-induced endothelial dysfunction and thrombus formation. Moreover, entospletinib blocked inflammation by different SARS-CoV-2 variants of concern. Combined, these data identify entospletinib as a promising treatment for severe COVID-19.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=136 SRC=\"FIGDIR/small/521247v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (36K):\norg.highwire.dtl.DTLVardef@edb3d5org.highwire.dtl.DTLVardef@1b99dd8org.highwire.dtl.DTLVardef@129ec7corg.highwire.dtl.DTLVardef@165000f_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Chiara E. Geyer", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Hung-Jen Chen", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Alexander P. Bye", - "author_inst": "University of Reading" - }, - { - "author_name": "Xue D. Manz", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Denise Guerra", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Tom G. Caniels", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Tom P. L. Bijl", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Guillermo R. Griffith", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Willianne Hoepel", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Steven W. de Taeye", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Jennifer Veth", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Alexander P.J. Vlaar", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "- Amsterdam UMC COVID-19 Biobank", - "author_inst": "-" - }, - { - "author_name": "Gestur Vidarsson", - "author_inst": "Sanquin Research" - }, - { - "author_name": "Harm Jan Bogaard", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Jurjan Aman", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Jonathan M. Gibbins", - "author_inst": "University of Reading" - }, - { - "author_name": "Marit J. van Gils", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Menno P. J. Winther", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Jeroen den Dunnen", - "author_inst": "Amsterdam UMC" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.12.20.521139", "rel_title": "Altered somatic hypermutation patterns in COVID-19 patients classifies disease severity", @@ -175229,6 +177178,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.12.20.521197", + "rel_title": "Genome-based comparison between the recombinant SARS-CoV-2 XBB and its parental lineages", + "rel_date": "2022-12-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.20.521197", + "rel_abs": "Recombination is the main contributor to RNA virus evolution, and SARS-CoV-2 during the pandemic produced several recombinants. The most recent SARS-CoV-2 recombinant is the lineage labeled XBB, also known as Gryphon, which arose from BJ.1 and BM. 1.1.1. Here we performed a genome-based survey aimed to compare the new recombinant with its parental lineages that never became dominant. Genetic analyses indicated that the recombinant XBB and its first descendant XBB.1 show an evolutionary condition typical of an evolutionary blind background with no further epidemiologically relevant descendant. Genetic variability and expansion capabilities are slightly higher than parental lineages. Bayesian Skyline Plot indicates that XBB reached its plateau around October 6, 2022 and after an initial rapid growth the viral population size did not further expand, and around November 10, 2022 its levels of genetic variability decreased. Simultaneously with the reduction of the XBB population size, an increase of the genetic variability of its first sub-lineage XBB.1 occurred, that in turn reached the plateau around November 9, 2022 showing a kind of vicariance with its direct progenitors. Structure analysis indicates that the affinity for ACE2 surface in XBB/XBB.1 RBDs is weaker than for BA.2 RBD. In conclusion, nowadays XBB and XBB.1 do not show evidence about a particular danger or high expansion capability. Genome-based monitoring must continue uninterrupted in order to individuate if further mutations can make XBB more dangerous or generate new subvariants with different expansion capability.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Fabio Scarpa", + "author_inst": "University of Sassari" + }, + { + "author_name": "Daria Sanna", + "author_inst": "Department of Biomedical Sciences, University of Sassari, Sassari, Italy" + }, + { + "author_name": "Ilenia Azzena", + "author_inst": "Department of Biomedical Sciences, University of Sassari, Sassari, Italy - Department of Veterinary Medicine, University of Sassari, Sassari, Italy;" + }, + { + "author_name": "Marco Casu", + "author_inst": "Department of Veterinary Medicine, University of Sassari, Sassari, Italy;" + }, + { + "author_name": "Piero Cossu", + "author_inst": "Department of Veterinary Medicine, University of Sassari, Sassari, Italy;" + }, + { + "author_name": "Pier Luigi Fiori", + "author_inst": "Department of Biomedical Sciences, University of Sassari, Sassari, Italy" + }, + { + "author_name": "Domenico Benvenuto", + "author_inst": "Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy" + }, + { + "author_name": "Elena Imperia", + "author_inst": "Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy - Unit of Gastroenterology, Department of Medicine, Un" + }, + { + "author_name": "Marta Giovanetti", + "author_inst": "Laboratorio de Flavivirus, Instituto Oswaldo Cruz, Fundacao Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil - Department of Science and Technology for Huma" + }, + { + "author_name": "Giancarlo Ceccarelli", + "author_inst": "Department of Public Health and Infectious Diseases, University Hospital Policlinico Umberto I, Sapienza University of Rome, Rome, Italy;" + }, + { + "author_name": "Roberto Cauda", + "author_inst": "UOC Malattie Infettive, Infectious Disease Department, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy" + }, + { + "author_name": "Antonio Cassone", + "author_inst": "Center of Genomic, Genetic and Biology, 53100 Siena, Italy" + }, + { + "author_name": "Stefano Pascarella", + "author_inst": "Department of Biochemical Sciences A. Rossi Fanelli, Sapienza Universita di Roma, 00185 Rome, Italy" + }, + { + "author_name": "Massimo Ciccozzi", + "author_inst": "Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Rome, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genetics" + }, { "rel_doi": "10.1101/2022.12.19.521129", "rel_title": "Rapid recall and de novo T cell responses during SARS-CoV-2 breakthrough infection", @@ -175948,117 +177968,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.12.18.22283593", - "rel_title": "Evaluation of bivalent Omicron BA.1 booster vaccination after different priming regimens in healthcare workers (SWITCH ON): a randomized controlled trial", - "rel_date": "2022-12-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.18.22283593", - "rel_abs": "Summary\n\nBackgroundBivalent mRNA-based COVID-19 vaccines encoding the ancestral and Omicron spike protein were developed as a countermeasure against antigenically distinct SARS-CoV-2 variants. We compared the (variant-specific) immunogenicity and reactogenicity of mRNA-based bivalent Omicron BA.1 vaccines in individuals who were primed with adenovirus- or mRNA-based vaccines.\n\nMethodsIn this open-label, multicenter, randomized, controlled trial, healthcare workers primed with Ad26.COV2.S or mRNA-based vaccines were boosted with mRNA-1273.214 or BNT162b2 OMI BA.1. The primary endpoint was the fold change in S1-specific IgG antibodies pre- and 28 days after booster vaccination. Secondary outcomes were fast response, (antibody levels on day 7), reactogenicity, neutralization of circulating variants and (cross-reactive) SARS-CoV-2-specific T-cell responses.\n\nFindingsNo effect of different priming regimens was observed on bivalent vaccination boosted S1-specific IgG antibodies. The largest increase in S1-specific IgG antibodies occurred between day 0 and 7 after bivalent booster. Neutralizing antibodies targeting the variants in the bivalent vaccine (ancestral SARS-CoV-2 and Omicron BA.1) were boosted. In addition, neutralizing antibodies against the circulating Omicron BA.5 variant increased after BA.1 bivalent booster. T-cell responses were boosted and retained reactivity with variants from the Omicron sub-lineage.\n\nInterpretationBivalent booster vaccination with mRNA-1273.214 or BNT162b2 OMI BA.1 resulted in a rapid recall of humoral and cellular immune responses independent of the initial priming regimen. Although no preferential boosting of variant-specific responses was observed, the induced antibodies and T-cells cross-reacted with Omicron BA.1 and BA.5. It remains crucial to monitor immunity at the population level, and simultaneously antigenic drift at the virus level, to determine the necessity (and timing) of COVID-19 booster vaccinations.\n\nFundingThe Netherlands Organization for Health Research and Development (ZonMw) grant agreement 10430072110001.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSVaccination against coronavirus disease-2019 (COVID-19) initially provided high levels of protection from both infection and severe disease. However, the emergence of antigenically distinct variants resulted in frequent breakthrough infections, especially with the emergence of variants from the Omicron sub-lineages. The frequent mutations in the Spike protein, and specifically the receptor binding domain (RBD), resulted in the recommendation by the WHO advisory group to update vaccines with novel antigens. Bivalent mRNA-based vaccines, encoding the Spike protein from both the ancestral SARS-CoV-2 and Omicron BA.1 (and later on BA.5) were subsequently introduced. Initial small comparative studies have been released on the evaluation of these bivalent vaccines, but it is essential is to evaluate the immunogenicity and reactogenicity of the vaccines against the background of different priming regimens.\n\nAdded value of this studyThe SWITCH ON trial evaluated the bivalent booster vaccines BNT162b2 OMI BA.1 and mRNA-1273.214 vaccine in a cohort of Dutch healthcare workers. Study participants were primed with either Ad26.COV2.S, mRNA-1273, or BNT162b2. The study investigated three important topics: (1) immunogenicity of Omicron BA.1 bivalent vaccines after Ad26.COV2.S- or mRNA-based vaccine priming, (2) rapid immunological recall responses, indicative of preserved humoral and cellular immunological memory, and (3) cross-reactivity with relevant variants after booster vaccination.\n\nImplication of all the available evidenceVaccination with the bivalent booster mRNA-1273.214 or BNT162b2 OMI BA.1 resulted in a rapid recall of humoral and cellular immune responses independent of the initial priming regimen. The largest fraction of (neutralizing) antibodies and virus-specific T-cells was recalled within 7 days post booster vaccination. Although no preferential boosting of variant-specific responses was observed, the induced antibodies and T-cells cross-reacted with Omicron BA.1, which was included in the vaccine, but also the more antigenically distinct BA.5. It remains crucial to monitor immunity at the population level, and simultaneously antigenic drift at the virus level, to determine the necessity (and timing) of COVID-19 booster vaccinations.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Ngoc Tan", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Daryl Geers", - "author_inst": "Erasmus Medical Centre: Erasmus MC" - }, - { - "author_name": "Roos Sablerolles", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Wim Rietdijk", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Bram Goorhuis", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Douwe Postma", - "author_inst": "UMCG" - }, - { - "author_name": "Leo Visser", - "author_inst": "LUMC" - }, - { - "author_name": "Susanne Bogers", - "author_inst": "Erasmus Medical Centre: Erasmus MC" - }, - { - "author_name": "Laura van Dijk", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Lennert Gommers", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Leanne van Leeuwen", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Annemarie Boerma", - "author_inst": "UMCG" - }, - { - "author_name": "Sander Nijhof", - "author_inst": "UMCG" - }, - { - "author_name": "Karel van Dort", - "author_inst": "Amsterdam UMC" - }, - { - "author_name": "Marion Koopmans", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Virgil A.S.H. Dalm", - "author_inst": "Erasmus Medical Centre: Erasmus MC" - }, - { - "author_name": "Melvin Lafeber", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Neeltje A. Kootstra", - "author_inst": "Amsterdam UMC, University of Amsterdam" - }, - { - "author_name": "Anke Huckriede", - "author_inst": "University Medical Center and University of Groningen" - }, - { - "author_name": "Debbie van Baarle", - "author_inst": "UMCG" - }, - { - "author_name": "Luca Zaeck", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Corine GeurtsvanKessel", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Rory D. de Vries", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Hugo van der Kuy", - "author_inst": "Erasmus MC" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pharmacology and therapeutics" - }, { "rel_doi": "10.1101/2022.12.17.520865", "rel_title": "A versatile and interoperable computational framework for the analysis and modeling of COVID-19 disease mechanisms", @@ -177411,6 +179320,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.12.15.22283533", + "rel_title": "Synthesizing evidence on the impacts of COVID-19 regulatory changes on methadone treatment for opioid use disorder: Implications for U.S. federal policy", + "rel_date": "2022-12-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.15.22283533", + "rel_abs": "As the U.S. faces a worsening overdose crisis, improving access to evidence-based treatment for opioid use disorder (OUD) remains a central policy priority. Federal regulatory changes in response to the COVID-19 pandemic significantly expanded flexibilities on take-home doses for methadone treatment for OUD. These changes have fueled critical questions about the impact of new regulations on OUD outcomes, and the potential health impact of permanently integrating these flexibilities into treatment policy going forward. To aide US policy makers as they consider implementing permanent methadone regulatory changes, we conducted a review synthesizing peer-reviewed research evidence on the impact of the COVID-19 methadone-take-home flexibilities on methadone program operations, OUD patient and provider experiences, and patient health outcomes. We interpret this evidence in the context of the federal rulemaking process and discuss avenues by which these important findings can be incorporated and implemented into U.S. substance use treatment policy going forward.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Noa Krawczyk", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "Bianca D. Rivera", + "author_inst": "NYU Grossman School of Medicine" + }, + { + "author_name": "Emily Levin", + "author_inst": "The George Washington University" + }, + { + "author_name": "Bridget C.E. Dooling", + "author_inst": "The George Washington University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "addiction medicine" + }, { "rel_doi": "10.1101/2022.12.15.22283529", "rel_title": "SARS-CoV-2-associated mortality with a principal cause other than COVID-19 during the Omicron epidemic in France and detection and treatment of Omicron infections in associated complications", @@ -177902,105 +179842,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.12.14.22283419", - "rel_title": "Using Social Media to Help Understand Long COVID Patient-Reported Health Outcomes: A Natural Language Processing Approach", - "rel_date": "2022-12-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.14.22283419", - "rel_abs": "BackgroundThere remains significant uncertainty in the definition of the long COVID disease, its expected clinical course, and its impact on daily functioning. Social media platforms can generate valuable insights into patient-reported health outcomes as the content is produced at high resolution by patients and caregivers, representing experiences that may be unavailable to most clinicians.\n\nObjectiveWe aim to determine the validity and effectiveness of advanced NLP approaches built to derive insight into Long COVID-related patient-reported health outcomes from social media platforms.\n\nMethodologyWe use Transformer-based BERT models to extract and normalize long COVID Symptoms and Conditions (SyCo) from English posts on Twitter and Reddit. Furthermore, we estimate the occurrence and co-occurrence of SyCo terms at any point or across time and locations. Finally, we compare the extracted health outcomes with human annotations and highly utilized clinical outcomes grounded in the medical literature.\n\nResultBased on our findings, the top three most commonly occurring groups of long COVID symptoms are systemic (such as \"fatigue\"), neuropsychiatric (such as \"anxiety\" and \"brain fog\"), and respiratory (such as \"shortness of breath\"). Regarding the co-occurring symptoms, the pair of fatigue & headaches is most common. In addition, we show that other conditions, such as infection, hair loss, and weight loss, as well as mentions of other diseases, such as flu, cancer, or Lyme disease, are among the top reported terms by social media users.\n\nConclusionThe outcome of our social media-derived pipeline is comparable with the outcomes of peer-reviewed articles relevant to long COVID symptoms. Overall, this study provides unique insights into patient-reported health outcomes from long COVID and valuable information about the patients journey that can help healthcare providers anticipate future needs.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Elham Dolatabadi", - "author_inst": "Vector Institute" - }, - { - "author_name": "Diana Moyano", - "author_inst": "Vector Institute" - }, - { - "author_name": "Michael Bales", - "author_inst": "Hoffmann-La Roche Ltd." - }, - { - "author_name": "Sofija Spasojevic", - "author_inst": "Hoffmann-La Roche Ltd." - }, - { - "author_name": "Rohan Bhambhoria", - "author_inst": "Queens University" - }, - { - "author_name": "Junaid Bhatti", - "author_inst": "Manulife, Ontario, Canada" - }, - { - "author_name": "Shyamolima Debnath", - "author_inst": "Deloitte, Ontario, Canada" - }, - { - "author_name": "Nicholas Hoell", - "author_inst": "Deloitte, Ontario, Canada" - }, - { - "author_name": "Xin Li", - "author_inst": "University of Toronto" - }, - { - "author_name": "Celine Leng", - "author_inst": "Hoffmann-La Roche Ltd., Ontario, Canada" - }, - { - "author_name": "Sasha Nanda", - "author_inst": "Deloitte, Ontario, Canada" - }, - { - "author_name": "Jad Saab", - "author_inst": "TELUS, Ontario, Canada" - }, - { - "author_name": "Esmat Sahak", - "author_inst": "University of Toronto" - }, - { - "author_name": "Fanny Sie", - "author_inst": "Hoffmann-La Roche Ltd., Ontario, Canada" - }, - { - "author_name": "Sara Uppal", - "author_inst": "TELUS, Ontario, Canada" - }, - { - "author_name": "Nirma Khatri Vadlamudi", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Antoaneta Vladimirova", - "author_inst": "Roche Information Solutions, CA, USA" - }, - { - "author_name": "Artur Yakimovich", - "author_inst": "Hoffmann-La Roche Ltd., Germany" - }, - { - "author_name": "Xiaoxue Yang", - "author_inst": "Deloitte, Ontario, Canada" - }, - { - "author_name": "Sedef Akinli Kocak", - "author_inst": "Vector Institute" - }, - { - "author_name": "Angela M. Cheung", - "author_inst": "University Health Network" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.12.16.520684", "rel_title": "Structural basis for the assembly of the DNA polymerase holoenzyme from a monkeypox virus variant", @@ -179089,6 +180930,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.12.13.22283434", + "rel_title": "Robust SARS-CoV-2 antibody and T cell immunity following three COVID-19 vaccine doses in inflammatory bowel disease patients receiving anti-TNF or alternative treatments", + "rel_date": "2022-12-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.13.22283434", + "rel_abs": "BACKGROUND AND AIMSVaccine-mediated immune responses in patients with inflammatory bowel disease (IBD) may be influenced by IBD therapies. We investigated in-depth humoral and T-cell responses to SARS-CoV-2 vaccination in IBD patients following three COVID-19 vaccine doses.\n\nMETHODSImmune responses of 100 SARS-CoV-2-uninfected IBD patients on varying treatments were compared to healthy controls (n=35). Anti-S1/2 and anti-RBD SARS-CoV-2-specific antibodies, CD4+ and CD8+ T-cell responses were measured at baseline and at five time-points after COVID-19 vaccination.\n\nRESULTSAnti-S1/2 and anti-RBD antibody concentrations at [~]1 month after second dose vaccination were significantly lower in anti-TNF-treated patients compared to non-TNF IBD patients and healthy controls (126.4 vs 262.1 and 295.5, p<0.0001). Anti-S1/2 antibodies remained reduced in anti-TNF treated patients before and after the third dose (285.7 vs 365.3, p=0.03), although anti-RBD antibodies reached comparable titres to non-TNF patients. Anti-RBD antibodies were higher in the vedolizumab group than controls after second dose (4.2 vs 3.6, p=0.003). Anti-TNF monotherapy was associated with increased CD4+ and CD8+ T-cell activation compared to combination anti-TNF patients after second dose, but comparable after third dose. Overall, IBD patients demonstrated similar CD4+/CD8+ T-cell responses compared to healthy controls regardless of treatment regimen.\n\nCONCLUSIONSAnti-TNFs impaired antibody concentrations when compared to non-TNF patients and controls after two vaccine doses. These differences were not observed after the third vaccine dose. However, vaccine induced SARS-CoV-2-specific T cell responses are robust in anti-TNF-treated patients. Our study supports the need for timely booster vaccination particularly in anti-TNF treated patients to minimise the risk of severe SARS-CoV-2 infection.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Eva Zhang", + "author_inst": "Royal Melbourne Hospital" + }, + { + "author_name": "Thi O Nguyen", + "author_inst": "Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Lilith Allen", + "author_inst": "Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Lukasz Kedzierski", + "author_inst": "Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Louise C Rowntree", + "author_inst": "Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "So Young Chang", + "author_inst": "Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Isabelle J Foo", + "author_inst": "Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Jennifer R Habel", + "author_inst": "Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Wuji Zhang", + "author_inst": "Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Tejas Menon", + "author_inst": "Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Jeni Mitchell", + "author_inst": "Royal Melbourne Hospital" + }, + { + "author_name": "Rupert Leong", + "author_inst": "Macquarie University" + }, + { + "author_name": "Katherine Bond", + "author_inst": "Royal Melbourne Hospital" + }, + { + "author_name": "Deborah A Williamson", + "author_inst": "Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Britt Christensen", + "author_inst": "Royal Melbourne Hospital" + }, + { + "author_name": "Katherine Kedzierska", + "author_inst": "University of Melbourne" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "gastroenterology" + }, { "rel_doi": "10.1101/2022.12.14.520006", "rel_title": "2-Thiouridine is a broad-spectrum antiviral nucleoside analogue against positive-strand RNA viruses", @@ -179880,65 +181800,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.12.12.22283336", - "rel_title": "Heat wave, COVID-19, and mortality excess in the 2022 summer: a cohort study on data from Italian surveillances.", - "rel_date": "2022-12-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.12.22283336", - "rel_abs": "We aimed to assess differences in the summer excess of mortality by COVID-19 history using data from the mortality and COVID-19 surveillances. We found 4% excess risk in 2022 summer, compared to 2015-2019. A mortality rate ratio of 1.59 (95%CI 1.39-1.82) for COVID-19 survivors compared to naive, was found. Both were higher in people aged [≥]75 years. During the July heat wave, the excess for COVID-19 survivors decreased and disappeared when excluding people living in nursing homes.\n\nFunding statementThis study was partially supported by the Italian Ministry of Health -CCM 2020 - \"Sorveglianza epidemiologica e controllo del COVID-19 in aree urbane metropolitane e per il contenimento della circolazione del Sars-CoV-2 nella popolazione immigrata in Italia\" and by the Ricerca Corrente 2023\n\nHighlightsO_LIthe excess of mortality in COVID-19 survivors is not exacerbated by heatwaves\nC_LIO_LIan excess of mortality during the whole summer in COVID-19 survivors aged over 75 suggest that no harvesting effect is appreciable in the older population that survived COVID-19\nC_LIO_LIFor COVID-19 survivors aged over 75, a lower mortality than the naive population was observed only during the July heat wave when we stratified by residency\nC_LI", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Francesco Venturelli", - "author_inst": "Epidemiology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy" - }, - { - "author_name": "Pamela Mancuso", - "author_inst": "Epidemiology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy" - }, - { - "author_name": "Massimo Vicentini", - "author_inst": "Epidemiology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy" - }, - { - "author_name": "Marta Ottone", - "author_inst": "Epidemiology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy" - }, - { - "author_name": "Cinzia Storchi", - "author_inst": "Epidemiology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy" - }, - { - "author_name": "Francesca Roncaglia", - "author_inst": "Epidemiology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy" - }, - { - "author_name": "Eufemia Bisaccia", - "author_inst": "Public Health Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy" - }, - { - "author_name": "Chiara Ferrarini", - "author_inst": "Epidemiology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy" - }, - { - "author_name": "Patrizio Pezzotti", - "author_inst": "Department of Infectious Diseases, Istituto Superiore di Sanita, Rome, Italy" - }, - { - "author_name": "Paolo Giorgi Rossi", - "author_inst": "Epidemiology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, Italy" - }, - { - "author_name": "- The Reggio Emilia COVID19 Working group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.12.09.22283280", "rel_title": "Identification of a protein expression signature distinguishing early from organising diffuse alveolar damage in COVID-19 patients.", @@ -181182,6 +183043,129 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.12.12.22283387", + "rel_title": "Seroprevalence of SARS-CoV-2 antibodies and retrospective mortality in two African settings: Lubumbashi, Democratic Republic of the Congo and Abidjan, Cote dIvoire", + "rel_date": "2022-12-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.12.22283387", + "rel_abs": "BackgroundAlthough seroprevalence studies have demonstrated the wide circulation of SARS-COV-2 in African countries, the impact on population health in these settings is still poorly understood. Using representative samples of the general population, we evaluated retrospective mortality and seroprevalence of anti-SARS-CoV-2 antibodies in Lubumbashi and Abidjan.\n\nMethodsThe studies included retrospective mortality surveys and nested anti-SARS-CoV-2 antibody prevalence surveys. In Lubumbashi the study took place during April-May 2021 and in Abidjan the survey was implemented in two phases: July-August 2021 and October-November 2021. Crude mortality rates were stratified between pre-pandemic and pandemic periods and further investigated by age group and COVID waves. Anti-SARS-CoV-2 seroprevalence was quantified by rapid diagnostic testing (RDT) and laboratory-based testing (ELISA in Lubumbashi and ECLIA in Abidjan).\n\nResultsIn Lubumbashi, the crude mortality rate (CMR) increased from 0.08 deaths per 10 000 persons per day (pre-pandemic) to 0.20 deaths per 10 000 persons per day (pandemic period). Increases were particularly pronounced among <5 years old. In Abidjan, no overall increase was observed during the pandemic period (pre-pandemic: 0.05 deaths per 10 000 persons per day; pandemic: 0.07 deaths per 10 000 persons per day). However, an increase was observed during the third wave (0.11 deaths per 10 000 persons per day). The estimated seroprevalence in Lubumbashi was 15.7% (RDT) and 43.2% (laboratory-based). In Abidjan, the estimated seroprevalence was 17.4% (RDT) and 72.9% (laboratory-based) during the first phase of the survey and 38.8% (RDT) and 82.2% (laboratory-based) during the second phase of the survey.\n\nConclusionAlthough circulation of SARS-CoV-2 seems to have been extensive in both settings, the public health impact varied. The increases, particularly among the youngest age group, suggest indirect impacts of COVID and the pandemic on population health. The seroprevalence results confirmed substantial underdetection of cases through the national surveillance systems.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Erica Simons", + "author_inst": "Epicentre" + }, + { + "author_name": "Birgit Nikolay", + "author_inst": "Epicentre" + }, + { + "author_name": "Pascal Ouedraogo", + "author_inst": "Epicentre" + }, + { + "author_name": "Estelle Pasquier", + "author_inst": "Epicentre" + }, + { + "author_name": "Carlos Tiemeni", + "author_inst": "Medecins Sans Frontieres" + }, + { + "author_name": "Ismael Adjaho", + "author_inst": "Medecins Sans Frontieres" + }, + { + "author_name": "Colette Badjo", + "author_inst": "Medecins Sans Frontieres" + }, + { + "author_name": "Kaouther Chamman", + "author_inst": "Epicentre" + }, + { + "author_name": "Mariam Diomand\u00e9", + "author_inst": "Medecins Sans Frontieres" + }, + { + "author_name": "Mireille Dosso", + "author_inst": "Institut Pasteur de C\u00f4te d'Ivoire: Institut Pasteur de Cote d'Ivoire" + }, + { + "author_name": "Moussa Doumbia", + "author_inst": "Institut Pasteur in Ivory Coast: Institut Pasteur de Cote d'Ivoire" + }, + { + "author_name": "Yves Asuni Izia", + "author_inst": "Medecins sans Frontieres" + }, + { + "author_name": "Hugues Kakompe", + "author_inst": "Ministry of Health, Democratic Republic of the Congo" + }, + { + "author_name": "Anne Marie Katsomya", + "author_inst": "Medecins Sans Frontieres" + }, + { + "author_name": "Vicky Kij", + "author_inst": "Ministry of Health, Democratic Republica of the Congo" + }, + { + "author_name": "Viviane Kouakou Akissi", + "author_inst": "Institut Pasteur de C\u00f4te d'Ivoire: Institut Pasteur de Cote d'Ivoire" + }, + { + "author_name": "Christopher Mambula", + "author_inst": "Medecins Sans Frontieres" + }, + { + "author_name": "Placide Mbala-Kingebeni", + "author_inst": "INRB: Institut National de Recherche Biomedicale" + }, + { + "author_name": "Jacques Muzinga", + "author_inst": "Laboratoire National de Lubumbashi" + }, + { + "author_name": "Basile Ngoy", + "author_inst": "Ministry of Health, Democratic Republic of the Congo" + }, + { + "author_name": "Lou Penali", + "author_inst": "Institut Pasteur de Cote d'Ivoire" + }, + { + "author_name": "Alessandro Pini", + "author_inst": "Epicentre" + }, + { + "author_name": "Klaudia Porten", + "author_inst": "Epicentre" + }, + { + "author_name": "Halidou Salou", + "author_inst": "Epicentre" + }, + { + "author_name": "Daouda Sevede", + "author_inst": "Institut Pasteur de C\u00f4te d'Ivoire: Institut Pasteur de Cote d'Ivoire" + }, + { + "author_name": "Francisco Luquero", + "author_inst": "Epicentre" + }, + { + "author_name": "Etienne Gignoux", + "author_inst": "Epicentre" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.12.13.520255", "rel_title": "Preclinical efficacy, safety, and immunogenicity of PHH-1V, a second-generation COVID-19 vaccine, in non-human primates", @@ -181597,29 +183581,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.12.10.518819", - "rel_title": "Identification of genomic signatures and multiple lineage markers from the second and third wave samples of COVID-19 in Western Rajasthan, India", - "rel_date": "2022-12-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.10.518819", - "rel_abs": "Most of the mutations occurred in SARS-CoV-2 are either relatively neutral or swiftly purged. However, some mutations have altered the functional aspects in terms of infectivity and transmission, host-viral interactions, disease severity and immune or vaccine escape. There are emerging evidence that certain mutations are jeopardizing the immune based therapies. The present research report is focused on the identification of genomic signatures of SARS-CoV-2 variant that caused mortality during second and third wave of COVID-19 in Western Rajasthan, India. We identified that Delta clade of SARS-CoV-2 is the predominant cause of mortality during second wave and even third wave in Western Rajasthan, India. Importantly, this study also revealed the unique and common substitution mutations within the spike domain, those are present in mortality and survived persons during the second and third wave of COVID-19 in India. In addition, this study also revealed the multiple lineage markers (Delta and Omicron), that would update with insightful understanding in the clade development of SARS-CoV-2.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ravisekhar Gadepalli", - "author_inst": "AIIMS Jodhpur" - }, - { - "author_name": "Naveen Prakash Bokolia", - "author_inst": "AIIMS Jodhpur" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2022.12.11.519990", "rel_title": "Immunogenic fusion proteins induce neutralizing SARS-CoV-2 antibodies in the serum and milk of sheep", @@ -182716,6 +184677,73 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.12.06.22283183", + "rel_title": "Lack of effectiveness of Bebtelovimab Monoclonal Antibody Among High-Risk Patients with SARS-Cov-2 Omicron During BA.2, BA.2.12.1 and BA.5 Subvariants Dominated Era", + "rel_date": "2022-12-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.06.22283183", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron subvariants are expected to be resistant to Bebtelovimab (BEB) monoclonal antibody (MAb) and the real-world experience regarding its effectiveness is scarce. This retrospective cohort study reports a data analysis in Banner Healthcare System (a large not-for-profit organization) between 4/5/2022 and 8/1/2022 and included 19,778 Coronavirus disease-19 (COVID-19) positive (by PCR or direct antigen testing) patients who were selected from Cerner-Electronic Health Record after the exclusions criteria were met. The study index date for cohort was determined as the date of BEB MAb administration or the date of the first positive COVID-19 testing. The cohort consist of COVID-19 infected patients who received BEB MAb (N=1,091) compared to propensity score (PS) matched control (N=1,091). The primary outcome was the incidence of 30-day all-cause hospitalization and/or mortality. All statistical analyses were conducted on the paired (matched) dataset. For the primary outcome, the event counts and percentages were reported. Ninety-five percent Clopper-Pearson confidence intervals for percentages were computed. The study cohorts were 1:1 propensity matched without replacement across 26 covariates using an optimal matching algorithm that minimizes the sum of absolute pairwise distance across the matched sample after fitting and using logistic regression as the distance function. The pairs were matched exactly on patient vaccination status, BMI group, age group and diabetes status. Compared to the PS matched control group (2.6%; 95% confidence interval [CI]: 1.7%, 3.7%), BEB MAb use (2.2%; 95% CI: 1.4%, 3.3%) did not significantly reduce the incidence of the primary outcome (p=0.67). In the subgroup analysis, we observed similar no-difference trends regarding the primary outcomes for the propensity rematched BEB MAb treated and untreated groups, stratified by patient vaccination status, age (<65 years or [≥]65), and immunocompromised status (patients with HIV/AIDS or solid organ transplants or malignancy including lymphoproliferative disorder). The number needed to treat (1/0.026-0.022) with BEB MAb was 250 to avoid one hospitalization and/or death over 30 days. The BEB MAb use lacked efficacy in patients with SARS-CoV-2 Omicron subvariants (mainly BA.2, BA.2.12.1, and BA.5) in the Banner Healthcare System in the Southwestern United States.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Srilekha Sridhara", + "author_inst": "The University of Arizona College of Medicine \u2013 Tucson: The University of Arizona College of Medicine Tucson" + }, + { + "author_name": "Ahmet B Gungor", + "author_inst": "Banner University Medical Center Tucson" + }, + { + "author_name": "Halil Kutlu Erol", + "author_inst": "The University of Arizona College of Medicine \u2013 Tucson: The University of Arizona College of Medicine Tucson" + }, + { + "author_name": "Mohanad Al-Obaidi", + "author_inst": "The University of Arizona College of Medicine \u2013 Tucson: The University of Arizona College of Medicine Tucson" + }, + { + "author_name": "Tirdad Zangeneh", + "author_inst": "The University of Arizona College of Medicine \u2013 Tucson: The University of Arizona College of Medicine Tucson" + }, + { + "author_name": "Edward Bedrick", + "author_inst": "The University of Arizona Mel and Enid Zuckerman College of Public Health" + }, + { + "author_name": "Venkatesh Ariyamuthu", + "author_inst": "The University of Arizona College of Medicine \u2013 Tucson: The University of Arizona College of Medicine Tucson" + }, + { + "author_name": "Aneesha Shetty", + "author_inst": "The University of Arizona College of Medicine \u2013 Tucson: The University of Arizona College of Medicine Tucson" + }, + { + "author_name": "Abd Assalam Qannus", + "author_inst": "The University of Arizona College of Medicine \u2013 Tucson: The University of Arizona College of Medicine Tucson" + }, + { + "author_name": "Katherine Mendoza", + "author_inst": "The University of Arizona College of Medicine \u2013 Tucson: The University of Arizona College of Medicine Tucson" + }, + { + "author_name": "Sangeetha Murugapandian", + "author_inst": "The University of Arizona College of Medicine \u2013 Tucson: The University of Arizona College of Medicine Tucson" + }, + { + "author_name": "Gaurav Gupta", + "author_inst": "Virginia Commonwealth University Medical Center" + }, + { + "author_name": "Bekir Tanriover", + "author_inst": "University of Arizona College of Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.12.06.22283000", "rel_title": "Emergence and antibody evasion of BQ and BA.2.75 SARS-CoV-2 sublineages in the face of maturing antibody breadth at the population level", @@ -183423,33 +185451,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.12.06.519378", - "rel_title": "The Australian academic STEMM workplace post-COVID: a picture of disarray", - "rel_date": "2022-12-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.06.519378", - "rel_abs": "In 2019 we surveyed Australian early career researchers (ECRs) working in STEMM (science, technology, engineering, mathematics and medicine). ECRs almost unanimously declared a \"love of research\", however, many reported frequent bullying and questionable research practices (QRPs), and that they intended to leave because of poor career stability. We replicated the survey in 2022 to determine the impact of the COVID-19 pandemic and sought more information on bullying and QRPs. Here, we compare data from 2019 (658 respondents) and 2022 (530 respondents), and detail poor professional and research conditions experienced by ECRs. Job satisfaction declined (62% versus 57%), workload concerns increased (48.6% versus 60.6%), more indicated \"now is a poor time to commence a research career\" (65% versus 76%) from 2019 to 2022, and roughly half reported experiencing bullying. Perhaps conditions could be tolerable if the ecosystem were yielding well-trained scientists and high-quality science. Unfortunately, there are signs of poor supervision and high rates of QRPs. ECRs detailed problems likely worthy of investigation, but few (22.4%) felt that their institute would act on a complaint. We conclude by suggesting strategies for ECR mentorship, training, and workforce considerations intended to maintain research excellence in Australia and improve ECR career stability.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Katherine Christian", - "author_inst": "Queensland University of Technology" - }, - { - "author_name": "Jo-ann Larkins", - "author_inst": "Federation University Australia" - }, - { - "author_name": "Michael Robert Doran", - "author_inst": "Queensland University of Technology" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "scientific communication and education" - }, { "rel_doi": "10.1101/2022.12.02.22283013", "rel_title": "Impact of COVID-19 Vaccinations in India - A Statewise Analysis", @@ -184626,6 +186627,141 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.12.04.22282902", + "rel_title": "SARS-CoV-2 infection induces the production of autoantibodies in severe COVID-19 patients in an age-dependent manner", + "rel_date": "2022-12-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.04.22282902", + "rel_abs": "Age is a significant risk factor for the coronavirus disease 2019 (COVID-19) outcomes due to immunosenescence and certain age-dependent medical conditions (e.g., obesity, cardiovascular disorder, diabetes, chronic respiratory disease). However, despite the well-known influence of age on autoantibody biology in health & disease, its impact on the risk of developing severe COVID-19 remains poorly explored. Here, we performed a cross-sectional study of autoantibodies directed against 58 targets associated with autoimmune diseases in 159 individuals with different COVID-19 outcomes (with 71 mild, 61 moderate, and 27 severe patients) and 73 healthy controls. We found that the natural production of autoantibodies increases with age and is exacerbated by SARS-CoV-2 infection, mostly in severe COVID-19 patients. Multivariate regression analysis showed that severe COVID-19 patients have a significant age-associated increase of autoantibody levels against 16 targets (e.g., amyloid {beta} peptide, {beta} catenin, cardiolipin, claudin, enteric nerve, fibulin, insulin receptor a, and platelet glycoprotein). Principal component analysis with spectrum decomposition based on these autoantibodies indicated an age-dependent stratification of severe COVID-19 patients. Random forest analysis ranked autoantibodies targeting cardiolipin, claudin, and platelet glycoprotein as the three most crucial autoantibodies for the stratification of severe elderly COVID-19 patients. Follow-up analysis using binomial regression found that anti-cardiolipin and anti-platelet glycoprotein autoantibodies indicated a significantly increased likelihood of developing a severe COVID-19 phenotype, presenting a synergistic effect on worsening COVID-19 outcomes. These findings provide new key insights to explain why elderly patients less favorable outcomes have than young individuals, suggesting new associations of distinct autoantibody levels with disease severity.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Dennyson Leandro M. Fonseca", + "author_inst": "Interunit Postgraduate Program on Bioinformatics, Institute of Mathematics and Statistics (IME), University of Sao Paulo" + }, + { + "author_name": "Igor Salerno Filgueiras", + "author_inst": "Department of Immunology, Institute of Biomedical Sciences, University of Sao Paulo" + }, + { + "author_name": "Alexandre HC Marques", + "author_inst": "Department of Immunology, Institute of Biomedical Sciences, University of Sao Paulo" + }, + { + "author_name": "Elroy Vojdani", + "author_inst": "Regenera Medical 11860 Wilshire Blvd., Ste. 301, Los Angeles" + }, + { + "author_name": "Gilad Halpert", + "author_inst": "Ariel University, Israel" + }, + { + "author_name": "Yuri Ostrinski", + "author_inst": "Ariel University, Israel" + }, + { + "author_name": "Gabriela Crispim Baiocchi", + "author_inst": "Department of Immunology, Institute of Biomedical Sciences, University of Sao Paulo" + }, + { + "author_name": "Desiree Rodrigues Placa", + "author_inst": "Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo" + }, + { + "author_name": "Paula P Freire", + "author_inst": "Department of Immunology, Institute of Biomedical Sciences, University of Sao Paulo" + }, + { + "author_name": "Shahab Zaki Pour", + "author_inst": "Laboratory of Molecular Evolution and Bioinformatics, Department of Microbiology, Biomedical Sciences Institute, University of Sao Paulo" + }, + { + "author_name": "Guido Moll", + "author_inst": "Departament of Nephrology and Internal Intensive Care Medicine, Charite University Hospital, Berlin, Germany" + }, + { + "author_name": "Rusan Catar", + "author_inst": "Departament of Nephrology and Internal Intensive Care Medicine, Charite University Hospital, Berlin, Germany" + }, + { + "author_name": "Yael Bublil Lavi", + "author_inst": "Department of Chemistry Ben Gurion University Beer-Sheva, Israel" + }, + { + "author_name": "Jonathan I. Silverberg", + "author_inst": "Department of Dermatology, George Washington University School of Medicine and Health Sciences, Washington, DC, USA" + }, + { + "author_name": "Jason Zimmerman", + "author_inst": "Maimonides Medical Center, Brooklyn, NY, USA" + }, + { + "author_name": "Gustavo Cabral de Miranda", + "author_inst": "Department of Immunology, Institute of Biomedical Sciences, University of Sao Paulo" + }, + { + "author_name": "Robson F Carvalho", + "author_inst": "Department of Structural and Functional Biology, Institute of Biosciences, Sao Paulo State University, Botucatu, Sao Paulo" + }, + { + "author_name": "Taj Ali Khan", + "author_inst": "Institute of Pathology and Diagnostic Medicine, Khyber Medical University, Peshawar, Pakistan" + }, + { + "author_name": "Harald Heidecke", + "author_inst": "CellTrend Gesellschaft mit beschrankter Haftung (GmbH), Luckenwalde, Germany" + }, + { + "author_name": "Rodrigo JS Dalmolin", + "author_inst": "Bioinformatics Multidisciplinary Environment, Federal University of Rio Grande do Norte, Natal, Brazil" + }, + { + "author_name": "Andre Ducati Luchessi", + "author_inst": "Department of Clinical and Toxicological Analyses, Federal University of Rio Grande do Norte, R.N., Brazil" + }, + { + "author_name": "Hans D. Ochs", + "author_inst": "Department of Pediatrics, University of Washington School of Medicine, and Seattle Children's Research Institute, Seattle, WA, USA" + }, + { + "author_name": "Lena F. Schimke", + "author_inst": "Department of Immunology, Institute of Biomedical Sciences, University of Sao Paulo" + }, + { + "author_name": "Howard Amital", + "author_inst": "Ariel University, Israel" + }, + { + "author_name": "Gabriela Riemekasten", + "author_inst": "Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lubeck, Lubeck, Germany" + }, + { + "author_name": "Israel Zyskind", + "author_inst": "Department of Pediatrics, NYU Langone Medical Center, New York, NY, USA" + }, + { + "author_name": "Avi Z Rosenberg", + "author_inst": "Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA" + }, + { + "author_name": "Aristo Vojdani", + "author_inst": "Department of Immunology, Immunosciences Laboratory, Inc., Los Angeles, CA, United States" + }, + { + "author_name": "Yehuda Shoenfeld", + "author_inst": "Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Hashomer, Israel" + }, + { + "author_name": "Otavio Cabral-Marques", + "author_inst": "Department of Immunology, Institute of Biomedical Sciences, University of Sao Paulo" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.12.01.22282932", "rel_title": "Antibody Affinity Maturation to SARS-CoV-2 Omicron Variants in a Teachers Cohort", @@ -184997,37 +187133,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.12.03.518963", - "rel_title": "Enhanced Protection from SARS-CoV-2 Variants by MVA-Based Vaccines Expressing Matched or Mismatched S Proteins Administered Intranasally to hACE2 Mice", - "rel_date": "2022-12-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.12.03.518963", - "rel_abs": "The continuous evolution of SARS-CoV-2 strains is contributing to the prolongation of the global pandemic. We previously reported the prevention or more rapid clearance of SARS-CoV-2 from the nasal turbinates and lungs of susceptible K18-hACE2 mice that had been vaccinated intranasally (IN) rather than intramuscularly (IM) with a recombinant MVA (rMVA) expressing a modified S protein of the ancestor SARS-CoV-2 strain. Here, we constructed additional rMVAs and pseudoviruses expressing modified S protein of SARS-CoV-2 variants and compared the ability of vaccines with S proteins that were matched or mismatched to neutralize variants, bind to S proteins and protect K18-hACE2 mice against SARS-CoV-2 challenge. Although vaccines with matched S proteins induced higher neutralizing antibodies, vaccines with mismatched S proteins still protected against severe disease and reduced virus and mRNAs in the lungs and nasal turbinates, though not as well as vaccines with matched S proteins. In mice earlier primed and boosted with rMVA expressing ancestral S, antibodies to the latter increased after one immunization with rMVA expressing Omicron S, but neutralizing antibody to Omicron required a second immunization. Passive transfer of Wuhan immune serum with Omicron S binding but undetectable neutralizing activities reduced infection of the lungs by the variant. Notably, the reduction in infection of the nasal turbinates and lungs was significantly greater when the rMVAs were administered IN rather than IM and this held true for vaccines that were matched or mismatched to the challenge SARS-CoV-2.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Catherine A Cotter", - "author_inst": "NIAID" - }, - { - "author_name": "Jeffrey L Americo", - "author_inst": "NIAID" - }, - { - "author_name": "Patricia L Earl", - "author_inst": "NIAID" - }, - { - "author_name": "Bernard Moss", - "author_inst": "NIAID, NIH" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.12.05.519085", "rel_title": "Convergent evolution of the SARS-CoV-2 Omicron subvariants leading to the emergence of BQ.1.1 variant", @@ -186260,6 +188365,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.12.02.22282935", + "rel_title": "Evaluating the use of social contact data to produce age-specific forecasts of SARS-CoV-2 incidence", + "rel_date": "2022-12-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.12.02.22282935", + "rel_abs": "Short-term forecasts can provide predictions of how an epidemic will change in the near future and form a central part of outbreak mitigation and control. Renewal-equation based models are increasingly popular. They infer key epidemiological parameters from historical epidemiological data and forecast future epidemic dynamics without requiring complex mechanistic assumptions. However, these models typically ignore interaction between age-groups, partly due to challenges in parameterising a time varying interaction matrix. Social contact data collected regularly by the CoMix survey during the COVID-19 epidemic in England, provide a means to inform interaction between age-groups in real-time.\n\nWe developed an age-specific forecasting framework and applied it to two age-stratified time-series: incidence of SARS-CoV-2 infection, estimated from a national infection and antibody prevalence survey; and, reported cases according to the UK national COVID-19 dashboard. Jointly fitting our model to social contact data from the CoMix study, we inferred a time-varying next generation matrix which we used to project infections and cases in the four weeks following each of 29 forecast dates between October 2021 and November 2022. We evaluated the forecasts using proper scoring rules and compared performance with three other models with alternative data and specifications alongside two naive baseline models.\n\nOverall, incorporating age-interaction improved forecasts of infections and the CoMix-data-informed model was the best performing model at time horizons between two and four weeks. However, this was not true when forecasting cases. We found that age-group-interaction was most important for predicting cases in children and older adults. The contact-data-informed models performed best during the winter months of 2020 - 2021, but performed comparatively poorly in other periods. We highlight challenges regarding the incorporation of contact data in forecasting and offer proposals as to how to extend and adapt our approach, which may lead to more successful forecasts in future.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "James D Munday", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Sam Abbott", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Sophie Meakin", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Sebastian Funk", + "author_inst": "London School of Hygiene & Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.12.01.22282842", "rel_title": "Analysis of the ARTIC V4 and V4.1 SARS-CoV-2 primers and their impact on the detection of Omicron BA.1 and BA.2 lineage defining mutations", @@ -187131,85 +189267,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.11.30.22282831", - "rel_title": "Severe acute infection and chronic pulmonary disease are risk factors for developing post-COVID-19 conditions", - "rel_date": "2022-12-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.30.22282831", - "rel_abs": "Post-COVID-19 conditions, also known as \"long COVID\", has significantly impacted the lives of many individuals, but the risk factors for this condition are poorly understood. In this study, we performed a retrospective EHR analysis of 89,843 individuals at a multi-state health system in the United States with PCR-confirmed COVID-19, including 1,086 patients diagnosed with long COVID and 1,086 matched controls not diagnosed with long COVID. For these two cohorts, we evaluated a wide range of clinical covariates, including laboratory tests, medication orders, phenotypes recorded in the clinical notes, and outcomes. We found that chronic pulmonary disease (CPD) was significantly more common as a pre-existing condition for the long COVID cohort than the control cohort (odds ratio: 1.9, 95% CI: [1.5, 2.6]). Additionally, long-COVID patients were more likely to have a history of migraine (odds ratio: 2.2, 95% CI: [1.6, 3.1]) and fibromyalgia (odds ratio: 2.3, 95% CI: [1.3, 3.8]). During the acute infection phase, the following lab measurements were abnormal in the long COVID cohort: high triglycerides (meanlongCOVID: 278.5 mg/dL vs. meancontrol: 141.4 mg/dL), low HDL cholesterol levels (meanlongCOVID: 38.4 mg/dL vs. meancontrol: 52.5 mg/dL), and high neutrophil-lymphocyte ratio (meanlongCOVID: 10.7 vs. meancontrol: 7.2). The hospitalization rate during the acute infection phase was also higher in the long COVID cohort compared to the control cohort (ratelongCOVID: 5% vs. ratecontrol: 1%). Overall, this study suggests that the severity of acute infection and a history of CPD, migraine, CFS, or fibromyalgia may be risk factors for long COVID symptoms. Our findings motivate clinical studies to evaluate whether suppressing acute disease severity proactively, especially in patients at high risk, can reduce incidence of long COVID.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Pritha Ghosh", - "author_inst": "nference Labs" - }, - { - "author_name": "Michiel JM Niesen", - "author_inst": "nference" - }, - { - "author_name": "Colin Pawlowski", - "author_inst": "nference" - }, - { - "author_name": "Hari Bandi", - "author_inst": "nference" - }, - { - "author_name": "Unice Yoo", - "author_inst": "nference" - }, - { - "author_name": "Patrick J Lenehan", - "author_inst": "nference" - }, - { - "author_name": "Praveen Kumar", - "author_inst": "nference Labs" - }, - { - "author_name": "Mihika Nadig", - "author_inst": "nference" - }, - { - "author_name": "Jason Ross", - "author_inst": "nference" - }, - { - "author_name": "Sankar Ardhanari", - "author_inst": "nference" - }, - { - "author_name": "John C O'Horo", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Aiveliagaram J Venkatakrishnan", - "author_inst": "nference" - }, - { - "author_name": "Clifford J Rosen", - "author_inst": "Maine Medical Center" - }, - { - "author_name": "Amalio Telenti", - "author_inst": "Vir Biotechnology, inc." - }, - { - "author_name": "Ryan Hurt", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Venky Soundararajan", - "author_inst": "nference" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.11.30.22282924", "rel_title": "Trends in patients' willingness for cancer care and the number of registered cancer cases in Ehime Prefecture during the COVID-19 pandemic", @@ -188202,6 +190259,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.11.28.22282808", + "rel_title": "Characteristics and outcomes of patients with COVID-19 at high-risk of disease progression receiving sotrovimab, oral antivirals or no treatment in England", + "rel_date": "2022-11-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.28.22282808", + "rel_abs": "IntroductionThere is limited real-world evidence surrounding the effectiveness of early, mild-to-moderate COVID-19 treatments following the emergence and dominance of Omicron SARS-CoV-2 subvariants. Here, characteristics and acute clinical outcomes are described for patients with COVID-19 treated with sotrovimab, nirmatrelvir/ritonavir or molnupiravir, or patients at highest risk per NHS criteria but who were untreated.\n\nMethodsRetrospective cohort study of non-hospitalised patients who received early treatment for, or were diagnosed with, COVID-19 between 1 December 2021 and 31 May 2022, using data from the Discover dataset in north-west London. Patients were included if aged [≥]12 years and treated with sotrovimab, nirmatrelvir/ritonavir or molnupiravir, or were untreated but expected to be eligible for early treatment per NHS highest-risk criteria at time of diagnosis. Outcomes were reported for 28 days from COVID-19 diagnosis (index). Subgroup analyses were conducted in patients with advanced renal disease, those aged 18-64 and [≥]65 years and by period of Omicron BA.1, BA.2 and BA.5 (post-hoc exploratory analysis) predominance.\n\nResultsA total of 696 patients prescribed sotrovimab, 337 prescribed nirmatrelvir/ritonavir, 470 prescribed molnupiravir and 4,044 eligible high-risk untreated patients were included. A high proportion of patients on sotrovimab had advanced renal disease (29.3%), [≥]3 high-risk comorbidities (47.6%) and were aged [≥]65 years (36.9%). In total, 5/696 (0.7%) patients on sotrovimab, <5/337 (0.3-1.2%) patients on nirmatrelvir/ritonavir, 10/470 (2.1%) patients on molnupiravir and 114/4,044 (2.8%) untreated patients were hospitalised with COVID-19 as the primary diagnosis. Similar results were observed across all subgroups and during Omicron subvariant periods.\n\nConclusionPatients who received sotrovimab appeared to show evidence of multiple comorbidities that may increase risk of severe COVID-19. Low hospitalisation rates were observed for all treated cohorts across subgroups and periods of predominant variants of concern. These descriptive results require confirmation with comparative effectiveness analyses adjusting for differences in underlying patient characteristics.\n\nKey pointsO_ST_ABSWhy carry out this study?C_ST_ABSO_LIThere is limited real-world evidence surrounding early, mild-to-moderate COVID-19 treatments, particularly during Omicron subvariant dominance periods, and the UK National Institute for Health and Care Excellence has recommended more is gathered.\nC_LIO_LIWe described patient characteristics and clinical outcomes among patients treated with sotrovimab, nirmatrelvir/ritonavir, molnupiravir or who met the highest-risk eligibility criteria but were untreated.\nC_LI\n\nWhat was learned from the study?O_LISotrovimab was often utilised amongst more elderly and at-risk patients, such as those with advanced renal disease, than patients treated with nirmatrelvir/ritonavir or molnupiravir.\nC_LIO_LIWe found that hospitalisation rates were low across all treated cohorts.\nC_LIO_LIFor patients treated with sotrovimab, clinical outcomes appeared consistent when observed across the age subgroups and Omicron subvariant periods, as well as among patients with advanced renal disease.\nC_LI", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Vishal Patel", + "author_inst": "GSK" + }, + { + "author_name": "Marcus J. Yarwood", + "author_inst": "Imperial College Health Partners" + }, + { + "author_name": "Bethany Levick", + "author_inst": "OPEN Health Evidence & Access" + }, + { + "author_name": "Daniel C. Gibbons", + "author_inst": "GSK" + }, + { + "author_name": "Myriam Drysdale", + "author_inst": "GSK" + }, + { + "author_name": "William Kerr", + "author_inst": "GSK" + }, + { + "author_name": "Jonathan D. Watkins", + "author_inst": "Imperial College Health Partners" + }, + { + "author_name": "Sophie Young", + "author_inst": "Imperial College Health Partners" + }, + { + "author_name": "Benjamin F. Pierce", + "author_inst": "Imperial College Health Partners" + }, + { + "author_name": "Emily J. Lloyd", + "author_inst": "GSK" + }, + { + "author_name": "Helen J. Birch", + "author_inst": "GSK" + }, + { + "author_name": "Tahereh Kamalati", + "author_inst": "Imperial College Health Partners" + }, + { + "author_name": "Stephen J. Brett", + "author_inst": "Department of Surgery and Cancer, Imperial College" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.11.28.22282412", "rel_title": "Evolving SARS-CoV-2 virulence among hospital and university affiliates in Spain and Greater Boston", @@ -188729,41 +190853,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2022.11.26.22282782", - "rel_title": "Rethinking Transfer Learning for Medical Image Classification", - "rel_date": "2022-11-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.26.22282782", - "rel_abs": "Transfer learning (TL) from pretrained deep models is a standard practice in modern medical image classification (MIC). However, what levels of features to be reused are problem-dependent, and uniformly finetuning all layers of pretrained models may be suboptimal. This insight has partly motivated the recent differential TL strategies, such as TransFusion (TF) and layer-wise finetuning (LWFT), which treat the layers in the pretrained models differentially. In this paper, we add one more strategy into this family, called TruncatedTL, which reuses and finetunes appropriate bottom layers and directly discards the remaining layers. This yields not only superior MIC performance but also compact models for efficient inference, compared to other differential TL methods. Our code is available at: https://github.com/sun-umn/TTL.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Le Peng", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Hengyue Liang", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Gaoxiang Luo", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Taihui Li", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Ju Sun", - "author_inst": "University of Minnesota" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2022.11.28.22282830", "rel_title": "Mortality due to SARS COV-2 And its Associated Factors in East Shewa Zone Treatment Centers, Ethiopia, 2022: A retrospective cross-sectional study", @@ -190040,6 +192129,117 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2022.11.28.518175", + "rel_title": "Fc mediated pan-sarbecovirus protection after alphavirus vector vaccination", + "rel_date": "2022-11-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.28.518175", + "rel_abs": "Two group 2B {beta}-coronaviruses (sarbecoviruses) have caused regional and global epidemics in modern history. The mechanisms of cross protection driven by the sarbecovirus spike, a dominant immunogen, are less clear yet critically important for pan-sarbecovirus vaccine development. We evaluated the mechanisms of cross-sarbecovirus protective immunity using a panel of alphavirus-vectored vaccines covering bat to human strains. While vaccination did not prevent virus replication, it protected against lethal heterologous disease outcomes in both SARS-CoV-2 and clade 2 bat sarbecovirus HKU3-SRBD challenge models. The spike vaccines tested primarily elicited a highly S1-specific homologous neutralizing antibody response with no detectable cross-virus neutralization. We found non-neutralizing antibody functions that mediated cross protection in wild-type mice were mechanistically linked to FcgR4 and spike S2-binding antibodies. Protection was lost in FcR knockout mice, further supporting a model for non-neutralizing, protective antibodies. These data highlight the importance of FcR-mediated cross-protective immune responses in universal pan-sarbecovirus vaccine designs.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Lily E. Adams", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Sarah R Leist", + "author_inst": "University of North Carolina" + }, + { + "author_name": "Kenneth H Dinnon III", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Ande West", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Kendra L Gully", + "author_inst": "University of North Carolina" + }, + { + "author_name": "Elizabeth Anderson", + "author_inst": "University of North Carolina" + }, + { + "author_name": "Jennifer F Loome", + "author_inst": "University of North Carolina" + }, + { + "author_name": "Emily Madden", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "John Powers", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Alexandra Schaefer", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Sanjay Sarkar", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Izabella Castillo", + "author_inst": "The University of North Carolina at Chapel Hill School of Medicine" + }, + { + "author_name": "Jenny Maron", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard University" + }, + { + "author_name": "Ryan P McNamara", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard University" + }, + { + "author_name": "Harry L Bertera", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard University" + }, + { + "author_name": "Mark R Zweigart", + "author_inst": "University of North Carolina" + }, + { + "author_name": "Jaclyn S Higgins", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Brea K Hampton", + "author_inst": "University of North Carolina" + }, + { + "author_name": "Prem Lakshmanane", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Galit Alter", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Stephanie Montgomery", + "author_inst": "Dallas Tissue Research" + }, + { + "author_name": "Victoria Baxter", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Mark T. Heise", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Ralph S. Baric", + "author_inst": "University of North Carolina at Chapel Hill" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.11.23.22280287", "rel_title": "How COVID-19 pandemic impacted the students and staff physical activity? A study in a Southern Brazilian University", @@ -190679,97 +192879,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2022.11.24.22282735", - "rel_title": "Immunogenicity and durability against Omicron BA.1, BA.2 and BA.4/5 variants at 3 to 4 months after a heterologous COVID-19 booster vaccine in healthy adults with a two-doses CoronaVac vaccination", - "rel_date": "2022-11-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.24.22282735", - "rel_abs": "ObjectivesSeveral countries have authorized a booster vaccine campaign to combat the spread of COVID-19. Data on persistence of booster vaccine-induced immunity against new Omicron subvariants are still limited. Therefore, our study aimed to determine the serological immune response of COVID-19 booster after CoronaVac-priming.\n\nMethodsA total of 187 CoronaVac-primed participants were enrolled and received an inactivated (BBIBP), viral vector (AZD1222) or mRNA vaccine (full-/half-dose BNT162B2, full-/half-dose mRNA-1273) as a booster dose. The persistence of humoral immunity both binding and neutralizing antibodies against wild-type and Omicron was determined on day 90- 120 after booster.\n\nResultsA waning of total RBD immunoglobulin (Ig) levels, anti-RBD IgG, and neutralizing antibodies against Omicron BA.1, BA.2, and BA.4/5 variants was observed 90-120 days after booster vaccination. Participants who received mRNA-1273 had the highest persistence of the immunogenicity response, followed by BNT162b2, AZD1222, and BBIBP-CorV. The responses between full and half doses of mRNA-1273 were comparable. The percentage reduction of binding antibody ranged from 50% to 75% among all booster vaccine.\n\nConclusionsThe antibody response substantially waned after 90-120 days post-booster dose. The heterologous mRNA and the viral vector booster demonstrated higher detectable rate of humoral immune responses against the Omicron variant compared to the inactivated BBIBP booster. Nevertheless, an additional fourth dose is recommended to maintain immune response against infection.\n\nHighlightsO_LIThe persistence of antibody responses is different among three vaccine platforms.\nC_LIO_LIHighly remained antibody levels were observed with the mRNA and viral vector booster.\nC_LIO_LIThe half-dose mRNA-1273 can be used interchangeably with the full-dose mRNA-1273.\nC_LIO_LIThe neutralizing activity against BA.5 was lower than wild type and BA.2 subvariant.\nC_LIO_LIA fourth dose is recommended for individuals who received an inactivated booster.\nC_LI", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Suvichada Assawakosri", - "author_inst": "Faculty of Medicine, Chulalongkorn University" - }, - { - "author_name": "Sitthichai Kanokudom", - "author_inst": "Faculty of Medicine, Chulalongkorn University" - }, - { - "author_name": "Nungruthai Suntronwong", - "author_inst": "Faculty of Medicine, Chulalongkorn University" - }, - { - "author_name": "Jira Chansaenroj", - "author_inst": "Faculty of Medicine, Chulalongkorn University" - }, - { - "author_name": "Chompoonut Auphimai", - "author_inst": "Faculty of Medicine, Chulalongkorn University" - }, - { - "author_name": "Pornjarim Nilyanimit", - "author_inst": "Chulalongkorn University Faculty of Medicine" - }, - { - "author_name": "Preeyaporn Vichaiwattana", - "author_inst": "Faculty of Medicine, Chulalongkorn University" - }, - { - "author_name": "Thanunrat Thongmee", - "author_inst": "Faculty of Medicine, Chulalongkorn University" - }, - { - "author_name": "Thaneeya Duangchinda", - "author_inst": "National Center for Genetic Engineering and Biotechnology (BIOTEC)" - }, - { - "author_name": "Warangkana Chantima", - "author_inst": "Division of Dengue Hemorrhagic Fever Research and Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine, Siriraj Hospital," - }, - { - "author_name": "Pattarakul Pakchotanon", - "author_inst": "National Center for Genetic Engineering and Biotechnology (BIOTEC)" - }, - { - "author_name": "Donchida Srimuan", - "author_inst": "Faculty of Medicine, Chulalongkorn University" - }, - { - "author_name": "Thaksaporn Thatsanatorn", - "author_inst": "Faculty of Medicine, Chulalongkorn University" - }, - { - "author_name": "Sirapa Klinfueng", - "author_inst": "Faculty of Medicine, Chulalongkorn University" - }, - { - "author_name": "Natthinee Sudhinaraset", - "author_inst": "Faculty of Medicine, Chulalongkorn University" - }, - { - "author_name": "Nasamon Wanlapakorn", - "author_inst": "Faculty of Medicine, Chulalongkorn University" - }, - { - "author_name": "Juthathip Mongkolsapaya", - "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford" - }, - { - "author_name": "Sittisak Honsawek", - "author_inst": "Faculty of Medicine, Chulalongkorn University" - }, - { - "author_name": "Yong Poovorawan", - "author_inst": "Chulalongkorn University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.11.23.22282679", "rel_title": "Substance use, psychiatric symptoms, personal mastery, and social support among COVID-19 long haulers: A compensatory model", @@ -191954,6 +194063,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.11.22.22282631", + "rel_title": "Modeling COVID-19 in different countries as sequences of SI waves", + "rel_date": "2022-11-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.22.22282631", + "rel_abs": "The COVID-19 pandemic has been a huge challenge worldwide for many institutions, researchers, national health organizations, and the pharmaceutical industry. As natural scientists and engineers, we attempted to contribute by calculating models and analyzing data to keep track of the pandemic.\n\nWhile a frequent goal is to predict the next pandemic wave by considering all influencing parameters, we examined methods to calculate a model course of the entire pandemic. This is done by reconstructing the course of infections into multiple model waves that sum up into a pandemic model that is close to the real course. The model wave parameters are varied by an algorithm, such as the Excel solver, to minimize the difference between the real and model courses.\n\nBy reconstructing the course of infections using the commonly known SIR model, we found that the calculated model parameters were ambiguous and difficult to interpret. In contrast, we found that sequenced SI model waves provide an astonishing precise digital representation of the pandemic course. Until November 2022, we found between six and 16 waves (depending on the country) in each of the 14 countries investigated.\n\nThe calculated parameters are easy to interpret and are comparable between different waves and countries. These wave parameters may be correlated with the virus types and measures in each country by other researchers. New waves are detectable early as they show a certain deviation from the actual model wave. After the maximum of the last real wave, the model indicates the further procedure for the pandemic course.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Rainer Janssen", + "author_inst": "janssen!plan engineering office" + }, + { + "author_name": "Juergen Mimkes", + "author_inst": "Paderborn University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.11.21.22282563", "rel_title": "Do Public Health Efforts Matter? Explaining Cross-Country Heterogeneity in Excess Death During the COVID-19 Pandemic", @@ -192569,25 +194701,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2022.11.19.22282451", - "rel_title": "Catch-up Routine Immunization to Restore Childhood Immunization Coverage following COVID-induced Declines in Zamboanga Peninsula, Philippines", - "rel_date": "2022-11-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.19.22282451", - "rel_abs": "Due to numerous waves of COVID-19 surge and a more focused government initiative to jump-start the COVID-19 vaccination in 2021, routine immunization was neglected in Zamboanga Peninsula, Philippines, ending the year with a fully-immunized coverage of only 59%. To address this, an intensified catch-up immunization campaign was conducted in April-June 2022 among children 0-23 months of age who missed their routine immunizations. A program case study is utilized to describe the catch-up immunization campaign conducted. The target for the catch-up immunization campaign was to vaccinate at least 80% of infants ages 0-23 months who missed any of their routine immunizations schedule. Online microplanning workshops and consultative meetings were conducted in preparation for the campaign. A record review was conducted from data from municipal and provincial health offices and then consolidated at the regional level. The coverage for all antigens at the regional level (all cities, and municipalities combined), was 49-60%, except for inactivated polio vaccine 2 (32%). In other words, approximately half of those children under 23 months who had missed doses got vaccinated during the catch-up vaccination activities. This was a relatively fair turnout of the campaign considering that the local government units are still transitioning to non-COVID health services. To address the immunization gap, the catch-up immunization campaign will continue to be conducted wherein local government unit health workers have already allotted one day every month to conduct house-to-house vaccination activity to track and vaccinate missed children.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Mary Germeyn Punzalan", - "author_inst": "Zamboanga City Medical Center" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.11.19.517207", "rel_title": "Evolution of the SARS-CoV-2 mutational spectrum", @@ -193824,6 +195937,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2022.11.17.22282447", + "rel_title": "Modeling analysis of COVID 19-related delays in colorectal cancer screening on simulated clinical outcomes", + "rel_date": "2022-11-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.17.22282447", + "rel_abs": "ObjectiveColorectal cancer (CRC) screening disruptions observed during the COVID-19 pandemic put patients at risk for more advanced-stage disease when diagnosed. This budget impact simulation model assessed increased use of multi-target stool DNA [mt-sDNA] or fecal immunochemical [FIT] tests to offset disruption in colonoscopy screening due to COVID-19 in adults at average-risk for CRC, from a United States payer perspective\n\nMain outcomes and measuresCompared to the base case (S0; 85% colonoscopy and 15% non-invasive tests), the estimated number of missed CRCs and advanced adenomas (AAs) were determined for four COVID-19-affected screening scenarios: S1, 9 months of CRC screening at 50% capacity, followed by 21 months at 75% capacity; S2, S1 followed by increasing stool-based testing by an average of 10% over 3-years; S3, 18 months of CRC screening at 50% capacity, followed by 12 months of 75% capacity; and S4, S3 followed by increasing stool-based testing by an average of 13% over 3-years.\n\nResultsIncreasing the proportional use of mt-sDNA improved AA detection by 6.0% (Scenario 2 versus 1) to 8.4% (Scenario 4 versus 3) and decreased the number of missed CRCs by 15.1% to 17.3%, respectively. Increasing FIT utilization improved the detection of AAs by 3.3% (Scenario 2 versus 1) to 4.6% (Scenario 4 versus 3) and decreased the number of missed CRCs by 12.9% to 14.9%, respectively. Across all scenarios, the number of AAs detected was higher for mt-sDNA than for FIT, and the number of missed CRCs was lower for mt-sDNA than for FIT.\n\nConclusions and relevanceUsing home-based stool tests for average-risk CRC screening can mitigate the consequences of reduced colonoscopy screening resulting from the COVID-19 pandemic. Use of mt-sDNA led to fewer missed CRCs and more AAs detected, compared to FIT.\n\nKey Points\n\nQuestionWhat is the impact of increasing the use of stool-based screening tests for colorectal cancer (CRC) during the COVID-19 pandemic in the United States?\n\nFindingsIn this simulation model, increasing the use of stool-based screening tests increased the number of advanced adenomas detected and decreased the number of missed CRC cases. Use of multi-target stool DNA (mt-sDNA) resulted in a higher number of advanced adenomas detected and a lower number of missed CRC cases compared to fecal immunochemical testing (FIT).\n\nMeaningIncreased use of mt-sDNA led to fewer missed CRC cases and more advanced adenomas detected, compared to FIT, when simulating reduced colonoscopy screening resulting from the COVID-19 pandemic.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Lesley-Ann Miller Wilson", + "author_inst": "Exact Sciences" + }, + { + "author_name": "Vahab Vahdat", + "author_inst": "Exact Sciences" + }, + { + "author_name": "Durado Brooks", + "author_inst": "Exact Sciences" + }, + { + "author_name": "Paul Limburg", + "author_inst": "Exact Sciences" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2022.11.15.22282337", "rel_title": "Did financial interventions offset the impact of financial adversity on mental health during the COVID-19 pandemic? A longitudinal analysis of the UCL COVID-19 Social Study", @@ -194279,53 +196423,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.11.18.517046", - "rel_title": "Rising SARS-CoV-2 Seroprevalence and Patterns of Cross-Variant Antibody Neutralization in UK Domestic Cats", - "rel_date": "2022-11-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.18.517046", - "rel_abs": "Recent evidence confirming cat-to-human SARS-CoV-2 transmission has highlighted the importance of monitoring infection in domestic cats. Although the effects of SARS-CoV-2 infection on feline health are poorly characterized, cats have close contact with humans, and with both domesticated and wild animals. Accordingly, they could act as a reservoir of infection, an intermediate host and a source of novel variants. To investigate the spread of the virus in the cat population, serum samples were tested for SARS-CoV-2 antibodies by ELISA and a pseudotype-based virus neutralization assay, designed to detect exposure to variants known to be circulating in the human population. Overall seroprevalence was 3.2%, peaking at 5.3% in autumn 2021. Variant-specific neutralizing antibody responses were detected with titers waning over time. The variant-specific response in the feline population correlated with and trailed the variants circulating in the human population, indicating multiple ongoing human-to-cat spill-over events.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Grace B Tyson", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Sarah Jones", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Nicola Logan", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Michael McDonald", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Pablo R Murcia", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "Brian J Willett", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - }, - { - "author_name": "William Weir", - "author_inst": "University of Glasgow" - }, - { - "author_name": "Margaret J Hosie", - "author_inst": "MRC-University of Glasgow Centre for Virus Research" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.11.18.517035", "rel_title": "Design and validation of an exposure system for efficient inter-animal SARS-CoV-2 airborne transmission in Syrian hamsters", @@ -195482,6 +197579,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical ethics" }, + { + "rel_doi": "10.1101/2022.11.15.516351", + "rel_title": "Molecularly distinct memory CD4+ T cells are induced by SARS-CoV-2 infection and mRNA vaccination", + "rel_date": "2022-11-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.15.516351", + "rel_abs": "Adaptive immune responses are induced by vaccination and infection, yet little is known about how CD4+ T cell memory differs when primed in these two contexts. Notably, viral infection is generally associated with higher levels of systemic inflammation than is vaccination. To assess whether the inflammatory milieu at the time of CD4+ T cell priming has long-term effects on memory, we compared Spike-specific memory CD4+ T cells in 22 individuals around the time of the participants third SARS-CoV-2 mRNA vaccination, with stratification by whether the participants first exposure to Spike was via virus or mRNA vaccine. Multimodal single-cell profiling of Spike-specific CD4+ T cells revealed 755 differentially expressed genes that distinguished infection- and vaccine-primed memory CD4+ T cells. Spike-specific CD4+ T cells from infection-primed individuals had strong enrichment for cytotoxicity and interferon signaling genes, whereas Spike-specific CD4+ T cells from vaccine-primed individuals were enriched for proliferative pathways by gene set enrichment analysis. Moreover, Spike-specific memory CD4+ T cells established by infection had distinct epigenetic landscapes driven by enrichment of IRF-family transcription factors, relative to T cells established by mRNA vaccination. This transcriptional imprint was minimally altered following subsequent mRNA vaccination or breakthrough infection, reflecting the strong bias induced by the inflammatory environment during initial memory differentiation. Together, these data suggest that the inflammatory context during CD4+ T cell priming is durably imprinted in the memory state at transcriptional and epigenetic levels, which has implications for personalization of vaccination based on prior infection history.\n\nOne Sentence SummarySARS-CoV-2 infection versus SARS-CoV-2 mRNA vaccination prime durable transcriptionally and epigenetically distinct Spike-specific CD4+ T cell memory landscapes.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Sophie L Gray-Gaillard", + "author_inst": "Department of Medicine, New York University Grossman School of Medicine; New York, NY, USA" + }, + { + "author_name": "Sabrina Solis", + "author_inst": "Department of Medicine, New York University Grossman School of Medicine; New York, NY, USA" + }, + { + "author_name": "Han Chen", + "author_inst": "Department of Medicine, New York University Grossman School of Medicine; New York, NY, USA" + }, + { + "author_name": "Clarice Monteiro", + "author_inst": "Department of Medicine, New York University Grossman School of Medicine; New York, NY, USA" + }, + { + "author_name": "Grace Ciabattoni", + "author_inst": "Department of Microbiology, New York University School of Medicine; New York, NY, USA" + }, + { + "author_name": "Marie I Samanovic", + "author_inst": "Department of Medicine, New York University Grossman School of Medicine; New York, NY, USA" + }, + { + "author_name": "Amber R Cornelius", + "author_inst": "Department of Medicine, New York University Grossman School of Medicine; New York, NY, USA" + }, + { + "author_name": "Tijaana Williams", + "author_inst": "Department of Medicine, New York University Grossman School of Medicine; New York, NY, USA" + }, + { + "author_name": "Emilie Geesey", + "author_inst": "Department of Medicine, New York University Grossman School of Medicine; New York, NY, USA" + }, + { + "author_name": "Miguel Rodriguez", + "author_inst": "Department of Medicine, New York University Grossman School of Medicine; New York, NY, USA" + }, + { + "author_name": "Mila Brum Ortigoza", + "author_inst": "Department of Medicine, New York University Grossman School of Medicine; New York, NY, USA" + }, + { + "author_name": "Ellie N Ivanova", + "author_inst": "Department of Pathology, New York University School of Medicine; New York, NY, USA" + }, + { + "author_name": "Sergei B Koralov", + "author_inst": "Department of Pathology, New York University School of Medicine; New York, NY, USA" + }, + { + "author_name": "Mark J Mulligan", + "author_inst": "Department of Medicine, New York University Grossman School of Medicine; New York, NY, USA" + }, + { + "author_name": "Ramin Sedaghat Herati", + "author_inst": "Department of Medicine, New York University Grossman School of Medicine; New York, NY, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.11.16.516726", "rel_title": "Beta-Cyclodextrins as affordable antivirals to treat coronavirus infection", @@ -196021,45 +198193,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.11.14.22282295", - "rel_title": "Detection of infectious SARS-CoV-2 in frozen aerosol samples collected from hospital rooms of patients with COVID-19", - "rel_date": "2022-11-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.14.22282295", - "rel_abs": "We isolated infectious SARS-CoV-2 from aerosol samples collected from hospital rooms of COVID19 patients. Isolated virus successfully replicated in cell cultures 14 months after collection, opening up prospects for retrospective analyses of samples stored during the previous waves of COVID-19.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Audray Fortin", - "author_inst": "CRCHUM" - }, - { - "author_name": "Marc Veillette", - "author_inst": "Centre de recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Quebec" - }, - { - "author_name": "Adriana Larrotta", - "author_inst": "Jewish General Hospital" - }, - { - "author_name": "Yves Longtin", - "author_inst": "McGill University" - }, - { - "author_name": "Caroline Duchaine", - "author_inst": "Centre de recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Quebec" - }, - { - "author_name": "Nathalie Grandvaux", - "author_inst": "Universite de Montreal" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.11.14.22282323", "rel_title": "Sensible Long-lead Forecast of COVID-19 Epidemic Outcomes", @@ -197164,6 +199297,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.11.09.22282122", + "rel_title": "SIR analytical model applied to 2020 Covid-19 data in Italy", + "rel_date": "2022-11-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.09.22282122", + "rel_abs": "A simple analytical Susceptible-Infectious-Recovered (SIR) model without vital dynamics is developed from basic assumptions. Based on the data available for the spread of the Covid 19 virus in Italy in 2020, the characteristic parameters of the model are estimated.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Roberto Simeone", + "author_inst": "None" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.11.07.22282049", "rel_title": "A myeloid program associated with COVID-19 severity is decreased by therapeutic blockade of IL-6 signaling", @@ -198035,29 +200187,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2022.11.10.22282181", - "rel_title": "WHAT IS THE RISK OF DEVELOPING A SEVERE FORM OF COVID-19 INFECTION AMONG ADULTS WHO CURRENTLY SMOKE COMPARED TO EX-SMOKERS? A protocol for systematic review and meta-analysis", - "rel_date": "2022-11-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.10.22282181", - "rel_abs": "IntroductionSmoking is one of the lifestyle choices associated with an increased risk of chronic health conditions and poorer COVID-19 outcomes. Because it is known that the lungs recover after quitting smoking, a direct comparison of the severity of COVID-19 infection in current and former smokers needs to be investigated.\n\nMethods and analysisThe Preferred Reporting Items for Systematic Reviews and Meta-Analyses Protocol (PRISMA-P) 2015 Checklist was used. Non-randomized studies will be searched in PubMed, Cochrane CENTRAL library, Embase, and Epistemonikos from December 2019 to the present. Hand-searching of grey literature, key journals, and reference lists will be conducted\n\nThis review will include studies of current and former smokers, with the main outcome being ICU admission, assisted respiration, or death. Two independent reviewers will select primary studies and abstract data from them. The Newcastle-Ottawa checklist will be used to assess the risk of bias, and the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) framework will be used to assess the quality of cumulative evidence. RevMan 5.4 will be used for data analysis.\n\nThe I2 statistic will be used to evaluate heterogeneity. For similar studies, the fixed-effect method of a meta-analysis will be used; otherwise, a random-effect model will be used. The qualitative synthesis will be used for studies that are ineligible for the quantitative approach.\n\nEthical consideration and disseminationBecause published data will be reviewed, no ethical approval is required. Our findings will be presented at national and/or international conferences, and they will be published in a peer-reviewed journal.\n\nPROSPERO registration number CRD42022368552\n\nARTICLE SUMMARY\n\nStrengths and limitations of this studyO_LIThis is a focused research question comparing the current and ex-smokers risk of contracting the severe form of COVID-19.\nC_LIO_LIThis systematic review and meta-analysis will provide evidence of the dangers of smoking during the COVID-19 pandemic.\nC_LIO_LIThe PRISMA-P reporting guidelines were strictly followed while writing this protocol.\nC_LIO_LIStudy selection will be carried out by two independent reviewers and a third person will intervene if a disagreement arises.\nC_LIO_LIA potential limitation is that an observational study design will be used in this systematic review.\nC_LI", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Taagbara Jolly Abaate", - "author_inst": "University of Port Harcourt Teaching Hospital" - }, - { - "author_name": "Abueh Nukoamene Prince", - "author_inst": "University of Port Harcourt Teaching Hospital" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.11.11.516111", "rel_title": "Attenuated humoral responses in HIV infection after SARS-CoV-2 vaccination are linked to global B cell defects and cellular immune profiles", @@ -199190,6 +201319,105 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.11.10.515993", + "rel_title": "An intranasal self-amplifying RNA SARS-CoV-2 vaccine produces durable respiratory and systemic immunity", + "rel_date": "2022-11-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.10.515993", + "rel_abs": "While mRNA vaccines have been effective in combating SARS-CoV-2, waning of vaccine-induced antibody responses and lack of vaccine-induced respiratory tract immunity contribute to ongoing infection and transmission. In this work, we compare and contrast intranasal (i.n.) and intramuscular (i.m.) administration of a SARS-CoV-2 self-amplifying RNA (saRNA) vaccine delivered by a nanostructured lipid carrier (NLC). Both i.m. and i.n. vaccines induce potent systemic serum neutralizing antibodies, bone marrow-resident IgG-secreting cells, and robust lymphoid tissue T cell immune responses. The i.n. vaccine additionally induces robust respiratory mucosal immune responses, including SARS-CoV-2-reactive lung-resident memory and lung-homing T cell populations. As a booster following previous i.m. vaccination, the i.n. vaccine also elicits the development of mucosal virus-specific T cells. Both the i.m. and i.n. administered vaccines protect hamsters from infection-associated morbidity upon viral challenge, significantly reducing viral loads and preventing challenged hamsters from transmitting virus to naive cagemates. This saRNA vaccines potent systemic immunogenicity, and additional mucosal immunogenicity when delivered i.n., may be key for combating SARS-CoV-2 and other respiratory pathogens.\n\nOne Sentence SummaryIntranasal SARS-CoV-2 saRNA vaccination induces systemic and mucosal immunity in mice, and prevents morbidity and blocks viral transmission in hamsters.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Madeleine F. Jennewein", + "author_inst": "Access to Advanced Health Institute" + }, + { + "author_name": "Michael D. Schultz", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Samuel Beaver", + "author_inst": "Access to Advanced Health Institute" + }, + { + "author_name": "Peter Battisti", + "author_inst": "Access to Advanced Health Institute" + }, + { + "author_name": "Julie Bakken", + "author_inst": "Access to Advanced Health Institute" + }, + { + "author_name": "Derek Hanson", + "author_inst": "Access to Advanced Health Institute" + }, + { + "author_name": "Jobaida Akther", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Raodoh Mohamath", + "author_inst": "Access to Advanced Health Institute" + }, + { + "author_name": "Jasneet Singh", + "author_inst": "Access to Advanced Health Institute" + }, + { + "author_name": "Noah Cross", + "author_inst": "Access to Advanced Health Institute" + }, + { + "author_name": "Sierra Reed", + "author_inst": "Access to Advanced Health Institute" + }, + { + "author_name": "Davies Kalange", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Jeremy B. Foote", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "R. Glenn King", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Aaron Silva-Sanchez", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Davide Botta", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Alana Gerhardt", + "author_inst": "Access to Advanced Health Institute" + }, + { + "author_name": "Corey Casper", + "author_inst": "Access to Advanced Health Institute" + }, + { + "author_name": "Troy D. Randall", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Frances E. Lund", + "author_inst": "University of Alabama at Birmingham" + }, + { + "author_name": "Emily A. Voigt", + "author_inst": "Access to Advanced Health Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.11.10.515939", "rel_title": "Precise identification of cell states altered indisease with healthy single-cell references", @@ -199701,61 +201929,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.11.08.515567", - "rel_title": "Enhanced stability of the SARS CoV-2 spike glycoprotein trimer following modification of an alanine cavity in the protein core.", - "rel_date": "2022-11-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.11.08.515567", - "rel_abs": "The spike (S) glycoprotein of SARS CoV-2 is the target of neutralizing antibodies (NAbs) that are crucial for vaccine effectiveness. The S1 subunit binds ACE2 while the S2 subunit mediates virus-cell membrane fusion. S2 is a class I fusion glycoprotein and contains a central coiled coil that acts as a scaffold for the conformational changes associated with fusion function. The coiled coil of S2 is unusual in that the 3-4 repeat of inward-facing positions are mostly occupied by polar residues that mediate few inter-helical contacts in the prefusion trimer. We examined how insertion of bulkier hydrophobic residues (Val, Leu, Ile, Phe) to fill a cavity formed by Ala1016 and Ala1020 that form part of the 3-4 repeat affects the stability and antigenicity of S trimers. Substitution of Ala1016 with bulkier hydrophobic residues in the context of a prefusion-stabilized S trimer, S2P-FHA, was associated with increased thermal stability. The trimer stabilizing effects of filling the Ala1016/Ala1020 cavity was linked to improved S glycoprotein membrane fusion function. When assessed as immunogens, two thermostable S2P-FHA mutants derived from the ancestral isolate, A1016L (16L) and A1016V/A1020I (VI) elicited very high titers of neutralizing antibodies to ancestral and Delta-derived viruses (1/2,700-1/5,110), while neutralization titer was somewhat reduced with Omicron BA.1 (1/210-1,1744). The antigens elicited antibody specificities that could compete with ACE2-Fc for binding to the receptor-binding motif (RBM) and NAbs directed to key neutralization epitopes within the receptor-binding domain (RBD), N-terminal domain (NTD) and stem region of S2. The VI mutation enabled the production of intrinsically stable Omicron BA.1 and Omicron BA.4/5 S ectodomain trimers in the absence of an external trimerization motif (T4 foldon). The VI mutation represents a method for producing an intrinsically stable trimeric S ectodomain glycoprotein vaccine in the absence of a foreign trimerization tag.\n\nAUTHOR SUMMARYFirst-generation SARS CoV-2 vaccines that generate immune responses to ancestral Spike glycoprotein sequences have averted at least 14.4 million deaths, but their effectiveness against the recently emerged Omicron lineages is reduced. The updating of booster vaccines with variant Spike sequences are therefore likely required to maintain immunity as the pandemic continues to evolve. The Spike is a trimeric integral membrane protein with a membrane spanning sequence at its C-terminus. The Spike protein-based vaccine that is currently licensed for human use is produced by a complex process that reconstitutes the Spike in an artificial membrane. Alternatively, production of the Spike trimer as a soluble protein generally requires replacement of the membrane spanning sequence with a foreign often highly immunogenic trimerization motif that can complicate clinical advancement. We used systematic structure-directed mutagenesis coupled with functional studies to identify an alternative stabilization approach that negates the requirement for an external trimerization motif or membrane-spanning sequence. The replacement of 2 alanine residues that form a cavity in the core of the Spike trimer with bulkier hydrophobic residues resulted in increased Spike thermal stability. Thermostable Spike mutants retained major conserved neutralizing antibody epitopes and the ability to elicit broad and potent neutralizing antibody responses. One such mutation, referred to as VI, enabled the production of intrinsically stable Omicron variant Spike ectodomain trimers in the absence of an external trimerization motif. The VI mutation potentially enables a simplified method for producing a stable trimeric S ectodomain glycoprotein vaccine.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Pantelis Poumbourios", - "author_inst": "Burnet Institute" - }, - { - "author_name": "Christine Langer", - "author_inst": "Burnet Institute" - }, - { - "author_name": "Irene Boo", - "author_inst": "Burnet Institute" - }, - { - "author_name": "Tasnin Zakir", - "author_inst": "Burnet Institute" - }, - { - "author_name": "Rob J Center", - "author_inst": "Burnet Institute" - }, - { - "author_name": "Anouschka Akerman", - "author_inst": "The Kirby Institute" - }, - { - "author_name": "Vanessa Milogiannakis", - "author_inst": "The Kirby Institute" - }, - { - "author_name": "Anupriya Aggarwal", - "author_inst": "The Kirby Institute" - }, - { - "author_name": "Stuart G Turville", - "author_inst": "The Kirby Institute" - }, - { - "author_name": "Heidi E Drummer", - "author_inst": "Burnet Institute" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.11.07.515545", "rel_title": "Optimization of the Illumina COVIDSeq\u2122 protocol for decentralized, cost-effective genomic surveillance", @@ -200632,6 +202805,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2022.11.03.22281898", + "rel_title": "Hospitalization forecast to inform COVID-19 pandemic planning and resource allocation using mathematical models", + "rel_date": "2022-11-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.11.03.22281898", + "rel_abs": "BackgroundThe COVID-19 pandemic has put tremendous pressure on hospital resources around the world. Forecasting demand for healthcare services is important generally, but crucial in epidemic contexts, both to facilitate resource planning and to inform situational awareness. There is abundant research on methods for predicting the spread of COVID-19 and even the arrival of COVID-19 patients to hospitals emergency departments. This study builds on that work to propose a hybrid tool, combining a stochastic Markov model and a discrete event simulation model to dynamically predict hospital admissions and total daily occupancy of hospital and ICU beds.\n\nMethodsThe model was developed and validated at San Juan de Alicante University Hospital from 10 July 2020 to 10 January 2022 and externally validated at Hospital Vega Baja. An admissions generator was developed using a stochastic Markov model that feeds a discrete event simulation model in R. Positive microbiological SARS-COV-2 results from the health departments catchment population were stratified by patient age to calculate the probabilities of hospital admission. Admitted patients follow distinct pathways through the hospital, which are simulated by the discrete event simulation model, allowing administrators to estimate the bed occupancy for the next week. The median absolute difference (MAD) between predicted and actual demand was used as a model performance measure.\n\nResultsWith respect to the San Juan hospital data, the admissions generator yielded a MAD of 6 admissions/week (interquartile range [IQR] 2-11). The MAD between the tools predictions and actual bed occupancy was 20 beds/day (IQR 5-43), or 5% of the hospital beds. The MAD between the intensive care unit (ICU)s predicted and actual occupancy was 4 beds/day (IQR 2-7), or 25% of the beds. When the model was further evaluated with data from Hospital Vega Baja, the admissions generator showed a MAD of 2.42 admissions/week (IQR 1.02-7.41). The MAD between the tools predictions and the actual bed occupancy was 18 beds/day (IQR 19.57-38.89), or 5.1% of the hospital beds. For ICU beds, the MAD was 3 beds/day (IQR 1-5), or 21.4% of the ICU beds.\n\nConclusionPredictions of hospital admissions, ward beds, and ICU occupancy for COVID-19 patients were very useful to hospital managers, allowing early planning of hospital resource allocation.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Philip Erick Wikman-Jorgensen", + "author_inst": "Hospital Universitari Sant Joan d'Alacant" + }, + { + "author_name": "Angel Ruiz", + "author_inst": "Laval University: Universite Laval" + }, + { + "author_name": "Vicente Giner-Galva\u00f1", + "author_inst": "Hospital Universitari Sant Joan d'Alacant" + }, + { + "author_name": "Jara Llenas-Garc\u00eda", + "author_inst": "Hospital Vega Baja" + }, + { + "author_name": "Jos\u00e9 Miguel Segu\u00ed-Ripoll", + "author_inst": "Hospital Universitari Sant Joan d'Alacant" + }, + { + "author_name": "Jose Mar\u00eda Salinas Serrano", + "author_inst": "Hospital Universitari Sant Joan d'Alacant" + }, + { + "author_name": "Emilio Borrajo", + "author_inst": "Hospital Vega Baja" + }, + { + "author_name": "Jos\u00e9 Mar\u00eda Ibarra S\u00e1nchez", + "author_inst": "Hospital Vega Baja" + }, + { + "author_name": "Jos\u00e9 Pedro Garc\u00eda-Sabater", + "author_inst": "Universitat Polit\u00e8cnica de Val\u00e8ncia: Universitat Politecnica de Valencia" + }, + { + "author_name": "Juan A Mar\u00edn-Garc\u00eda", + "author_inst": "Universitat Polit\u00e8cnica de Val\u00e8ncia: Universitat Politecnica de Valencia" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2022.11.03.22281912", "rel_title": "Antibody response durability following three-dose COVID-19 vaccination in people with HIV receiving suppressive ART", @@ -201267,37 +203495,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.10.30.22281737", - "rel_title": "Spatial Optimization to Improve COVID-19 Vaccine Allocation", - "rel_date": "2022-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.30.22281737", - "rel_abs": "Early distribution of COVID-19 vaccines was largely driven by population size and did not account for COVID-19 prevalence nor location characteristics. In this study, we applied an optimization framework to identify distribution strategies that would have lowered COVID-19 related morbidity and mortality. Optimized vaccine allocation would have decreased case incidence by 8% with 5,926 fewer COVID-19 cases, 106 fewer deaths, and 4.5 million dollars in healthcare cost saved during the first half of 2021. As COVID-19 variants continue to be identified, and the likelihood of future pandemics remains high, application of resource optimization should be a priority for policy makers.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Justin Goodson", - "author_inst": "Saint Louis University" - }, - { - "author_name": "Stephen Scroggins", - "author_inst": "Saint Louis University" - }, - { - "author_name": "Tasnova Afroze", - "author_inst": "Saint Louis University" - }, - { - "author_name": "Enbal Shacham", - "author_inst": "Saint Louis University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.10.31.513793", "rel_title": "Antiviral effect of candies containing persimmon-derived tannin against SARS-CoV-2 delta strain", @@ -202366,6 +204563,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.10.31.514572", + "rel_title": "Improving the preclinical and clinical success rates of LMW drugs depends on radical revisions to the status quo scientific foundations of medicinal chemistry: a case study on COVID Mpro inhibition", + "rel_date": "2022-11-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.31.514572", + "rel_abs": "The poor preclinical and clinical success rates of low molecular weight (LMW) compounds can be partially attributed to the inherent trial-and-error nature of pharmaceutical research, which is limited largely to retrospective data-driven, rather than prospective prediction-driven human relevant workflows stemming from: 1) inadequate scientific understanding of structure-activity, structure-property, and structure-free energy relationships; 2) disconnects between empirical models derived from in vitro equilibrium data (e.g., Hill and Michaelis-Menten models) vis-a-vis the native non-equilibrium cellular setting (where the pertinent metrics consist of rates, rather than equilibrium state distributions); and 3) inadequate understanding of the non-linear dynamic (NLD) basis of cellular function and disease. We argue that the limit of understanding of cellular function/dysfunction and pharmacology based on empirical principles (observation/inference) has been reached, and that further progress depends on understanding these phenomena at the first principles theoretical level. Toward that end, we have been developing and applying a theory (called \"Biodynamics\") on the general mechanisms by which: 1) cellular functions are conveyed by dynamic multi-molecular/-ionic (multi-flux) systems operating in the NLD regime; 2) cellular dysfunction results from molecular dysfunction; 3) molecular structure and function are powered by covalent/non-covalent forms of free energy; and 4) cellular dysfunction is corrected pharmacologically. Biodynamics represents a radical departure from the status quo empirical science and reduction to practice thereof, replacing: 1) the interatomic contact model of structure-free energy and structure-property relationships with a solvation free energy model; 2) equilibrium drug-target occupancy models with dynamic models accounting for time-dependent drug and target/off-target binding site buildup and decay; and 3) linear models of molecular structure-function and multi-molecular/-ionic systems conveying cellular function and dysfunction with NLD models that more realistically capture the emergent non-linear behaviors of such systems. Here, we apply our theory to COVID Mpro inhibition and overview its implications for a holistic, in vivo relevant approach to drug design.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Robert Alan Pearlstein", + "author_inst": "Novartis Institutes for BioMedical Research" + }, + { + "author_name": "Hongbin Wan", + "author_inst": "Novartis Institutes for BioMedical Research Inc" + }, + { + "author_name": "Sarah Williams", + "author_inst": "Novartis Institutes for BioMedical Research" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2022.11.01.514696", "rel_title": "Education in the Time of COVID-19: The Improvised Experiment of Virtual Assessments", @@ -202860,20 +205084,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.10.31.22281748", - "rel_title": "A cohort study of Post COVID-19 Condition across the Beta, Delta and Omicron waves in South Africa: 6-month follow up of hospitalised and non-hospitalised participants", - "rel_date": "2022-11-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.31.22281748", - "rel_abs": "BackgroundA third of people may experience persistent symptoms following COVID-19. With over 90% of South Africans having evidence of prior SARS-CoV-2 infection, it is likely that many people could be affected by Post COVID-19 Condition (PCC).\n\nMethodsThe was a prospective, longitudinal observational cohort study recruiting hospitalised and non-hospitalised participants, infected during the periods that Beta, Delta and Omicron BA.1 variants dominated in South Africa. Participants aged 18 years or older were randomly selected to undergo telephone assessment at 1, 3 and 6 months after hospital discharge or laboratory-confirmed SARS-CoV-2 infection. Participants were assessed using a standardised questionnaire for evaluation of symptoms and health-related quality of life. We used negative binomial regression models to determine factors associated with the presence of [≥]1 symptoms at 6 months.\n\nFindingsAmong hospitalised and non-hospitalised participants, 46.7% (1,227/2,626) and 18.5% (199/1,074) had [≥]1 symptoms at 6 months (p=<0.001). Among hospitalised participants 59.5%, 61.2% and 18.5% experienced [≥]1 symptoms at 6 months among individuals infected during the Beta, Delta and Omicron dominant waves respectively. Among PLWH who were hospitalised, 40.4% had [≥]1 symptoms at 6 months compared to 47.1% among HIV-uninfected participants (p=0.108).\n\nRisk factors for PCC included older age, female sex, non-black race, the presence of a comorbidity, greater number of acute COVID-19 symptoms, hospitalisation/ COVID-19 severity and wave period (individuals infected during the Omicron-dominated wave had a lower risk of persistent symptoms [adjusted Incident Risk Ratio 0.45; 95% Confidence Interval 0.36 - 0.57] compared to those infected during the Beta-dominated wave). There were no associations between self-reported vaccination status before or after SARS-CoV-2 infection with persistent symptoms.\n\nInterpretationThe study revealed a high prevalence of persistent symptoms among South African participants at 6 months although decreased risk for PCC among participants infected during the Omicron BA.1 wave. These findings have serious implications for countries with resource-constrained healthcare systems.\n\nFundingBill & Melinda Gates Foundation, UK Foreign, Commonwealth & Development Office, and Wellcome.", - "rel_num_authors": 0, - "rel_authors": null, - "version": "1", - "license": "", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.10.31.22281766", "rel_title": "Effectiveness of mRNA COVID-19 vaccine booster doses against Omicron severe outcomes", @@ -203683,6 +205893,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.10.28.22281646", + "rel_title": "Machine learning models for predicting severe COVID-19 outcomes in hospitals", + "rel_date": "2022-10-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.28.22281646", + "rel_abs": "The aim of this observational retrospective study is to improve early risk stratification of hospitalized Covid-19 patients by predicting in-hospital mortality, transfer to intensive care unit (ICU) and mechanical ventilation from electronic health record data of the first 24 hours after admission. Our machine learning model predicts in-hospital mortality (AUC=0.918), transfer to ICU (AUC=0.821) and the need for mechanical ventilation (AUC=0.654) from a few laboratory data of the first 24 hours after admission. Models based on dichotomous features indicating whether a laboratory value exceeds or falls below a threshold perform nearly as good as models based on numerical features. We devise completely data-driven and interpretable machine-learning models for the prediction of in-hospital mortality, transfer to ICU and mechanical ventilation for hospitalized Covid-19 patients within 24 hours after admission. Numerical values of CRP and blood sugar and dichotomous indicators for increased partial thromboplastin time (PTT) and glutamic oxaloacetic transaminase (GOT) are amongst the best predictors.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Philipp Wendland", + "author_inst": "University of Applied Sciences Koblenz, Department of Mathematics and Technology" + }, + { + "author_name": "Vanessa Schmitt", + "author_inst": "University of Applied Sciences Koblenz, Department of Mathematics and Technology" + }, + { + "author_name": "Joerg Zimmermann", + "author_inst": "University of Applied Sciences Koblenz, Department of Mathematics and Technology" + }, + { + "author_name": "Lukas Haeger", + "author_inst": "University Clinic Tuebingen, Department of Internal Medicine" + }, + { + "author_name": "Siri Goepel", + "author_inst": "University Clinic Tuebingen, Department of Internal Medicine" + }, + { + "author_name": "Christof Schenkel-Haeger", + "author_inst": "University of Applied Sciences Koblenz, Department of Economics and Social Care" + }, + { + "author_name": "Maik Kschischo", + "author_inst": "University of Applied Sciences Koblenz, Department of Mathematics and Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.10.27.22281603", "rel_title": "Preliminary report: Safety and immunogenicity of an inactivated SARS-CoV-2 vaccine, KD-414, in healthy adult participants: a non-randomized, open-label phase 2/3 clinical study in Japan", @@ -204222,61 +206475,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2022.10.25.22281469", - "rel_title": "Graph-based Fusion Modeling and Explanation for Disease Trajectory Prediction", - "rel_date": "2022-10-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.25.22281469", - "rel_abs": "We propose a relational graph to incorporate clinical similarity between patients while building personalized clinical event predictors with a focus on hospitalized COVID-19 patients. Our graph formation process fuses heterogeneous data, i.e., chest X-rays as node features and non-imaging EHR for edge formation. While node represents a snap-shot in time for a single patient, weighted edge structure encodes complex clinical patterns among patients. While age and gender have been used in the past for patient graph formation, our method incorporates complex clinical history while avoiding manual feature selection. The model learns from the patients own data as well as patterns among clinically-similar patients. Our visualization study investigates the effects of neighborhood of a node on its predictiveness and showcases the models tendency to focus on edge-connected patients with highly suggestive clinical features common with the node. The proposed model generalizes well by allowing edge formation process to adapt to an external cohort.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Amara Tariq", - "author_inst": "Mayo Clinic, AZ" - }, - { - "author_name": "Siyi Tang", - "author_inst": "Stanford University" - }, - { - "author_name": "Hifza Sakhi", - "author_inst": "Philadelphia College of Osteopathic Medicine - Georgia Campus" - }, - { - "author_name": "Leo Anthony G. Celi", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Janice Newsome", - "author_inst": "Emory University Hospital" - }, - { - "author_name": "Daniel Rubin", - "author_inst": "Stanford University" - }, - { - "author_name": "Hari Trivedi", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Judy W Gicchoya", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Bhavik Patel", - "author_inst": "Mayo Clinic Arizona" - }, - { - "author_name": "Imon Banerjee", - "author_inst": "Mayo Clinic, AZ" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2022.10.25.22281427", "rel_title": "Viral load of SARS-CoV-2 Omicron BA.5 is lower than that of BA.2 despite the higher infectivity of BA.5", @@ -206233,6 +208431,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.10.24.22281485", + "rel_title": "Epigenetic and transcriptomic reprogramming in monocytes of severe COVID-19 patients reflects alterations in myeloid differentiation and the influence of inflammatory cytokines", + "rel_date": "2022-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.24.22281485", + "rel_abs": "COVID-19 manifests with a wide spectrum of clinical phenotypes, ranging from asymptomatic and mild to severe and critical. Severe and critical COVID-19 patients are characterized by marked changes in the myeloid compartment, especially monocytes. However, little is known about the epigenetic alterations that occur in these cells during hyperinflammatory responses in severe COVID-19 patients. In this study, we obtained the DNA methylome and transcriptome of peripheral blood monocytes from severe COVID-19 patients. DNA samples extracted from CD14+CD15-monocytes of 48 severe COVID-19 patients and 11 healthy controls were hybridized on MethylationEPIC BeadChip arrays. In parallel, single-cell transcriptomics of 10 severe COVID-19 patients were generated. CellPhoneDB was used to infer changes in the crosstalk between monocytes and other immune cell types. We observed DNA methylation changes in CpG sites associated with interferon-related genes and genes associated with antigen presentation, concordant with gene expression changes. These changes significantly overlapped with those occurring in bacterial sepsis, although specific DNA methylation alterations in genes specific to viral infection were also identified. We also found these alterations to comprise some of the DNA methylation changes occurring during myeloid differentiation and under the influence of inflammatory cytokines. A progression of DNA methylation alterations in relation to the Sequential Organ Failure Assessment (SOFA) score was found to be related to interferon-related genes and T-helper 1 cell cytokine production. CellPhoneDB analysis of the single-cell transcriptomes of other immune cell types suggested the existence of altered crosstalk between monocytes and other cell types like NK cells and regulatory T cells. Our findings show the occurrence of an epigenetic and transcriptional reprogramming of peripheral blood monocytes, which could be associated with the release of aberrant immature monocytes, increased systemic levels of pro-inflammatory cytokines, and changes in immune cell crosstalk in these patients.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Gerard Godoy-Tena", + "author_inst": "Josep Carreras Research Institute (IJC)" + }, + { + "author_name": "Anis Barmada", + "author_inst": "Wellcome Sanger Institute" + }, + { + "author_name": "Octavio Morante-Palacios", + "author_inst": "Josep Carreras Research Institute (IJC)" + }, + { + "author_name": "Carlos de la Calle-Fabregat", + "author_inst": "Josep Carreras Research Institute (IJC)" + }, + { + "author_name": "Ricardo Martins-Ferreira", + "author_inst": "Josep Carreras Research Institute (IJC)" + }, + { + "author_name": "Anna G Ferrete-Bonastre", + "author_inst": "Josep Carreras Research Institute (IJC)" + }, + { + "author_name": "Laura Ciudad", + "author_inst": "Josep Carreras Resaerch Institute (IJC)" + }, + { + "author_name": "Adolfo Ruiz-Sanmartin", + "author_inst": "Hospital Vall d'Hebron" + }, + { + "author_name": "Monica Martinez-Gallo", + "author_inst": "Hospital Vall d'Hebron" + }, + { + "author_name": "Ricard Ferrer", + "author_inst": "Hospital Vall d'Hebron" + }, + { + "author_name": "Juan C Ruiz-Rodriguez", + "author_inst": "Hospital Vall d'Hebron" + }, + { + "author_name": "Javier Rodriguez-Ubreva", + "author_inst": "Josep Carreras Research Institute (IJC)" + }, + { + "author_name": "Roser Vento-Tormo", + "author_inst": "Wellcome Sanger Institute" + }, + { + "author_name": "Esteban Ballestar", + "author_inst": "Josep Carreras Research Institute (IJC)" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2022.10.24.22281450", "rel_title": "Impact of COVID-19 on the national development of countries: implications for the public health", @@ -206628,65 +208897,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.10.25.513760", - "rel_title": "One for all - Human kidney Caki-1 cells are highly susceptible to infection with corona- and other respiratory viruses", - "rel_date": "2022-10-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.25.513760", - "rel_abs": "In vitro investigations of host-pathogen interactions of viruses are reliant on suitable cell and tissue culture models. Results are only as good as the model they have been generated in. However, choosing cell models for in vitro work often depends on what is available in labs or what has previously been used. Despite the vast increase in coronavirus research activity over the past few years, researchers are still heavily reliant on: non-human cells, for example Vero E6, highly heterogeneous or not fully differentiated cells, such as Calu-3, or naturally unsusceptible cells requiring overexpression of receptors and other accessory factors, such as ACE2 and TMPRSS2. Complex cell models, such as primary cell-derived air-liquid interface epithelial models are highly representative of human tissues but are expensive and time-consuming to develop and maintain. They have limited suitability for large-scale and high-throughput analysis.\n\nUsing tissue-specific expression pattern as a selection criteria, we identified human kidney cells as an ideal target for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and broader coronavirus infection. We show the use of the highly characterized human kidney cell line Caki-1 for infection with three human coronaviruses: Betacoronaviruses SARS-CoV-2 and Middle Eastern respiratory syndrome coronavirus (MERS-CoV) and Alphacoronavirus human coronavirus 229E (hCoV-229E). Caki-1 cells show equal or superior susceptibility to all three coronaviruses when compared to other commonly used cell lines for the cultivation of the respective virus. Antibody staining against SARS-CoV-2 N protein shows comparable replication rates. Using a panel of 21 antibodies in infected Caki-1 cells using immunocytochemistry shows the location of viral proteins during replication. In addition, Caki-1 cells were found to be susceptible to two other human respiratory viruses, influenza A virus and respiratory syncytial virus, making them an ideal model for cross-comparison of not only a broad range of coronaviruses but respiratory viruses in general.\n\nAuthor SummaryInvestigating how viruses interact with their host relies models used for laboratory research. The closer a model matches the host, the more conclusive results are. Complex cell systems based on primary epithelial or stem cells are the gold standard of in vitro research. However, they are expensive, time consuming, and laborious to establish. Therefore, cell lines remain the backbone of virus research.\n\nDespite vastly increased research into human coronaviruses following the COVID-19 pandemic, researchers continue to rely on suboptimal cell line models, for example ells of non-human origin like the VeroE6 African Green Monkey cell line. Using known expression patterns of the entry factors of the COVID-19 causative agent severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) we identified the Caki-1 cell line as a target for SARS-CoV-2. This cell line could be shown to be infectable with a wide range of coronaviruses including common cold virus hCoV-229E, epidemic virus MERS-CoV, and SARS-CoV-2 as well as other important respiratory viruses influenza A virus and respiratory syncytial virus. We could show that SARS-CoV-2 proteins can be stained for and localized in Caki-1 cells and the cells are competent of forming a cellular immune response. Together, this makes Caki-1 cells a unique tool for cross-virus comparison in one cell line.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Alison Daniels", - "author_inst": "The University Of Edinburgh" - }, - { - "author_name": "Sarah Louise Fletcher", - "author_inst": "The University Of Edinburgh" - }, - { - "author_name": "Holly E. M. Kerr", - "author_inst": "The University Of Edinburgh" - }, - { - "author_name": "Annika Kratzel", - "author_inst": "University of Bern" - }, - { - "author_name": "Nisha Kriplani", - "author_inst": "The University Of Edinburgh" - }, - { - "author_name": "Nicky Craig", - "author_inst": "The University Of Edinburgh" - }, - { - "author_name": "C James Hastie", - "author_inst": "The University of Dundee" - }, - { - "author_name": "Paul Davies", - "author_inst": "The University of Dundee" - }, - { - "author_name": "Paul Digard", - "author_inst": "The University Of Edinburgh" - }, - { - "author_name": "Volker Thiel", - "author_inst": "University of Bern" - }, - { - "author_name": "Christine Tait-Burkard", - "author_inst": "The University Of Edinburgh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.10.21.22281363", "rel_title": "COVID-19 vaccine equity and the right to health for displaced Venezuelans in Latin America", @@ -208555,6 +210765,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.10.21.22281382", + "rel_title": "Abnormal renal function tests at presentation in severe COVID 19 pneumonia and its effect on clinical outcomes", + "rel_date": "2022-10-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.21.22281382", + "rel_abs": "AimTo determine the incidence of abnormal renal function tests at presentation in South Asian patients admitted with severe COVID 19 pneumonia and determine its effect on disease severity and clinical outcomes\n\nMethodsThis was a retrospective cross-sectional study conducted at the COVID Intensive care unit of a large tertiary care government hospital in Karachi, Pakistan. 190 patients admitted over five months from 1/5/2021 till 30/6/2021 were included in the study. Patient demographic characteristics, comorbidities, and clinical manifestations of COVID 19 infection were recorded. Laboratory values at the time of presentation, including Hemoglobin, NLR, platelets, blood urea nitrogen, glomerular filtration rate (GFR), inflammatory markers, liver function tests, and electrolytes were recorded. Patient outcome and need for mechanical ventilation were assessed 28 days after admission and compared with the incidence of abnormal renal functions at presentation.\n\nResultsMean GFR and BUN at presentation were 69.7 and 28.4 respectively. 109 (50.4%) patients had abnormal renal function tests at the time of presentation. 76 (40.0%) patients had low GFR and 33 (17.4%) had only raised BUN with normal GFR. Mean GFR was lower in non-survivors vs survivors (p-value 0.000) and in patients who required mechanical ventilation (p-value 0.008). Patients who had low GFR showed greater mortality than those with normal GFR (p-value 0.04) and were more likely to require mechanical ventilation (p-value 0.04).\n\nConclusionLow GFR at presentation is common in patients with severe COVID 19 pneumonia and is associated with a higher in-hospital mortality rate and need for mechanical ventilation.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Naveed Iqbal", + "author_inst": "Benazir Bhutto Hospital" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.10.21.22281343", "rel_title": "Receipt of COVID-19 and seasonal influenza vaccines in California (USA) during the 2021-2022 influenza season", @@ -208998,49 +211227,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2022.10.20.22281298", - "rel_title": "Virtual care use prior to emergency department admissions during a stable COVID-19 period in Ontario, Canada", - "rel_date": "2022-10-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.20.22281298", - "rel_abs": "BackgroundThe increased use of telemedicine during the pandemic has led to concerns about potential increased emergency department (ED) admissions and outpatient service use prior to such admissions. We examined the frequency of telemedicine use prior to ED admissions and characterized the patients with prior telemedicine use and the physicians who provided these outpatient visits.\n\nMethodsWe conducted a retrospective, population-based, cross-sectional analysis using linked health administrative data in Ontario, Canada to identify patients who had an ED admission between July 1 and September 30, 2021 and patients with an ED admissions during the same period in 2019. We grouped patients based on their use of outpatient services in the 7 days prior to admission and reported their sociodemographic characteristics and healthcare utilization.\n\nResultsThere were 1,080,334 ED admissions in 2021 vs. 1,113,230 in 2019. In 2021, 74% of these admissions had no prior outpatient visits (virtual or in-person) within 7 days of admission, compared to 75% in 2019. Only 3% of ED admissions had both virtual and in-person visits in the 7 days prior to ED admission. Patients with prior virtual care use were more likely to be hospitalized than those without any outpatient care (13% vs 7.7.%).\n\nInterpretationThe net amount of ED admissions and outpatient care prior to admission remained the same over a period of the COVID-19 pandemic when cases were relatively stable. Virtual care seems to be able to appropriately triage patients to the ED and may even prove beneficial for diverting patients away from the ED when an ED admission is not appropriate.\n\nThe COVID-19 pandemic has led to the emergence of standard use of telemedicine in health care across the globe(1,2). In Ontario, Canada the proportion of ambulatory visits completed virtually has been maintained at slightly above 50% from 2020 to 2021 (3). Despite its widespread adoption, it is still unclear when virtual visits are clinically appropriate and how such wide use of telemedicine impacts patient outcomes and healthcare utilization metrics.\n\nBefore the pandemic, there had been concerns that telemedicine may lead to an increased use of outpatient services with patients having both a virtual and an in-person visit for the same clinical issue(4,5). For example, pre-pandemic data (2007-2016) from Manitoba showed that telemedicine users had on average 1.3 times more ambulatory visits than non-users.(6) In addition, studies have produced mixed evidence with regard to the effect of telemedicine on urgent services such as emergency department (ED) admissions and hospitalizations (7). Many of the studies reported in the literature are based on data from site-specific programs and therefore have limited generalizability. Finally, policymakers and some physicians have become concerned that the high rates of telemedicine during COVID-19 have led to an increase in emergency department admissions because of poor access to in-person outpatient care (8). This concern is exacerbated when one considers rural and lower socioeconomic status patients who already had poor access to care before the pandemic(9). Combined with reports of lower uptake of telemedicine among these patients(10,11), it is not clear how the transition of care from in-person to virtual impacts ED use.\n\nThe high adoption of telemedicine during the pandemic, in the context of a publicly funded healthcare system allowing us access to most visits across the entire population, offers a unique opportunity to examine the frequency of telemedicine use prior to ED admissions. Therefore, the goal of this study was to characterize the frequency and modality (in-person vs virtual) of outpatient care prior to ED admissions. We examined whether there was an overall increase in outpatient visits prior to ED admissions during a period of the pandemic when access to telemedicine was available compared to a seasonality matched period before the pandemic where access to telemedicine was quite limited.\n\nWe also aimed to characterize the patients who had a telemedicine visit prior to an ED admission vs. those who had an in-person visit and the physicians who saw patients with virtual only visits prior to their ED admission compared to those who saw patients virtually or in-person prior to their ED admission.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Vess Stamenova", - "author_inst": "Women's College Hospital" - }, - { - "author_name": "Cherry Chu", - "author_inst": "Women's College Hospital" - }, - { - "author_name": "Emily Borgundvaag", - "author_inst": "ICES" - }, - { - "author_name": "Cathleen Fleury", - "author_inst": "Women's College Hospital" - }, - { - "author_name": "Janette Brual", - "author_inst": "Women's College Hospital" - }, - { - "author_name": "Onil Bhattacharyya", - "author_inst": "Women's College Hospital" - }, - { - "author_name": "Mina Tadrous", - "author_inst": "University of Toronto Leslie Dan Faculty of Pharmacy" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2022.10.20.22281311", "rel_title": "Meeting the 2030 End TB goals in the wake of COVID-19: a modelling study of countries in the USAID TB portfolio", @@ -210437,6 +212623,25 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.10.20.513136", + "rel_title": "Diversity, composition, and networking of saliva microbiota distinguish the severity of COVID-19 episodes as revealed by an analysis of 16S rRNA variable V1-V3 regions sequences", + "rel_date": "2022-10-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.20.513136", + "rel_abs": "BackgroundStudies on the role of the oral microbiome in SARS-CoV-2 infection and severity of the disease are limited. We aimed to characterize the bacterial communities present in the saliva of patients with varied COVID-19 severity to learn if there are differences in the characteristics of the microbiome among the clinical groups.\n\nMethodsWe included asymptomatic subjects with no previous COVID-19 infection or vaccination; patients with mild respiratory symptoms, positive or negative for SARS-CoV-2 infection; patients that required hospitalization because of severe COVID-19 with oxygen saturation below 92%, and fatal cases of COVID-19. Saliva samples collected before any treatment were tested for SARS-CoV-2 by PCR. Oral microbiota in saliva was studied by amplification and sequencing of the V1-V3 variable regions of 16S gene using a Illumina MiSeq platform.\n\nResultsWe found significant changes in diversity, composition, and networking in saliva microbiota of patients with COVID-19, as well as patterns associated with severity of disease. The presence or abundance of several commensal species and opportunistic pathogens were associated with each clinical stage. Patterns of networking were also found associated with severity of disease: a highly regulated bacterial community (normonetting) was found in healthy people whereas poorly regulated populations (disnetting) were characteristic of severe cases.\n\nConclusionsCharacterization of microbiota in saliva may offer important clues in the pathogenesis of COVID-19 and may also identify potential markers for prognosis in the severity of the disease.\n\nImportance of the workSARS-CoV-2 infection is the most severe pandemic of humankind in the last hundred years. The outcome of the infection ranges from asymptomatic or mild to severe and even fatal cases, but reasons for this remain unknown. Microbes normally colonizing the respiratory tract form communities that may mitigate the transmission, symptoms, and severity of viral infections, but very little is known on the role of these microbial communities in the severity of COVID-19. We aimed to characterize the bacterial communities in saliva of patients with different severity of COVID-19 disease, from mild to fatal cases. Our results revealed clear differences in the composition and in the nature of interactions (networking) of the bacterial species present in the different clinical groups and show community-patterns associated with disease severity. Characterization of the microbial communities in saliva may offer important clues to learn ways COVID-19 patients may suffer from different disease severities.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Javier Torres", + "author_inst": "Instituto Mexicano del Seguro Social" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.10.18.512756", "rel_title": "Endonuclease fingerprint indicates a synthetic origin of SARS-CoV-2", @@ -211128,49 +213333,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2022.10.18.22281202", - "rel_title": "Alternative splicing in the lung influences COVID-19 severity and respiratory diseases.", - "rel_date": "2022-10-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.18.22281202", - "rel_abs": "Hospital admission for COVID-19 remains common despite the successful development of vaccines and treatments. Thus, there is an ongoing need to identify targets for new COVID-19 therapies. Alternative splicing is an essential mechanism for generating functional diversity in protein isoforms and influences immune response to infection. However, the causal role of alternative splicing in COVID-19 severity and its potential therapeutic relevance is not fully understood. In this study, we evaluated the causal role of alternative splicing in COVID-19 severity and susceptibility using Mendelian randomization (MR). To do so, we performed two-sample MR to assess whether cis-sQTLs spanning 8,172 gene splicing in 5,295 genes were associated with COVID-19 outcomes in the COVID-19 Host Genetics Initiative, including up to 158,840 COVID-19 cases and 2,782,977 population controls. We identified that alternative splicing in lungs, rather than total RNA expression of OAS1, ATP11A, DPP9 and NPNT, was associated with COVID-19 severity. MUC1 splicing was associated with COVID-19 susceptibility. Further colocalization analyses supported a shared genetic mechanism between COVID-19 severity with idiopathic pulmonary fibrosis at ATP11A and DPP9 loci, and with chronic obstructive lung diseases at NPNT. We lastly showed that ATP11A, DPP9, NPNT, and MUC1 were highly expressed in lung alveolar epithelial cells, both in COVID-19 uninfected and infected samples. Taken together, these findings clarify the importance of alternative splicing of proteins in the lung for COVID-19 and other respiratory diseases, providing isoform-based targets for drug discovery.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Tomoko Nakanishi", - "author_inst": "McGill University" - }, - { - "author_name": "Yossi Yossi Farjoun", - "author_inst": "McGill University" - }, - { - "author_name": "Julian Daniel Sunday Willett", - "author_inst": "McGill University" - }, - { - "author_name": "Richard J Allen", - "author_inst": "University of Leicester" - }, - { - "author_name": "Beatriz Guillen-Guio", - "author_inst": "University of Leicester" - }, - { - "author_name": "Sirui Zhou", - "author_inst": "Lady Davis Institute of Jewish General Hospital" - }, - { - "author_name": "J Brent Richards", - "author_inst": "McGill University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2022.10.14.22280869", "rel_title": "MULTISYSTEM INFLAMMATORY SYNDROME IN CHILDREN COURSE AMID COVID-19 PANDEMIC IN THE REBUBLIC OF BELARUS", @@ -212583,6 +214745,41 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2022.10.17.512617", + "rel_title": "Infection of primary nasal epithelial cells differentiates among lethal and seasonal human coronaviruses", + "rel_date": "2022-10-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.17.512617", + "rel_abs": "The nasal epithelium is the initial entry portal and primary barrier to infection by all human coronaviruses (HCoVs). We utilize primary nasal epithelial cells grown at air-liquid interface, which recapitulate the heterogeneous cellular population as well as mucociliary clearance functions of the in vivo nasal epithelium, to compare lethal (SARS-CoV-2 and MERS-CoV) and seasonal (HCoV-NL63 and HCoV-229E) HCoVs. All four HCoVs replicate productively in nasal cultures but diverge significantly in terms of cytotoxicity induced following infection, as the seasonal HCoVs as well as SARS-CoV-2 cause cellular cytotoxicity as well as epithelial barrier disruption, while MERS-CoV does not. Treatment of nasal cultures with type 2 cytokine IL-13 to mimic asthmatic airways differentially impacts HCoV replication, enhancing MERS-CoV replication but reducing that of SARS-CoV-2 and HCoV-NL63. This study highlights diversity among HCoVs during infection of the nasal epithelium, which is likely to influence downstream infection outcomes such as disease severity and transmissibility.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Clayton Otter", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Alejandra Fausto", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Li Hui Tan", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Noam A Cohen", + "author_inst": "Uniersity of Pennsylvania" + }, + { + "author_name": "Susan R Weiss", + "author_inst": "University of Pennsylvania" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.10.13.22281012", "rel_title": "COVID-19 Vaccine Effectiveness against SARS-CoV-2 Infections with the Delta Variant among Ages >=12 Years in Utah", @@ -213206,77 +215403,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.10.17.22281085", - "rel_title": "COVID-19 among adults living with HIV: Correlates of mortality in a general population in a resource-limited setting", - "rel_date": "2022-10-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.17.22281085", - "rel_abs": "IntroductionWhile a large proportion of people with HIV (PWH) have experienced SARS-CoV-2 infections, there is uncertainty about the role of HIV disease severity on COVID-19 outcomes, especially in lower income settings. We studied the association between mortality and characteristics of HIV severity and management, and vaccination, among adult PWH.\n\nMethodsWe analysed observational cohort data on all PWH aged [≥]15 years experiencing a diagnosed SARS-CoV-2 infection (until March 2022), who accessed public sector healthcare in the Western Cape province of South Africa. Logistic regression was used to study the association of mortality with CD4 cell count, viral load, evidence of ART, time since first HIV evidence, and vaccination, adjusting for demographic characteristics, comorbidities, admission pressure, location and time period.\n\nResultsMortality occurred in 5.7% (95% CI: 5.3,6.0) of 17 831 first diagnosed infections. Higher mortality was associated with lower recent CD4, no evidence of ART collection, high or unknown recent viral load (among those with ART evidence), and recent first HIV evidence, differentially by age. Vaccination was protective. The burden of comorbidities was high, and tuberculosis, chronic kidney disease, diabetes and hypertension were associated with higher mortality, more strongly in younger adults.\n\nConclusionsMortality was strongly associated with suboptimal HIV control, and prevalence of these risk factors increased in later COVID-19 waves. It remains a public health priority to ensure PWH are on suppressive ART and vaccinated, and manage any disruptions in care that occurred during the pandemic. The diagnosis and management of comorbidities, including for tuberculosis, should be optimised.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Reshma Kassanjee", - "author_inst": "School of Public Health, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Mary-Ann Davies", - "author_inst": "School of Public Health, University of Cape Town, Cape Town, South Africa; Western Cape Government: Health and Wellness, Cape Town, South Africa" - }, - { - "author_name": "Olina Ngwenya", - "author_inst": "Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Af" - }, - { - "author_name": "Richard Osei-Yeboah", - "author_inst": "Division of Computational Biology, Integrative Biomedical Sciences Department, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Theuns Jacobs", - "author_inst": "School of Public Health, University of Cape Town, Cape Town, South Africa; Western Cape Government: Health and Wellness, Cape Town, South Africa" - }, - { - "author_name": "Erna Morden", - "author_inst": "School of Public Health, University of Cape Town, Cape Town, South Africa; Western Cape Government: Health and Wellness, Cape Town, South Africa" - }, - { - "author_name": "Venessa Timmerman", - "author_inst": "Western Cape Government: Health and Wellness, Cape Town, South Africa" - }, - { - "author_name": "Stefan Britz", - "author_inst": "Department of Statistical Sciences, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Marc Mendelson", - "author_inst": "Division of Infectious Diseases and HIV Medicine, Department of Medicine, Groote Schuur Hospital, University of Cape Town, South Africa" - }, - { - "author_name": "Jantjie Taljaard", - "author_inst": "Division of Infectious Diseases, Department of Medicine, Tygerberg Hospital, Stellenbosch University, South Africa" - }, - { - "author_name": "Julien Riou", - "author_inst": "Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Andrew Boulle", - "author_inst": "School of Public Health, University of Cape Town, Cape Town, South Africa; Western Cape Government: Health and Wellness, Cape Town, South Africa" - }, - { - "author_name": "Nicki Tiffin", - "author_inst": "Western Cape Government: Health and Wellness, Cape Town, South Africa; University of the Western Cape, Cape Town, South Africa" - }, - { - "author_name": "Nesbert Zinyakatira", - "author_inst": "School of Public Health, University of Cape Town, Cape Town, South Africa; Western Cape Government: Health and Wellness, Cape Town, South Africa" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.10.15.22281123", "rel_title": "Investigating the cause of a 2021 winter wave of COVID-19 in a border region in Eastern Germany: a mixed-methods study, August to November 2021", @@ -214425,6 +216551,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.10.12.511991", + "rel_title": "Rapid transmission and tight bottlenecks constrain the evolution of highly transmissible SARS-CoV-2 variants", + "rel_date": "2022-10-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.12.511991", + "rel_abs": "Transmission bottlenecks limit the spread of novel mutations and reduce the efficiency of natural selection along a transmission chain. Many viruses exhibit tight bottlenecks, and studies of early SARS-CoV-2 lineages identified a bottleneck of 1-3 infectious virions. While increased force of infection, host receptor binding, or immune evasion may influence bottleneck size, the relationship between transmissibility and the transmission bottleneck is unclear. Here, we compare the transmission bottleneck of non-variant-of-concern (non-VOC) SARS-CoV-2 lineages to those of the Alpha, Delta, and Omicron variants. We sequenced viruses from 168 individuals in 65 multiply infected households in duplicate to high depth of coverage. In 110 specimens collected close to the time of transmission, within-host diversity was extremely low. At a 2% frequency threshold, 51% had no intrahost single nucleotide variants (iSNV), and 42% had 1-2 iSNV. In 64 possible transmission pairs with detectable iSNV, we identified a bottleneck of 1 infectious virion (95% CI 1-1) for Alpha, Delta, and Omicron lineages and 2 (95% CI 2-2) in non-VOC lineages. The latter was driven by a single iSNV shared in one non-VOC household. The tight transmission bottleneck in SARS-CoV-2 is due to low genetic diversity at the time of transmission, a relationship that may be more pronounced in rapidly transmissible variants. The tight bottlenecks identified here will limit the development of highly mutated VOC in typical transmission chains, adding to the evidence that selection over prolonged infections in immunocompromised patients may drive their evolution.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Emily E. Bendall", + "author_inst": "University of Michigan" + }, + { + "author_name": "Amy Callear", + "author_inst": "University of Michigan" + }, + { + "author_name": "Amy Getz", + "author_inst": "University of Michigan" + }, + { + "author_name": "Kendra Goforth", + "author_inst": "University of Michigan" + }, + { + "author_name": "Drew Edwards", + "author_inst": "University of Michigan" + }, + { + "author_name": "Arnold Monto", + "author_inst": "University of Michigan" + }, + { + "author_name": "Emily Toth Martin", + "author_inst": "University of Michigan" + }, + { + "author_name": "Adam S. Lauring", + "author_inst": "University of Michigan" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.10.13.512127", "rel_title": "SARS-CoV-2 immune complex triggers human monocyte necroptosis", @@ -215372,41 +217545,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.10.11.22280963", - "rel_title": "Age-stratified infection fatality rate of COVID-19 in the non-elderly informed from pre-vaccination national seroprevalence studies", - "rel_date": "2022-10-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.11.22280963", - "rel_abs": "The infection fatality rate (IFR) of COVID-19 among non-elderly people in the absence of vaccination or prior infection is important to estimate accurately, since 94% of the global population is younger than 70 years and 86% is younger than 60 years. In systematic searches in SeroTracker and PubMed (protocol: https://osf.io/xvupr), we identified 40 eligible national seroprevalence studies covering 38 countries with pre-vaccination seroprevalence data. For 29 countries (24 high-income, 5 others), publicly available age-stratified COVID-19 death data and age-stratified seroprevalence information were available and were included in the primary analysis. The IFRs had a median of 0.035% (interquartile range (IQR) 0.013 - 0.056%) for the 0-59 years old population, and 0.095% (IQR 0.036 - 0.125%,) for the 0-69 years old. The median IFR was 0.0003% at 0-19 years, 0.003% at 20-29 years, 0.011% at 30-39 years, 0.035% at 40-49 years, 0.129% at 50-59 years, and 0.501% at 60-69 years. Including data from another 9 countries with imputed age distribution of COVID-19 deaths yielded median IFR of 0.025-0.032% for 0-59 years and 0.063-0.082% for 0-69 years. Meta-regression analyses also suggested global IFR of 0.03% and 0.07%, respectively in these age groups. The current analysis suggests a much lower pre-vaccination IFR in non-elderly populations than previously suggested. Large differences did exist between countries and may reflect differences in comorbidities and other factors. These estimates provide a baseline from which to fathom further IFR declines with the widespread use of vaccination, prior infections, and evolution of new variants.\n\nHighlights*Across 31 systematically identified national seroprevalence studies in the pre-vaccination era, the median infection fatality rate of COVID-19 was estimated to be 0.035% for people aged 0-59 years people and 0.095% for those aged 0-69 years.\n\n*The median IFR was 0.0003% at 0-19 years, 0.003% at 20-29 years, 0.011% at 30-39 years, 0.035% at 40-49 years, 0.129% at 50-59 years, and 0.501% at 60-69 years.\n\n*At a global level, pre-vaccination IFR may have been as low as 0.03% and 0.07% for 0-59 and 0-69 year old people, respectively.\n\n*These IFR estimates in non-elderly populations are lower than previous calculations had suggested.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Angelo Maria Pezzullo", - "author_inst": "Universita Cattolica del Sacro Cuore" - }, - { - "author_name": "Cathrine Axfors", - "author_inst": "Stanford University" - }, - { - "author_name": "Despina G Contopoulos-Ioannidis", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Alexandre Apostolatos", - "author_inst": "Universite de Montreal" - }, - { - "author_name": "John P.A. Ioannidis", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.10.12.22280917", "rel_title": "Evaluating an epidemiologically motivated surrogate model of a multi-model ensemble", @@ -216439,6 +218577,153 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.10.10.511571", + "rel_title": "GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics.", + "rel_date": "2022-10-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.10.511571", + "rel_abs": "We seek to transform how new and emergent variants of pandemiccausing viruses, specifically SARS-CoV-2, are identified and classified. By adapting large language models (LLMs) for genomic data, we build genome-scale language models (GenSLMs) which can learn the evolutionary landscape of SARS-CoV-2 genomes. By pretraining on over 110 million prokaryotic gene sequences and finetuning a SARS-CoV-2-specific model on 1.5 million genomes, we show that GenSLMs can accurately and rapidly identify variants of concern. Thus, to our knowledge, GenSLMs represents one of the first whole genome scale foundation models which can generalize to other prediction tasks. We demonstrate scaling of GenSLMs on GPU-based supercomputers and AI-hardware accelerators utilizing 1.63 Zettaflops in training runs with a sustained performance of 121 PFLOPS in mixed precision and peak of 850 PFLOPS. We present initial scientific insights from examining GenSLMs in tracking evolutionary dynamics of SARS-CoV-2, paving the path to realizing this on large biological data.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Max T. Zvyagin", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Alexander Brace", + "author_inst": "University of Chicago" + }, + { + "author_name": "Kyle Hippe", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Yuntian Deng", + "author_inst": "NVIDIA Inc" + }, + { + "author_name": "Bin Zhang", + "author_inst": "Cerebras Systems" + }, + { + "author_name": "Cindy Orozco Bohorquez", + "author_inst": "Cerebras Systems" + }, + { + "author_name": "Austin Clyde", + "author_inst": "University of Chicago" + }, + { + "author_name": "Bharat Kale", + "author_inst": "Northern Illinois University" + }, + { + "author_name": "Danilo Perez-Rivera", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Heng Ma", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Carla M. Mann", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Michael Irvin", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "J. Gregory Pauloski", + "author_inst": "University of Chicago" + }, + { + "author_name": "Logan Ward", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Valerie Hayot", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Murali Emani", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Sam Foreman", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Zhen Xie", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Diangen Lin", + "author_inst": "University of Chicago" + }, + { + "author_name": "Maulik Shukla", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Weili Nie", + "author_inst": "NVIDIA Inc" + }, + { + "author_name": "Josh Romero", + "author_inst": "NVIDIA Inc" + }, + { + "author_name": "Christian Dallago", + "author_inst": "NVIDIA Inc" + }, + { + "author_name": "Arash Vahdat", + "author_inst": "NVIDIA Inc" + }, + { + "author_name": "Chaowei Xiao", + "author_inst": "NVIDIA Inc" + }, + { + "author_name": "Thomas Gibbs", + "author_inst": "NVIDIA Inc" + }, + { + "author_name": "Ian Foster", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "James J. Davis", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Michael E. Papka", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Thomas Brettin", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Anima Anandkumar", + "author_inst": "NVIDIA Inc" + }, + { + "author_name": "Venkatram Vishwanath", + "author_inst": "Argonne National Laboratory" + }, + { + "author_name": "Arvind Ramanathan", + "author_inst": "Argonne National Laboratory" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.10.10.511623", "rel_title": "Genomic tracking of SARS-COV-2 variants in Myanmar", @@ -217038,53 +219323,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.10.09.22280877", - "rel_title": "COVID19 Diagnosis Using Chest X-rays and Transfer Learning", - "rel_date": "2022-10-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.10.09.22280877", - "rel_abs": "A pandemic of respiratory illnesses from a novel coronavirus known as Sars-CoV-2 has swept across the globe since December of 2019. This is calling upon the research community including medical imaging to provide effective tools for use in combating this virus. Research in biomedical imaging of viral patients is already very active with machine learning models being created for diagnosing Sars-CoV-2 infections in patients using CT scans and chest x-rays. We aim to build upon this research. Here we used a transfer-learning approach to develop models capable of diagnosing COVID19 from chest x-ray. For this work we compiled a dataset of 112120 negative images from the Chest X-Ray 14 and 2725 positive images from public repositories. We tested multiple models, including logistic regression and random forest and XGBoost with and without principal components analysis, using five-fold cross-validation to evaluate recall, precision, and f1-score. These models were compared to a pre-trained deep-learning model for evaluating chest x-rays called COVID-Net. Our best model was XGBoost with principal components with a recall, precision, and f1-score of 0.692, 0.960, 0.804 respectively. This model greatly outperformed COVID-Net which scored 0.987, 0.025, 0.048. This model, with its high precision and reasonable sensitivity, would be most useful as \"rule-in\" test for COVID19. Though it outperforms some chemical assays in sensitivity, this model should be studied in patients who would not ordinarily receive a chest x-ray before being used for screening.\n\nCCS CONCEPTSO_LILife and Medical Sciences * Machine Learning * Artificial Intelligence\nC_LI\n\nReference formatJonathan Stubblefield, Jason Causey, Dakota Dale, Jake Qualls, Emily Bellis, Jennifer Fowler, Karl Walker and Xiuzhen Huang. 2022. COVID19 Diagnosis Using Chest X-Rays and Transfer Learning.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Jonathan Stubblefield", - "author_inst": "Arkansas State University" - }, - { - "author_name": "Jason Causey", - "author_inst": "Arkansas State University" - }, - { - "author_name": "Dakota Dale", - "author_inst": "University of Arkansas at Fayetteville" - }, - { - "author_name": "Jake Qualls", - "author_inst": "Arkansas State University" - }, - { - "author_name": "Emily Bellis", - "author_inst": "Arkansas State University" - }, - { - "author_name": "Jennifer Fowler", - "author_inst": "Arkansas State University" - }, - { - "author_name": "Karl Walker", - "author_inst": "University of Arkansas at Pine Bluff" - }, - { - "author_name": "Xiuzhen Huang", - "author_inst": "Arkansas State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2022.10.08.22280863", "rel_title": "A Third Dose COVID-19 Vaccination in Allogeneic Hematopoietic Stem Cell Transplantation Patients", @@ -218529,6 +220767,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2022.10.08.511397", + "rel_title": "SiRNA Molecules as Potential RNAi Therapeutics to Silence RdRP Region and N-Gene of SARS-CoV-2: An In Silico Approach", + "rel_date": "2022-10-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.08.511397", + "rel_abs": "COVID-19 pandemic keeps pressing onward and effective treatment option against it is still far-off. Since the onslaught in 2020, 13 different variants of SARS-CoV-2 have been surfaced including 05 different variants of concern. Success in faster pandemic handling in the future largely depends on reinforcing therapeutics along with vaccines. As a part of RNAi therapeutics, here we developed a computational approach for predicting siRNAs, which are presumed to be intrinsically active against two crucial mRNAs of SARS-CoV-2, the RNA-dependent RNA polymerase (RdRp), and the nucleocapsid phosphoprotein gene (N gene). Sequence conservancy among the alpha, beta, gamma, and delta variants of SARS-CoV-2 was integrated in the analyses that warrants the potential of these siRNAs against multiple variants. We preliminary found 13 RdRP-targeting and 7 N gene-targeting siRNAs using the siDirect V.2.0. These siRNAs were subsequently filtered through different parameters at optimum condition including macromolecular docking studies. As a result, we selected 4 siRNAs against the RdRP and 3 siRNAs against the N-gene as RNAi candidates. Development of these potential siRNA therapeutics can significantly synergize COVID-19 mitigation by lessening the efforts, furthermore, can lay a rudimentary base for the in silico design of RNAi therapeutics for future emergencies.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Mahedi Hasan", + "author_inst": "Department of Biochemistry and Molecular Biology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh." + }, + { + "author_name": "Atiya Tahira Tasnim", + "author_inst": "Department of Biochemistry and Molecular Biology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh." + }, + { + "author_name": "Arafat Islam Ashik", + "author_inst": "Department of Biochemistry and Molecular Biology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh." + }, + { + "author_name": "Md Belal Chowdhury", + "author_inst": "Department of Biochemistry and Molecular Biology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh." + }, + { + "author_name": "Zakia Sultana Nishat", + "author_inst": "Department of Biochemistry and Molecular Biology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh." + }, + { + "author_name": "Khandaker Atkia Fariha", + "author_inst": "Department of Biochemistry and Molecular Biology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh." + }, + { + "author_name": "Tanvir Hossain", + "author_inst": "Department of Biochemistry and Molecular Biology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh." + }, + { + "author_name": "Shamim Ahmed", + "author_inst": "Department of Biochemistry and Molecular Biology, School of Life Sciences, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.10.07.511351", "rel_title": "Inhibition of the SARS-CoV-2 helicase at single-nucleotide resolution.", @@ -218964,117 +221249,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.10.06.511203", - "rel_title": "Incipient parallel evolution of SARS-CoV-2 Deltacron variant in South Brazil", - "rel_date": "2022-10-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.06.511203", - "rel_abs": "With the coexistence of multiple lineages and increased international travel, recombination and gene flow are likely to become increasingly important in the adaptive evolution of SARS-CoV-2. This could result in the incipient parallel evolution of multiple recombinant lineages. However, identifying recombinant lineages is challenging, and the true extent of recombinant evolution in SARS-CoV-2 may be underestimated. This study describes the first SARS-CoV-2 Deltacron recombinant case identified in Brazil. We demonstrate that the recombination breakpoint is at the beginning of Spike gene (S). The 5' genome portion (circa 22 kb) resembles the AY.101 lineage (VOC Delta), and the 3' genome portion (circa 8 kb nucleotides) is most similar to the BA.1.1 lineage (VOC Omicron). Furthermore, evolutionary genomic analyses indicate that the new strain emerged after a single recombination event between lineages of diverse geographical locations in December 2021 in South Brazil. This Deltacron, named AYBA-RS, is one out of almost 30 recombinants described this year. The submission of only four sequences in the GISAID database suggests that this Brazilian lineage had a minor epidemiological impact. On the other hand, the recent emergence of this and various other Deltacron recombinant lineages (i.e., XD, XF, and XS) suggests that gene flow and recombination may play an increasingly important role in the COVID-19 pandemic. We explain the evolutionary and population genetic theory that support this assertion, and we conclude that this stresses the need for continued genomic and epidemiological surveillance. This is particularly important for countries where multiple variants are present, as well as for countries that receive significant inbound international travel.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Fernando H Sant Anna", - "author_inst": "Hospital Moinhos de Vento" - }, - { - "author_name": "Tiago F Andreis", - "author_inst": "Hospital Moinhos de Vento" - }, - { - "author_name": "Richard S Salvato", - "author_inst": "CDCT/CEVS/SES-RS" - }, - { - "author_name": "Ana P Muterle", - "author_inst": "Hospital Moinhos de Vento" - }, - { - "author_name": "Juliana Comerlato", - "author_inst": "Hospital Moinhos de Vento" - }, - { - "author_name": "Tatiana S Gregianini", - "author_inst": "LACEN/CEVS/SES-RS" - }, - { - "author_name": "Regina B Barcellos", - "author_inst": "CDCT/CEVS/SES-RS" - }, - { - "author_name": "Fernanda M Godinho", - "author_inst": "CDCT/CEVS/SES-RS" - }, - { - "author_name": "Paola C Resende", - "author_inst": "FIOCRUZ" - }, - { - "author_name": "Gabriel L Wallau", - "author_inst": "FIOCRUZ-PE" - }, - { - "author_name": "Thais R Castro", - "author_inst": "Universidade Federal de Santa Maria" - }, - { - "author_name": "Bruna C Casarin", - "author_inst": "Universidade Federal de Santa Maria" - }, - { - "author_name": "Andressa A Vieira", - "author_inst": "Universidade Federal de Santa Maria" - }, - { - "author_name": "Alexandre V Schwarzbold", - "author_inst": "Universidade Federal de Santa Maria" - }, - { - "author_name": "Priscila A Trindade", - "author_inst": "Universidade Federal de Santa Maria" - }, - { - "author_name": "Gabriela LT Giannini", - "author_inst": "Hospital Moinhos de Vento" - }, - { - "author_name": "Luana Freese", - "author_inst": "Hospital Moinhos de Vento" - }, - { - "author_name": "Giovana Bristot", - "author_inst": "Hospital Moinhos de Vento" - }, - { - "author_name": "Carolina S Brasil", - "author_inst": "Hospital Moinhos de Vento" - }, - { - "author_name": "Bruna O Rocha", - "author_inst": "Hospital Moinhos de Vento" - }, - { - "author_name": "Paloma B Martins", - "author_inst": "Hospital Moinhos de Vento" - }, - { - "author_name": "Francine H Oliveira", - "author_inst": "Hospital Moinhos de Vento" - }, - { - "author_name": "Cock v Oosterhout", - "author_inst": "University of East Anglia" - }, - { - "author_name": "Eliana Wendland", - "author_inst": "UFCSPA" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2022.10.07.511263", "rel_title": "Neutralization of SARS-CoV-2 Omicron BA.4/BA.5 subvariant by a booster dose of bivalent adjuvanted subunit vaccine containing Omicron BA.4/BA.5 and BA.1 subvariants", @@ -220327,6 +222501,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.10.04.510919", + "rel_title": "Real-time inactivation of airborne SARS-CoV-2 using ultraviolet-C", + "rel_date": "2022-10-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.04.510919", + "rel_abs": "COVID-19 is a life-threatening respiratory infection that has had a profound impact on indoor air quality awareness. Ultraviolet-C (UV-C) is a physical disinfection process that triggers microbial inactivation through creating irreversible genetic material damage. An upper room device equipped with germicidal UV-C (UR GUV) was evaluated against airborne SARS-CoV-2 for antimicrobial efficacy using a robust aerosol testing protocol. In 30 minutes, it led to a virucidal efficacy of 99.994 % in a large, room-sized chamber. UR GUV is a promising mitigation strategy for airborne pathogens.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Carolina Koutras", + "author_inst": "R-Zero Systems" + }, + { + "author_name": "Richard L Wade", + "author_inst": "R-Zero Systems" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.10.05.510928", "rel_title": "A novel antiviral formulation inhibits SARS-CoV-2 infection of human bronchial epithelium", @@ -221026,57 +223223,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.09.30.510319", - "rel_title": "Minor intron containing genes: Achilles' heel of viruses?", - "rel_date": "2022-10-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.30.510319", - "rel_abs": "The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) revealed the worlds unpreparedness to deal with the emergence of novel pathogenic viruses, pointing to the urgent need to identify targets for broad-spectrum antiviral strategies. Here, we report that proteins encoded by Minor Intron-containing Genes (MIGs) are significantly enriched in datasets of cellular proteins that are leveraged by SARS-CoV-2 and other viruses. Pointing to a general gateway for viruses to tap cellular machinery, MIG-encoded proteins (MIG-Ps) that react to the disruption of the minor spliceosome are most important points of viral attack, suggesting that MIG-Ps may pan-viral drug targets. While contemporary anti-viral drugs shun MIG-Ps, we surprisingly found that anti-cancer drugs that have been repurposed to combat SARS-CoV-2, indeed target MIG-Ps, suggesting that such genes can potentially be tapped to efficiently fight viruses.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Stefan Wuchty", - "author_inst": "Univ. of Miami" - }, - { - "author_name": "Alisa K. White", - "author_inst": "Univ. of Connecticut" - }, - { - "author_name": "Anouk M. Olthof", - "author_inst": "Univ. of Connecticut" - }, - { - "author_name": "Kyle Drake", - "author_inst": "Univ. of Connecticut" - }, - { - "author_name": "Adam J. Hume", - "author_inst": "Boston Univ." - }, - { - "author_name": "Judith Olejnik", - "author_inst": "Boston Univ." - }, - { - "author_name": "Elke Muehlberger", - "author_inst": "Boston Univ." - }, - { - "author_name": "Vanessa Aguiar-Pulido", - "author_inst": "Univ. of Miami" - }, - { - "author_name": "Rahul N. Kanadia", - "author_inst": "Univ. of Connecticut" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "systems biology" - }, { "rel_doi": "10.1101/2022.09.27.22280428", "rel_title": "Impact of Fluvoxamine on outpatient treatment of COVID-19 in Honduras", @@ -222449,6 +224595,181 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.10.03.510566", + "rel_title": "Intranasal delivery of NS1-deleted influenza virus vectored COVID-19 vaccine restrains the SARS-CoV-2 inflammatory response", + "rel_date": "2022-10-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.10.03.510566", + "rel_abs": "The emergence of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) variants and \"anatomical escape\" characteristics threaten the effectiveness of current coronavirus disease (COVID-19) vaccines. There is an urgent need to understand the immunological mechanism of broad-spectrum respiratory tract protection to guide broader vaccines development. In this study, we investigated immune responses induced by an NS1-deleted influenza virus vectored intranasal COVID-19 vaccine (dNS1-RBD) which provides broad-spectrum protection against SARS-CoV-2 variants. Intranasal delivery of dNS1-RBD induced innate immunity, trained immunity and tissue-resident memory T cells covering the upper and lower respiratory tract. It restrained the inflammatory response by suppressing early phase viral load post SARS-CoV-2 challenge and attenuating pro-inflammatory cytokine (IL-6, IL-1B, and IFN-{gamma}) levels, thereby reducing excess immune-induced tissue injury compared with the control group. By inducing local cellular immunity and trained immunity, intranasal delivery of NS1-deleted influenza virus vectored vaccine represents a broad-spectrum COVID-19 vaccine strategy to reduce disease burden.", + "rel_num_authors": 40, + "rel_authors": [ + { + "author_name": "Liang Zhang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Yao Jiang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Jinhang He", + "author_inst": "Xiamen University" + }, + { + "author_name": "Junyu Chen", + "author_inst": "Xiamen University" + }, + { + "author_name": "Ruoyao Qi", + "author_inst": "Xiamen University" + }, + { + "author_name": "Lunzhi Yuan", + "author_inst": "Xiamen University" + }, + { + "author_name": "Tiange Shao", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Congjie Chen", + "author_inst": "Xiamen University" + }, + { + "author_name": "Yaode Chen", + "author_inst": "Xiamen University" + }, + { + "author_name": "Xijing Wang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Xing Lei", + "author_inst": "Xiamen University" + }, + { + "author_name": "Qingxiang Gao", + "author_inst": "Xiamen University" + }, + { + "author_name": "Chunlan Zhuang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Ming Zhou", + "author_inst": "Xiamen University" + }, + { + "author_name": "Jian Ma", + "author_inst": "Xiamen University" + }, + { + "author_name": "Wei Liu", + "author_inst": "Xiamen University" + }, + { + "author_name": "Man Yang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Rao Fu", + "author_inst": "Xiamen University" + }, + { + "author_name": "Yangtao Wu", + "author_inst": "Xiamen University" + }, + { + "author_name": "Feng Chen", + "author_inst": "Xiamen University" + }, + { + "author_name": "Hualong Xiong", + "author_inst": "Xiamen University" + }, + { + "author_name": "Meifeng Nie", + "author_inst": "Xiamen University" + }, + { + "author_name": "Yiyi Chen", + "author_inst": "Xiamen University" + }, + { + "author_name": "Kun Wu", + "author_inst": "Xiamen University" + }, + { + "author_name": "Mujing Fang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Yingbin Wang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Zizheng Zheng", + "author_inst": "Xiamen University" + }, + { + "author_name": "Shoujie Huang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Shengxiang Ge", + "author_inst": "Xiamen University" + }, + { + "author_name": "Shih-Chin Cheng", + "author_inst": "Xiamen University" + }, + { + "author_name": "Huachen Zhu", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Tong Chen", + "author_inst": "Xiamen University" + }, + { + "author_name": "Quan Yuan", + "author_inst": "Xiamen University" + }, + { + "author_name": "Ting Wu", + "author_inst": "Xiamen University" + }, + { + "author_name": "Jun Zhang", + "author_inst": "Xiamen University" + }, + { + "author_name": "Yixin Chen", + "author_inst": "Xiamen University" + }, + { + "author_name": "Tianying Zhang", + "author_inst": "School of Public Health, Xiamen University" + }, + { + "author_name": "Hai Qi", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Yi Guan", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Ningshao Xia", + "author_inst": "Xiamen University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.09.30.510274", "rel_title": "Reproducibility of spatial summation of pain effect during COVID-19 pandemic", @@ -223024,45 +225345,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.09.29.22280526", - "rel_title": "Effectiveness and Duration of Protection of a Fourth Dose of COVID-19 mRNA Vaccine among Long-Term Care Residents in Ontario, Canada", - "rel_date": "2022-09-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.29.22280526", - "rel_abs": "BackgroundAs of December 30, 2021, Ontario long-term care (LTC) residents who received a third dose of COVID-19 vaccine [≥]84 days previously were offered a fourth dose to prevent a surge in COVID-19-related morbidity and mortality due to the Omicron variant. Seven months have passed since fourth doses were implemented, allowing for the examination of fourth dose protection over time.\n\nMethodsWe used a test-negative design and linked databases to estimate the marginal effectiveness (4 versus 3 doses) and vaccine effectiveness (VE; 2, 3, or 4 doses versus no doses) of mRNA vaccines among Ontario LTC residents aged [≥]60 years who were tested for SARS-CoV-2 between December 30, 2021 and August 3, 2022. Outcome measures included any Omicron infection, symptomatic infection, and severe outcomes (hospitalization or death).\n\nResultsWe included 21,275 Omicron cases and 273,466 test-negative controls. The marginal effectiveness of a fourth dose <84 days ago compared to a third dose received [≥]84 days ago was 23% (95% Confidence Interval [CI] 17-29%), 36% (95%CI 26-44%), and 37% (95%CI 24-48%) against SARS-CoV-2 infection, symptomatic infection, and severe outcomes, respectively. Additional protection provided by a fourth dose compared to a third dose was negligible against all outcomes [≥]168 days after vaccination. Compared to unvaccinated individuals, vaccine effectiveness (VE) of a fourth dose decreased from 49% (95%CI 44%-54%) to 18% (95%CI 5-28%) against infection, 69% (95%CI 62-75%) to 44% (95%CI 24-59%) against symptomatic infection, and 82% (95%CI 77-86%) to 74% (95%CI 62-82%) against severe outcomes <84 days versus [≥]168 days after vaccination.\n\nConclusionsOur findings suggest that fourth doses of mRNA COVID-19 vaccines provide additional protection against Omicron-related outcomes in LTC residents, but the protection wanes over time, with more waning seen against infection than severe outcomes.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Ramandip Grewal", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Lena Nguyen", - "author_inst": "ICES" - }, - { - "author_name": "Sarah A Buchan", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Sarah E Wilson", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Andrew P Costa", - "author_inst": "McMaster University" - }, - { - "author_name": "Jeffrey C Kwong", - "author_inst": "ICES" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.09.29.22280448", "rel_title": "Retrospective and prospective studies evaluating the performance of the SARS-Cov-2 \"AQ+ COVID-19 Ag Rapid Test\" from InTec on symptomatic and non-symptomatic patients", @@ -224183,6 +226465,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.09.27.509803", + "rel_title": "Activation of SARS-CoV-2 by trypsin-like proteases in the clinical specimens of patients with COVID-19", + "rel_date": "2022-09-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.27.509803", + "rel_abs": "SARS-CoV-2 enters host cells through the angiotensin converting enzyme 2 (ACE2) receptor and/or transmembrane protease, serine 2 (TMPRSS2). Serine proteases, such as TMPRSS2 and trypsin, promote viral entry.\n\nIn this study, we investigated whether proteases increased SARS-CoV-2 infectivity using pseudotyped viruses and clinical specimens from patients with COVID-19. First, we investigated how trypsin increased infectivity using the pseudotyped virus. Our findings revealed that trypsin increased infectivity after the virus was adsorbed on the cells, but no increase in infectivity was observed when the virus was treated with trypsin. We examined the effect of trypsin on SARS-CoV-2 infection in clinical specimens and found that the infectivity of the SARS-CoV-2 delta variant increased 36,000-fold after trypsin treatment. By contrast, the infectivity of SARS-CoV-2 omicron variant increased to less than 20-fold in the clinical specimens. Finally, infectivity of clinical specimens containing culture supernatants of Fusobacterium necrophorum was increased from several- to 10-fold. Because SARS-CoV-2 infectivity increases in the oral cavity, which may contain anaerobic bacteria, keeping the oral cavities clean may help prevent SARS-CoV-2 infection.\n\nImportanceIn this study, we examined whether trypsin-like proteases increased the infectivity of SARS-CoV-2. We found that trypsin-like proteases increased the infectivity of both the pseudotyped viruses and the live virus in the clinical specimens. The increase in infectivity was significantly higher for the delta than the omicron variant. A large amount of protease in the oral cavity during SARS-CoV-2 infection is expected to increase infectivity. Therefore, keeping the oral cavity clean is important for preventing infection.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Emiko Igarashi", + "author_inst": "Toyama Institute of Health" + }, + { + "author_name": "Takahisa Shimada", + "author_inst": "Toyama Institute of Health" + }, + { + "author_name": "Shunsuke Yazawa", + "author_inst": "Toyama Institute of Health" + }, + { + "author_name": "Yumiko Saga", + "author_inst": "Toyama Institute of Health" + }, + { + "author_name": "Masae Itamochi", + "author_inst": "Toyama Institute of Health" + }, + { + "author_name": "Noriko Inasaki", + "author_inst": "Toyama Institute of Health" + }, + { + "author_name": "Yoshitomo Morinaga", + "author_inst": "University of Toyama" + }, + { + "author_name": "Kazunori Oishi", + "author_inst": "Toyama Institute of Health" + }, + { + "author_name": "Hideki Tani", + "author_inst": "Toyama Institute of Health" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.09.27.509738", "rel_title": "IgG3 subclass antibodies recognize antigenically drifted influenza viruses and SARS-CoV-2 variants through efficient bivalent binding", @@ -224922,117 +227255,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.09.25.22280081", - "rel_title": "Evaluation of S/F94 as a proxy for COVID-19 severity", - "rel_date": "2022-09-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.25.22280081", - "rel_abs": "Optimising statistical power in early-stage trials and observational studies accelerates discovery and improves the reliability of results. Ideally, intermediate outcomes should be continuously distributed and lie on the causal pathway between an intervention and a definitive outcome such as mortality. In order to optimise power for an intermediate outcome in the RECOVERY trial, we devised and evaluated a modification to a simple, pragmatic measure of oxygenation function - the SaO2/FIO2 (S/F) ratio.\n\nWe demonstrate that, because of the ceiling effect in oxyhaemoglobin saturation, S/F ceases to reflect pulmonary oxygenation function at high values of SaO2. Using synthetic and real data, we found that the correlation of S/F with a gold standard (PaO2/FIO2, P/F ratio) improved substantially when measurements with SaO2 [≥] 0.94 are excluded (Spearman r, synthetic data: S/F : 0.31; S/F94: 0.85). We refer to this measure as S/F94.\n\nIn order to test the underlying assumptions and validity of S/F94 as a predictor of a definitive outcome (mortality), we collected an observational dataset including over 39,000 hospitalised patients with COVID-19 in the ISARIC4C study. We first demonstrated that S/F94 is predictive of mortality in COVID-19. We then compared the sample sizes required for trials using different outcome measures (S/F94, the WHO ordinal scale, sustained improvement at day 28 and mortality at day 28) ensuring comparable effect sizes. The smallest sample size was needed when S/F94 on day 5 was used as an outcome measure.\n\nTo facilitate future study design, we provide an online user interface to quantify real-world power for a range of outcomes and inclusion criteria, using a synthetic dataset retaining the population-level clinical associations in real data accrued in ISARIC4C https://isaric4c.net/endpoints.\n\nWe demonstrated that S/F94 is superior to S/F as a measure of pulmonary oxygenation function and is an effective intermediate outcome measure in COVID-19. It is a simple and non-invasive measurement, representative of disease severity and provides greater statistical power to detect treatment differences than other intermediate endpoints.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Maaike C Swets", - "author_inst": "Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom" - }, - { - "author_name": "Steven Kerr", - "author_inst": "Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom" - }, - { - "author_name": "James Scott-Brown", - "author_inst": "School of Informatics, University of Edinburgh, Edinburgh, UK" - }, - { - "author_name": "Adam B Brown", - "author_inst": "Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom" - }, - { - "author_name": "Rishi K Gupta", - "author_inst": "Institute for Global Health, University College London, London, UK" - }, - { - "author_name": "Jonathan E Millar", - "author_inst": "Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom" - }, - { - "author_name": "Enti Spata", - "author_inst": "Medical Research Council Population Health Research Unit at the University of Oxford, Nuffield Department of Population Health (NDPH), Oxford, UK" - }, - { - "author_name": "Fiona McCurrach", - "author_inst": "EMERGE, NHS Lothian, Royal Infirmary Edinburgh, Edinburgh, UK" - }, - { - "author_name": "Andrew D Bretherick", - "author_inst": "MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK" - }, - { - "author_name": "Annemarie B Docherty", - "author_inst": "Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom" - }, - { - "author_name": "David Harrison", - "author_inst": "Intensive Care National Audit & Research Centre, London, UK" - }, - { - "author_name": "Kathy Rowan", - "author_inst": "Intensive Care National Audit & Research Centre, London, UK" - }, - { - "author_name": "Neil Young", - "author_inst": "Department of Anaesthesia, Critical Care and Pain Medicine, Royal Infirmary of Edinburgh, Edinburgh, UK" - }, - { - "author_name": "- ISARIC4C", - "author_inst": "" - }, - { - "author_name": "Geert H Groeneveld", - "author_inst": "Department of Infectious Diseases, Leiden University Medical Center, Leiden University, Leiden, The Netherlands" - }, - { - "author_name": "Jake Dunning", - "author_inst": "Pandemic Sciences Institute, University of Oxford, Oxford, UK" - }, - { - "author_name": "Jonathan S Nguyen-Van-Tam", - "author_inst": "Population and Lifespan Health, University of Nottingham School of Medicine, Nottingham, UK" - }, - { - "author_name": "Peter JM Openshaw", - "author_inst": "National Heart and Lung Institute, Imperial College London, London, UK" - }, - { - "author_name": "Peter W Horby", - "author_inst": "Pandemic Sciences Institute, University of Oxford, Oxford, UK" - }, - { - "author_name": "Ewen M Harrison", - "author_inst": "Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom" - }, - { - "author_name": "Natalie Staplin", - "author_inst": "Medical Research Council Population Health Research Unit at the University of Oxford, Nuffield Department of Population Health (NDPH), Oxford, UK" - }, - { - "author_name": "Malcolm G Semple", - "author_inst": "Institute of Infection, Veterinary and Ecological Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK" - }, - { - "author_name": "Nazir Lone", - "author_inst": "Centre for Medical Informatics, Usher Institute, University of Edinburgh, Edinburgh, United Kingdom" - }, - { - "author_name": "J Kenneth Baillie", - "author_inst": "Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.09.26.22280293", "rel_title": "Long-term mental health outcomes after SARS-CoV-2 infection: prospective cohort study", @@ -226169,6 +228391,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.09.25.22280335", + "rel_title": "Impact of cross-coronavirus immunity in post-acute sequelae of COVID-19", + "rel_date": "2022-09-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.25.22280335", + "rel_abs": "Beyond the unpredictable acute illness caused by SARS-CoV-2, one-fifth of infections unpredictably result in long-term persistence of symptoms despite the apparent clearance of infection. Insights into the mechanisms that underlie post-acute sequelae of COVID-19 (PASC) will be critical for the prevention and clinical management of long-term complications of COVID-19. Several hypotheses have been proposed that may account for the development of PASC, including persistence of virus or the dysregulation of immunity. Among the immunological changes noted in PASC, alterations in humoral immunity have been observed in some patient subsets. To begin to determine whether SARS-CoV-2 or other pathogen specific humoral immune responses evolve uniquely in PASC, we performed comprehensive antibody profiling against SARS-CoV-2 and a panel of endemic pathogens or routine vaccine antigens using Systems Serology in a cohort of patients with pre-existing rheumatic disease who either developed or did not develop PASC. A distinct humoral immune response was observed in individuals with PASC. Specifically, individuals with PASC harbored less inflamed and weaker Fc{gamma} receptor binding anti-SARS-CoV-2 antibodies and a significantly expanded and more inflamed antibody response against endemic Coronavirus OC43. Individuals with PASC, further, generated more avid IgM responses and developed an expanded inflammatory OC43 S2-specific Fc-receptor binding response, linked to cross reactivity across SARS-CoV-2 and common coronaviruses. These findings implicate previous common Coronavirus imprinting as a marker for the development of PASC.\n\nOne Sentence SummaryThrough high dimensional humoral immune profiling we uncovered the potential importance of previous common Coronavirus imprinting as a novel marker and potential mechanism of an endotype of PASC.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Jonathan D Herman", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Caroline Atyeo", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Yonatan Zur", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Claire E Cook", + "author_inst": "Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital" + }, + { + "author_name": "Naomi J Patel", + "author_inst": "Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital" + }, + { + "author_name": "Kathleen M Vanni", + "author_inst": "Division of Rheumatology, Inflammation, and Immunity, Brigham and Womens Hospital" + }, + { + "author_name": "Emily N Kowalski", + "author_inst": "Division of Rheumatology, Inflammation, and Immunity, Brigham and Womens Hospital" + }, + { + "author_name": "Grace Qian", + "author_inst": "Division of Rheumatology, Inflammation, and Immunity, Brigham and Womens Hospital" + }, + { + "author_name": "Nancy A Shadick", + "author_inst": "Division of Rheumatology, Inflammation, and Immunity, Brigham and Womens Hospital" + }, + { + "author_name": "Douglas A Lauffenburger", + "author_inst": "Department of Biological Engineering, Massachusetts Institute of Technology" + }, + { + "author_name": "Zachary S Wallace", + "author_inst": "Division of Rheumatology, Allergy, and Immunology, Massachusetts General Hospital" + }, + { + "author_name": "Jeffrey A Sparks", + "author_inst": "Division of Rheumatology, Inflammation, and Immunity, Brigham and Womens Hospital" + }, + { + "author_name": "Galit Alter", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.09.25.22280341", "rel_title": "Protection of homologous and heterologous boosters after primary schemes of rAd26-rAd5, ChAdOx1 nCoV-19 and BBIBP-CorV during the Omicron outbreak in adults of 50 years and older in Argentina: a test-negative case-control study.", @@ -226764,93 +229053,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.09.26.509529", - "rel_title": "SARS-CoV-2 Uses Nonstructural Protein 16 to Evade Restriction by IFIT1 and IFIT3", - "rel_date": "2022-09-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.26.509529", - "rel_abs": "Understanding the molecular basis of innate immune evasion by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an important consideration for designing the next wave of therapeutics. Here, we investigate the role of the nonstructural protein 16 (NSP16) of SARS-CoV-2 in infection and pathogenesis. NSP16, a ribonucleoside 2-O methyltransferase (MTase), catalyzes the transfer of a methyl group to mRNA as part of the capping process. Based on observations with other CoVs, we hypothesized that NSP16 2-O MTase function protects SARS-CoV-2 from cap-sensing host restriction. Therefore, we engineered SARS-CoV-2 with a mutation that disrupts a conserved residue in the active site of NSP16. We subsequently show that this mutant is attenuated both in vitro and in vivo, using a hamster model of SARS-CoV-2 infection. Mechanistically, we confirm that the NSP16 mutant is more sensitive to type I interferon (IFN-I) in vitro. Furthermore, silencing IFIT1 or IFIT3, IFN-stimulated genes that sense a lack of 2-O methylation, partially restores fitness to the NSP16 mutant. Finally, we demonstrate that sinefungin, a methyltransferase inhibitor that binds the catalytic site of NSP16, sensitizes wild-type SARS-CoV-2 to IFN-I treatment. Overall, our findings highlight the importance of SARS-CoV-2 NSP16 in evading host innate immunity and suggest a possible target for future antiviral therapies.\n\nImportanceSimilar to other coronaviruses, disruption of SARS-CoV-2 NSP16 function attenuates viral replication in a type I interferon-dependent manner. In vivo, our results show reduced disease and viral replication at late times in the hamster lung, but an earlier titer deficit for the NSP16 mutant (dNSP16) in the upper airway. In addition, our results confirm a role for IFIT1, but also demonstrate the necessity of IFIT3 in mediating dNSP16 attenuation. Finally, we show that targeting NSP16 activity with a 2-O methyltransferase inhibitor in combination with type I interferon offers a novel avenue for antiviral development.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Craig Schindewolf", - "author_inst": "The University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Kumari Lokugamage", - "author_inst": "The University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Michelle Vu", - "author_inst": "University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Bryan A Johnson", - "author_inst": "The University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Dionna Scharton", - "author_inst": "The University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Jessica A Plante", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Birte K Kalveram", - "author_inst": "The University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Patricia A Crocquet-Valdes", - "author_inst": "The University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Stephanea L Sotcheff", - "author_inst": "The University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Elizabeth Jaworski", - "author_inst": "The University of Texas Medical Branch at Galveston" - }, - { - "author_name": "R. Elias Alvarado", - "author_inst": "The University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Kari Debbink", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Matthew D Daugherty", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Scott Weaver", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Andrew Laurence Routh", - "author_inst": "University of Texas Medical Branch, Galveston" - }, - { - "author_name": "David H. Walker", - "author_inst": "The University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Kenneth S Plante", - "author_inst": "The University of Texas Medical Branch at Galveston" - }, - { - "author_name": "Vineet D Menachery", - "author_inst": "The University of Texas Medical Branch at Galveston" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.09.22.22280247", "rel_title": "Abatacept for Treatment of Adults Hospitalized with Moderate or Severe Covid-19", @@ -228855,6 +231057,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.09.21.22280208", + "rel_title": "Less invasive SARS-CoV-2 testing for children: A comparison of saliva and a novel Anterior Nasal Swab", + "rel_date": "2022-09-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.21.22280208", + "rel_abs": "Reducing procedural discomfort for children requiring respiratory testing for SARS-CoV-2 is important in supporting testing strategies for case identification. Alternative sampling methods to nose and throat swabs, which can be self-collected, may reduce laboratory-based testing requirements and provide rapid results for clearance to attend school or hospital settings. The aim of this study was to compare preference and diagnostic sensitivity of a novel anterior nasal swab (ANS), and saliva, with a standard combined nose and throat (CTN) swab. The three samples were self-collected by children aged 5-18 years who had COVID-19 or were a household close contact. Samples were analysed by reverse transcription polymerase chain reaction (RT-PCR) on the Allplex SARS-CoV-2 Assay. Most children and parents preferred the ANS and saliva swab over the CTN swab for future testing. The ANS was highly sensitive (sensitivity 1.000 (95% Confidence Interval (CI) 0.920, 1.000)) for SARS-CoV-2 detection, compared to saliva (sensitivity 0.886, 95% CI 0.754, 0.962). We conclude the novel ANS is a highly sensitive and more comfortable method for SARS-CoV-2 detection when compared to CTN swab.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Shidan Tosif", + "author_inst": "Murdoch Childrens Research Institute" + }, + { + "author_name": "Lai-Yang Lee", + "author_inst": "Royal Childrens Hospital Melbourne" + }, + { + "author_name": "Jill Nguyen", + "author_inst": "Murdoch Childrens Research Institute" + }, + { + "author_name": "Chris Selman", + "author_inst": "Murdoch Childrens Research Institute" + }, + { + "author_name": "Anneke Grobler", + "author_inst": "Murdoch Children's Research Institute" + }, + { + "author_name": "Alissa McMinn", + "author_inst": "Murdoch Childrens Research Institute" + }, + { + "author_name": "Andrew Steer", + "author_inst": "Murdoch Childrens Research Institute" + }, + { + "author_name": "Andrew Daley", + "author_inst": "Royal Childrens Hospital Melbourne" + }, + { + "author_name": "Nigel Crawford", + "author_inst": "Murdoch Childrens Research Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2022.09.23.22280264", "rel_title": "Post-COVID-19 syndrome: retinal microcirculation as a potential marker for chronic fatigue", @@ -229438,73 +231691,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.09.23.22280263", - "rel_title": "Natural ventilation, low CO2 and air filtration are associated with reduced indoor air respiratory pathogens", - "rel_date": "2022-09-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.23.22280263", - "rel_abs": "Currently, the real-life impact of indoor climate, human behavior, ventilation and air filtration on respiratory pathogen detection and concentration are poorly understood. This hinders the interpretability of bioaerosol quantification in indoor air to surveil respiratory pathogens and transmission risk. We tested 341 indoor air samples from 21 community settings for 29 respiratory pathogens using qPCR. On average, 3.9 pathogens were positive per sample and 85.3% of samples tested positive for at least one. The number of detected pathogens and their respective concentrations varied significantly by pathogen, month, and age group in generalized linear (mixed) models and generalized estimating equations. High CO2 and low natural ventilation were independent risk factors for detection. CO2 concentration and air filtration were independently associated with their concentration. Occupancy, sampling time, mask wearing, vocalization, temperature, humidity and mechanical ventilation were not significant. Our results support the importance of ventilation and air filtration to reduce transmission.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Joren Raymenants", - "author_inst": "KU Leuven" - }, - { - "author_name": "Caspar Geenen", - "author_inst": "KU Leuven" - }, - { - "author_name": "Lore Budts", - "author_inst": "University Hospitals Leuven" - }, - { - "author_name": "Jonathan Thibaut", - "author_inst": "KU Leuven" - }, - { - "author_name": "Marijn Thijssen", - "author_inst": "KU Leuven" - }, - { - "author_name": "Hannelore De Mulder", - "author_inst": "KU Leuven" - }, - { - "author_name": "Sarah Gorissen", - "author_inst": "KU Leuven" - }, - { - "author_name": "Bastiaan Craessaerts", - "author_inst": "University Hospitals Leuven" - }, - { - "author_name": "Lies Laenen", - "author_inst": "University Hospitals Leuven" - }, - { - "author_name": "Kurt Beuselinck", - "author_inst": "University Hospitals Leuven" - }, - { - "author_name": "Sien Ombelet", - "author_inst": "University Hospitals Leuven" - }, - { - "author_name": "Els Keyaerts", - "author_inst": "University Hospitals Leuven" - }, - { - "author_name": "Emmanuel Andre", - "author_inst": "KU Leuven" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.09.20.22276701", "rel_title": "Dose of approved COVID-19 vaccines is based on weak evidence: a review of early-phase, dose-finding trials", @@ -230793,6 +232979,133 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.09.20.508614", + "rel_title": "Parallel use of pluripotent human stem cell lung and heart models provide new insights for treatment of SARS-CoV-2", + "rel_date": "2022-09-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.20.508614", + "rel_abs": "SARS-CoV-2 primarily infects the respiratory tract, but pulmonary and cardiac complications occur in severe COVID-19. To elucidate molecular mechanisms in the lung and heart, we conducted paired experiments in human stem cell-derived lung alveolar type II (AT2) epithelial cell and cardiac cultures infected with SARS-CoV-2. With CRISPR- Cas9 mediated knock-out of ACE2, we demonstrated that angiotensin converting enzyme 2 (ACE2) was essential for SARS-CoV-2 infection of both cell types but further processing in lung cells required TMPRSS2 while cardiac cells required the endosomal pathway. Host responses were significantly different; transcriptome profiling and phosphoproteomics responses depended strongly on the cell type. We identified several antiviral compounds with distinct antiviral and toxicity profiles in lung AT2 and cardiac cells, highlighting the importance of using several relevant cell types for evaluation of antiviral drugs. Our data provide new insights into rational drug combinations for effective treatment of a virus that affects multiple organ systems.\n\nOne-sentence summaryRational treatment strategies for SARS-CoV-2 derived from human PSC models", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Rajeev Rudraraju", + "author_inst": "The Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, 3000, Victoria, A" + }, + { + "author_name": "Matthew J Gartner", + "author_inst": "The Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, 3000, Victoria, A" + }, + { + "author_name": "Jessica A Neil", + "author_inst": "The Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, 3000, Victoria, A" + }, + { + "author_name": "Elizabeth S Stout", + "author_inst": "The Novo Nordisk Foundation Centre for Stem Cell Medicine (reNEW), Murdoch Childrens Research Institute, Melbourne, 3052, Victoria, Australia" + }, + { + "author_name": "Joseph Chen", + "author_inst": "Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia" + }, + { + "author_name": "Elise J Needham", + "author_inst": "Charles Perkins Centre and School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camperdown, NSW 2006 Australia." + }, + { + "author_name": "Michael See", + "author_inst": "The Novo Nordisk Foundation Centre for Stem Cell Medicine (reNEW), Murdoch Childrens Research Institute, Melbourne, 3052, Victoria, Australia." + }, + { + "author_name": "Charley Mackenzie-Kludas", + "author_inst": "The Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, 3000, Victoria, A" + }, + { + "author_name": "Leo Yi Yang", + "author_inst": "The Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, 3000, Victoria, A" + }, + { + "author_name": "Mingyang Wang", + "author_inst": "The Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, 3000, Victoria, A" + }, + { + "author_name": "Hayley Pointer", + "author_inst": "The Novo Nordisk Foundation Centre for Stem Cell Medicine (reNEW), Murdoch Childrens Research Institute, Melbourne, 3052, Victoria, Australia" + }, + { + "author_name": "Kathy Karavendzas", + "author_inst": "The Novo Nordisk Foundation Centre for Stem Cell Medicine (reNEW), Murdoch Childrens Research Institute, Melbourne, 3052, Victoria, Australia" + }, + { + "author_name": "Dad Abu-Bonsrah", + "author_inst": "The Novo Nordisk Foundation Centre for Stem Cell Medicine (reNEW), Murdoch Childrens Research Institute, Melbourne, 3052, Victoria, Australia" + }, + { + "author_name": "Damien Drew", + "author_inst": "Infection and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Victoria, Australia" + }, + { + "author_name": "Yu Bo Yang Sun", + "author_inst": "Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia" + }, + { + "author_name": "Jia Ping Tan", + "author_inst": "Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia" + }, + { + "author_name": "Guizhi Sun", + "author_inst": "Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia" + }, + { + "author_name": "Abbas Salavaty", + "author_inst": "Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia" + }, + { + "author_name": "Natalie Charitakis", + "author_inst": "The Novo Nordisk Foundation Centre for Stem Cell Medicine (reNEW), Murdoch Childrens Research Institute, Melbourne, 3052, Victoria, Australia" + }, + { + "author_name": "Hieu T Nim", + "author_inst": "The Novo Nordisk Foundation Centre for Stem Cell Medicine (reNEW), Murdoch Childrens Research Institute, Melbourne, 3052, Victoria, Australia" + }, + { + "author_name": "Peter D Currie", + "author_inst": "Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia" + }, + { + "author_name": "Wai-Hong Tham", + "author_inst": "Infection and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Victoria, Australia" + }, + { + "author_name": "Enzo Porrello", + "author_inst": "The Novo Nordisk Foundation Centre for Stem Cell Medicine (reNEW), Murdoch Childrens Research Institute, Melbourne, 3052, Victoria, Australia." + }, + { + "author_name": "Jose Polo", + "author_inst": "Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia" + }, + { + "author_name": "Sean J Humphrey", + "author_inst": "Charles Perkins Centre and School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Camperdown, NSW 2006 Australia" + }, + { + "author_name": "Mirana Ramialison", + "author_inst": "The Novo Nordisk Foundation Centre for Stem Cell Medicine (reNEW), Murdoch Childrens Research Institute, Melbourne, 3052, Victoria, Australia" + }, + { + "author_name": "David A Elliott", + "author_inst": "The Novo Nordisk Foundation Centre for Stem Cell Medicine (reNEW), Murdoch Childrens Research Institute, Melbourne, 3052, Victoria, Australia" + }, + { + "author_name": "Kanta Subbarao", + "author_inst": "The Peter Doherty Institute for Infection and Immunity" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.09.19.22280133", "rel_title": "Therapeutic and Interventional Bronchoscopy Performed in Critically ill COVID-19 patients: A Systematic Review", @@ -231360,61 +233673,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.09.18.508418", - "rel_title": "Guild-level microbiome signature associated with COVID-19 severity and prognosis", - "rel_date": "2022-09-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.18.508418", - "rel_abs": "COVID-19 severity has been associated with alterations of the gut microbiota. However, the relationship between gut microbiome alterations and COVID-19 prognosis remains elusive. Here, we performed a genome-resolved metagenomic analysis on fecal samples collected from 300 in-hospital COVID-19 patients at time of admission. Among the 2,568 high quality metagenome-assembled genomes (HQMAGs), Redundancy Analysis identified 33 HQMAGs which showed differential distribution among mild, moderate, and severe/critical severity groups. Random Forest model based on these 33 HQMAGs classified patients from different severity groups (average AUC = 0.79). Co-abundance network analysis found that the 33 HQMAGs were organized as two competing guilds. Guild 1 harbored more genes for short-chain fatty acid biosynthesis, and fewer genes for virulence and antibiotic resistance, compared with Guild 2. Random Forest regression showed that these 33 HQMAGs at admission had the capacity to predict 8 clinical parameters, which are predictors for COVID-19 prognosis, at Day 7 in hospital. Moreover, the dominance of Guild 1 over Guild 2 at admission predicted the death/discharge outcome of the critical patients (AUC = 0.92). Random Forest models based on these 33 HQMAGs classified patients with different COVID-19 symptom severity, and differentiated COVID-19 patients from healthy subjects, non-COVID-19, and pneumonia controls in three independent datasets. Thus, this genome-based guild-level signature may facilitate early identification of hospitalized COVID-19 patients with high risk of more severe outcomes at time of admission.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Mingquan Guo", - "author_inst": "Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Fudan University" - }, - { - "author_name": "Guojun Wu", - "author_inst": "Rutgers University" - }, - { - "author_name": "Yun Tan", - "author_inst": "Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine" - }, - { - "author_name": "Yan Li", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Xin Jin", - "author_inst": "Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Fudan University" - }, - { - "author_name": "Weiqiang Qi", - "author_inst": "Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Fudan University" - }, - { - "author_name": "Xiaokui Guo", - "author_inst": "School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine" - }, - { - "author_name": "Chenhong Zhang", - "author_inst": "Shanghai Jiao Tong University" - }, - { - "author_name": "Zhaoqin Zhu", - "author_inst": "Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Fudan University" - }, - { - "author_name": "Liping Zhao", - "author_inst": "Rutgers University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.09.18.508442", "rel_title": "HCR Lateral Flow Assays for Amplified Instrument-Free At-Home SARS-CoV-2 Testing", @@ -232627,6 +234885,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.09.15.22279958", + "rel_title": "Prevalence and risk factors for long COVID after mild disease: a longitudinal study with a symptomatic control group.", + "rel_date": "2022-09-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.15.22279958", + "rel_abs": "BackgroundThere is limited data on the prevalence and risk factors for long COVID, with a shortage of prospective studies with appropriate control groups and adequate sample size. We therefore performed a prospective study to determine the prevalence and risk factors for long COVID.\n\nMethodsWe recruited patients age [≥] 15 years who were clinically suspected of having acute SARS-CoV-2 infection from September 2020 to April 2021. Nasopharyngeal swabs were collected for RT-PCR 3-5 days post symptom onset. Clinical and sociodemographic characteristics were collected using structured questionnaires from persons positive and negative for SARS-COV-2. Follow-up was performed by telephone interview to assess early outcomes and persistent symptoms. For COVID-19 cases, 5D-3L EuroQol questionnaire was used to assess the impact of symptoms on quality of life.\n\nResultsWe followed 814 participants (412 COVD-19 positive and 402 COVID-19 negative persons) of whom the majority (741 / 814) had mild symptoms. Both the COVID-19 positive and the COVID-19 negative groups had similar sociodemographic and clinical characteristics, except for the rate of hospitalization (15.8% vs 1.5%, respectively). One month after disease onset, 122 (29.6%) individuals reported residual symptoms in the COVID-19 positive group or the long COVID group versus 24 (6%) individuals in the COVID-19 negative group. In the long COVID group, fatigue, olfactory disorder, and myalgia were the most frequent symptoms which occurred in the acute phase. Compared to recovered patients, female sex, older age and having > 5 symptoms during the acute phase were risk factors for long COVID. Quality of life was evaluated in 102 out of 122 cases of long COVID with 57 (55.9%) reporting an impact in at least one dimension of the EuroQol 5D-3L questionnaire.\n\nConclusionIn this prospective study consisting predominantly of patients with mild disease, the persistence of symptoms after acute disease was highly associated with long COVID-19 (29.6% vs 6% of COVID negative group). The risk factors for long COVID were older age, female sex, and polysymptomatic acute disease.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Ana Beatriz C Caze", + "author_inst": "Federal University of Bahia" + }, + { + "author_name": "Thiago Cerqueira Silva", + "author_inst": "LIB and LEITV Laboratories, Instituto Goncalo Moniz, Fiocruz, Salvador, Bahia, Brazil; Universidade Federal da Bahia, Salvador, Bahia, Brazil" + }, + { + "author_name": "Adriele Pinheiro Bomfim", + "author_inst": "Instituto Goncalo Muniz, Fiocruz, Salvador, Brazil; Universidade Federal da Bahia, Salvador, Bahia, Brazil" + }, + { + "author_name": "Gisley Lima de Souza", + "author_inst": "Escola de Medicina e Saude Publica da Bahia; Instituto Goncalo Moniz, Fiocruz, Salvador, Bahia, Brazil" + }, + { + "author_name": "Amanda Canario Andrade Azevedo", + "author_inst": "Hospital Santa Izabel, Santa Casa da Bahia, Salvador, Bahia, Brazil" + }, + { + "author_name": "Michelle Queiroz Aguiar Brasil", + "author_inst": "Instituto Goncalo Moniz, Fiocruz, Salvador, Bahia, Brazil; Federal University of Bahia, Salvador, Bahia, Brazil" + }, + { + "author_name": "Nara Rubia Santos", + "author_inst": "Departamento de Vigilancia em Saude/Vigilancia Epidemiologica, Campo Formoso, Bahia Brazil" + }, + { + "author_name": "Ricardo Khouri", + "author_inst": "Centro de Pesquisas Goncalo Moniz" + }, + { + "author_name": "Jennifer Dan", + "author_inst": "UCSD: University of California San Diego" + }, + { + "author_name": "Antonio Carlos Bandeira", + "author_inst": "UNI-FTC-Faculdade Tecnologia Ciencias Medical School, Bahia; Central State Laboratory LACEN-Bahia; Infectious Diseases Advisor" + }, + { + "author_name": "Luciano Pamplona de Goes Cavalcanti", + "author_inst": "Universidade Federal do Ceara, Fortaleza, Ceara, Brazil; Centro Universitario Christus, Fortaleza, Ceara, Brazil" + }, + { + "author_name": "Manoel Barral Netto", + "author_inst": "LIB and LEITV Laboratories, Instituto Goncalo Moniz, Fiocruz, Salvador, Bahia, Brazil; Universidade Federal da Bahia, Salvador, Bahia, Brazil" + }, + { + "author_name": "Aldina Maria Prado Barral", + "author_inst": "Instituto Goncalo Moniz, Fundacao Oswaldo Cruz, Salvador, Bahia, Brazil; Instituto de Investigacao em Imunologia, Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Cynara Gomes Barbosa", + "author_inst": "Universidade Federal da Bahia, Salvador, Brazil" + }, + { + "author_name": "Viviane S Boaventura", + "author_inst": "Federal University of Bahia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.09.15.22280010", "rel_title": "Estimation of mRNA COVID-19 Vaccination Effectiveness in Tokyo for Omicron Variants BA.2 and BA.5 -Effect of Social Behavior-", @@ -233198,93 +235531,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.09.16.507742", - "rel_title": "Genome characterization of monkeypox cases detected in India: Identification of three sub clusters among A.2 lineage", - "rel_date": "2022-09-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.16.507742", - "rel_abs": "Since May 2022, Monkeypox, a zoonotic Orthopox DNA virus was reported in more than 102 countries indicating expansion of its geographic range. We analyzed the complete genomes sequences of Monkeypox cases from Kerala (n=5 travelled from UAE) and Delhi (n=5 no travel history), India confirmed during July to August 2022. All the retrieved MPXV sequences from India covering 90 to 99% genome belong to A.2 lineage of clade IIb. The A.2 MPXV lineage divided in three sub clusters; first cluster Kerala n=5, Delhi n=2 aligned with the USA-2022 ON674051.1; while second of Delhi n=3 aligned with USA-2022 ON675438.1 and third consists of the UK, USA and Thailand. Recent update in MPXV lineage designated all the five sequences from Kerala as A.2.1. In addition to known 16 single nucleotide polymorphisms (SNPs) along with 13 APOBEC3 cytosine deaminase activity determined specific lineage defining mutations in A.2 lineage, 25 additional APOBEC3 mutations were found in 10 reported sequences. The study emphasizes need of enhancing genomic surveillance to understand the mutation and its linkage.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Anita M Shete", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" - }, - { - "author_name": "Pragya D Yadav", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" - }, - { - "author_name": "Abhinendra Kumar", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" - }, - { - "author_name": "Savita Patil", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" - }, - { - "author_name": "Deepak Y Patil", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" - }, - { - "author_name": "Yash Joshi", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" - }, - { - "author_name": "Triparna Majumdar", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" - }, - { - "author_name": "Vineet Relhan", - "author_inst": "Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India, Pin-110002" - }, - { - "author_name": "Rima R Sahay", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" - }, - { - "author_name": "Meenakshy Vasu", - "author_inst": "Public Health Department of Kerala, Directorate of Health Services (IDSP), Thiruvananthapuram, India, Pin - 695 035" - }, - { - "author_name": "Pranita Gawande", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" - }, - { - "author_name": "Ajay Verma", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" - }, - { - "author_name": "Arbind Kumar", - "author_inst": "All India Institute of Medical Sciences, New Delhi, India, Pin-110029" - }, - { - "author_name": "Shivram Dhakad", - "author_inst": "All India Institute of Medical Sciences, New Delhi, India, Pin-110029" - }, - { - "author_name": "Anukumar Bala Krishnan", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Alappuzha, Kerala, India, Pin-688005" - }, - { - "author_name": "Shubin Chenayil", - "author_inst": "State Surveillance Unit (IDSP), Directorate of Health Services (IDSP), Malappuram, Kerala, India, Pin-676505" - }, - { - "author_name": "Suresh Kumar", - "author_inst": "Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, India, Pin-110002" - }, - { - "author_name": "Priya Abraham", - "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.09.16.508299", "rel_title": "Omicron sublineage BA.2.75.2 exhibits extensive escape from neutralising antibodies", @@ -234597,6 +236843,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2022.09.14.22279932", + "rel_title": "Rationale, Design, and Baseline Characteristics of the VALIANT (COVID-19 in Older Adults: A Longitudinal Assessment) Cohort", + "rel_date": "2022-09-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.14.22279932", + "rel_abs": "BackgroundMost older adults hospitalized with COVID-19 survive their acute illness. The impact of COVID-19 hospitalization on patient-centered outcomes, such as physical function, cognitive function, and symptoms, is not well understood. We sought to address this knowledge gap by collecting longitudinal data about these issues from a cohort of older adult survivors of COVID-19 hospitalization.\n\nMethodsWe undertook a prospective study of community-living persons age [≥]60 years who were hospitalized with COVID-19 from June 2020 to June 2021. A baseline interview was conducted during or up to two weeks after hospitalization. Follow-up interviews occurred at one, three, and six months post-discharge. In interviews, participants completed comprehensive assessments of physical and cognitive function, symptoms, and psychosocial factors. If a participant was too impaired to complete an interview, an abbreviated assessment was performed with a proxy. Additional information was collected from the electronic health record. Baseline characteristics of the cohort are reported here.\n\nResultsAmong 341 participants, the mean age was 71.4 (SD 8.4) years, 51% were women, and 37% were of Black race or Hispanic ethnicity. Median length of hospitalization was 8 (IQR 6-12) days. All but 4% of participants required supplemental oxygen and 21% required a higher level of care in an intensive care unit or stepdown unit. Nearly half (47%) reported at least one disability in physical function, 45% demonstrated cognitive impairment, and 67% were pre-frail or frail. Participants reported a mean of 9 of 14 (SD 3) COVID-19-related symptoms.\n\nConclusionsOlder adults hospitalized with COVID-19 demonstrated high rates of baseline physical and cognitive impairment as well as high symptom burden. Longitudinal findings from this cohort will advance our understanding of outcome trajectories of great importance to older survivors of COVID-19.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Andrew B Cohen", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Gail McAvay", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Mary Geda", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Sumon Chattopadhyay", + "author_inst": "University of Utah" + }, + { + "author_name": "Seohyuk Lee", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Denise Acampora", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Katy Araujo", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Peter Charpentier", + "author_inst": "CRI Web Tools" + }, + { + "author_name": "Thomas M Gill", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Alexandra Hajduk", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Lauren Ferrante", + "author_inst": "Yale School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "geriatric medicine" + }, { "rel_doi": "10.1101/2022.09.13.507829", "rel_title": "SARS-CoV-2 Protein Nsp2 Stimulates Translation Under Normal and Hypoxic Conditions", @@ -235184,37 +237489,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2022.09.13.22279846", - "rel_title": "Pregnant women's attitudes and behaviours towards antenatal vaccination against Influenza and COVID-19 in the Liverpool City Region, United Kingdom: cross-sectional survey", - "rel_date": "2022-09-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.13.22279846", - "rel_abs": "ObjectiveInfluenza poses a serious health risk to pregnant women and their babies. Despite this risk, influenza vaccine uptake in pregnant women in the UK is less than 50%. Little is known about how COVID-19 affects pregnant women, but its management may affect attitudes and behaviours towards vaccination in pregnancy. The study objectives were to establish attitudes and knowledge of pregnant women towards influenza disease and influenza vaccination and to compare these to attitudes and knowledge about COVID-19 and COVID-19 vaccination.\n\nDesignA cross-sectional survey was conducted using an online questionnaire distributed through local advertisement and social media outlets. Information was sought on attitudes and knowledge of influenza and COVID-19 and their respective vaccines.\n\nParticipants and settingPregnant women residing in Liverpool City Region, UK\n\nResultsOf the 237 respondents, 73.8% reported receiving an influenza vaccine. Over half (56.5%) perceived themselves to be at risk from influenza, 70.5% believed that if they got influenza, their baby would get ill, and 64.6% believed getting influenza could hurt their baby, 60.3% believed that the influenza vaccine would prevent their baby from getting ill, and 70.8% believed it would protect their baby. Only 32.9% of respondents stated they would receive the COVID-19 vaccine if it were available to them. However, 80.2% stated they would receive a COVID-19 vaccine if they were not pregnant. Most of the women stated that they would accept a vaccine if recommended to them by healthcare professionals.\n\nConclusionsAcceptance of the influenza and COVID-19 vaccines during pregnancy seems to be more related to the safety of the baby rather than the mother. Women perceived their child to be more at risk than themselves. Information about influenza and COVID-19 vaccine safety as well as healthcare provider recommendations play an important role in vaccine uptake in pregnant women.\n\nStrengths and limitations of this studyO_LIThe study provides information on how a pandemic affects vaccine attitudes and behaviours during pregnancy.\nC_LIO_LIThe study compares and contrasts attitudes and behaviours towards influenza and COVID-19 vaccines.\nC_LIO_LIThe study provides new information relating to barriers to COVID-19 vaccine acceptance and provides insights into mechanisms for improving uptake.\nC_LIO_LIThe sample size is small and self-selected which might lead to an over-representation of women likely to accept or have strong opinions on vaccinations.\nC_LIO_LIResponses to the questions on vaccine status are self-reported, not provided from healthcare records.\nC_LI", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Samantha Kilada", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Neil French", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Elizabeth Perkins", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Daniel Hungerford", - "author_inst": "University of Liverpool" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.09.12.22279862", "rel_title": "The epidemiology of long COVID in US adults two years after the start of the US SARS-CoV-2 pandemic", @@ -236347,6 +238621,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.09.11.22279823", + "rel_title": "Effects of the COVID-19 pandemic on the mental health of clinically extremely vulnerable children and children living with clinically extremely vulnerable people in Wales: A data linkage study", + "rel_date": "2022-09-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.11.22279823", + "rel_abs": "ObjectivesTo determine whether clinically extremely vulnerable (CEV) children or children living with a CEV person in Wales were at greater risk of presenting with anxiety or depression in primary or secondary care during the COVID-19 pandemic compared with children in the general population, and to compare patterns of anxiety and depression during the pandemic (23rd March 2020-31st January 2021, referred to as 2020/21) and before the pandemic (March 23rd 2019-January 31st 2020, referred to as 2019/20), between CEV children and the general population.\n\nDesignPopulation-based cross-sectional cohort study using anonymised, linked, routinely collected health and administrative data held in the Secure Anonymised Information Linkage Databank. CEV individuals were identified using the COVID-19 Shielded Patient List.\n\nSettingPrimary and secondary healthcare settings covering 80% of the population of Wales.\n\nParticipantsChildren aged 2-17 in Wales: CEV (3,769); living with a CEV person (20,033); or neither (415,009).\n\nPrimary outcome measureFirst record of anxiety or depression in primary or secondary healthcare in 2019/20 and 2020/21, identified using Read and ICD-10 codes.\n\nResultsA Cox regression model adjusted for demographics and history of anxiety or depression revealed that only CEV children were at greater risk of presenting with anxiety or depression during the pandemic compared with the general population (Hazard Ratio=2.27, 95% Confidence Interval=1.94-2.66, p<0.001). Compared with the general population, the risk amongst CEV children was higher in 2020/21 (Risk Ratio 3.04) compared with 2019/20 (Risk Ratio 1.90). In 2020/21, the cumulative incidence of anxiety or depression increased slightly amongst CEV children, but declined amongst the general population.\n\nConclusionsDifferences in the cumulative incidences of recorded anxiety or depression in healthcare between CEV children and the general population were largely driven by a reduction in presentations to healthcare services by children in the general population during the pandemic.\n\nStrengths and limitations of this studyO_LIStrengths of this study include its novelty, national focus and clinical relevance; to date this is the first population-based study examining the effects of the COVID-19 pandemic on healthcare use for anxiety or depression amongst clinically extremely vulnerable (CEV) children and children living with a CEV person in Wales\nC_LIO_LIWe compared 2020/21 data with pre-pandemic 2019/20 data for CEV children and children in the general population, to place the impact of the COVID-19 pandemic in the context of longer-term patterns of healthcare use\nC_LIO_LIWe used a novel approach and linked multiple datasets to identify a cohort of children living with a CEV person in Wales during the COVID-19 pandemic\nC_LIO_LIThere was heterogeneity within the Shielded Patient List that was used to create the cohorts of children identified as CEV or living with a CEV person, in terms of the type and severity of individuals underlying conditions; the manner in which people were added to the list; the time point that people were added to the list; and the extent to which people followed the shielding guidance\nC_LIO_LIRoutinely collected healthcare data does not capture self-reported health, and is likely to underestimate the burden of common mental disorders in the population\nC_LI", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Laura Elizabeth Cowley", + "author_inst": "Swansea University" + }, + { + "author_name": "Karen Hodgson", + "author_inst": "Public Health Wales" + }, + { + "author_name": "Jiao Song", + "author_inst": "Public Health Wales" + }, + { + "author_name": "Tony Whiffen", + "author_inst": "Welsh Government" + }, + { + "author_name": "Jacinta Tan", + "author_inst": "University of Oxford" + }, + { + "author_name": "Ann John", + "author_inst": "Swansea University" + }, + { + "author_name": "Amrita Bandyopadhyay", + "author_inst": "Swansea University" + }, + { + "author_name": "Alisha R Davies", + "author_inst": "Public Health Wales" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2022.09.12.22279847", "rel_title": "Multicentre diagnostic evaluation of OnSite COVID-19 Rapid Test (CTK Biotech) among symptomatic individuals in Brazil and The United Kingdom", @@ -236866,141 +239187,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sexual and reproductive health" }, - { - "rel_doi": "10.1101/2022.09.09.22279787", - "rel_title": "SARS-CoV-2 Serosurveys: How antigen, isotype and threshold choices affect the outcome", - "rel_date": "2022-09-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.09.22279787", - "rel_abs": "BackgroundEvaluating the performance of SARS-CoV-2 serological assays and clearly articulating the utility of selected antigen, isotypes and thresholds is crucial to understanding the prevalence of infection within selected communities.\n\nMethodsThis cross-sectional study, implemented in 2020, screened PCR-confirmed COVID-19 patients (n=86), banked pre-pandemic and negative donors (n=96), health care workers and family members (n=552), and university employees (n=327) for anti-SARS-CoV-2 receptor-binding domain (RBD), trimeric spike protein (S), and nucleocapsid protein (N) IgG and IgA antibodies with a laboratory developed Enzyme-Linked Immunosorbent Assay (ELISA) and tested how antigen, isotype and threshold choices affected the seroprevalence. The following threshold methods were evaluated: (i) mean + 3 standard deviations of the negative controls; (ii) 100% specificity for each antigen/isotype combination; and (iii) the maximal Youden index.\n\nResultsWe found vastly different seroprevalence estimates depending on selected antigens, isotypes and the applied threshold method, ranging from 0.0% to 85.4%. Subsequently, we maximized specificity and reported a seroprevalence, based on more than one antigen, ranging from 9.3% to 25.9%.\n\nConclusionsThis study revealed the importance of evaluating serosurvey tools for antigen, isotype, and threshold-specific sensitivity and specificity, in order to interpret qualitative serosurvey outcomes reliably and consistently across studies.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "Raquel A. Binder", - "author_inst": "Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA" - }, - { - "author_name": "Gavin F. Fujimori", - "author_inst": "Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA" - }, - { - "author_name": "Catherine S. Forconi", - "author_inst": "Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA" - }, - { - "author_name": "George W. Reed", - "author_inst": "Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA" - }, - { - "author_name": "Leandro S. Silva", - "author_inst": "Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA" - }, - { - "author_name": "Priya Saikumar Lakshmi", - "author_inst": "Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA" - }, - { - "author_name": "Amanda Higgins", - "author_inst": "Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA" - }, - { - "author_name": "Lindsey Cincotta", - "author_inst": "Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA" - }, - { - "author_name": "Protiva Dutta", - "author_inst": "Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA" - }, - { - "author_name": "Marie-Claire Salive", - "author_inst": "Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA" - }, - { - "author_name": "Virginia Mangolds", - "author_inst": "Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA" - }, - { - "author_name": "Otuwe Anya", - "author_inst": "Department of Emergency Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA" - }, - { - "author_name": "J. Mauricio Calvo Calle", - "author_inst": "Department of Pathology, University of Massachusetts Chan Medical School, Worcester, MA, USA" - }, - { - "author_name": "Thomas Nixon", - "author_inst": "Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, USA" - }, - { - "author_name": "Qiushi Tang", - "author_inst": "Horae Gene Therapy Center, University of Massachusetts Chan Medical School, Worcester, MA, USA" - }, - { - "author_name": "Mireya Wessolossky", - "author_inst": "Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA" - }, - { - "author_name": "Yang Wang", - "author_inst": "MassBiologics of the University of Massachusetts Chan Medical School, Boston, MA, USA" - }, - { - "author_name": "Dominic A. Ritacco", - "author_inst": "Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA" - }, - { - "author_name": "Courtney S. Bly", - "author_inst": "Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA" - }, - { - "author_name": "Stephanie Fischinger", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Caroline Atyeo", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Peter O. Oluoch", - "author_inst": "Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, USA" - }, - { - "author_name": "Boaz Odwar", - "author_inst": "Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA" - }, - { - "author_name": "Jeffrey A. Bailey", - "author_inst": "Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI, USA" - }, - { - "author_name": "Ana Maldonado-Contreras", - "author_inst": "Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, USA" - }, - { - "author_name": "John P. Haran", - "author_inst": "Department of Emergency Medicine and Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA, USA" - }, - { - "author_name": "Aaron G. Schmidt", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Lisa Cavacini", - "author_inst": "MassBiologics of the University of Massachusetts Chan Medical School, Boston, MA, USA" - }, - { - "author_name": "Galit Alter", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Ann M. Moormann", - "author_inst": "Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.09.09.22279771", "rel_title": "THE EFFECT OF THE MEASLES, MUMPS AND RUBELLA VACCINE ON INNATE AND ADAPTIVE IMMUNE RESPONSES IN PERSONS RECEIVING A SARS-COV-2 mRNA VACCINE.A SUB-STUDY OF THE CROWN CORONATION TRIAL", @@ -238769,6 +240955,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2022.09.07.22279682", + "rel_title": "Psychological factors associated with reporting side effects following COVID-19 vaccination: a prospective cohort study (CoVAccS - wave 3)", + "rel_date": "2022-09-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.07.22279682", + "rel_abs": "ObjectiveTo investigate symptom reporting following the first and second COVID-19 vaccine doses, attribution of symptoms to the vaccine, and factors associated with symptom reporting.\n\nMethodsProspective cohort study (T1: 13-15 January 2021, T2: 4-15 October 2021). Participants were aged 18 years or older, living in the UK. Personal, clinical, and psychological factors were investigated at T1. Symptoms were reported at T2. We used logistic regression analyses to investigate associations.\n\nResultsAfter the first COVID-19 vaccine dose, 74.1% (95% CI 71.4% to 76.7%, n=762/1028) of participants reported at least one injection-site symptom, while 65.0% (95% CI 62.0% to 67.9%, n=669/1029) reported at least one other (non-injection-site) symptom. Symptom reporting was associated with being a woman and younger. After the second dose, 52.9% (95% CI 49.8% to 56.0%, n=532/1005) of participants reported at least one injection-site symptom and 43.7% (95% CI 40.7% to 46.8%, n=440/1006) reported at least one other (non-injection-site) symptom. Symptom reporting was associated with having reported symptoms after the first dose, having an illness that put one at higher risk of COVID-19 (non-injection-site symptoms only), and not believing that one had enough information about COVID-19 to make an informed decision about vaccination (injection-site symptoms only).\n\nConclusionsWomen and younger people were more likely to report symptoms from vaccination. People who had reported symptoms from previous doses were also more likely to report symptoms subsequently, although symptom reporting following the second vaccine was lower than following the first vaccine. Few psychological factors were associated with symptom reporting.\n\nHighlightsO_LIWe measured symptom reporting and attributions from the COVID-19 vaccines.\nC_LIO_LIA prospective cohort study was used (T1: January 2021, T2: October 2021).\nC_LIO_LIWomen and younger people were more likely to report side effects.\nC_LIO_LISide effects reporting after the first and second dose was strongly associated.\nC_LI", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Louise E. Smith", + "author_inst": "King's College London" + }, + { + "author_name": "Julius Sim", + "author_inst": "Keele University" + }, + { + "author_name": "Susan Mary Sherman", + "author_inst": "Keele University" + }, + { + "author_name": "Richard Aml\u00f4t", + "author_inst": "UK Health Security Agency" + }, + { + "author_name": "Megan Cutts", + "author_inst": "Keele University" + }, + { + "author_name": "Hannah Dasch", + "author_inst": "King's College London" + }, + { + "author_name": "Nick Sevdalis", + "author_inst": "King's College London" + }, + { + "author_name": "James Rubin", + "author_inst": "King's College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.09.05.22279616", "rel_title": "Impact of the COVID-19 pandemic on tuberculosis notification in Brazil", @@ -239144,81 +241377,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2022.09.07.22279692", - "rel_title": "Improved Robustness of SARS-CoV-2 Whole-Genome Sequencing from Wastewater with a Nonselective Virus Concentration Method", - "rel_date": "2022-09-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.07.22279692", - "rel_abs": "The sequencing of human virus genomes from wastewater samples is an efficient method for tracking viral transmission and evolution at the community level. However, this requires the recovery of viral nucleic acids of high quality. We developed a reusable tangential-flow filtration system to concentrate and purify viruses from wastewater for whole-genome sequencing. A pilot study was conducted with 94 wastewater samples from four local sewersheds, from which viral nucleic acids were extracted, and the whole genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was sequenced using the ARTIC V4.0 primers. Our method yielded a high probability (0.9) of recovering complete or near-complete SARS-CoV-2 genomes (>90% coverage at 10x depth) from wastewater when the COVID-19 incidence rate exceeded 33 cases per 100 000 people. The relative abundances of sequenced SARS-CoV-2 variants followed the trends observed from patient-derived samples. We also identified SARS-CoV-2 lineages in wastewater that were underrepresented or not present in the clinical whole-genome sequencing data. The developed tangential-flow filtration system can be easily adopted for the sequencing of other viruses in wastewater, particularly those at low concentrations.\n\nSYNOPSISThe tangential-flow filtration method extracts viral nucleic acids of high enough quality from wastewater for robust and successful whole-genome sequencing.\n\nGRAPHIC FOR TABLE OF CONTENTS (TOC)\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC=\"FIGDIR/small/22279692v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (22K):\norg.highwire.dtl.DTLVardef@566377org.highwire.dtl.DTLVardef@19c3ba7org.highwire.dtl.DTLVardef@106c70org.highwire.dtl.DTLVardef@3f3f8f_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Emily Segelhurst", - "author_inst": "Department of Civil, Structural and Environmental Engineering, University at Buffalo, Buffalo, New York 14260, United States" - }, - { - "author_name": "Jonathan E Bard", - "author_inst": "UB Genomics and Bioinformatics Core, University at Buffalo, Buffalo, New York 14203, United States; Department of Biochemistry, Jacobs School of Medicine and Bi" - }, - { - "author_name": "Annemarie N Pillsbury", - "author_inst": "Department of Civil, Structural and Environmental Engineering, University at Buffalo, Buffalo, New York 14260, United States" - }, - { - "author_name": "Md Mahbubul Alam", - "author_inst": "Department of Civil, Structural and Environmental Engineering, University at Buffalo, Buffalo, New York 14260, United States" - }, - { - "author_name": "Natalie A Lamb", - "author_inst": "UB Genomics and Bioinformatics Core, University at Buffalo, Buffalo, New York 14203, United States" - }, - { - "author_name": "Chonglin Zhu", - "author_inst": "Department of Civil, Structural and Environmental Engineering, University at Buffalo, Buffalo, New York 14260, United States" - }, - { - "author_name": "Alyssa Pohlman", - "author_inst": "UB Genomics and Bioinformatics Core, University at Buffalo, Buffalo, New York 14203, United States" - }, - { - "author_name": "Amanda Boccolucci", - "author_inst": "UB Genomics and Bioinformatics Core, University at Buffalo, Buffalo, New York 14203, United States" - }, - { - "author_name": "Jamaal Emerson", - "author_inst": "Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203, United States" - }, - { - "author_name": "Brandon J Marzullo", - "author_inst": "UB Genomics and Bioinformatics Core, University at Buffalo, Buffalo, New York 14203, United States; Department of Biochemistry, Jacobs School of Medicine and Bi" - }, - { - "author_name": "Donald A Yergeau", - "author_inst": "UB Genomics and Bioinformatics Core, University at Buffalo, Buffalo, New York 14203, United States" - }, - { - "author_name": "Norma J Nowak", - "author_inst": "UB Genomics and Bioinformatics Core, University at Buffalo, Buffalo, New York 14203, United States; Department of Biochemistry, Jacobs School of Medicine and Bi" - }, - { - "author_name": "Ian M Bradley", - "author_inst": "Department of Civil, Structural and Environmental Engineering, University at Buffalo, Buffalo, New York 14260, United States; Research and Education in Energy, " - }, - { - "author_name": "Jennifer A Surtees", - "author_inst": "Department of Biochemistry, Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences; Research and Education in Energy, Envi" - }, - { - "author_name": "Yinyin Ye", - "author_inst": "Department of Civil, Structural and Environmental Engineering, University at Buffalo, Buffalo, New York 14260, United States" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.09.09.22279754", "rel_title": "Contact patterns of UK home delivery drivers and their use of protective measures during the COVID-19 pandemic: a cross-sectional study", @@ -240539,6 +242697,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.09.06.22279625", + "rel_title": "Mucosal immunity and antibody anergy in COVID-exposed Covishield vaccinees", + "rel_date": "2022-09-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.06.22279625", + "rel_abs": "Knowledge is limited on mucosal immunity induction and longitudinal responses to vaccination against SARS-CoV2. Here, we determined serum/salivary antibodies and cytokines after three Covishield vaccine doses. Sera from 205 healthcare workers (HCWs) one-month after first- dose; one-, three- and six-months after second-dose; paired sera and stimulated whole mouth fluid (SWMF) from 10 HCWs one-, three- and six-months after third-dose were tested for anti- spike SARS-CoV2 antibodies by ECLIA and for cytokines by ELISA/cytokine bead arrays. One-month after second-dose, antibodies had increased significantly (6-fold) in COVID-naive group, but declined (1.5-fold) in those previously exposed to COVID. At one-month after first- dose, IL-10 levels were statistically higher in the previously COVID-exposed group compared to COVID-naive group (p<0.02). Breakthrough infections were 44% in COVID-naive group, while re-infections were 27% in COVID-exposed group (p<0.02). Proinflammatory cytokines-IL- 17/IL-21 at one-month after first- and second-doses, and memory cytokines-IL-7/IL-15 at three- and six-months after second-dose were minimal. Antibodies spiked at one-month after third- dose and declined by three- and six-months after third-dose similar to post-second-dose. Paired sera and SWMF at one- and six-months after third-dose lacked adaptive immunity cytokine expression. Innate immunity cytokines (MIG, MCP-1, IL-8, TNF-, IL-6, IL-1{beta}) showed a declining trend in serum, but were sustained in SWMF. Thus, our findings suggest that first-dose acts as an antibody boost, while second-dose induces antibody anergy in the previously COVID- exposed group. Rapidly declining antibodies and minimal T cell cytokines raises concerns over their durability in subsequent virus exposures. Sustained innate cytokines emanating from the oral mucosa warrant further in-depth explorations.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Priya Kannian", + "author_inst": "The Voluntary Health Services Hospital" + }, + { + "author_name": "Pasuvaraj Mahanathi", + "author_inst": "The Voluntary Health Services Hospital, Chennai, India" + }, + { + "author_name": "Arul Gracemary", + "author_inst": "The Voluntary Health Services Hospital, Chennai, India" + }, + { + "author_name": "Nagalingeswaran Kumarasamy", + "author_inst": "The Voluntary Health Services Hospital, Chennai, India" + }, + { + "author_name": "Stephen J Challacombe", + "author_inst": "King's College London" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.09.04.22279588", "rel_title": "The prevalence of SARS-CoV-2 infection and long COVID in US adults during the BA.5 surge, June-July 2022", @@ -241098,37 +243291,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2022.09.06.506814", - "rel_title": "Climate change has affected the spillover risk of bat-borne pathogens", - "rel_date": "2022-09-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.09.06.506814", - "rel_abs": "Bat-borne viruses are a threat to global health and have in recent history had major impacts to human morbidity and mortality. Examples include diseases such as rabies, Ebola, SARS-Cov-1, and SARS-Cov-2 (COVID-19). Climate change could exacerbate the emergence of bat-borne pathogens by affecting the distribution and abundance of bats in tropical ecosystems. Here we report an assessment of historical climate and vampire bat occurrence data for the last century, which revealed a relationship between climatic variation and risk of disease spillover triggered by changes in bat distributions. This report represents one of the first examples of empirical evidence of global change effects on continental patterns of bat-borne pathogen transmission risk. We therefore recommend that more research is necessary on the impacts of climate change on bat-borne pathogen spillover risk, and that climate change impacts on bat-borne disease should be considered in global security initiatives.\n\nHighlightsO_LIBat-borne viruses are a threat to global health and include diseases such as rabies, Ebola, SARS-Cov-1, and SARS-Cov-2 (COVID-19).\nC_LIO_LIClimate change could exacerbate the emergence of bat-borne pathogens by affecting the distribution and abundance of bats.\nC_LIO_LIHere we report an assessment of historical climate and vampire-bat occurrence data for the last century, which reveals a relationship between climatic variation and risk of disease spillover triggered by changes in bat distributions.\nC_LI", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Paige Van de Vuurst", - "author_inst": "Virgina Tech" - }, - { - "author_name": "Huijie Qiao", - "author_inst": "3Institute of Zoology, Chinese Academy of Sciences, Beijing, China" - }, - { - "author_name": "Diego Soler-Tovar", - "author_inst": "Universidad de La Salle, Bogota, Colombia." - }, - { - "author_name": "Luis E Escobar", - "author_inst": "Virginia Tech" - } - ], - "version": "1", - "license": "cc_no", - "type": "confirmatory results", - "category": "systems biology" - }, { "rel_doi": "10.1101/2022.09.06.22279606", "rel_title": "The COVID-19 Pandemic as an Opportunity for Unravelling the Causative Association between Respiratory Viruses and Pneumococcus-Associated Disease in Young Children: A Prospective Cohort Study", @@ -242573,6 +244735,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.08.30.22279415", + "rel_title": "Spatial analysis of COVID-19 booster vaccine uptake in Scotland, and projection of future distributions", + "rel_date": "2022-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.30.22279415", + "rel_abs": "Vaccination is a critical tool for controlling infectious diseases, with its use to protect against COVID-19 being a prime example. Where a disease is highly transmissible, even a small proportion of unvaccinated individuals can have substantial implications for disease burdens and compromise efforts for control. As socio-demographic factors such as deprivation and ethnicity have been shown to influence uptake rates, identifying how vaccine uptake varies with socio-demographic indicators is a critical step for reducing vaccine hesitancy and issues of access, and identifying plausible future uptake patterns.\n\nHere, we analyse the numbers of COVID-19 vaccinations subdivided by age, gender, date, dose and geographical location. We use publicly available socio-demographic data, and use random forest models to capture patterns of uptake at high spatial resolution, with systematic variation restricted to fine spatial scale (~ 1km in urban areas). We show that uptake of first vaccine booster doses in Scotland can be used to predict with high precision the distribution of second booster doses across deprivation deciles, age and gender despite the substantially lower uptake of second boosters compared to first.\n\nThis analysis shows that while age and gender have the greatest impact on the model fit, there is a substantial influence of several deprivation factors and the proportion of BAME residents. The high correlation amongst these factors also suggests that, should vaccine uptake decrease, the impact of deprivation is likely to increase, furthering the disproportionate impact of COVID-19 on individuals living in highly deprived areas. As our analysis is based solely on publicly available socio-demographic data and readily recorded vaccination uptake figures, it would be easily adaptable to analysing vaccination uptake data from countries where data recording is similar, and for aiding vaccination campaigns against other infectious diseases.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Anthony J Wood", + "author_inst": "The University of Edinburgh" + }, + { + "author_name": "Anne Marie MacKintosh", + "author_inst": "University of Stirling" + }, + { + "author_name": "Martine Stead", + "author_inst": "University of Stirling" + }, + { + "author_name": "Rowland Raymond Kao", + "author_inst": "University of Edinburgh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.08.31.22279432", "rel_title": "COVID-19 disruptions of food systems and nutrition services in Ethiopia: Evidence of the impacts and policy responses", @@ -243136,105 +245329,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2022.09.02.22279398", - "rel_title": "COVID-19-associated AKI in hospitalized US patients: incidence, temporal trends, geographical distribution, risk factors and mortality", - "rel_date": "2022-09-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.09.02.22279398", - "rel_abs": "BackgroundAcute kidney injury (AKI) is associated with mortality in patients hospitalized with COVID-19, however, its incidence, geographic distribution, and temporal trends since the start of the pandemic are understudied.\n\nMethodsElectronic health record data were obtained from 53 health systems in the United States (US) in the National COVID Cohort Collaborative (N3C). We selected hospitalized adults diagnosed with COVID-19 between March 6th, 2020, and January 6th, 2022. AKI was determined with serum creatinine (SCr) and diagnosis codes. Time were divided into 16-weeks (P1-6) periods and geographical regions into Northeast, Midwest, South, and West. Multivariable models were used to analyze the risk factors for AKI or mortality.\n\nResultsOut of a total cohort of 306,061, 126,478 (41.0 %) patients had AKI. Among these, 17.9% lacked a diagnosis code but had AKI based on the change in SCr. Similar to patients coded for AKI, these patients had higher mortality compared to those without AKI. The incidence of AKI was highest in P1 (49.3%), reduced in P2 (40.6%), and relatively stable thereafter. Compared to the Midwest, the Northeast, South, and West had higher adjusted AKI incidence in P1, subsequently, the South and West regions continued to have the highest relative incidence. In multivariable models, AKI defined by either SCr or diagnostic code, and the severity of AKI was associated with mortality.\n\nConclusionsUncoded cases of COVID-19-associated AKI are common and associated with mortality. The incidence and distribution of COVID-19-associated AKI have changed since the first wave of the pandemic in the US.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Yun Jae Yoo", - "author_inst": "Stony Brook University" - }, - { - "author_name": "Kenneth J Wilkins", - "author_inst": "NIH" - }, - { - "author_name": "Fadhl Alakwaa", - "author_inst": "University of Michigan" - }, - { - "author_name": "Feifan Liu", - "author_inst": "University of Massachusetts Chan Medical School" - }, - { - "author_name": "Luke A Torre-Healy", - "author_inst": "Stony Brook University" - }, - { - "author_name": "Spencer Krichevsky", - "author_inst": "Stony Brook University" - }, - { - "author_name": "Stephanie S Hong", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Ankit Sakhuja", - "author_inst": "West Virginia United Health System: WVU Medicine" - }, - { - "author_name": "Chetan K Potu", - "author_inst": "Stony Brook University" - }, - { - "author_name": "Joel Saltz", - "author_inst": "Stony Brook University" - }, - { - "author_name": "Rajiv Saran", - "author_inst": "University of Michigan" - }, - { - "author_name": "Richard L Zhu", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Soko Setoguchi", - "author_inst": "Rutgers Robert Wood Johnson Medical School and School of Public Health" - }, - { - "author_name": "Sandra L Kane-Gill", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Sandeep Mallipattu", - "author_inst": "Stony Brook University" - }, - { - "author_name": "Yongqun He", - "author_inst": "University of Michigan" - }, - { - "author_name": "David H Ellison", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "James B Byrd", - "author_inst": "5570C MSRB II" - }, - { - "author_name": "Chirag R Parikh", - "author_inst": "Johns Hopkins School of Medicine" - }, - { - "author_name": "Richard A Moffitt", - "author_inst": "Stony Brook University" - }, - { - "author_name": "FARRUKH KORAISHY", - "author_inst": "Stony Brook University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "nephrology" - }, { "rel_doi": "10.1101/2022.08.31.22279422", "rel_title": "Zero-COVID policy or Living-with-COVID policy? Analysis Based on Percent Excess Mortality", @@ -244355,6 +246449,129 @@ "type": "new results", "category": "systems biology" }, + { + "rel_doi": "10.1101/2022.08.29.22279359", + "rel_title": "Prophylactic Treatment of COVID-19 in Care Homes Trial (PROTECT-CH)", + "rel_date": "2022-08-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.29.22279359", + "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19) is associated with significant mortality and morbidity in care homes. Novel or repurposed antiviral drugs may reduce infection and disease severity through reducing viral replication and inflammation.\n\nObjectiveTo compare the safety and efficacy of antiviral agents (ciclesonide, niclosamide) for preventing SARS-CoV-2 infection and COVID-19 severity in care home residents.\n\nDesignCluster-randomised open-label blinded endpoint platform clinical trial testing antiviral agents in a post-exposure prophylaxis paradigm.\n\nSettingCare homes across all four United Kingdom member countries.\n\nParticipantsCare home residents 65 years of age or older.\n\nInterventionsCare homes were to be allocated at random by computer to 42 days of antiviral agent plus standard care versus standard of care and followed for 60 days after randomisation.\n\nMain outcome measuresThe primary four-level ordered categorical outcome with participants classified according to the most serious of all-cause mortality, all-cause hospitalisation, SARS-CoV-2 infection and no infection. Analysis using ordinal logistic regression was by intention to treat. Other outcomes included the components of the primary outcome and transmission.\n\nResultsDelays in contracting between NIHR and the manufacturers of potential antiviral agents significantly delayed any potential start date. Having set up the trial (protocol, approvals, insurance, website, database, routine data algorithms, training materials), the trial was stopped in September 2021 prior to contracting of care homes and general practitioners in view of the success of vaccination in care homes with significantly reduced infections, hospitalisations and deaths. As a result, the sample size target (based on COVID-19 rates and deaths occurring in February-June 2020) became unfeasible.\n\nLimitationsCare home residents were not approached about the trial and so were not consented and did not receive treatment. Hence, the feasibility of screening, consent, treatment and data acquisition, and potential benefit of post exposure prophylaxis were never tested. Further, contracting between the University of Nottingham and the PIs, GPs and care homes was not completed, so the feasibility of contracting with all the different groups at the scale needed was not tested.\n\nConclusionsThe role of post exposure prophylaxis of COVID-19 in care home residents was not tested because of changes in COVID-19 incidence, prevalence and virulence as a consequence of the vaccination programme that rendered the study unfeasible. Significant progress was made in describing and developing the infrastructure necessary for a large scale Clinical Trial of Investigational Medicinal Products in care homes in all four UK nations.\n\nFuture workThe role of post-exposure prophylaxis of COVID-19 in care home residents remains to be defined. Significant logistical barriers to conducting research in care homes during a pandemic need to be removed before such studies are possible in the required short timescale.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Philip M Bath", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Jonathan Ball", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Matthew Boyd", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Heather Gage", + "author_inst": "University of Surrey" + }, + { + "author_name": "Matthew Glover", + "author_inst": "University of Surrey" + }, + { + "author_name": "Maureen Godfrey", + "author_inst": "Private person" + }, + { + "author_name": "Bruce Guthrie", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Jonathan Hewitt", + "author_inst": "Llandough Hospital" + }, + { + "author_name": "Robert Howard", + "author_inst": "University College London" + }, + { + "author_name": "Thomas Jaki", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Edmund Juszczak", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Daniel Lasserson", + "author_inst": "University of Warwick" + }, + { + "author_name": "Paul Leighton", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Val Leyland", + "author_inst": "Private person" + }, + { + "author_name": "Wei Shen Lim", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Pip Logan", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Garry Meakin", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Alan Montgomery", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Reuben Ogollah", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Peter Passmore", + "author_inst": "Queen's University Belfast" + }, + { + "author_name": "Philip Quinlan", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Caroline Rick", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Simon Royal", + "author_inst": "Cripps Health Centre" + }, + { + "author_name": "Susan D Shenkin", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Clare Upton", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Adam L Gordon", + "author_inst": "University of Nottingham" + }, + { + "author_name": "- PROTECT-CH Trialists", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.08.25.22279235", "rel_title": "How Important Are Study Designs? A Simulation Assessment of Vaccine Effectiveness Estimation Bias with Time-Varying Vaccine Coverage, and Heterogeneous Testing and Baseline Attack Rates", @@ -244742,65 +246959,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.08.29.22279327", - "rel_title": "Effectiveness of endurance training rehabilitation after hospitalisation in intensive care for COVID-19-related acute respiratory distress syndrome on dyspnoea (RECOVER): a randomised controlled, open-label multicentre trial", - "rel_date": "2022-08-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.29.22279327", - "rel_abs": "BackgroundCOVID-19-related Acute Respiratory Distress Syndrome (CARDS) is the severe evolution of the Sars-Cov-2 infection leading to an intensive care unit (ICU) stay. Its onset is associated with \"long-covid\" including persisting respiratory disorders up to one year. Rehabilitation is suggested by most guidelines in the treatment of \"long-covid\". As no randomised controlled trial did support its use in \"long-covid\" we aimed to evaluate the effects of endurance training rehabilitation (ETR) on dyspnoea in \"long-covid\" following CARDS.\n\nMethodsIn this multicentre, two-arm, parallel, open, assessor-blinded, randomised, controlled trial performed in three French ICU, we enrolled adults previously admitted for CARDS, discharged for at least three months and presenting an mMRC dyspnea scale score > 1. Eligible patients were randomly allocated (1:1) to receive either ETR or standard physiotherapy (SP), both for three months. Outcomes assessors were masked to treatment assignment. Primary outcome was dyspnoeas evolution, measured by Multidimensional Dyspnea Profile (MDP) at inclusion and after 90 days.\n\nResultsBetween August 7, 2020 and January 26, 2022, 871 COVID-19 patients were screened, of whom 60 were randomly assigned to ETR (n=27) or SP (n=33). Mean MDP score after treatment was significantly lower in the ETR group than in the SP group (26.15 [SD 15.48] vs. 44.76 [SD 19.25]; mean difference -18.61 [95% CI -27.78 to -9.44]; p<0.0001).\n\nConclusionCARDS patients suffering from breathlessness three months after discharge improved their dyspnoea significantly more when treated with ETR for three months rather than with SP.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Christophe Romanet", - "author_inst": "Intensive care department, Groupe hospitalier Paris Saint Joseph, Paris, France" - }, - { - "author_name": "Johan Wormser", - "author_inst": "Intensive care department, Groupe hospitalier Paris Saint Joseph, Paris, France" - }, - { - "author_name": "Audrey Fels", - "author_inst": "Department of clinical research. Groupe Hospitalier Paris Saint Joseph, Paris, France" - }, - { - "author_name": "Pauline Lucas", - "author_inst": "Department of Intensive Care, Hopital Cochin - Port Royal, Paris, France" - }, - { - "author_name": "Camille Prudat", - "author_inst": "Department of Intensive Care, Groupe Hospitalier Paris Saint Joseph, Paris, France" - }, - { - "author_name": "Emmanuelle Sacco", - "author_inst": "Department of Clinical Research, Groupe Hospitalier Paris Saint Joseph, Paris, France" - }, - { - "author_name": "Cedric Bruel", - "author_inst": "Intensive care department, Groupe hospitalier Paris Saint Joseph, Paris, France" - }, - { - "author_name": "Gaetan Pantefeve", - "author_inst": "Department of Intensive Care, Centre Hospitalier Victor Dupouy, Argenteuil, France" - }, - { - "author_name": "Frederic Pene", - "author_inst": "Department of Medical Intensive Care, Hopital Cochin - Port Royal, Paris, France" - }, - { - "author_name": "Gilles Chatellier", - "author_inst": "Department of Clinical Research, Groupe Hospitalier Paris Saint Joseph, Paris, France" - }, - { - "author_name": "Francois Philippart", - "author_inst": "Intensive care department, Groupe hospitalier Paris Saint Joseph, Paris, France" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2022.08.26.22279232", "rel_title": "UB-612 Multitope Vaccine Targeting SARS-CoV-2 Spike and Non-Spike Proteins Provides Broad and Durable Immune Responses", @@ -245913,6 +248071,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.25.505365", + "rel_title": "Antimicrobial copper as an effective and practical deterrent to surface transmission of SARS-CoV-2", + "rel_date": "2022-08-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.25.505365", + "rel_abs": "The aerosols are critical for SARS-CoV-2 transmission, however in areas with high confluence of people the contaminated surfaces take an important role that we could attack using antimicrobial surfaces including copper. In this study, we wanted to challenge infectious SARS-CoV-2 with two samples of copper surfaces and one plastic surface as control at different direct times contact. To evaluate and quantify virucidal activity of copper against SARS-CoV-2, two methods of experimental infection were performed, TCID50 and plaque assays on VeroE6 cells, showing significant inactivation of high titer of SARS-CoV-2 within minutes reaching 99.9 % of inactivation of infectivity on both copper surfaces. Daily high demand surfaces contamination is an issue that we have to worry about not only during the actual pandemic time but also for future, where copper or its alloys will have a pivotal role.\n\nImportanceQuantitative data obtained of TCID50 and plaque assay with infectious SARS-CoV-2 virus showed that after direct contact with copper or copper alloys, viruses were inactivated within minutes. Notably, the SARS-CoV-2 virus used in these assays was in high titer (106 PFU/mL) showing strong copper inactivation of the infectious SARS-CoV-2.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Jorge Vera-Otarola", + "author_inst": "Pontificia Universidad Catolica de Chile" + }, + { + "author_name": "Nicolas Mendez", + "author_inst": "The Clean Copper Company, LLC" + }, + { + "author_name": "Constanza Mart\u00ednez-Valdebenito", + "author_inst": "Pontificia Universidad Catolica de Chile" + }, + { + "author_name": "Rodolfo Mannheim", + "author_inst": "Universidad de Santiago de Chile" + }, + { + "author_name": "Kenneth Lu", + "author_inst": "University of California" + }, + { + "author_name": "Steve Rhodes", + "author_inst": "The Clean Copper Company, LLC" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "confirmatory results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.08.25.22279195", "rel_title": "Are female-specific cancers long-term sequelae of COVID-19? Evidence from a large-scale genome-wide cross-trait analysis", @@ -246664,45 +248861,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.08.25.22279237", - "rel_title": "Predicting the efficacy of variant-modified COVID-19 vaccine boosters", - "rel_date": "2022-08-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.25.22279237", - "rel_abs": "As a result of the emergence and circulation of antigenically distinct SARS-CoV-2 variants, a number of variant-modified COVID-19 vaccines have been developed. Here we perform a meta-analysis of the available data on neutralisation titres from clinical studies comparing booster vaccination with either the current ancestral-based vaccines or variant-modified vaccines. We then use this to predict the relative efficacies of these booster vaccines under different scenarios.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "David S Khoury", - "author_inst": "Kirby Institute, UNSW Sydney" - }, - { - "author_name": "Steffen S Docken", - "author_inst": "Kirby Institute, UNSW Sydney" - }, - { - "author_name": "Kanta Subbarao", - "author_inst": "The Peter Doherty Institute for Infection and Immunity" - }, - { - "author_name": "Stephen Kent", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Miles Philip Davenport", - "author_inst": "Kirby Institute, UNSW Sydney" - }, - { - "author_name": "Deborah Cromer", - "author_inst": "UNSW Australia" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.08.25.505316", "rel_title": "Enhancer deregulation in TET2 Mutant Clonal Hematopoiesis is associated with increased COVID-19 related inflammation severity and mortality", @@ -248003,6 +250161,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.08.25.22279225", + "rel_title": "Multisystem Inflammatory Syndrome in Children Managed in the Outpatient Setting: An EHR-based cohort study from the RECOVER program", + "rel_date": "2022-08-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.25.22279225", + "rel_abs": "Using electronic health record data combined with primary chart review, we identified 7 children across 8 pediatric medical centers with a diagnosis of Multisystem Inflammatory Syndrome in Children (MIS-C) who were managed as outpatients. These findings should prompt a discussion about modifying the case definition to allow for such a possibility.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Ravi Jhaveri", + "author_inst": "Ann & Robert H. Lurie Children's Hospital of Chicago" + }, + { + "author_name": "Ryan Webb", + "author_inst": "Children's Hospital of Philadelphia" + }, + { + "author_name": "Hanieh Razzaghi", + "author_inst": "Children's Hospital of Philadelphia" + }, + { + "author_name": "Julia Schurchard", + "author_inst": "Children's Hospital of Philadelphia" + }, + { + "author_name": "Asuncion Mejias", + "author_inst": "Nationwide Children's Hospital" + }, + { + "author_name": "Tellen D Bennett", + "author_inst": "University of Colorado School of Medicine" + }, + { + "author_name": "Pei-Ni Jone", + "author_inst": "Children's Hospital of Colorado" + }, + { + "author_name": "Deepika Thacker", + "author_inst": "Nemours" + }, + { + "author_name": "Grant R. Schulert", + "author_inst": "Cincinnati Children's Hospital & Medical Center" + }, + { + "author_name": "Colin Rogerson", + "author_inst": "Riley Children's Hospital" + }, + { + "author_name": "Jonathan D. Cogen", + "author_inst": "Seattle Children's Hospital" + }, + { + "author_name": "L. Charles Bailey", + "author_inst": "Children's Hospital of Philadelphia" + }, + { + "author_name": "Christopher B. Forrest", + "author_inst": "Children's Hospital of Philadelphia" + }, + { + "author_name": "Grace M. Lee", + "author_inst": "Stanford Children's Hospital" + }, + { + "author_name": "Suchitra Rao", + "author_inst": "University of Colorado School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2022.08.23.504944", "rel_title": "COVID-19 Contact Tracing Analysis with Bluetooth Technology Using Raspberry Pis", @@ -248402,105 +250635,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.08.23.22279120", - "rel_title": "Design and Analysis of Outcomes following SARS-CoV-2 Infection in Veterans", - "rel_date": "2022-08-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.23.22279120", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSBackgroundC_ST_ABSUnderstanding how SARS-CoV-2 infection impacts long-term patient outcomes requires identification of comparable persons with and without infection. We report the design and implementation of a matching strategy employed by the Department of Veterans Affairs (VA) COVID-19 Observational Research Collaboratory (CORC) to develop comparable cohorts of SARS-CoV-2 infected and uninfected persons for the purpose of inferring potential causative long-term adverse effects of SARS-CoV-2 infection in the Veteran population.\n\nMethodsIn a retrospective cohort study, we identified VA health care system patients who were and were not infected with SARS-CoV-2 on a rolling monthly basis. We generated matched cohorts utilizing a combination of exact and time-varying propensity score matching based on electronic health record (EHR)-derived covariates that can be confounders or risk factors across a range of outcomes.\n\nResultsFrom an initial pool of 126,689,864 person-months of observation, we generated final matched cohorts of 208,536 Veterans infected between March 2020-April 2021 and 3,014,091 uninfected Veterans. Matched cohorts were well-balanced on all 38 covariates used in matching after excluding patients for: no VA health care utilization; implausible age, weight, or height; living outside of the 50 states or Washington, D.C.; prior SARS-CoV-2 diagnosis per Medicare claims; or lack of a suitable match. Most Veterans in the matched cohort were male (88.3%), non-Hispanic (87.1%), white (67.2%), and living in urban areas (71.5%), with a mean age of 60.6, BMI of 31.3, Gagne comorbidity score of 1.4 and a mean of 2.3 CDC high-risk conditions. The most common diagnoses were hypertension (61.4%), diabetes (34.3%), major depression (32.2%), coronary heart disease (28.5%), PTSD (25.5%), anxiety (22.5%), and chronic kidney disease (22.5%).\n\nConclusionsThis successful creation of matched SARS-CoV-2 infected and uninfected patient cohorts from the largest integrated health system in the United States will support cohort studies of outcomes derived from EHRs and sample selection for qualitative interviews and patient surveys. These studies will increase our understanding of the long-term outcomes of Veterans who were infected with SARS-CoV-2.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Valerie A. Smith", - "author_inst": "Center of Innovation to Accelerate Discovery and Practice Transformation, Durham VA Medical Center, Durham, NC; Department of Population Health Sciences, Duke U" - }, - { - "author_name": "Theodore S.Z. Berkowitz", - "author_inst": "Center of Innovation to Accelerate Discovery and Practice Transformation, Durham VA Medical Center, Durham, NC" - }, - { - "author_name": "Paul Hebert", - "author_inst": "Health Services Research & Development Center of Innovation for Veteran-Centered and Value-Driven Care, and Gastroenterology section, Veterans Affairs Puget Sou" - }, - { - "author_name": "Edwin S. Wong", - "author_inst": "Health Services Research & Development Center of Innovation for Veteran-Centered and Value-Driven Care, and Gastroenterology section, Veterans Affairs Puget Sou" - }, - { - "author_name": "Meike Niederhausen", - "author_inst": "Center to Improve Veteran Involvement in Care, VA Portland Health Care System, Portland, OR; Oregon Health & Science University (OHSU), Portland, OR ; Portland " - }, - { - "author_name": "John A. Pura", - "author_inst": "Center of Innovation to Accelerate Discovery and Practice Transformation, Durham VA Medical Center, Durham, NC" - }, - { - "author_name": "Kristin Berry", - "author_inst": "Health Services Research & Development Center of Innovation for Veteran-Centered and Value-Driven Care, and Gastroenterology section, Veterans Affairs Puget Sou" - }, - { - "author_name": "Pamela Green", - "author_inst": "Health Services Research & Development Center of Innovation for Veteran-Centered and Value-Driven Care, and Gastroenterology section, Veterans Affairs Puget Sou" - }, - { - "author_name": "Anna Korpak", - "author_inst": "Seattle Epidemiologic Research and Information Center, VA Puget Sound, Seattle, WA" - }, - { - "author_name": "Alexandra Fox", - "author_inst": "Seattle Epidemiologic Research and Information Center, VA Puget Sound, Seattle, WA" - }, - { - "author_name": "Aaron Baraff", - "author_inst": "Seattle Epidemiologic Research and Information Center, VA Puget Sound, Seattle, WA" - }, - { - "author_name": "Alexandra Hickok", - "author_inst": "Center to Improve Veteran Involvement in Care, VA Portland Health Care System, Portland, OR" - }, - { - "author_name": "Troy A. Shahoumian", - "author_inst": "Population Health: Health Solutions, Veterans Health Administration, Washington, DC" - }, - { - "author_name": "Amy S.B. Bohnert", - "author_inst": "VA Center for Clinical Management Research, Ann Arbor VA, Ann Arbor, MI; Departments of Anesthesiology and Psychiatry, University of Michigan Medical School, An" - }, - { - "author_name": "Denise Hynes", - "author_inst": "Center to Improve Veteran Involvement in Care, VA Portland Health Care System, Portland, OR; College of Public Health and Human Sciences and Center for Quantita" - }, - { - "author_name": "Edward J. Boyko", - "author_inst": "Seattle Epidemiologic Research and Information Center, VA Puget Sound, Seattle, WA" - }, - { - "author_name": "George N. Ioannou", - "author_inst": "Health Services Research & Development Center of Innovation for Veteran-Centered and Value-Driven Care, and Gastroenterology section, Veterans Affairs Puget Sou" - }, - { - "author_name": "Theodore J. Iwashyna", - "author_inst": "VA Center for Clinical Management Research, Ann Arbor VA, Ann Arbor, MI; National Clinical Scholars Program, University of Michigan Medical School, Ann Arbor, M" - }, - { - "author_name": "C. Barrett Bowling", - "author_inst": "Center of Innovation to Accelerate Discovery and Practice Transformation, Durham VA Medical Center, Durham, NC; Geriatric Research Education and Clinical Center" - }, - { - "author_name": "Ann M. O'Hare", - "author_inst": "; Division of Nephrology, University of Washington, Seattle, WA" - }, - { - "author_name": "Matthew L. Maciejewski", - "author_inst": "Center of Innovation to Accelerate Discovery and Practice Transformation, Durham VA Medical Center, Durham, NC; Department of Population Health Sciences, Duke U" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.08.23.22279026", "rel_title": "Immune protection against SARS-CoV-2 re-reinfection and immune imprinting", @@ -249717,6 +251851,29 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2022.08.22.504823", + "rel_title": "Effective Matrix Designs for COVID-19 Group Testing", + "rel_date": "2022-08-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.22.504823", + "rel_abs": "BackgroundGrouping samples with low prevalence of positives into pools and testing these pools can achieve considerable savings in testing resources compared with individual testing in the context of COVID-19. We review published pooling matrices, which encode the assignment of samples into pools and describe decoding algorithms, which decode individual samples from pools. Based on the findings we propose new one-round pooling designs with high compression that can efficiently be decoded by combinatorial algorithms. This expands the admissible parameter space for the construction of pooling matrices compared to current methods.\n\nResultsBy arranging samples in a grid and using polynomials to construct pools, we develop direct formulas for an Algorithm (Polynomial Pools (PP)) to generate assignments of samples into pools. Designs from PP guarantee to correctly decode all samples with up to a specified number of positive samples. PP includes recent combinatorial methods for COVID-19, and enables new constructions that can result in more effective designs.\n\nConclusionFor low prevalences of COVID-19, group tests can save resources when compared to individual testing. Constructions from the recent literature on combinatorial methods have gaps with respect to the designs that are available. We develop a method (PP), which generalizes previous constructions and enables new designs that can be advantageous in various situations.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "David Brust", + "author_inst": "German Aerospace Center (DLR)" + }, + { + "author_name": "Johannes J Brust", + "author_inst": "University of California San Diego" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.08.23.503528", "rel_title": "An outbreak of SARS-CoV-2 in big hairy armadillos (Chaetophractus villosus) associated with Gamma variant in Argentina three months after being undetectable in humans", @@ -250264,41 +252421,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.08.18.22278968", - "rel_title": "Evaluation of RT-PCR pooling test for the detection of SARS-CoV-2 in low-resource setting", - "rel_date": "2022-08-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.18.22278968", - "rel_abs": "BackgroundSpecimen pooling is an efficient method when there is limited accessibility or scarcity of test kits and reagents for nucleic acid extraction and molecular detection. We evaluated the ability of the standard real-time reverse transcriptase-polymerase chain reaction (RT-PCR) test for detecting a single positive sample of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within a pool of negative samples and to find out the maximum pool dilution limit up to which a single positive sample can be detected.\n\nMethodsRNA extracts from nasopharyngeal and oropharyngeal samples were pooled for the detection of the SARS-CoV-2 virus by RT-PCR. Positive samples were serially diluted in negative samples pools with dilutions ranging from 1/2 to 1/64 to estimate the optimal pool size. The viral transport medium (VTM) of three positive samples was also evaluated for optimal pool size determination.\n\nResultsA single positive sample with a Cycle threshold (Ct) value range from 16-23 (high viral load) can be detected in dilution pools upto1/64 for both genes. In pooling before RNA extraction, a positive sample with a low Ct value (13) and intermediate Ct value (25) was detected till 1/32 dilution pool but a positive sample with a high Ct value (32) was not detected further 1/4 dilution. Besides, two positive VTM samples were detected in pools of sizes 5, 8, and 10.\n\nConclusionsThis study concluded that sample testing by pooling is reliable if done properly and can help increase testing capacity in a low-resource setting.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Narayani Maharjan", - "author_inst": "Wuhan University Second Clinical Hospital: Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Niresh Thapa", - "author_inst": "Karnali Academy of Health Sciences" - }, - { - "author_name": "Bibek Pun Magar", - "author_inst": "Karnali Academy of Health Sciences" - }, - { - "author_name": "Muna Maharjan", - "author_inst": "Karnali Academy of Health Sciences" - }, - { - "author_name": "Jiancheng Tu", - "author_inst": "Wuhan University Second Clinical Hospital: Zhongnan Hospital of Wuhan University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.08.21.22278552", "rel_title": "Neutralizing Antibody to Omicron BA.1, BA.2 and BA.5 in COVID-19 Patients", @@ -251495,6 +253617,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.21.22279031", + "rel_title": "Neutrophil proteomics identifies temporal changes and hallmarks of delayed recovery in COVID19", + "rel_date": "2022-08-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.21.22279031", + "rel_abs": "RationaleNeutrophils are important in the pathophysiology of COVID19 but the molecular changes contributing to altered neutrophil phenotypes following SARS-CoV-2 infection are not fully understood.\n\nObjectivesTo use quantitative mass spectrometry-based proteomics to explore neutrophil phenotypes following acute SARS-CoV-2 infection and during recovery.\n\nMethodsProspective observational study of hospitalised patients with PCR-confirmed SARS-CoV-2 infection (May 2020-December 2020). Patients were enrolled within 96 hours of admission, with longitudinal sampling up to 29 days. Control groups comprised non-COVID19 acute lower respiratory tract infection (LRTI) and age-matched non-infected controls. Neutrophils isolated from peripheral blood were processed for mass spectrometry. COVID19 severity and recovery were defined using the WHO ordinal scale.\n\nMeasurements and Main Results84 COVID19 patients were included and compared to 91 LRTI patients and 42 controls. 5,800 neutrophil proteins were identified and 1,748 proteins were significantly different (q-value<0.05) in neutrophils from COVID19 patients compared to those of non-infected controls, including a robust interferon response at baseline, which was lost in severe patients one week after enrolment. Neutrophil changes associated with COVID19 disease severity and prolonged illness were characterized and candidate targets for modulation of neutrophil function were identified. Delayed recovery from COVID19 was associated with changes in metabolic and signalling proteins, complement, chemokine and leukotriene receptors, integrins and inhibitory receptors.\n\nConclusionsSARS-CoV-2 infection results in the sustained presence of recirculating neutrophils with distinct metabolic profiles and altered capacities to respond to migratory signals and cues from other immune cells, pathogens or cytokines.\n\nScientific Knowledge on the SubjectInflammation is the primary driver of morbidity and mortality in severe COVID19. Type I interferon responses, T-cell exhaustion, cytokine storm, emergency myelopoiesis, myeloid compartment dysregulation and procoagulant pathway activation are well established contributors to COVID19 disease severity. Neutrophils play an important role in COVID19, with elevated neutrophil-to-lymphocyte ratios and the emergence of a circulating immature neutrophil population in individuals with severe symptoms. Neutrophil infiltration in the lungs coupled with the release of neutrophil extracellular traps has also been reported in severe and fatal COVID19. The aim of this study was to quantitatively map the proteomes of peripheral blood neutrophils from a cohort of hospitalised COVID19 patients to understand how SARS-CoV-2 infection changes neutrophil phenotypes and functional capacity.\n\nWhat this study adds to the fieldHigh-resolution mass spectrometry was used to characterise the proteomes of peripheral blood neutrophils from >200 individuals at different stages of disease. This work has comprehensively mapped neutrophil molecular changes associated with mild and severe COVID19 and identified significant quantitative changes in more than 1700 proteins in neutrophils from patients hospitalised with COVID19 versus patients with non-COVID19 acute respiratory infections. The study identifies neutrophil protein signatures associated with COVID19 disease severity. The data also show that alterations in neutrophil proteomes can persist in fully recovered patients and identify distinct neutrophil proteomes in recovered versus non recovered patients. Our study provides novel insights into neutrophil responses during acute COVID19 and reveals that altered neutrophil phenotypes persist in convalescent COVID19 patients.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Merete B Long", + "author_inst": "University of Dundee" + }, + { + "author_name": "Andrew JM Howden", + "author_inst": "University of Dundee" + }, + { + "author_name": "Holly R Keir", + "author_inst": "University of Dundee" + }, + { + "author_name": "Christina M Rollings", + "author_inst": "University of Dundee" + }, + { + "author_name": "Yan Hui Giam", + "author_inst": "University of Dundee" + }, + { + "author_name": "Thomas Pembridge", + "author_inst": "University of Dundee" + }, + { + "author_name": "Hani Abo-Leyah", + "author_inst": "University of Dundee" + }, + { + "author_name": "Amy Lloyd", + "author_inst": "University of Dundee" + }, + { + "author_name": "Gabriel Sollberger", + "author_inst": "Max Planck Institute for infection biology" + }, + { + "author_name": "Rebecca Hull", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Amy Gilmour", + "author_inst": "University of Dundee" + }, + { + "author_name": "Chloe Hughes", + "author_inst": "University of Dundee" + }, + { + "author_name": "Benjamin JM New", + "author_inst": "NHS Tayside" + }, + { + "author_name": "Diane Cassidy", + "author_inst": "University of Dundee" + }, + { + "author_name": "Amelia Shoemark", + "author_inst": "University of Dundee" + }, + { + "author_name": "Hollian Richardson", + "author_inst": "University of Dundee" + }, + { + "author_name": "Angus I Lamond", + "author_inst": "University of Dundee" + }, + { + "author_name": "Doreen Cantrell", + "author_inst": "University of Dundee" + }, + { + "author_name": "James Chalmers", + "author_inst": "University of Dundee" + }, + { + "author_name": "Alejandro J Brenes", + "author_inst": "University of Dundee" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2022.08.22.504819", "rel_title": "The butterfly effect: mutational bias of SARS-CoV-2 affects its pattern of molecular evolution on synonymous and nonsynonymous levels", @@ -252030,77 +254247,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.08.18.22278939", - "rel_title": "Demographic and Outcome Characteristics of Children Hospitalized with Acute COVID-19 versus Multisystem Inflammatory Syndrome in Children in Canada", - "rel_date": "2022-08-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.18.22278939", - "rel_abs": "Direct comparisons of pediatric hospitalizations for acute COVID-19 and multisystem inflammatory syndrome in children (MIS-C) can inform health system planning. While there were more hospitalizations and deaths from acute COVID-19 amongst Canadian children between March 2020-May 2021, MIS-C cases were more severe, requiring more intensive care and vasopressor support.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Daniel Stephen Farrar", - "author_inst": "The Hospital for Sick Children" - }, - { - "author_name": "Charlotte Moore Hepburn", - "author_inst": "The Hospital for Sick Children" - }, - { - "author_name": "Olivier Drouin", - "author_inst": "CHU Sainte-Justine" - }, - { - "author_name": "Tala El Tal", - "author_inst": "The Hospital for Sick Children" - }, - { - "author_name": "Marie-Paule Morin", - "author_inst": "CHU Sainte-Justine" - }, - { - "author_name": "Roberta A. Berard", - "author_inst": "London Health Sciences Centre" - }, - { - "author_name": "Melanie King", - "author_inst": "Canadian Paediatric Society" - }, - { - "author_name": "Melanie Laffin Thibodeau", - "author_inst": "Canadian Paediatric Society" - }, - { - "author_name": "Elie Haddad", - "author_inst": "CHU Sainte-Justine" - }, - { - "author_name": "Rosie Scuccimarri", - "author_inst": "Montreal Children's Hospital and McGill University Health Centre" - }, - { - "author_name": "Rae S. M. Yeung", - "author_inst": "The Hospital for Sick Children" - }, - { - "author_name": "Fatima Kakkar", - "author_inst": "University of Montreal, CHU Sainte-Justine" - }, - { - "author_name": "Shaun K Morris", - "author_inst": "The Hospital for Sick Children" - }, - { - "author_name": "- Canadian Paediatric Surveillance Program COVID-19 Study Team", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.08.17.22278898", "rel_title": "Within-host genetic diversity of SARS-CoV-2 in the context of large-scale hospital-associated genomic surveillance", @@ -253229,6 +255375,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.08.15.22278787", + "rel_title": "The impact of the Covid-19 pandemic on Italian population-based cancer screening activities and test coverage: results from national cross-sectional repeated surveys", + "rel_date": "2022-08-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.15.22278787", + "rel_abs": "BackgroundIn Italy, population-based screening programs for breast, cervical and colorectal cancers are mandatory, and Regions are in charge of their delivery. From March to May 2020, a severe lockdown was imposed due to the Covid-19 pandemic by the Italian Ministry of Health, with the suspension of screening programs. This paper describes the impact of the pandemic on Italian screening activities and test coverage in 2020.\n\nMethodsThe regional number of subjects invited and of screening tests performed in 2020 were compared with those in 2019. Invitation and examination coverage were also calculated. PASSI surveillance system, through telephone interviews, investigated the population screening test coverage, before and during the pandemic, accordingly to educational attainment, perceived economic difficulties and citizenship.\n\nResultsA reduction of subjects invited and tests performed, with differences among periods and geographic macro areas, was observed in 2020 vs. 2019. The reduction in examination coverage was larger than that in invitation coverage for all screening campaigns. From the second half of 2020, the trend for test coverage showed a decrease in all the macro areas for all the screening campaigns. Compared with the pre-pandemic period, there was a greater difference according to level of education in the odds of having had a test last year vs. never having been screened or not being up to date with screening tests. In addition, foreigners had less access to screening than Italians did.\n\nConclusionsThe lockdown and the ongoing Covid-19 emergency caused an important delay in screening activities. This increased the pre-existing individual and geographical inequalities in access. The opportunistic screening did not mitigate the pandemic impact.\n\nFundingThis study was partially supported by Italian Ministry of Health - Ricerca Corrente Annual Program 2023.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Paolo Giorgi Rossi", + "author_inst": "Azienda Sanitaria Unit\u00e0 Locale di Reggio Emilia" + }, + { + "author_name": "Giuliano Carrozzi", + "author_inst": "Azienda Unit\u00e0 Sanitaria Locale - Modena" + }, + { + "author_name": "Patrizia Falini", + "author_inst": "Institute for cancer research, prevention and clinical network (ISPRO), Florence, Italy" + }, + { + "author_name": "Letizia Sampaolo", + "author_inst": "Azienda Unit\u00e0 Sanitaria Locale - Modena" + }, + { + "author_name": "Giuseppe Gorini", + "author_inst": "Institute for cancer research, prevention and clinical network (ISPRO), Florence, Italy" + }, + { + "author_name": "Manuel Zorzi", + "author_inst": "Registro Tumori del Veneto, Azienda Zero" + }, + { + "author_name": "Paola Armaroli", + "author_inst": "Centro di Prevenzione Oncologica, Azienda Ospedaliero-Universitaria Citt\u00e0 della Salute e della Scienza di Torino" + }, + { + "author_name": "Carlo Senore", + "author_inst": "Centro di Prevenzione Oncologica, Azienda Ospedaliero-Universitaria Citt\u00e0 della Salute e della Scienza di Torino" + }, + { + "author_name": "Priscilla Sassoli de Bianchi", + "author_inst": "Servizio Prevenzione Collettiva e Sanit\u00e0 Pubblica, Direzione Generale Cura della Persona, Salute e Welfare, Regione Emilia-Romagna" + }, + { + "author_name": "Maria Masocco", + "author_inst": "Istituto Superiore di Sanita, Rome" + }, + { + "author_name": "Marco Zappa", + "author_inst": "Retired, Institute for cancer research, prevention and clinical network (ISPRO), Florence, Italy" + }, + { + "author_name": "Francesca Battisti", + "author_inst": "Institute for cancer research, prevention and clinical network (ISPRO), Florence, Italy" + }, + { + "author_name": "Paola Mantellini", + "author_inst": "Institute for cancer research, prevention and clinical network (ISPRO), Florence, Italy" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.08.15.22278703", "rel_title": "Long-term changes in human mobility responses to COVID-19-related information in Japan", @@ -253716,109 +255929,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.08.14.22278762", - "rel_title": "The COVID HOME study research protocol: Prospective cohort study of non-hospitalised COVID-19 patients", - "rel_date": "2022-08-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.14.22278762", - "rel_abs": "BackgroundGuidelines on COVID-19 management are developed as we learn from this pandemic. However, most research has been done on hospitalised patients and the impact of the disease on non-hospitalised and their role in transmission are not yet well understood.\n\nThe COVID HOME study conducts research among COVID-19 patients and their family members who were not hospitalised during acute disease, to guide patient care and inform public health guidelines for infection prevention and control in the community and household.\n\nMethodsAn ongoing prospective longitudinal observational study of COVID-19 outpatients was established in March 2020 in the Netherlands. Laboratory confirmed SARS-CoV-2 infected individuals of all ages that did not merit hospitalisation, and their household (HH) members, were enrolled after written informed consent. Enrolled participants were visited at home within 48 hours after initial diagnosis, and then weekly on days 7, 14 and 21 to obtain clinical data, a blood sample for biochemical parameters/cytokines and serological determination; and a nasopharyngeal/throat swab plus urine, stool and sperm or vaginal secretion (if consenting) to test for SARS-CoV-2 by RT-PCR (viral shedding) and for viral culturing. Weekly nasopharyngeal/throat swabs and stool samples, plus a blood sample on days 0 and 21 were also taken from HH members to determine whether and when they became infected. All participants were invited to continue follow-up at 3-, 6-, 12- and 18-months post-infection to assess long-term sequelae and immunological status.\n\nPreliminary ResultsA total of 256 participants belonging to 103 HH were included of which, 190 (74.2%) were positive for SARS-CoV-2 infection. Most individuals (183/190, 96.3%) developed mild to moderate disease. At the time of writing, all participants had reached the 3 and 6 month time-points of the long-term follow-up, while approximately 78% reached 12 month and 23% the 18 month time-point. Preliminary analysis showed that 43% (52/121) positive individuals reported having complaints at 3 months post-infection, while 42.7% (61/143) had complaints at 6 months.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Adriana Tami", - "author_inst": "University Medical Centre Groningen: Universitair Medisch Centrum Groningen" - }, - { - "author_name": "Bernardina TF van der Gun", - "author_inst": "University Medical Centre Groningen: Universitair Medisch Centrum Groningen" - }, - { - "author_name": "Karin I Wold", - "author_inst": "University Medical Centre Groningen: Universitair Medisch Centrum Groningen" - }, - { - "author_name": "Maria F. Vincenti-Gonzalez", - "author_inst": "University Medical Centre Groningen: Universitair Medisch Centrum Groningen" - }, - { - "author_name": "Linda ACM Veloo", - "author_inst": "University Medical Centre Groningen: Universitair Medisch Centrum Groningen" - }, - { - "author_name": "Marjolein Knoester", - "author_inst": "University Medical Centre Groningen: Universitair Medisch Centrum Groningen" - }, - { - "author_name": "Valerie PR Harmsma", - "author_inst": "University Medical Centre Groningen: Universitair Medisch Centrum Groningen" - }, - { - "author_name": "Gerolf C de Boer", - "author_inst": "University Medical Centre Groningen: Universitair Medisch Centrum Groningen" - }, - { - "author_name": "Anke LW Huckriede", - "author_inst": "University Medical Centre Groningen: Universitair Medisch Centrum Groningen" - }, - { - "author_name": "Daniele Pantano", - "author_inst": "University Medical Centre Groningen: Universitair Medisch Centrum Groningen" - }, - { - "author_name": "Lilli Gard", - "author_inst": "University Medical Centre Groningen: Universitair Medisch Centrum Groningen" - }, - { - "author_name": "Izabela A Rodenhuis-Zybert", - "author_inst": "University Medical Centre Groningen: Universitair Medisch Centrum Groningen" - }, - { - "author_name": "Vinit Upasani", - "author_inst": "University Medical Centre Groningen: Universitair Medisch Centrum Groningen" - }, - { - "author_name": "Jolanda Smit", - "author_inst": "University Medical Centre Groningen: Universitair Medisch Centrum Groningen" - }, - { - "author_name": "Akkelies E Dijkstra", - "author_inst": "University Medical Centre Groningen: Universitair Medisch Centrum Groningen" - }, - { - "author_name": "Jacco J de Haan", - "author_inst": "University Medical Centre Groningen: Universitair Medisch Centrum Groningen" - }, - { - "author_name": "Jip M van Elst", - "author_inst": "University Medical Centre Groningen: Universitair Medisch Centrum Groningen" - }, - { - "author_name": "Jossy van den Boogaard", - "author_inst": "Rijksinstituut voor Volksgezondheid en Milieu Centrum Infectieziektebestrijding" - }, - { - "author_name": "Shennae O\u2019Boyle", - "author_inst": "London School of Hygiene and Tropical Medicine Faculty of Infectious and Tropical Diseases" - }, - { - "author_name": "Luis Nacul", - "author_inst": "London School of Hygiene and Tropical Medicine Department of Clinical Research" - }, - { - "author_name": "Bert HGM Niesters", - "author_inst": "University Medical Centre Groningen: Universitair Medisch Centrum Groningen" - }, - { - "author_name": "Alex W Friedriach", - "author_inst": "University Medical Centre Groningen: Universitair Medisch Centrum Groningen" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.08.13.22278733", "rel_title": "QCovid 4 - Predicting risk of death or hospitalisation from COVID-19 in adults testing positive for SARS-CoV-2 infection during the Omicron wave in England", @@ -254975,6 +257085,65 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.08.12.503750", + "rel_title": "Sphingosine kinases promote Ebola virus infection and can be targeted to inhibit filoviruses, coronaviruses, and arenaviruses using late endocytic trafficking to enter cells", + "rel_date": "2022-08-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.12.503750", + "rel_abs": "Entry of enveloped viruses in host cells requires the fusion of the viral and host cell membranes, a process that is facilitated by viral fusion proteins protruding from the viral envelope. For fusion, viral fusion proteins need to be triggered by host factors and for some viruses, such as Ebola virus (EBOV) and Lassa fever virus, this event occurs inside endosomes and/or lysosomes. Consequently, these late-penetrating viruses must be internalized and delivered to entry-conducive intracellular vesicles. Because endocytosis and vesicular trafficking are tightly regulated cellular processes, late penetrating viruses also depend on specific host factors, such as signaling molecules, for efficient viral delivery to the site of fusion, suggesting that these could be targeted for antiviral therapy. In this study, we investigated a role for sphingosine kinases (SKs) in viral entry and found that chemical inhibition of sphingosine kinase 1 (SK1) and/or SK2 and knockdown of SK1 or SK2, inhibited entry of EBOV into host cells. Mechanistically, inhibition of SK1 and/or SK2 prevented EBOV from reaching late-endosomes and lysosomes that are positive for the EBOV receptor, Niemann Pick C1 (NPC1). Furthermore, we present evidence that suggests the trafficking defect caused by SK1/2 inhibition occurs independently of S1P signaling through cell-surface S1PRs. Lastly, we found that chemical inhibition of SKs prevents entry of other late-penetrating viruses, including arenaviruses and coronaviruses, in addition to inhibiting infection by replication competent EBOV and SARS-CoV-2 in Huh7.5 cells. In sum, our results highlight an important role played by SKs in endocytic trafficking which can be targeted to inhibit entry of late-penetrating viruses. SK inhibitors could serve as a starting point for the development of broad-spectrum antiviral therapeutics.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Corina M Stewart", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Yuxia Bo", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Kathy Fu", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Mable Chan", + "author_inst": "University of Manitoba" + }, + { + "author_name": "Robert Kozak", + "author_inst": "Sunnybrook Health Sciences Center" + }, + { + "author_name": "Kim Yang-Ping Apperley", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Genevieve Laroche", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Andre Beauchemin", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Gary Kobinger", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Darwyn Kobasa", + "author_inst": "University of Manitoba" + }, + { + "author_name": "Marceline Cote", + "author_inst": "University of Ottawa" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.08.12.22278708", "rel_title": "Estimation of the Total Number of Infected Cases in the 5th Wave of COVID-19 in Hong Kong", @@ -255650,73 +257819,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.08.10.22278639", - "rel_title": "Humoral immune responses remain quantitatively impaired but improve qualitatively in anti-CD20 treated patients with multiple sclerosis after three or four COVID-19 vaccinations", - "rel_date": "2022-08-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.10.22278639", - "rel_abs": "BackgroundHumoral immune responses to COVID-19 vaccination are diminished in anti-CD20 treated patients with multiple sclerosis (pwMS). In healthy individuals, neutralizing antibodies against the SARS-CoV-2 Omicron variant are only detected after three COVID-19 vaccinations. It was hitherto unknown whether a third or fourth COVID-19 vaccination of anti-CD20 treated pwMS improves SARS-CoV-2 specific humoral immune responses, including neutralizing antibodies against Omicron.\n\nMethodsAnti-CD20 treated pwMS vaccinated two (n=61), three (n=57) or four (n=15) times and healthy controls (n=10) vaccinated thrice were included in a prospective cohort study. Anti-SARS-CoV-2 spike S1 IgG and IgA levels, maturation of SARS-CoV-2 IgG avidity, neutralizing capacity against the SARS-CoV-2 Omicron BA.2 variant and SARS-CoV-2 specific T cell responses were analyzed.\n\nResultsThe proportion of anti-CD20 treated pwMS with detectable SARS-CoV-2 S1 IgG was similar after the second (31/61, 50.8%), third (31/57, 54.4%) and fourth (8/15, 53.3%) vaccination. In pwMS with detectable SARS-CoV-2 IgG, the proportion with high affinity antibodies increased from the second (6/31, 19.4%) to the third (17/31, 54.8%) and fourth (6/8, 75%) vaccination. While none (0/10) of the anti-CD20 treated pwMS vaccinated twice had Omicron specific neutralizing antibodies, 3/10 (30%) pwMS vaccinated thrice and 3/5 (60%) pwMS vaccinated four times generated Omicron specific neutralizing antibodies.\n\nConclusionAlthough SARS-CoV-2 specific humoral immune responses remain quantitatively impaired, in those anti-CD20 treated pwMS who do develop SARS-CoV-2 antibodies, the functionality of SARS-CoV-2 antibodies, including neutralizing antibodies against Omicron, improves after three and four SARS-CoV-2 vaccinations, supporting current recommendations for one or two booster vaccination in anti-CD20 treated pwMS.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Carolin Otto", - "author_inst": "Department of Neurology, Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin and Humboldt-Universitaet zu Berlin, Berlin, Germa" - }, - { - "author_name": "Tatjana Schwarz", - "author_inst": "Institute of Virology, Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin and Humboldt-Universitaet zu Berlin, Berlin, Germany" - }, - { - "author_name": "Lara M Jeworowski", - "author_inst": "2Institute of Virology, Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin and Humboldt-Universitaet zu Berlin, Berlin, German" - }, - { - "author_name": "Marie L Schmidt", - "author_inst": "Institute of Virology, Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin and Humboldt-Universitaet zu Berlin, Berlin, Germany" - }, - { - "author_name": "Felix Walper", - "author_inst": "Institute of Virology, Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin and Humboldt-Universitaet zu Berlin, Berlin, Germany" - }, - { - "author_name": "Florence Pache", - "author_inst": "Department of Neurology, Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin and Humboldt-Universitaet zu Berlin, Berlin, Germa" - }, - { - "author_name": "Patrick Schindler", - "author_inst": "Department of Neurology, Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin and Humboldt-Universitaet zu Berlin, Berlin, Germa" - }, - { - "author_name": "Moritz Niederschweiberer", - "author_inst": "Department of Neurology, Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin and Humboldt-Universitaet zu Berlin, Berlin, Germa" - }, - { - "author_name": "Andi Krumbholz", - "author_inst": "Institute for Infection Medicine, Christian-Albrechts-Universitaet zu Kiel and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany" - }, - { - "author_name": "Ruben Rose", - "author_inst": "Institute for Infection Medicine, Christian-Albrechts-Universitaet zu Kiel and University Medical Center Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany" - }, - { - "author_name": "Christian Drosten", - "author_inst": "Institute of Virology, Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin and Humboldt-Universitaet zu Berlin, Berlin, Germany" - }, - { - "author_name": "Klemens Ruprecht", - "author_inst": "Department of Neurology, Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin and Humboldt-Universitaet zu Berlin, Berlin, Germa" - }, - { - "author_name": "Victor M Corman", - "author_inst": "Institute of Virology, Charite - Universitaetsmedizin Berlin, corporate member of Freie Universitaet Berlin and Humboldt-Universitaet zu Berlin, Berlin, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2022.08.10.22278638", "rel_title": "Assessment of COVID-19 Effect on the Health of Families in South-West, Nigeria", @@ -257361,6 +259463,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.09.22278505", + "rel_title": "Safety and Immunogenicity of Intradermal Administration of Fractional Dose CoronaVac(R), ChAdOx1 nCoV-19 and BNT162b2 as Primary Series Vaccination", + "rel_date": "2022-08-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.09.22278505", + "rel_abs": "There is a limited supply of COVID-19 vaccines, with less than 20% of eligible populations in low-income countries having received one dose. Intradermal delivery of fractional dose vaccines is one way to improve global vaccine access, but no studies have reported data on intradermal delivery of COVID-19 primary series vaccination. We conducted a pilot study to examine the safety and immunogenicity of three intradermal primary series regimens - heterologous regimen of CoronaVac and ChAdOx1 (CoronaVac-ChAdOx1), homologous regimen of ChAdOx1 (ChAdOx1-ChAdOx1), and homologous regimen of BNT162b2 (BNT162b2-BNT162b2). Each dose was 1/5th or 1/6th of the standard dose. Two additional exploratory arms of intradermal vaccination for the second dose following an intramuscular first dose of ChAdOx1 and BNT162b2 were included. Intradermal vaccination was found to be immunogenic and safe. The antibody responses generated by the intradermal primary series were highest in the BNT162b2 arms. The anti-receptor binding domain (anti-RBD) IgG concentration following fractional dose intradermal vaccination was similar to that of standard dose intramuscular vaccination of the same regimen, except for BNT162b2. The BNT162b2 intradermal series generated a lower antibody concentration than the reference intramuscular series, despite generating the highest antibody concentration of all three intradermal primary series regimens. Neutralizing antibody responses against the SARS-CoV-2 ancestral strain were consistent with what was observed for anti-RBD IgG, with lower titers for SARS-CoV-2 variants. The FRNT50 titers were lowest against the omicron variant, being undetectable (GMT[≤]10) in about a quarter of study participants. T-cell responses against spike- and nucleocapsid-membrane-open reading frame proteins were also detected following intradermal vaccination. Adverse effects following intradermal vaccination were generally comparable with post-intramuscular vaccination effects. Taken together, our data suggest that intradermal vaccination using 1/5th or 1/6th of standard COVID-19 intramuscular vaccination dosing generates similar immune responses with tendency of lower systemic adverse reactions than intramuscular vaccination. Our findings have implications in settings where COVID-19 vaccines are in shortage.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Somruedee Chatsiricharoenkul", + "author_inst": "Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand" + }, + { + "author_name": "Suvimol Niyomnaitham", + "author_inst": "Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand" + }, + { + "author_name": "H. Joshua Posen", + "author_inst": "Division of Infectious Diseases, Hospital for Sick Children, Toronto, Canada" + }, + { + "author_name": "Zheng Quan Toh", + "author_inst": "Murdoch Children Research Institute, Parkville, Victoria, Australia" + }, + { + "author_name": "Paul V Licciardi", + "author_inst": "Murdoch Children's Research Institute" + }, + { + "author_name": "Patimaporn Wongprompitak", + "author_inst": "Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand" + }, + { + "author_name": "Thaneeya Duangchinda", + "author_inst": "Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand" + }, + { + "author_name": "Pattarakul Pakchotanon", + "author_inst": "Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand" + }, + { + "author_name": "Warangkana Chantima", + "author_inst": "Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand" + }, + { + "author_name": "Kulkanya Chokephaibulkit", + "author_inst": "Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.08.09.22278555", "rel_title": "What rate of air filtration (ACH) can emulate protection of an N95 respirator in an unventilated room and how can it be checked?", @@ -258052,61 +260209,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.08.08.503267", - "rel_title": "COVID-19 pandemic responses may impact the spread of antibiotic-resistant bacteria: a modelling study", - "rel_date": "2022-08-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.08.503267", - "rel_abs": "Non-pharmaceutical interventions implemented to block SARS-CoV-2 transmission in early 2020 led to global reductions in the incidence of invasive pneumococcal disease (IPD). By contrast, most European countries reported an increase in antibiotic resistance among invasive Streptococcus pneumoniae isolates from 2019 to 2020, while an increasing number of studies reported stable pneumococcal carriage prevalence over the same period. To disentangle the impacts of the COVID-19 pandemic on pneumococcal epidemiology in the community setting, we propose a mathematical model formalizing simultaneous transmission of SARS-CoV-2 and antibiotic-sensitive and -resistant strains of S. pneumoniae. To test hypotheses underlying these trends five mechanisms were built in into the model and examined: (1) a population-wide reduction of antibiotic prescriptions in the community, (2) lockdown effect on pneumococcal transmission, (3) a reduced risk of developing an IPD due to the absence of common respiratory viruses, (4) community azithromycin use in COVID-19 infected individuals, (5) and a longer carriage duration of antibiotic-resistant pneumococcal strains. Among 31 possible pandemic scenarios involving mechanisms individually or in combination, model simulations surprisingly identified only two scenarios that reproduced the reported trends in the general population. They included factors (1), (3), and (4). These scenarios replicated a nearly 50% reduction in annual IPD, and an increase in antibiotic resistance from 20% to 22%, all while maintaining a relatively stable pneumococcal carriage. Exploring further, higher SARS-CoV-2 R0 values and synergistic within-host virus- bacteria interaction mechanisms could have additionally contributed to the observed antibiotic resistance increase. Our work demonstrates the utility of the mathematical modeling approach in unraveling the complex effects of the COVID-19 pandemic responses on AMR dynamics.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Aleksandra Kovacevic", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "David R. M. Smith", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Eve Rahb\u00e9", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Sophie Novelli", - "author_inst": "INSERM" - }, - { - "author_name": "Paul Henriot", - "author_inst": "CNAM: Conservatoire National des Arts et Metiers" - }, - { - "author_name": "Emmanuelle Varon", - "author_inst": "CNRP" - }, - { - "author_name": "Robert Cohen", - "author_inst": "ACTIV" - }, - { - "author_name": "Corinne Levy", - "author_inst": "ACTIV" - }, - { - "author_name": "Laura Temime", - "author_inst": "CNAM: Conservatoire National des Arts et Metiers" - }, - { - "author_name": "Lulla Opatowski", - "author_inst": "Institut Pasteur" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2022.08.08.22278547", "rel_title": "Infectiousness of SARS-CoV-2 breakthrough infections and reinfections during the Omicron wave", @@ -259395,6 +261497,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.06.503019", + "rel_title": "Evolutionary progression of collective mutations in Omicron sub-lineages towards efficient RBD-hACE2: allosteric communications between and within viral and human proteins", + "rel_date": "2022-08-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.06.503019", + "rel_abs": "The interaction between the Spike (S) protein of SARS-CoV-2 and the human angiotensin converting enzyme 2 (hACE2) is essential for infection, and is a target for neutralizing antibodies. Consequently, selection of mutations in the S protein is expected to be driven by the impact on the interaction with hACE2 and antibody escape. Here, for the first time, we systematically characterized the collective effects of mutations in each of the Omicron sub-lineages (BA.1, BA.2, BA.3 and BA.4) on both the viral S protein receptor binding domain (RBD) and the hACE2 protein using post molecular dynamics studies and dynamic residue network (DRN) analysis. Our analysis suggested that Omicron sub-lineage mutations result in altered physicochemical properties that change conformational flexibility compared to the reference structure, and may contribute to antibody escape. We also observed changes in the hACE2 substrate binding groove in some sub-lineages. Notably, we identified unique allosteric communication paths in the reference protein complex formed by the DRN metrics betweenness centrality and eigencentrality hubs, originating from the RBD core traversing the receptor binding motif of the S protein and the N-terminal domain of the hACE2 to the active site. We showed allosteric changes in residue network paths in both the RBD and hACE2 proteins due to Omicron sub-lineage mutations. Taken together, these data suggest progressive evolution of the Omicron S protein RBD in sub-lineages towards a more efficient interaction with the hACE2 receptor which may account for the increased transmissibility of Omicron variants.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Victor Barozi", + "author_inst": "Rhodes University" + }, + { + "author_name": "Adrienne L Edkins", + "author_inst": "Rhodes University" + }, + { + "author_name": "Ozlem Tastan Bishop", + "author_inst": "Rhodes University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.08.06.503050", "rel_title": "The Defenders of the Alveolus Succumb in COVID-19 Pneumonia to SARS-CoV-2, Necroptosis, Pyroptosis and Panoptosis", @@ -260070,41 +262199,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.08.05.22278480", - "rel_title": "Rapid threat detection in SARS-CoV-2", - "rel_date": "2022-08-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.05.22278480", - "rel_abs": "This paper presents a novel virus surveillance framework, completely independent of phylogeny-based methods. The framework issues timely alerts with an accuracy exceeding 85% that are based on the co-evolutionary relations between sites of the viral multiple sequence array (MSA). This set of relations is formalized via a motif complex, whose dynamics contains key information about the emergence of viral threats without the referencing of strain prevalence. Our notion of threat is centered at the emergence of a certain type of critical cluster consisting of key co-evolving sites. We present three case studies, based on GISAID data from UK, US and New York, where we perform our surveillance. We alert on May 16, 2022, based on GISAID data from New York, to a critical cluster of co-evolving sites mapping to the Pango-designation, BA.5. The alert specifies a cluster of seven genomic sites, one of which exhibits D3N on the M (membrane) protein-the distinguishing mutation of BA.5, three encoding ORF6:D61L and the remaining three exhibiting the synonymous mutations C26858T, C27889T and A27259C. New insight is obtained: when projected onto sequences, this cluster splits into two, mutually exclusive blocks of co-evolving sites (m:D3N,nuc:C27889T) linked to the five reverse mutations (nuc:C26858T,nuc:A27259C,ORF6:D61L). We furthermore provide an in depth analysis of all major signaled threats, during which we discover a specific signature concerning linked reverse mutation in the critical cluster.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Christopher L. Barrett", - "author_inst": "University of Virginia" - }, - { - "author_name": "Fenix W.D. Huang", - "author_inst": "University of Virginia" - }, - { - "author_name": "Thomas J.X. Li", - "author_inst": "University of Virginia" - }, - { - "author_name": "Andrew S. Warren", - "author_inst": "University of Virginia" - }, - { - "author_name": "Christian M. Reidys", - "author_inst": "University of Virginia" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.08.05.22278489", "rel_title": "Heterologous vaccination as a strategy to minimize inequity in COVID-19 vaccine access: A modeling study in Thailand", @@ -261665,6 +263759,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.08.03.22278013", + "rel_title": "Spatio-temporal characteristics of the SARS-CoV-2 Omicron variant spread at fine geographical scales, and comparison to earlier variants", + "rel_date": "2022-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.03.22278013", + "rel_abs": "For the long term control of an infectious disease such as COVID-19, it is crucial to identify the most likely individuals to become infected and the role that differences in demographic characteristics play in the observed patterns of infection. As high-volume surveillance winds down, testing data from earlier periods are invaluable for studying risk factors for infection in detail. Observed changes in time during these periods may then inform how stable the pattern will be in the long term.\n\nTo this end we analyse the distribution of cases of COVID-19 across Scotland in 2021, where the location (census areas of order 500-1,000 residents) and reporting date of cases are known. We consider over 450,000 individually recorded cases, in two infection waves triggered by different lineages: B.1.1.529 (\"Omicron\") and B.1.617.2 (\"Delta\"). We use random forests, informed by measures of geography, demography, testing and vaccination. We show that the distributions are only adequately explained when considering multiple explanatory variables, implying that case heterogeneity arose from a combination of individual behaviour, immunity, and testing frequency.\n\nDespite differences in virus lineage, time of year, and interventions in place, we find the risk factors remained broadly consistent between the two waves. Many of the observed smaller differences could be reasonably explained by changes in control measures.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Anthony J Wood", + "author_inst": "The Roslin Institute, University of Edinburgh" + }, + { + "author_name": "Aeron R Sanchez", + "author_inst": "The Roslin Institute, University of Edinburgh" + }, + { + "author_name": "Paul R Bessell", + "author_inst": "The Roslin Institute, University of Edinburgh" + }, + { + "author_name": "Rebecca Wightman", + "author_inst": "Edinburgh Medical School, University of Edinburgh" + }, + { + "author_name": "Rowland R Kao", + "author_inst": "Royal (Dick) School of Veterinary Studies, University of Edinburgh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.08.02.22278212", "rel_title": "One Health Genomic Surveillance and Response to a University-Based Outbreak of the SARS-CoV-2 Delta AY.25 Lineage, Arizona, 2021", @@ -262400,85 +264529,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.08.04.22278378", - "rel_title": "Viral Kinetics of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Omicron Infection in mRNA-Vaccinated Individuals Treated and Not Treated with Nirmatrelvir-Ritonavir", - "rel_date": "2022-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.04.22278378", - "rel_abs": "We measured viral kinetics of SARS-CoV-2 Omicron infection in 36 mRNA-vaccinated individuals, 11 of whom were treated with nirmatrelvir-ritonavir (NMV-r). We found that NMV-r was associated with greater incidence of viral rebound compared to no treatment. For those that did not rebound, NMV-r significantly reduced time to PCR conversion.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Eric Y. Dai", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Kannon A. Lee", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Audrey B. Nathanson", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Ariana T. Leonelli", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Brittany A Petros", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Taylor Brock-Fisher", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Sabrina T. Dobbins", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Bronwyn L. MacInnis", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Amelia Capone", - "author_inst": "Beth Israel Lahey Health Primary Care - Chelsea" - }, - { - "author_name": "Nancy Littlehale", - "author_inst": "Beth Israel Lahey Health Primary Care - Chelsea" - }, - { - "author_name": "Julie Boucau", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Caitlin Marino", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Amy K. Barczak", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Pardis C. Sabeti", - "author_inst": "Harvard University; The Broad Institute or MIT and Harvard; Howard Hughes Medical Institute" - }, - { - "author_name": "Michael Springer", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Kathryn E. Stephenson", - "author_inst": "Beth Israel Deaconess Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.08.04.22278204", "rel_title": "\"I don't know what to do or where to go\". experiences of accessing healthcare support from the perspectives of people living with Long Covid and healthcare professionals: A qualitative study in Bradford, UK.", @@ -263571,6 +265621,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.08.01.22278262", + "rel_title": "An integrated epidemiologic and economic model to assess optimal COVID-19 pandemic policy", + "rel_date": "2022-08-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.08.01.22278262", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSBackgroundC_ST_ABSIdentifying optimal COVID-19 policies is challenging. For Victoria, Australia (6.6 million people), we evaluated 104 policy packages (two levels of stringency of public health and social measures [PHSMs], by two levels each of mask-wearing and respirator provision during large outbreaks, by 13 vaccination schedules) for nine future SARS-CoV-2 variant scenarios.\n\nMethodsWe used an agent-based model to estimate morbidity, mortality, and costs over 12 months from October 2022 for each scenario. The 104 policies (each averaged over the nine future variant scenarios) were ranked based on four evenly weighted criteria: cost-effectiveness from (a) health system only and (b) health system plus GDP perspectives, (c) deaths and (d) days exceeding hospital occupancy thresholds.\n\nFindingsMore compared to less stringent PHSMs reduced cumulative infections, hospitalisations and deaths but also increased time in stage [≥]3 PHSMs. Any further vaccination from October 2022 decreased hospitalisations and deaths by 12% and 27% respectively compared to no further vaccination and was usually a cost-saving intervention from a health expenditure plus GDP perspective. High versus low vaccine coverage decreased deaths by 15% and reduced time in stage [≥]3 PHSMs by 20%. The modelled mask policies had modest impacts on morbidity, mortality, and health system pressure. The highest-ranking policy combination was more stringent PHSMs, two further vaccine doses (an Omicron-targeted vaccine followed by a multivalent vaccine) for [≥]30-year-olds with high uptake, and promotion of increased mask wearing (but not Government provision of respirators).\n\nInterpretationOngoing vaccination and PHSMs continue to be key components of the COVID-19 pandemic response. Integrated epidemiologic and economic modelling, as exemplified in this paper, can be rapidly updated and used in pandemic decision making.\n\nFundingAnonymous donation, University of Melbourne funding.\n\nAO_SCPLOWBSTRACTC_SCPLOW\n\nBackgroundIdentifying optimal COVID-19 policies is challenging. For Victoria, Australia (6.6 million people), we evaluated 104 policy packages: (a) two levels of stringency of public health and social measures (PHSMs; lower, higher), by (b) two levels each of mask wearing (low, high) and Government respirator provision (nil, yes) during large outbreaks (defined as when the projected number of people in hospital reached >270 or >130 per million population for lower and higher stringency PHSM settings respectively), by (c) 13 vaccination schedules (nil, and four combinations of low/high coverage for [≥]30/60-year-olds, each with an Omicron-targeted (OT) booster in the last quarter of 2022 followed by one of: nil, another OT booster in the second quarter of 2023, or a multivalent booster in the second quarter of 2023). These policies were modelled in the setting of nine future SARS-CoV-2 variant scenarios (no major new variant of concern and one of eight variants arriving in November 2022 with different virulence, antigenic, and immune escape profiles).\n\nMethodsWe used an agent-based model to estimate morbidity, mortality, and costs over 12 months from October 2022 for each scenario. The 104 policies (each averaged over the nine future variant scenarios) were ranked based on four evenly weighted criteria: cost-effectiveness from (a) health system only and (b) health system plus GDP perspectives (HALYs valued at AUD 70,000; discount rate 3%), (c) deaths and (d) days exceeding hospital occupancy thresholds.\n\nFindingsMore compared to less stringent PHSMs reduced cumulative infections, hospitalisations and deaths by an average of 25%, 24% and 24% respectively across 468 policy comparisons (other policy and variant scenarios held constant), but also increased time in stage [≥]3 (out of 5) PHSMs by an average of 42 days (23 days for low virulence and 70 days for high virulence variants).\n\nAny further vaccination from October 2022 decreased hospitalisations and deaths by 12% and 27% respectively compared to no further vaccination, however the cumulative number of infections increased by 10% due to vaccination preferentially decreasing hospitalisation rates that were used to dynamically set PHSM stages. Any further vaccination was of marginal cost-effectiveness from a health system perspective (an average of AUD 77,500 per HALY gained for vaccinating [≥]60-year-olds, and AUD 41,600 for 30- to 59-year-olds incremental to [≥]60-year-olds), but vaccination also resulted in 36% fewer days in Stage [≥]3 PHSMs usually making it a cost-saving intervention from a health expenditure plus GDP perspective. High versus low vaccine coverage reduced deaths by 15% and reduced time in Stage [≥]3 PHSMs by 20%.\n\nPromotion to increase mask wearing or government provision of respirators during large outbreaks reduced cumulative infections, hospitalisations and deaths over the 12 months by 1% to 2%, and reduced days with hospital occupancy exceeding 750 COVID-19 patients by 2% (4% to 5% in the context of highly virulent variants).\n\nThe highest-ranking policy combination was more stringent PHSMs, two further vaccine doses (an Omicron-targeted vaccine followed by a multivalent vaccine) for [≥]30-year-olds with high uptake, and promotion of increased mask wearing (but not Government provision of respirators).\n\nInterpretationOngoing vaccination and PHSMs continue to be key components of the COVID-19 pandemic response. Integrated epidemiologic and economic modelling, as exemplified in this paper, can be rapidly updated and used in pandemic decision making.\n\nFundingAnonymous donation, University of Melbourne funding.\n\nRO_SCPLOWESEARCHC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWINC_SCPLOWO_SCPCAP C_SCPCAPO_SCPLOWCONTEXTC_SCPLOW\n\nEvidence before this studyWe searched Ovid MEDLINE to 28 July 2022 for studies using the terms (economic evaluation.mp. OR cost effectiveness.mp. OR health economic*.mp.) AND (simulation.mp. OR model*.mp.) AND pandemic*.mp. to identify existing simulation modelling analyses of pandemic preparedness and response that incorporated cost effectiveness considerations. All identified literature examined pandemic influenza and COVID-19 and was highly heterogeneous in terms of modelled interventions (which included school closures, masks, hand hygiene, vaccination, testing strategies, antiviral medication, physical distancing measures, indoor ventilation, and personal protective equipment), quality, context, model structure, and economic evaluation approach.\n\nSystematic reviews of COVID-19 modelling studies that include a health economic component generally indicate that SARS-CoV-2 testing, personal protective equipment, masks, and physical distancing measures are cost-effective. However, few prior studies consider optimal packages of interventions (as opposed to standalone interventions), and none explicitly account for ongoing viral evolution or accurately capture the complexities of vaccine- or natural infection-derived immunity to SARS-CoV-2.\n\nFor example, a previous study integrating a dynamic SARS-CoV-2 transmission model with an economic analysis using a net monetary benefit approach published in early 2021 emphasized the combined public health and economic advantages of COVID-19 vaccination combined with physical distancing measures in the UK. However, considering current knowledge regarding the substantial waning of vaccine effectiveness and relatively low protection against infection conferred by vaccination (compared to more severe clinical outcomes), this model likely over-estimated the impact of COVID-19 vaccination on viral transmission. Scenarios that considered the emergence of SARS-CoV-2 variants of concern and thus associated changes in viral transmissibility, immune escape capacity (which has, in the case of the Omicron variant, greatly reduced protection following vaccination and prior infection) or virulence were also not modelled.\n\nAdded value of this studyTo our knowledge, our study is the first that utilises a dynamic disease transmission model combined with an integrated economic evaluation framework to systematically compare COVID-19 policy intervention packages while accounting for ongoing SARS-CoV-2 evolution and waning population immunity. At a high-level, we found that a considerable degree of COVID-19 disease burden should be expected in the future, with modelled interventions only able to partly mitigate pandemic-associated morbidity and mortality in the medium-term.\n\nAcross nine plausible future SARS-CoV-2 variant scenarios, higher stringency PHSMs notably reduced cumulative infections, hospitalisations and deaths in the 12-month period modelled but had the tradeoff of higher expected societal economic losses. Increasing community mask-wearing and substituting cloth and surgical masks for government supplied respirators during periods of high SARS-CoV-2 morbidity both reduced the number of days with hospital occupancy exceeding 750 COVID-19 patients by 2% on average across scenarios, and minimally reduced the cumulative infection, hospitalization and death burden. Compared to no further vaccines, the modelled vaccination schedules (with next-generation vaccines; one or two further doses) reduced hospitalisations by an average of 12%, and deaths by 27%. Vaccinating [≥]30-year-olds was modestly superior to just vaccinating [≥]60-year-olds (reducing cumulative deaths, for example, by 3.1%).\n\nConsidering all policy options together, and ranking by optimality on cost-effectiveness, health system pressure and deaths, the highest ranking policy combinations tended to be a mix of higher stringency PHSMs, promotion to increase mask wearing but no Government-funded respirator provision during large outbreaks, and the administration of two booster vaccine doses within the 12-month period to [≥]30-year-olds with associated high coverage (noting gains from vaccinating [≥]30-year-olds compared to [≥]60-year-olds were modest).\n\nImplications of all the available evidenceThe policy implications of this study are three-fold. Firstly, it reinforces the cost-effectiveness of ongoing vaccination of the public to mitigate morbidity and mortality associated with COVID-19. Secondly, the characteristics of emerging SARS-CoV-2 variants, outside the control of policy makers, will likely substantially influence public health outcomes associated with the pandemic in the future. Finally, at a phase of the pandemic characterised by growing intervention options urgently requiring prioritisation by decision makers alongside a large degree of ongoing uncertainty about future variants, this study provides a framework within which to systematically compare the health and economic benefits and burdens of packages of interventions that can be rapidly updated with new information (such as estimated effectiveness and waning kinetics of newly-developed vaccines) to support policy making.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Joshua Szanyi", + "author_inst": "Melbourne School of Population and Global Health, The University of Melbourne" + }, + { + "author_name": "Tim Wilson", + "author_inst": "Melbourne School of Population and Global Health, The University of Melbourne" + }, + { + "author_name": "Samantha Howe", + "author_inst": "Melbourne School of Population and Global Health, The University of Melbourne" + }, + { + "author_name": "Jessie Zeng", + "author_inst": "Melbourne School of Population and Global Health, The University of Melbourne" + }, + { + "author_name": "Hassan Andrabi", + "author_inst": "Melbourne School of Population and Global Health, The University of Melbourne" + }, + { + "author_name": "Shania Rossiter", + "author_inst": "Melbourne School of Population and Global Health, The University of Melbourne" + }, + { + "author_name": "Tony Blakely", + "author_inst": "Melbourne School of Population and Global Health, The University of Melbourne" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.08.02.22277351", "rel_title": "Development, testing and validation of a SARS-CoV-2 multiplex panel for detection of the five major variants of concern on a portable PCR platform", @@ -264141,73 +266234,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.08.02.502461", - "rel_title": "Omicron BA.2 breakthrough infection enhances cross-neutralization of BA.2.12.1 and BA.4/BA.5", - "rel_date": "2022-08-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.08.02.502461", - "rel_abs": "Recently, we reported that BNT162b2-vaccinated individuals after Omicron BA.1 breakthrough infection have strong serum neutralizing activity against Omicron BA.1, BA.2, and previous SARS-CoV-2 variants of concern (VOCs), yet less against the highly contagious Omicron sublineages BA.4 and BA.5 that have displaced previous variants. As the latter sublineages are derived from Omicron BA.2, we characterized serum neutralizing activity of COVID-19 mRNA vaccine triple-immunized individuals who experienced BA.2 breakthrough infection. We demonstrate that sera of these individuals have broadly neutralizing activity against previous VOCs as well as all tested Omicron sublineages, including BA.2 derived variants BA.2.12.1, BA.4/BA.5. Furthermore, applying antibody depletion we showed that neutralization of BA.2 and BA.4/BA.5 sublineages by BA.2 convalescent sera is driven to a significant extent by antibodies targeting the N-terminal domain (NTD) of the spike glycoprotein, whereas their neutralization by Omicron BA.1 convalescent sera depends exclusively on antibodies targeting the receptor binding domain (RBD). These findings suggest that exposure to Omicron BA.2, in contrast to BA.1 spike glycoprotein, triggers significant NTD specific recall responses in vaccinated individuals and thereby enhances the neutralization of BA.4/BA.5 sublineages. Given the current epidemiology with a predominance of BA.2 derived sublineages like BA.4/BA.5 and rapidly ongoing evolution, these findings are of high relevance for the development of Omicron adapted vaccines.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Alexander Muik", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Bonny Gaby Lui", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Maren Bacher", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Ann-Kathrin Wallisch", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Aras Toker", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Andrew Finlayson", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Kimberly Krueger", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Orkun Ozhelvaci", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Katharina Grikscheit", - "author_inst": "Institute for Medical Virology, University Hospital, Goethe University Frankfurt" - }, - { - "author_name": "Sebastian Hoehl", - "author_inst": "Institute for Medical Virology, University Hospital, Goethe University Frankfurt" - }, - { - "author_name": "Sandra Ciesek", - "author_inst": "Goethe Universtiy Frankfurt" - }, - { - "author_name": "Oezlem Tuereci", - "author_inst": "BioNTech SE" - }, - { - "author_name": "Ugur Sahin", - "author_inst": "BioNTech" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.08.02.502427", "rel_title": "UVC-based air disinfection system for rapid inactivation of SARS-CoV-2 present in the air", @@ -265324,6 +267350,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.28.22278142", + "rel_title": "Priority age targets for COVID-19 vaccination in Ethiopia under limited vaccine supply", + "rel_date": "2022-07-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.28.22278142", + "rel_abs": "BackgroundThe worldwide inequitable access to vaccination claims for a re-assessment of policies that could minimize the COVID-19 burden in low-income countries. An illustrative example is what occurred in Ethiopia, where nine months after the launch of the national vaccination program in March 2021, only 3% of the population received two doses of COVID-19 vaccine. In the meantime, a new wave of cases caused by the emergence of Delta variant of SARS-CoV-2 was observed between July and November 2021.\n\nMethodsWe used a SARS-CoV-2 transmission model to estimate the level of immunity accrued before the launch of vaccination in the Southwest Shewa Zone (SWSZ) and to evaluate the impact of alternative age priority vaccination targets in a context of limited vaccine supply. The model was informed with available epidemiological evidence and detailed contact data collected across different socio-demographic settings.\n\nResultsWe found that, during the first year of the pandemic, 46.1-58.7% of SARS-CoV-2 infections and 24.9-48% of critical cases occurred in SWSZ were likely associated with infectors under 30 years of age. During the Delta wave, the contribution of this age group in causing critical cases was estimated to increase to 66.7-70.6%. However, our findings suggest that, when considering the vaccine product available at the time (ChAdOx1 nCoV-19; 65% efficacy against infection after 2 doses), prioritizing the elderly for vaccination remained the best strategy to minimize the disease burden caused by Delta, irrespectively to the number of available doses. Vaccination of all individuals aged 50{square}years or older would have averted 40 (95%CI: 18-60), 90 (95%CI: 61-111), and 62 (95%CI: 21-108) critical cases per 100,000 residents in urban, rural, and remote areas, respectively. Vaccination of all individuals aged 30{square}years or more would have averted an average of 86-152 critical cases per 100,000 individuals, depending on the setting considered.\n\nConclusionsDespite infections among children and young adults likely caused 70% of critical cases during the Delta wave in SWSZ, most vulnerable ages should remain a key priority target for vaccination against COVID-19.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Margherita Galli", + "author_inst": "Fondazione Bruno Kessler" + }, + { + "author_name": "Agnese Zardini", + "author_inst": "Fondazione Bruno Kessler" + }, + { + "author_name": "Worku Nigussa Gamshie", + "author_inst": "Doctors with Africa CUAMM" + }, + { + "author_name": "Stefano Santini", + "author_inst": "Doctors with Africa CUAMM" + }, + { + "author_name": "Ademe Tsegaye", + "author_inst": "Doctors with Africa CUAMM" + }, + { + "author_name": "Filippo Trentini", + "author_inst": "Bocconi University" + }, + { + "author_name": "Valentina Marziano", + "author_inst": "Fondazione Bruno Kessler" + }, + { + "author_name": "Giorgio Guzzetta", + "author_inst": "Fondazione Bruno Kessler" + }, + { + "author_name": "Mattia Manica", + "author_inst": "Fondazione Bruno Kessler" + }, + { + "author_name": "Valeria d'Andrea", + "author_inst": "Fondazione Bruno Kessler" + }, + { + "author_name": "Giovanni Putoto", + "author_inst": "Doctors with Africa CUAMM" + }, + { + "author_name": "Fabio Manenti", + "author_inst": "Doctors with Africa CUAMM" + }, + { + "author_name": "Marco Ajelli", + "author_inst": "Indiana University School of Public Health, Bloomington, US" + }, + { + "author_name": "Piero Poletti", + "author_inst": "Bruno Kessler Foundation" + }, + { + "author_name": "Stefano Merler", + "author_inst": "Fondazione Bruno Kessler" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.07.28.22278141", "rel_title": "Seroprevalence of anti-SARS-CoV-2 IgG antibodies in Tyrol, Austria: Updated analysis involving 22,607 blood donors covering the period October 2021 to April 2022", @@ -265919,37 +268020,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.07.29.22278191", - "rel_title": "Has the pandemic enhanced and sustained digital health-seeking behaviour? A big-data interrupted time-series analysis of Google Trends", - "rel_date": "2022-07-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.29.22278191", - "rel_abs": "BackgroundDue to the emergency responses early in the pandemic, the use of digital health in healthcare increased abruptly, yet it remains unclear whether this introduction was sustainable on the long term. We explore trends in digital health-seeking behaviour as proxy for readiness to adopt digital health as a mainstream form of healthcare.\n\nMethodsWe use weekly Google Trends data from February 2019 to August 2021 in Canada, United States, United Kingdom, New Zealand, Australia, and Ireland. We used five keywords to monitor online search interests in Google Trends: online doctor, telehealth, online health, telemedicine, and health app. Data are analysed using an interrupted time-series analysis with break-points on 11 March 2020 and 20 December 2020.\n\nResultsDigital health searches immediately increased in all countries after the pandemic announcement. There was some variance in what keywords were used per country. However, searches declined after this immediate spike, sometimes towards pre-pandemic levels. The exception is the search volume of health app, which showed to either remain stable or gradually increase during the pandemic.\n\nInterpretationOur findings suggest that digital health-seeking behavioural patterns associated with the pandemic are currently not sustainable. Further building of digital health capacity and development of robust digital governance and literacy frameworks remain crucial to more structurally facilitate digital health transformation across countries.\n\nFundingNot applicable.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Robin van Kessel", - "author_inst": "Maastricht University" - }, - { - "author_name": "Ilias Kyriopoulos", - "author_inst": "London School of Economics and Political Science" - }, - { - "author_name": "Brian Li Han Wong", - "author_inst": "I-DAIR" - }, - { - "author_name": "Elias Mossialos", - "author_inst": "London School of Economics and Political Science" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.07.27.22278107", "rel_title": "Psychological impacts of COVID-19 outbreak in Ethiopia: a systematic review and meta-analysis", @@ -267106,6 +269176,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.07.28.22278138", + "rel_title": "An agent-based modelling framework for assessing SARS-CoV-2 indoor airborne transmission risk", + "rel_date": "2022-07-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.28.22278138", + "rel_abs": "We develop a framework for modelling the risk of infection from airborne Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in well-mixed environments in the presence of interventions designed to reduce infection risk. Our framework allows development of models that are highly tailored to the specifics of complex indoor environments, including layout, people movements, and ventilation. We explore its utility through case studies, two of which are based on actual sites.\n\nOur results reflect previously quantified benefits of masks and vaccinations. We also produce quantitative estimates of the effects of air filters, and reduced indoor occupancy for which we cannot find quantitative estimates but for which positive benefits have been postulated.\n\nWe find that increased airflow reduces risk due to dilution, even if that airflow is via recirculation in a large space. Our case studies have identified interventions which seem to generalise, and others which seem to be dependent on site-specific factors, such as occupant density.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Simon O Knapp", + "author_inst": "CSIRO" + }, + { + "author_name": "Rob Dunne", + "author_inst": "CSIRO" + }, + { + "author_name": "Bruce Tabor", + "author_inst": "CSIRO" + }, + { + "author_name": "Roslyn I Hickson", + "author_inst": "CSIRO" + }, + { + "author_name": "Simon Dunstall", + "author_inst": "CSIRO" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.07.29.502072", "rel_title": "Infection- or vaccine mediated immunity reduces SARS-CoV-2 transmission, but increases competitiveness of Omicron in hamsters", @@ -267933,45 +270038,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.07.28.501852", - "rel_title": "P2G3 human monoclonal antibody neutralizes SARS-CoV-2 Omicron subvariants including BA.4 and BA.5 and Bebtelovimab escape mutants", - "rel_date": "2022-07-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.28.501852", - "rel_abs": "The rapid evolution of SARS-CoV-2 has led to a severe attrition of the pool of monoclonal antibodies still available for COVID-19 prophylaxis or treatment. Omicron subvariants notably escape most antibodies developed so far, with Bebtelovimab last amongst clinically approved therapeutic antibodies to display still good activity against all of them including the currently dominant BA.4/BA.5. We recently described P2G3, a broadly active SARS-CoV-2 monoclonal antibody, which targets a region of Spike partly overlapping with the site recognized by Bebtelovimab. Here, we reveal that P2G3 efficiently neutralizes SARS-CoV-2 omicron subvariants including BA.4/BA.5. We further demonstrate that P2G3 neutralizes Omicron BA.2 and BA.4 mutants escaping Bebtelovimab blockade, whereas the converse is not true.\n\nFundingEU COVICIS program; private foundation advised by CARIGEST SA.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Priscilla Turelli", - "author_inst": "EPFL" - }, - { - "author_name": "Craig Fenwick", - "author_inst": "Lausanne University Hospital" - }, - { - "author_name": "Charlene Raclot", - "author_inst": "EPFL" - }, - { - "author_name": "Vanessa Genet", - "author_inst": "EPFL" - }, - { - "author_name": "Giuseppe Pantaleo", - "author_inst": "Lausanne University Hospital" - }, - { - "author_name": "Didier Trono", - "author_inst": "EPFL" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.07.28.501901", "rel_title": "Effect of Delta and Omicron mutations on the RBD-SD1 do-main of the Spike protein in SARS-CoV-2 and the Omicron mutations on RBD-ACE2 interface complex", @@ -268920,6 +270986,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, + { + "rel_doi": "10.1101/2022.07.25.22278025", + "rel_title": "Plasma proteomics of SARS-CoV-2 infection and severity reveals impact on Alzheimer and coronary disease pathways", + "rel_date": "2022-07-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.25.22278025", + "rel_abs": "Identification of the plasma proteomic changes of Coronavirus disease 2019 (COVID-19) is essential to understanding the pathophysiology of the disease and developing predictive models and novel therapeutics. We performed plasma deep proteomic profiling from 332 COVID-19 patients and 150 controls and pursued replication in an independent cohort (297 cases and 76 controls) to find potential biomarkers and causal proteins for three COVID-19 outcomes (infection, ventilation, and death). We identified and replicated 1,449 proteins associated with any of the three outcomes (841 for infection, 833 for ventilation, and 253 for death) that can be query on a web portal (https://covid.proteomics.wustl.edu/). Using those proteins and machine learning approached we created and validated specific prediction models for ventilation (AUC>0.91), death (AUC>0.95) and either outcome (AUC>0.80). These proteins were also enriched in specific biological processes, including immune and cytokine signaling (FDR [≤] 3.72x10-14), Alzheimers disease (FDR [≤] 5.46x10-10) and coronary artery disease (FDR [≤] 4.64x10-2). Mendelian randomization using pQTL as instrumental variants nominated BCAT2 and GOLM1 as a causal proteins for COVID-19. Causal gene network analyses identified 141 highly connected key proteins, of which 35 have known drug targets with FDA-approved compounds. Our findings provide distinctive prognostic biomarkers for two severe COVID-19 outcomes (ventilation and death), reveal their relationship to Alzheimers disease and coronary artery disease, and identify potential therapeutic targets for COVID-19 outcomes.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Carlos Cruchaga", + "author_inst": "Washington University School of Medicine, St Louis, MO, USA" + }, + { + "author_name": "Lihua Wang", + "author_inst": "Washington University School of Medicine, St Louis, MO, USA" + }, + { + "author_name": "Yun Ju Sung", + "author_inst": "Washington University School of Medicine, St Louis, MO, USA" + }, + { + "author_name": "Dan Western", + "author_inst": "Washington University School of Medicine, St Louis, MO, USA" + }, + { + "author_name": "Jigyasha Timsina", + "author_inst": "Washington University School of Medicine, St Louis, MO, USA" + }, + { + "author_name": "Charlie Repaci", + "author_inst": "Washington University School of Medicine, St Louis, MO, USA" + }, + { + "author_name": "Won-Min Song", + "author_inst": "Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA" + }, + { + "author_name": "Joanne Norton", + "author_inst": "Washington University School of Medicine, St Louis, MO, USA" + }, + { + "author_name": "Pat Kohlfeld", + "author_inst": "Washington University School of Medicine, St Louis, MO, USA" + }, + { + "author_name": "John Budde", + "author_inst": "Washington University School of Medicine, St Louis, MO, USA" + }, + { + "author_name": "Sharlee Climer", + "author_inst": "University of Missouri-St. Louis, St. Louis, MO, USA" + }, + { + "author_name": "Omar H. Bbut", + "author_inst": "Washington University School of Medicine, St Louis, MO, USA" + }, + { + "author_name": "Daniel A Jacobson", + "author_inst": "Oak Ridge National Laboratory" + }, + { + "author_name": "Michael R Garvin", + "author_inst": "UT-BATTELLE, LLC-OAK RIDGE NATIONAL LAB" + }, + { + "author_name": "Alan R. Templeton", + "author_inst": "Washington University School of Medicine, St Louis, MO, USA" + }, + { + "author_name": "Shawn Campagna", + "author_inst": "University of Tennessee, Knoxville, TN, USA" + }, + { + "author_name": "Jane O'Halloran", + "author_inst": "Washington University in St. Louis School of Medicine" + }, + { + "author_name": "Rachel Presti", + "author_inst": "Washington University School of Medicine, St Louis, MO, USA" + }, + { + "author_name": "Charles William Goss", + "author_inst": "Washington University in St. Louis School of Medicine" + }, + { + "author_name": "Philip A Mudd", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Beau M. Ances", + "author_inst": "Washington University School of Medicine, St Louis, MO, USA" + }, + { + "author_name": "Bin Zhang", + "author_inst": "Icahn School of Medicine at Mount Sinai, New York, New York, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.07.25.22277980", "rel_title": "Lowered quality of life in Long COVID is strongly predicted by affective symptoms and chronic fatigue syndrome which are associated with inflammatory processes during the acute infectious phase and consequent neuroimmunotoxic pathways.", @@ -269463,85 +271632,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.07.23.501235", - "rel_title": "Multi-omics integrated analysis reveals a specific phenotype of CD8+ T cell may contribute to immunothromosis via Th17 response in severe and critical COVID-19", - "rel_date": "2022-07-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.23.501235", - "rel_abs": "T lymphocyte reduction and immunosenescence frequently occur in severe and critical coronavirus disease 2019 (COVID-19) patients, which may cause immunothrombosis and numerous sequelae. This study integrated analyzed multi-omics data from healthy donors, pneumonia, COVID-19 patients (mild & moderate, severe, and critical), and convalescences, including clinical, laboratory test, PBMC bulk RNA-seq, PBMC scRNA-seq and TCR-seq, BAL scRNA-seq, and lung proteome. We revealed that there are certain associations among T lymphocyte reduction, CD8+ T cell senescence, Th17 immune activation, and immunothrombosis. A specific phenotype (S. P.) CD8+ T cells were identified in severe and critical COVID-19 patients in both PBMC and BAL scRNA-seq, which showed highly TCR homology with terminal effector CD8+ T cells and senescent CD8+ T cells. Pseudotime analysis showed that the S. P. CD8+ T cells were located in the transition trajectory from mild to severe disease. Which may be activated by terminal effector CD8+ T cells or senescent CD8+ T cells, thereby promoting Th17 cell differentiation. This phenomenon was absent in healthy donors, mild and moderate COVID-19 patients, or convalescences. Our findings are an important reference for avoiding the conversion of patients with mild to severe diseases and provide insight into the future prevention and control of COVID-19 and its variants.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Wen-Xing Li", - "author_inst": "School of Basic Medical Sciences, Southern Medical University" - }, - { - "author_name": "San-Qi An", - "author_inst": "Guangxi Medical University" - }, - { - "author_name": "Shao-Xing Dai", - "author_inst": "Kunming University of Science and Technology" - }, - { - "author_name": "Zhao-Ming Zhou", - "author_inst": "School of Public Health, Southern Medical University" - }, - { - "author_name": "Xin Zeng", - "author_inst": "School of Public Health, Southern Medical University" - }, - { - "author_name": "Guan-Hua Deng", - "author_inst": "Guangdong Sanjiu Brain Hospital" - }, - { - "author_name": "Ying-Ying Huang", - "author_inst": "Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences" - }, - { - "author_name": "Quan Yin", - "author_inst": "Southwest University" - }, - { - "author_name": "Ling-Yu Shen", - "author_inst": "Department of Nephrology, Zhujiang Hospital, Southern Medical University" - }, - { - "author_name": "An-Qi Xu", - "author_inst": "Department of Cerebrovascular Surgery, Zhujiang Hospital, Southern Medical University" - }, - { - "author_name": "Yao Lin", - "author_inst": "Guangxi Medical University" - }, - { - "author_name": "Jun-Jun Jiang", - "author_inst": "Guangxi Medical University" - }, - { - "author_name": "Wu Wei", - "author_inst": "Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences" - }, - { - "author_name": "Hao Liang", - "author_inst": "Guangxi Medical University" - }, - { - "author_name": "Dao-Gang Guan", - "author_inst": "School of Basic Medical Sciences, Southern Medical University" - }, - { - "author_name": "Cheng Zhou", - "author_inst": "Department of Radiation Oncology, Nanfang Hospital, Southern Medical University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2022.07.25.501370", "rel_title": "Poor sensitivity of iPSC-derived neural progenitors and glutamatergic neurons to SARS-CoV-2", @@ -270746,6 +272836,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2022.07.21.22277909", + "rel_title": "Early COVID-19 Pandemic Response in Western Visayas, Philippines", + "rel_date": "2022-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.21.22277909", + "rel_abs": "The COVID-19 pandemic has burdened the public health system in the Philippines since January 2020. In Western Visayas (Region 6), Philippines, issues have been raised on the limitations of the governments response on testing, contact tracing, and augmentation of healthcare facilities. Using data from the Western Visayas - Regional Epidemiologic Surveillance Unit (WV - RESU) from March 20 - June 20, 2020, the following observations were made: 1) Of the 6 provinces, Iloilo had the highest % tests done per capita which may be linked to the presence of the only regional COVID-19 testing facility in the province at that time, 2) There were delays in the overall processing times for specimens from Antique and Negros Occidental which may be linked to transport logistics and/or laboratory processing, 3) Contact tracing and testing were de-linked - tracing was adequate (3,420/3,503, 97.63%), but less than 50% of these (1,668/3,420) were tested, 4) Hospital and quarantine facility capacities were still adequate, but their utilization rates needed to be monitored continuously for further augmentation, if needed. This data shows the challenges of establishing a pandemic response in one of the regions in the Philippines.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Pia Regina Fatima Zamora", + "author_inst": "University of San Agustin" + }, + { + "author_name": "Jonathan Adam Rico", + "author_inst": "University of San Agustin" + }, + { + "author_name": "Dominic Karl Bolinas", + "author_inst": "University of the Philippines Manila" + }, + { + "author_name": "Jesus Emmanuel Sevilleja", + "author_inst": "National Center for Mental Health" + }, + { + "author_name": "Romulo de Castro", + "author_inst": "University of San Agustin" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.07.19.22277801", "rel_title": "How the Malian press treated hydroxychloroquine at the beginning of the COVID-19 pandemic", @@ -271193,109 +273318,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.07.21.501031", - "rel_title": "Suppression of systemic T cell immunity to viral infection during liver injury is prevented by inhibition of interferon and IL-10 signaling", - "rel_date": "2022-07-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.21.501031", - "rel_abs": "Patients with liver injury such as cirrhosis are at increased risk of intractable viral infections and are hyporesponsive to vaccination. Here, we report that liver injury leads to inhibition of systemic T cell immunity (LIST), which abrogated anti-viral immunity and caused persistent infection in preclinical liver injury models. Enhanced gut microbial-translocation but not dysbiosis induced tonic type-I-interferon (IFN) signaling in hepatic myeloid cells, which was responsible for their excessive production of IL-10 after viral infection. Antibiotic treatment reducing intestinal microbial burden or inhibition of IFN- and IL-10-signaling all restored anti-viral immunity without immune pathology. Importantly, inhibition of IL-10 restored virus-specific immune responses to vaccination in cirrhotic patients. Thus, LIST results from sequential events involving intestinal microbial translocation, hepatic myeloid cell-derived IFN-/IL-10 expression, and finally inhibitory IL-10 receptor-signaling in T cells, of which IL-10R-signaling may serve as target to reconstitute anti-viral T cell immunity in cirrhotic patients.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Philipp Carl Hackstein", - "author_inst": "Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, UK and 1Institute of Molecular Medicine and Experimental Im" - }, - { - "author_name": "Jasper Spitzer", - "author_inst": "Institute of Innate Immunity, University Hospital Bonn, Germany" - }, - { - "author_name": "Konstantinos Symeonidis", - "author_inst": "Institute of Molecular Medicine and Experimental Immunology, University Hospital Bonn, Germany" - }, - { - "author_name": "Helena Horvatic", - "author_inst": "Institute of Molecular Medicine and Experimental Immunology, University Hospital Bonn, Germany" - }, - { - "author_name": "Tanja Bedke", - "author_inst": "Medizinische Klinik und Poliklinik, Hamburg Center for Translational Immunology (HCTI), Universitaetsklinikum Hamburg-Eppendorf, Hamburg, Germany" - }, - { - "author_name": "Babett Steglich", - "author_inst": "Universitaetsklinikum Hamburg-Eppendorf, Hamburg, Germany" - }, - { - "author_name": "Lisa Assmus", - "author_inst": "Institute of Molecular Medicine and Experimental Immunology, University Hospital Bonn, Germany" - }, - { - "author_name": "Alexandru Odainic", - "author_inst": "2Institute of Innate Immunity, University Hospital Bonn, Germany" - }, - { - "author_name": "Nina Kessler", - "author_inst": "University of Bonn" - }, - { - "author_name": "Sabine Klein", - "author_inst": "Medizinische Klinik 1. Universitaetsklinikum Frankfurt. Goethe Universitaet. Germany" - }, - { - "author_name": "Marc Beyer", - "author_inst": "DZNE, Bonn, Germany" - }, - { - "author_name": "Ricarda Schmithausen", - "author_inst": "University Hospital Bonn, Germany" - }, - { - "author_name": "Eicke Latz", - "author_inst": "University Hospital Bonn: Universitatsklinikum Bonn" - }, - { - "author_name": "Christian Kurts", - "author_inst": "University Hospital Bonn" - }, - { - "author_name": "Jonel Trebicka", - "author_inst": "Medizinische Klinik 1. Universitaetsklinikum Frankfurt. Goethe Universitaet, Germany" - }, - { - "author_name": "Richard Flavell", - "author_inst": "Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA" - }, - { - "author_name": "Natalio Garbi", - "author_inst": "Institute of Molecular Medicine and Experimental Immunology, University of Bonn" - }, - { - "author_name": "Axel Roers", - "author_inst": "Institute of Immunology, University of Heidelberg, Germany" - }, - { - "author_name": "Samuel Huber", - "author_inst": "Universitatsklinikum Hamburg-Eppendorf" - }, - { - "author_name": "Susanne Schmidt", - "author_inst": "2Institute of Innate Immunity, University Hospital Bonn, Germany" - }, - { - "author_name": "Percy Knolle", - "author_inst": "Institute of Molecular Immunology and Experimental Oncology, Technical University of Munich, Germany" - }, - { - "author_name": "Zeinab Abdullah", - "author_inst": "1Institute of Molecular Medicine and Experimental Immunology, University Hospital Bonn, Germany" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.07.21.500931", "rel_title": "Decoding the Effects of Spike Receptor Binding Domain Mutations on Antibody Escape Abilities of Omicron Variants", @@ -272456,6 +274478,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.07.19.22277798", + "rel_title": "Co-designing an intervention to strengthen vaccine uptake in Congolese migrants in the UK (LISOLO MALAMU): a participatory study protocol", + "rel_date": "2022-07-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.19.22277798", + "rel_abs": "IntroductionAdult migrants are at risk of under-immunisation and are likely to need catch-up vaccination to bring them in line with the UK schedule. The COVID-19 pandemic has highlighted and exacerbated inequities in vaccine uptake, with migrants facing additional barriers to information, low vaccine confidence, and access to vaccine services. There is a need for participatory and theory-based research that meaningfully engages underserved migrant groups to make sense of their experiences and beliefs about vaccination and uses these insights to co-produce tailored interventions which can increase uptake. COVID-19 vaccination provides a unique entry-point and opportunity to explore these issues in tandem with addressing routine immunisation gaps and developing more culturally-sensitive routine vaccination services.\n\nMethods and analysisLISOLO MALAMU ( Good Talk) is a community-based participatory research study which uses co-design, design thinking and behaviour change theory to engage adult Congolese migrants in developing a tailored intervention to increase vaccine uptake. A community-academic coalition will lead and co-design the study. The study will involve i) in-depth interviews with adult Congolese migrants (foreign-born, >18 years), ii-iii) interviews and consensus workshops with clinical, public health and community stakeholders, and iv) co-design workshops with adult Congolese migrants. Qualitative data will be analysed iteratively, using Thematic Analysis, and mapped to the Theoretical Domains Framework, with participation from the coalition in discussing and interpreting findings and selecting intervention functions to guide the co-design workshops. Sociodemographic data of interview participants will be summarised using descriptive statistics. The study will run from approximately November 2021-November 2022.\n\nEthics and disseminationEthics approval has been granted by the St Georges University Research Ethics Committee (REC reference 2021.0128). Study findings will be widely disseminated by the coalition through local community organisations in Hackney and broader academic and policy stakeholders, including a final celebration event. Recommendations for a future larger scale study and testing of prototyped interventions will be made.\n\nStrengths and limitations of this study\n\nStrengthsO_LIThis study will directly respond to ongoing calls for community-centred and participatory approaches to engaging migrants in routine and COVID-19 vaccination, by implementing a value-driven and reciprocal approach to conducting a study addressing the needs of an underserved community.\nC_LIO_LIThe target population was selected following a comprehensive systematic review of the evidence (1) and pre-engagement scoping work conducted with migrant community representatives in London, UK. (2, 3)\nC_LIO_LIIt aims to co-produce a tailored intervention to address specific barriers to, and strengthen, vaccine uptake for COVID-19 and routine vaccines in adult Congolese migrants (including MMR, Td/IPV, and HPV) as set out by UKHSA guidance (4), and has been co-designed with, and will be co-delivered by, a coalition formed of academic researchers, a council for voluntary service (a local charity which offers services and support for local voluntary and community organisations), and a Congolese community-based organisation.\nC_LI\n\nLimitationsO_LIAs this study is tailored to the Congolese migrant population, other migrants who also face barriers to vaccine uptake are not included. Whilst we can draw some conclusions about the experiences of other Black migrants who face similar historical and cultural barriers to uptake of routine and COVID-19 vaccines, our ability to generalise the findings to all migrant communities might be limited.\nC_LIO_LICo-designed intervention prototypes will not be formally implemented and evaluated in this study, however recommendations will be made so that this can be done in a future phase.\nC_LI", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Alison F Crawshaw Ms", + "author_inst": "St George's, University of London" + }, + { + "author_name": "Caroline Hickey Ms", + "author_inst": "Hackney CVS" + }, + { + "author_name": "Laura Muzinga Lutumba", + "author_inst": "Hackney Congolese Women Support Group" + }, + { + "author_name": "Lusau Mimi Kitoko", + "author_inst": "Hackney Congolese Women Support Group" + }, + { + "author_name": "Sarah Luti Nkembi", + "author_inst": "Hackney Congolese Women Support Group" + }, + { + "author_name": "Felicity Knights", + "author_inst": "St George's, University of London" + }, + { + "author_name": "Yusuf Ciftci", + "author_inst": "Doctors of the World UK" + }, + { + "author_name": "Lucy P Goldsmith", + "author_inst": "St George's, University of London" + }, + { + "author_name": "Tushna Vandrevala", + "author_inst": "Kingston University and St George's" + }, + { + "author_name": "Alice S Forster", + "author_inst": "Our Future Health" + }, + { + "author_name": "Sally Hargreaves", + "author_inst": "St George's, University of London" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.07.18.22277769", "rel_title": "Impact of SARS-Cov-2 on Clinical Trial Unit Staff: The EPIC Observational Study", @@ -273011,61 +275092,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.07.18.500565", - "rel_title": "The First Geographic Identification by Country of Sustainable Mutations of SARS-COV-2 Sequence Samples: Worldwide Natural Selection Trends", - "rel_date": "2022-07-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.18.500565", - "rel_abs": "The high mutation rates of RNA viruses, coupled with short generation times and large population sizes, allow viruses to evolve rapidly and adapt to the host environment. The rapidity of viral mutation also causes problems in developing successful vaccines and antiviral drugs. With the spread of SARS-CoV-2 worldwide, thousands of mutations have been identified, some of which have relatively high incidences, but their potential impacts on virus characteristics remain unknown. The present study analyzed mutation patterns, SARS-CoV-2 AASs retrieved from the GISAID database containing 10,500,000 samples. Python 3.8.0 programming language was utilized to pre-process FASTA data, align to the reference sequence, and analyze the sequences. Upon completion, all mutations discovered were categorized based on geographical regions and dates. The most stable mutations were found in nsp1(8% S135R), nsp12(99.3% P323L), nsp16 (1.2% R216C), envelope (30.6% T9I), spike (97.6% D614G), and Orf8 (3.5% S24L), and were identified in the United States on April 3, 2020, and England, Gibraltar, and, New Zealand, on January 1, 2020, respectively. The study of mutations is the key to improving understanding of the function of the SARS-CoV-2, and recent information on mutations helps provide strategic planning for the prevention and treatment of this disease. Viral mutation studies could improve the development of vaccines, antiviral drugs, and diagnostic assays designed with high accuracy, specifically useful during pandemics. This knowledge helps to be one step ahead of new emergence variants.\n\nIMPORTANCEMore than two years into the global COVID-19 pandemic, the focus of attention is shifted to the emergence and spread of the SARS-CoV-2 variants that cause the evolutionary trend.\n\nHere, we analyzed and compared about 10.5 million sequences of SARS-CoV-2 to extract the stable mutations, frequencies and the substitute amino acid that changed with the wild-type one in the evolutionary trend.\n\nAlso, developing and designing accurate vaccines could prepare long-term immunization against different local variants. In addition, according to the false negative results of the COVID-19 PCR test report in the diagnosis of new strains, investigating local mutation patterns could help to design local primer and vaccine.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "mohammadamin Mahmanzar", - "author_inst": "University of Hawaii John A. Burns School of Medicine" - }, - { - "author_name": "Seyed Taleb Houseini", - "author_inst": "Islamic Azad University, Mazandaran, Iran" - }, - { - "author_name": "Karim Rahimian", - "author_inst": "Tarbiat Modares University" - }, - { - "author_name": "Arsham Mikaeili Namini", - "author_inst": "Kharazmi University" - }, - { - "author_name": "Amir Gholamzad", - "author_inst": "Islamic Azad University Medical Branch of Tehran" - }, - { - "author_name": "Samaneh Tokhanbigli", - "author_inst": "Islamic Azad University Pharmaceutical Sciences Branch" - }, - { - "author_name": "Mahsa Mollapour Sisakht", - "author_inst": "ErasmusMC" - }, - { - "author_name": "Amin Farhadi", - "author_inst": "Payame Noor University" - }, - { - "author_name": "Donna Lee Kuehu", - "author_inst": "University of Hawaii John A. Burns School of Medicine" - }, - { - "author_name": "Youping Deng", - "author_inst": "University of Hawaii John A. Burns School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2022.07.18.500332", "rel_title": "Neutralizing antibody evasion and receptor binding features of SARS-CoV-2 Omicron BA.2.75", @@ -274358,6 +276384,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2022.07.15.22276814", + "rel_title": "Assessment of COVID-19 hospitalization risk during SARS-CoV-2 Omicron relative to Delta variant predominance, New York City, August 2021-January 2022", + "rel_date": "2022-07-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.15.22276814", + "rel_abs": "ImportanceAssessing relative disease severity of SARS-CoV-2 variants in populations with varied vaccination and infection histories can help characterize emerging variants and support healthcare system preparedness.\n\nObjectiveTo assess COVID-19 hospitalization risk for patients infected with Omicron (BA.1 and sublineages) compared with Delta SARS-CoV-2 variants.\n\nDesignObservational cohort study.\n\nSettingNew York City Department of Health and Mental Hygiene population-based COVID-19 disease registry, linked with laboratory results, immunization registry, and supplemental hospitalization data sources.\n\nParticipantsNew York City residents with positive laboratory-based SARS-CoV-2 tests during August 2021-January 2022. A secondary analysis restricted to patients with whole-genome sequencing results, comprising 1%-18% of weekly confirmed cases.\n\nExposuresDiagnosis during periods when [≥]98% of sequencing results were Delta (August-November 2021) or Omicron (January 2022). A secondary analysis defined variant exposure using patient-level sequencing results.\n\nMain outcomes and measuresCOVID-19 hospitalization, defined as a positive SARS-CoV-2 test 14 days before or 3 days after hospital admission.\n\nResultsAmong 646,852 persons with a positive laboratory-based SARS-CoV-2 test, hospitalization risk was lower for patients diagnosed when Omicron predominated (16,025/488,053, 3.3%) than when Delta predominated (8,268/158,799, 5.2%). In multivariable analysis adjusting for demographic characteristics and prior diagnosis and vaccination status, patients diagnosed when Omicron relative to Delta predominated had 0.72 (95% confidence interval [CI]: 0.63, 0.82) times the hospitalization risk. In a secondary analysis of 55,138 patients with sequencing results, hospitalization risk was similar for patients infected with Omicron (2,042/29,866, 6.8%) relative to Delta (1,780/25,272, 7.0%) and higher among those who received two mRNA vaccine doses (adjusted relative risk 1.64, 95% CI: 1.44, 1.87).\n\nConclusions and relevanceIllness severity was lower for patients diagnosed when Omicron (BA.1 and sublineages) relative to Delta predominated. This finding was consistent after adjusting for prior diagnosis and vaccination status, suggesting intrinsic virologic properties, not population-based immunity, accounted for the lower severity. A secondary analysis demonstrated collider bias from the sequencing sampling frame changing over time in ways associated with disease severity. Investing in representative data collection is necessary to avoid bias in assessing relative disease severity as new variants emerge, immunity wanes, and additional COVID-19 vaccines are administered.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Sharon K. Greene", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Alison K. Levin-Rector", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Elizabeth Luoma", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Helly Amin", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Emily McGibbon", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Robert W. Mathes", + "author_inst": "New York City Department of Health and Mental Hygiene" + }, + { + "author_name": "Shama D. Ahuja", + "author_inst": "New York City Department of Health and Mental Hygiene" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.07.16.22277702", "rel_title": "Extended compartmental model for modeling COVID-19 epidemic in Slovenia", @@ -274793,37 +276862,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.07.15.22277675", - "rel_title": "COVID-19 Prevention at Institutions of Higher Education, United States, 2020 -- 2021: Implementation of Nonpharmaceutical Interventions", - "rel_date": "2022-07-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.15.22277675", - "rel_abs": "BackgroundIn early 2020, following the start of the coronavirus disease 2019 (COVID-19) pandemic, institutions of higher education (IHEs) across the United States rapidly pivoted to distance learning to reduce risk of on-campus virus transmission.\n\nObjectiveTo explore IHE use of nonpharmaceutical interventions (NPIs) during the subsequent pandemic-affected academic year 2020-2021.\n\nDesignCross-sectional study of data collected January - June 2021. Setting: US four-year, undergraduate IHEs.\n\nPatients (or Participants)All public (n=547) and a stratified random sample of private (n=300) IHEs.\n\nMeasurementsFrom IHE websites, we documented NPIs, including changes to the calendar, learning environment, housing, common areas, and dining; COVID-19 testing; and facemask protocols, and performed weighted analysis to assess congruence with the US Centers for Disease Control and Prevention (CDC) guidance for IHEs. We used weighted multivariable linear regression to explore the association between IHE characteristics and the summated number of implemented NPIs.\n\nResultsOverall, 20% of IHEs implemented all surveyed CDC-recommended NPIs. The most frequently utilized were learning environment changes (91%), practiced as one or more of the following: distance or hybrid learning opportunities (98%), 6-feet spacing (60%), and reduced class sizes (51%). Additionally, 88% of IHEs specified facemask protocols, 78% physically modified common areas, and 67% offered COVID-19 testing. Among the 33% of IHEs offering [≥]50% of courses in person, having <1,000 students was associated with having implemented fewer NPIs than IHEs with [≥]1,000 students.\n\nLimitationsData collected from publicly available sources may introduce observation biases but allow for large sample size.\n\nConclusionOnly 1 in 5 IHEs implemented all surveyed CDC recommendations, while a majority implemented a subset. IHE size and location were associated with degree of NPI implementation. Additional research is needed to assess adherence to NPI implementation in IHE settings.\n\nFunding SourceUnited States Centers for Disease Control and Prevention", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Sarah Moreland", - "author_inst": "Centers for Disease Control and Prevention, Oak Ridge Institute for Science and Education" - }, - { - "author_name": "Nicole Zviedrite", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Faruque Ahmed", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Amra Uzicanin", - "author_inst": "Centers for Disease Control and Prevention" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.07.15.22277665", "rel_title": "Differential symptoms among COVID-19 outpatients before and during periods of SARS-CoV-2 Omicron variant dominance in Blantyre, Malawi: a prospective observational study", @@ -276536,6 +278574,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.12.22277539", + "rel_title": "Vaccine, Booster and Natural Antibody Binding to SARS-CoV-2 Omicron (BA.1) Spike Protein and Vaccine Efficacy", + "rel_date": "2022-07-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.12.22277539", + "rel_abs": "The SARS-CoV-2 Omicron variant (BA.1) has 25 unique mutations to the Spike glycoprotein, suggesting the efficacy of current vaccines against the new variant may be seriously degraded. A fully quantitative antibody binding study was performed for Spike Omicron (SO) and original Spike (S) proteins simultaneously on three cohorts of patients: convalescent following RT-PCR-confirmed infection in early 2020, double-vaccinated at [≥]2 weeks, and vaccine boosters. The average (mode) of the booster cohort response distributions were 15.1 mg/L and 13.4 mg/L for S and SO, respectively, compared with the significantly lower double-vaccinated average, S=2.4 mg/L, SO=2.0 mg/L, and natural infections average S=2.0 mg/L, SO = 1.8 mg/L. A preliminary epitope degradation screen was performed for a panel of antibodies raised to the S1 and S2 regions of the original S protein. The panel showed significant degradation to antibody epitopes in the S1 region. Differential antibody binding of the vaccine response to S and SO suggests vaccine efficacy may be reduced by up to 50% against the Omicron variant.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Philip H James-Pemberton", + "author_inst": "University of Exeter" + }, + { + "author_name": "Mark W Helliwell", + "author_inst": "Attomarker Ltd" + }, + { + "author_name": "Rouslan V Olkhov", + "author_inst": "Attomarker Ltd" + }, + { + "author_name": "Shivali Kohli", + "author_inst": "Attomarker Ltd" + }, + { + "author_name": "Aaron C Westlake", + "author_inst": "Attomarker Ltd" + }, + { + "author_name": "Benjamin M Farrar", + "author_inst": "Attomarker Ltd" + }, + { + "author_name": "Ben J Sutton", + "author_inst": "Attomarker Ltd" + }, + { + "author_name": "Nicholas D Ager", + "author_inst": "Attomarker Ltd" + }, + { + "author_name": "Andrew M Shaw", + "author_inst": "University of Exeter" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.07.13.22277580", "rel_title": "Procalcitonin for Antimicrobial Stewardship Among Cancer Patients Admitted with COVID-19", @@ -277011,33 +279100,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.07.14.22277622", - "rel_title": "Application of Carleman approximants for the estimation of epidemic parameters from incidence data time-series", - "rel_date": "2022-07-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.14.22277622", - "rel_abs": "We have analyzed the possibility of estimating epidemiological parameters from daily infection incidence data. In particular, we have focused on the determination of the instantaneous reproduction number, the contagion period and the duration of the infectious period using only the reported incidence time-series information. We have developed a data-driven method based on the instantaneous mapping of the infection incidence data on the simplest (two parameter) SIR model, along the progression of an epidemy. The mapping is carried out via Carleman linearization of the non-linear model equations. We concluded that the daily infection incidence series on its own does not carry enough information to provide estimates for the above time scales and hence additional measurements and/or hypotheses must be considered. In contrast, the prevalence time-series does allow for accurate estimates. For the case in which the characteristic infectious period is available, a new algebraic formula for the instantaneous reproduction number has been derived.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Juan C. Mu\u00f1oz-S\u00e1nchez", - "author_inst": "Institute for Integrative Systems Biology and Theoretical Physics Department of University of Valencia" - }, - { - "author_name": "Santiago F. Elena", - "author_inst": "Institute for Integrative Systems Biology and Santa Fe Institute" - }, - { - "author_name": "Jos\u00e9-Angel Oteo", - "author_inst": "Institute for Integrative Systems Biology and Theoretical Physics Department of University of Valencia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.07.13.22277613", "rel_title": "Assessing Risk Exposure of COVID-19 in Indonesian Government-owned Public Health Center Physicians", @@ -278082,6 +280144,37 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.07.13.499586", + "rel_title": "Structural basis for the enhanced infectivity and immune evasion of Omicron subvariants", + "rel_date": "2022-07-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.07.13.499586", + "rel_abs": "The Omicron variants of SARS-CoV-2 have recently become the globally dominant variants of concern in the COVID-19 pandemic. At least five major Omicron sub-lineages have been characterized: BA.1, BA.2, BA.3, BA.4 and BA.5. They all possess over 30 mutations on the Spike (S) protein. Here we report the cryo-EM structures of the trimeric S proteins from the five subvariants, of which BA.4 and BA.5 share the same mutations of S protein, each in complex with the surface receptor ACE2. All three receptor binding domains of S protein from BA.2 and BA.4/BA.5 are \"up\", while the BA.1 S protein has two \"up\" and one \"down\". The BA.3 S protein displays increased heterogeneity, with the majority in the all \"up\" RBD state. The differentially preferred conformations of the S protein are consistent with their varied transmissibilities. Analysis of the well defined S309 and S2K146 epitopes reveals the underlie immune evasion mechanism of Omicron subvariants.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Yaning Li", + "author_inst": "School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China. School of Life Sciences, Tsinghua University, Beijing 100084, China." + }, + { + "author_name": "Yaping Shen", + "author_inst": "School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China." + }, + { + "author_name": "Yuanyuan Zhang", + "author_inst": "School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China." + }, + { + "author_name": "Renhong Yan", + "author_inst": "School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2022.07.13.499346", "rel_title": "Nitazoxanide is a potent inhibitor of human seasonal coronaviruses acting at postentry level: effect on viral spike glycoprotein", @@ -278725,53 +280818,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, - { - "rel_doi": "10.1101/2022.07.07.22277315", - "rel_title": "The uncoupling of all-cause excess mortality from Covid-19 cases and associated hospitalizations in late winter and spring of 2022 in a highly vaccinated state.", - "rel_date": "2022-07-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.07.22277315", - "rel_abs": "IntroductionSince March 2020, all-cause excess mortality--the number of all-cause deaths exceeding the baseline number of expected deaths--has been observed in waves coinciding with Covid-19 outbreaks in the United States. We recently described high levels of excess mortality in Massachusetts during the initial 8-week Omicron wave. However, whether excess mortality continued after that period--during which an outbreak of Omicron subvariants occurred--is unknown.\n\nMethodsWe applied seasonal autoregressive integrated moving averages to five years of pre-pandemic data provided by the Massachusetts Registry of Vital Records and Statistics (MRVRS) to project the weekly populations and expected deaths for the pandemic period. Observed deaths during the pandemic were also provided by MRVRS and are >99% complete for all study weeks.\n\nResultsDuring the 18-week Omicron subvariant period (the week ending February 27, 2022, through June 26, 2022) the incidence of all-cause excess mortality was 0.1 per 100,000-person weeks, corresponding to 148 excess deaths (95%. CI -907 to 1153), representing a 97.1% decrease from the initial Omicron period (during which all-cause excess mortality was 4.0 per 100,000-person-weeks), and a 91.9% reduction from the Delta and Delta-Omicron transition period (during which all-cause excess mortality was 1.5 per 100,000-person-weeks), despite >226,000 reported new Covid-19 cases during the subvariant/spring period. However, Covid-19-associated hospitalizations were observed during the subvariant/spring 2022 period.\n\nConclusionIn a highly vaccinated state with a recent wave of SARS-CoV-2, all-cause excess mortality was uncoupled from new case counts, indicating the possibility of temporary protection from the most severe outcomes related to Covid-19 among high-risk individuals. However, given the possibility of waning immunity and the emerging of new variants, continued monitoring is warranted.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Jeremy Faust", - "author_inst": "Brigham and Women's Hospital, Harvard Medical School" - }, - { - "author_name": "Benjamin Renton", - "author_inst": "Ariadne Labs, Brigham and Women's Hospital" - }, - { - "author_name": "Alexander Junxiang Chen", - "author_inst": "Harvard University" - }, - { - "author_name": "Chengan Du", - "author_inst": "Center for Outcomes Research and Evaluation, Yale University School of Medicine, New Haven, Connecticut" - }, - { - "author_name": "Chenxue Liang", - "author_inst": "Center for Outcomes Research and Evaluation, Yale University School of Medicine, New Haven, Connecticut" - }, - { - "author_name": "Shu-Xia Li", - "author_inst": "Center for Outcomes Research and Evaluation, Yale University School of Medicine, New Haven, Connecticut" - }, - { - "author_name": "Zhenqiu Lin", - "author_inst": "Center for Outcomes Research and Evaluation, Yale University School of Medicine, New Haven, Connecticut" - }, - { - "author_name": "Harlan Krumholz", - "author_inst": "Center for Outcomes Research and Evaluation, Yale University School of Medicine, New Haven, Connecticut" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.07.11.22277504", "rel_title": "Estimation of disease burden and clinical severity of COVID-19 caused by Omicron BA.2 in Shanghai, February-June 2022", @@ -280176,6 +282222,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.07.22277353", + "rel_title": "Assessing the impact of SARS-CoV-2 lineages and mutations on patient survival", + "rel_date": "2022-07-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.07.22277353", + "rel_abs": "After more than two years of COVID-19 pandemic, SARS-CoV-2 still remains a global public health problem. Successive waves of infection have produced new SARS-CoV-2 variants with new mutations whose impact on COVID-19 severity and patient survival is uncertain. A total of 764 SARS-CoV-2 genomes sequenced from COVID-19 patients, hospitalized from 19th February 2020 to 30st April 2021, along with their clinical data, were used for survival analysis. A significant association of B.1.1.7, the alpha lineage, with patient mortality (Log Hazard ratio LHR=0.51, C.I.=[0.14,0.88]) was found upon adjustment by all the covariates known to affect COVID-19 prognosis. Moreover, survival analysis of mutations in the SARS-CoV-2 genome rendered 27 of them significantly associated with higher mortality of patients. Most of these mutations were located in the S, ORF8 and N proteins. This study illustrates how a combination of genomic and clinical data provide solid evidence on the impact of viral lineage on patient survival.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Carlos Loucera", + "author_inst": "Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Sevilla, 41013, Spain" + }, + { + "author_name": "Javier Perez-Florido", + "author_inst": "Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Sevilla, 41013, Spain" + }, + { + "author_name": "Carlos S Casimiro-Soriguer", + "author_inst": "Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Sevilla, 41013, Spain" + }, + { + "author_name": "Francisco M Ortuno", + "author_inst": "Department of Computer Architecture and Computer Technology, University of Granada, 18011, Granada, Spain" + }, + { + "author_name": "Rosario Carmona", + "author_inst": "Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Sevilla, 41013, Spain" + }, + { + "author_name": "Gerrit Bostelmann", + "author_inst": "Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Sevilla, 41013, Spain" + }, + { + "author_name": "Luis Javier Martinez-Gonzalez", + "author_inst": "GENYO. Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, 18016 Granada, Spain" + }, + { + "author_name": "Dolores Dolores Munoyerro-Muniz", + "author_inst": "Subdireccion Tecnica Asesora de Gestion de la Informacion. Servicio Andaluz de Salud, 41001, Sevilla, Spain." + }, + { + "author_name": "Roman Villegas", + "author_inst": "Subdireccion Tecnica Asesora de Gestion de la Informacion. Servicio Andaluz de Salud, 41001, Sevilla, Spain." + }, + { + "author_name": "Jesus Rodriguez-Bano", + "author_inst": "Unidad Clinica de Enfermedades Infecciosas, Microbiologia y Medicina Preventiva, Hospital Universitario Virgen Macarena, 41009, Sevilla, Spain." + }, + { + "author_name": "Manuel Romero-Gomez", + "author_inst": "Servicio de Aparato Digestivo. Hospital Universitario Virgen del Rocio. 41013, Sevilla. Spain." + }, + { + "author_name": "Nicola Lorusso", + "author_inst": "Direccion General de Salud Publica. Consejeria de Salud y Familias. Junta de Andalucia. 41020, Sevilla, Spain" + }, + { + "author_name": "Javier Garcia-Leon", + "author_inst": "Departamento de Metafisica y Corrientes Actuales de la Filosofia, Etica y Filosofia Politica. Universidad de Sevilla, 41004, Sevilla, Spain" + }, + { + "author_name": "Jose M Navarro-Mari", + "author_inst": "Servicio de Microbiologia, Hospital Virgen de las Nieves, 18014, Granada, Spain." + }, + { + "author_name": "Pedro Camacho-Martinez", + "author_inst": "Servicio de Microbiologia. Unidad Clinica Enfermedades Infecciosas, Microbiologia y Medicina Preventiva. Hospital Universitario Virgen del Rocio. 41013. Sevilla" + }, + { + "author_name": "Laura Merino-Diaz", + "author_inst": "Servicio de Microbiologia. Unidad Clinica Enfermedades Infecciosas, Microbiologia y Medicina Preventiva. Hospital Universitario Virgen del Rocio. 41013. Sevilla" + }, + { + "author_name": "Adolfo de Salazar", + "author_inst": "Servicio de Microbiologia. Hospital Universitario San Cecilio. 18016, Granada, Spain." + }, + { + "author_name": "Laura Vinuela", + "author_inst": "Servicio de Microbiologia. Hospital Universitario San Cecilio. 18016, Granada, Spain." + }, + { + "author_name": "- The Andalusian COVID-19 sequencing initiative", + "author_inst": "" + }, + { + "author_name": "Jose A Lepe", + "author_inst": "Servicio de Microbiologia. Unidad Clinica Enfermedades Infecciosas, Microbiologia y Medicina Preventiva. Hospital Universitario Virgen del Rocio. 41013. Sevilla" + }, + { + "author_name": "Federico Garcia", + "author_inst": "Servicio de Microbiologia. Hospital Universitario San Cecilio. 18016, Granada, Spain." + }, + { + "author_name": "Joaquin Dopazo", + "author_inst": "Computational Medicine, Andalusian Public Foundation Progress and Health-FPS, Sevilla, 41013, Spain" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.07.07.22277128", "rel_title": "SARS-CoV-2 Omicron BA.5: Evolving tropism and evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern.", @@ -282430,6 +284579,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.06.22277066", + "rel_title": "Association between nursing home crowding and outbreak-associated respiratory infection and death prior to the COVID-19 pandemic between 2014 and 2019 in Ontario, Canada", + "rel_date": "2022-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.06.22277066", + "rel_abs": "ImportanceResident crowding in nursing homes is associated with larger SARS-CoV-2 outbreaks. However, this association has not been previously documented for non-SARS-CoV-2 respiratory infections.\n\nObjectiveWe sought to measure the association between nursing home crowding and respiratory infections in Ontario nursing homes prior to the COVID-19 pandemic.\n\nDesign, Setting, and ParticipantsWe conducted a retrospective cohort study of nursing home residents in Ontario, Canada over a five-year period prior to the COVID-19 pandemic, between September 2014 and August 2019.\n\nExposureUsing administrative data, we estimated the crowding index equal to the mean number of residents per bedroom and bathroom (residents / [0.5*bedrooms+0.5*bathrooms]).\n\nOutcomesThe incidence of outbreak-associated infections and mortality per 100 nursing home residents per year. We also examined infection and mortality outcomes for outbreaks due to 7 specific pathogens: coronaviruses (OC43, 229E, NL63, HKU1), influenza A, influenza B, human metapneumovirus, parainfluenza virus, respiratory syncytial virus, rhinovirus/enterovirus.\n\nResultsThere was one or more respiratory outbreak in 93.9% (588/626) nursing homes in Ontario. There were 4,921 outbreaks involving 64,829 cases of respiratory infection, and 1,969 deaths. Outbreaks attributable to a single identified pathogen were principally caused by influenza A (29%), rhinovirus (11.7%), influenza B (8.1%), and respiratory syncytial virus (6.1%). Among homes, 42.7% (251/588) homes had a high crowding index ([≥] 2.0). After adjustment, more crowded homes had higher outbreak-associated respiratory infection incidence (aRR 1.89; 95% 1.64-2.18) and mortality incidence (aRR 2.28; 95% 1.84-2.84). More crowded homes had higher adjusted estimates of the incidence of infection and mortality for each of the 7 respiratory pathogens examined.\n\nConclusions and RelevanceResidents of crowded nursing homes experienced more respiratory-outbreak infections and mortality due to influenza and other non-SARS-CoV-2 respiratory pathogens. Decreasing crowding in nursing homes is an important patient safety target beyond the COVID-19 pandemic.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Pamela Leece", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Michael Whelan", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Andrew P Costa", + "author_inst": "McMaster University" + }, + { + "author_name": "Nick Daneman", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Jennie Johnstone", + "author_inst": "Mount Sinai Hospital" + }, + { + "author_name": "Allison McGeer", + "author_inst": "Mount Sinai Hospital" + }, + { + "author_name": "Paula Rochon", + "author_inst": "Womens College Hospital" + }, + { + "author_name": "Kevin L Schwartz", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Kevin Antoine Brown", + "author_inst": "Public Health Ontario" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.07.06.22277341", "rel_title": "Prevalence and factors associated with antigen test positivity following SARS-CoV-2 infection among healthcare workers in Los Angeles", @@ -282882,53 +285082,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.07.02.22277181", - "rel_title": "Integrative analysis of viral entry networks and clinical outcomes identifies a protective role for spironolactone in severe COVID-19", - "rel_date": "2022-07-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.02.22277181", - "rel_abs": "Treatment strategies that target host entry factors have proven an effective means of impeding viral entry in HIV and may be more robust to viral evolution than drugs targeting viral proteins directly. High-throughput functional screens provide an unbiased means of identifying genes that influence the infection of host cells, while retrospective cohort analysis can measure the real-world, clinical potential of repurposing existing therapeutics as antiviral treatments. Here, we combine these two powerful methods to identify drugs that alter the clinical course of COVID-19 by targeting host entry factors. We demonstrate that integrative analysis of genome-wide CRISPR screening datasets enables network-based prioritization of drugs modulating viral entry, and we identify three common medications (spironolactone, quetiapine, and carvedilol) based on their network proximity to putative host factors. To understand the drugs real-world impact, we perform a propensity-score-matched, retrospective cohort study of 64,349 COVID-19 patients and show that spironolactone use is associated with improved clinical prognosis, measured by both ICU admission and mechanical ventilation rates. Finally, we show that spironolactone exerts a dose-dependent inhibitory effect on viral entry in a human lung epithelial cell line. Our results suggest that spironolactone may improve clinical outcomes in COVID-19 through tissue-dependent inhibition of viral entry. Our work further provides a potential approach to integrate functional genomics with real-world evidence for drug repurposing.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Henry Cousins", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Adrienne Sarah Kline", - "author_inst": "Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Chengkun Wang", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Yuanhao Qu", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Mengdi Wang", - "author_inst": "Princeton University" - }, - { - "author_name": "Russ Altman", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Yuan Luo", - "author_inst": "Feinberg School of Medicine, Northwestern University" - }, - { - "author_name": "Le Cong", - "author_inst": "Stanford University School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.07.03.22277169", "rel_title": "Clinical advancement of patients infected with SARS-CoV-2 Omicron variant in Shanghai, China", @@ -284344,6 +286497,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.07.02.22277186", + "rel_title": "Inferring the differences in incubation-period and generation-interval distributions of the Delta and Omicron variants of SARS-CoV-2", + "rel_date": "2022-07-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.02.22277186", + "rel_abs": "Estimating the differences in the incubation-period, serial-interval, and generation-interval distributions of SARS-CoV-2 variants is critical to understanding their transmission and control. However, the impact of epidemic dynamics is often neglected in estimating the timing of infection and transmission--for example, when an epidemic is growing exponentially, a cohort of infected individuals who developed symptoms at the same time are more likely to have been infected recently. Here, we re-analyze incubation-period and serial-interval data describing transmissions of the Delta and Omicron variants from the Netherlands at the end of December 2021. Previous analysis of the same data set reported shorter mean observed incubation period (3.2 days vs 4.4 days) and serial interval (3.5 days vs 4.1 days) for the Omicron variant, but the number of infections caused by the Delta variant decreased during this period as the number of Omicron infections increased. When we account for growth-rate differences of two variants during the study period, we estimate similar mean incubation periods (3.8-4.5 days) for both variants but a shorter mean generation interval for the Omicron variant (3.0 days; 95% CI: 2.7-3.2 days) than for the Delta variant (3.8 days; 95% CI: 3.7-4.0 days). We further note that the differences in estimated generation intervals may be driven by the \"network effect\"--higher effective transmissibility of the Omicron variant can cause faster susceptible depletion among contact networks, which in turn prevents late transmission (therefore shortening realized generation intervals). Using up-to-date generation-interval distributions is critical to accurately estimating the reproduction advantage of the Omicron variant.\n\nSignificanceRecent studies suggest that individuals infected with the Omicron variant develop symptoms earlier (shorter incubation period) and transmit faster (shorter generation interval) than those infected with the Delta variant. However, these studies typically neglect population-level effects: when an epidemic is growing, a greater proportion of current cases were infected recently, biasing us toward observing faster transmission events. Accounting for this dynamical bias, we find that Omicron infections from the Netherlands at the end of December 2021 had similar incubation periods, but shorter generation intervals, compared to Delta infections from the same period. Shorter generation intervals of the Omicron variant might be due to its higher effective reproduction number, which can cause faster local susceptible depletion around the contact network.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Sang Woo Park", + "author_inst": "Princeton University" + }, + { + "author_name": "Kaiyuan Sun", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Sam Abbott", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Ron Sender", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Yinon M. Bar-On", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Joshua S Weitz", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Sebastian Funk", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Bryan Grenfell", + "author_inst": "Princeton University" + }, + { + "author_name": "Jantien A. Backer", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Jacco Wallinga", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Cecile Viboud", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Jonathan Dushoff", + "author_inst": "McMaster University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.07.02.22277179", "rel_title": "Using machine learning probabilities to identify effects of COVID-19", @@ -285824,85 +288040,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.06.29.498117", - "rel_title": "COVID-19 Neuropathology: evidence for SARS-CoV-2 invasion of Human Brainstem Nuclei", - "rel_date": "2022-07-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.29.498117", - "rel_abs": "Neurological manifestations are common in COVID-19, the disease caused by SARS-CoV-2. Despite reports of SARS-CoV-2 detection in the brain and cerebrospinal fluid of COVID-19 patients, its still unclear whether the virus can infect the central nervous system, and which neuropathological alterations can be ascribed to viral tropism, rather than immune-mediated mechanisms.\n\nHere, we assess neuropathological alterations in 24 COVID-19 patients and 18 matched controls who died due to pneumonia / respiratory failure. Aside from a wide spectrum of neuropathological alterations, SARS-CoV-2-immunoreactive neurons were detected in specific brainstem nuclei of 5 COVID-19 subjects. Viral RNA was also detected by real-time RT-PCR. Quantification of reactive microglia revealed an anatomically segregated pattern of inflammation within affected brainstem regions, and was higher when compared to controls. While the results of this study support the neuroinvasive potential of SARS-CoV-2, the role of SARS-CoV-2 neurotropism in COVID-19 and its long-term sequelae require further investigation.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Aron Emmi", - "author_inst": "Institute of Human Anatomy, Department of Neuroscience, University of Padova, Italy" - }, - { - "author_name": "Stefania Rizzo", - "author_inst": "Department of Cardio-Thoracic-Vascular Sciences & Public Health, University of Padova, Italy" - }, - { - "author_name": "Luisa Barzon", - "author_inst": "Department of Molecular Medicine, University of Padova, Padova, Italy" - }, - { - "author_name": "Michele Sandre", - "author_inst": "Movement Disorders Unit, Neurology Clinic, Department of Neuroscience, University of Padova" - }, - { - "author_name": "Elisa Carturan", - "author_inst": "Department of Cardio-Thoracic-Vascular Sciences & Public Health, University of Padova, Italy" - }, - { - "author_name": "Alessandro Sinigaglia", - "author_inst": "Department of Molecular Medicine, University of Padova, Padova, Italy" - }, - { - "author_name": "Silvia Riccetti", - "author_inst": "Department of Molecular Medicine, University of Padova, Padova, Italy" - }, - { - "author_name": "Mila della Barbera", - "author_inst": "Department of Cardio-Thoracic-Vascular Sciences & Public Health, University of Padova, Italy" - }, - { - "author_name": "Rafael Boscolo-Berto", - "author_inst": "Institute of Human Anatomy, Department of Neuroscience, University of Padova, Italy" - }, - { - "author_name": "Patrizia Cocco", - "author_inst": "Pathology and Histopathology Unit, Ospedali Riuniti Padova Sud, Padova, Italy" - }, - { - "author_name": "Veronica Macchi", - "author_inst": "Institute of Human Anatomy, Department of Neuroscience, University of Padova, Italy" - }, - { - "author_name": "Angelo Antonini", - "author_inst": "Movement Disorders Unit, Neurology Clinic, Department of Neuroscience, University of Padova" - }, - { - "author_name": "Monica De Gaspari", - "author_inst": "Department of Cardio-Thoracic-Vascular Sciences & Public Health, University of Padova, Italy" - }, - { - "author_name": "Cristina Basso", - "author_inst": "Department of Cardio-Thoracic-Vascular Sciences & Public Health, University of Padova, Italy" - }, - { - "author_name": "Raffaele De Caro", - "author_inst": "Institute of Human Anatomy, Department of Neuroscience, University of Padova, Italy" - }, - { - "author_name": "Andrea Porzionato", - "author_inst": "Institute of Human Anatomy, Department of Neuroscience, University of Padova, Italy" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "neuroscience" - }, { "rel_doi": "10.1101/2022.07.05.498834", "rel_title": "Comparing the evolutionary dynamics of predominant SARS-CoV-2 virus lineages co-circulating in Mexico", @@ -287398,6 +289535,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.07.01.22277137", + "rel_title": "The decline of COVID-19 severity and lethality over two years of pandemic", + "rel_date": "2022-07-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.07.01.22277137", + "rel_abs": "Undernotification of SARS-CoV-2 infections has been a major obstacle to the tracking of critical quantities such as infection attack rates and the probability of severe and lethal outcomes. We use a model of SARS-CoV-2 transmission and vaccination informed by epidemiological and genomic surveillance data to estimate the number of daily infections occurred in Italy in the first two years of pandemic. We estimate that the attack rate of ancestral lineages, Alpha, and Delta were in a similar range (10-17%, range of 95% CI: 7-23%), while that of Omicron until February 20, 2022, was remarkably higher (51%, 95%CI: 33-70%). The combined effect of vaccination, immunity from natural infection, change in variant features, and improved patient management massively reduced the probabilities of hospitalization, admission to intensive care, and death given infection, with 20 to 40-fold reductions during the period of dominance of Omicron compared to the initial acute phase.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Valentina Marziano", + "author_inst": "Bruno Kessler Foundation" + }, + { + "author_name": "Giorgio Guzzetta", + "author_inst": "Bruno Kessler Foundation" + }, + { + "author_name": "Francesco Menegale", + "author_inst": "University of Trento" + }, + { + "author_name": "Chiara Sacco", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Daniele Petrone", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Alberto Mateo Urdiales", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Martina Del Manso", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Antonino Bella", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Massimo Fabiani", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Maria Fenicia Vescio", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Flavia Riccardo", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Piero Poletti", + "author_inst": "Bruno Kessler Foundation" + }, + { + "author_name": "Mattia Manica", + "author_inst": "Bruno Kessler Foundation" + }, + { + "author_name": "Agnese Zardini", + "author_inst": "Bruno Kessler Foundation" + }, + { + "author_name": "Valeria d'Andrea", + "author_inst": "Bruno Kessler Foundation" + }, + { + "author_name": "Filippo Trentini", + "author_inst": "Bocconi University" + }, + { + "author_name": "Paola Stefanelli", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Giovanni Rezza", + "author_inst": "Ministry of Health" + }, + { + "author_name": "Anna Teresa Palamara", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Silvio Brusaferro", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Marco Ajelli", + "author_inst": "Indiana University School of Public Health" + }, + { + "author_name": "Patrizio Pezzotti", + "author_inst": "Istituto Superiore di Sanita" + }, + { + "author_name": "Stefano Merler", + "author_inst": "Bruno Kessler Foundation" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.06.30.22277079", "rel_title": "Rucaparib blocks SARS-CoV-2 virus binding to cells and interleukin-6 release in a model of COVID-19", @@ -287842,53 +290086,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2022.06.30.498338", - "rel_title": "Transcriptional Profiles Analysis of COVID-19 and Malaria Patients Reveals Potential Biomarkers in Children", - "rel_date": "2022-07-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.30.498338", - "rel_abs": "The clinical presentation overlap between malaria and COVID-19 poses special challenges for rapid diagnosis in febrile children. In this study, we collected RNA-seq data of children with malaria and COVID-19 infection from the public databases as raw data in fastq format paired end files. A group of six, five and two biological replicates of malaria, COVID-19 and healthy donors respectively were used for the study. We conducted differential gene expression analysis to visualize differences in the expression profiles. Using edgeR, we explored particularly gene expression levels in different phenotype groups and found that 1084 genes and 2495 genes were differentially expressed in the malaria samples and COVID-19 samples respectively when compared to healthy controls. The highly expressed gene in the COVID-19 group we found CD151 gene which is facilitates in T cell proliferation, while in the malaria group, among the highly expressed gene we identified GBP5 gene which involved in inflammatory response and response to bacterium. By comparing both malaria and COVID-19 infections, the overlap of 62 differentially expressed genes patterns were identified. Among them, three genes (ENSG00000234998, H2AC19 and TXNDC5) were highly upregulated in both infections. Strikingly, we observed 13 genes such as HBQ1, HBM, SLC7A5, SERINC2, ATP6V0C, ST6GALNAC4, RAD23A, PNPLA2, GAS2L1, TMEM86B, SLC6A8, UBALD1, RNF187 were downregulated in children with malaria and uniquely upregulated in children with COVID-19, thus may be further validated as potential biomarkers to delineate COVID-19 from malaria-related febrile infection. The hemoglobin complexes and lipid metabolism biological pathways are highly expressed in both infections. Our study provided new insights for further investigation of the biological pattern in hosts with malaria and COVID-19 coinfection.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Nzungize Lambert", - "author_inst": "Liverpool School of Tropical Medicine Research Unit, Centre for Research in Infectious Diseases (CRID), P.O. Box 13591 Cameroon." - }, - { - "author_name": "Kengne-Ouafo A. Jonas", - "author_inst": "Liverpool School of Tropical Medicine Research Unit, Centre for Research in Infectious Diseases (CRID), P.O. Box 13591, Cameroon." - }, - { - "author_name": "Wesonga Makokha Rissy", - "author_inst": "African institute of Biomedical science and technology(AiBST), Zimbabwe" - }, - { - "author_name": "Umuhoza Diane", - "author_inst": "Rwanda Agriculture and Animal Ressources Board (RAB), Rwanda" - }, - { - "author_name": "Ken Murithi", - "author_inst": "International Center of Insect Physiology and Ecology, Kenya" - }, - { - "author_name": "Kimani Peter", - "author_inst": "International Center of Insect Physiology and Ecology, Kenya" - }, - { - "author_name": "Olaitan I. Awe", - "author_inst": "University of Ibadan, Ibadan, Oyo State, Nigeria" - }, - { - "author_name": "Allissa Dillman", - "author_inst": "National Institutes of Health, Bethesda, MD, U.S.A." - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2022.07.01.496571", "rel_title": "CovidOutcome2: a tool for SARS-CoV2 mutation identification and for disease severity prediction", @@ -288900,6 +291097,145 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.06.28.22276303", + "rel_title": "Effectiveness of vaccines in preventing hospitalization due to COVID-19: A multicenter hospital-based case-control study, Germany, June 2021 to January 2022", + "rel_date": "2022-06-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.28.22276303", + "rel_abs": "We included 852 patients in a prospectively recruiting multicenter matched case-control study in Germany to assess vaccine effectiveness (VE) in preventing COVID-19-associated hospitalization (Delta-variant dominance). Two-dose VE was 89% (95%CI 84-93%) overall, 79% in patients with >2 comorbidities and 77% in adults aged 60-75 years. A third dose increased VE to >93% in all patient-subgroups.", + "rel_num_authors": 31, + "rel_authors": [ + { + "author_name": "Anna Stoliaroff", + "author_inst": "Robert Koch-Institute" + }, + { + "author_name": "Caroline Peine", + "author_inst": "Robert Koch-Institute" + }, + { + "author_name": "Tim Herath", + "author_inst": "Robert Koch-Institute" + }, + { + "author_name": "Johannes Lachmann", + "author_inst": "Robert Koch-Institute" + }, + { + "author_name": "Achim Doerre", + "author_inst": "Robert Koch-Institute" + }, + { + "author_name": "Delphine Perriat", + "author_inst": "Robert Koch-Institute" + }, + { + "author_name": "Andreas Nitsche", + "author_inst": "Robert Koch Institute" + }, + { + "author_name": "Janine Michel", + "author_inst": "Robert Koch-Institute" + }, + { + "author_name": "Thomas Rinner", + "author_inst": "Robert Koch-Institute" + }, + { + "author_name": "Daniel Stern", + "author_inst": "Robert Koch-Institute" + }, + { + "author_name": "Fridolin Treindl", + "author_inst": "Robert Koch-Institute" + }, + { + "author_name": "Natalie Hofmann", + "author_inst": "Robert Koch-Institute" + }, + { + "author_name": "Marica Grossegesse", + "author_inst": "Robert Koch Institute" + }, + { + "author_name": "Claudia Kohl", + "author_inst": "Robert Koch-Institute" + }, + { + "author_name": "Annika Brinkmann", + "author_inst": "Robert Koch-Institute" + }, + { + "author_name": "Tanja Meyer", + "author_inst": "Robert Koch-Institute" + }, + { + "author_name": "Brigitte Dorner", + "author_inst": "Robert Koch-Institute" + }, + { + "author_name": "Sascha Hein", + "author_inst": "Paul-Ehrlich-Institute" + }, + { + "author_name": "Laura Werel", + "author_inst": "Paul-Ehrlich-Institute" + }, + { + "author_name": "Eberhard Hildt", + "author_inst": "Paul-Ehrlich-Institute" + }, + { + "author_name": "Sven Glaeser", + "author_inst": "Vivantes Netzwerk fuer Gesundheit GmbH" + }, + { + "author_name": "Helmut Schuehlen", + "author_inst": "Vivantes Netzwerk fuer Gesundheit GmbH" + }, + { + "author_name": "Caroline Isner", + "author_inst": "Vivantes Netzwerk fuer Gesundheit GmbH" + }, + { + "author_name": "Alexander Peric", + "author_inst": "Vivantes Netzwerk fuer Gesundheit GmbH" + }, + { + "author_name": "Ammar Ghouzi", + "author_inst": "Schoen Klinik Duesseldorf" + }, + { + "author_name": "Annette Reichardt", + "author_inst": "Helios Klinikum Berlin-Buch" + }, + { + "author_name": "Matthias Janneck", + "author_inst": "Albertinen Krankenhaus Hamburg" + }, + { + "author_name": "Guntram Lock", + "author_inst": "Albertinen Krankenhaus Hamburg" + }, + { + "author_name": "Lars Schaade", + "author_inst": "Robert Koch-Institute" + }, + { + "author_name": "Ole Wichmann", + "author_inst": "Robert Koch-Institute" + }, + { + "author_name": "Thomas Harder", + "author_inst": "Robert Koch-Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.06.28.22277028", "rel_title": "Masks Do No More Than Prevent Transmission:Theory and Data Undermine the Variolation Hypothesis", @@ -289408,85 +291744,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.06.27.497749", - "rel_title": "The RNA demethylase FTO controls m6A marking on SARS-CoV-2 and classifies COVID-19 severity in patients", - "rel_date": "2022-06-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.27.497749", - "rel_abs": "The RNA modification N6-methyladenosine (m6A) plays a key role in the life cycles of several RNA viruses. Whether this applies to SARS-CoV-2 and whether m6A affects the outcome of COVID-19 disease is still poorly explored. Here we report that the RNA demethylase FTO strongly affects both m6A marking of SARS-CoV-2 and COVID-19 severity. By m6A profiling of SARS-CoV-2, we confirmed in infected cultured cells and showed for the first time in vivo in hamsters that the regions encoding TRS_L and the nucleocapsid protein are multiply marked by m6A, preferentially within RRACH motifs that are specific to {beta}-coronaviruses and well conserved across SARS-CoV-2 variants. In cells, downregulation of the m6A demethylase FTO, occurring upon SARS-CoV-2 infection, increased m6A marking of SARS-CoV-2 RNA and slightly promoted viral replication. In COVID-19 patients, a negative correlation was found between FTO expression and both SARS-CoV-2 expression and disease severity. FTO emerged as a classifier of disease severity and hence a potential stratifier of COVID-19 patients.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Lionel Malbec", - "author_inst": "University of Brussels" - }, - { - "author_name": "Margot Celerier", - "author_inst": "University of Brussels" - }, - { - "author_name": "Martin Bizet", - "author_inst": "University of Brussels" - }, - { - "author_name": "Emilie Calonne", - "author_inst": "University of Brussels" - }, - { - "author_name": "Heike Hofmann-Winkler", - "author_inst": "German Primate Center" - }, - { - "author_name": "Bram Boeckx", - "author_inst": "University of Leuven" - }, - { - "author_name": "Rana Abdelnabi", - "author_inst": "University of Leuven" - }, - { - "author_name": "Pascale Putmans", - "author_inst": "University of Brussels" - }, - { - "author_name": "Bouchra Hassabi", - "author_inst": "University of Brussels" - }, - { - "author_name": "Lieve Naesens", - "author_inst": "University of Leuven" - }, - { - "author_name": "Diether Lambrechts", - "author_inst": "University of Leuven" - }, - { - "author_name": "Stefan P\u00f6hlmann", - "author_inst": "German Primate Center" - }, - { - "author_name": "Rachel Deplus", - "author_inst": "University of Brussels" - }, - { - "author_name": "Leen Delang", - "author_inst": "University of Leuven" - }, - { - "author_name": "Jana Jeschke", - "author_inst": "University of Brussels" - }, - { - "author_name": "Francois Fuks", - "author_inst": "University of Brussels" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2022.06.24.22276872", "rel_title": "An evaluation of the introduction of telehealth for remote antenatal and postnatal contacts in Bangladesh and Lao People's Democratic Republic during the COVID-19 pandemic", @@ -290838,6 +293095,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rehabilitation medicine and physical therapy" }, + { + "rel_doi": "10.1101/2022.06.24.22276853", + "rel_title": "Algorithmic Fairness and Bias Mitigation for Clinical Machine Learning: A New Utility for Deep Reinforcement Learning", + "rel_date": "2022-06-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.24.22276853", + "rel_abs": "As machine learning-based models continue to be developed for healthcare applications, greater effort is needed in ensuring that these technologies do not reflect or exacerbate any unwanted or discriminatory biases that may be present in the data. In this study, we introduce a reinforcement learning framework capable of mitigating biases that may have been acquired during data collection. In particular, we evaluated our model for the task of rapidly predicting COVID-19 for patients presenting to hospital emergency departments, and aimed to mitigate any site-specific (hospital) and ethnicity-based biases present in the data. Using a specialized reward function and training procedure, we show that our method achieves clinically-effective screening performances, while significantly improving outcome fairness compared to current benchmarks and state-of-the-art machine learning methods. We performed external validation across three independent hospitals, and additionally tested our method on a patient ICU discharge status task, demonstrating model generalizability.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Jenny Yang", + "author_inst": "The University of Oxford" + }, + { + "author_name": "Andrew AS Soltan", + "author_inst": "University of Oxford" + }, + { + "author_name": "David A Clifton", + "author_inst": "The University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2022.06.23.22276827", "rel_title": "HIV and SARS-CoV-2 infection in postpartum Kenyan women and their infants", @@ -291250,101 +293534,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.06.22.22276744", - "rel_title": "Vaccination saves lives: How do patients with chronic diseases and severe COVID-19 fare? Analysis from Indias National Clinical registry for COVID-19", - "rel_date": "2022-06-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.22.22276744", - "rel_abs": "ObjectivesThis study aims to describe the demographic and clinical profile and ascertain the determinants of outcome among hospitalised COVID-19 adult patients enrolled in the National Clinical Registry for COVID-19 (NCRC).\n\nMethodsNCRC is an on-going data collection platform operational in 42 hospitals across India. Data of hospitalized COVID-19 patients enrolled in NCRC between 1st September 2020 to 26th October 2021 were examined.\n\nResultsAnalysis of 29,509 hospitalised, adult COVID-19 patients [mean (SD) age: 51.1 (16.2) year; male: 18752 (63.6%)] showed that 15678 (53.1%) had at least one comorbidity. Among 25715 (87.1%) symptomatic patients, fever was the commonest symptom (72.3%) followed by shortness of breath (48.9%) and dry cough (45.5%). In-hospital mortality was 14.5% (n=3957). Adjusted odds of dying were significantly higher in age-group [≥]60 years, males, with diabetes, chronic kidney diseases, chronic liver disease, malignancy, and tuberculosis, presenting with dyspnea and neurological symptoms. WHO ordinal scale 4 or above at admission carried the highest odds of dying [5.6 (95% CI: 4.6, 7.0)]. Patients receiving one [OR: 0.5 (95% CI: 0.4, 0.7)] or two doses of anti-SARS CoV-2 vaccine [OR: 0.4 (95% CI: 0.3, 0.7)] were protected from in-hospital mortality.\n\nConclusionsWHO ordinal scale at admission is the most important independent predictor for in-hospital death in COVID-19 patients. Anti-SARS-CoV2 vaccination provides significant protection against mortality.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Aparna Mukherjee", - "author_inst": "Indian Council of Medical Research" - }, - { - "author_name": "Gunjan Kumar", - "author_inst": "Indian Council of Medical Research" - }, - { - "author_name": "Alka Turuk", - "author_inst": "Indian Council of Medical Research" - }, - { - "author_name": "Ashish Bhalla", - "author_inst": "PGIMER: Post Graduate Institute of Medical Education and Research" - }, - { - "author_name": "Thrilok Chander Bingi", - "author_inst": "Gandhi Medical College and Hospital" - }, - { - "author_name": "Pankaj Bhardwaj", - "author_inst": "All India Institute of Medical Sciences - Jodhpur" - }, - { - "author_name": "Tridip Dutta Baruah", - "author_inst": "All India Institute of Medical Sciences - Raipur" - }, - { - "author_name": "Subhasis Mukherjee", - "author_inst": "College of Medicine and Sagore Dutta Hospital" - }, - { - "author_name": "Arunansu Talukdar", - "author_inst": "Medical College and Hospital Kolkata" - }, - { - "author_name": "Yogiraj Ray", - "author_inst": "Infectious Disease And Beliaghata Hospital" - }, - { - "author_name": "Mary John", - "author_inst": "Christian Medical College and Hospital Ludhiana" - }, - { - "author_name": "Janakkumar R Khambholja", - "author_inst": "Smt NHL Municipal Medical College" - }, - { - "author_name": "Amit H Patel", - "author_inst": "CIMS Hospital" - }, - { - "author_name": "Sourin Bhuniya", - "author_inst": "All India Institute of Medical Sciences - Bhubaneswar" - }, - { - "author_name": "Rajnish Joshi", - "author_inst": "All India Institute of Medical Science - Bhopal" - }, - { - "author_name": "Geetha R Menon", - "author_inst": "National Institute of Medical Statistics" - }, - { - "author_name": "Damodar Sahu", - "author_inst": "National Institute of Medical Statistics" - }, - { - "author_name": "Vishnu Vardhan Rao", - "author_inst": "National Institute of Medical Statistics" - }, - { - "author_name": "Balram Bhargava", - "author_inst": "Indian Council of Medical Research" - }, - { - "author_name": "Samiran Panda", - "author_inst": "Indian Council of Medical Research" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.06.26.497669", "rel_title": "Antiviral T-cell Biofactory platform for SARS-CoV-2", @@ -292416,6 +294605,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.06.22.22276690", + "rel_title": "Long-term immune persistence induced by two-dose BBIBP-CorV vaccine with different intervals, and immunogenicity and safety of a homologous booster dose in high-risk occupational population. Secondary Study Based on a Randomized Clinical Trial", + "rel_date": "2022-06-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.22.22276690", + "rel_abs": "BackgroundBBIBP-CorV vaccine with two doses and an interval of 3-4 weeks had been proved to have good immunogenicity and efficacy as well as an acceptable safety profile according to our initial research and other similar studies. Maintaining adequate neutralizing antibody levels is also necessary for long-term protection, especially in the midst of the COVID-19 pandemic. Our aim was to evaluate the immune persistence of neutralizing antibody elicited by BBIBP-CorV vaccines with day 0-14, 0-21 and 0-28 schedule, and assess the immunogenicity and safety of a homologous booster dose in the high-risk occupational population aged 18-59 years.\n\nMethodsA total of 809 eligible participants, aged 18-59 years, were recruited and randomly allocated to receive BBIBP-CorV vaccine with day 0-14, 0-21 or 0-28 schedule respectively between January and May 2021 in Taiyuan City, Shanxi Province, China among the public security officers and the airport ground staff in initial study. In this secondary study, the responders (GMT [≥] 16) at day 28 after priming two-dose vaccine were followed up at months 3, 6 and 10 to evaluate the immune persistence of three two-dose schedules. At month 10, eligible participants of three two-dose schedules were received a homologous booster dose respectively (hereafter abbreviated as 0-14d-10m group, 0-21d-10m group and 0-28d-10m group), and followed up at day 28 post-booster to assess the safety and immunogenicity of the booster dose. The contents of follow-up included the blood samples, oropharyngeal/nasal swabs, and adverse reactions collection. The main outcomes of the study included geometric mean titers (GMT) of neutralizing antibody to live SARS-CoV-2, the positive rates of different criteria and the constituent ratio of GMT of neutralizing antibodies at different follow-up point. Meanwhile, we explored the kinetics of antibody levels of different vaccination regimens by generalized estimating equations (GEE) and used exponent curve model to predict the duration of maintaining protected antibody after the booster dose. We also determined predictors of maintaining protected antibody level within 10 months after the second dose by Cox proportional hazards regression model and nomogram. The trial was registered with ChiCTR.org.cn (ChiCTR2100041705, ChiCTR2100041706).\n\nResultsThe number of 241, 247 and 256 responders (GMT [≥] 16) at day 28 after two-dose BBIBP-CorV vaccine in 0-14d, 0-21d and 0-28d schedule were followed-up at months 3, 6, and 10 for immune persistence evaluation. At month 10, a total of 390 participants were eligible and received a booster dose with 130 participants in the 0-14d-10m, 0-21d-10m and 0-28d-10m group respectively, of whom 74.1% (289/390) were male, with a mean age of 37.1{+/-}10.3 years. The GMT of neutralizing antibody in 0-28d-10m and 0-21d-10m group were significantly higher than 0-14d-10m group at month 3 (GMT: 71.6 & 64.2 vs 46.4, P<0.0001), month 6 (GMT: 47.1 & 42.8 vs 30.5, P < 0.0001) and month 10 (GMT: 32.4 vs 20.3, P < 0.0001; 28.8 vs 20.3, P=0.0004) after the second dose. A sharply decrease by 4.85-fold (GMT: 94.4-20.3), 4.67-fold (GMT: 134.4-28.8) and 4.49-fold (GMT: 145.5-32.4) was observed from day 28 to month 10 after the second dose in 0-14d-10m, 0-21d-10m and 0-28d-10m group, respectively, and they had similar decline kinetics (P=0.67). At 28 days after booster dose, a remarkable rebound in neutralizing antibody (GMT: 246.2, 277.5 and 288.6) were observed in three groups, respectively. Notably, the GMT after booster dose was not affected by priming two-dose schedule. The predictive duration of neutralizing antibody declining to the cutoff level of positive antibody response may be 18.08 months, 18.83 months and 19.08 months after booster dose in three groups, respectively. Long-term immune persistence within 10 months after the second dose was associated with age<40, female, and history of influenza vaccination. All adverse reactions were mild after the booster injection. None of the participants were infected SARS-CoV-2 during the trial period.\n\nConclusionsThe priming two-dose BBIBP-CorV vaccine with 0-28 days and 0-21 days schedule could lead a longer persistence of neutralizing antibody than 0-14 days schedule. Maintaining long-term immune persistence was also associated with age<40, female, and history of influenza vaccination. Regardless of priming two-doses vaccination regimens, a homologous booster dose led to a strong rebound in neutralizing antibody and might elicit satisfactory persistent immunity.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Tian Yao", + "author_inst": "First Hospital/First Clinical Medical College of Shanxi Medical University" + }, + { + "author_name": "Xiaohong Zhang", + "author_inst": "Shanxi Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Shengcai Mu", + "author_inst": "Shanxi Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Yana Guo", + "author_inst": "School of Public Health, Shanxi Medical University" + }, + { + "author_name": "Xiuyang Xu", + "author_inst": "School of Public Health, Shanxi Medical University" + }, + { + "author_name": "Junfeng Huo", + "author_inst": "Shanxi Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Zhiyun Wei", + "author_inst": "Shanxi Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Ling Liu", + "author_inst": "Shanxi Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Xiaoqing Li", + "author_inst": "Shanxi Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Hong Li", + "author_inst": "Shanxi Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Rongqin Xing", + "author_inst": "Outpatient Department of Shanxi Aviation Industry Group Co. LTD" + }, + { + "author_name": "Yongliang Feng", + "author_inst": "School of Public Health, Shanxi Medical University" + }, + { + "author_name": "Jing Chen", + "author_inst": "Shanxi Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Lizhong Feng", + "author_inst": "Shanxi Provincial Center for Disease Control and Prevention" + }, + { + "author_name": "Suping Wang", + "author_inst": "School of Public Health, Shanxi Medical University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.06.24.22276867", "rel_title": "The mental wellbeing of prison staff in England during the COVID-19 pandemic: a cross-sectional study", @@ -292900,81 +295164,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.06.23.497404", - "rel_title": "The Functional Landscape of SARS-CoV-2 3CL Protease", - "rel_date": "2022-06-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.23.497404", - "rel_abs": "SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) as the etiologic agent of COVID-19 (coronavirus disease 2019) has drastically altered life globally. Numerous efforts have been placed on the development of therapeutics to treat SARS-CoV-2 infection. One particular target is the 3CL protease (3CLpro), which holds promise as it is essential to the virus and highly conserved among coronaviruses, suggesting that it may be possible to find broad inhibitors that treat not just SARS-CoV-2 but other coronavirus infections as well. While the 3CL protease has been studied by many groups for SARS-CoV-2 and other coronaviruses, our understanding of its tolerance to mutations is limited, knowledge which is particularly important as 3CL protease inhibitors become utilized clinically. Here, we develop a yeast-based deep mutational scanning approach to systematically profile the activity of all possible single mutants of the SARS-CoV-2 3CLpro, and validate our results both in yeast and in authentic viruses. We reveal that the 3CLpro is highly malleable and is capable of tolerating mutations throughout the protein, including within the substrate binding pocket. Yet, we also identify specific residues that appear immutable for function of the protease, suggesting that these interactions may be novel targets for the design of future 3CLpro inhibitors. Finally, we utilize our screening results as a basis to identify E166V as a resistance-conferring mutation against the therapeutic 3CLpro inhibitor, nirmatrelvir, in clinical use. Collectively, the functional map presented herein may serve as a guide for further understanding of the biological properties of the 3CL protease and for drug development for current and future coronavirus pandemics.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Sho Iketani", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Seo Jung Hong", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Jenny Sheng", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Farideh Bahari", - "author_inst": "University of Tehran" - }, - { - "author_name": "Bruce Culbertson", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Fereshteh Fallah Atanaki", - "author_inst": "University of Tehran" - }, - { - "author_name": "Arjun K. Aditham", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Alexander F. Kratz", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Maria I. Luck", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Ruxiao Tian", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Stephen P. Goff", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Hesam Montazeri", - "author_inst": "University of Tehran" - }, - { - "author_name": "Yosef Sabo", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "David D. Ho", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Alejandro Chavez", - "author_inst": "Columbia University Irving Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.06.23.497239", "rel_title": "Investigating the mutations in the SARS-CoV-2 proteins among European countries", @@ -294374,6 +296563,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.06.23.22276812", + "rel_title": "On the impacts of the COVID-19 pandemic on mortality: Lost years or lost days?", + "rel_date": "2022-06-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.23.22276812", + "rel_abs": "ObjectiveTo quantify the (direct and indirect) impacts of the COVID-19 pandemic on mortality for actual populations of persons living in 12 European countries in 2020.\n\nMethodBased on demographic and mortality data, as well as remaining life expectancies found in the Human Mortality Database, we calculated a \"population life lost\" in 2020 for men and women living in Belgium, Croatia, Denmark, Finland, Hungary, Lithuania, Luxembourg, Norway, Portugal, Spain, Sweden and Switzerland. This quantity was obtained by dividing the total number of years lost in 2020 (estimated from all-cause mortality data and attributed directly or indirectly to COVID-19) by the size of the population.\n\nResultsA significant population life loss was found in 8 countries in 2020, with men losing an average of 8.7, 5.0, 4.4, 4.0, 3.7, 3.4, 3.1 and 2.7 days in Lithuania, Spain, Belgium, Hungary, Croatia, Portugal, Switzerland and Sweden, respectively. For women, this loss was 5.5, 4.3, 3.7, 3.7, 3.1, 2.4, 1.6 and 1.4 days, respectively. No significant losses were found in Finland, Luxembourg, Denmark and Norway. Life loss was highly dependent on age, reaching 40 days at the age of 90 in some countries, while only a few significant losses occurred under the age of 60. Even in countries with a significant population life loss in 2020, it was on average about 30 times lower than in 1918, at the time of the Spanish flu.\n\nConclusionsOur results based on the concept of population life loss were consistent with those based on the classical concept of life expectancy, confirming the significant impact of COVID-19 on mortality in 8 European countries in 2020. However, while life expectancy losses were typically counted in months or years, population life losses could be counted in days, a potentially useful piece of information from a public health perspective.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Valentin Rousson", + "author_inst": "University of Lausanne" + }, + { + "author_name": "Isabella Locatelli", + "author_inst": "Unisante (University of Lausanne)" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.06.22.22276789", "rel_title": "Association of physical activity and the risk of COVID-19 hospitalization: a dose-response meta-analysis", @@ -294690,149 +296902,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.06.21.22276660", - "rel_title": "Evidence of recent Epstein-Barr virus reactivation in individuals experiencing Long COVID", - "rel_date": "2022-06-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.21.22276660", - "rel_abs": "The presence and reactivation of chronic viral infections such as Epstein-Barr virus (EBV), cytomegalovirus (CMV) and human immunodeficiency virus (HIV) have been proposed as potential contributors to Long COVID (LC), but studies in well-characterized post-acute cohorts of individuals with COVID-19 over a longer time course consistent with current case definitions of LC are limited. In a cohort of 280 adults with prior SARS-CoV-2 infection, we observed that LC symptoms such as fatigue and neurocognitive dysfunction at a median of 4 months following initial diagnosis were independently associated with serological evidence of recent EBV reactivation (early antigen-D [EA-D] IgG positivity) or high nuclear antigen IgG levels, but not with ongoing EBV viremia. Evidence of EBV reactivation (EA-D IgG) was most strongly associated with fatigue (OR 2.12). Underlying HIV infection was also independently associated with neurocognitive LC (OR 2.5). Interestingly, participants who had serologic evidence of prior CMV infection were less likely to develop neurocognitive LC (OR 0.52) and tended to have less severe (>5 symptoms reported) LC (OR 0.44). Overall, these findings suggest differential effects of chronic viral co-infections on the likelihood of developing LC and predicted distinct syndromic patterns. Further assessment during the acute phase of COVID-19 is warranted.\n\nSUMMARYThe authors found that Long COVID symptoms in a post-acute cohort were associated with serological evidence of recent EBV reactivation and pre-existing HIV infection when adjusted for participant factors, sample timing, comorbid conditions and prior hospitalization, whereas underlying CMV infection was associated with a decreased risk of Long COVID.", - "rel_num_authors": 32, - "rel_authors": [ - { - "author_name": "Michael J Peluso", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Tyler-Marie Deveau", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Sadie E Munter", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Dylan Ryder", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Amanda Buck", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Gabrielle Beck-Engeser", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Fay Chan", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Scott Lu", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Sarah A Goldberg", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Rebecca Hoh", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Viva Tai", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Leonel Torres", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Nikita S Iyer", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Monika Deswal", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Lynn H Ngo", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Melissa Buitrago", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Antonio Rodriguez", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Jessica Y Chen", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Brandon C Yee", - "author_inst": "Monogram Biosciences" - }, - { - "author_name": "Ahmed Chenna", - "author_inst": "Monogram Biosciences" - }, - { - "author_name": "John W Winslow", - "author_inst": "Monogram Biosciences" - }, - { - "author_name": "Christos J Petropoulos", - "author_inst": "Monogram Biosciences" - }, - { - "author_name": "Amelia N Deitchman", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Joanna Hellmuth", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Matthew A Spinelli", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Matthew S Durstenfeld", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Priscilla Y Hsue", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "J Daniel Kelly", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Jeffrey N Martin", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Steven G Deeks", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Peter W Hunt", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Timothy J Henrich", - "author_inst": "University of California, San Francisco" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.06.21.22276720", "rel_title": "Effects of the COVID-19 pandemic on self-reported 12-month pneumococcal vaccination series completion rates in Canada: An interrupted time-series analysis", @@ -296268,6 +298337,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2022.06.19.22276620", + "rel_title": "Emotions in the time of COVID-19: A sentiment analysis of tweets during the nationwide lockdown in India", + "rel_date": "2022-06-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.19.22276620", + "rel_abs": "BackgroundCOVID-19 pandemic is unprecedented in terms of burden, nature and quantum of control measures and public reactions. We report trends in public emotions and sentiments before and during the nation-wide lockdown implemented since 25th March 2020 in India.\n\nMethodsWe collected a sample of tweets containing the keywords coronavirus or COVID-19 published between 12th March and 14th April in India. After pre-processing, the tweets were subjected to sentiment analysis using natural language processing algorithms.\n\nResultsOur analysis of 226170 tweets revealed a positive public sentiment (mean sentiment score=0.25). Tweets expressing a given sentiment showed significant (p<0.001) waning of negativity; negative tweets decreased (39.3% to 35.9%) and positive tweets increased (49.8% to 51.8%). Trust (0.85 words/tweet/day) and fear (0.66 words/tweet/day) were the dominant positive and negative emotions, respectively.\n\nConclusionsPositive sentiments dominated during the COVID-19 lockdown in India. A surveillance system monitoring public sentiments on public health interventions for COVID-19 should be established.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Rizwan Suliankatchi Abdulkader", + "author_inst": "ICMR-National Institute of Epidemiology" + }, + { + "author_name": "Kathiresan Jeyashree", + "author_inst": "ICMR-National Institute of Epidemiology" + }, + { + "author_name": "Deneshkumar Venugopal", + "author_inst": "Manonmaniam Sundaranar University" + }, + { + "author_name": "K Senthamarai Kannan", + "author_inst": "Manonmaniam Sundaranar University" + }, + { + "author_name": "Manickam Ponnaiah", + "author_inst": "ICMR-National Institute of Epidemiology" + }, + { + "author_name": "Manoj Murhekar", + "author_inst": "ICMR-National Insitute of Epidemiology" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2022.06.16.22276531", "rel_title": "Vaccination and testing as a means of ending the COVID-19 pandemic: comparative and statistical analysis", @@ -296712,65 +298820,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.06.14.22276397", - "rel_title": "Association between Bisphosphonate use and COVID-19 related outcomes: a retrospective cohort study", - "rel_date": "2022-06-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.14.22276397", - "rel_abs": "BackgroundAlthough there are several efficacious vaccines against COVID-19, vaccination rates in many regions around the world remain insufficient to prevent continued high disease burden and emergence of viral variants. Repurposing of existing therapeutics that prevent or mitigate severe COVID-19 could help to address these challenges. The objective of this study was to determine whether prior use of bisphosphonates is associated with reduced incidence and/or severity of COVID-19.\n\nMethodsA retrospective cohort study utilizing payer-complete health insurance claims data from 8,239,790 patients with continuous medical and prescription insurance from 1-1-2019 to 6-30-2020 was performed. The primary exposure of interest was use of any bisphosphonate from 1-1-2019 to 2-29-2020. Outcomes of interest included: (a) testing for SARS-CoV-2 infection; (b) COVID-19 diagnosis; and (c) hospitalization with COVID-19 diagnosis between 3-1-2020 and 6-30-2020.\n\nResults7,906,603 patients for whom continuous medical and prescription insurance information was available were selected. 450,366 bisphosphonate users were identified and 1:1 propensity score-matched to bisphosphonate non-users by age, gender, insurance type, primary-care-provider visit in 2019, and comorbidity burden. Bisphosphonate users had lower odds ratios (OR) of testing for SARS-CoV-2 infection (OR=0.22; 95%CI:0.21-0.23; p<0.001), COVID-19 diagnosis (OR=0.23; 95%CI:0.22-0.24; p<0.001), and COVID-19-related hospitalization (OR=0.26; 95%CI:0.24-0.29; p<0.001). Sensitivity analyses yielded results consistent with the primary analysis. Bisphosphonate-use was also associated with decreased odds of acute bronchitis (OR=0.23; 95%CI:0.22-0.23; p<0.001) or pneumonia (OR=0.32; 95%CI:0.31-0.34; p<0.001) in 2019, suggesting that bisphosphonates may protect against respiratory infections by a variety of pathogens, including but not limited to SARS-CoV-2.\n\nConclusionsPrior bisphosphonate-use was associated with dramatically reduced odds of SARS-CoV-2 testing, COVID-19 diagnosis, and COVID-19-related hospitalizations. Prospective clinical trials will be required to establish a causal role for bisphosphonate-use in COVID-19-related outcomes.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Ulrich H von Andrian", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Jeffrey Thompson", - "author_inst": "Cerner Enviza" - }, - { - "author_name": "Yidi Wang", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Tobias Dreischulte", - "author_inst": "Ludwig-Maximilians-University" - }, - { - "author_name": "Olga Barreiro", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Rodrigo J Gonzalez", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Colette Matysiak", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Harold R Neely", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Marietta Rottenkolber", - "author_inst": "Ludwig-Maximilians-University" - }, - { - "author_name": "Thmoas Haskell", - "author_inst": "Cerner Enviza" - }, - { - "author_name": "Stefan Endres", - "author_inst": "Ludwig-Maximilians-University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.06.20.22276641", "rel_title": "Can we mitigate the psychological impacts of social isolation using behavioural activation? Long-term results of the UK BASIL Urgent Public Health COVID-19 pilot randomised controlled trial and living systematic review", @@ -298002,6 +300051,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.06.16.496375", + "rel_title": "An S1 subunit vaccine and combination adjuvant (COVAC-1) elicits robust protection against SARS-CoV-2 challenge in African green monkeys", + "rel_date": "2022-06-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.16.496375", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the agent responsible for the ongoing global pandemic. With over 500 million cases and more than 6 million deaths reported globally, the need for access to effective vaccines is clear. An ideal SARS-CoV-2 vaccine will prevent pathology in the lungs and prevent virus replication in the upper respiratory tract, thus reducing transmission. Here, we assessed the efficacy of an adjuvanted SARS-CoV-2 S1 subunit vaccine, called COVAC-1, in an African green monkey (AGM) model. AGMs immunized and boosted with COVAC-1 were protected from SARS-CoV-2 challenge compared to unvaccinated controls based on reduced pathology and reduced viral RNA levels and infectious virus in the respiratory tract. Both neutralizing antibodies and antibodies capable of mediating antibody-dependent cell-mediated cytotoxicity (ADCC) were observed in vaccinated animals prior to the challenge. COVAC-1 induced effective protection, including in the upper respiratory tract, thus supporting further development and utility for determining the mechanism that confers this protection.\n\nAUTHOR SUMMARYVaccines that can prevent the onward transmission of SARS-CoV-2 and prevent disease are highly desirable. Whether this can be accomplished without mucosal immunization by a parenterally administered subunit vaccine is not well established. Here we demonstrate that following two vaccinations, a protein subunit vaccine containing the S1 portion of the SARS-CoV-2 spike glycoprotein and the novel adjuvant TriAdj significantly reduces the amount of virus in the lungs and also mediates rapid clearance of the virus from the upper respiratory tract. Further support of the effectiveness of COVAC-1 was the observation of reduced pathology in the lungs and viral RNA being largely absent from tissues, blood, and rectal swabs. Thus COVAC-1 appears promising at mediating protection in both the upper and lower respiratory tract and may be capable of reducing subsequent transmission of SARS-CoV-2. Further investigation into the mechanism of protection in the upper respiratory tract and the initial immune response that supports this would be warranted.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Lauren Garnett", + "author_inst": "University of Manitoba Max Rady College of Medicine" + }, + { + "author_name": "Kaylie Tran", + "author_inst": "National Microbiology Laboratory" + }, + { + "author_name": "Mable Chan", + "author_inst": "National Microbiology Laboratory" + }, + { + "author_name": "Kevin Tierney", + "author_inst": "National Microbiology Laboratory" + }, + { + "author_name": "Zachary Schiffman", + "author_inst": "National Microbiology Laboratory" + }, + { + "author_name": "Jonathan Audet", + "author_inst": "National Microbiology Laboratory" + }, + { + "author_name": "Jocelyne Lew", + "author_inst": "University of Saskatchewan" + }, + { + "author_name": "Courtney Meilleur", + "author_inst": "National Microbiology Laboratory" + }, + { + "author_name": "Michael Chan", + "author_inst": "National Microbiology Laboratory" + }, + { + "author_name": "Kathy Manguiat", + "author_inst": "National Microbiology Laboratory" + }, + { + "author_name": "Nikesh Tailor", + "author_inst": "National Microbiology Laboratory" + }, + { + "author_name": "Robert Vendramelli", + "author_inst": "National Microbiology Laboratory" + }, + { + "author_name": "Yvon Deschambault", + "author_inst": "National Microbiology Laboratory" + }, + { + "author_name": "Guillaume Beaudoin-Bussi\u00e8res", + "author_inst": "University of Montreal: Universite de Montreal" + }, + { + "author_name": "Jonathan Richard", + "author_inst": "University of Montreal: Universite de Montreal" + }, + { + "author_name": "Andr\u00e9s Finzi", + "author_inst": "University of Montreal: Universite de Montreal" + }, + { + "author_name": "Rick Higgins", + "author_inst": "University of Manitoba Max Rady College of Medicine" + }, + { + "author_name": "Sylvia van den Hurk", + "author_inst": "University of Saskatchewan" + }, + { + "author_name": "Volker Gerdts", + "author_inst": "University of Saskatchewan" + }, + { + "author_name": "James Strong", + "author_inst": "National Microbiology Laboratory" + }, + { + "author_name": "Darryl Falzarano", + "author_inst": "University of Saskatchewan" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.06.16.22276514", "rel_title": "High Mortality among Older Patients Hospitalized with COVID-19 during the First Pandemic Wave", @@ -298658,77 +300806,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.06.17.22276478", - "rel_title": "The prevalence, incidence and longevity of antibodies against SARS-CoV-2 among primary healthcare providers in Belgium: a prospective cohort study with 12 months of follow-up", - "rel_date": "2022-06-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.17.22276478", - "rel_abs": "ObjectivesTo estimate the prevalence, incidence, and longevity of antibodies against SARS-CoV-2 among primary healthcare providers (PHCPs).\n\nDesignProspective cohort study with 12 months of follow-up.\n\nSettingPrimary care in Belgium\n\nParticipantsAny general practitioner (GP) working in primary care in Belgium and any other PHCP from the same GP practice who physically manages (examines, tests, treats) patients were eligible. A convenience sample of 3,648 eligible PHCPs from 2,001 GP practices registered for this study (3,044 and 604 to start in December 2020 and January 2021, respectively). 3,390 PHCPs (92,9%) participated in their first testing timepoint (2,820 and 565, respectively) and 2,557 PHCPs (70,1%) in the last testing timepoint (December 2021).\n\nInterventionsParticipants were asked to perform a rapid serological test (RST) targeting IgM and IgG against the receptor binding domain (RBD) of SARS-CoV-2 and to complete an online questionnaire at each of maximum 8 testing timepoints.\n\nPrimary and secondary outcome measuresThe prevalence, incidence, and longevity of antibodies against SARS-CoV-2 both after natural infection and after vaccination.\n\nResultsAmong all participants, 67% were women and 77% GPs. Median age was 43 years. The seroprevalence in December 2020 (before vaccination availability) was 15.1% (95% CI: 13.5% to 16.6%), increased to 84.2% (95% CI: 82.9% to 85.5%) in March 2021 (after vaccination availability) and reached 93.9% (95% CI: 92.9% to 94.9%) in December 2021 (during booster vaccination availability and fourth (delta variant dominant) covid wave). Among not (yet) vaccinated participants the first monthly incidence of antibodies against SARS-CoV-2 was estimated to be 2.91% (95% CI: 1.80% to 4.01%). The longevity of antibodies is higher in PHCPs with self-reported COVID-19 infection.\n\nConclusionsThis study confirms that occupational health measures provided sufficient protection when managing patients. High uptake of vaccination resulted in high seroprevalence of SARS-CoV-2 antibodies in PHCPs in Belgium. Longevity of antibodies was supported by booster vaccination and virus circulation.\n\nRegistrationTrial registration number: NCT04779424\n\nStrengths and limitations of this studyO_LIThis large cohort study with 12 months follow-up could provide precise estimates of the prevalence and incidence of antibodies against SARS-CoV-2 among primary health care providers (PHCPs) at national and regional level in Belgium.\nC_LIO_LIThe rapid serological test (RST) used targets IgM and IgG against the receptor binding domain of SARS-CoV-2 and could therefore also assess the antibody response after vaccination, and longevity of antibodies against SARS-CoV-2 both after natural infection and after vaccination, but cannot distinguish between both.\nC_LIO_LIThe results in PHCPs could be compared to that of the general population and other population groups, e.g. health care workers in hospitals and nursing homes.\nC_LIO_LIThe use of a convenience sample, missing data points and reduced RST accuracy when performed and interpreted by many different participants could limit the validity of the study results.\nC_LI", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Niels Adriaenssens", - "author_inst": "University of Antwerp" - }, - { - "author_name": "Beatrice Scholtes", - "author_inst": "University of Liege" - }, - { - "author_name": "Robin Bruyndonckx", - "author_inst": "University of Antwerp" - }, - { - "author_name": "Pauline Van Ngoc", - "author_inst": "University of Liege" - }, - { - "author_name": "Jan Y Verbakel", - "author_inst": "KU Leuven" - }, - { - "author_name": "An De Sutter", - "author_inst": "Ghent University" - }, - { - "author_name": "Stefan Heytens", - "author_inst": "Ghent University" - }, - { - "author_name": "Ann Van den Bruel", - "author_inst": "KU Leuven" - }, - { - "author_name": "Isabelle Desombere", - "author_inst": "Sciensano" - }, - { - "author_name": "Pierre Van Damme", - "author_inst": "University of Antwerp" - }, - { - "author_name": "Herman Goossens", - "author_inst": "University of Antwerp" - }, - { - "author_name": "Laetitia Buret", - "author_inst": "University of Liege" - }, - { - "author_name": "Els Duysburgh", - "author_inst": "Sciensano" - }, - { - "author_name": "Samuel Coenen", - "author_inst": "University of Antwerp" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "primary care research" - }, { "rel_doi": "10.1101/2022.06.16.22276503", "rel_title": "Home-use Photobiomodulation Device Treatment Outcomes for COVID-19", @@ -300040,6 +302117,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.06.14.22276401", + "rel_title": "Persistent circulating SARS-CoV-2 spike is associated with post-acute COVID-19 sequelae", + "rel_date": "2022-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.14.22276401", + "rel_abs": "The diagnosis and management of post-acute sequelae of COVID-19 (PASC) poses an ongoing medical challenge. Identifying biomarkers associated with PASC would immensely improve the classification of PASC patients and provide the means to evaluate treatment strategies. We analyzed plasma samples collected from a cohort of PASC and COVID-19 patients (n = 63) to quantify circulating viral antigens and inflammatory markers. Strikingly, we detect SARS-CoV-2 spike antigen in a majority of PASC patients up to 12 months post-diagnosis, suggesting the presence of an active persistent SARS-CoV-2 viral reservoir. Furthermore, temporal antigen profiles for many patients show the presence of spike at multiple time points over several months, highlighting the potential utility of the SARS-CoV-2 full spike protein as a biomarker for PASC.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Zoe Swank", + "author_inst": "Brigham and Women's Hospital, Harvard Medical School" + }, + { + "author_name": "Yasmeen Senussi", + "author_inst": "Brigham and Women's Hospital, Harvard Medical School" + }, + { + "author_name": "Galit Alter", + "author_inst": "Ragon Institute of MGH, MIT and Harvard" + }, + { + "author_name": "David R. Walt", + "author_inst": "Brigham and Women's Hospital/Harvard Medical School" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pathology" + }, { "rel_doi": "10.1101/2022.06.16.22276476", "rel_title": "Moral injury and psychological wellbeing in UK healthcare staff", @@ -300520,41 +302628,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.06.15.22276436", - "rel_title": "Global estimates of the fitness advantage of SARS-CoV-2 variant Omicron", - "rel_date": "2022-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.15.22276436", - "rel_abs": "New variants of SARS-CoV-2 show remarkable heterogeneity in their relative fitness both over time and space. In this paper we extend a previously published model for estimating the selection strength for new SARS-CoV-2 variants to a hierarchical, mixed-effects, renewal equation model. This formulation allows us to globally estimate selection effects at different spatial levels while controlling for complex patterns of transmission and jointly inferring the effects of unit-level covariates in the spatial heterogeneity of SARS-CoV-2 selection effects. Applying this model to the spread of Omicron in 40 counties finding evidence for very strong (64%) but very heterogeneous selection effects at the country level. We further considered different measures of vaccination levels and measures of recent population-level infection as possible explanations. However, none of those variables were found to explain a significant proportion of the heterogeneity in country-level selection effects. We did find a significant positive correlation between the selection advantage of Delta and Omicron at the country level, suggesting that region-specific explanatory variables of fitness differences do exist. Our method is implemented in the Stan programming language, can be run on standard commercial-grade computing resources, and should be straightforward to apply to future variants.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Christiaan H van Dorp", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Emma E Goldberg", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Nick Hengartner", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Ruian Ke", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Ethan O Romero-Severson", - "author_inst": "Los Alamos National Laboratory" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.06.12.22276299", "rel_title": "A Systematic Review on COVID-19 Vaccine preferences using Discrete Choice Experiments", @@ -302226,6 +304299,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.06.11.22276248", + "rel_title": "Assessing COVID-19 vaccination strategies in varied demographics using an individual-based model", + "rel_date": "2022-06-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.11.22276248", + "rel_abs": "BackgroundNew variants of SARS-CoV-2 are constantly discovered. Administration of COVID-19 vaccines and booster doses, combined with applications of non-pharmaceutical interventions (NPIs), is often used to prevent outbreaks of emerging variants. Such outbreak dynamics are further complicated by the populations behavior and demographic composition. Hence, realistic simulations are needed to estimate the efficiency of proposed vaccination strategies in conjunction with NPIs.\n\nMethodsWe developed an individual-based model of COVID-19 dynamics that considers age-dependent parameters such as contact matrices, probabilities of symptomatic and severe disease, and households age distribution. As a case study, we simulate outbreak dynamics under the demographic compositions of two Israeli cities with different household sizes and age distributions. We compare two vaccination strategies: vaccinate individuals in a currently prioritized age group, or dynamically prioritize neighborhoods with a high estimated reproductive number. Total infections and hospitalizations are used to compare the efficiency of the vaccination strategies under the two demographic structures, in conjunction with different NPIs.\n\nResultsWe demonstrate the effectiveness of vaccination strategies targeting highly infected localities and of NPIs actively detecting asymptomatic infections. We further show that there are different optimal vaccination strategies for each demographic composition of sub-populations, and that their application is superior to a uniformly applied strategy.\n\nConclusionOur study emphasizes the importance of tailoring vaccination strategies to subpopulations infection rates and to the unique characteristics of their demographics (e.g., household size and age distributions). The presented simulation framework and our findings can help better design future responses against the following emerging variants.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Noam Ben-Zuk", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Yair Daon", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Amit Sasson", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Dror Ben-Adi", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Amit Huppert", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Daniel Nevo", + "author_inst": "Tel Aviv University" + }, + { + "author_name": "Uri Obolski", + "author_inst": "Tel Aviv University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.06.11.22276266", "rel_title": "Stratifying elicited antibody dynamics after two doses of SARS-CoV-2 vaccine in a community-based cohort in Fukushima, Japan", @@ -302750,53 +304866,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.06.09.22276150", - "rel_title": "Antigen test swabs are comparable to nasopharyngeal swabs for sequencing of SARS-CoV-2", - "rel_date": "2022-06-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.09.22276150", - "rel_abs": "Viral genomic surveillance has been integral in the global response to the SARS-CoV-2 pandemic. Surveillance efforts rely on the availability of representative clinical specimens from ongoing testing activities. However, testing practices have recently shifted due to the widespread availability and use of rapid antigen tests, which could lead to gaps in future monitoring efforts. As such, genomic surveillance strategies must adapt to include laboratory workflows that are robust to sample type. To that end, we compare the results of RT-qPCR and viral genome sequencing using samples from positive BinaxNOW COVID-19 Antigen Card swabs (N=555) to those obtained from previously collected nasopharyngeal (NP) swabs used for nucleic acid amplification testing (N=135). We show that swabs obtained from antigen cards are comparable in performance to clinical excess samples from NP swabs, providing a viable alternative. This validation permits the reliable expansion of viral genomic surveillance to cases identified in the clinic or home setting where rapid antigen tests are used.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Sayf Al-Deen Hassouneh", - "author_inst": "University of Central Florida, Orlando, FL" - }, - { - "author_name": "Alexa Trujillo", - "author_inst": "University of Central Florida, Orlando, FL" - }, - { - "author_name": "Sobur Ali", - "author_inst": "University of Central Florida, Orlando, FL" - }, - { - "author_name": "Eleonora Cella", - "author_inst": "University of Central Florida, Orlando, FL" - }, - { - "author_name": "Catherine G Johnston", - "author_inst": "University of Central Florida, Orlando, FL" - }, - { - "author_name": "Katherine C DeRuff", - "author_inst": "2Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA" - }, - { - "author_name": "Pardis C Sabeti", - "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA" - }, - { - "author_name": "Taj Azarian", - "author_inst": "University of Central Florida, Orlando, FL" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.06.09.22276226", "rel_title": "American Covid: An Econometric Analysis of Variants.", @@ -304240,6 +306309,29 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.06.13.495792", + "rel_title": "Antigenic escape accelerated by the presence of immunocompromised hosts", + "rel_date": "2022-06-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.13.495792", + "rel_abs": "The repeated emergence of SARS-CoV-2 escape mutants from host immunity has obstructed the containment of the current pandemic and poses a serious threat to humanity. Prolonged infection in immunocompromised patients has received increasing attention as a driver of immune escape, and accumulating evidence suggests that viral genomic diversity and emergence of immune-escape mutants are promoted in immunocompromised patients. However, because immunocompromised patients comprise a small proportion of the host population, whether they have a significant impact on antigenic evolution at the population level is unknown. We used an evolutionary epidemiological model combining antigenic evolution and epidemiological dynamics in host populations with heterogeneity in immune competency to determine the impact of immunocompromised patients on the pathogen evolutionary dynamics of antigenic escape from host immunity. We derived analytical formulae of the speed of antigenic evolution in heterogeneous host populations and found that even a small number of immunocompromised hosts in the population significantly accelerates antigenic evolution. Our results demonstrate that immunocompromised hosts play a key role in viral adaptation at the population level and emphasize the importance of critical care and surveillance of immunocompromised hosts.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Ryuichi Kumata", + "author_inst": "The Graduate University of Advanced Studies" + }, + { + "author_name": "Akira Sasaki", + "author_inst": "Department of Evolutionary Studies of Biosystems, The Graduate University of Advanced Studies, SOKENDAI, Hayama, Kanagawa 2400139, Japan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2022.06.14.496021", "rel_title": "Protective efficacy of COVAXIN(R) against Delta and Omicron variants in hamster model", @@ -304736,41 +306828,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.06.13.495912", - "rel_title": "Accurate and Fast Clade Assignment via Deep Learning and Frequency Chaos Game Representation", - "rel_date": "2022-06-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.13.495912", - "rel_abs": "BackgroundSince the beginning of the COVID-19 pandemic there has been an explosion of sequencing of the SARS-CoV-2 virus, making it the most widely sequenced virus in the history. Several databases and tools have been created to keep track of genome sequences and variants of the virus, most notably the GISAID platform hosts millions of complete genome sequences, and it is continuously expanding every day. A challenging task is the development of fast and accurate tools that are able to distinguish between the different SARS-CoV-2 variants and assign them to a clade.\n\nResultsIn this paper, we leverage the Frequency Chaos Game Representation (FCGR) and Convolutional Neural Networks (CNNs) to develop an original method that learns how to classify genome sequences that we implement into CouGaR-g, a tool for the clade assignment problem on SARS-CoV-2 sequences. On a testing subset of the GISAID, CouGaR-g achieves an 96.29% overall accuracy, while a similar tool, Covidex, obtained a 77, 12% overall accuracy. As far as we know, our method is the first using Deep Learning and FCGR for intra-species classification. Furthermore, by using some feature importance methods CouGaR-g allows to identify k-mers that matches SARS-CoV-2 marker variants.\n\nConclusionsBy combining FCGR and CNNs, we develop a method that achieves a better accuracy than Covidex (which is based on Random Forest) for clade assignment of SARS-CoV-2 genome sequences, also thanks to our training on a much larger dataset, with comparable running times. Our method implemented in CouGaR-g is able to detect k-mers that capture relevant biological information that distinguishes the clades, known as marker variants.\n\nAvailabilityThe trained models can be tested online providing a FASTA file (with one or multiple sequences) at https://huggingface.co/spaces/BIASLab/sars-cov-2-classification-fcgr. CouGaR-g is also available at https://github.com/AlgoLab/CouGaR-g under the GPL.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Jorge Avila Cartes", - "author_inst": "Department of Computer Science, Systems and Communications. University of Milano--Bicocca, Italy" - }, - { - "author_name": "Santosh Anand", - "author_inst": "Department of Computer Science, Systems and Communications. University of Milano--Bicocca, Italy" - }, - { - "author_name": "Simone Ciccolella", - "author_inst": "Department of Computer Science, Systems and Communications. University of Milano--Bicocca, Italy" - }, - { - "author_name": "Paola Bonizzoni", - "author_inst": "Department of Computer Science, Systems and Communications. University of Milano--Bicocca, Italy" - }, - { - "author_name": "Gianluca Della Vedova", - "author_inst": "Department of Computer Science, Systems and Communications. University of Milano--Bicocca, Italy" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2022.06.12.495856", "rel_title": "SARS2Mutant: SARS-CoV-2 Amino-Acid Mutation Atlas Database", @@ -305770,6 +307827,73 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2022.06.09.495472", + "rel_title": "Tracking infectious entry routes of SARS-CoV-2", + "rel_date": "2022-06-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.09.495472", + "rel_abs": "SARS-CoV-2 cell entry starts with membrane attachment and ends with spike-protein (S) catalyzed membrane fusion depending on two cleavage steps, one usually by furin in producing cells and the second by TMPRSS2 on target cells. Endosomal cathepsins can carry out both. Using real-time 3D single virion tracking, we show fusion and genome penetration requires virion exposure to an acidic milieu of pH 6.2-6.8, even when furin and TMPRSS2 cleavages have occurred. We detect the sequential steps of S1-fragment dissociation, fusion, and content release from the cell surface in TMPRRS2 overexpressing cells only when exposed to acidic pH. We define a key role of an acidic environment for successful infection, found in endosomal compartments and at the surface of TMPRSS2 expressing cells in the acidic milieu of the nasal cavity.\n\nSignificance StatementInfection by SARS-CoV-2 depends upon the S large spike protein decorating the virions and is responsible for receptor engagement and subsequent fusion of viral and cellular membranes allowing release of virion contents into the cell. Using new single particle imaging tools, to visualize and track the successive steps from virion attachment to fusion, combined with chemical and genetic perturbations of the cells, we provide the first direct evidence for the cellular uptake routes of productive infection in multiple cell types and their dependence on proteolysis of S by cell surface or endosomal proteases. We show that fusion and content release always require the acidic environment from endosomes, preceded by liberation of the S1 fragment which depends on ACE2 receptor engagement.\n\nOne sentence summaryDetailed molecular snapshots of the productive infectious entry pathway of SARS-CoV-2 into cells", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Louis-Marie Bloyet", + "author_inst": "Washington University in St Louis" + }, + { + "author_name": "Spencer Stumpf", + "author_inst": "Washington University in St Louis" + }, + { + "author_name": "Zhuoming Liu", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Ravi Ojha", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Markku T Patjas", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Ahmed Geneid", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Catherine A Doyle", + "author_inst": "University of Virginia" + }, + { + "author_name": "Sanna Toppila-Salmi", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Antti Makitie", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Volker Kiessling", + "author_inst": "University of Virginia" + }, + { + "author_name": "Olli Vapalahti", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Sean P. J. Whelan", + "author_inst": "Washington University in Saint Louis" + }, + { + "author_name": "Giuseppe Balistreri", + "author_inst": "University of Helsinki" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.06.09.495433", "rel_title": "A cellular assay for spike/ACE2 fusion: quantification of fusion-inhibitory antibodies after COVID-19 and vaccination", @@ -306270,117 +308394,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2022.06.07.495149", - "rel_title": "SARS-CoV-2 spike protein induces long-term TLR4-mediated synapse and cognitive loss recapitulating Post-COVID syndrome", - "rel_date": "2022-06-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.07.495149", - "rel_abs": "Cognitive dysfunction is often reported in post-COVID patients, but its underlying mechanisms remain unknown. While some evidence indicate that SARS-CoV-2 can reach and directly impact the brain, others suggest viral neuroinvasion as a rare event. Independently of brain viral infection, the ability of SARS-CoV-2 spike (S) protein to cross the BBB and reach memory-related brain regions has already been shown. Here, we demonstrate that brain infusion of S protein in mice induces late cognitive impairment and increases serum levels of neurofilament light chain (NFL), which recapitulates post-COVID features. Neuroinflammation, hippocampal microgliosis and synapse loss are induced by S protein. Increased engulfment of hippocampal presynaptic terminals late after S protein brain infusion were found to temporally correlate with cognitive deficit in mice. Blockage of TLR4 signaling prevented S-associated detrimental effects on synapse and memory loss. In a cohort of 86 patients recovered from mild COVID-19, genotype GG TLR4 -2604G>A (rs10759931) was associated with poor cognitive outcome. Collectively, these findings indicate that S protein directly impacts the brain and suggest that TLR4 is a potential target to prevent post-COVID cognitive dysfunction.\n\nOne Sentence SummaryTLR4 mediates long-term cognitive impairment in mice and its genetic variant increases the risk of poor cognitive outcome in post-COVID patients.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Fabricia Lima Fontes-Dantas", - "author_inst": "School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil; Department of Pharmacology, Institute of Biology, Rio de Janeiro State Uni" - }, - { - "author_name": "Gabriel G Fernandes", - "author_inst": "School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil" - }, - { - "author_name": "Elisa G. Gutman", - "author_inst": "Translational Neuroscience Laboratory (LabNet), Post-Graduate Program in Neurology, Federal University of Rio de Janeiro State, RJ, Brazil." - }, - { - "author_name": "Emanuelle V. De Lima", - "author_inst": "School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil." - }, - { - "author_name": "Leticia S. Antonio", - "author_inst": "School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil." - }, - { - "author_name": "Mariana B. Hammerle", - "author_inst": "Clinical Medicine post-graduation program, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil" - }, - { - "author_name": "Hannah P. Mota-Araujo", - "author_inst": "School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil" - }, - { - "author_name": "Lilian C. Colodeti", - "author_inst": "School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil" - }, - { - "author_name": "Suzana M. B. Araujo", - "author_inst": "School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil" - }, - { - "author_name": "Talita N. da Silva", - "author_inst": "School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil" - }, - { - "author_name": "Larissa A. Duarte", - "author_inst": "Translational Neuroscience Laboratory (LabNet), Post-Graduate Program in Neurology, Federal University of Rio de Janeiro State, RJ, Brazil" - }, - { - "author_name": "Andreza L. Salvio", - "author_inst": "Translational Neuroscience Laboratory (LabNet), Post-Graduate Program in Neurology, Federal University of Rio de Janeiro State, RJ, Brazil" - }, - { - "author_name": "Karina L. Pires", - "author_inst": "Neurology Department of Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Brazil" - }, - { - "author_name": "Luciane A. A. Leon", - "author_inst": "Laboratorio de Desenvolvimento Tecnologico em Virologia. IOC/FIOCRUZ, Rio de Janeiro, Brasil" - }, - { - "author_name": "Claudia C. F. Vasconcelos", - "author_inst": "Neurology Department of Federal University of the State of Rio de Janeiro (UNIRIO), Rio de Janeiro, Brazil" - }, - { - "author_name": "Luciana Romao", - "author_inst": "Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21944-590, Brazil" - }, - { - "author_name": "Luiz E.B. Savio", - "author_inst": "Institute of Biophysics Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21944-590, Brazil" - }, - { - "author_name": "Jerson L. Silva", - "author_inst": "Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21944-590, Brazil" - }, - { - "author_name": "Robson da Costa", - "author_inst": "School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil" - }, - { - "author_name": "Julia R. Clarke", - "author_inst": "Institute of Biomedical Sciences, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21944-590, Brazil" - }, - { - "author_name": "Andrea T. Da Poian", - "author_inst": "Institute of Medical Biochemistry Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21944-590, Brazil" - }, - { - "author_name": "Soniza V. Alves-Leon", - "author_inst": "Division of Neurology, Hospital Clementino Fraga Filho, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil" - }, - { - "author_name": "Giselle F. Passos", - "author_inst": "School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil" - }, - { - "author_name": "Claudia P. Figueiredo", - "author_inst": "School of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "neuroscience" - }, { "rel_doi": "10.1101/2022.06.07.495215", "rel_title": "Efficacy of Parainfluenza Virus 5 (PIV5)-vectored Intranasal COVID-19 Vaccine as a Single Dose Vaccine and as a Booster against SARS-CoV-2 Variants", @@ -307932,6 +309945,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.06.04.22275989", + "rel_title": "Predictors of second COVID-19 booster dose or new COVID-19 vaccine hesitancy among nurses: a cross-sectional study", + "rel_date": "2022-06-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.04.22275989", + "rel_abs": "Aims and objectivesTo assess the levels of second COVID-19 booster dose or new COVID-19 vaccine hesitancy among nurses and explore the potential predictors of vaccine hesitancy.\n\nBackgroundCOVID-19 full vaccination seems to be highly effective against highly contagious variants of SARS-CoV-2. Healthcare workers are a high-risk group since they have experienced high levels of COVID-19-associated morbidity and mortality.\n\nMethodsAn on-line cross-sectional study was carried out in Greece in May 2022, using a self-administered questionnaire. The study population included nurses in healthcare services who were fully vaccinated against COVID-19 at the time of study. We considered socio-demographic characteristics, COVID-19-related variables, and attitudes toward COVID-19 vaccination and pandemic as potential predictors of vaccine hesitancy.\n\nResultsAmong 795 nurses, 30.9% were hesitant toward a second booster dose or a new COVID-19 vaccine. Independent predictors of hesitancy included lower educational level, absence of a chronic condition, good/very good self-perceived physical health, lack of flu vaccination during 2021, front-line nurses that provided healthcare to COVID-19 patients during the pandemic, nurses that had not been diagnosed with COVID-19 during the pandemic, and nurses that had at least one relative/friend that has died from COVID-19. Moreover, increased compliance with hygiene measures, increased fear of a second booster dose/new COVID-19 vaccine, and decreased trust in COVID-19 vaccination were associated with increased hesitancy.\n\nConclusionsOur study shows that a significant percentage of nurses are hesitant toward a second booster dose/new COVID-19 vaccine. This initial hesitancy could be a barrier to efforts to control the COVID-19 pandemic. There is a need to communicate COVID-19 vaccine science in a way that is accessible to nurses in order to decrease COVID-19 vaccine hesitancy.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Petros A Galanis", + "author_inst": "National and Kapodistrian University of Athens" + }, + { + "author_name": "Irene Vraka", + "author_inst": "P. and A. Kyriakou Childrens Hospital" + }, + { + "author_name": "Aglaia Katsiroumpa", + "author_inst": "Faculty of Nursing, National and Kapodistrian University of Athens" + }, + { + "author_name": "Olga Siskou", + "author_inst": "University of Piraeus" + }, + { + "author_name": "Olympia Konstantakopoulou", + "author_inst": "Faculty of Nursing, National and Kapodistrian University of Athens" + }, + { + "author_name": "Theodoros Katsoulas", + "author_inst": "Faculty of Nursing, National and Kapodistrian University of Athens" + }, + { + "author_name": "Theodoros Mariolis-Sapsakos", + "author_inst": "Faculty of Nursing, National and Kapodistrian University of Athens" + }, + { + "author_name": "Daphne Kaitelidou", + "author_inst": "Faculty of Nursing, National and Kapodistrian University of Athens" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.06.06.22276032", "rel_title": "Understanding COVID-19 admissions in the UK; Analysis of Freedom of Information Requests", @@ -308372,61 +310432,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2022.06.05.493249", - "rel_title": "Pathogen-Host Adhesion between SARS-CoV-2 S Proteins from Different Variants and Human ACE2 Probed at Single-Molecule and Single-Cell Levels", - "rel_date": "2022-06-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.05.493249", - "rel_abs": "Pathogen-Host adhesion is considered the first step of infection for many pathogens such as bacteria and virus. The binding of the receptor binding domain (RBD) of SARS-CoV-2 Spike protein (S protein) onto human angiotensin-converting enzyme 2 (ACE2) is considered as the first step for the SARS-CoV-2 to adhere onto the host cells during the infection. Within three years, a number of variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have been found all around the world. Here, we investigated the adhesion of S Proteins from different variants and ACE2 using atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) and single-cell force spectroscopy (SCFS). We found that the unbinding force and binding probability of the S protein from Delta variant to the ACE2 was the highest among the variants tested in our study at both single-molecule and single-cell levels. Molecular dynamics simulation showed that ACE2-RBD (Omicron) complex is destabilized by the E484A and Y505H mutations and stabilized by S477N and N501Y mutations, when compared with Delta variant. In addition, a neutralizing antibody, produced by immunization with wild type RBD of S protein, could effectively inhibit the binding of S proteins from wild type, Delta and Omicron variants onto ACE2. Our results provide new insight for the molecular mechanism of the adhesive interactions between S protein and ACE2 and suggest that effective monoclonal antibody can be prepared using wild type S protein against the different variants.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Xiaoxu Zhang", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Jialin Chen", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Bixia Hong", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Haifeng Xu", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Pengfei Pei", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Long Chen", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Yigang Tong", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Shi-Zhong Luo", - "author_inst": "Beijing university of chemcial technology" - }, - { - "author_name": "Huahao Fan", - "author_inst": "Beijing University of Chemical Technology" - }, - { - "author_name": "Chengzhi He", - "author_inst": "Beijing University of Chemical Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2022.06.05.22276008", "rel_title": "Transplantation of solid organs recovered from deceased donors recently infected by SARS-CoV-2 in the United States", @@ -309702,6 +311707,25 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2022.06.03.494608", + "rel_title": "Taxonium: a web-based tool for exploring large phylogenetic trees", + "rel_date": "2022-06-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.06.03.494608", + "rel_abs": "The COVID-19 pandemic has resulted in a step change in the scale of sequencing data, with more genomes of SARS-CoV-2 having been sequenced than any other organism on earth. These sequences reveal key insights when represented as a phylogenetic tree, which captures the evolutionary history of the virus, and allows the identification of transmission events and the emergence of new variants. However, existing web-based tools for exploring phylogenies do not scale to the size of datasets now available for SARS-CoV-2. We have developed Taxonium, a new tool that uses WebGL to allow the exploration of trees with tens of millions of nodes in the browser for the first time. Taxonium links each node to associated metadata and supports mutation-annotated trees, which are able to capture all known genetic variation in a dataset. It can either be run entirely locally in the browser, from a server-based backend, or as a desktop application. We describe insights that analysing a tree of five million sequences can provide into SARS-CoV-2 evolution, and provide a tool at cov2tree.org for exploring a public tree of more than five million SARS-CoV-2 sequences. Taxonium can be applied to any tree, and is available at taxonium.org, with source code at github.com/theosanderson/taxonium.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Theo Sanderson", + "author_inst": "Francis Crick Institute" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.06.02.493651", "rel_title": "Distinct antibody responses to endemic coronaviruses pre- and post-SARS-CoV-2 infection in Kenyan infants and mothers", @@ -310162,49 +312186,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.06.02.22275918", - "rel_title": "Delays in COVID-19 Diagnosis and Hospitalization and Outcomes -- New York City, New York, USA, October 2020-November 2021", - "rel_date": "2022-06-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.06.02.22275918", - "rel_abs": "COVID-19 patients diagnosed [≥]3 days after symptom onset had increased odds of hospitalization. The 75th percentile for diagnosis delay was 5 days for residents of low-privilege areas and Black and Hispanic people diagnosed before SARS-CoV-2 Delta predominance, compared with 4 days for other patients, indicating inequities in prompt diagnosis.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Laura E Graf", - "author_inst": "New York City Department of Health and Mental Hygiene" - }, - { - "author_name": "Eric R Peterson", - "author_inst": "New York City Department of Health and Mental Hygiene" - }, - { - "author_name": "Jennifer Baumgartner", - "author_inst": "New York City Department of Health and Mental Hygiene" - }, - { - "author_name": "Anne Fine", - "author_inst": "New York City Department of Health and Mental Hygiene" - }, - { - "author_name": "Corinne N Thompson", - "author_inst": "New York City Department of Health and Mental Hygiene" - }, - { - "author_name": "Kathleen Blaney", - "author_inst": "New York City Department of Health and Mental Hygiene" - }, - { - "author_name": "Sharon K Greene", - "author_inst": "New York City Department of Health and Mental Hygiene" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.06.03.22275961", "rel_title": "Genetic Diversity and Evolutionary Convergence of Cryptic SARS-CoV-2 Lineages Detected Via Wastewater Sequencing", @@ -311568,6 +313549,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2022.05.31.22275831", + "rel_title": "WAVES (Web-based tool for Analysis and Visualization of Environmental Samples) - a web application for visualization of wastewater pathogen sequencing results", + "rel_date": "2022-06-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.31.22275831", + "rel_abs": "Environmental monitoring of pathogens provides an accurate and timely source of information for public health authorities and policymakers. In the last two years, wastewater sequencing proved to be an effective way of detection and quantification of SARS-CoV-2 variants circulating in population. Wastewater sequencing produces substantial amounts of geographical and genomic data. Proper visualization of spatial and temporal patterns in this data is crucial for the assessment of the epidemiological situation and forecasting. Here, we present a web-based dashboard application for visualization and analysis of data obtained from sequencing of environmental samples. The dashboard provides multi-layered visualization of geographical and genomic data. It allows to display frequencies of detected pathogen variants as well as individual mutation frequencies. The features of WAVES for early tracking and detection of novel variants in the wastewater are demonstrated in an example of BA.1 variant and the signature Spike mutation S:E484A. WAVES dashboard is easily customized through the editable configuration file and can be used for different types of pathogens and environmental samples.\n\nAvailabilityWAVES source code is freely available at https://github.com/ptriska/WavesDash under MIT license.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Petr Triska", + "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences" + }, + { + "author_name": "Fabian Amman", + "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences" + }, + { + "author_name": "Lukas Endler", + "author_inst": "CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences" + }, + { + "author_name": "Andreas Bergthaler", + "author_inst": "Medical University of Vienna" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.06.01.22275842", "rel_title": "The spread of infectious diseases from a physics perspective", @@ -312032,41 +314044,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.05.31.22275746", - "rel_title": "Symptom variation, correlations, and relationship to physical activity in Long Covid: intensive longitudinal study", - "rel_date": "2022-06-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.31.22275746", - "rel_abs": "BackgroundPeople with Long Covid (Post-Acute Sequelae of Covid-19) describe multiple symptoms which vary between and within individuals over relatively short time intervals. We aimed to describe the real-time associations between different symptoms and between symptoms and physical activity at the individual patient level.\n\nMethods and FindingsIntensive longitudinal study of 82 adults with self-reported Long Covid (median duration 12-18 months). Data collection involved a smartphone app with 5 daily entries over 14 days and continuous wearing of a wrist accelerometer. Data items included 7 symptoms (Visual Analog Scales) and perceived demands in the preceding period (Likert scales). Activity was measured using mean acceleration in the 3-hour periods preceding and following app data entry. Analysis used within-person correlations of symptoms pairs and both pooled and individual symptom networks derived from graphical vector autoregression.\n\nApp data was suitable for analysis from 74 participants (90%) comprising 4022 entries representing 77.6% of possible entries. Symptoms varied substantially within individuals and were only weakly auto-correlated. The strongest between-subject symptom correlations were of fatigue with pain (partial coefficient 0.5) and cognitive difficulty with light-headedness (0.41). Pooled within-subject correlations showed fatigue correlated with cognitive difficulty (partial coefficient 0.2) pain (0.19) breathlessness (0.15) and light-headedness (0.12) but not anxiety. Cognitive difficulty was correlated with anxiety and light-headedness (partial coefficients 0.16 and 0.17). Individual participant correlation heatmaps and symptom networks showed no clear patterns indicative of distinct phenotypes.\n\nSymptoms, including fatigue, were inconsistently correlated with prior or subsequent physical activity: this may reflect adjustment of activity in response to symptoms. Delayed worsening of symptoms after the highest activity peak was observed in 7 participants.\n\nConclusionSymptoms of Long Covid vary within individuals over short time scales, with heterogenous patterns of symptom correlation. The findings are compatible with altered central symptom processing as an additional factor in Long Covid.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Christopher Burton", - "author_inst": "University of Sheffield" - }, - { - "author_name": "Helen Dawes", - "author_inst": "University of Exeter" - }, - { - "author_name": "Simon Goodwill", - "author_inst": "Sheffield Hallam University" - }, - { - "author_name": "Michael Thelwell", - "author_inst": "Sheffield Hallam University" - }, - { - "author_name": "Caroline Dalton", - "author_inst": "Sheffield Hallam University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.06.01.22275858", "rel_title": "Vaccine effectiveness against SARS-CoV-2 reinfection during periods of Alpha (B.1.1.7), Delta (B.1.617.2) or Omicron (B.1.1.529) dominance: A Danish nationwide study", @@ -313278,6 +315255,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.05.30.22275757", + "rel_title": "Young age, student status and reported non-binary gender associate strongly with decreased functioning during Covid-19 pandemic in a university community.", + "rel_date": "2022-05-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.30.22275757", + "rel_abs": "BackgroundCovid-19 pandemic has had detrimental effects on physical and mental well-being whereas there are fewer studies on Covid-19 effects on everyday functioning.\n\nAimsWe aimed to investigate effects of Covid-19 on functioning and related factors in a university community.\n\nMethodIn all, 2004 students and university personnel responded to a Webropol survey in May 2021, when the measures for preventing Covid-19 infections had sustained about a year and a half. Functioning included Visual Analog Scale (0 to 10) assessments on ability to function and ability to work.\n\nResultsYoung age, reported non-binary gender, being student, low resilience, loneliness, received mental care and minor physical exercise, as well as depressive symptoms associated with inferior functioning and negative effects of Covid-19 on functioning. Good school performance at adolescence associated with better, while childhood adversities associated with poorer functioning.\n\nConclusionsIn the university community, young age and non-binary gender associated with decreased functioning during Covid-19 pandemic. Functioning of students was lower than in that of the university personnel. The need for therapeutic counselling and interventions is greatest among young students.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Raimo K. R. Salokangas", + "author_inst": "University of Turku" + }, + { + "author_name": "Tiina From", + "author_inst": "University of Turku" + }, + { + "author_name": "Jarmo Hietala", + "author_inst": "University of Turku and Turku University Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.05.25.22275569", "rel_title": "Modelling patterns of SARS-CoV-2 circulation in the Netherlands, August 2020-February 2022, revealed by a nationwide sewage surveillance program", @@ -313698,49 +315702,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.05.29.22275262", - "rel_title": "Incidence of Post-Covid Syndrome and Associated Symptoms in Outpatient Care in Bavaria, Germany", - "rel_date": "2022-05-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.29.22275262", - "rel_abs": "ObjectivesTo estimate the treatment incidence of Post-Covid Syndrome in the context of office-based care in Bavaria, Germany, and to establish whether related diagnoses occur more frequently than in patients with no known history of COVID-19.\n\nDesignRetrospective analysis of routinely collected claims data.\n\nSettingOffice-based care in Bavaria, Germany.\n\nParticipants391,990 patients with confirmed COVID-19 diagnosis, 62,659 patients with other respiratory infection, and a control group of 659,579 patients with no confirmed or suspected diagnosis COVID-19.\n\nPrimary and Secondary Outcome MeasuresPrimary outcome is diagnosis of a Post-COVID Syndrome by an office-based physician. Secondary outcomes are: Chronic Fatigue Syndrome (CFS), psychological disorder, fatigue, mild cognitive impairment, disturbances of taste and smell, dyspnea, pulmonary embolism and myalgia.\n\nResultsAmong all patients with confirmed COVID-19 infection, 14.2% (95% CI: 14.0-14.5) received a diagnosis of a Post-COVID Syndrome, and 6.7% (6.5-6.9) received the diagnosis in at least two quarterly periods during a two-year follow-up. Compared with patients with other respiratory infections and with controls, patients with COVID-19 more frequently received a variety of diagnoses including CFS (1.6% vs. 0.6% and 0.3%, respectively), fatigue (13.3% vs. 9.2% and 6.0%), dyspnea (9.9% vs. 5.1% and 3.2%) and disturbances of taste and smell (3.2% vs. 1.2% and 0.5%). The treatment incidence of Post-COVID Syndrome was highest among adults aged 40-59 (19.0%) and lowest among children aged below 12 years (2.6%).\n\nConclusionsOur results demonstrate a moderately high incidence of Post-COVID Syndrome two years after infection with COVID-19. There is an urgent need to find efficient and effective solutions to help patients with mental disorders, dyspnea, fatigue and loss of smell. Guidelines and treatment algorithms, including referral criteria, occupational and physical therapy, require promptly and coherent implementation. Further research is required both to find new therapeutic options and to assess the implications of Post-COVID Syndrome for health services.\n\nStrengths and Limitations of the Study\n\nO_LIThe data cover all statutory health insurance companies in Bavaria and have high generalisability to the general population.\nC_LIO_LIBy considering the proportion of COVID-19 patients consulting a physician, our results are better able to differentiate between everyday complaints and medically significant illness than data from a self-reported questionnaire.\nC_LIO_LIFollow-up of up to two years enables first assessment of the proportion requiring continuous care for a Post-COVID Syndrome.\nC_LIO_LIThe routinely collected data are not audited and contain little information regarding the severity of the symptoms.\nC_LI", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ewan Donnachie", - "author_inst": "Bavarian Association of Statutory Health Insurance Physicians" - }, - { - "author_name": "Alexander Hapfelmeier", - "author_inst": "Technical University Munich" - }, - { - "author_name": "Klaus Linde", - "author_inst": "Technical University Munich" - }, - { - "author_name": "Martin Tauscher", - "author_inst": "Bavarian Association of Statutory Health Insurance Physicians" - }, - { - "author_name": "Roman Gerlach", - "author_inst": "Bavarian Association of Statutory Health Insurance Physicians" - }, - { - "author_name": "Anna Greissel", - "author_inst": "Technical University Munich" - }, - { - "author_name": "Antonius Schneider", - "author_inst": "Technical University Munich" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.05.29.22273082", "rel_title": "Increased ambulance attendances related to suicide and self-injury in response to the pandemic", @@ -314756,6 +316717,149 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.05.25.22274904", + "rel_title": "Immunogenicity and Safety of Beta Adjuvanted Recombinant Booster Vaccine", + "rel_date": "2022-05-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.25.22274904", + "rel_abs": "BackgroundVariant-adaptated vaccines against coronavirus disease 2019 (COVID-19) as boosters are needed to increase a broader protection against SARS CoV-2 variants. New adjuvanted recombinant protein vaccines as heterologous boosters could maximize the response.\n\nMethodsIn this randomized, single-blinded, multicenter trial, adults who had received two doses of Pfizer-BioNTech mRNA vaccine (BNT162b2) 3 to7 months before were randomly assigned to receive a boost of BNT162b2, Sanofi/GSK SARS-CoV-2 adjuvanted recombinant protein MV D614 (monovalent parental formulation) or SARS-CoV-2 adjuvanted recombinant protein MV B.1.351 vaccine (monovalent Beta formulation). The primary endpoint was the percentage of subjects with a [≥]10-fold increase in neutralizing antibody titers for the Wuhan (D614) and B.1.351 (Beta) SARS-CoV-2 viral strains between day 0 and day 15.\n\nFindingsThe percentages of participants whose neutralizing antibody titers against the Wuhan (D614) SARS-CoV-2 strain increased by a factor [≥]10 between day 0 and day 15 was 55.3% (95% CI 43.4-66.7) in MV D614 group (n=76), 76.1% (64.5-85.4) in MV B.1.351 (Beta) group (n=71) and 63.2% (51.3-73.9) in BNT162b2 group (n=76). These percentages were 44.7% (33.3-56.6), 84.5% (74.0-92.0) and 51.3% (39.6-63.0) for the B.1.351 (Beta) viral strain, respectively. Higher neutralizing antibodies rates against Delta and Omicron BA.1 variants were also elicited after Sanofi/GSK MV Beta vaccine compared to the other vaccines. Comparable reactogenicity profile was observed with the three vaccines.\n\nInterpretationHeterologous boosting with the Sanofi/GSK Beta formulation vaccine resulted in a higher neutralizing antibody response against Beta variant but also the original strain and Delta and Omicron BA.1 variants, compared with mRNA BNT162b2 vaccine or the Sanofi/GSK MVD614 formulation. New vaccines containing Beta spike protein may represent an interesting strategy for broader protection against SARS CoV-2 variants.\n\nFundingFrench Ministries of Solidarity and Health and Research and Sanofi\n\nTrial registration numberClinicalTrials.gov identifier NCT05124171; EudraCT identifier 2021-004550-33.", + "rel_num_authors": 32, + "rel_authors": [ + { + "author_name": "Odile LAUNAY", + "author_inst": "AP-HP, H\u00f4pital Cochin; Inserm CIC 1417, Paris, France, Universit\u00e9 Paris Cit\u00e9, Facult\u00e9 de m\u00e9decine, Paris, France, F-CRIN, I REIVAC/COVIREIVAC, France" + }, + { + "author_name": "Marine Cachanado", + "author_inst": "Department of Clinical Pharmacology and Clinical Research Platform Paris-East (URCEST-CRC-CRB), APHP, H\u00f4pital St Antoine, Paris, France" + }, + { + "author_name": "Liem Binh Luong Ng\u0169yen", + "author_inst": "AP-HP, H\u00f4pital Cochin; Inserm CIC 1417, Paris, France; F-CRIN, I REIVAC/COVIREIVAC, France" + }, + { + "author_name": "Laetitia Ninove", + "author_inst": "Unit\u00e9 des Virus \u00c9mergents, UVE: Aix Marseille Univ, IRD 190, INSERM 1207, Marseille, France" + }, + { + "author_name": "Marie Lach\u00e2tre", + "author_inst": "AP-HP, H\u00f4pital Cochin; Inserm CIC 1417, Paris, France; F-CRIN, I REIVAC/COVIREIVAC, France" + }, + { + "author_name": "In\u00e8s Ben Ghezala", + "author_inst": "Inserm, CIC 1432, Clinical Investigation Center, Clinical Epidemiology/Clinical Trials Unit, University Hospital, Dijon, France" + }, + { + "author_name": "Marc Bardou", + "author_inst": "Inserm, CIC 1432, Clinical Investigation Center, Clinical Epidemiology/Clinical Trials Unit, University Hospital, Dijon, France; F-CRIN, I REIVAC/COVIREIVAC, Fr" + }, + { + "author_name": "Catherine Schmidt -Mutter", + "author_inst": "CIC Inserm 1434, H\u00f4pitaux Universitaires de Strasbourg, France, F-CRIN, I REIVAC/COVIREIVAC, France" + }, + { + "author_name": "Renaud Felten", + "author_inst": "CIC Inserm 1434, H\u00d4pitaux Universitaires de Strasbourg, France; F-CRIN, I REIVAC/COVIREIVAC, France" + }, + { + "author_name": "Karine Lacombe", + "author_inst": "Sorbonne Universit\u00e9, IPLESP Inserm UMR-S1136, H\u00f4pital St Antoine, AP-HP, Paris, France; F-CRIN, I REIVAC/COVIREIVAC, France" + }, + { + "author_name": "Laure Surgers", + "author_inst": "Sorbonne Universit\u00e9, IPLESP Inserm UMR-S1136, H\u00d4pital St Antoine, AP-HP, Paris, France; F-CRIN, I REIVAC/COVIREIVAC, France" + }, + { + "author_name": "Fabrice Laine", + "author_inst": "INSERM, CIC1414, CHU Rennes, Rennes, France; F-CRIN, I REIVAC/COVIREIVAC, France" + }, + { + "author_name": "Jean-Sebastien Allain", + "author_inst": "INSERM, CIC1414, CHU Rennes, Rennes, France; F-CRIN, I REIVAC/COVIREIVAC, France" + }, + { + "author_name": "Elisabeth Botelho-Nevers", + "author_inst": "Service d infectiologie, CIC1408, Inserm, CHU de Saint-Etienne, 42055 Saint-Etienne, France; F-CRIN, I REIVAC/COVIREIVAC, France" + }, + { + "author_name": "Marie-Pierre Tavolacci", + "author_inst": "Normandie Univ, UNIROUEN, U1073, CHU Rouen, and CIC-CRB 1404, F-76000 Rouen, France; F-CRIN, I REIVAC/COVIREIVAC, France" + }, + { + "author_name": "christian Chidiac", + "author_inst": "Maladies Infectieuses, GHN Croix Rousse, Hospices Civils de Lyon, UFR de M\u00e9decine et Ma&eutique Lyon Sud Universit\u00e9 Claude Bernard Lyon1, Universit&ea de Lyon, " + }, + { + "author_name": "Patricia Pavese", + "author_inst": "Maladies infectieuses et tropicales, CHU de Grenoble Alpes, France; F-CRIN, I REIVAC/COVIREIVAC, France" + }, + { + "author_name": "Bertrand Dussol", + "author_inst": "CIC 14-09, INSERM - Aix Marseille Universit\u00e9 H\u00f4pitaux Universitaires de Marseille; F-CRIN, I REIVAC/COVIREIVAC, France" + }, + { + "author_name": "Stephane Priet", + "author_inst": "Unit\u00e9 des Virus \u00c9mergents, UVE: Aix Marseille Univ, IRD 190, INSERM 1207, Marseille, France" + }, + { + "author_name": "Dominique Deplanque", + "author_inst": "Univ. Lille, Inserm, CHU Lille, CIC 1403 Centre d investigation clinique, F- 59000 Lille, France; F-CRIN, I REIVAC/COVIREIVAC, France" + }, + { + "author_name": "Amel Touati", + "author_inst": "Department of Clinical Pharmacology and Clinical Research Platform Paris-East (URCEST-CRC-CRB), APHP, H\u00f4pital St Antoine, Paris, France" + }, + { + "author_name": "Laureen Curci", + "author_inst": "AP-HP, H\u00f4pital Cochin; Inserm CIC 1417, Paris, France; F-CRIN, I REIVAC/COVIREIVAC, France" + }, + { + "author_name": "Eleine Konate", + "author_inst": "AP-HP, H\u00f4pital Cochin; Inserm CIC 1417, Paris, France; F-CRIN, I REIVAC/COVIREIVAC, France" + }, + { + "author_name": "Nadine Ben Hamouda", + "author_inst": "Service Immunologie Biologique, APHP, H\u00f4pital Europ\u00e9en Georges Pompidou, 75015 Paris, France ; PARCC, INSERM U970, Universit\u00e9 de Paris, 75006 Paris, France" + }, + { + "author_name": "Anissa Besbes", + "author_inst": "Service Immunologie Biologique, APHP, H\u00f4pital Europ\u00e9en Georges Pompidou, 75015 Paris, France ; PARCC, INSERM U970, Universit\u00e9 de Paris, 75006 Paris, France" + }, + { + "author_name": "Eunice Nubret", + "author_inst": "APHP, Direction de la Recherche Clinique et de l Innovation (DRCI), Paris, France" + }, + { + "author_name": "Florence Capelle", + "author_inst": "D\u00e9partement des Essais Cliniques de l AGEPS, DRCI-APHP, Paris, France" + }, + { + "author_name": "Laurence Berard", + "author_inst": "Department of Clinical Pharmacology and Clinical Research Platform Paris-East (URCEST-CRC-CRB), APHP, H\u00f4pital St Antoine, Paris, France" + }, + { + "author_name": "Alexandra Rousseau", + "author_inst": "Department of Clinical Pharmacology and Clinical Research Platform Paris-East (URCEST-CRC-CRB), APHP, H\u00d4pital St Antoine, Paris, France" + }, + { + "author_name": "Eric Tartour", + "author_inst": "Service d Immunologie Biologique, APHP, H\u00f4pital Europ\u00e9en Georges Pompidou, 75015 Paris, France ; PARCC, INSERM U970, Universit\u00e9 de Paris, 75006 Paris, France" + }, + { + "author_name": "Tabassome Simon", + "author_inst": "Department of Clinical Pharmacology and Clinical Research Platform Paris-East (URCEST-CRC-CRB), APHP, H\u00f4pital St Antoine, Paris, France" + }, + { + "author_name": "Xavier De Lamballerie", + "author_inst": "Unit\u00e9 des Virus \u00c9mergents, UVE: Aix Marseille Univ, IRD 190, INSERM 1207, Marseille, France" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.05.27.493569", "rel_title": "Spike mutation resilient scFv76 antibody counteracts SARS-CoV-2 lung damage upon aerosol delivery", @@ -315380,57 +317484,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2022.05.27.493400", - "rel_title": "The Glycan-Specificity of the Pineapple Lectin AcmJRL and its Carbohydrate-Dependent Binding of the SARS-CoV-2 Spike Protein", - "rel_date": "2022-05-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.27.493400", - "rel_abs": "The current SARS-CoV-2 pandemic has become one of the most challenging global health threats, with over 530 million reported infections by May 2022. In addition to vaccines, research and development have also been directed towards novel drugs. Since the highly glycosylated spike protein of SARS-CoV-2 is essential for infection, it constitutes a prime target for antiviral agents. The pineapple-derived jacalin-related lectin (AcmJRL) is present in the medication bromelain in significant quantities and has previously been described to bind mannosides. Here, we elucidated its ligand specificity by glycan array analysis, quantified the interaction with carbohydrates and validated high-mannose glycans as preferred ligands. Because the SARS-CoV-2 spike protein was previously reported to carry a high proportion of high-mannose N-glycans, we tested the binding of AcmJRL to recombinantly produced spike protein. We could demonstrate that AcmJRL binds the spike protein with a low micromolar KD in a carbohydrate-dependent fashion, suggesting its use as a potential SARS-CoV-2 neutralising agent.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Joscha Meiers", - "author_inst": "Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)" - }, - { - "author_name": "Jan Dastbaz", - "author_inst": "Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)" - }, - { - "author_name": "Sebastian Adam", - "author_inst": "Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)" - }, - { - "author_name": "Sari Rasheed", - "author_inst": "Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)" - }, - { - "author_name": "Susanne H Kirsch", - "author_inst": "Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)" - }, - { - "author_name": "Peter Meiser", - "author_inst": "Ursapharm" - }, - { - "author_name": "Peter Gross", - "author_inst": "Hochschule Kaiserslautern" - }, - { - "author_name": "Rolf Mueller", - "author_inst": "Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)" - }, - { - "author_name": "Alexander Titz", - "author_inst": "Helmholtz-Institut fuer Pharmazeutische Forschung Saarland" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2022.05.27.22275675", "rel_title": "A Model-Based Strategy on COVID-19 Vaccine Roll-out in the Philippines", @@ -317226,6 +319279,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.05.25.22275300", + "rel_title": "Limited induction of lung-resident memory T cell responses against SARS-CoV-2 by mRNA vaccination", + "rel_date": "2022-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.25.22275300", + "rel_abs": "Resident memory T cells (TRM) present at the respiratory tract may be essential to enhance early SARS-CoV-2 viral clearance, thus limiting viral infection and disease. While long-term antigen (Ag)-specific TRM are detectable beyond 11 months in the lung of convalescent COVID-19 patients after mild and severe infection, it is unknown if mRNA vaccination encoding for the SARS-CoV-2 S-protein can induce this frontline protection. We found that the frequency of CD4+ T cells secreting interferon (IFN){gamma} in response to S-peptides was variable but overall similar in the lung of mRNA-vaccinated patients compared to convalescent-infected patients. However, in vaccinated patients, lung responses presented less frequently a TRM phenotype compared to convalescent infected individuals and polyfunctional CD107a+ IFN{gamma}+ TRM were virtually absent. Thus, a robust and broad TRM response established in convalescent-infected individuals may be advantageous in limiting disease if the virus is not blocked by initial mechanisms of protection, such as neutralization. Still, mRNA vaccines might induce responses within the lung parenchyma, potentially contributing to the overall disease control.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Daan K.J. Pieren", + "author_inst": "Vall d'Hebron Research Institute (VHIR)" + }, + { + "author_name": "Sebasti\u00e1n G. Kuguel", + "author_inst": "Vall d'Hebron Research Institute (VHIR)" + }, + { + "author_name": "Joel Rosado", + "author_inst": "Vall d'Hebron Research Institute (VHIR)" + }, + { + "author_name": "Alba G. Robles", + "author_inst": "Vall d'Hebron Research Institute (VHIR)" + }, + { + "author_name": "Joan Rey-Cano", + "author_inst": "Vall d'Hebron Research Institute (VHIR)" + }, + { + "author_name": "Cristina Mancebo", + "author_inst": "Vall d'Hebron Research Institute (VHIR)" + }, + { + "author_name": "Juliana Esperalba", + "author_inst": "Vall d'Hebron Research Institute (VHIR)" + }, + { + "author_name": "Vicen\u00e7 Falc\u00f3", + "author_inst": "Vall d'Hebron Research Institute (VHIR)" + }, + { + "author_name": "Mar\u00eda J. Buz\u00f3n", + "author_inst": "Vall d'Hebron Research Institute (VHIR)" + }, + { + "author_name": "Meritxell Genesc\u00e0", + "author_inst": "Vall d'Hebron Research Institute (VHIR)" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.05.25.22275487", "rel_title": "Modelling the impacts of public health interventions and weather on SARS-CoV-2 Omicron outbreak in Hong Kong", @@ -317738,29 +319846,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2022.05.21.22275421", - "rel_title": "Analysis of the genetic diversity of SARS-CoV-2 genomes carrying the Omicron B.1.1.529 mutation", - "rel_date": "2022-05-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.21.22275421", - "rel_abs": "In this work, we evaluated the levels of genetic diversity in 95 genomes of the carriers of the Omicron B.1.1.529 mutation in SARS-CoV-2 from South Africa, Asia, Massachusetts-USA, Rhode Island-USA, United Kingdom and Germany. All with 29,996pb extension and recovered from GENBANK and publicly available at the National Center for Biotechnology and Information (NCBI). All gaps and conserved sites were extracted for the construction of a phylogenetic tree and for specific methodologies of estimates of paired FST, Molecular Variance (AMOVA), Genetic Distance, Incompatibility, demographic expansion analyses, molecular diversity and of evolutionary divergence time analyses, always with 20,000 random permutations. The results revealed the presence of only 75 parsimony-informative sites, sites among the 29,996bp analyzed. The analyses based on FST values, confirmed the absence of distinct genetic structuring with fixation index of 98% and with a greater component of population variation (6%) for a \"p\" 0.05. Tau variations (related to the ancestry of the groups), did not reveal significant moments of divergence, supported by the incompatible analysis of the observed distribution ({tau} = 0%). It is safe to say that the large number of existing polymorphisms reflects major changes in the protein products of viral populations in all countries and especially In South Africa. This consideration provides the safety that, because there are large differences between the haplotypes studied, these differences are minimal within the populations analyzed geographically and, therefore, it does not seem safe to extrapolate the results of polymorphism and molecular diversity levels found in the Variant Omicron B.1.529 of SARS-CoV-2 for wild genomes or other mutants. This warns us that, due to their higher transmission speed and infection, possible problems of molecular adjustments in vaccines already in use may be necessary in the near future.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Br\u00e1ulio Wagner Correia da Silva", - "author_inst": "Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA, Vit\u00f3ria de Santo Ant\u00e3o, Pernambuco, Brazil" - }, - { - "author_name": "Pierre Teodosio Felix Sr.", - "author_inst": "Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA, Vit\u00f3ria de Santo Ant\u00e3o, Pernambuco, Brazil" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.05.23.22275445", "rel_title": "Post-covid medical complaints after SARS-CoV-2 Omicron vs Delta variants -a prospective cohort study", @@ -319060,6 +321145,141 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2022.05.24.22275398", + "rel_title": "Generalizable Long COVID Subtypes: Findings from the NIH N3C and RECOVER Programs", + "rel_date": "2022-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.24.22275398", + "rel_abs": "Accurate stratification of patients with post-acute sequelae of SARS-CoV-2 infection (PASC, or long COVID) would allow precision clinical management strategies. However, the natural history of long COVID is incompletely understood and characterized by an extremely wide range of manifestations that are difficult to analyze computationally. In addition, the generalizability of machine learning classification of COVID-19 clinical outcomes has rarely been tested. We present a method for computationally modeling PASC phenotype data based on electronic healthcare records (EHRs) and for assessing pairwise phenotypic similarity between patients using semantic similarity. Our approach defines a nonlinear similarity function that maps from a feature space of phenotypic abnormalities to a matrix of pairwise patient similarity that can be clustered using unsupervised machine learning procedures. Using k-means clustering of this similarity matrix, we found six distinct clusters of PASC patients, each with distinct profiles of phenotypic abnormalities. There was a significant association of cluster membership with a range of pre-existing conditions and with measures of severity during acute COVID-19. Two of the clusters were associated with severe manifestations and displayed increased mortality. We assigned new patients from other healthcare centers to one of the six clusters on the basis of maximum semantic similarity to the original patients. We show that the identified clusters were generalizable across different hospital systems and that the increased mortality rate was consistently observed in two of the clusters. Semantic phenotypic clustering can provide a foundation for assigning patients to stratified subgroups for natural history or therapy studies on PASC.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Justin Reese", + "author_inst": "Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA" + }, + { + "author_name": "Hannah Blau", + "author_inst": "The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA" + }, + { + "author_name": "Timothy Bergquist", + "author_inst": "Sage Bionetworks. Seattle, WA, USA" + }, + { + "author_name": "Johanna J. Loomba", + "author_inst": "The Integrated Translational Health Research Institute of Virginia (iTHRIV), University of Virginia, Charlottesville, Virginia, USA." + }, + { + "author_name": "Tiffany Callahan", + "author_inst": "Department of Biomedical Informatics, Columbia University, New York, NY, USA" + }, + { + "author_name": "Bryan Laraway", + "author_inst": "University of Colorado Anschutz Medical Campus, Aurora, CO, USA" + }, + { + "author_name": "Corneliu Antonescu", + "author_inst": "University of Arizona - Banner Health, Phoenix, AZ" + }, + { + "author_name": "Elena Casiraghi", + "author_inst": "AnacletoLab, Dipartimento di Informatica, Universita degli Studi di Milano, Italy" + }, + { + "author_name": "Ben Coleman", + "author_inst": "The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA" + }, + { + "author_name": "Michael Gargano", + "author_inst": "The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA" + }, + { + "author_name": "Kenneth Wilkins", + "author_inst": "Biostatistics Program, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA." + }, + { + "author_name": "Luca Cappelletti", + "author_inst": "AnacletoLab, Dipartimento di Informatica, Universita degli Studi di Milano, Italy" + }, + { + "author_name": "Tommaso Fontana", + "author_inst": "AnacletoLab, Dipartimento di Informatica, Universita degli Studi di Milano, Italy" + }, + { + "author_name": "Nariman Ammar", + "author_inst": "University of Tennessee Health Science Center, Memphis, TN, USA" + }, + { + "author_name": "Blessy Antony", + "author_inst": "Department of Computer Science, Virginia Tech, Blacksburg, VA, USA." + }, + { + "author_name": "T. M. Murali", + "author_inst": "Department of Computer Science, Virginia Tech, Blacksburg, VA, USA." + }, + { + "author_name": "Guy Karlebach", + "author_inst": "The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA" + }, + { + "author_name": "Julie A. McMurry", + "author_inst": "University of Colorado Anschutz Medical Campus, Aurora, CO, USA" + }, + { + "author_name": "Andrew Williams", + "author_inst": "Tufts Medical Center Clinical and Translational Science Institute, Tufts Medical Center, Boston, MA, USA" + }, + { + "author_name": "Richard Moffitt", + "author_inst": "Stony Brook University Department of Biomedical Informatics and Stony Brook Cancer Center, Stony Brook, NY, USA" + }, + { + "author_name": "Jineta Banerjee", + "author_inst": "Sage Bionetworks. Seattle, WA, USA" + }, + { + "author_name": "Anthony E. Solomonides", + "author_inst": "NorthShore University HealthSystem Research Institute, Evanston, IL" + }, + { + "author_name": "Hannah Davis", + "author_inst": "Patient-Led Research Collaborative, NY, USA" + }, + { + "author_name": "Kristin Kostka", + "author_inst": "Northeastern University, OHDSI Center at the Roux Institute, Boston, MA, USA" + }, + { + "author_name": "Giorgio Valentini", + "author_inst": "AnacletoLab, Dipartimento di Informatica, Universita degli Studi di Milano, Italy" + }, + { + "author_name": "David Sahner", + "author_inst": "Axle Informatics, Rockville, MD, USA" + }, + { + "author_name": "Christopher G. Chute", + "author_inst": "Schools of Medicine, Public Health, and Nursing, Johns Hopkins University, Baltimore, MD" + }, + { + "author_name": "Charisse Madlock-Brown", + "author_inst": "University of Tennessee Health Science Center, Memphis, TN, USA" + }, + { + "author_name": "Melissa A. Haendel", + "author_inst": "University of Colorado Anschutz Medical Campus, Aurora, CO, USA" + }, + { + "author_name": "Peter N. Robinson", + "author_inst": "The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT, USA" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.05.24.22275498", "rel_title": "Health workers Perspective on the Feasibility and Acceptability of the Introduction of AgRDT for COVID-19 in Kisumu County, Western Kenya", @@ -319528,153 +321748,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.05.22.22275417", - "rel_title": "Comparative effectiveness of sotrovimab and molnupiravir for prevention of severe COVID-19 outcomes in non-hospitalised patients: an observational cohort study using the OpenSAFELY platform", - "rel_date": "2022-05-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.22.22275417", - "rel_abs": "ObjectiveTo compare the effectiveness of sotrovimab (a neutralising monoclonal antibody) vs. molnupiravir (an antiviral) in preventing severe COVID-19 outcomes in non-hospitalised high-risk COVID-19 adult patients.\n\nDesignWith the approval of NHS England, we conducted a real-world cohort study using the OpenSAFELY-TPP platform.\n\nSettingPatient-level electronic health record data were obtained from 24 million people registered with a general practice in England that uses TPP software. The primary care data were securely linked with data on COVID-19 infection and therapeutics, hospital admission, and death within the OpenSAFELY-TPP platform, covering a period where both medications were frequently prescribed in community settings.\n\nParticipantsNon-hospitalised adult COVID-19 patients at high risk of severe outcomes treated with sotrovimab or molnupiravir since December 16, 2021.\n\nInterventionsSotrovimab or molnupiravir administered in the community by COVID-19 Medicine Delivery Units.\n\nMain outcome measureCOVID-19 related hospitalisation or COVID-19 related death within 28 days after treatment initiation.\n\nResultsBetween December 16, 2021 and February 10, 2022, 3331 and 2689 patients were treated with sotrovimab and molnupiravir, with no substantial differences in their baseline characteristics. The mean age of all 6020 patients was 52 (SD=16) years; 59% were female, 89% White and 88% had three or more COVID-19 vaccinations. Within 28 days after treatment initiation, 87 (1.4%) COVID-19 related hospitalisations/deaths were observed (32 treated with sotrovimab and 55 with molnupiravir). Cox proportional hazards models stratified by area showed that after adjusting for demographics, high-risk cohort categories, vaccination status, calendar time, body mass index and other comorbidities, treatment with sotrovimab was associated with a substantially lower risk than treatment with molnupiravir (hazard ratio, HR=0.54, 95% CI: 0.33 to 0.88; P=0.014). Consistent results were obtained from propensity score weighted Cox models (HR=0.50, 95% CI: 0.31 to 0.81; P=0.005) and when restricted to fully vaccinated people (HR=0.53, 95% CI: 0.31 to 0.90; P=0.019). No substantial effect modifications by other characteristics were detected (all P values for interaction>0.10). Findings were similar in an exploratory analysis of patients treated between February 16 and May 1, 2022 when the Omicron BA.2 variant was dominant in England.\n\nConclusionIn routine care of non-hospitalised high-risk adult patients with COVID-19 in England, those who received sotrovimab were at lower risk of severe COVID-19 outcomes than those receiving molnupiravir.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Bang Zheng", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Amelia CA Green", - "author_inst": "University of Oxford" - }, - { - "author_name": "John Tazare", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Helen J Curtis", - "author_inst": "University of Oxford" - }, - { - "author_name": "Louis Fisher", - "author_inst": "University of Oxford" - }, - { - "author_name": "Linda Nab", - "author_inst": "University of Oxford" - }, - { - "author_name": "Anna Schultze", - "author_inst": "London School of Hygiene and Trop. Med." - }, - { - "author_name": "Viyaasan Mahalingasivam", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Edward Parker", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "William J Hulme", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sebastian CJ Bacon", - "author_inst": "University of Oxford" - }, - { - "author_name": "Nicholas J DeVito", - "author_inst": "University of Oxford" - }, - { - "author_name": "Christopher Bates", - "author_inst": "TPP" - }, - { - "author_name": "David Evans", - "author_inst": "University of Oxford" - }, - { - "author_name": "Peter Inglesby", - "author_inst": "University of Oxford" - }, - { - "author_name": "Henry Drysdale", - "author_inst": "University of Oxford" - }, - { - "author_name": "Simon Davy", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jonathan Cockburn", - "author_inst": "TPP" - }, - { - "author_name": "Caroline E Morton", - "author_inst": "University of Oxford" - }, - { - "author_name": "George Hickman", - "author_inst": "University of Oxford" - }, - { - "author_name": "Tom Ward", - "author_inst": "University of Oxford" - }, - { - "author_name": "Rebecca M Smith", - "author_inst": "University of Oxford" - }, - { - "author_name": "John Parry", - "author_inst": "TPP" - }, - { - "author_name": "Frank Hester", - "author_inst": "TPP" - }, - { - "author_name": "Sam Harper", - "author_inst": "TPP" - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "University of Oxford" - }, - { - "author_name": "Rosalind M Eggo", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Alex J Walker", - "author_inst": "University of Oxford" - }, - { - "author_name": "Stephen JW Evans", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Ian J Douglas", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Brian MacKenna", - "author_inst": "University of Oxford" - }, - { - "author_name": "Ben Goldacre", - "author_inst": "University of Oxford" - }, - { - "author_name": "Laurie A Tomlinson", - "author_inst": "London School of Hygiene and Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.05.20.22275396", "rel_title": "Omicron and vaccines: An analysis on the decline in COVID-19 mortality", @@ -321170,6 +323243,169 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, + { + "rel_doi": "10.1101/2022.05.19.22275214", + "rel_title": "Antibody levels following vaccination against SARS-CoV-2: associations with post-vaccination infection and risk factors", + "rel_date": "2022-05-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.19.22275214", + "rel_abs": "SARS-CoV-2 antibody levels can be used to assess humoral immune responses following SARS-CoV-2 infection or vaccination, and may predict risk of future infection. From cross-sectional antibody testing of 9,361 individuals from TwinsUK and ALSPAC UK population-based longitudinal studies (jointly in April-May 2021, and TwinsUK only in November 2021-January 2022), we tested associations between antibody levels following vaccination and: (1) SARS-CoV-2 infection following vaccination(s); (2) health, socio-demographic, SARS-CoV-2 infection and SARS-CoV-2 vaccination variables.\n\nWithin TwinsUK, single-vaccinated individuals with the lowest 20% of anti-Spike antibody levels at initial testing had 3-fold greater odds of SARS-CoV-2 infection over the next six to nine months, compared to the top 20%. In TwinsUK and ALSPAC, individuals identified as at increased risk of COVID-19 complication through the UK \"Shielded Patient List\" had consistently greater odds (2 to 4-fold) of having antibody levels in the lowest 10%. Third vaccination increased absolute antibody levels for almost all individuals, and reduced relative disparities compared with earlier vaccinations.\n\nThese findings quantify the association between antibody level and risk of subsequent infection, and support a policy of triple vaccination for the generation of protective antibodies.\n\nLay summaryIn this study, we analysed blood samples from 9,361 participants from two studies in the UK: an adult twin registry, TwinsUK (4,739 individuals); and the Avon Longitudinal Study of Parents and Children, ALSPAC (4,622 individuals). We did this work as part of the UK Government National Core Studies initiative researching COVID-19. We measured blood antibodies which are specific to SARS-CoV-2 (which causes COVID-19). Having a third COVID-19 vaccination boosted antibody levels. More than 90% of people from TwinsUK had levels after third vaccination that were greater than the average level after second vaccination. Importantly, this was the case even in individuals on the UK \"Shielded Patient List\". We found that people with lower antibody levels after first vaccination were more likely to report having COVID-19 later on, compared to people with higher antibody levels. People on the UK \"Shielded Patient List\", and individuals who reported that they had poorer general health, were more likely to have lower antibody levels after vaccination. In contrast, people who had had a previous COVID-19 infection were more likely to have higher antibody levels following vaccination compared to people without infection. People receiving the Oxford/AstraZeneca rather than the Pfizer BioNTech vaccine had lower antibody levels after one or two vaccinations. However, after a third vaccination, there was no difference in antibody levels between those who had Oxford/AstraZeneca and Pfizer BioNTech vaccines for their first two doses. These findings support having a third COVID-19 vaccination to boost antibodies.", + "rel_num_authors": 37, + "rel_authors": [ + { + "author_name": "Nathan J Cheetham", + "author_inst": "King's College London" + }, + { + "author_name": "Milla Kibble", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Andrew Wong", + "author_inst": "University College London" + }, + { + "author_name": "Richard J Silverwood", + "author_inst": "University College London" + }, + { + "author_name": "Anika Knuppel", + "author_inst": "University College London" + }, + { + "author_name": "Dylan M Williams", + "author_inst": "University College London" + }, + { + "author_name": "Olivia K L Hamilton", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Paul H Lee", + "author_inst": "University of Leicester" + }, + { + "author_name": "Charis Bridger Staatz", + "author_inst": "University College London" + }, + { + "author_name": "Giorgio Di Gessa", + "author_inst": "University College London" + }, + { + "author_name": "Jingmin Zhu", + "author_inst": "University College London" + }, + { + "author_name": "Srinivasa Vittal Katikireddi", + "author_inst": "University of Glasgow" + }, + { + "author_name": "George B Ploubidis", + "author_inst": "University College London" + }, + { + "author_name": "Ellen J Thompson", + "author_inst": "King's College London" + }, + { + "author_name": "Ruth C E Bowyer", + "author_inst": "King's College London" + }, + { + "author_name": "Xinyuan Zhang", + "author_inst": "King's College London" + }, + { + "author_name": "Golboo Abbasian", + "author_inst": "King's College London" + }, + { + "author_name": "Maria Paz Garcia", + "author_inst": "King's College London" + }, + { + "author_name": "Deborah Hart", + "author_inst": "King's College London" + }, + { + "author_name": "Jeffrew Seow", + "author_inst": "King's College London" + }, + { + "author_name": "Carl Graham", + "author_inst": "King's College London" + }, + { + "author_name": "Neophytos Kouphou", + "author_inst": "King's College London" + }, + { + "author_name": "Sam Acors", + "author_inst": "King's College London" + }, + { + "author_name": "Michael H Malim", + "author_inst": "King's College London" + }, + { + "author_name": "Ruth E Mitchell", + "author_inst": "University of Bristol" + }, + { + "author_name": "Kate Northstone", + "author_inst": "University of Bristol" + }, + { + "author_name": "Daniel Major-Smith", + "author_inst": "University of Bristol" + }, + { + "author_name": "Sarah Matthews", + "author_inst": "University of Bristol" + }, + { + "author_name": "Thomas Breeze", + "author_inst": "University of Bristol" + }, + { + "author_name": "Michael Crawford", + "author_inst": "University of Bristol" + }, + { + "author_name": "Lynn Molloy", + "author_inst": "University of Bristol" + }, + { + "author_name": "Alex Siu Fung Kwong", + "author_inst": "University of Bristol" + }, + { + "author_name": "Katie J Doores", + "author_inst": "King's College London" + }, + { + "author_name": "Nishi Chaturvedi", + "author_inst": "University College London" + }, + { + "author_name": "Emma L Duncan", + "author_inst": "King's College London" + }, + { + "author_name": "Nicholas J Timpson", + "author_inst": "University of Bristol" + }, + { + "author_name": "Claire J Steves", + "author_inst": "King's College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.05.20.22275359", "rel_title": "Targeting SARS-CoV-2 superspreading infections could dramatically improve the efficiency of epidemic control strategies in resource-limited contexts", @@ -321578,37 +323814,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.05.18.22275240", - "rel_title": "Exploring barriers and facilitators to physical activity during the COVID-19 pandemic: a qualitative study", - "rel_date": "2022-05-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.18.22275240", - "rel_abs": "ObjectivesQuantitative data show that physical activity (PA) reduced during the COVID-19 pandemic, with differential impacts across demographic groups. Qualitative research is limited, so reasons for this have not been explored in-depth. This study aimed to understand barriers and facilitators to PA during the pandemic, focusing on groups more likely to have been affected by restrictions, and to map these onto the Capability, Opportunity, Motivation Model of Behaviour (COM-B).\n\nDesignSemi-structured qualitative interview study.\n\nMethodsOne-to-one telephone/videocall interviews were conducted with younger (aged 18-24) and older adults (aged 70+), those with long-term physical health conditions or mental health conditions, and parents of young children, probing about their experiences of PA. Barriers and facilitators were identified using reflexive thematic analysis, and themes were mapped onto COM-B dimensions.\n\nResults116 participants were included (18-93 years old, 61% female, 71% White British). Key themes were the importance of the outdoor environment, impact of COVID-19 restrictions, fear of contracting COVID-19, and level of engagement with home exercise. Caring responsibilities and conflicting priorities were a barrier. PA as a method of socialising, establishing new routines, and the importance of PA for protecting mental health were motivators. Most themes mapped onto the physical opportunity (environmental factors) and reflective motivation (evaluations and plans) COM-B domains.\n\nConclusionsFuture interventions should increase physical opportunity and reflective motivation for PA during pandemics, to avoid further negative health outcomes following periods of lockdown. Strategies could include tailoring PA guidance depending on location and giving education on the health benefits of PA.\n\nStatement of ContributionO_ST_ABSWhat is already known on this subject?C_ST_ABSO_LIPhysical activity (PA) levels reduced during the COVID-19 pandemic.\nC_LIO_LIThe extent of this reduction varied across demographic groups.\nC_LIO_LIVery few qualitative studies have explored reasons for these changes.\nC_LI\n\nWhat does this study add?O_LINovel interview data, giving context to existing quantitative data.\nC_LIO_LIInsight into which themes were important for different demographic groups.\nC_LIO_LISuggestions for increasing PA in future pandemics, by mapping findings to a theoretical framework.\nC_LI", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Charlotte Roche", - "author_inst": "University College London" - }, - { - "author_name": "Abigail Fisher", - "author_inst": "University College London" - }, - { - "author_name": "Daisy Fancourt", - "author_inst": "University College London" - }, - { - "author_name": "Alexandra Burton", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.05.20.22275313", "rel_title": "Neonatal outcomes and indirect consequences following maternal SARS-CoV-2 infection in pregnancy: A systematic review", @@ -322944,6 +325149,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, + { + "rel_doi": "10.1101/2022.05.18.22275203", + "rel_title": "Prevalence and determinants of mental well-being and satisfaction with life among university students amidst COVID-19 pandemic", + "rel_date": "2022-05-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.18.22275203", + "rel_abs": "BackgroundThe COVID-19 pandemic has caused a slew of mental illnesses due to a lack of cures and vaccinations, as well as concerns about students well-being and satisfaction with life, resulting in psychological symptoms and dissatisfaction with their lives. As students are highly susceptible to mental health issues, researchers discovered that perceived SWL and MWB decreased. The present study investigated the prevalence and determinants of mental well-being and satisfaction with life among university students in Bangladesh.\n\nMethodsAn e-survey based cross-sectional study was carried out from February to April 2021 among 660 students. A purposive sampling technique was utilized in the study. Self-reported mental well-being and satisfaction with life psychological tools were also used. The e-questionnaire survey was conducted with informed consent and questions were related to socio-demographics, satisfaction with life, and mental well-being scales. Descriptive statistics and multiple regression analysis were performed. The data were rechecked and analyzed with the R programming language\n\nResultsThe prevalence estimates of mental well-being and satisfaction with life were 27% and 13%, respectively. In a total of 660 participants, 58.2% of them were male and the rest of them were female (41.8%). Among the participants, 22.5% suffer the worst conditions regarding their financial conditions, and 16.5% badly seek a job for livelihood.\n\nConclusionThe present findings revealed that the COVID-19 pandemic and longtime educational institution closure significantly affect the students mental health. Students mental well-being was in vulnerable conditions and their satisfaction with life was extremely poor. A comprehensive student psychological support service should be expanded to help students mental health.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Md. Safaet Hossain Sujan", + "author_inst": "Department of Public Health and Informatics, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh bCentre for Advanced Research Excellence in Public Health" + }, + { + "author_name": "Atefehsadat Haghighathoseini Haghighathoseini", + "author_inst": "Department of Health Administration and Policy, George Mason University" + }, + { + "author_name": "Rafia Tasnim", + "author_inst": "Department of Public Health and Informatics, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh bCentre for Advanced Research Excellence in Public Health, " + }, + { + "author_name": "Rezaul Karim Ripon", + "author_inst": "Department of Public Health and Informatics, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh" + }, + { + "author_name": "Sayem Ahmed Ripon", + "author_inst": "Department of Geography and Environmental studies. University of Chittagong" + }, + { + "author_name": "Mohammad Mohiuddin Hasan", + "author_inst": "Hospital Services Management, DGHS, Mohakhali, Dhaka-1212, Bangladesh" + }, + { + "author_name": "Muhammad Ramiz Uddin", + "author_inst": "Department of Chemistry and Biochemistry, The university of Oklahoma, Norman, USA" + }, + { + "author_name": "Most. Zannatul Ferdous", + "author_inst": "Jahangirnagar University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2022.05.20.22275350", "rel_title": "Parents' intention to vaccinate their child for COVID-19: a cross-sectional survey (CoVAccS - wave 3)", @@ -323452,89 +325704,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.05.17.22275154", - "rel_title": "COVID-19 booster dose antibody response in pregnant, lactating, and nonpregnant women", - "rel_date": "2022-05-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.17.22275154", - "rel_abs": "BACKGROUNDWhile emerging data during the SARS-CoV-2 pandemic have demonstrated robust mRNA vaccine-induced immunogenicity across populations, including pregnant and lactating individuals, the rapid waning of vaccine-induced immunity and the emergence of variants of concern motivated the use of mRNA vaccine booster doses. Whether all populations, including pregnant and lactating individuals, will mount a comparable response to a booster dose is not known.\n\nOBJECTIVEWe sought to profile the humoral immune response to a COVID-19 mRNA booster dose in a cohort of pregnant, lactating, and age-matched nonpregnant women.\n\nSTUDY DESIGNWe characterized the antibody response against ancestral Spike and Omicron in a cohort of 31 pregnant, 12 lactating and 20 nonpregnant age-matched controls who received a BNT162b2 or mRNA-1273 booster dose after primary COVID-19 vaccination. We also examined the vaccine-induced antibody profiles of 15 maternal:cord dyads at delivery.\n\nRESULTSReceipt of a booster dose during pregnancy resulted in increased IgG1 against Omicron Spike (post-primary vaccination vs post-booster, p = 0.03). Pregnant and lactating individuals exhibited equivalent Spike-specific total IgG1, IgM and IgA levels and neutralizing titers against Omicron compared to nonpregnant women. Subtle differences in Fc-receptor binding and antibody subclass profiles were observed in the immune response to a booster dose in pregnant compared to nonpregnant individuals. Analysis of maternal and cord antibody profiles at delivery demonstrated equivalent total Spike-specific IgG1 in maternal and cord blood, yet higher Spike-specific Fc{gamma}R3a-binding antibodies in the cord relative to maternal blood (p = 0.002), consistent with preferential transfer of highly functional IgG. Spike-specific IgG1 levels in the cord were positively correlated with time elapsed since receipt of the booster dose (Spearman R 0.574, p = 0.035).\n\nCONCLUSIONSThese data suggest that receipt of a booster dose during pregnancy induces a robust Spike-specific humoral immune response, including against Omicron. If boosting occurs in the third trimester, higher Spike-specific cord IgG1 levels are achieved with greater time elapsed between receipt of the booster and delivery. Receipt of a booster dose has the potential to augment maternal and neonatal immunity.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Caroline Atyeo PhD", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA; PhD Program in Virology, Division of Medical Sciences, Harvard University, Boston, MA, USA" - }, - { - "author_name": "Lydia L Shook MD", - "author_inst": "Department of Obstetrics & Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Vincent Center for Reproductive Biology, Massach" - }, - { - "author_name": "Nadege Nziza PhD", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Elizabeth A DeRiso PhD", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Cordelia Muir", - "author_inst": "Department of Obstetrics & Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Arantxa Medina Baez", - "author_inst": "Department of Obstetrics & Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Rosiane S Lima", - "author_inst": "Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA" - }, - { - "author_name": "Stepan Demidkin", - "author_inst": "Department of Obstetrics & Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Vincent Center for Reproductive Biology, Massach" - }, - { - "author_name": "Sara Brigida", - "author_inst": "Department of Obstetrics & Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Vincent Center for Reproductive Biology, Massach" - }, - { - "author_name": "Rose M De Guzman PhD", - "author_inst": "Department of Obstetrics & Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Vincent Center for Reproductive Biology, Massach" - }, - { - "author_name": "Madeleine D Burns", - "author_inst": "Department of Obstetrics & Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Department of Pediatrics, Massachusetts General " - }, - { - "author_name": "Alejandro B Balazs PhD", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Alessio Fasano MD", - "author_inst": "Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA" - }, - { - "author_name": "Lael M Yonker MD", - "author_inst": "Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA" - }, - { - "author_name": "Kathryn J Gray MD PhD", - "author_inst": "Department of Obstetrics and Gynecology, Brigham and Womens Hospital, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Galit Alter PhD", - "author_inst": "Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Andrea G Edlow MD MSc", - "author_inst": "Department of Obstetrics & Gynecology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA; Vincent Center for Reproductive Biology, Massach" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2022.05.15.22275071", "rel_title": "Fear of Infection and Sufficient Vaccine Reservation Information Might Drive Rapid Coronavirus Disease 2019 Vaccination in Japan: Evidence from Twitter Analysis", @@ -324662,6 +326831,69 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2022.05.16.22274439", + "rel_title": "Neuropathic symptoms with SARS-CoV-2 vaccination", + "rel_date": "2022-05-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.16.22274439", + "rel_abs": "Background and ObjectivesVarious peripheral neuropathies, particularly those with sensory and autonomic dysfunction may occur during or shortly after acute COVID-19 illnesses. These appear most likely to reflect immune dysregulation. If similar manifestations can occur with the vaccination remains unknown.\n\nResultsIn an observational study, we studied 23 patients (92% female; median age 40years) reporting new neuropathic symptoms beginning within 1 month after SARS-CoV-2 vaccination. 100% reported sensory symptoms comprising severe face and/or limb paresthesias, and 61% had orthostasis, heat intolerance and palpitations. Autonomic testing in 12 identified seven with reduced distal sweat production and six with positional orthostatic tachycardia syndrome. Among 16 with lower-leg skin biopsies, 31% had diagnostic/subthreshold epidermal neurite densities ([≤]5%), 13% were borderline (5.01-10%) and 19% showed abnormal axonal swelling. Biopsies from randomly selected five patients that were evaluated for immune complexes showed deposition of complement C4d in endothelial cells. Electrodiagnostic test results were normal in 94% (16/17). Together, 52% (12/23) of patients had objective evidence of small-fiber peripheral neuropathy. 58% patients (7/12) treated with oral corticosteroids had complete or near-complete improvement after two weeks as compared to 9% (1/11) of patients who did not receive immunotherapy having full recovery at 12 weeks. At 5-9 months post-symptom onset, 3 non-recovering patients received intravenous immunoglobulin with symptom resolution within two weeks.\n\nConclusionsThis observational study suggests that a variety of neuropathic symptoms may manifest after SARS-CoV-2 vaccinations and in some patients might be an immune-mediated process.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Farinaz Safavi", + "author_inst": "NINDS,NIH" + }, + { + "author_name": "Lindsey Gustafson", + "author_inst": "NINDS, NIH" + }, + { + "author_name": "Brian Walitt", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Tanya Lehky", + "author_inst": "NINDS, NIH" + }, + { + "author_name": "Sara Dehbashi", + "author_inst": "Jefferson University" + }, + { + "author_name": "Amanda Wiebold", + "author_inst": "NINDS, NIH" + }, + { + "author_name": "Yair Mina", + "author_inst": "NINDS, NIH" + }, + { + "author_name": "Susan Shin", + "author_inst": "Ichan School of Medicine at Mt Sinai" + }, + { + "author_name": "Baohan Pan", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Michael Polydefkis", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Anne Louise Oaklander", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Avindra Nath", + "author_inst": "National Institutes of Health" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2022.05.12.22274953", "rel_title": "Racial differences in vaccine acceptance in a rural southern US state", @@ -325058,85 +327290,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.05.16.22275163", - "rel_title": "Performance and validation of an adaptable multiplex assay for detection of serologic response to SARS-CoV-2 infection or vaccination.", - "rel_date": "2022-05-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.16.22275163", - "rel_abs": "Measurement of quantitative antibody responses are increasingly important in evaluating the immune response to infection and vaccination. In this study we describe the validation of a quantitative, multiplex serologic assay utilising an electrochemiluminescence platform, which measures IgG against the receptor binding domain (RBD), spike S1 and S2 subunits and nucleocapsid antigens of SARS-CoV-2. The assay displayed a sensitivity ranging from 73-91% and specificity from 90 to 96% in detecting previous infection with SARS-CoV-2 depending on antigenic target and time since infection, and this assay highly correlated with commercially available assays. The within-plate coefficient of variation ranged from 3.8-3.9% and the inter-plate coefficient of variation from 11-13% for each antigen.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Grace Kenny", - "author_inst": "Centre for Experimental Pathogen Host Research, University College Dublin, Ireland" - }, - { - "author_name": "Riya Negi", - "author_inst": "Centre for Experimental Pathogen Host Research, University College Dublin, Ireland" - }, - { - "author_name": "Sophie O'Reilly", - "author_inst": "Centre for Experimental Pathogen Host Research, University College Dublin, Ireland" - }, - { - "author_name": "Alejandro Abner Garcia Leon", - "author_inst": "Centre for Experimental Pathogen Host Research, University College Dublin, Ireland" - }, - { - "author_name": "Dana Alalwan", - "author_inst": "Centre for Experimental Pathogen Host Research, University College Dublin, Ireland" - }, - { - "author_name": "Colette Marie Gaillard", - "author_inst": "Centre for Experimental Pathogen Host Research, University College Dublin, Ireland" - }, - { - "author_name": "Gurvin Saini", - "author_inst": "Centre for Experimental Pathogen Host Research, University College Dublin, Ireland" - }, - { - "author_name": "Rosanna Inzitari", - "author_inst": "School of Medicine, University College Dublin, Ireland" - }, - { - "author_name": "Eoin Feeney", - "author_inst": "Centre for Experimental Pathogen Host Research, University College Dublin, Ireland; Department of Infectious Diseases, St Vincent's University Hospital, Irelan" - }, - { - "author_name": "Aoife G Cotter", - "author_inst": "Centre for Experimental Pathogen Host Research, University College Dublin, Ireland; Department of Infectious Diseases, Mater Misericordiae University Hospital," - }, - { - "author_name": "Eoghan de Barra", - "author_inst": "Department of Infectious Diseases, Beaumont Hospital, Ireland, Department of International Health and Tropical Medicine, Royal College of Surgeons in Ireland" - }, - { - "author_name": "Corinna Sadlier", - "author_inst": "Department of Infectious Diseases, Cork University Hospital, Ireland" - }, - { - "author_name": "Fiona Crispie", - "author_inst": "Teagasc Food Research Centre and APC Microbiome Ireland" - }, - { - "author_name": "Virginie Gautier", - "author_inst": "Centre for Experimental Pathogen Host Research, University College Dublin, Ireland" - }, - { - "author_name": "Patrick Mallon", - "author_inst": "Centre for Experimental Pathogen Host Research, University College Dublin, Ireland" - }, - { - "author_name": "- All Ireland Infectious Diseases Cohort Study", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.05.17.22275193", "rel_title": "Antibody response to SARS-CoV2 among COVID-19 confirmed cases, and correlates with neutralizing assay in a subgroup of patients in Delhi National Capital Region, India", @@ -326304,6 +328457,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "transplantation" }, + { + "rel_doi": "10.1101/2022.05.12.22274799", + "rel_title": "A Universal Day Zero Infectious Disease Testing Strategy Leveraging CRISPR-based Sample Depletion and Metagenomic Sequencing", + "rel_date": "2022-05-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.12.22274799", + "rel_abs": "The lack of preparedness for detecting the highly infectious SARS-CoV-2 pathogen, the pathogen responsible for the COVID-19 disease, has caused enormous harm to public health and the economy. It took [~]60 days for the first reverse transcription quantitative polymerase chain reaction (RT-qPCR) tests for SARS-CoV-2 infection developed by the United States Centers for Disease Control (CDC) to be made publicly available. It then took >270 days to deploy 800,000 of these tests at a time when the estimated actual testing needs required over 6 million tests per day. Testing was therefore limited to individuals with symptoms or in close contact with confirmed positive cases. Testing strategies deployed on a population scale at Day Zero i.e., at the time of the first reported case, would be of significant value. Next Generation Sequencing (NGS) has such Day Zero capabilities with the potential for broad and large-scale testing. However, it has limited detection sensitivity for low copy numbers of pathogens which may be present. Here we demonstrate that by using CRISPR-Cas9 to remove abundant sequences that do not contribute to pathogen detection, NGS detection sensitivity of COVID-19 is comparable to RT-qPCR. In addition, we show that this assay can be used for variant strain typing, co-infection detection, and individual human host response assessment, all in a single workflow using existing open-source analysis pipelines. This NGS workflow is pathogen agnostic, and therefore has the potential to transform how both large-scale pandemic response and focused clinical infectious disease testing are pursued in the future.\n\nSIGNIFICANCE STATEMENTThe lack of preparedness for detecting infectious pathogens has had a devastating effect on the global economy and society. Thus, a Day Zero testing strategy, that can be deployed at the first reported case and expanded to population scale, is required. Next generation sequencing enables Day Zero capabilities but is inadequate for detecting low levels of pathogen due to abundant sequences of little biological interest. By applying the CRISPR-Cas system to remove these sequences in vitro, we show sensitivity of pathogen detection equivalent to RT-qPCR. The workflow is pathogen agnostic, and enables detection of strain types, co-infections and human host response with a single workflow and open-source analysis tools. These results highlight the potential to transform future large-scale pandemic response.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Agnes P Chan", + "author_inst": "The Translational Genomics Research Institute (TGen)" + }, + { + "author_name": "Azeem Siddique", + "author_inst": "Jumpcode Genomics" + }, + { + "author_name": "Yvain Desplat", + "author_inst": "Jumpcode Genomics" + }, + { + "author_name": "Yongwook Choi", + "author_inst": "TGen" + }, + { + "author_name": "Sridhar Ranganathan", + "author_inst": "Jumpcode Genomics" + }, + { + "author_name": "Kumari Sonal Choudhary", + "author_inst": "Jumpcode Genomics" + }, + { + "author_name": "Josh Diaz", + "author_inst": "Jumpcode Genomics" + }, + { + "author_name": "Jon Bezney", + "author_inst": "Jumpcode Genomics" + }, + { + "author_name": "Dante DeAscanis", + "author_inst": "Jumpcode Genomics" + }, + { + "author_name": "Zenas George", + "author_inst": "Jumpcode Genomics" + }, + { + "author_name": "Shukmei Wong", + "author_inst": "TGen" + }, + { + "author_name": "William Selleck", + "author_inst": "TGen" + }, + { + "author_name": "Jolene Bowers", + "author_inst": "TGen" + }, + { + "author_name": "Victoria Zismann", + "author_inst": "TGen" + }, + { + "author_name": "Lauren Reining", + "author_inst": "TGen" + }, + { + "author_name": "Sarah Highlander", + "author_inst": "TGen" + }, + { + "author_name": "Yaron Hakak", + "author_inst": "Jumpcode Genomics" + }, + { + "author_name": "Keith Brown", + "author_inst": "Jumpcode Genomics" + }, + { + "author_name": "Jon Armstrong", + "author_inst": "Jumpcode Genomics" + }, + { + "author_name": "Nicholas J Schork", + "author_inst": "The Translational Genomics Research Institute (TGen)" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.05.12.22274991", "rel_title": "Elevated expression of RGS2 may underlie reduced olfaction in COVID-19 patients", @@ -326764,41 +329012,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2022.05.13.491763", - "rel_title": "AI-based search for convergently expanding, advantageous mutations in SARS-CoV-2 by focusing on oligonucleotide frequencies", - "rel_date": "2022-05-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.13.491763", - "rel_abs": "Among mutations that occur in SARS-CoV-2, efficient identification of mutations advantageous for viral replication and transmission is important to characterize and defeat this rampant virus. Mutations rapidly expanding frequency in a viral population are candidates for advantageous mutations, but neutral mutations hitchhiking with advantageous mutations are also likely to be included. To distinguish these, we focus on mutations that appear to occur independently in different lineages and expand in frequency in a convergent evolutionary manner. Batch-learning SOM (BLSOM) can separate SARS-CoV-2 genome sequences according by lineage from only providing the oligonucleotide composition. Focusing on remarkably expanding 20-mers, each of which is only represented by one copy in the viral genome, allows us to correlate the expanding 20-mers to mutations. Using visualization functions in BLSOM, we can efficiently identify mutations that have expanded remarkably both in the Omicron lineage, which is phylogenetically distinct from other lineages, and in other lineages. Most of these mutations involved changes in amino acids, but there were a few that did not, such as an intergenic mutation.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Toshimichi Ikemura", - "author_inst": "Nagahama Institute of Bio-Science and Technology" - }, - { - "author_name": "Yuki Iwasaki", - "author_inst": "Nagahama Institute of Bio-Science and Technology" - }, - { - "author_name": "Kennosuke Wada", - "author_inst": "Nagahama Institute of Bio-Science and Technology" - }, - { - "author_name": "Yoshiko Wada", - "author_inst": "Nagahama Institute of Bio-Science and Technology" - }, - { - "author_name": "Takashi Abe", - "author_inst": "Niigata University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2022.05.13.491916", "rel_title": "A SCID mouse model to evaluate the efficacy of antivirals against SARS-CoV-2 infection", @@ -327926,6 +330139,137 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.05.13.491770", + "rel_title": "Structural insights for neutralization of BA.1 and BA.2 Omicron variants by a broadly neutralizing SARS-CoV-2 antibody", + "rel_date": "2022-05-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.13.491770", + "rel_abs": "The SARS-CoV-2 BA.1 and BA.2 (Omicron) variants contain more than 30 mutations within the spike protein and evade therapeutic monoclonal antibodies (mAbs). Here, we report a receptor-binding domain (RBD) targeting human antibody (002-S21F2) that effectively neutralizes live viral isolates of SARS-CoV-2 variants of concern (VOCs) including Alpha, Beta, Gamma, Delta, and Omicron (BA.1 and BA.2) with IC50 ranging from 0.02 - 0.05 g/ml. This near germline antibody 002-S21F2 has unique genetic features that are distinct from any reported SARS-CoV-2 mAbs. Structural studies of the full-length IgG in complex with spike trimers (Omicron and WA.1) reveal that 002-S21F2 recognizes an epitope on the outer face of RBD (class-3 surface), outside the ACE2 binding motif and its unique molecular features enable it to overcome mutations found in the Omicron variants. The discovery and comprehensive structural analysis of 002-S21F2 provide valuable insight for broad and potent neutralization of SARS-CoV-2 Omicron variants BA.1 and BA.2.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Sanjeev Kumar", + "author_inst": "ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India" + }, + { + "author_name": "Anamika Patel", + "author_inst": "Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA." + }, + { + "author_name": "Lilin Lai", + "author_inst": "Department of Pediatrics, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA" + }, + { + "author_name": "Chennareddy Chakravarthy", + "author_inst": "Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University" + }, + { + "author_name": "Rajesh Valanparambil", + "author_inst": "Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University" + }, + { + "author_name": "Meredith E. Davis-Gardner", + "author_inst": "Department of Pediatrics, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA" + }, + { + "author_name": "Venkata Viswanadh Edara", + "author_inst": "Department of Pediatrics, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA" + }, + { + "author_name": "Susanne Linderman", + "author_inst": "Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University" + }, + { + "author_name": "Elluri Seetharami Reddy", + "author_inst": "ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India; Kusuma School of Biological Sciences, Indi" + }, + { + "author_name": "Kamalvishnu Gottimukkala", + "author_inst": "ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India" + }, + { + "author_name": "Kaustuv Nayak", + "author_inst": "ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India" + }, + { + "author_name": "Prashant Bajpai", + "author_inst": "ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India" + }, + { + "author_name": "Vanshika Singh", + "author_inst": "ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India" + }, + { + "author_name": "Filipp Frank", + "author_inst": "Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA." + }, + { + "author_name": "Narayanaiah Cheedarla", + "author_inst": "Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA" + }, + { + "author_name": "Hans Verkerke", + "author_inst": "Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA; Department of Pathology, Brigham and Womens Hospit" + }, + { + "author_name": "Andrew S. Neish", + "author_inst": "Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA" + }, + { + "author_name": "John D. Roback", + "author_inst": "Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA" + }, + { + "author_name": "Grace Mantus", + "author_inst": "Department of Pediatrics, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 303" + }, + { + "author_name": "Pawan Kumar Goel", + "author_inst": "Shaheed Hasan Khan Mewat Government Medical College, Haryana, India" + }, + { + "author_name": "Manju Rahi", + "author_inst": "Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, 110029, India" + }, + { + "author_name": "Carl W. Davis", + "author_inst": "Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University" + }, + { + "author_name": "Jens Wrammert", + "author_inst": "Department of Pediatrics, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University, Atlanta, GA 303" + }, + { + "author_name": "Mehul S. Suthar", + "author_inst": "Department of Pediatrics, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA" + }, + { + "author_name": "Rafi Ahmed", + "author_inst": "Department of Microbiology and Immunology, Emory University School of Medicine, Emory University, Atlanta, GA 30322, USA; Emory Vaccine Center, Emory University" + }, + { + "author_name": "Eric Ortlund", + "author_inst": "Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA." + }, + { + "author_name": "Amit Sharma", + "author_inst": "ICMR-National Institute of Malaria Research, Dwarka, New Delhi, 110077, India; Structural Parasitology Group, International Center for Genetic Engineering and B" + }, + { + "author_name": "Kaja Murali Krishna", + "author_inst": "ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India; Emory Vaccine Center and Department of Ped" + }, + { + "author_name": "Anmol Chandele", + "author_inst": "ICGEB-Emory Vaccine Center, International Center for Genetic Engineering and Biotechnology, New Delhi, 110067, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.04.02.22273339", "rel_title": "Factors Related to Stress in Children with Online Media Learning Methods during a Pandemic at Jaya Mulya 1 Elementary School, Karawang-Indonesia", @@ -328246,77 +330590,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2022.05.12.491597", - "rel_title": "Delivery of Circular mRNA via Degradable Lipid Nanoparticles against SARS-COV-2 Delta Variant", - "rel_date": "2022-05-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.12.491597", - "rel_abs": "mRNA vaccines have emerged as a most promising and potent platform in the fight against various diseases including the COVID-19 pandemic. However, the intrinsic instability, varying side effects associated with the delivery systems, and continuous emergence of virus variants highlight the urgent need for the development of stable, safe and efficacious mRNA vaccines. In this study, by screening a panel of proprietary biodegradable ionizable lipidoids, we reported on a novel mRNA vaccine (cmRNA-1130) formed from a biodegradable lipidoid with eight ester bonds in the branched tail (AX4) and synthetic circular mRNA (cmRNA) encoding the trimeric Delta receptor binding domain (RBD) of SARS-CoV-2 spike protein for the induction of robust immune activation. The AX4-based lipid nanoparticles (AX4-LNP) revealed much faster elimination rate from liver and spleen in comparison with commercialized MC3-based LNP (MC3-LNP) and afforded normal level of alanine transferase (ALT), aspartate aminotransferase (AST), and creatinine (CRE) in BALB/c mice. Following intramuscular (IM) administration in BALB/c mice, cmRNA-1130 elicited potent and sustained neutralizing antibodies, RBD-specific CD4+ and CD8+ T effector memory cells (Tem), and Th1-biased T cell activations. cmRNA-1130 vaccine showed excellent stability against 6-month storage at 4 {degrees}C and freezing-thawing cycles. In brief, our study highlights mRNA vaccines based on cmRNA and biodegradable AX4 lipids hold great potential as superb therapeutic platforms for the treatment of varying diseases.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Ke Huang", - "author_inst": "Suzhou CureMed Biopharma Technology Co., Ltd." - }, - { - "author_name": "Na Li", - "author_inst": "Suzhou CureMed Biopharma Technology Co., Ltd." - }, - { - "author_name": "Yingwen Li", - "author_inst": "Suzhou CureMed Biopharma Technology Co., Ltd." - }, - { - "author_name": "Jiafeng Zhu", - "author_inst": "Suzhou CureMed Biopharma Technology Co., Ltd." - }, - { - "author_name": "Qianyi Fan", - "author_inst": "Suzhou CureMed Biopharma Technology Co., Ltd." - }, - { - "author_name": "Jiali Yang", - "author_inst": "Suzhou CureMed Biopharma Technology Co., Ltd." - }, - { - "author_name": "Yinjia Gao", - "author_inst": "Suzhou CureMed Biopharma Technology Co., Ltd." - }, - { - "author_name": "Yuping Liu", - "author_inst": "Suzhou CureMed Biopharma Technology Co., Ltd." - }, - { - "author_name": "Qiangbo Hou", - "author_inst": "Suzhou CureMed Biopharma Technology Co., Ltd." - }, - { - "author_name": "Shufeng Gao", - "author_inst": "Suzhou CureMed Biopharma Technology Co., Ltd." - }, - { - "author_name": "Ke Wei", - "author_inst": "Hunan University of Chinese Medicine" - }, - { - "author_name": "Chao Deng", - "author_inst": "Soochow University" - }, - { - "author_name": "Chijian Zuo", - "author_inst": "Suzhou CureMed Biopharma Technology Co., Ltd." - }, - { - "author_name": "Zhenhua Sun", - "author_inst": "Suzhou CureMed Biopharma Technology Co., Ltd." - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.05.10.22274813", "rel_title": "Inhaled CO2 concentration while wearing face masks: a pilot study using capnography.", @@ -329608,6 +331881,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2022.05.06.22274739", + "rel_title": "PixelPrint: Three-dimensional printing of realistic patient-specific lung phantoms for validation of computed tomography post-processing and inference algorithms", + "rel_date": "2022-05-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.06.22274739", + "rel_abs": "BackgroundRadiomics and other modern clinical decision-support algorithms are emerging as the next frontier for diagnostic and prognostic medical imaging. However, heterogeneities in image characteristics due to variations in imaging systems and protocols hamper the advancement of reproducible feature extraction pipelines. There is a growing need for realistic patient-based phantoms that accurately mimic human anatomy and disease manifestations to provide consistent ground-truth targets when comparing different feature extraction or image cohort normalization techniques.\n\nMaterials and MethodsPixelPrint was developed for 3D-printing lifelike lung phantoms for computed tomography (CT) by directly translating clinical images into printer instructions that control the density on a voxel-by-voxel basis. CT datasets of three COVID-19 pneumonia patients served as input for 3D-printing lung phantoms. Five radiologists rated patient and phantom images for imaging characteristics and diagnostic confidence in a blinded reader study. Linear mixed models were utilized to evaluate effect sizes of evaluating phantom as opposed to patient images. Finally, PixelPrints reproducibility was evaluated by producing four phantoms from the same clinical images.\n\nResultsEstimated mean differences between patient and phantom images were small (0.03-0.29, using a 1-5 scale). Effect size assessment with respect to rating variabilities revealed that the effect of having a phantom in the image is within one-third of the inter- and intra-reader variabilities. PixelPrints production reproducibility tests showed high correspondence among four phantoms produced using the same patient images, with higher similarity scores between high-dose scans of the different phantoms than those measured between clinical-dose scans of a single phantom.\n\nConclusionsWe demonstrated PixelPrints ability to produce lifelike 3D-printed CT lung phantoms reliably. These can provide ground-truth targets for validating the generalizability of inference-based decision-support algorithms between different health centers and imaging protocols, as well as for optimizing scan protocols with realistic patient-based phantoms.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Nadav Shapira", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Kevin Donovan", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Kai Mei", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Michael Geagan", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Leonid Roshkovan", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Grace Gang", + "author_inst": "John Hopkins University" + }, + { + "author_name": "Mohammed Abed", + "author_inst": "Ibn Sina University of Medical and Pharmaceutical Sciences" + }, + { + "author_name": "Nathaniel B Linna", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Coulter P Cranston", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Ali H Dhanaliwala", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Despina Kontos", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Harold I Litt", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "J Webster Stayman", + "author_inst": "John Hopkins University" + }, + { + "author_name": "Russell T Shinohara", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Peter B No\u00ebl", + "author_inst": "University of Pennsylvania" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2022.05.08.22274817", "rel_title": "High but Short-lived anti-SARS-CoV2 neutralizing, IgM, IgA, and IgG levels among mRNA-vaccinees compared to naturally-infected participants", @@ -330252,81 +332600,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2022.05.10.22272976", - "rel_title": "Have the COVID-19 Pandemic and Lockdown Affected Children's Mental Health in Long Term? A Repeated Cross-Sectional Study.", - "rel_date": "2022-05-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.10.22272976", - "rel_abs": "ObjectiveThe study aimed to evaluate the impact of the COVID-19 pandemic on levels of anxiety and depressive symptoms in children and adolescents.\n\nDesignCross-sectional surveys were carried out on the mental health of children; one survey was conducted before the COVID-19 pandemic and one into the pandemic, 15 months after the implementation of lockdown, social distancing, and school closures. Demographic data and COVID-19 pandemic-related data were collected from specific parent-report and self-report questionnaires.\n\nParticipantsParticipants included children and adolescents between ages 6-16 years, attending a tertiary care hospital without any diagnosed major psychiatric disorder or chronic disorder.\n\nAnalysisData was collected at two points (before the COVID-19 pandemic and during it) and compared. Levels of anxiety and depressive symptoms were compared and tested for statistically significant differences between these two points using appropriate statistical tests. Regression models were constructed to predict the factors affecting increased anxiety levels and depressive symptoms in the COVID-19 period.\n\nResults832 and 1255 children/adolescents were included in the study during the pre-COVID-19 and COVID-19 times, respectively. The median age of the participants was 10 years [Interquartile Range (IQR) = 4 years). The median (IQR) Spence Childrens Anxiety Scale score was 24 (12) at the pre-COVID-19 point and 31 (13) during the COVID-19 pandemic (p<0.001, r=-0.27). 11% and 16% of children reported being depressed at these two-time points, respectively (p=0.004, {varphi}c=-0.063). Regression analysis showed that many factors, including the duration of smartphone use, female gender, and only child status, were associated with increased anxiety or depression levels.\n\nConclusionA large proportion of children had elevated anxiety and depressive symptoms during the pandemic relative to before the pandemic, suggesting a need for measures to engage children in healthy habits to protect childrens mental health and continuous monitoring of children during such scenarios.\n\nSTRENGTHS AND LIMITATIONSO_LIWith the availability of pre-pandemic data, the repeated cross-sectional study design allowed us to compare the anxiety symptoms and prevalence of depression in children and adolescents during and before the COVID-19 lockdown and school closures.\nC_LIO_LIThe study is one of the few studies from low-to-middle income countries on this topic with large sample size.\nC_LIO_LIThe data was collected hospital setting, and all of the participants were attending a hospital, which could have resulted in a sampling bias. Although it is a tertiary care hospital, all of the patients included in the study came to us for primary care and were not referred.\nC_LIO_LIWe used standardised scales that are usually used for screening and evaluation purposes and not for diagnostic purposes.\nC_LIO_LIWe were unable to perform a longitudinal study with a follow-up that would offer clear evidence of any fluctuation in mental health during the course of the pandemic.\nC_LI", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Manas Pustake", - "author_inst": "Department of Pediatrics, Grant Government Medical College and Sir J.J. Group of Hospitals, Mumbai, 400008, India" - }, - { - "author_name": "Sushant Mane", - "author_inst": "Department of Pediatrics, Grant Government Medical College and Sir J.J. Group of Hospitals, Mumbai, 400008, India" - }, - { - "author_name": "Mohammad Arfat Ganiyani", - "author_inst": "Department of Pediatrics, Grant Government Medical College and Sir J.J. Group of Hospitals, Mumbai, 400008, India" - }, - { - "author_name": "Sayan Mukherjee", - "author_inst": "Department of Pediatrics, Grant Government Medical College and Sir J.J. Group of Hospitals, Mumbai, 400008, India" - }, - { - "author_name": "Misba Sayed", - "author_inst": "Department of Pediatrics, Grant Government Medical College and Sir J.J. Group of Hospitals, Mumbai, 400008, India" - }, - { - "author_name": "Varada Mithbavkar", - "author_inst": "Department of Pediatrics, Grant Government Medical College and Sir J.J. Group of Hospitals, Mumbai, 400008, India" - }, - { - "author_name": "Zaid Memon", - "author_inst": "Department of Community Medicine, Mahatma Gandhi Mission Medical College, Navi Mumbai, 410 219, India." - }, - { - "author_name": "Abdus Samad Momin", - "author_inst": "Department of Pediatrics, Grant Government Medical College and Sir J.J. Group of Hospitals, Mumbai, 400008, India" - }, - { - "author_name": "Krishna Deshmukh", - "author_inst": "Department of Pediatrics, Grant Government Medical College and Sir J.J. Group of Hospitals, Mumbai, 400008, India" - }, - { - "author_name": "Ayush Chordia", - "author_inst": "Department of Pediatrics, Grant Government Medical College and Sir J.J. Group of Hospitals, Mumbai, 400008, India" - }, - { - "author_name": "Sabyasachi Parida", - "author_inst": "Department of Pediatrics, Grant Government Medical College and Sir J.J. Group of Hospitals, Mumbai, 400008, India" - }, - { - "author_name": "Ajit Bhagwat", - "author_inst": "Department of Pediatrics, Grant Government Medical College and Sir J.J. Group of Hospitals, Mumbai, 400008, India" - }, - { - "author_name": "Alan Johnson", - "author_inst": "Department of Pediatrics, Grant Government Medical College and Sir J.J. Group of Hospitals, Mumbai, 400008, India" - }, - { - "author_name": "Deepankar Varma", - "author_inst": "Department of Pediatrics, Grant Government Medical College and Sir J.J. Group of Hospitals, Mumbai, 400008, India" - }, - { - "author_name": "Sanket Warghade", - "author_inst": "Department of Pediatrics, Grant Government Medical College and Sir J.J. Group of Hospitals, Mumbai, 400008, India" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2022.05.09.22274842", "rel_title": "Knowledge mobilization activities to support decision-making by youth, parents, and adults using a systematic and living map of evidence and recommendations on COVID-19: protocol for a randomized controlled trial", @@ -331618,6 +333891,37 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.05.06.490962", + "rel_title": "The bacterial lysate Lantigen B reduces the expression of ACE2 on primary oropharyngeal cells", + "rel_date": "2022-05-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.06.490962", + "rel_abs": "Angiotensin-converting enzyme2 (ACE2) is the main cell surface receptor of the SARS-CoV-2 spike protein and is expressed in a variety of cell types, including cells of the respiratory tract. A bacterial lysate used for the prophylaxis of respiratory infections (OM-85), was recently shown to downregulate the expression of ACE2 in epithelial cells, suggesting its possible role as a prophylaxis of the onset of COVID19. Another bacterial lysate (Lantigen B, administered sublingually) is used in the prophylaxis of recurrent respiratory tract infections. It contains antigens obtained by chemical lysis from the most representative microbes of the respiratory tract. In this in vitro study, the capacity of Lantigen B to decrease ACE2 in human oropharyngeal cells was evaluated. The study was carried out in 40 healthy donors undergoing oropharyngeal swab for routine SARS-CoV-2 detection. Cells were treated in vitro with a 1:2 of Lantigen B. ACE2 expression was evaluated using a fluorescent anti-ACE2 monoclonal antibody and flow cytometry. A reduction in the number of positive cells was observed in 72% of the patients, while a modulation of ACE2 expression was observed in 62% of the samples. As a control, the expression of the CD54 rhinovirus receptor in the same cells was unaffected. To evaluate the functional effects of down regulation, in a subset of samples, the same oropharynx cells were incubated with Lantigen B and infected with wild-type SARS-CoV-2. After 24 hours, viral RNA, as assessed by rt-PCR, was significantly lower in samples treated with Lantigen B. In conclusion, this study demonstrates that Lantigen B, at a pharmacological dose, modulates the expression of the main SARS-CoV-2 receptor in oropharyngeal cells, and reduces viral yield. This activity could be synergistic with other approaches (vaccination and therapy) by reducing the number of potentially infected cells and thus reducing the effects of SARS-CoV-2 infection.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Caterina Pizzimenti", + "author_inst": "Department of Research and Development, Bruschettini Ltd, Via Isonzo 6, 16147, Genova, Italy" + }, + { + "author_name": "Paola Pirrello", + "author_inst": "Department of Research and Development, Bruschettini Ltd, Via Isonzo 6, 16147, Genova, Italy" + }, + { + "author_name": "Alessia Ruiba", + "author_inst": "Klinik fur Medicinische Onkologie und Hamatologie, Kantonsspital St. Gallen, Rorschacher Strasse 95, 9007 St Gallen" + }, + { + "author_name": "Giovanni Melioli", + "author_inst": "Laboratory Medicine, Albaro Site, Alliance Medical Diagnostic Ltd, Via Boselli 30, 16146, Genova, Italy" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2022.05.07.491038", "rel_title": "Simultaneous and sequential multi-species coronavirus vaccination", @@ -332058,177 +334362,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.05.05.22273234", - "rel_title": "Changes in English medication safety indicators throughout the COVID-19 pandemic: a federated analysis of 57 million patients' primary care records in situ using OpenSAFELY", - "rel_date": "2022-05-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.05.22273234", - "rel_abs": "ObjectiveTo describe the impact of the COVID-19 pandemic on safe prescribing, using the PINCER prescribing indicators; to implement complex prescribing indicators at national scale using GP data.\n\nDesignPopulation based cohort study, with the approval of NHS England using the OpenSAFELY platform.\n\nSettingElectronic health record data from 56.8 million NHS patients general practice records.\n\nParticipantsAll NHS patients registered at a GP practice using TPP or EMIS computer systems and recorded as at risk of at least one potentially hazardous PINCER indicator between September 2019 and September 2021.\n\nMain outcome measureMonthly trends and between-practice variation for compliance with 13 PINCER measures between September 2019 and September 2021.\n\nResultsThe indicators were successfully implemented across GP data in OpenSAFELY. Hazardous prescribing remained largely unchanged during the COVID-19 pandemic, with only small reductions in achievement of the PINCER indicators. There were transient delays in blood test monitoring for some medications, particularly ACE inhibitors. All indicators exhibited substantial recovery by September 2021. We identified 1,813,058 patients at risk of at least one hazardous prescribing event.\n\nConclusionGood performance was maintained during the COVID-19 pandemic across a diverse range of widely evaluated measures of safe prescribing.\n\nSummary box O_TEXTBOXWHAT IS ALREADY KNOWN ON THIS TOPICO_LIPrimary care services were substantially disrupted by the COVID-19 pandemic.\nC_LIO_LIDisruption to safe prescribing during the pandemic has not previously been evaluated.\nC_LIO_LIPINCER is a nationally adopted programme of activities that aims to identify and correct hazardous prescribing in GP practices, by conducting manual audit on subgroups of practices.\nC_LI\n\nWHAT THIS STUDY ADDSO_LIFor the first time, we were able to successfully generate data on PINCER indicators for almost the whole population of England, in a single analysis.\nC_LIO_LIOur study is the most comprehensive assessment of medication safety during the COVID-19 pandemic in England, covering 95% of the population using well-validated measures.\nC_LIO_LIGood performance was maintained across many PINCER indicators throughout the pandemic.\nC_LIO_LIDelays in delivering some medication-related blood test monitoring were evident though considerable recovery was made by the end of the study period.\nC_LI\n\nC_TEXTBOX", - "rel_num_authors": 39, - "rel_authors": [ - { - "author_name": "Louis Fisher", - "author_inst": "Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Lisa E M Hopcroft", - "author_inst": "Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Sarah Rodgers", - "author_inst": "PRIMIS, School of Medicine, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK" - }, - { - "author_name": "James Barrett", - "author_inst": "PRIMIS, School of Medicine, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK" - }, - { - "author_name": "Kerry Oliver", - "author_inst": "PRIMIS, School of Medicine, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK" - }, - { - "author_name": "Anthony J Avery", - "author_inst": "Centre for Academic Primary Care, School of Medicine, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK" - }, - { - "author_name": "Dai Evans", - "author_inst": "PRIMIS, School of Medicine, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK" - }, - { - "author_name": "Helen Curtis", - "author_inst": "Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Richard Croker", - "author_inst": "Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Orla Macdonald", - "author_inst": "Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Jessica Morley", - "author_inst": "Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Seb Bacon", - "author_inst": "Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Simon Davy", - "author_inst": "Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Iain Dillingham", - "author_inst": "Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "David Evans", - "author_inst": "Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "George Hickman", - "author_inst": "Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Peter Inglesby", - "author_inst": "Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Caroline E Morton", - "author_inst": "Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Becky Smith", - "author_inst": "Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Tom Ward", - "author_inst": "Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "William Hulme", - "author_inst": "Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Amelia Green", - "author_inst": "Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Jon Massey", - "author_inst": "Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Alex J Walker", - "author_inst": "Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Chris Bates", - "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX" - }, - { - "author_name": "Jonathan Cockburn", - "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX" - }, - { - "author_name": "John Parry", - "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX" - }, - { - "author_name": "Frank Hester", - "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX" - }, - { - "author_name": "Sam Harper", - "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX" - }, - { - "author_name": "Shaun O'Hanlon", - "author_inst": "EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA" - }, - { - "author_name": "Alex Eavis", - "author_inst": "EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA" - }, - { - "author_name": "Richard Jarvis", - "author_inst": "EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA" - }, - { - "author_name": "Dima Avramov", - "author_inst": "EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA" - }, - { - "author_name": "Paul Griffiths", - "author_inst": "EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA" - }, - { - "author_name": "Aaron Fowles", - "author_inst": "EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA" - }, - { - "author_name": "Nasreen Parkes", - "author_inst": "EMIS Health, Fulford Grange, Micklefield Lane, Rawdon, Leeds, LS19 6BA" - }, - { - "author_name": "Ben Goldacre", - "author_inst": "Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - }, - { - "author_name": "Brian MacKenna", - "author_inst": "Bennett Institute of Applied Data Science, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "primary care research" - }, { "rel_doi": "10.1101/2022.05.04.22274667", "rel_title": "Screening for safe opening of universities under Omicron and Delta variants of COVID-19: When less is more", @@ -333336,6 +335469,73 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2022.05.06.490867", + "rel_title": "SARS-CoV-2 evolution and patient immunological history shape the breadth and potency of antibody-mediated immunity", + "rel_date": "2022-05-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.06.490867", + "rel_abs": "Since the emergence of SARS-CoV-2, humans have been exposed to distinct SARS-CoV-2 antigens, either by infection with different variants, and/or vaccination. Population immunity is thus highly heterogeneous, but the impact of such heterogeneity on the effectiveness and breadth of the antibody-mediated response is unclear. We measured antibody-mediated neutralisation responses against SARS-CoV-2Wuhan, SARS-CoV-2, SARS-CoV-2{delta} and SARS-CoV-2o pseudoviruses using sera from patients with distinct immunological histories, including naive, vaccinated, infected with SARS-CoV-2Wuhan, SARS-CoV-2 or SARS-CoV-2{delta}, and vaccinated/infected individuals. We show that the breadth and potency of the antibody-mediated response is influenced by the number, the variant, and the nature (infection or vaccination) of exposures, and that individuals with mixed immunity acquired by vaccination and natural exposure exhibit the broadest and most potent responses. Our results suggest that the interplay between host immunity and SARS-CoV-2 evolution will shape the antigenicity and subsequent transmission dynamics of SARS-CoV-2, with important implications for future vaccine design.\n\nAuthor SummaryNeutralising antibodies provide protection against viruses and are generated because of vaccination or prior infections. The main target of anti-SARS-CoV-2 neutralising antibodies is a protein called Spike, which decorates the viral particle and mediates viral entry into cells. As SARS-CoV-2 evolves, mutations accumulate in the spike protein, allowing the virus to escape antibody-mediated immunity and decreasing vaccine effectiveness. Multiple SARS-CoV-2 variants have appeared since the start of the COVID-19 pandemic, causing various waves of infection through the population and infecting-in some cases-people that had been previously infected or vaccinated. Since the antibody response is highly specific, individuals infected with different variants are likely to have different repertoires of neutralising antibodies. We studied the breadth and potency of the antibody-mediated response against different SARS-CoV-2 variants using sera from vaccinated people as well as from people infected with different variants. We show that potency of the antibody response against different SARS-CoV-2 variants depends on the particular variant that infected each person, the exposure type (infection or vaccination) and the number and order of exposures. Our study provides insight into the interplay between virus evolution and immunity, as well as important information for the development of better vaccination strategies.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Maria Manali", + "author_inst": "MRC-University of Glasgow Centre for Virus Research" + }, + { + "author_name": "Laura A Bissett", + "author_inst": "MRC-University of Glasgow Centre for Virus Research" + }, + { + "author_name": "Julien Amat", + "author_inst": "MRC-University of Glasgow Centre for Virus Research" + }, + { + "author_name": "Nicola Logan", + "author_inst": "MRC-University of Glasgow Centre for Virus Research" + }, + { + "author_name": "Sam Scott", + "author_inst": "MRC-University of Glasgow Centre for Virus Research" + }, + { + "author_name": "Ellen Hughes", + "author_inst": "MRC-University of Glasgow Centre for Virus Research" + }, + { + "author_name": "William Harvey", + "author_inst": "MRC-University of Glasgow Centre for Virus Research" + }, + { + "author_name": "Richard Orton", + "author_inst": "MRC-University of Glasgow Centre for Virus Research" + }, + { + "author_name": "Emma Thomson", + "author_inst": "MRC-University of Glasgow Centre for Virus Research" + }, + { + "author_name": "Rory Gunson", + "author_inst": "NHS Greater Glasgow and Clyde" + }, + { + "author_name": "Mafalda Viana", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Brian Willett", + "author_inst": "MRC-University of Glasgow Centre for Virus Research" + }, + { + "author_name": "Pablo Ramiro Murcia", + "author_inst": "MRC-University of Glasgow Centre for Virus Research" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.05.02.22273554", "rel_title": "Longitudinal analyses of depression and anxiety highlight greater prevalence during COVID-19 lockdowns in the Dutch general population and a continuing increase in suicidal ideation in young adults", @@ -333748,61 +335948,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2022.05.04.22274657", - "rel_title": "Have infection control and prevention measures resulted in any adverse outcomes for care home and domiciliary care residents and staff?", - "rel_date": "2022-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.05.04.22274657", - "rel_abs": "TOPLINE SUMMARYO_ST_ABSWhat is a Rapid Review?C_ST_ABSOur rapid reviews use a variation of the systematic review approach, abbreviating or omitting some components to generate the evidence to inform stakeholders promptly whilst maintaining attention to bias. They follow the methodological recommendations and minimum standards for conducting and reporting rapid reviews, including a structured protocol, systematic search, screening, data extraction, critical appraisal and evidence synthesis to answer a specific question and identify key research gaps. They take 1-2 months, depending on the breadth and complexity of the research topic/question(s), the extent of the evidence base and type of analysis required for synthesis.\n\nBackground / Aim of Rapid ReviewCare for older and vulnerable people must sustain core infection prevention and control (IPC) practices and remain vigilant for COVID-19 transmission to prevent virus spread and protect residents and healthcare professionals from severe infections, hospitalisations and death.\n\nHowever, these measures could potentially lead to adverse outcomes such as decreased mental wellbeing in patients and staff. A recent publication by Public Health England examines the effectiveness of IPC practices for reducing COVID-19 transmission in care homes (Duval et al., 2021). We explore evidence relating to adverse outcomes from IPC practices to help inform policy recommendations and identify gaps within the literature where further research can be prioritised.\n\nKey FindingsO_ST_ABSExtent of the evidence baseC_ST_ABSO_LI15 studies were identified: 14 primary studies and one rapid review\nC_LI\n\nRecency of the evidence baseO_LIOf the primary studies, six were published in 2020 and eight were published in 2021\nC_LIO_LIThe rapid review was published in 2021.\nC_LI\n\nSummary of findingsThis rapid review focuses on adverse outcomes resulting from increased IPC measures put in place during the COVID-19 pandemic. Whilst there is some evidence to show that there may be a link between IPC measures and adverse outcomes, causation cannot be assumed.\n\nO_LIDuring the COVID-19 restrictions, the cognition, mental wellbeing and behaviour of residents in care homes were negatively affected\nC_LIO_LIIncreased IPC procedures during the COVID-19 pandemic increased stress and burden among care staff because of increased workload and dilemmas between adhering well to IPC procedures and providing the best care for the care recipients\nC_LIO_LICOVID-19 IPC procedures were not well developed at the beginning of the COVID-19 pandemic, but evidence from 2021 suggests that good adherence to IPC measures can enable visitations by family members and medical professionals into care homes\nC_LIO_LIOnly one study investigating domiciliary care was found. Therefore, it is difficult to make conclusions related specifically to this care setting\nC_LIO_LINo published studies have reported on the costs or cost-effectiveness of IPC measures or have explored the cost implications of adverse outcomes associated with IPC measures\nC_LI\n\nBest quality evidenceOnly one study was deemed as high quality based on the quality appraisal checklist ranking. This was a mixed methods study design (Tulloch et al., 2021).\n\nPolicy ImplicationsSince March 2020, there have been many changes to government guidelines relating to procedures to keep the population safe from COVID-19 harm. Policies vary according to country, even within the UK. Important issues such as care home visitation policies have changed in such a way that care home staff have felt it difficult to keep up with the changes, which in itself increased the burden on those staff. The following implications were identified from this work:\n\nO_LIIPC policies should be clear, concise and tailored to care homes and domiciliary care settings\nC_LIO_LIIncreased attention to workforce planning is needed to ensure adequate staffing and to reduce individual burden\nC_LIO_LIRestrictions (e.g. visitation) for care home residents needs to be balanced by additional psychological support\nC_LIO_LIFurther research with robust methods in this area is urgently needed especially in the domiciliary care setting\nC_LI\n\nStrength of EvidenceOne limitation is the lack of high-quality evidence from the included studies. Confidence in the strength of evidence about adverse outcomes of COVID-19 IPC procedures was rated as low overall. Whilst the majority of studies achieved a moderate score based on the quality appraisal tools used, due to the nature of the methods used, the overall quality of evidence is low.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Llinos Haf Spencer", - "author_inst": "Bangor University" - }, - { - "author_name": "Ned Hartfiel", - "author_inst": "Bangor University" - }, - { - "author_name": "Annie Hendry", - "author_inst": "Bangor University" - }, - { - "author_name": "Bethany Fern Anthony", - "author_inst": "Bangor University" - }, - { - "author_name": "Abraham Makanjuola", - "author_inst": "Bangor University" - }, - { - "author_name": "Nathan Bray", - "author_inst": "Bangor University" - }, - { - "author_name": "Dyfrig A. Hughes", - "author_inst": "Bangor University" - }, - { - "author_name": "Clare Wilkinson", - "author_inst": "Bangor University" - }, - { - "author_name": "Deborah Fitzsimmons", - "author_inst": "Swansea University" - }, - { - "author_name": "Rhiannon Tudor Edwards", - "author_inst": "Bangor University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2022.05.03.22274592", "rel_title": "Durability of the immune response to a third BNT162b2 dose; five months follow-up", @@ -335358,6 +337503,53 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.05.03.490409", + "rel_title": "Sensitivity of novel SARS-CoV-2 Omicron subvariants, BA.2.11, BA.2.12.1, BA.4 and BA.5 to therapeutic monoclonal antibodies", + "rel_date": "2022-05-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.05.03.490409", + "rel_abs": "As of May 2022, Omicron BA.2 variant is the most dominant variant in the world. Thereafter, Omicron subvariants have emerged and some of them began outcompeting BA.2 in multiple countries. For instance, Omicron BA.2.11, BA.2.12.1 and BA.4/5 subvariants are becoming dominant in France, the USA and South Africa, respectively. In this study, we evaluated the sensitivity of these new Omicron subvariants (BA.2.11, BA.2.12.1 and BA.4/5) to eight therapeutic monoclonal antibodies (bamlanivimab, bebtelovimab, casirivimab, cilgavimab, etesevimab, imdevimab, sotrovimab and tixagevimab). Notably, we showed that although cilgavimab is antiviral against BA.2, BA.4/5 exhibits higher resistance to this antibody compared to BA.2. Since mutations are accumulated in the spike proteins of newly emerging SARS-CoV-2 variants, we suggest the importance of rapid evaluation of the efficiency of therapeutic monoclonal antibodies against novel SARS-CoV-2 variants.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Daichi Yamasoba", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Yusuke Kosugi", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Izumi Kimura", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Shigeru Fujita", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Keiya Uriu", + "author_inst": "The University of Tokyo" + }, + { + "author_name": "Jumpei Ito", + "author_inst": "The Institute of Medical Science, The University of Tokyo" + }, + { + "author_name": "Kei Sato", + "author_inst": "Institute of Medical Science, The University of Tokyo" + }, + { + "author_name": "- The Genotype to Phenotype Japan (G2P-Japan) Consortium", + "author_inst": "-" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.05.03.22274602", "rel_title": "Accident and emergency (AE) attendance in England following infection with SARS-CoV-2 Omicron or Delta", @@ -335890,201 +338082,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2022.04.30.489997", - "rel_title": "BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection", - "rel_date": "2022-05-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.30.489997", - "rel_abs": "SARS-CoV-2 Omicron sublineages BA.2.12.1, BA.4 and BA.5 exhibit higher transmissibility over BA.21. The new variants receptor binding and immune evasion capability require immediate investigation. Here, coupled with Spike structural comparisons, we show that BA.2.12.1 and BA.4/BA.5 exhibit comparable ACE2-binding affinities to BA.2. Importantly, BA.2.12.1 and BA.4/BA.5 display stronger neutralization evasion than BA.2 against the plasma from 3-dose vaccination and, most strikingly, from post-vaccination BA.1 infections. To delineate the underlying antibody evasion mechanism, we determined the escaping mutation profiles2, epitope distribution3 and Omicron neutralization efficacy of 1640 RBD-directed neutralizing antibodies (NAbs), including 614 isolated from BA.1 convalescents. Interestingly, post-vaccination BA.1 infection mainly recalls wildtype-induced humoral memory. The resulting elicited antibodies could neutralize both wildtype and BA.1 and are enriched on non-ACE2-competing epitopes. However, most of these cross-reactive NAbs are heavily escaped by L452Q, L452R and F486V. BA.1 infection can also induce new clones of BA.1-specific antibodies that potently neutralize BA.1; nevertheless, these NAbs are largely escaped by BA.2/BA.4/BA.5 due to D405N and F486V, and react weakly to pre-Omicron variants, exhibiting poor neutralization breadths. As for therapeutic NAbs, Bebtelovimab4 and Cilgavimab5 can effectively neutralize BA.2.12.1 and BA.4/BA.5, while the S371F, D405N and R408S mutations would undermine most broad sarbecovirus NAbs. Together, our results indicate that Omicron may evolve mutations to evade the humoral immunity elicited by BA.1 infection, suggesting that BA.1-derived vaccine boosters may not achieve broad-spectrum protection against new Omicron variants.", - "rel_num_authors": 45, - "rel_authors": [ - { - "author_name": "Yunlong Richard Cao", - "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University" - }, - { - "author_name": "Ayijiang Yisimayi", - "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University" - }, - { - "author_name": "Fanchong Jian", - "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University" - }, - { - "author_name": "Weiliang Song", - "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University" - }, - { - "author_name": "Tianhe Xiao", - "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University" - }, - { - "author_name": "Lei Wang", - "author_inst": "CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences" - }, - { - "author_name": "Shuo Du", - "author_inst": "School of Life Sciences, Peking University" - }, - { - "author_name": "Jing Wang", - "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University" - }, - { - "author_name": "Qianqian Li", - "author_inst": "Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC)" - }, - { - "author_name": "Xiaosu Chen", - "author_inst": "Institute for Immunology, College of Life Sciences, Nankai University" - }, - { - "author_name": "Yuanling Yu", - "author_inst": "Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijin" - }, - { - "author_name": "Peng Wang", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Zhiying Zhang", - "author_inst": "School of Life Sciences, Peking University" - }, - { - "author_name": "Pulan Liu", - "author_inst": "School of Life Sciences, Peking University" - }, - { - "author_name": "Ran An", - "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University" - }, - { - "author_name": "Xiaohua Hao", - "author_inst": "Beijing Ditan Hospital, Capital Medical University" - }, - { - "author_name": "Yao Wang", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Jing Wang", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Rui Feng", - "author_inst": "CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences" - }, - { - "author_name": "Haiyan Sun", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Lijuan Zhao", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Wen Zhang", - "author_inst": "Beijing Ditan Hospital, Capital Medical University" - }, - { - "author_name": "Dong Zhao", - "author_inst": "Beijing Ditan Hospital, Capital Medical University" - }, - { - "author_name": "Jiang Zheng", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Lingling Yu", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Can Li", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Na Zhang", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Rui Wang", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Xiao Niu", - "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University" - }, - { - "author_name": "Sijie Yang", - "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University" - }, - { - "author_name": "Xuetao Song", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Yangyang Chai", - "author_inst": "Institute for Immunology, College of Life Sciences, Nankai University" - }, - { - "author_name": "Ye Hu", - "author_inst": "Institute for Immunology, College of Life Sciences, Nankai University" - }, - { - "author_name": "Yansong Shi", - "author_inst": "Institute for Immunology, College of Life Sciences, Nankai University" - }, - { - "author_name": "Linlin Zheng", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Zhiqiang Li", - "author_inst": "Peking-Tsinghua Center for Life Sciences, Peking University" - }, - { - "author_name": "Qingqing Gu", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Fei Shao", - "author_inst": "Changping Laboratory" - }, - { - "author_name": "Weijin Huang", - "author_inst": "Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC)" - }, - { - "author_name": "Ronghua Jin", - "author_inst": "Beijing Ditan Hospital, Capital Medical University" - }, - { - "author_name": "Zhongyang Shen", - "author_inst": "Organ Transplant Center, NHC Key Laboratory for Critical Care Medicine, Tianjin First Central Hospital, Nankai University" - }, - { - "author_name": "Youchun Wang", - "author_inst": "Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC)" - }, - { - "author_name": "Xiangxi Wang", - "author_inst": "CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences" - }, - { - "author_name": "Junyu Xiao", - "author_inst": "School of Life Sciences, Peking University" - }, - { - "author_name": "Xiaoliang Sunney Xie", - "author_inst": "Biomedical Pioneering Innovation Center (BIOPIC), Peking University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.04.30.486882", "rel_title": "The highly conserved stem-loop II motif is important for the lifecycle of astroviruses but dispensable for SARS-CoV-2", @@ -337476,6 +339473,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.04.29.22274455", + "rel_title": "Protection against Omicron re-infection conferred by prior heterologous SARS-CoV-2 infection, with and without mRNA vaccination", + "rel_date": "2022-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.29.22274455", + "rel_abs": "ImportanceOmicron is phylogenetically- and antigenically-distinct from earlier SARS-CoV-2 variants and the original vaccine strain. Protection conferred by prior SARS-CoV-2 infection against Omicron re-infection, and the added value of vaccination, require quantification.\n\nObjectiveTo estimate protection against Omicron re-infection and hospitalization conferred by prior heterologous SARS-CoV-2 (non-Omicron) infection and/or up to three doses of (ancestral, Wuhan-like) mRNA vaccine.\n\nDesignTest-negative study between December 26 (epi-week 52), 2021 and March 12 (epi-week 10), 2022.\n\nSettingPopulation-based, province of Quebec, Canada\n\nParticipantsCommunity-dwelling [≥]12-year-olds tested for SARS-CoV-2.\n\nExposuresPrior laboratory-confirmed infection with/without mRNA vaccination.\n\nOutcomesLaboratory-confirmed SARS-CoV-2 re-infection and hospitalization, presumed Omicron by genomic surveillance. The odds of prior non-Omicron infection with/without vaccination were compared among Omicron cases/hospitalizations versus test-negative controls (single randomly-selected per individual). Adjusted odds ratios controlled for age, sex, testing-indication and epi-week. Analyses were stratified by severity and time since last non-Omicron infection or vaccine dose.\n\nResultsWithout vaccination, prior non-Omicron infection reduced the Omicron re-infection risk by 44% (95%CI:38-48), decreasing from 66% (95%CI:57-73) at 3-5 months to 35% (95%CI:21-47) at 9-11 months post-infection and <30% thereafter. The more severe the prior infection, the greater the risk reduction: 8% (95%CI:17-28), 43% (95%CI:37-49) and 68% (95%CI:51-80) for prior asymptomatic, symptomatic ambulatory or hospitalized infections. mRNA vaccine effectiveness against Omicron infection was consistently significantly higher among previously-infected vs. non-infected individuals at 65% (95%CI:63-67) vs. 20% (95%CI:16-24) for one-dose; 68% (95%CI:67-70) vs. 42% (95%CI:41-44) for two doses; and 83% (95%CI:81-84) vs. 73% (95%CI:72-73) for three doses.\n\nInfection-induced protection against Omicron hospitalization was 81% (95%CI: 66-89) increasing to 86% (95%CI:77-99) with one, 94% (95%CI:91-96) with two and 97%(95%CI:94-99) with three mRNA vaccine doses. Two-dose effectiveness against hospitalization among previously-infected individuals did not wane across 11 months and did not significantly differ from three-dose effectiveness despite longer follow-up (median 158 and 27 days, respectively).\n\nConclusions and relevancePrior heterologous SARS-CoV-2 infection provided substantial and sustained protection against Omicron hospitalization, greatest among those also vaccinated. In the context of program goals to prevent severe outcomes and preserve healthcare system capacity, >2 doses of ancestral Wuhan-like vaccine may be of marginal incremental value to previously-infected individuals.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Sara Carazo", + "author_inst": "Biological and occupational risks unit. Institut national de sant\u00e9 publique du Qu\u00e9bec, Quebec city, Quebec, Canada" + }, + { + "author_name": "Danuta M Skowronski", + "author_inst": "BC Centre for Disease Control, Vancouver, British Columbia, Canada" + }, + { + "author_name": "Marc Brisson", + "author_inst": "Centre Hospitalier Universitaire (CHU) de Qu\u00e9bec Universit\u00e9 Laval Research Center, Quebec city, Quebec, Canada" + }, + { + "author_name": "Chantal Sauvageau", + "author_inst": "Biological and occupational risks unit. Institut national de sant\u00e9 publique du Qu\u00e9bec, Quebec city, Quebec, Canada" + }, + { + "author_name": "Nicholas Brousseau", + "author_inst": "Biological and occupational risks unit. Institut national de sant\u00e9 publique du Qu\u00e9bec, Quebec city, Quebec, Canada" + }, + { + "author_name": "Rodica Gilca", + "author_inst": "Biological and occupational risks unit. Institut national de sant\u00e9 publique du Qu\u00e9bec, Quebec city, Quebec, Canada" + }, + { + "author_name": "Manale Ouakki", + "author_inst": "Biological and occupational risks unit. Institut national de sant\u00e9 publique du Qu\u00e9bec, Quebec city, Quebec, Canada" + }, + { + "author_name": "Sapha Barkati", + "author_inst": "Department of Medicine, Division of infectious diseases, McGill University Health Center, McGill University, Montreal, Quebec, Canada" + }, + { + "author_name": "Judith Fafard", + "author_inst": "Laboratoire de Sant\u00e9 Publique du Qu\u00e9bec, Institut national de sant\u00e9 publique du Qu\u00e9bec, Sainte-Anne-de-Bellevue, Quebec, Canada" + }, + { + "author_name": "Denis Talbot", + "author_inst": "Centre Hospitalier Universitaire (CHU) de Qu\u00e9bec Universit\u00e9 Laval Research Center, Quebec city, Quebec, Canada" + }, + { + "author_name": "Vladimir Gilca", + "author_inst": "Biological and occupational risks unit. Institut national de sant\u00e9 publique du Qu\u00e9bec, Quebec city, Quebec, Canada" + }, + { + "author_name": "Genevi\u00e8ve Deceuninck", + "author_inst": "Centre Hospitalier Universitaire (CHU) de Qu\u00e9bec Universit\u00e9 Laval Research Center, Quebec city, Quebec, Canada" + }, + { + "author_name": "Christophe Garenc", + "author_inst": "Biological and occupational risks unit. Institut national de sant\u00e9 publique du Qu\u00e9bec, Quebec city, Quebec, Canada" + }, + { + "author_name": "Alex Carignan", + "author_inst": "Department of microbiology and infectious diseases, Sherbrook University, Sherbrook, Quebec, Canada" + }, + { + "author_name": "Philippe De Wals", + "author_inst": "Biological and occupational risks unit. Institut national de sant\u00e9 publique du Qu\u00e9bec, Quebec city, Quebec, Canada" + }, + { + "author_name": "Gaston De Serres", + "author_inst": "Biological and occupational risks unit. Institut national de sant\u00e9 publique du Qu\u00e9bec, Quebec city, Quebec, Canada" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.04.27.22274270", "rel_title": "Clinical Features and Outcomes of COVID-19 at a Teaching Hospital in Kingston, Jamaica", @@ -337948,49 +340024,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.04.26.22274264", - "rel_title": "Pilot study on the use of low molecular weight heparins in the prevention of thromboembolic disease during pregnancy and puerperium.", - "rel_date": "2022-04-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.26.22274264", - "rel_abs": "A pregnant woman is 4 to 5 times more likely to suffer a thromboembolic event than a non-pregnant woman. Furthermore, an increase in these episodes has been observed in women infected with SARS-CoV-2. Consequently, the prophylactic prescription of low-molecular-weight heparins (LMWH) in pregnant women is undergoing an increase that has not been evaluated yet. The aim of this study was to determine the prevalence of LMWH prescription in pregnant women at the Hospital Universitario Puerta de Hierro Majadahonda (HUPHM), according to their level of risk and its variation due to SARS-CoV-2 infection. To answer this question, a retrospective cohort of 113 women who gave birth during the month of February at the HUPHM was designed. The level of individual risk of thromboembolism, according to the Royal College guidelines (37a), was calculated with an interview to complete a questionnaire and the analysis of their clinical records. 53.6% of the women were prescribed LMWH as indicated in the guidelines. This high prevalence is explained by the high age of the pregnant women (over 35 years), the wave of the omicron variant (December 2021) and a high rate of cesarean sections (25%). On the other hand, the percentage of patients with COVID-19 was 17.6% but only 53% of them had received LMWH. In conclusion, LMWH is a very common prescription in obstetrics, mostly during puerperium, and has become even more relevant due to the COVID-19 pandemic", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Paloma Anchustegui-Mendizabal", - "author_inst": "UNIVERSIDAD AUTONOMA MADRID" - }, - { - "author_name": "Patricia Anchustegui-Mendizabal", - "author_inst": "UNIVERSIDAD AUTONOMA MADRID" - }, - { - "author_name": "Laura Arechabala-Palacios", - "author_inst": "UNIVERSIDAD AUTONOMA DE MADRID" - }, - { - "author_name": "Laura Fernandez-Gonzalez", - "author_inst": "UNIVERSIDAD AUTONOMA DE MADRID" - }, - { - "author_name": "Clara Garcia-Gil", - "author_inst": "UNIVERSIDAD AUTONOMA DE MADRID" - }, - { - "author_name": "Jesus Miguel Hernandez-Guijo", - "author_inst": "UNIVERSIDAD.AUTONOMA DE MADRID" - }, - { - "author_name": "Oscar Martinez Perez", - "author_inst": "Puerta de Hierro University Hospital" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2022.04.27.22274357", "rel_title": "Observed strong pervasive positive selection in the N-terminal domain, receptor-binding domain and furin-cleavage sites of SARS-CoV-2 Spike protein sampled from Zimbabwean COVID-19 patients.", @@ -339466,6 +341499,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.04.25.22274187", + "rel_title": "Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1", + "rel_date": "2022-04-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.25.22274187", + "rel_abs": "Mutations in the viral genome of SARS-CoV-2 can impact the performance of molecular diagnostic assays. In some cases, such as S gene target failure, the impact can serve as a unique indicator of a particular SARS-CoV-2 variant and provide a method for rapid detection. Here we describe partial ORF1ab gene target failure (pOGTF) on the cobas(R) SARS-CoV-2 assays, defined by a [≥]2 thermocycles delay in detection of the ORF1ab gene compared to the E gene. We demonstrate that pOGTF is 97% sensitive and 99% specific for SARS-CoV-2 lineage BA.2.12.1, an emerging variant in the United States with spike L452Q and S704L mutations that may impact transmission, infectivity, and/or immune evasion. Increasing rates of pOGTF closely mirrored rates of BA.2.12.1 sequences uploaded to public databases, and, importantly increasing local rates of pOGTF also mirrored increasing overall test positivity. Use of pOGTF as a proxy for BA.2.12.1 provides faster tracking of the variant than whole-genome sequencing and can benefit laboratories without sequencing capabilities.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Kyle G Rodino", + "author_inst": "University of Pennsylvania Perelman School of Medicine" + }, + { + "author_name": "David R. Peaper", + "author_inst": "Yale University" + }, + { + "author_name": "Brendan J Kelly", + "author_inst": "University of Pennsylvania Perelman School of Medicine" + }, + { + "author_name": "Frederic Bushman", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Andrew Marques", + "author_inst": "University of Pennsylvania Perelman School of Medicine" + }, + { + "author_name": "Hriju Adhikari", + "author_inst": "University of Pennsylvania Perelman School of Medicine" + }, + { + "author_name": "Zheng Jin Tu", + "author_inst": "Cleveland Clinic" + }, + { + "author_name": "Rebecca Marrero Rolon", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Lars F Westblade", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Daniel Green", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Gregory J Berry", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Fann Wu", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Medini K Annavajhala", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Anne-Catrin Uhlemann", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Bijal A Parikh", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Tracy McMillen", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Krupa Jani", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "N. Esther Babady", + "author_inst": "Memorial Sloan Kettering Cancer Center" + }, + { + "author_name": "Anne M Hahn", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Robert T Koch", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Nathan D Grubaugh", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "- Yale SARS-CoV-2 Genomic Surveillance Initiative", + "author_inst": "" + }, + { + "author_name": "Daniel D Rhoads", + "author_inst": "Cleveland Clinic" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.04.26.22274335", "rel_title": "Incorporating Vaccination into Compartment Models for Infectious Diseases", @@ -339850,65 +341990,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.04.28.489772", - "rel_title": "Structural and functional characteristics of SARS-CoV-2 Omicron subvariant BA.2 spike", - "rel_date": "2022-04-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.28.489772", - "rel_abs": "The Omicron subvariant BA.2 has become the dominant circulating strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in many countries. We have characterized structural, functional and antigenic properties of the full-length BA.2 spike (S) protein and compared replication of the authentic virus in cell culture and animal model with previously prevalent variants. BA.2 S can fuse membranes more efficiently than Omicron BA.1, mainly due to lack of a BA.1-specific mutation that may retard the receptor engagement, but still less efficiently than other variants. Both BA.1 and BA.2 viruses replicated substantially faster in animal lungs than the early G614 (B.1) strain in the absence of pre-existing immunity, possibly explaining the increased transmissibility despite their functionally compromised spikes. As in BA.1, mutations in the BA.2 S remodel its antigenic surfaces leading to strong resistance to neutralizing antibodies. These results suggest that both immune evasion and replicative advantage may contribute to the heightened transmissibility for the Omicron subvariants.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Tang Weichun", - "author_inst": "United States Food and Drug Administration" - }, - { - "author_name": "Christy Lavine", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Haisun Zhu", - "author_inst": "Institute for Protein Innovation" - }, - { - "author_name": "Krishna Anand", - "author_inst": "Institute for Protein Innovation" - }, - { - "author_name": "Martina Kosikova", - "author_inst": "United States Food and Drug Administration" - }, - { - "author_name": "Hyung Joon Kwon", - "author_inst": "United States Food and Drug Administration" - }, - { - "author_name": "Shaowei Wang", - "author_inst": "Codex BioSolutions, Inc." - }, - { - "author_name": "Megan L. Mayer", - "author_inst": "The Harvard Cryo-EM Center for Structural Biology" - }, - { - "author_name": "Michael S. Seaman", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Jianming Lu", - "author_inst": "Codex BioSolutions, Inc." - }, - { - "author_name": "Hang Xie", - "author_inst": "Center for Biologics Evaluation and Research, US Food and Drug Administration" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.04.28.489537", "rel_title": "The spike gene is a major determinant for the SARS-CoV-2 Omicron-BA.1 phenotype", @@ -341088,6 +343169,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.04.26.22274244", + "rel_title": "The impact of COVID-19 pandemic on bronchiolitis (lower respiratory tract infection) due to respiratory syncytial virus: A systematic review and meta-analysis", + "rel_date": "2022-04-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.26.22274244", + "rel_abs": "BackgroundThe COVID-19 pandemic has changed the epidemiology of RSV infection which accounts for most bronchiolitis cases and viral pneumonias in infants.\n\nAimThis systematic review and meta-analysis aimed to quantitatively assess the effect of COVID-19 pandemic on respiratory syncytial virus (RSV) associated bronchiolitis among hospitalised infants globally.\n\nMethodsThe study protocol was registered in the PROSPERO database (CRD42022314000) and was designed based on PRISMA guidelines updated in May 2020. An electronic search of PubMed/MEDLINE, Scopus and Google Scholar was carried out for articles regarding the impact of the COVID-19 pandemic on bronchiolitis or lower respiratory tract infection due to the respiratory syncytial virus in English published between January 2019 and March 2022. The meta-analysis component was modified appropriately to synthesise the pooled proportion of infants having RSV-associated bronchiolitis before the COVID-19 pandemic in 2019 and during the pandemic with 95% confidence interval (CI).\n\nResultsWe screened 189 articles and systematically reviewed fifty studies reporting RSV-associated bronchiolitis cases in infants before the pandemic in 2019 and during the pandemic in 2020/2021. Eight qualified studies from Europe and China, which reported RSV-bronchiolitis both in 2019 and in 2020/21 were pooled by random-effects meta-analysis. These studies comprised 109,186 symptomatic cases of bronchiolitis before the pandemic in 2019 and 61,982 cases in 2020-2021. The quantitative analysis included laboratory-confirmed RSV infection in 7691 infants with bronchiolitis reported before the pandemic in 2019. Meanwhile, during the pandemic, 4964 bronchiolitis cases were associated with RSV infection. The pooled proportion of RSV-associated bronchiolitis cases before the pandemic in 2019 was 16.74% (95% CI 11.73, 22.43%, 95% prediction interval 0.032, 34.16). The pooled proportion of confirmed RSV cases during the pandemic in 2020/2021 was 19.20 % (95% CI 12.01, 27.59%, 95% prediction interval 0.046, 42.35).\n\nConclusionThere was an increase in RSV activity after the relaxation of stringent public health measures during the COVID-19 pandemic.\n\nKey Messages (Provide appropriate messages of about 35-50 words to be printed in centre box)O_LIThis systematic review and meta-analysis reports the pooled proportion of RSV associated bronchiolitis cases in 2019 (before the COVID-19 pandemic) and during the pandemic.\nC_LIO_LIEight observational studies from China and Europe were qualified for the meta-analysis.\nC_LIO_LIA decline in reported cases of bronchiolitis was observed during the COVID-19 pandemic which might be attributed to non-pharmaceutical measures and a fall in the hospitalisation rates of respiratory non-SARS-CoV-2 infections.\nC_LIO_LIThe pooled proportion of RSV positivity rate among bronchiolitis cases was more during the COVID-19 pandemic.\nC_LI", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Sasidharanpillai Sabeena", + "author_inst": "Independent Researcher" + }, + { + "author_name": "Nagaraja Ravishankar", + "author_inst": "Vallabhbhai Patel Chest Institute, New Delhi" + }, + { + "author_name": "Sudandiradas Robin", + "author_inst": "Manipal Academy of Higher Education" + }, + { + "author_name": "Sabitha Sasidharan Pillai", + "author_inst": "Warren Alpert Medical School of Brown University, Providence, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.04.26.489630", "rel_title": "P681 mutations within the polybasic motif of spike dictate fusogenicity and syncytia formation of SARS CoV-2 variants", @@ -341588,29 +343700,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.04.22.22274058", - "rel_title": "Coronavirus and incomes: the COVID-19 pandemic dynamics in Africa in February 2022", - "rel_date": "2022-04-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.22.22274058", - "rel_abs": "The relative accumulated and daily characteristics of the COVID-19 pandemic dynamics in Africa were used to find links with the gross domestic product per capita (GDP), percentages of fully vaccinated people and daily numbers of tests per case. A simple statistical analysis of datasets corresponding to February 1, 2022 showed that accumulated and daily numbers of cases per capita, daily numbers of deaths per capita and vaccination levels increase with the increase of GDP. As in the case of Europe, the smoothed daily numbers of new cases per capita in Africa increase with the increasing of the vaccination level. But the increase of the accumulated numbers of cases and daily number of deaths with increasing the vaccination level was revealed in Africa. In comparison with Europe, no significant correlation was revealed between the vaccination level and the number of deaths per case. As in the case of Europe, African countries demonstrate no statistically significant links between the pandemic dynamics characteristics and the daily number of tests per case. It looks that countries with very small GDP are less affected by the COVID-19 pandemic. The cause of this phenomenon requires further research, but it is possible that low incomes limit the mobility of the population and reduce the number of contacts with infected people. In order to overcome the pandemic, quarantine measures and social distance should not be neglected (this also applies to countries with a high level of income and vaccination).", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Igor Nesteruk", - "author_inst": "Institute of Hydromechanics National Academy of sciences of Ukraine" - }, - { - "author_name": "Oleksii Rodionov", - "author_inst": "Private consulting office, Kyiv, Ukraine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.04.22.22274169", "rel_title": "Global burden of mental health problems among children and adolescents during COVID-19 pandemic: A systematic umbrella review", @@ -342918,6 +345007,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2022.04.22.22274137", + "rel_title": "A within-host model of SARS-CoV-2 infection", + "rel_date": "2022-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.22.22274137", + "rel_abs": "Within-host models have been used to successfully describe the dynamics of multiple viral infections, however, the dynamics of SARS-CoV-2 virus infection remain poorly understood. A greater understanding of how the virus interacts with the host can contribute to more realistic epidemiological models and help evaluate the effect of antiviral therapies and vaccines. Here, we present a within-host model to describe SARS-CoV-2 viral dynamics in the upper respiratory tract of individuals enrolled in the UK COVID-19 Human Challenge Study. Using this model, we investigate the viral dynamics and provide timescales of infection that independently verify key epidemiological parameters important in the management of an epidemic. In particular, we estimate that an infected individual is first capable of transmitting the virus after approximately 2.1 days, remains infectious for a further 8.3 days, but can continue to test positive using a PCR test for up to 27 days.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jonathan Carruthers", + "author_inst": "United Kingdom Health Security Agency" + }, + { + "author_name": "Jingsi Xu", + "author_inst": "University of Manchester" + }, + { + "author_name": "Thomas James Ronald Finnie", + "author_inst": "United Kingdom Health Security Agency" + }, + { + "author_name": "Ian Hall", + "author_inst": "University of Manchester" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.04.22.22274163", "rel_title": "Predicting past and future SARS-CoV-2-related sick leave using discrete time Markov modelling", @@ -343338,101 +345458,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.04.21.22274082", - "rel_title": "COVID-19 patients share common, corticosteroid-independent features of impaired host immunity to pathogenic molds", - "rel_date": "2022-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.21.22274082", - "rel_abs": "Patients suffering from coronavirus disease-2019 (COVID-19) are at high risk for deadly secondary fungal infections such as COVID-19-associated pulmonary aspergillosis (CAPA) and COVID-19-associated mucormycosis (CAM). Despite this clinical observation, direct experimental evidence for severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2)-driven alterations of antifungal immunity is scarce. Using an ex-vivo whole blood (WB) stimulation assay, we challenged blood from twelve COVID-19 patients with Aspergillus fumigatus and Rhizopus arrhizus antigens and studied the expression of activation, maturation, and exhaustion markers, as well as cytokine secretion. Compared to healthy controls, T-helper cells from COVID-19 patients displayed increased expression levels of the exhaustion marker PD-1 and weakened A. fumigatus- and R. arrhizus-induced activation. While baseline secretion of proinflammatory cytokines was massively elevated, WB from COVID-19 patients elicited diminished release of T-cellular (e.g., IFN-{gamma}, IL-2) and innate immune cell-derived (e.g., CXCL9, CXCL10) cytokines in response to A. fumigatus and R. arrhizus antigens. Additionally, samples from COVID-19 patients showed deficient granulocyte activation by mold antigens and reduced fungal killing capacity of neutrophils. These features of weakened anti-mold immune responses were largely decoupled from COVID-19 severity, the time elapsed since diagnosis of COVID-19, and recent corticosteroid uptake, suggesting that impaired anti-mold defense is a common denominator of the underlying SARS-CoV-2 infection. Taken together, these results expand our understanding of the immune predisposition to post-viral mold infections and could inform future studies of immunotherapeutic strategies to prevent and treat fungal superinfections in COVID-19 patients.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Beeke Tappe", - "author_inst": "Department of Internal Medicine II, University Hospital of Wuerzburg, Wuerzburg, Germany." - }, - { - "author_name": "Chris David Lauruschkat", - "author_inst": "Department of Internal Medicine II, University Hospital of Wuerzburg, Wuerzburg, Germany." - }, - { - "author_name": "Lea Strobel", - "author_inst": "Department of Internal Medicine II, University Hospital of Wuerzburg, Wuerzburg, Germany." - }, - { - "author_name": "Jezreel Pantaleon Garcia", - "author_inst": "Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, USA." - }, - { - "author_name": "Oliver Kurzai", - "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany. Leibniz Institute for Natural Product Research and Infection Biology Hans K" - }, - { - "author_name": "Silke Rebhan", - "author_inst": "Department of Internal Medicine II, University Hospital of Wuerzburg, Wuerzburg, Germany." - }, - { - "author_name": "Sabrina Kraus", - "author_inst": "Department of Internal Medicine II, University Hospital of Wuerzburg, Wuerzburg, Germany." - }, - { - "author_name": "Elena Pfeuffer-Jovic", - "author_inst": "Missionsaerztliche Klinik Wuerzburg, Wuerzburg, Germany." - }, - { - "author_name": "Lydia Bussemer", - "author_inst": "Department of Internal Medicine II, University Hospital of Wuerzburg, Wuerzburg, Germany." - }, - { - "author_name": "Lotte Possler", - "author_inst": "Main-Klinik Ochsenfurt, Wuerzburg, Germany." - }, - { - "author_name": "Matthias Held", - "author_inst": "Missionsaerztliche Klinik Wuerzburg, Wuerzburg, Germany." - }, - { - "author_name": "Kerstin Huenniger", - "author_inst": "Institute for Hygiene and Microbiology, University of Wuerzburg, Wuerzburg, Germany. Leibniz Institute for Natural Product Research and Infection Biology Hans K" - }, - { - "author_name": "Olaf Kniemeyer", - "author_inst": "Leibniz Institute for Natural Product Research and Infection Biology Hans Knoell Institute, Jena, Germany." - }, - { - "author_name": "Sascha Schaeuble", - "author_inst": "Leibniz Institute for Natural Product Research and Infection Biology Hans Knoell Institute, Jena, Germany." - }, - { - "author_name": "Axel Brakhage", - "author_inst": "Leibniz Institute for Natural Product Research and Infection Biology Hans Knoell Institute, Jena, Germany. Department of Microbiology and Molecular Biology, Ins" - }, - { - "author_name": "Gianni Panagiotou", - "author_inst": "Leibniz Institute for Natural Product Research and Infection Biology Hans Knoell Institute, Jena, Germany." - }, - { - "author_name": "Lewis P. White", - "author_inst": "Public Health Wales, Microbiology Cardiff, Wales, UK." - }, - { - "author_name": "Hermann Einsele", - "author_inst": "Department of Internal Medicine II, University Hospital of Wuerzburg, Wuerzburg, Germany." - }, - { - "author_name": "Juergen Loeffler", - "author_inst": "Department of Internal Medicine II, University Hospital of Wuerzburg, Wuerzburg, Germany." - }, - { - "author_name": "Sebastian Wurster", - "author_inst": "Department of Infectious Diseases, Infection Control and Employee Health, The University of Texas MD Anderson Cancer Center, Houston, USA." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.04.21.22274138", "rel_title": "Epidemiological investigation of the COVID-19 outbreak in Vellore district in South India using Geographic Information Surveillance (GIS)", @@ -346172,6 +348197,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.04.18.22273880", + "rel_title": "Changes of LipoxinA4 Levels Following Early Hospital Management of Patients with Non-Severe COVID-19: A Pilot Study", + "rel_date": "2022-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.18.22273880", + "rel_abs": "LipoxinA4 (LXA4) is an anti-inflammatory biomarker participating in the active process of inflammation resolution, which is suggested to be effective on infectious and inflammatory diseases like COVID-19. In this study, we hypothesized that LXA4 levels may increase following COVID-19 treatment and are even more accurate than commonly used inflammatory markers such as erythrocyte sedimentation rate (ESR), c-reactive protein (CRP), and ferritin. To test this hypothesis, a pilot study was conducted with 31 adult hospitalized patients with non-severe COVID-19. LXA4 levels were measured at the baseline and 48-72 hours later. Accordingly, ESR and CRP levels were collected on the first day of hospitalization. Moreover, the maximum serum ferritin levels were collected during the five days. LXA4 levels significantly increased at 48-72 hours compared to the baseline. ESR, CRP, and ferritin levels were positively correlated with the increased LXA4. In contrast, aging was shown to negatively correlate with the increased LXA4 levels. LXA4 may be known as a valuable marker to assess the treatment response among non-elderly patients with non-severe COVID-19. Furthermore, LXA4 could be considered as a potential treatment option under inflammatory conditions. Further studies are necessary to clarify LXA4 role in COVID-19 pathogenesis, as well as the balance between such pro-resolving mediators and inflammatory parameters.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Farzaneh Jamali", + "author_inst": "Tehran University of Medical Sciences" + }, + { + "author_name": "Bita Shahrami", + "author_inst": "Tehran University of Medical Sciences" + }, + { + "author_name": "Amirmahdi Mojtahedzadeh", + "author_inst": "Semmelweis University" + }, + { + "author_name": "Farhad Najmeddin", + "author_inst": "Tehran University of Medical Sciences" + }, + { + "author_name": "Amir Ahmad Arabzadeh", + "author_inst": "Ardabil University of Medical Sciences" + }, + { + "author_name": "Azar Hadadi", + "author_inst": "Tehran University of Medical Sciences" + }, + { + "author_name": "Mohammad Sharifzadeh", + "author_inst": "Tehran University of Medical Sciences" + }, + { + "author_name": "Mojtaba Mojtahedzadeh", + "author_inst": "Tehran University of Medical Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.04.19.22274056", "rel_title": "Effectiveness of Primary and Booster COVID-19 mRNA Vaccination against Infection Caused by the SARS-CoV-2 Omicron Variant in People with a Prior SARS-CoV-2 Infection", @@ -346800,89 +348872,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2022.04.20.22274061", - "rel_title": "Vaccine effectiveness against SARS-CoV-2 infection and COVID-19-related hospitalization with the Alpha, Delta and Omicron SARS-CoV-2 variants: a nationwide Danish cohort study", - "rel_date": "2022-04-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.20.22274061", - "rel_abs": "BackgroundThe continued occurrence of more contagious SARS-CoV-2 variants and waning immunity over time require ongoing re-evaluation of the vaccine effectiveness (VE). This study aimed to estimate the effectiveness in two age groups (12-59 and 60 years or above) of two and three vaccine doses (BNT162b2 mRNA or mRNA-1273 vaccine) by time since vaccination against SARS-CoV-2 infection and COVID-19-related hospitalization in an Alpha, Delta and Omicron dominated period.\n\nMethodsA Danish nationwide cohort study design was used to estimate VE against SARS-CoV-2 infection and COVID-19-related hospitalization with the Alpha, Delta and Omicron variants. Information was obtained from nationwide registries and linked using a unique personal identification number. The study included all residents in Denmark aged 12 years or above (18 years or above for the analysis of three doses) in the Alpha (February 20 to June 15, 2021), Delta (July 4 to November 20, 2021) and Omicron (December 21, 2021 to January 31, 2022) dominated periods. VE estimates including 95% confidence intervals (CIs) were calculated using Cox proportional hazard regression models with adjustments for age, sex and geographical region. Vaccination status was included as a time-varying exposure.\n\nFindingsIn the oldest age group, VE against infection after two doses was 91.0% (95% CI: 88.5; 92.9) for the Alpha variant, 82.2% (95% CI: 75.3; 87.1) for the Delta variant and 39.9% (95% CI: 26.4; 50.9) for the Omicron variant 14-30 days since vaccination. The VE waned over time and was 71.5% (95% CI: 54.7; 82.8), 49.8% (95% CI: 46.5; 52.8) and 4.7% (95% CI: 0.2; 8.9) >120 days since vaccination against the three variants, respectively. Higher estimates were observed after the third dose with VE estimates against infection of 86.0% (Delta, 95% CI: 83.3; 88.3) and 57.6% (Omicron, 95% CI: 55.8; 59.4) 14-30 days since vaccination. Among both age groups, VE against COVID-19-related hospitalization 14-30 days since vaccination with two or three doses was 94.8% or above for the Alpha and Delta variants, whereas among the youngest age group, VE estimates against the Omicron variant after two and three doses were 62.4% (95% CI: 46.3; 73.6) and 89.8% (95% CI: 87.9; 91.3), respectively.\n\nConclusionsTwo vaccine doses provided high protection against SARS-CoV-2 infection and COVID-19-related hospitalization with the Alpha and Delta variants with protection waning over time. Two vaccine doses provided only limited protection against SARS-CoV-2 infection and COVID-19-related hospitalization with the Omicron variant. The third vaccine dose substantially increased the protection against Delta and Omicron.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Mie Agermose Gram", - "author_inst": "Statens Serum Institut" - }, - { - "author_name": "Hanne-Dorthe Emborg", - "author_inst": "SSI: Statens Serum Institut" - }, - { - "author_name": "Astrid Blicher Schelde", - "author_inst": "SSI: Statens Serum Institut" - }, - { - "author_name": "Nikolaj Ulrik Friis", - "author_inst": "SSI: Statens Serum Institut" - }, - { - "author_name": "Katrine Finderup Nielsen", - "author_inst": "Statens Serum Institut" - }, - { - "author_name": "Ida Rask Moustsen-Helms", - "author_inst": "SSI: Statens Serum Institut" - }, - { - "author_name": "Rebecca Legarth", - "author_inst": "SSI: Statens Serum Institut" - }, - { - "author_name": "Janni Uyen Hoa Lam", - "author_inst": "SSI: Statens Serum Institut" - }, - { - "author_name": "Manon Chaine", - "author_inst": "SSI: Statens Serum Institut" - }, - { - "author_name": "Aisha Zahoor Malik", - "author_inst": "SSI: Statens Serum Institut" - }, - { - "author_name": "Morten Rasmussen", - "author_inst": "SSI: Statens Serum Institut" - }, - { - "author_name": "Jannik Fonager", - "author_inst": "SSI: Statens Serum Institut" - }, - { - "author_name": "Raphael Niklaus Sieber", - "author_inst": "SSI: Statens Serum Institut" - }, - { - "author_name": "Marc Stegger", - "author_inst": "SSI: Statens Serum Institut" - }, - { - "author_name": "Steen Ethelberg", - "author_inst": "SSI: Statens Serum Institut" - }, - { - "author_name": "Palle Valentiner-Branth", - "author_inst": "SSI: Statens Serum Institut" - }, - { - "author_name": "Christian Holm Hansen", - "author_inst": "SSI: Statens Serum Institut" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.04.14.22273903", "rel_title": "Effects of COVID-19 in Care Homes - A Mixed Methods Review", @@ -348002,6 +349991,41 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.04.18.488640", + "rel_title": "BCG vaccination of Diversity Outbred mice induces cross-reactive antibodies to SARS-CoV-2 spike protein", + "rel_date": "2022-04-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.18.488640", + "rel_abs": "The Bacillus Calmette-Guerin (BCG) vaccine, the only vaccine against tuberculosis, induces cross-protection against pathogens unrelated to Mycobacterium, including viruses. Epidemiological studies have identified potential benefits of BCG vaccination against SARS-CoV-2 infection. While BCGs heterologous effects have been widely attributable to trained immunity, we hypothesized BCG vaccination could induce cross-reactive antibodies against the spike protein of SARS-CoV-2 Wuhan-Hu-1. The concentration of IgG reactive to SARS-CoV-2 spike protein from the sera of BCG-vaccinated, Diversity Outbred (DO) mice and C57BL/6J inbred mice was measured using ELISA. Sera from 10/15 BCG-vaccinated DO mice possessed more IgG reactive to recombinant spike protein than sera from BCG-vaccinated C57BL/6J mice and unvaccinated DO mice. Amino acid sequences common to BCG cell wall/membrane proteins and SARS-CoV-2 spike protein were identified as potential antigen candidates for future study. These results imply a humoral mechanism, influenced by genotype, by which BCG vaccination could confer immunity to SARS-CoV-2.\n\nGraphic Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC=\"FIGDIR/small/488640v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (23K):\norg.highwire.dtl.DTLVardef@1ff9d16org.highwire.dtl.DTLVardef@a2302dorg.highwire.dtl.DTLVardef@8ee2borg.highwire.dtl.DTLVardef@4c7b55_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Aubrey G. Specht", + "author_inst": "Department of Infectious Disease and Global Health, Cummings SVM at Tufts University, North Grafton, MA, USA" + }, + { + "author_name": "Sherry L. Kurtz", + "author_inst": "Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA" + }, + { + "author_name": "Karen L. Elkins", + "author_inst": "Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA" + }, + { + "author_name": "Harrison Specht", + "author_inst": "Department of Bioengineering and Barnett Institute, Northeastern University, Boston, MA, USA" + }, + { + "author_name": "Gillian Beamer", + "author_inst": "Department of Infectious Disease and Global Health, Cummings SVM at Tufts University, North Grafton, MA, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.04.19.488806", "rel_title": "The Spike protein of SARS-CoV-2 impairs lipid metabolism and increases susceptibility to lipotoxicity: implication for a role of Nrf2", @@ -348430,25 +350454,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.04.13.22273837", - "rel_title": "How did the COVID-19 Pandemic impact self-reported cancer screening rates in 12 Midwestern states?", - "rel_date": "2022-04-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.13.22273837", - "rel_abs": "ObjectiveIn the early months of the COVID-19 pandemic, the U.S. healthcare system reallocated resources to emergency response and mitigation. This reallocation impacted essential healthcare services, including cancer screenings.\n\nMethodsTo examine how the pandemic impacted cancer screenings at the population-level, this study analyzes 2018 and 2020 Behavioral Risk Factor Surveillance System (BRFSS) data to estimate the change in the proportion of eligible adults reporting a recent cancer screen (mammogram, pap smear, colon/sigmoidoscopy, blood stool test). All analyses accounted for response rates and sampling weights, and explored differences by gender and region across 12 Midwestern states.\n\nResultsWe found that the proportion of adult women completing a mammogram declined across all states (-0.9% to -18.1%). The change in colon/sigmoidoscopies, pap smears, and blood stool tests were mixed, ranging from a 9.7% decline in pap smears to a 7.1% increase in blood stool tests. Declines varied considerably between states and within states by gender or metro/urban/rural status.\n\nConclusionsThe COVID-19 pandemic led to delayed breast, cervical, and colorectal cancer detection services. Policymakers should aim to advance cancer control efforts by implementing targeted screening initiatives.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Jason Semprini", - "author_inst": "University of Iowa" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.04.18.22273967", "rel_title": "A boost with SARS-CoV-2 BNT162b2 mRNA vaccine elicits strong humoral responses independently of the interval between the first two doses", @@ -349788,6 +351793,45 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.04.13.22273200", + "rel_title": "Pre-procedural testing improves estimated COVID-19 prevalence and trends", + "rel_date": "2022-04-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.13.22273200", + "rel_abs": "BackgroundCOVID-19 positivity rates reported to the public may provide a distorted view of community trends because they tend to be inflated by high-risk groups, such as symptomatic patients and individuals with known exposures to COVID-19. This positive bias within high-risk groups has also varied over time, depending on testing capability and indications for being tested. In contrast, throughout the pandemic, routine COVID-19 screening tests for elective procedures and operations unrelated to COVID-19 risk have been administered by medical facilities to reduce transmission to medical staffing and other patients. We propose the use of these pre-procedural COVID-19 patient datasets to reduce biases in community trends and better understand local prevalence.\n\nMethodsUsing patient data from the Maui Medical Group clinic, we analyzed 12,640 COVID-19 test results from May 1, 2020 to March 16, 2021, divided into two time periods corresponding with Mauis outbreak.\n\nResultsMean positivity rates were 0.1% for the pre-procedural group, 3.9% for the symptomatic group, 4.2% for the exposed group, and 2.0% for the total study population. Post-outbreak, the mean positivity rate of the pre-procedural group was significantly lower than the aggregate group (all other clinic groups combined). The positivity rates of both pre-procedural and aggregate groups increased over the study period, although the pre-procedural group showed a smaller rise in rate.\n\nConclusionsPre-procedural groups may produce different trends compared to high-risk groups and are sufficiently robust to detect small changes in positivity rates. Considered in conjunction with high-risk groups, pre-procedural marker groups used to monitor understudied, low-risk subsets of a community may improve our understanding of community COVID-19 prevalence and trends.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "GENEVIEVE C. PANG", + "author_inst": "Hawaii Department of Health" + }, + { + "author_name": "Amy T. Hou", + "author_inst": "Maui Medical Group" + }, + { + "author_name": "Krizhna L. Bayudan", + "author_inst": "Hawaii State Department of Health" + }, + { + "author_name": "Ethan A. Frank", + "author_inst": "Hawaii State Department of Health" + }, + { + "author_name": "Jennifer Pastiglione", + "author_inst": "Maui Medical Group" + }, + { + "author_name": "Lorrin W. Pang", + "author_inst": "Hawaii State Department of Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.04.14.22273896", "rel_title": "COVID-19 vaccine effectiveness against severe disease from the Omicron BA.1 and BA.2 subvariants: surveillance results from southern Sweden, December 2021 to March 2022", @@ -350140,57 +352184,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2022.04.15.22273460", - "rel_title": "Coronavirus infection in neonates: Neurodevelopmental outcomes at 18 months of age", - "rel_date": "2022-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.15.22273460", - "rel_abs": "BackgroundAlthough most neonates with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections have mild disease, the impact on neurodevelopmental outcomes is unknown. This study aimed to assess 18-month neurodevelopmental outcomes of neonates infected with SARS-CoV-2 infection.\n\nMethodsWe conducted a prospective cohort study of neonates diagnosed with SARS-CoV-2 infection between June 2020-August 2020 through nasopharyngeal coronavirus disease 2019 (COVID-19) PCR testing. A total of 58 neonates were identified from the Kuwait national COVID-19 registry and were enrolled. Historical controls were selected from the neonatal follow-up registry and matched 2:1 based on sex and gestational age. At 18 months of age, neurodevelopmental outcomes were assessed using Bayley Scales of Infant and Toddler Development-3rd Edition (BSID-III) by two trained assessors.\n\nResultsA total of 40 children were diagnosed with SARS-CoV-2 infection and included in the final analysis. The median age at infection was 18 days (range: 10-26 days). Eighteen (45%) were asymptomatic, 15 (37.5%) had a sepsis-like presentation, 5 (12.5%) had respiratory distress and 2 (5%) had a multisystem inflammatory syndrome in children (MIS-C)-like presentation. At 18 months follow up, only one child had severe developmental delay, and one child had a language delay. BSID-III outcomes did not significantly differ between the SARS-CoV-2 infected group and the control group.\n\nConclusionsThere is no difference in neurodevelopmental outcomes in children infected with SARS-CoV-2 infection at 18 months compared to controls, although longer neurodevelopmental follow-up studies are required.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Mariam Ayed", - "author_inst": "Farwaniya Hospital" - }, - { - "author_name": "Zainab Alsaffar", - "author_inst": "Farwaniya Hospital" - }, - { - "author_name": "Zainab Bahzad", - "author_inst": "Farwaniya Hospital" - }, - { - "author_name": "Yasmin Buhamad", - "author_inst": "Farwaniya Hospital" - }, - { - "author_name": "Ali Abdulkareem", - "author_inst": "Farwaniya Hospital" - }, - { - "author_name": "Alaa AlQattan", - "author_inst": "Farwaniya Hospital" - }, - { - "author_name": "Alia Embaireeg", - "author_inst": "Farwaniya Hospital" - }, - { - "author_name": "Mais Kartam", - "author_inst": "Farwaniya Hospital" - }, - { - "author_name": "Hessa Alkandari", - "author_inst": "Population Health Department, Dasman Diabetes Institute, Kuwait" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2022.04.14.22273413", "rel_title": "Vaccine effectiveness of CanSino (Adv5-nCoV) COVID-19 vaccine among childcare workers -- Mexico, March-December 2021", @@ -351478,6 +353471,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.04.11.22273644", + "rel_title": "COVID-19 vaccine coverage among immigrants and refugees in Alberta: a population-based cross-sectional study", + "rel_date": "2022-04-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.11.22273644", + "rel_abs": "IntroductionStudies have shown that immigrants have lower vaccination rates than the Canadian-born population. We sought to assess COVID-19 vaccine coverage and factors associated with uptake among foreign-born immigrants relative to the non-immigrant population in Alberta, Canada.\n\nMethodsIn this cross-sectional study, we analyzed population-based linked administrative health data from Alberta to examine vaccine coverage for 3,931,698 Albertans, of which 731,217 were immigrants. We calculated COVID-19 vaccination coverage as the proportion of eligible Albertans with a record of receiving at least one dose of a COVID-19 vaccine as of November 29, 2021. We used multivariable logistic regression to examine the association of vaccine coverage with migration status (immigrants: four categories based on time since migration and non-immigrants) adjusting for socio-demographic variables.\n\nResultsOverall, COVID-19 vaccination coverage was higher among immigrants (78.2%; 95% CI: 78.1%-78.3%) compared to non-immigrants (76.0%; 95% CI: 75.9%-76.0%). Coverage among immigrants differed by continent of origin, with North America, Oceania, and Europe having the lowest coverage. Although vaccine coverage was relatively uniform across neighborhood income quintiles for immigrants, immigrants living in rural areas had lower vaccine coverage compared to non-immigrants living in rural areas. Multivariable logistic regression analysis showed a significant interaction between age category and migration status. While immigrants below 50 years of age generally had significantly higher vaccine coverage compared to non-immigrants, there was some variation based on time since migration. Immigrants above 50 years of age showed significantly lower coverage compared to non-immigrants of the same age.\n\nConclusionPublic health interventions should focus on older immigrants, immigrants living in rural areas, and immigrants from specific continental backgrounds in order to improve COVID-19 vaccination coverage.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Shannon E MacDonald", + "author_inst": "University of Alberta" + }, + { + "author_name": "Yuba Raj Paudel", + "author_inst": "University of Alberta" + }, + { + "author_name": "Crystal Du", + "author_inst": "University of Alberta" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.04.07.22273578", "rel_title": "Disentangling the rhythms of human activity in the built environment for airborne transmission risk", @@ -351802,69 +353822,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, - { - "rel_doi": "10.1101/2022.04.15.22273412", - "rel_title": "COVID-19 vaccine effectiveness against SARS-CoV-2 infection in the United States prior to the Delta and Omicron-associated surges: a retrospective cohort study of repeat blood donors", - "rel_date": "2022-04-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.15.22273412", - "rel_abs": "To inform public health policy, it is critical to monitor COVID-19 vaccine effectiveness (VE), including against acquiring infection. We estimated VE using a retrospective cohort study among repeat blood donors who donated during the first half of 2021, demonstrating a viable approach for monitoring of VE via serological surveillance. Using Poisson regression, we estimated overall VE was 88.8% (95% CI: 86.2-91.1), adjusted for demographic covariates and variable baseline risk. Time since first reporting vaccination, age, race-ethnicity, region, and calendar time were statistically significant predictors of incident infection. Studies of VE during periods of Delta and Omicron spread are underway.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Eduard Grebe", - "author_inst": "Vitalant Research Institute" - }, - { - "author_name": "Elaine A. Yu", - "author_inst": "Vitalant Research Institute" - }, - { - "author_name": "Marjorie D. Bravo", - "author_inst": "Vitalant" - }, - { - "author_name": "Alex Welte", - "author_inst": "Stellenbosch University" - }, - { - "author_name": "Roberta L. Bruhn", - "author_inst": "Vitalant Research Institute" - }, - { - "author_name": "Mars Stone", - "author_inst": "Vitalant Research Institiute" - }, - { - "author_name": "Valerie Green", - "author_inst": "Creative Testing Solutions" - }, - { - "author_name": "Phillip C. Williamson", - "author_inst": "Creative Testing Solutions" - }, - { - "author_name": "Leora R. Feldstein", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Jefferson M. Jones", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Michael P. Busch", - "author_inst": "Vitalant Research Institute" - }, - { - "author_name": "Brian Custer", - "author_inst": "Vitalant Research Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.04.15.22273449", "rel_title": "Using a real-world network to model the tradeoff between stay-at-home restriction, vaccination, social distancing and working hours on COVID-19 dynamics.", @@ -352980,6 +354937,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/105437", + "rel_title": "The Arabidopsis Framework Model version 2 predicts the organism-level effects of circadian clock gene mis-regulation", + "rel_date": "2022-04-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/105437", + "rel_abs": "Predicting a multicellular organisms phenotype quantitatively from its genotype is challenging, as genetic effects must propagate across scales. Circadian clocks are intracellular regulators that control temporal gene expression patterns and hence metabolism, physiology and behaviour. Here we explain and predict canonical phenotypes of circadian timing in a multicellular, model organism. We used diverse metabolic and physiological data to combine and extend mathematical models of rhythmic gene expression, photoperiod-dependent flowering, elongation growth and starch metabolism within a Framework Model for the vegetative growth of Arabidopsis thaliana, sharing the model and data files in a structured, public resource. The calibrated model predicted the effect of altered circadian timing upon each particular phenotype in clock-mutant plants under standard laboratory conditions. Altered night-time metabolism of stored starch accounted for most of the decrease in whole-plant biomass, as previously proposed. Mobilisation of a secondary store of malate and fumarate was also mis-regulated, accounting for any remaining biomass defect. We test three candidate mechanisms for the accumulation of these organic acids. Our results link genotype through specific processes to higher-level phenotypes, formalising our understanding of a subtle, pleiotropic syndrome at the whole-organism level, and validating the systems approach to understand complex traits starting from intracellular circuits.\n\nThis work updates the first biorXiv version, February 2017, https://doi.org/10.1101/105437, with an expanded description and additional analysis of the same core data sets and the same FMv2 model, summary tables and supporting, follow-on data from three further studies with further collaborators. This biorXiv revision constitutes the second version of this report.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Abigail Vanderheiden", + "author_inst": "Emory University" + }, + { + "author_name": "Philipp Ralfs", + "author_inst": "Emory University" + }, + { + "author_name": "Tatiana Chirkova", + "author_inst": "Emory University" + }, + { + "author_name": "Amit A Upadhyay", + "author_inst": "Emory University" + }, + { + "author_name": "Matthew G Zimmerman", + "author_inst": "Emory University" + }, + { + "author_name": "Shamika Bedoya", + "author_inst": "Emory University" + }, + { + "author_name": "Hadj Aoued", + "author_inst": "Emory University" + }, + { + "author_name": "Gregory K Tharp", + "author_inst": "Emory University" + }, + { + "author_name": "Kathryn Pellegrini", + "author_inst": "Emory University" + }, + { + "author_name": "Anice C Lowen", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Vineet D. Menachery", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Larry J Anderson", + "author_inst": "University of Emory School of Medicine" + }, + { + "author_name": "Arash Grakoui", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Steven E. Bosinger", + "author_inst": "Emory University" + }, + { + "author_name": "Mehul S Suthar", + "author_inst": "Emory University" + } + ], + "version": "2", + "license": "cc_no", + "type": "new results", + "category": "plant biology" + }, { "rel_doi": "10.1101/2022.04.08.22273322", "rel_title": "Correlations between kidney and heart function bioindicators and the expressions of Toll-Like, ACE2, and NRP-1 receptors in COVID-19", @@ -353363,77 +355395,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.04.12.22273761", - "rel_title": "Multiplex RT-qPCR assay (N200) to detect and estimate prevalence of multiple SARS-CoV-2 Variants of Concern in wastewater", - "rel_date": "2022-04-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.12.22273761", - "rel_abs": "Wastewater-based surveillance (WBS) has become an effective tool around the globe for indirect monitoring of COVID-19 in communities. Quantities of viral fragments of SARS-CoV-2 in wastewater are related to numbers of clinical cases of COVID-19 reported within the corresponding sewershed. Variants of Concern (VOCs) have been detected in wastewater by use of reverse transcription quantitative polymerase chain reaction (RT-qPCR) or sequencing. A multiplex RT-qPCR assay to detect and estimate the prevalence of multiple VOCs, including Omicron/Alpha, Beta, Gamma, and Delta, in wastewater RNA extracts was developed and validated. The probe-based multiplex assay, named \"N200\" focuses on amino acids 199-202, a region of the N gene that contains several mutations that are associated with variants of SARS- CoV-2 within a single amplicon. Each of the probes in the N200 assay are specific to the targeted mutations and worked equally well in single- and multi-plex modes. To estimate prevalence of each VOC, the abundance of the targeted mutation was compared with a non- mutated region within the same amplified region. The N200 assay was applied to monitor frequencies of VOCs in wastewater extracts from six sewersheds in Ontario, Canada collected between December 1, 2021, and January 4, 2022. Using the N200 assay, the replacement of the Delta variant along with the introduction and rapid dominance of the Omicron variant were monitored in near real-time, as they occurred nearly simultaneously at all six locations. The N200 assay is robust and efficient for wastewater surveillance can be adopted into VOC monitoring programs or replace more laborious assays currently being used to monitor SARS- CoV-2 and its VOCs.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Meghan L.M. Fuzzen", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Nathanael BJ Harper", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Hadi A Dhiyebi", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Nivetha Srikanthan", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Samina Hayat", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Shelley W Peterson", - "author_inst": "National Microbiology Laboratory, Public Health Agency of Canada" - }, - { - "author_name": "Ivy Yang", - "author_inst": "University of Toronto" - }, - { - "author_name": "Jianxian X Sun", - "author_inst": "University of Toronto" - }, - { - "author_name": "Elizabeth A Edwards", - "author_inst": "University of Toronto" - }, - { - "author_name": "John P Giesy", - "author_inst": "University of Saskatchewan" - }, - { - "author_name": "Chand S Mangat", - "author_inst": "National Microbiology Laboratory, Public Health Agency of Canada" - }, - { - "author_name": "Tyson E Graber", - "author_inst": "Children's Hospital of Eastern Ontario Research Institute" - }, - { - "author_name": "Robert E Delatolla", - "author_inst": "University of Ottawa" - }, - { - "author_name": "Mark R Servos", - "author_inst": "University of Waterloo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.04.13.22273825", "rel_title": "Effectiveness of COVID-19 vaccines against hospitalization and death in Canada: A multiprovincial test-negative design study", @@ -354949,6 +356910,20 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.04.10.22273660", + "rel_title": "Lowered oxygen saturation and increased body temperature in acute COVID-19 largely predict chronic fatigue syndrome and affective symptoms due to LONG COVID: a precision nomothetic approach", + "rel_date": "2022-04-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.10.22273660", + "rel_abs": "BackgroundLong coronavirus disease 2019 (LC) is a chronic sequel of acute COVID-19. The exact pathophysiology of the affective, chronic fatigue and physiosomatic symptoms (labeled as \"physio-affective phenome\") of LC has remained elusive.\n\nObjectiveThe current study aims to delineate the effects of oxygen saturation (SpO2) and body temperature during the acute phase on the physio-affective phenome of LC.\n\nMethodWe recruited 120 LC patients and 36 controls. For all participants, we assessed the lowest SpO2 and peak body temperature during acute COVID-19, and the Hamilton Depression and Anxiety Rating Scale (HAMD/HAMA) and Fibro Fatigue (FF) scales 3 to 4 months later.\n\nResultsLowered SpO2 and increased body temperature during the acute phase and female sex predict 60.7% of the variance in the physio-affective phenome of LC. Using unsupervised learning techniques we were able to delineate a new endophenotype class, which comprises around 26.7% of the LC patients and is characterized by very low SpO2 and very high body temperature, and depression, anxiety, chronic fatigue, and autonomic and gastro-intestinal symptoms scores. Single latent vectors could be extracted from both biomarkers, depression, anxiety and FF symptoms or from both biomarkers, insomnia, chronic fatigue, gastro-intestinal and autonomic symptoms.\n\nConclusionThe newly constructed endophenotype class and pathway phenotypes indicate that the physio-affective phenome of LC is at least in part the consequence of the pathophysiology of acute COVID-19, namely the combined effects of lowered SpO2, increased body temperature and the associated immune-inflammatory processes and lung lesions.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2022.04.11.22273729", "rel_title": "Intensity and longevity of SARS-CoV-2 vaccination response and efficacy of adjusted vaccination schedules in patients with immune-mediated inflammatory disease", @@ -355199,49 +357174,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.04.07.22273593", - "rel_title": "Inequities in COVID-19 vaccine and booster coverage across Massachusetts ZIP codes: large gaps persist after the 2021/22 Omicron wave", - "rel_date": "2022-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.07.22273593", - "rel_abs": "BackgroundInequities in COVID-19 vaccine coverage may contribute to future disparities in morbidity and mortality between Massachusetts (MA) communities.\n\nMethodsWe obtained public-use data on residents vaccinated and boosted by ZIP code (and by age group: 5-19, 20-39, 40-64, 65+) from MA Department of Public Health. We constructed population denominators for postal ZIP codes by aggregating Census-tract population estimates from the 2015-2019 American Community Survey. We excluded non-residential ZIP codes and the smallest ZIP codes containing 1% of the states population. We mapped variation in ZIP-code level primary series vaccine and booster coverage and used regression models to evaluate the association of these measures with ZIP-code-level socioeconomic and demographic characteristics. Because age is strongly associated with COVID-19 severity and vaccine access/uptake, we assessed whether observed socioeconomic and racial inequities persisted after adjusting for age composition and plotted age-specific vaccine and booster coverage by deciles of ZIP-code characteristics.\n\nResultsWe analyzed data on 418 ZIP codes. We observed wide geographic variation in primary series vaccination and booster rates, with marked inequities by ZIP-code-level education, median household income, essential worker share, and racial-ethnic composition. In age-stratified analyses, primary series vaccine coverage was very high among the elderly. However, we found large inequities in vaccination rates among younger adults and children, and very large inequities in booster rates for all age groups. In multivariable regression models, each 10 percentage point increase in \"percent college educated\" was associated with a 5.0 percentage point increase in primary series vaccine coverage and a 4.9 percentage point increase in booster coverage. Although ZIP codes with higher \"percent Black/Latino/Indigenous\" and higher \"percent essential workers\" had lower vaccine coverage, these associations became strongly positive after adjusting for age and education, consistent with high demand for vaccines among Black/Latino/Indigenous and essential worker populations.\n\nConclusionOne year into MAs vaccine rollout, large disparities in COVID-19 primary series vaccine and booster coverage persist across MA ZIP codes.\n\nO_TEXTBOXKey Messages\n\nO_LIAs of March 2022, in the wake of MAs Omicron wave, there were large inequities in ZIP-code-level vaccine and booster coverage by income, education, percent Black/Latino/Indigenous, and percent essential workers.\nC_LIO_LIEducation was the strongest predictor of ZIP-code vaccine coverage in MA.\nC_LIO_LICoverage gaps in ZIP codes with many essential workers and large Black/Latino/Indigenous populations are troubling, as these groups face disproportionate risk for COVID-19 infection and severe illness. However, we found no evidence that \"hesitancy\" drives vaccination gaps. After adjusting for age and education levels, vaccine uptake was higher in ZIP codes with many Black/Latino/Indigenous residents or essential workers.\nC_LIO_LIGaps in vaccine and booster coverage among vulnerable groups may lead to excess morbidity, mortality, and economic losses during the next COVID-19 wave. These burdens will not be equitably shared and are preventable.\nC_LI\n\nC_TEXTBOX", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Jacob Bor", - "author_inst": "Boston University" - }, - { - "author_name": "Sabrina A Assoumou", - "author_inst": "Boston Medical Center" - }, - { - "author_name": "Kevin Lane", - "author_inst": "Boston University" - }, - { - "author_name": "Yareliz Diaz", - "author_inst": "Boston University" - }, - { - "author_name": "Bisola Ojikutu", - "author_inst": "Boston Public Health Commission" - }, - { - "author_name": "Julia Raifman", - "author_inst": "Boston University" - }, - { - "author_name": "Jonathan I Levy", - "author_inst": "Boston University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.04.07.22273534", "rel_title": "Quantifying the relationship between SARS-CoV-2 wastewater concentrations and building-level COVID-19 prevalence at an isolation residence using a passive sampling approach", @@ -356245,6 +358177,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.04.08.22273628", + "rel_title": "Implications of red state/blue state differences in COVID-19 death rates", + "rel_date": "2022-04-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.08.22273628", + "rel_abs": "The study objective was to explore state death rates pre- and post- 4/19/2021 (date vaccines were assumed available) and the relative contributions of 3 factors to state death rates post- 4/19/2021: 1) vaccination rates, 2) prevalence of obesity, hypertension, diabetes, COPD, cardiovascular disease, and asthma and 3) red vs. blue states, to better understand options for reducing deaths. The ratio of red to blue state deaths/million was 1.6 pre-4/19/2021 and 2.3 between 4/19 and 2/28/2022 resulting in >222,000 extra deaths in red states or 305/ day. Adjusted betas from linear regression showed state vaccination rates had the strongest effect on death rates while red vs. blue states explained more of the difference in state death rates (60% vs. 46% for vaccination rates) with mean vaccination rates ~10% higher in blue states. Results suggest that increasing vaccination rates in red states could potentially save thousands of lives as the pandemic continues.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Mary Adams", + "author_inst": "On Target Health Data LLC" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.04.06.22273535", "rel_title": "Effectiveness of 2 and 3 mRNA COVID-19 Vaccines Doses against Omicron and Delta-Related Outpatient Illness among Adults, October 2021 - February 2022", @@ -356781,109 +358732,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.04.07.487528", - "rel_title": "Cryo-EM structures of SARS-CoV-2 Omicron BA.2 spike", - "rel_date": "2022-04-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.07.487528", - "rel_abs": "The BA.2 sub-lineage of the SARS-CoV-2 Omicron variant has gained in proportion relative to BA.1. As differences in spike (S) proteins may underlie differences in their pathobiology, here we determine cryo-EM structures of a BA.2 S ectodomain and compare these to previously determined BA.1 S structures. BA.2 Receptor Binding Domain (RBD) mutations induced remodeling of the internal RBD structure resulting in its improved thermostability and tighter packing within the 3-RBD-down spike. In the S2 subunit, the fusion peptide in BA.2 was less accessible to antibodies than in BA.1. Pseudovirus neutralization and spike binding assays revealed extensive immune evasion while defining epitopes of two RBD-directed antibodies, DH1044 and DH1193, that bound the outer RBD face to neutralize both BA.1 and BA.2. Taken together, our results indicate that stabilization of the 3-RBD-down state through interprotomer RBD-RBD packing is a hallmark of the Omicron variant, and reveal differences in key functional regions in the BA.1 and BA.2 S proteins.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Victoria Stalls", - "author_inst": "Duke University" - }, - { - "author_name": "Jared Lindenberger", - "author_inst": "Duke University" - }, - { - "author_name": "Sophie Gobeil", - "author_inst": "Duke School of Medicine" - }, - { - "author_name": "Rory Henderson", - "author_inst": "Duke University" - }, - { - "author_name": "Rob Parks", - "author_inst": "Duke University" - }, - { - "author_name": "Maggie Barr", - "author_inst": "Duke University" - }, - { - "author_name": "Margaret Deyton", - "author_inst": "Duke University" - }, - { - "author_name": "Mitchell Martin", - "author_inst": "Duke University" - }, - { - "author_name": "Katarzyna Janowska", - "author_inst": "Duke University" - }, - { - "author_name": "Xiao Huang", - "author_inst": "Duke University" - }, - { - "author_name": "Aaron May", - "author_inst": "Duke University" - }, - { - "author_name": "Micah Speakman", - "author_inst": "Duke University" - }, - { - "author_name": "Esther Beaudoin", - "author_inst": "Duke University" - }, - { - "author_name": "Bryan Kraft", - "author_inst": "Duke University" - }, - { - "author_name": "Xiaozhi Lu", - "author_inst": "Duke University" - }, - { - "author_name": "Robert J Edwards", - "author_inst": "Duke University" - }, - { - "author_name": "Amanda Eaton", - "author_inst": "Duke University" - }, - { - "author_name": "David Montefiori", - "author_inst": "Duke University" - }, - { - "author_name": "Wilton Williams", - "author_inst": "Duke University" - }, - { - "author_name": "Kevin Wiehe", - "author_inst": "Duke University" - }, - { - "author_name": "Barton F Haynes", - "author_inst": "Duke University" - }, - { - "author_name": "Priyamvada Acharya", - "author_inst": "Duke University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2022.04.08.487623", "rel_title": "SARS-CoV-2 mutations affect proteasome processing to alter CD8+ T cell responses", @@ -358271,6 +360119,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.30.22271928", + "rel_title": "Multiplexed biosensor for point-of-care COVID-19 monitoring: CRISPR-powered unamplified RNA diagnostics and protein-based therapeutic drug management", + "rel_date": "2022-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.30.22271928", + "rel_abs": "In late 2019 SARS-CoV-2 rapidly spread to become a global pandemic, therefore, measures to attenuate chains of infection, such as high-throughput screenings and isolation of carriers were taken. Prerequisite for a reasonable and democratic implementation of such measures, however, is the availability of sufficient testing opportunities (beyond reverse transcription PCR, the current gold standard). We, therefore, propose an electrochemical, microfluidic multiplexed biosensor in combination with CRISPR/Cas-powered assays for point-of-care nucleic acid testing. In this study, we simultaneously screen for and identify SARS-CoV-2 infections (Omicron-variant) in clinical specimens (Sample-to-result time: [~]30 min), employing LbuCas13a, whilst bypassing reverse transcription as well as target amplification of the viral RNA, both of which are necessary for detection via PCR and multiple other methods. In addition, we demonstrate the feasibility of combining assays based on different classes of biomolecules, in this case protein-based antibiotic detection, on the same device. The programmability of the effector and multiplexing capacity (up to six analytes) of our platform, in combination with a miniaturized measurement setup, including a credit card sized near field communication (NFC) potentiostat and a microperistaltic pump, provide a promising on-site tool for identifying individuals infected with variants of concern and monitoring their disease progression alongside other potential biomarkers or medication clearance.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Midori Johnston", + "author_inst": "University of Freiburg" + }, + { + "author_name": "H. Ceren Ates", + "author_inst": "University of Freiburg" + }, + { + "author_name": "Regina T. Glatz", + "author_inst": "University of Freiburg" + }, + { + "author_name": "Hasti Mohsenin", + "author_inst": "University of Freiburg" + }, + { + "author_name": "Rosanne Schmachtenberg", + "author_inst": "University of Freiburg" + }, + { + "author_name": "Nathalie G\u00f6ppert", + "author_inst": "University of Freiburg" + }, + { + "author_name": "Daniela Huzly", + "author_inst": "University of Freiburg" + }, + { + "author_name": "Gerald A. Urban", + "author_inst": "University of Freiburg" + }, + { + "author_name": "Wilfried Weber", + "author_inst": "University of Freiburg" + }, + { + "author_name": "Can Dincer", + "author_inst": "University of Freiburg" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.04.05.22273453", "rel_title": "Unsuppressed HIV infection impairs T cell responses to SARS-CoV-2 infection and abrogates T cell cross-recognition", @@ -358819,49 +360722,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.04.06.22273512", - "rel_title": "Pandemic-EBT and grab-and-go school Meals: Costs, reach, and benefits of two approaches to keep children fed during school closures due to COVID-19", - "rel_date": "2022-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.06.22273512", - "rel_abs": "ImportanceSchool meals improve nutrition and health for millions of U.S. children. School closures due to the COVID-19 pandemic disrupted childrens access to school meals. Two policy approaches were activated to replace missed meals for children from low-income families. The Pandemic Electronic Benefit Transfer (P-EBT) program provided the cash value of missed meals directly to families on debit-like cards to use for making food purchases. The grab-and-go meals program offered prepared meals from school kitchens at community distribution points. The effectiveness of these programs at reaching those who needed them and their costs were unknown.\n\nObjectiveTo determine how many eligible children were reached by P-EBT and grab-and-go meals, how many meals or benefits were received, and how much each program cost to implement.\n\nDesignCross-sectional study, Spring 2020.\n\nSettingNational.\n\nParticipantsAll children <19 years old and children age 6-18 eligible to receive free or reduced price meals (FRPM).\n\nExposure(s)Receipt of P-EBT or grab-and-go school meals.\n\nMain Outcome(s) and Measure(s)Percentage of children reached by P-EBT and grab-and-go school meals; average benefit received per recipient; and average cost, including implementation costs and time costs to families, per meal distributed.\n\nResultsGrab-and-go school meals reached about 10.5 million children (17% of all US children), most of whom were FRPM-eligible students. Among FRPM-eligible students only, grab-and-go meals reached 27%, compared to 89% reached by P-EBT. Among those receiving benefits, the average monthly benefit was larger for grab-and-go school meals ($148) relative to P-EBT ($110). P-EBT had lower costs per meal delivered - $6.51 - compared to $8.20 for grab- and-go school meals. P-EBT had lower public sector implementation costs but higher uncompensated time costs to families (e.g., preparation time for meals) compared to grab-and-go school meals.\n\nConclusions and RelevanceBoth programs supported childrens access to food when schools were closed and in complementary ways. P-EBT is an efficient and effective policy option to support food access for eligible children when school is out.\n\nKEY POINTSO_ST_ABSQuestionC_ST_ABSWhat were the operating costs, costs and benefits to families, and proportion of eligible children who received benefits of two programs aimed at replacing school meals missed when schools were closed due to COVID-19?\n\nFindingsIn this cross sectional analysis, we found that the Pandemic-Electronic Benefit Transfer program, in which state agencies sent debit cards loaded with the cash value of missed school meals directly to families, reached nearly all low income students (89%) and cost relatively little per meal provided. In comparison, grab-and-go school meals, in which school food service departments provided prepared meals for offsite consumption, reached 27% of low income children and was associated with larger per meal costs.\n\nMeaningDuring times when children cannot access school meals, state and federal agencies should support cost-efficient programs for schools to distribute prepared meals and activate programs like P-EBT to efficiently reach eligible children.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Erica L Kenney", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Lina Pinero Walkinshaw", - "author_inst": "University of Washington" - }, - { - "author_name": "Ye Shen", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Sheila E Fleischhacker", - "author_inst": "Georgetown University Law Center" - }, - { - "author_name": "Jessica Jones-Smith", - "author_inst": "University of Washington" - }, - { - "author_name": "Sara N Bleich", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "James W Krieger", - "author_inst": "University of Washington" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "nutrition" - }, { "rel_doi": "10.1101/2022.04.04.22273058", "rel_title": "Delta/ Omicron and Omicron/BA.2 co-infections occurring in Immunocompromised hosts", @@ -360041,6 +361901,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2022.04.03.22273268", + "rel_title": "Classification of Omicron BA.1, BA.1.1 and BA.2 sublineages by TaqMan assay consistent with whole genome analysis data", + "rel_date": "2022-04-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.03.22273268", + "rel_abs": "ObjectiveRecently, the Omicron strain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread and replaced the previously dominant Delta strain. Several Omicron sublineages (BA.1, BA.1.1 and BA.2) have been identified, with in vitro and preclinical reports showing that the pathogenicity and therapeutic efficacy differs between BA.1 and BA.2. We sought to develop a TaqMan assay to identify these subvariants.\n\nMethodsA TaqMan assay was constructed for rapid identification and genotyping of Omicron sublineages. We analyzed three characteristic mutations of the spike gene, {Delta}69-70, G339D and Q493R, by TaqMan assay. The accuracy of the TaqMan assay was examined by comparing its results with the results of whole genome sequencing (WGS) analysis.\n\nResultsA total of 169 SARS-CoV-2 positive samples were analyzed by WGS and TaqMan assay. The 127 samples determined as BA.1/BA.1.1 by WGS were all positive for {Delta}69-70, G339D and Q493R by TaqMan assay. Forty-two samples determined as BA.2 by WGS were negative for {Delta}69-70 but positive for G339D and Q493R by TaqMan. The concordance rate between WGS and the TaqMan assay was 100% (169/169).\n\nConclusionTaqMan assays targeting characteristic mutations are useful for identification and discrimination of Omicron sublineages.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Yosuke Hirotsu", + "author_inst": "Yamanashi Central Hospital" + }, + { + "author_name": "Makoto Maejima", + "author_inst": "Yamanashi Central Hospital" + }, + { + "author_name": "Masahiro Shibusawa", + "author_inst": "Yamanashi Central Hospital" + }, + { + "author_name": "Yume Natori", + "author_inst": "Yamanashi Central Hospital" + }, + { + "author_name": "Yuki Nagakubo", + "author_inst": "Yamanashi Central Hospital" + }, + { + "author_name": "Kazuhiro Hosaka", + "author_inst": "Yamanashi Central Hospital" + }, + { + "author_name": "Hitomi Sueki", + "author_inst": "Yamanashi Central Hospital" + }, + { + "author_name": "Hitoshi Mochizuki", + "author_inst": "Yamanashi Central Hospital" + }, + { + "author_name": "Toshiharu Tsutsui", + "author_inst": "Yamanashi Central Hospital" + }, + { + "author_name": "Yumiko Kakizaki", + "author_inst": "Yamanashi Central Hospital" + }, + { + "author_name": "Yoshihiro Miyashita", + "author_inst": "Yamanashi Central Hospital" + }, + { + "author_name": "Masao Omata", + "author_inst": "Yamanashi Central Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.04.04.22273429", "rel_title": "Viral dynamics of Omicron and Delta SARS-CoV-2 variants with implications for timing of release from isolation: a longitudinal cohort study", @@ -360445,53 +362368,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.04.03.22273370", - "rel_title": "Automated method to extract and purify RNA from wastewater enables more sensitive detection of SARS-CoV-2 markers in community sewersheds", - "rel_date": "2022-04-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.03.22273370", - "rel_abs": "Wastewater based epidemiology (WBE) has emerged as a strategy to identify, locate, and manage outbreaks of COVID19, and thereby possibly prevent surges in cases, which overwhelm local to global health care networks. The WBE process is based on assaying municipal wastewater for molecular markers of the SARS-CoV-2 virus. The standard process for sampling municipal wastewater is both time-consuming and requires the handling of large quantities of wastewater, which negatively affect throughput and timely reporting, and can increase safety risks. We report on a method to assay multiple sub-samples of a bulk wastewater sample. We document the effectiveness of this new approach by way of comparison of technologies for automating RNA purification from wastewater samples. We compared processes using the Perkin-Elmer Chemagic 360 to a PEG/NaCl/Qiagen protocol that is used for detection of N1 and N2 SARS-CoV-2 markers by the majority of 19 pandemic wastewater testing labs in the State of Michigan. Specifically, we found that the Chemagic 360 lowered handling time, decreased the amount of wastewater required by 10-fold, increased the amount of RNA isolated per {micro}l of final elution product by approximately five-fold, and had no deleterious effect on subsequent ddPCR analysis. Moreover, for detection of markers on the borderline of detectability, we found that use of the Chemagic 360 enabled the detection of viral markers in a significant number of samples for which the result with the PEG/NaCl/Qiagen method was below the level of detectability. This improvement in detectability of the viral markers might be particularly important for early warning to public health authorities at the beginning of an outbreak.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Nicholas W. West", - "author_inst": "Wayne State University" - }, - { - "author_name": "Adrian A. Vasquez", - "author_inst": "Wayne State University" - }, - { - "author_name": "Azadeh Bahmani", - "author_inst": "Wayne State University" - }, - { - "author_name": "Mohammed Khan", - "author_inst": "Wayne State University" - }, - { - "author_name": "James Hartrick", - "author_inst": "LimnoTech, 501 Avis Dr., Ann Arbor, MI 48108" - }, - { - "author_name": "Carrie L. Turner", - "author_inst": "LimnoTech, 501 Avis Dr., Ann Arbor, MI 48108" - }, - { - "author_name": "William Shuster", - "author_inst": "Wayne State University" - }, - { - "author_name": "Jeffrey L. Ram", - "author_inst": "Wayne State University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.04.05.22273169", "rel_title": "Changing patterns of SARS-CoV-2 infection through Delta and Omicron waves by vaccination status, previous infection and neighbourhood deprivation: A cohort analysis of 2.7M people.", @@ -361907,6 +363783,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2022.04.02.486853", + "rel_title": "Dietary \u03b1KG inhibits SARS CoV-2 infection and rescues inflamed lungs to restore normal O2 saturation in animals", + "rel_date": "2022-04-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.04.02.486853", + "rel_abs": "Our recent works described the rescue effect of -ketoglutarate (KG, a metabolite of Krebs cycle) on thrombosis and inflammation in animals. KG augments activity of prolyl hydroxylase 2 (PHD2), which in turn degrades proline residues of substrates like phosphorylated Akt (pAkt) and hypoxia inducible factor (HIF). Here we describe the inhibitory effect of octyl KG on pAkt as well as on HIF1/HIF2, and in turn decreasing SARS CoV-2 replication in Vero E6 cells. KG failed to inhibit the viral replication and Akt phosphorylation in PHD2-knockdown U937 cells transiently expressing ACE2. Contrastingly, triciribine (TCN, an Akt-inhibitor) inhibited viral replication alongside a downmodulation of pAkt in PHD2-KD cells. Dietary KG significantly inhibited viral infection and rescued hamsters from thrombus formation and inflammation in lungs, the known causes of acute respiratory distress syndrome (ARDS) in COVID-19. KG supplementation also reduced the apoptotic death of lung tissues in infected animals, alongside a downmodulation of pAkt and HIF2. KG supplementation neither affected IgG levels against SARS CoV-2 RBD protein nor altered the neutralization antibody response against SARS CoV-2. It did not interfere with the percentage of interferon-{gamma} positive (IFN{gamma}+) CD4+ and IFN{gamma}+CD8+ T cells in infected animals. The extended work in balb/c mice transiently expressing ACE2 showed a similar effect of KG in reducing accumulation of inflammatory immune cells and cytokines, including IL6, IL1{beta} and TNF, in lungs as well as in circulation of infected animals. Pro-thrombotic markers like platelet microparticles and platelet-leukocyte aggregates were reduced significantly in infected mice after KG supplementation. Importantly, KG supplementation restored the O2 saturation (SpO2) in circulation of SARS CoV-2 infected hamsters and mice, suggesting a potential therapeutic role of this metabolite in COVID-19 treatment.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Sakshi Agarwal", + "author_inst": "Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, India" + }, + { + "author_name": "Simrandeep Kaur", + "author_inst": "Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, India" + }, + { + "author_name": "Tejeswara Rao Asuru", + "author_inst": "Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, India" + }, + { + "author_name": "Garima Joshi", + "author_inst": "Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, India" + }, + { + "author_name": "Nishith M Shrimali", + "author_inst": "Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, India" + }, + { + "author_name": "Anamika Singh", + "author_inst": "Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, India" + }, + { + "author_name": "Oinam N Singh", + "author_inst": "Translational Health Science Technology Institute, National Capital Region Biotech Science Cluster, Faridabad, India." + }, + { + "author_name": "Puneet Srivastva", + "author_inst": "Translational Health Science Technology Institute, National Capital Region Biotech Science Cluster, Faridabad, India." + }, + { + "author_name": "Tripti Shrivastava", + "author_inst": "Translational Health Science Technology Institute, National Capital Region Biotech Science Cluster, Faridabad, India." + }, + { + "author_name": "Sudhanshu Vrati", + "author_inst": "Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, India" + }, + { + "author_name": "Milan Surjit", + "author_inst": "Translational Health Science Technology Institute, National Capital Region Biotech Science Cluster, Faridabad, India." + }, + { + "author_name": "Prasenjit Guchhait", + "author_inst": "Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, India;" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2022.04.03.486854", "rel_title": "Conformational Flexibility in Neutralization of SARS-CoV-2 by Naturally Elicited Anti-SARS-CoV-2 Antibodies", @@ -362495,61 +364434,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.31.22273111", - "rel_title": "Predictors of all-cause mortality among patients hospitalized with influenza, respiratory syncytial virus, or SARS-CoV-2", - "rel_date": "2022-04-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.31.22273111", - "rel_abs": "BackgroundShared and divergent predictors of clinical severity across respiratory viruses may support clinical and community responses in the context of a novel respiratory pathogen.\n\nMethodsWe conducted a retrospective cohort study to identify predictors of 30-day all-cause mortality following hospitalization with influenza (N=45,749; 2011-09 to 2019-05), respiratory syncytial virus (RSV; N=24,345; 2011-09 to 2019-04), or severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; N=8,988; 2020-03 to 2020-12; pre-vaccine) using population-based health administrative data from Ontario, Canada. Multivariable modified Poisson regression was used to assess associations between potential predictors and mortality. We compared the direction, magnitude, and confidence intervals of risk ratios to identify shared and divergent predictors of mortality.\n\nResults3,186 (7.0%), 697 (2.9%) and 1,880 (20.9%) patients died within 30 days of hospital admission with influenza, RSV, and SARS-CoV-2, respectively. Shared predictors of increased mortality included: older age, male sex, residence in a long-term care home, and chronic kidney disease. Positive associations between age and mortality were largest for patients with SARS-CoV-2. Few comorbidities were associated with mortality among patients with SARS-CoV-2 as compared to those with influenza or RSV.\n\nConclusionsOur findings may help identify patients at greatest risk of illness secondary to a respiratory virus, anticipate hospital resource needs, and prioritize local prevention and therapeutic strategies to communities with higher prevalence of risk factors.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Mackenzie A. Hamilton", - "author_inst": "MAP Centre for Urban Health Solutions" - }, - { - "author_name": "Ying Liu", - "author_inst": "ICES" - }, - { - "author_name": "Andrew Calzavara", - "author_inst": "ICES" - }, - { - "author_name": "Maria E. Sundaram", - "author_inst": "Marshfield Clinic Research Institute" - }, - { - "author_name": "Mohamed Djebli", - "author_inst": "ICES" - }, - { - "author_name": "Dariya Darvin", - "author_inst": "University of Toronto, Department of Medicine" - }, - { - "author_name": "Stefan Baral", - "author_inst": "JHSPH" - }, - { - "author_name": "Rafal Kustra", - "author_inst": "Dalla Lana School of Public Health, University of Toronto" - }, - { - "author_name": "Jeffrey C. Kwong", - "author_inst": "ICES" - }, - { - "author_name": "Sharmistha Mishra", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.31.22272957", "rel_title": "Clinical and Economic Impact of Differential COVID-19 Vaccine Effectiveness in the United States", @@ -363721,6 +365605,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2022.04.01.22273316", + "rel_title": "Modeling and Global Sensitivity Analysis of Strategies to Mitigate Covid-19 Transmission on a Structured College Campus", + "rel_date": "2022-04-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.01.22273316", + "rel_abs": "In response to the COVID-19 pandemic, many higher educational institutions moved their courses on-line in hopes of slowing disease spread. The advent of multiple highly-effective vaccines offers the promise of a return to \"normal\" in-person operations, but it is not clear if--or for how long--campuses should employ non-pharmaceutical interventions such as requiring masks or capping the size of in-person courses. In this study, we develop and fine-tune a model of COVID-19 spread to UC Merceds student and faculty population. We perform a global sensitivity analysis to consider how both pharmaceutical and non-pharmaceutical interventions impact disease spread. Our work reveals that vaccines alone may not be sufficient to eradicate disease dynamics and that significant contact with an infectious surrounding community will maintain infections on-campus. Our work provides a foundation for higher-education planning allowing campuses to balance the benefits of in-person instruction with the ability to quarantine/isolate infectious individuals.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Lihong Zhao", + "author_inst": "University of California Merced" + }, + { + "author_name": "Fabian Santiago", + "author_inst": "University of California, Merced" + }, + { + "author_name": "Erica M. Rutter", + "author_inst": "University of California, Merced" + }, + { + "author_name": "Shilpa Khatri", + "author_inst": "University of California, Merced" + }, + { + "author_name": "Suzanne Sindi", + "author_inst": "University of California, Merced" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.04.01.22273281", "rel_title": "Effectiveness of COVID-19 vaccines against Omicron and Delta hospitalisation: test negative case-control study", @@ -364169,25 +366088,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2022.04.01.22273291", - "rel_title": "Metabolic alkalosis and mortality in COVID-19", - "rel_date": "2022-04-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.04.01.22273291", - "rel_abs": "BackgroundAs a new infectious disease affecting the world, COVID-19 has caused a huge impact on countries around the world. At present, its specific pathophysiological mechanism has not been fully clarified. We found in the analysis of the arterial blood gas data of critically ill patients that the incidence of metabolic alkalosis in such patients is high.\n\nMethodWe retrospectively analyzed the arterial blood gas analysis results of a total of 16 critically ill patients in the intensive ICU area of Xiaogan Central Hospital and 42 severe patients in the intensive isolation ward, and analyzed metabolic acidosis and respiratory acidosis. Metabolic alkalosis and respiratory alkalosis, and the relationship between metabolic alkalosis and death.\n\nResultAmong the 16 critically ill patients, the incidence of metabolic alkalosis was 100%, while the incidence of metabolic alkalosis in severe patients was 50%; the mortality rate in critically ill patients was 81.3%, and 21.4% in severe patients; The mortality of all patients with metabolic alkalosis is 95.5%,and 4.5% in without metabolic alkalosis.\n\nConclusionThe incidence of metabolic alkalosis in critically ill COVID-19 patients is high, and it is associated with high mortality.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Zhifeng Jiang", - "author_inst": "Xiaogan Hospital Affiliated to Wuhan University of Science and Technology" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.31.22273242", "rel_title": "If you build it, will they use it? Use of a Digital Assistant for Self-Reporting of COVID-19 Rapid Antigen Test Results during Large Nationwide Community Testing Initiative", @@ -365703,6 +367603,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.24.22272732", + "rel_title": "Transcriptomic profiling of cardiac tissues from SARS-CoV-2 patients identifies DNA damage", + "rel_date": "2022-03-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.24.22272732", + "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is known to present with pulmonary and extra-pulmonary organ complications. In comparison with the 2009 pandemic (pH1N1), SARS-CoV-2 infection is likely to lead to more severe disease, with multi-organ effects, including cardiovascular disease. SARS-CoV-2 has been associated with acute and long-term cardiovascular disease, but the molecular changes govern this remain unknown.\n\nIn this study, we investigated the landscape of cardiac tissues collected at rapid autopsy from SARS-CoV-2, pH1N1, and control patients using targeted spatial transcriptomics approaches. Although SARS-CoV-2 was not detected in cardiac tissue, host transcriptomics showed upregulation of genes associated with DNA damage and repair, heat shock, and M1-like macrophage infiltration in the cardiac tissues of COVID-19 patients. The DNA damage present in the SARS-CoV-2 patient samples, were further confirmed by {gamma}-H2Ax immunohistochemistry. In comparison, pH1N1 showed upregulation of Interferon-stimulated genes (ISGs), in particular interferon and complement pathways, when compared with COVID-19 patients.\n\nThese data demonstrate the emergence of distinct transcriptomic profiles in cardiac tissues of SARS-CoV-2 and pH1N1 influenza infection supporting the need for a greater understanding of the effects on extra-pulmonary organs, including the cardiovascular system of COVID-19 patients, to delineate the immunopathobiology of SARS-CoV-2 infection, and long term impact on health.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Arutha Kulasinghe", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Ning Liu", + "author_inst": "The Walter and Eliza Hall Institute" + }, + { + "author_name": "Chin Wee Tan", + "author_inst": "The Walter and Eliza Hall Institute" + }, + { + "author_name": "James Monkman", + "author_inst": "The University of Queensland Diamantina Institute" + }, + { + "author_name": "Jane E Sinclair", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Dharmesh D Bhuva", + "author_inst": "The Walter and Eliza Hall Institute" + }, + { + "author_name": "David Godbolt", + "author_inst": "The Prince Charles Hospital" + }, + { + "author_name": "Liuliu Pan", + "author_inst": "Nanostring Technologies" + }, + { + "author_name": "Andy Nam", + "author_inst": "Nanostring Technologies" + }, + { + "author_name": "Habib Sadeghirad", + "author_inst": "The University of Queensland Diamantina Institute" + }, + { + "author_name": "Kei Sato", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Gianluigi Li Bassi", + "author_inst": "University of Queensland" + }, + { + "author_name": "Ken O'Byrne", + "author_inst": "Princess Alexandra Hospital" + }, + { + "author_name": "Camila Hartmann", + "author_inst": "Pontifical Catholic University of Parana" + }, + { + "author_name": "Anna Flavia Ribeiro dos Santos Miggiolaro", + "author_inst": "Pontifical Catholic University of Parana" + }, + { + "author_name": "Gustavo Lenci Marques", + "author_inst": "Pontifical Catholic University of Parana" + }, + { + "author_name": "Lidia Zytynski Moura", + "author_inst": "Pontifical Catholic University of Parana" + }, + { + "author_name": "Derek Richard", + "author_inst": "Queensland University of Technology" + }, + { + "author_name": "Mark N Adams", + "author_inst": "Queensland University of Technology" + }, + { + "author_name": "Lucia Noronha", + "author_inst": "Pontifical Catholic University of Parana" + }, + { + "author_name": "Cristina Pellegrino Baena", + "author_inst": "Pontifical Catholic University of Parana" + }, + { + "author_name": "Jacky Suen", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Rakesh Arora", + "author_inst": "The University of Manitoba" + }, + { + "author_name": "Gabrielle T Belz", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Kirsty Short", + "author_inst": "University of Queensland" + }, + { + "author_name": "Melissa J Davis", + "author_inst": "The Walter and Eliza Hall Institute" + }, + { + "author_name": "Fernando SF Guimaraes", + "author_inst": "The University of Queensland Diamantina Institute" + }, + { + "author_name": "John F Fraser", + "author_inst": "The University of Queensland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.27.22273007", "rel_title": "Global Reports of Myocarditis Following COVID-19 Vaccination: A Systematic Review and Meta-Analysis", @@ -366035,317 +368062,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, - { - "rel_doi": "10.1101/2022.03.30.22273206", - "rel_title": "Remdesivir for the treatment of hospitalised patients with COVID-19: final results from the DisCoVeRy randomised, controlled, open-label trial", - "rel_date": "2022-03-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.30.22273206", - "rel_abs": "BackgroundThe antiviral efficacy of remdesivir is still controversial. We aimed at evaluating its clinical effectiveness in hospitalised patients with COVID-19, with indication of oxygen and/or ventilator support. Following prior publication of preliminary results, here we present the final results after completion of data monitoring.\n\nMethodsIn this European multicentre, open-label, parallel-group, randomised, controlled trial (DisCoVeRy, NCT04315948; EudraCT2020-000936-23), participants were randomly allocated to receive usual standard of care (SoC) alone or in combination with remdesivir, lopinavir/ritonavir, lopinavir/ritonavir and IFN-{beta}-1a, or hydroxychloroquine. Adult patients hospitalised with COVID-19 were eligible if they had clinical evidence of hypoxemic pneumonia, or required oxygen supplementation. Exclusion criteria included elevated liver enzyme, severe chronic kidney disease, any contra-indication to one of the studied treatments or their use in the 29 days before randomization, or use of ribavirin, as well as pregnancy or breast-feeding. Here, we report results for remdesivir + SoC versus SoC alone. Remdesivir was administered as 200 mg infusion on day 1, followed by once daily infusions of 100 mg up to 9 days, for a total duration of 10 days. It could be stopped after 5 days if the participant was discharged. Treatment assignation was performed via web-based block randomisation stratified on illness severity and administrative European region. The primary outcome was the clinical status at day 15 measured by the WHO 7-point ordinal scale, assessed in the intention-to-treat population.\n\nFindingsBetween March 22nd, 2020 and January 21st, 2021, 857 participants were randomised to one of the two arms in 5 European countries and 843 participants were included for the evaluation of remdesivir (control, n=423; remdesivir, n=420).\n\nAt day 15, the distribution of the WHO ordinal scale was as follow in the remdesivir and control groups, respectively: Not hospitalized, no limitations on activities: 62/420 (14.8%) and 72/423 (17.0%); Not hospitalized, limitation on activities: 126/420 (30%) and 135/423 (31.9%); Hospitalized, not requiring supplemental oxygen: 56/420 (13.3%) and 31/423 (7.3%); Hospitalized, requiring supplemental oxygen: 75/420 (17.9%) and 65/423 (15.4%); Hospitalized, on non-invasive ventilation or high flow oxygen devices: 16/420 (3.8%) and 16/423 (3.8%); Hospitalized, on invasive mechanical ventilation or ECMO: 64/420 (15.2%) and 80/423 (18.9%); Death: 21/420 (5%) and 24/423 (5.7%). The difference between treatment groups was not statistically significant (OR for remdesivir, 1.02, 95% CI, 0.62 to 1.70, P=0.93). There was no significant difference in the occurrence of Serious Adverse Events between treatment groups (remdesivir, n=147/410, 35.9%, versus control, n=138/423, 32.6%, p=0.29).\n\nInterpretationRemdesivir use for the treatment of hospitalised patients with COVID-19 was not associated with clinical improvement at day 15.\n\nFundingEuropean Union Commission, French Ministry of Health, DIM One Health Ile-de-France, REACTing, Fonds Erasme-COVID-ULB; Belgian Health Care Knowledge Centre (KCE), AGMT gGmbH, FEDER \"European Regional Development Fund\", Portugal Ministry of Health, Portugal Agency for Clinical Research and Biomedical Innovation. Remdesivir was provided free of charge by Gilead.", - "rel_num_authors": 74, - "rel_authors": [ - { - "author_name": "Florence Ader", - "author_inst": "CHU Lyon" - }, - { - "author_name": "Maude Bouscambert Duchamp", - "author_inst": "CHU Lyon" - }, - { - "author_name": "Maya Hites", - "author_inst": "CHU Erasme" - }, - { - "author_name": "Nathan Peiffer Smadja", - "author_inst": "CHU Bichat" - }, - { - "author_name": "Julien Poissy", - "author_inst": "CHU Lille" - }, - { - "author_name": "Drifa Belhadi", - "author_inst": "CHU Bichat" - }, - { - "author_name": "Alpha Diallo", - "author_inst": "ANRS" - }, - { - "author_name": "Christelle Delmas", - "author_inst": "ANRS" - }, - { - "author_name": "Juliette Saillard", - "author_inst": "Inserm" - }, - { - "author_name": "Aline Dechanet", - "author_inst": "CHU Bichat" - }, - { - "author_name": "Claire Fougerou", - "author_inst": "CHU Rennes" - }, - { - "author_name": "Minh Patrick Le", - "author_inst": "CHU Bichat" - }, - { - "author_name": "Gilles Peytavin", - "author_inst": "CHU Bichat" - }, - { - "author_name": "Noemie Mercier", - "author_inst": "ANRS" - }, - { - "author_name": "Priyanka Velou", - "author_inst": "CHU Bichat" - }, - { - "author_name": "Sarah Tubiana", - "author_inst": "CHU Bichat" - }, - { - "author_name": "Xavier Lescure", - "author_inst": "CHU Bichat" - }, - { - "author_name": "Emmanuel Faure", - "author_inst": "CHU Lille" - }, - { - "author_name": "Saad Nseir", - "author_inst": "CHU Lille" - }, - { - "author_name": "Jean Christophe Richard", - "author_inst": "CHU Lyon" - }, - { - "author_name": "Florent Wallet", - "author_inst": "CHU Lyon" - }, - { - "author_name": "Francois Goehringer", - "author_inst": "CHU Nancy" - }, - { - "author_name": "Benjamin Lefevre", - "author_inst": "CHU Nancy" - }, - { - "author_name": "Antoine Kimmoun", - "author_inst": "CHU Nancy" - }, - { - "author_name": "Francois Raffi", - "author_inst": "CHU Nantes" - }, - { - "author_name": "Bejamin Gaborit", - "author_inst": "CHU Nantes" - }, - { - "author_name": "Jean Reignier", - "author_inst": "CHU Nantes" - }, - { - "author_name": "Jean Philippe Lanoix", - "author_inst": "CHU Amiens" - }, - { - "author_name": "Claire Andrejak", - "author_inst": "CHU Amiens" - }, - { - "author_name": "Yoann Zerbib", - "author_inst": "CHU Amiens" - }, - { - "author_name": "Firouze Bani Sadr", - "author_inst": "CHU Reims" - }, - { - "author_name": "Bruno Mourvilliers", - "author_inst": "CHU Reims" - }, - { - "author_name": "Francois Danion", - "author_inst": "CHU Strasbourg" - }, - { - "author_name": "Yvon Ruch", - "author_inst": "CHU Strasbourg" - }, - { - "author_name": "Raphael Clere Jehl", - "author_inst": "CHU Strasbourg" - }, - { - "author_name": "Vincent Le Moing", - "author_inst": "CHU Montpellier" - }, - { - "author_name": "Kada Klouche", - "author_inst": "CHU Montpellier" - }, - { - "author_name": "Karine Lacombe", - "author_inst": "CHU Saint Antoine" - }, - { - "author_name": "Guillaume Martin Blondel", - "author_inst": "CHU Toulouse" - }, - { - "author_name": "Fanny Vardon Bounes", - "author_inst": "CHU Toulouse" - }, - { - "author_name": "Andre Cabie", - "author_inst": "CHU Fort de France" - }, - { - "author_name": "Jean Marie Turmel", - "author_inst": "CHU Fort de France" - }, - { - "author_name": "Lionel Piroth", - "author_inst": "CHU Dijon" - }, - { - "author_name": "Mathieu Blot", - "author_inst": "CHU Dijon" - }, - { - "author_name": "Elisabeth Botelho Nevers", - "author_inst": "CHU Saint Etienne" - }, - { - "author_name": "Amandine Gagneux Brunon", - "author_inst": "CHU Saint Etienne" - }, - { - "author_name": "Guillaume Thiery", - "author_inst": "CHU St Etienne" - }, - { - "author_name": "Francois Benezit", - "author_inst": "CHU Rennes" - }, - { - "author_name": "Rostane Gaci", - "author_inst": "CHR Mets-Thionville" - }, - { - "author_name": "Joy Mootien", - "author_inst": "CH Mulhouse" - }, - { - "author_name": "Sebastien Gallien", - "author_inst": "CHU Mondor" - }, - { - "author_name": "Denis Garot", - "author_inst": "CHU Tours" - }, - { - "author_name": "Kevin Bouiller", - "author_inst": "CHU Besancon" - }, - { - "author_name": "Loic Epelboin", - "author_inst": "CH Cayenne" - }, - { - "author_name": "Stephane Jaureguiberry", - "author_inst": "CHU Bicetre" - }, - { - "author_name": "Alexandre Gaymard", - "author_inst": "CHU Lyon" - }, - { - "author_name": "Gil Verschelden", - "author_inst": "CHU Erasme" - }, - { - "author_name": "Sandra Braz", - "author_inst": "CHU Lisboa Norte" - }, - { - "author_name": "Joao Miguel Ferreira Ribeiro", - "author_inst": "CHU Lisboa Norte" - }, - { - "author_name": "Michael Joannidis", - "author_inst": "CHU Innsbruck" - }, - { - "author_name": "Therese Staub", - "author_inst": "CHU Luxembourg" - }, - { - "author_name": "Antoine Altdorfer", - "author_inst": "CHR Citadelle" - }, - { - "author_name": "Richard Greil", - "author_inst": "CHU Salzburg" - }, - { - "author_name": "Alexander Egle", - "author_inst": "CHU Salzburg" - }, - { - "author_name": "Jeremie Guedj", - "author_inst": "Inserm" - }, - { - "author_name": "Marion Noret", - "author_inst": "CH Annecy Gennevois" - }, - { - "author_name": "Roberto Roncon Albuquerque", - "author_inst": "CHU Sao Joao" - }, - { - "author_name": "Jose Artur Paiva", - "author_inst": "CHU Sao Joao" - }, - { - "author_name": "Bruno Lina", - "author_inst": "CHU Lyon" - }, - { - "author_name": "Dominique Costagliola", - "author_inst": "Inserm" - }, - { - "author_name": "Yazdan Yazdanpanah", - "author_inst": "CHU Bichat" - }, - { - "author_name": "Charles Burdet", - "author_inst": "CHU Bichat" - }, - { - "author_name": "France Mentre", - "author_inst": "CHU Bichat" - }, - { - "author_name": "- DisCoVeRy Study Group", - "author_inst": "#N/A" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.26.22272979", "rel_title": "Impact of the Russian invasion of Ukraine onthe COVID-19 pandemic dynamics", @@ -368213,6 +369929,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.03.25.22272948", + "rel_title": "Labor market position and depression during the COVID-19 epidemic among young adults (18 to 30 years): a nationally representative study in France.", + "rel_date": "2022-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.25.22272948", + "rel_abs": "ObjectiveTo examine the relationship between young adults labor force participation and depression in the context of the COVID-19 pandemic.\n\nDesign, Setting, ParticipantsData come from the nationally-representative EPICOV cohort study set up in France, and were collected in 2020 and 2021 (3 waves of online or telephone interviews) among 2217 participants aged 18-30 years. Participants with prior mental health disorder (n=50) were excluded from the statistical analyses.\n\nResultsUsing Generalized Estimating Equation (GEE) models controlled for participants socio-demographic and health characteristics and weighted to be nationally-representative, we found that compared to young adults who were employed, those who were studying or unemployed were significantly more likely to experience depression assessed using the PHQ-9 (multivariate ORs respectively: OR: 1.29, 95% CI 1.05-1.60 and OR: 1.50, 1.13-1.99). Stratifying the analyses by age, we observed than unemployment was more strongly associated with depression among participants 25-30 years than among those who were 18-24 years (multivariate ORs respectively 1.78, 95% CI 1.17-2.71 and 1.41, 95% CI 0.96-2.09). Being out of the labor force was, to the contrary, more significantly associated with depression among participants 18-24 years (multivariate OR: 1.71, 95% CI 1.04-2.82, vs. 1.00, 95% CI 0.53-1.87 among participants 25-30 years). Stratifying the analyses by sex, we found no significant differences in the relationships between labor market characteristics and depression (compared to participants who were employed, multivariate ORs associated with being a student: men: 1.33, 95% CI 1.01-1.76; women: 1.19, 95% CI 0.85-1.67, multivariate ORs associated with being unemployed: men: 1.60, 95% CI 1.04-2.45; women: 1.47, 95% CI 1.01-2.15).\n\nConclusions and relevanceOur study shows that in addition to students, young adults who are unemployed also experience elevated levels of depression in the context of the COVID-19 pandemic. These two groups should be the focus of specific attention in terms of prevention and mental health treatment. Supporting employment could also be a propitious way of reducing the burden of the Covid-19 pandemic on the mental health of young adults.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSIs labor force participation associated with young adults likelihood of depression during the COVID-19 pandemic?\n\nFindingsIn a nationally-representative cohort study in France, compared to young adults who are employed, those who are studying or experience unemployment had elevated odds of depression in 2020 and 2021.\n\nMeaningYoung people are experiencing the highest burden of mental health problems in the context of the COVID-19 epidemic - our study implies that those who are studying or are unemployed are at especially high risk and should be the focus of attention in terms of prevention and treatment.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Maria Melchior", + "author_inst": "INSERM" + }, + { + "author_name": "Aline-Marie Florence", + "author_inst": "INSERM" + }, + { + "author_name": "Camille Davisse-Paturet", + "author_inst": "INSERM" + }, + { + "author_name": "Bruno Falissard", + "author_inst": "Paris Saclay" + }, + { + "author_name": "Cedric Galera", + "author_inst": "Bordeaux University" + }, + { + "author_name": "Jean-Baptiste Hazo", + "author_inst": "Ministry of Health" + }, + { + "author_name": "Cecile Vuillermoz", + "author_inst": "INSERM" + }, + { + "author_name": "Josiane WARSZAWSKI", + "author_inst": "INSERM CESP Universite Paris-Saclay, Service de sante publique, AP-HP" + }, + { + "author_name": "Fallou Dione", + "author_inst": "INSERM" + }, + { + "author_name": "Alexandra Rouquette", + "author_inst": "Paris Saclay" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.03.28.22273029", "rel_title": "Healthcare workers perceptions and medically approved COVID-19 infection risk: understanding the mental health dimension of the pandemic. A German hospital case study", @@ -368701,121 +370472,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.03.29.486253", - "rel_title": "Discovery of a druggable copper-signaling pathway that drives cell plasticity and inflammation", - "rel_date": "2022-03-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.29.486253", - "rel_abs": "Inflammation is a complex physiological process triggered in response to harmful stimuli. It involves specialized cells of the immune system able to clear sources of cell injury and damaged tissues to promote repair. Excessive inflammation can occur as a result of infections and is a hallmark of several diseases. The molecular basis underlying inflammatory responses are not fully understood. Here, we show that the cell surface marker CD44, which characterizes activated immune cells, acts as a metal transporter that promotes copper uptake. We identified a chemically reactive pool of copper(II) in mitochondria of inflammatory macrophages that catalyzes NAD(H) redox cycling by activating hydrogen peroxide. Maintenance of NAD+ enables metabolic and epigenetic programming towards the inflammatory state. Targeting mitochondrial copper(II) with a rationally-designed dimer of metformin triggers distinct metabolic and epigenetic states that oppose macrophage activation. This drug reduces inflammation in mouse models of bacterial and viral (SARS-CoV-2) infections, improves well-being and increases survival. Identifying mechanisms that regulate the plasticity of immune cells provides the means to develop next-generation medicine. Our work illuminates the central role of copper as a regulator of cell plasticity and unveils a new therapeutic strategy based on metabolic reprogramming and the control of epigenetic cell states.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Stephanie Solier", - "author_inst": "Institut Curie" - }, - { - "author_name": "Sebastian Muller", - "author_inst": "Institut Curie" - }, - { - "author_name": "Tatiana Caneque", - "author_inst": "Institut Curie" - }, - { - "author_name": "Antoine Versini", - "author_inst": "Institut Curie" - }, - { - "author_name": "Leeroy Baron", - "author_inst": "Institut Curie" - }, - { - "author_name": "Pierre Gestraud", - "author_inst": "Institut Curie" - }, - { - "author_name": "Nicolas Servant", - "author_inst": "Institut Curie" - }, - { - "author_name": "Laila Emam", - "author_inst": "Paris-Saclay" - }, - { - "author_name": "Arnaud Mansart", - "author_inst": "Paris-Saclay" - }, - { - "author_name": "G. Dan Pantos", - "author_inst": "University of Bath" - }, - { - "author_name": "Vincent Gandon", - "author_inst": "Ecole Polytechnique" - }, - { - "author_name": "Valentin Sencio", - "author_inst": "University of Lille" - }, - { - "author_name": "Cyril Robin", - "author_inst": "University of Lille" - }, - { - "author_name": "Francois Trottein", - "author_inst": "University of Lille" - }, - { - "author_name": "Anne-Laure Begue", - "author_inst": "Institut Curie" - }, - { - "author_name": "Helene Salmon", - "author_inst": "Institut Curie" - }, - { - "author_name": "Sylvere Durand", - "author_inst": "Institut Curie" - }, - { - "author_name": "Ting-Di Wu", - "author_inst": "Institut Curie" - }, - { - "author_name": "Nicolas Manel", - "author_inst": "Institut Curie" - }, - { - "author_name": "Alain Puisieux", - "author_inst": "Institut Curie" - }, - { - "author_name": "Mark A. Dawson", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Sarah Watson", - "author_inst": "Institut Curie" - }, - { - "author_name": "Guido Kroemer", - "author_inst": "Sorbonne University" - }, - { - "author_name": "Djillali Annane", - "author_inst": "Hospital Raymond Poincare" - }, - { - "author_name": "Raphael Rodriguez", - "author_inst": "Institut Curie" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2022.03.29.482838", "rel_title": "Subcellular mapping of the protein landscape of SARS-CoV-2 infected cells for target-centric drug repurposing", @@ -370619,6 +372275,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, + { + "rel_doi": "10.1101/2022.03.23.22270017", + "rel_title": "Serological Response to Three, Four and Five Doses of SARS-CoV-2 Vaccine in Kidney Transplant Recipients", + "rel_date": "2022-03-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.23.22270017", + "rel_abs": "Mortality from COVID-19 among kidney transplant recipients (KTR) is high, and their response to three vaccinations against SARS-CoV-2 is strongly impaired.\n\nWe retrospectively analyzed serological response of up to five doses of SARS-CoV-2 vaccine in KTR from December 27, 2020, until December 31, 2021. Particularly, the influence of different dose adjustment regimens for mycophenolic acid (MPA) on serological response to fourth vaccination was analyzed.\n\nIn total, 4.277 vaccinations against SARS-CoV-2 in 1.478 patients were analyzed. Serological response was 19.5% after 1.203 basic immunizations, and increased to 29.4%, 55.6%, and 57.5% in response to 603 third, 250 fourth and 40 fifth vaccinations, resulting in a cumulative response rate of 88.7%.\n\nIn patients with calcineurin inhibitor and MPA maintenance immunosuppression, pausing MPA and adding 5 mg prednisolone equivalent before the fourth vaccination increased serological response rate to 75% in comparison to no dose adjustment (52%) or dose reduction (46%). Belatacept-treated patients had a response rate of 8.7% (4/46) after three vaccinations and 12.5% (3/25) after four vaccinations.\n\nExcept for belatacept-treated patients, repeated SARS-CoV-2 vaccination of up to five times effectively induces serological response in kidney transplant recipients. It can be enhanced by pausing MPA at the time of vaccination.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Bilgin Osmanodja", + "author_inst": "Department of Nephrology and Medical Intensive Care, Charite Berlin, Berlin, Germany" + }, + { + "author_name": "Simon Ronicke", + "author_inst": "Department of Nephrology and Medical Intensive Care, Charite Berlin, Berlin, Germany" + }, + { + "author_name": "Klemens Budde", + "author_inst": "Department of Nephrology and Medical Intensive Care, Charite Berlin, Berlin, Germany" + }, + { + "author_name": "Annika Jens", + "author_inst": "Department of Nephrology and Medical Intensive Care, Charite Berlin, Berlin, Germany" + }, + { + "author_name": "Charlotte Hammett", + "author_inst": "Department of Nephrology and Medical Intensive Care, Charite Berlin, Berlin, Germany" + }, + { + "author_name": "Nadine Koch", + "author_inst": "Department of Nephrology and Medical Intensive Care, Charite Berlin, Berlin, Germany" + }, + { + "author_name": "Evelyn Seelow", + "author_inst": "Department of Nephrology and Medical Intensive Care, Charite Berlin, Berlin, Germany" + }, + { + "author_name": "Johannes Waiser", + "author_inst": "Department of Nephrology and Medical Intensive Care, Charite Berlin, Berlin, Germany" + }, + { + "author_name": "Bianca Zukunft", + "author_inst": "Department of Nephrology and Medical Intensive Care, Charite Berlin, Berlin, Germany" + }, + { + "author_name": "Friederike Bachmann", + "author_inst": "Department of Nephrology and Medical Intensive Care, Charite Berlin, Berlin, Germany" + }, + { + "author_name": "Mira Choi", + "author_inst": "Department of Nephrology and Medical Intensive Care, Charite Berlin, Berlin, Germany" + }, + { + "author_name": "Ulrike Weber", + "author_inst": "Department of Nephrology and Medical Intensive Care, Charite Berlin, Berlin, Germany" + }, + { + "author_name": "Bettina Ebersp\u00e4cher", + "author_inst": "Labor Berlin-Charite Vivantes GmbH, Berlin, Germany" + }, + { + "author_name": "J\u00f6rg Hofmann", + "author_inst": "Labor Berlin-Charite Vivantes GmbH, Berlin, Germany" + }, + { + "author_name": "Fritz Grunow", + "author_inst": "Department of Nephrology and Medical Intensive Care, Charite Berlin, Berlin, Germany" + }, + { + "author_name": "Michael Mikhailov", + "author_inst": "Department of Nephrology and Medical Intensive Care, Charite Berlin, Berlin, Germany" + }, + { + "author_name": "Lutz Liefeldt", + "author_inst": "Department of Nephrology and Medical Intensive Care, Charite Berlin, Berlin, Germany" + }, + { + "author_name": "Kai-Uwe Eckardt", + "author_inst": "Department of Nephrology and Medical Intensive Care, Charite Berlin, Berlin, Germany" + }, + { + "author_name": "Fabian Halleck", + "author_inst": "Department of Nephrology and Medical Intensive Care, Charite Berlin, Berlin, Germany" + }, + { + "author_name": "Eva Schrezenmeier", + "author_inst": "Department of Nephrology and Medical Intensive Care, Charite Berlin, Berlin, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, { "rel_doi": "10.1101/2022.03.24.22272871", "rel_title": "Detection and prevalence of SARS-CoV-2 co-infections during the Omicron variant circulation, France, December 2021 - February 2022", @@ -371315,45 +373066,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2022.03.24.485734", - "rel_title": "SARS-CoV-2 harnesses host translational shutoff and autophagy to optimize virus yields: The role of the envelope (E) protein", - "rel_date": "2022-03-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.24.485734", - "rel_abs": "The SARS-CoV-2 virion is composed of four structural proteins: spike (S), nucleocapsid (N), membrane (M), and envelope (E). E spans the membrane a single time and is the smallest, yet most enigmatic of the structural proteins. E is conserved among coronaviruses and has an essential role in virus-mediated pathogenesis. We found that ectopic expression of E had deleterious effects on the host cell as it activated stress responses, leading to phosphorylation of the translation initiation factor eIF2 and LC3 lipidation that resulted in host translational shutoff. During infection E is highly expressed although only a small fraction is incorporated into virions, suggesting that E activity is regulated and harnessed by the virus to its benefit. In support of this, we found that the {gamma}1 34.5 protein of herpes simplex virus 1 (HSV-1) prevented deleterious effects of E on the host cell and allowed for E protein accumulation. This observation prompted us to investigate whether other SARS-CoV-2 structural proteins regulate E. We found that the N and M proteins enabled E protein accumulation, whereas S prevented E accumulation. While {gamma}1 34.5 protein prevented deleterious effects of E on the host cells, it had a negative effect on SARS-CoV-2 replication. This negative effect of {gamma}1 34.5 was most likely associated with failure of SARS-CoV-2 to divert the translational machinery and with deregulation of autophagy pathways. Overall, our data suggest that SARS-CoV-2 causes stress responses and subjugates these pathways, including host protein synthesis (phosphorylated eIF2) and autophagy, to support optimal virus production.\n\nImportanceIn 2020, a new {beta}-coronavirus, SARS-CoV-2, entered the human population that has caused a pandemic resulting in 6 million deaths worldwide. Although closely related to SARS-CoV, the mechanisms of SARS-CoV-2 pathogenesis are not fully understood. We found that ectopic expression of the SARS-CoV-2 E protein had detrimental effects on the host cell, causing metabolic alterations including shutoff of protein synthesis and mobilization of cellular resources through autophagy activation. Co-expression of E with viral proteins known to subvert host antiviral responses such as autophagy and translational inhibition, either from SARS-CoV-2 or from heterologous viruses increased cell survival and E protein accumulation. However, such factors were found to negatively impact SARS-CoV-2 infection, as autophagy contributes to formation of viral membrane factories, and translational control offers an advantage for viral gene expression. Overall, SARS-CoV-2 has evolved mechanisms to harness host functions that are essential for virus replication.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Hope Waisner", - "author_inst": "University of Kansas Medical Center" - }, - { - "author_name": "Brandon Grieshaber", - "author_inst": "University of Kansas Medical Center" - }, - { - "author_name": "Rabina Saud", - "author_inst": "University of Kansas Medical Center" - }, - { - "author_name": "Wyatt Henke", - "author_inst": "University of Kansas Medical Center" - }, - { - "author_name": "Edward Brice Stephens", - "author_inst": "University of Kansas Medical Center" - }, - { - "author_name": "Maria Kalamvoki", - "author_inst": "University of Kansas Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.03.24.485222", "rel_title": "A Computational Pipeline to Identify Potential Drug Targets and Interacting Chemotypes in SARS-CoV-2", @@ -372229,6 +373941,65 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.03.22.485425", + "rel_title": "Influenza infection in ferrets with SARS-CoV-2 infection history", + "rel_date": "2022-03-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.22.485425", + "rel_abs": "Non-pharmaceutical interventions (NPIs) to contain the SARS-CoV-2 pandemic drastically reduced human-to-human interactions, decreasing the circulation of other respiratory viruses as well. As a consequence, influenza virus circulation - normally responsible for 3-5 million hospitalizations per year globally - was significantly reduced. With downscaling the NPI countermeasures, there is a concern for increased influenza disease, particularly in individuals suffering from post-acute effects of SARS-CoV-2 infection. To investigate this possibility, we performed a sequential influenza H1N1 infection 4 weeks after an initial SARS-CoV-2 infection in the ferret model. Upon H1N1 infection, ferrets that were previously infected with SARS-CoV-2 showed an increased tendency to develop clinical symptoms compared to the control H1N1 infected animals. Histopathological analysis indicated only a slight increase for type II pneumocyte hyperplasia and bronchitis. The effects of the sequential infection thus appeared minor. However, ferrets were infected with B.1.351-SARS-CoV-2, the beta variant of concern, which replicated poorly in our model. The histopathology of the respiratory organs was mostly resolved 4 weeks after SARS-CoV-2 infection, with only reminiscent histopathological features in the upper respiratory tract. Nevertheless, SARS-CoV-2 specific cellular and humoral responses were observed, confirming an established infection. Thus, there may likely be a SARS-CoV-2 variant-dependent effect on the severity of disease upon a sequential influenza infection as we observed mild effects upon a mild infection. It, however, remains to be determined what the impact is of more virulent SARS-CoV-2 variants.\n\nImportanceDuring the COVID-19 pandemic, the use of face masks, social distancing and isolation were not only effective in decreasing the circulation of SARS-CoV-2, but also in reducing other respiratory viruses such as influenza. With less restrictions, influenza is slowly returning. In the meantime, people still suffering from long-COVID, could be more vulnerable to an influenza virus infection and develop more severe influenza disease. This study provides directions to the effect of a previous SARS-CoV-2 exposure on influenza disease severity in the ferret model. This model is highly valuable to test sequential infections under controlled settings for translation to humans. We could not induce clear long-term COVID-19 effects as SARS-CoV-2 infection in ferrets was mild. However, we still observed a slight increase in influenza disease severity compared to ferrets that had not encountered SARS-CoV-2 before. It may therefore be advisable to include long-COVID patients as a risk group for influenza vaccination.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Caroline Vilas Boas de Melo", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Florence Peters", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Harry van Dijken", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Stefanie Lenz", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Koen van de Ven", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Lisa Wijsman", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Ang\u00e9la Gommersbach", + "author_inst": "Poonawalla Science Park" + }, + { + "author_name": "Tanja Schouten", + "author_inst": "Poonawalla Sciencepark" + }, + { + "author_name": "Puck B van Kasteren", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Judith M.A. van den Brand", + "author_inst": "University of Utrecht" + }, + { + "author_name": "Jorgen de Jonge", + "author_inst": "National Institute for Public Health and the Environment" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2022.03.24.485596", "rel_title": "Differences in neuroinflammation in the olfactory bulb between D614G, Delta and Omicron BA.1 SARS-CoV-2 variants in the hamster model", @@ -372677,61 +374448,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.03.24.22272892", - "rel_title": "The modified COVID-19 Yorkshire Rehabilitation Scale (C19-YRSm) patient-reported outcome measure for Long Covid or Post-COVID syndrome", - "rel_date": "2022-03-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.24.22272892", - "rel_abs": "BackgroundThe C19-YRS was the first validated scale reported in the literature for patient assessment and monitoring in Long Covid or Post-COVID syndrome. The 22-item scale contains four subscales measuring symptom severity, functional disability, overall health and additional symptoms.\n\nObjectivesThis study aimed to modify and refine the scale based on psychometric properties, emerging evidence on additional Long Covid symptoms, and feedback from a working group of patients and healthcare professionals.\n\nMethodsData were collected from 370 patients who completed the C19-YRS scale in a community Long COVID service. The psychometric properties of the Symptom Severity and Functional Disability subscales were assessed using a Rasch Measurement Theory framework, where all individual scale items were assessed for model fit, local dependency, response category functioning and differential item functioning (DIF) by age group and sex. Additionally, the subscales were assessed for targeting, reliability and unidimensionality. The overall health subscale is a single item, and the additional symptoms subscale is not intended to be summed, therefore neither is appropriate for Rasch analyses. Psychometric results and implications were relayed back to the working group for discussion, alongside clinical evidence of emerging and relevant symptoms not covered by the original C19-YRS.\n\nResultsRasch analysis revealed promising psychometric properties of the symptom severity and functional disability subscales, with both displaying good targeting and reliability, although some individual measurement anomalies were noted. The original 0-10 item response category structure did not operate as intended for both the subscales. Post-hoc rescoring suggested that a 4-point response category structure would be more appropriate for both the subscales, and this aligned with patient feedback. This scoring change was implemented, alongside changes in the item composition of the symptom severity and additional symptoms subscales. The functional disability item set, and the overall health single-item subscale remained unchanged.\n\nConclusionA modified version of the C19-YRS was developed based on a combination of psychometric evidence, clinical relevance of the content and feedback from the working group (comprising patients and healthcare professionals). Future studies including NIHR funded LOCOMOTION study will undertake large-scale, multi-centre validation of the modified C19-YRS.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Manoj Sivan", - "author_inst": "University of Leeds" - }, - { - "author_name": "Nick J Preston", - "author_inst": "University of Leeds" - }, - { - "author_name": "Amy Parkin", - "author_inst": "Leeds Teaching Hospitals NHS Trust" - }, - { - "author_name": "Sophie Makower", - "author_inst": "Leeds Community Healthcare NHS Trust" - }, - { - "author_name": "Jeremy Gee", - "author_inst": "Airedale Hospitals NHS Trust" - }, - { - "author_name": "Denise Ross", - "author_inst": "Leeds Teaching Hospitals NHS Trust" - }, - { - "author_name": "Rachel Tarrant", - "author_inst": "Leeds Community Healthcare NHS Trust" - }, - { - "author_name": "Jennifer Davison", - "author_inst": "Leeds Community Healthcare NHS Trust" - }, - { - "author_name": "Stephen Halpin", - "author_inst": "University of Leeds" - }, - { - "author_name": "Mike Horton", - "author_inst": "University of Leeds" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "rehabilitation medicine and physical therapy" - }, { "rel_doi": "10.1101/2022.03.24.22272883", "rel_title": "Production of anti-spike antibodies in response to COVID vaccine in lymphoma patients", @@ -374095,6 +375811,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.22.22272773", + "rel_title": "Risk of SARS-CoV-2 transmission by fomites: a clinical observational study in highly infectious COVID-19 patients", + "rel_date": "2022-03-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.22.22272773", + "rel_abs": "BackgroundThe contribution of droplet-contaminated surfaces for virus transmission has been discussed controversially in the context of the current Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic. Importantly, the risk of fomite-based transmission has not been systematically addressed.\n\nMethodsWe initiated this single-center observational study to evaluate whether hospitalized COVID-19 patients can contaminate stainless steel carriers by coughing or intensive moistening with saliva and to assess the risk of SARS-CoV-2 transmission upon detection of viral loads and infectious virus in cell culture. Fifteen hospitalized patients with a high baseline viral load (CT value [≤] 25) shortly after admission were included. We documented clinical and laboratory parameters and used patient samples to perform virus culture, quantitative PCR and virus sequencing.\n\nResultsNasopharyngeal and oropharyngeal swabs of all patients were positive for viral RNA on the day of the study. Infectious SARS-CoV-2 could be isolated from 6 patient swabs (46.2 %). While after coughing, no infectious virus could be recovered, intensive moistening with saliva resulted in successful viral recovery from steel carriers of 5 patients (38.5 %).\n\nConclusionsTransmission of infectious SARS-CoV-2 via fomites is possible upon extensive moistening, but unlikely to occur in real-life scenarios and from droplet-contaminated fomites.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Toni Luise Meister", + "author_inst": "Ruhr University Bochum" + }, + { + "author_name": "Marielen Dreismeier", + "author_inst": "Ruhr University Bochum" + }, + { + "author_name": "Elena Vidal Blanco", + "author_inst": "Ruhr University Bochum" + }, + { + "author_name": "Yannick Brueggemann", + "author_inst": "Ruhr University Bochum" + }, + { + "author_name": "Natalie Heinen", + "author_inst": "Ruhr University Bochum" + }, + { + "author_name": "Guenter Kampf", + "author_inst": "University Medicine Greifswald" + }, + { + "author_name": "Daniel Todt", + "author_inst": "Ruhr University Bochum" + }, + { + "author_name": "Huu Phuc Nguyen", + "author_inst": "Ruhr University Bochum" + }, + { + "author_name": "Joerg Steinmann", + "author_inst": "Paracelsus Medical University" + }, + { + "author_name": "Wolfgang Ekkehard Schmidt", + "author_inst": "Ruhr University Bochum" + }, + { + "author_name": "Eike Steinmann", + "author_inst": "Ruhr University Bochum" + }, + { + "author_name": "Daniel Robert Quast", + "author_inst": "Ruhr University Bochum" + }, + { + "author_name": "Stephanie Pfaender", + "author_inst": "Ruhr University Bochum" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.22.22272758", "rel_title": "Mathematical modelling of COVID-19 transmission dynamics with vaccination: A case study in Ethiopia", @@ -374739,53 +376522,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.21.22272358", - "rel_title": "Undiagnosed COVID-19 in households with a child with mitochondrial disease", - "rel_date": "2022-03-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.21.22272358", - "rel_abs": "BackgroundThe impact of the COVID-19 pandemic on medically fragile populations, who are at higher risk of severe illness and sequelae, has not been well characterized. Viral infection is a major cause of morbidity in children with mitochondrial disease (MtD), and the COVID-19 pandemic represents an opportunity to study this vulnerable population.\n\nMethodsA convenience sampling cross-sectional serology study was conducted (October 2020 to June 2021) in households (N = 20) containing a child with MtD (N = 22). Samples (N = 83) were collected in the home using a microsampling apparatus and shipped to investigators. Antibodies against SARS-CoV-2 nucleocapsid (IgG), spike protein (IgG, IgM, IgA), and receptor binding domain (IgG, IgM, IgA) were determined by enzyme linked immunosorbent assay.\n\nResultsWhile only 4.8% of participants were clinically diagnosed for SARS-CoV-2 infection, 75.9% of study participants were seropositive for SARS-CoV-2 antibodies. Most samples were IgM positive for spike or RBD (70%), indicating that infection was recent. This translated to all 20 families showing evidence of infection in at least one household member. For the children with MtD, 91% had antibodies against SARS-CoV-2 and had not experienced any adverse outcomes at the time of assessment. For children with recent infections (IgM+ only), serologic data suggest household members as a source.\n\nConclusionsCOVID-19 was highly prevalent and undiagnosed in households with a child with MtD through the 2020-2021 winter wave of the pandemic. In this first major wave, children with MtD tolerated SARS-CoV-2 infection well, potentially due to household adherence to CDC recommendations for risk mitigation.\n\nFundingThis study was funded by the Intramural Research Program of the National Institutes of Health (HG200381-03).\n\nClinical trial numberNCT04419870", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Eliza M. Gordon-Lipkin", - "author_inst": "National Human Genome Research Institute, National Institutes of Health" - }, - { - "author_name": "Christopher Marcum", - "author_inst": "National Institute of Allergy and Infectious Disease, National Institutes of Health" - }, - { - "author_name": "Shannon Kruk", - "author_inst": "National Human Genome Research Institute, National Institutes of Health" - }, - { - "author_name": "Elizabeth Thompson", - "author_inst": "National Human Genome Research Institute, National Institutes of Health" - }, - { - "author_name": "Sophie E.M. Kelly", - "author_inst": "National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health" - }, - { - "author_name": "Heather Kalish", - "author_inst": "National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health" - }, - { - "author_name": "Kaitlyn Sadtler", - "author_inst": "National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health" - }, - { - "author_name": "Peter McGuire", - "author_inst": "NIH" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2022.03.21.22271747", "rel_title": "Clinical validation and the evaluation of a colorimetric SARS-CoV-2 RT-LAMP assay identify its robustness against RT-PCR", @@ -376077,6 +377813,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.03.18.22272462", + "rel_title": "A fast and sensitive absolute quantification assay for the detection of SARS-CoV-2 peptides using Parallel Reaction Monitoring Mass Spectrometry", + "rel_date": "2022-03-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.18.22272462", + "rel_abs": "The on-going SARS-CoV-2 (COVID-19) pandemic has called for an urgent need for rapid and high-throughput methods for mass testing for early detection, prevention and surveillance of the disease. Here, we tested if targeted parallel reaction monitoring (PRM) quantification using high resolution Orbitrap instruments can provide the sensitivity and speed required for a high-throughput method that could be used for clinical diagnosis. Here we report a high-throughput and sensitive PRM-MS assay that enables absolute quantification of SARS-CoV-2 nucleocapsid peptides with short turn-around times. Concatenated peptides (QconCAT) synthesized using isotopically labelled SARS-CoV-2 were used for absolute quantification. We developed a fast and high-throughput S-trap-based sample preparation method, which was then successfully utilized for testing 25 positive and 25 negative heat-inactivated nasopharyngeal swab samples for SARS-CoV-2 detection. The method was able to differentiate between negative and positive patients accurately within its limits of detection. Moreover, extrapolating from the QconCAT absolute quantification, our data show that patients with Ct values as low as 17.5 have NCAP protein amounts of around 7.5 pmol in swab samples. The present high-throughput method could potentially be utilized in specialized clinics as an alternative tool for detection of SARS-CoV-2.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Akshada Gajbhiye", + "author_inst": "Newcastle University" + }, + { + "author_name": "Atakan Nalbant", + "author_inst": "Newcastle University" + }, + { + "author_name": "Tiaan Heunis", + "author_inst": "Newcastle University" + }, + { + "author_name": "Frances Sidgwick", + "author_inst": "Newcastle University" + }, + { + "author_name": "Andrew Porter", + "author_inst": "Newcastle University" + }, + { + "author_name": "Yusri Taha", + "author_inst": "The Newcastle upon Tyne Hospitals NHS Foundation Trust" + }, + { + "author_name": "Matthias Trost", + "author_inst": "Newcastle University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.03.21.22272687", "rel_title": "Cost-effectiveness of antigen testing for ending COVID-19 isolation", @@ -376425,161 +378204,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2022.03.20.485044", - "rel_title": "Robust and durable prophylactic protection conferred by RNA interference in preclinical models of SARS-CoV-2", - "rel_date": "2022-03-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.20.485044", - "rel_abs": "RNA interference is a natural antiviral mechanism that could be harnessed to combat SARS-CoV-2 infection by targeting and destroying the viral genome. We screened lipophilic small-interfering RNA (siRNA) conjugates targeting highly conserved regions of the SARS-CoV-2 genome and identified leads targeting outside of the spike-encoding region capable of achieving [≥]3-log viral reduction. Serial passaging studies demonstrated that a two-siRNA combination prevented development of resistance compared to a single-siRNA approach. A two-siRNA combination delivered intranasally protected Syrian hamsters from weight loss and lung pathology by viral infection upon prophylactic administration but not following onset of infection. Together, the data support potential utility of RNAi as a prophylactic approach to limit SARS-CoV-2 infection that may help combat emergent variants, complement existing interventions, or protect populations where vaccines are less effective. Most importantly, this strategy has implications for developing medicines that may be valuable in protecting against future coronavirus pandemics.", - "rel_num_authors": 35, - "rel_authors": [ - { - "author_name": "Yesseinia I Anglero-Rodriguez", - "author_inst": "Alnylam Pharmaceuticals" - }, - { - "author_name": "Florian A Lempp", - "author_inst": "VIR Biotechnology" - }, - { - "author_name": "James McIninch", - "author_inst": "Alnylam Pharmaceuticals" - }, - { - "author_name": "Mark K Schlegel", - "author_inst": "Alnylam Pharmaceuticals" - }, - { - "author_name": "Christopher R Brown", - "author_inst": "Alnylam Pharmaceuticals" - }, - { - "author_name": "Donald J Foster", - "author_inst": "Alnylam Pharmaceuticals" - }, - { - "author_name": "Adam B Castoreno", - "author_inst": "Alnylam Pharmaceuticals" - }, - { - "author_name": "Tuyen Nguyen", - "author_inst": "Alnylam Pharmaceuticals" - }, - { - "author_name": "Megha Subramanian", - "author_inst": "Alnylam Pharmaceuticals" - }, - { - "author_name": "Martin Montiel-Ruiz", - "author_inst": "VIR Biotechnology" - }, - { - "author_name": "Hannah Kaiser", - "author_inst": "VIR Biotechnology" - }, - { - "author_name": "Anna Sahakyan", - "author_inst": "VIR Biotechnology" - }, - { - "author_name": "Roberto Spreafico", - "author_inst": "VIR Biotechnology" - }, - { - "author_name": "Svetlana Shulga Morskaya", - "author_inst": "Alnylam Pharmaceuticals" - }, - { - "author_name": "Joseph D Barry", - "author_inst": "Alnylam Pharmaceuticals" - }, - { - "author_name": "Daniel Berman", - "author_inst": "Alnylam Pharmaceuticals" - }, - { - "author_name": "Stephanie Lefebvre", - "author_inst": "Alnylam Pharmaceuticals" - }, - { - "author_name": "Anne Kasper", - "author_inst": "Alnylam Pharmaceuticals" - }, - { - "author_name": "Timothy Racie", - "author_inst": "Alnylam Pharmaceuticals" - }, - { - "author_name": "Diann Weddle", - "author_inst": "Alnylam Pharmaceuticals" - }, - { - "author_name": "Melissa Mobley", - "author_inst": "Alnylam Pharmaceuticals" - }, - { - "author_name": "Arlin Rogers", - "author_inst": "Alnylam Pharmaceuticals" - }, - { - "author_name": "Joseph Dybowski", - "author_inst": "Alnylam Pharmaceuticals" - }, - { - "author_name": "Saheo Chong", - "author_inst": "Alnylam Pharmaceuticals" - }, - { - "author_name": "Jayprakash Nair", - "author_inst": "Alnylam Pharmaceuticals" - }, - { - "author_name": "Amy Simon", - "author_inst": "Alnylam Pharmaceuticals" - }, - { - "author_name": "Kevin Sloan", - "author_inst": "Alnylam Pharmaceuticals" - }, - { - "author_name": "Seungmin Hwang", - "author_inst": "VIR Biotechnology" - }, - { - "author_name": "Herbert W Virgin", - "author_inst": "VIR Biotechnology" - }, - { - "author_name": "Kevin Fitzgerald", - "author_inst": "Alnylam Pharmaceuticals" - }, - { - "author_name": "Martin A Maier", - "author_inst": "Alnylam Pharmaceuticals" - }, - { - "author_name": "Gregory Hinkle", - "author_inst": "Alnylam Pharmaceuticals" - }, - { - "author_name": "Christy Hebner", - "author_inst": "Alnylam Pharmaceuticals" - }, - { - "author_name": "Akin Akinc", - "author_inst": "Alnylam Pharmaceuticals" - }, - { - "author_name": "Vasant Jadhav", - "author_inst": "Alnylam Pharmaceuticals" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2022.03.18.22272624", "rel_title": "A 16-Month Longitudinal Investigation of Risk and Protective Factors for Mental Health Outcomes Throughout Three National Lockdowns and a Mass Vaccination Campaign: Evidence from a Weighted Israeli Sample During COVID-19", @@ -378171,6 +379795,37 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.03.18.484954", + "rel_title": "Peptidome Surveillance Across Evolving SARS-CoV-2 Lineages Reveals HLA Binding Conservation in Nucleocapsid Among Variants With Most Potential for T-Cell Epitope Loss In Spike", + "rel_date": "2022-03-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.18.484954", + "rel_abs": "To provide a unique global view of the relative potential for evasion of CD8+ and CD4+ T cells by SARS-CoV-2 lineages as they evolve over time, we performed a comprehensive analysis of predicted HLA-I and HLA-II binding peptides in spike (S) and nucleocapsid (N) protein sequences of all available SARS-CoV-2 genomes as provided by NIH NCBI at a bi-monthly interval between March and December of 2021. A data supplement of all B.1.1.529 (Omicron) genomes from GISAID in early December was also used to capture the rapidly spreading variant. A key finding is that throughout continued viral evolution and increasing rates of mutations occurring at T-cell epitope hotspots, protein instances with worst case binding loss did not become the most frequent for any Variant of Concern (VOC) or Variant of Interest (VOI) lineage; suggesting T-cell evasion is not likely to be a dominant evolutionary pressure on SARS-CoV-2. We also determined that throughout the course of the pandemic in 2021, there remained a relatively steady ratio of viral variants that exhibit conservation of epitopes in the N protein, despite significant potential for epitope loss in S relative to other lineages. We further localized conserved regions in N with high epitope yield potential, and illustrated HLA-I binding heterogeneity across the S protein consistent with empirical observations. Although Omicrons high volume of mutations caused it to exhibit more epitope loss potential than most frequently observed versions of proteins in almost all other VOCs, epitope candidates across its most frequent N proteins were still largely conserved. This analysis adds to the body of evidence suggesting that N may have merit as an additional antigen to elicit immune responses to vaccination with increased potential to provide sustained protection against COVID-19 disease in the face of emerging variants.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Kamil Wnuk", + "author_inst": "ImmunityBio, Inc." + }, + { + "author_name": "Jeremi Sudol", + "author_inst": "ImmunityBio, Inc." + }, + { + "author_name": "Patricia R Spilman", + "author_inst": "ImmunityBio, Inc." + }, + { + "author_name": "Patrick Soon-Shiong", + "author_inst": "ImmunityBio, Inc" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.03.18.484956", "rel_title": "Human Galectin-9 Potently Enhances SARS-CoV-2 Replication and Inflammation in Airway Epithelial Cells", @@ -378671,153 +380326,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, - { - "rel_doi": "10.1101/2022.03.17.22272589", - "rel_title": "A multiplexed Cas13-based assay with point-of-care attributes for simultaneous COVID-19 diagnosis and variant surveillance", - "rel_date": "2022-03-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.17.22272589", - "rel_abs": "Point-of-care (POC) nucleic acid detection technologies are poised to aid gold-standard technologies in controlling the COVID-19 pandemic, yet shortcomings in the capability to perform critically needed complex detection--such as multiplexed detection for viral variant surveillance--may limit their widespread adoption. Herein, we developed a robust multiplexed CRISPR-based detection using LwaCas13a and PsmCas13b to simultaneously diagnose SARS-CoV-2 infection and pinpoint the causative SARS-CoV-2 variant of concern (VOC)-- including globally dominant VOCs Delta (B.1.617.2) and Omicron (B.1.1.529)--all while maintaining high levels of accuracy upon the detection of multiple SARS-CoV-2 gene targets. The platform has several attributes suitable for POC use: premixed, freeze-dried reagents for easy use and storage; convenient direct-to-eye or smartphone-based readouts; and a one-pot variant of the multiplexed detection. To reduce reliance on proprietary reagents and enable sustainable use of such a technology in low- and middle-income countries, we locally produced and formulated our own recombinase polymerase amplification reaction and demonstrated its equivalent efficiency to commercial counterparts. Our tool--CRISPR-based detection for simultaneous COVID-19 diagnosis and variant surveillance which can be locally manufactured--may enable sustainable use of CRISPR diagnostics technologies for COVID- 19 and other diseases in POC settings.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Maturada Patchsung", - "author_inst": "School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand" - }, - { - "author_name": "Aimorn Homchan", - "author_inst": "School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Department of Biochemistry, Facul" - }, - { - "author_name": "Kanokpol Aphicho", - "author_inst": "School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand" - }, - { - "author_name": "Surased Suraritdechachai", - "author_inst": "School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand" - }, - { - "author_name": "Thanyapat Wanitchanon", - "author_inst": "School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand" - }, - { - "author_name": "Archiraya Pattama", - "author_inst": "Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Khomkrit Sappakhaw", - "author_inst": "School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand" - }, - { - "author_name": "Piyachat Meesawat", - "author_inst": "School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand" - }, - { - "author_name": "Thanakrit Wongsatit", - "author_inst": "School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand" - }, - { - "author_name": "Artittaya Athipanyasilp", - "author_inst": "School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand" - }, - { - "author_name": "Krittapas Jantarug", - "author_inst": "School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand" - }, - { - "author_name": "Niracha Athipanyasilp", - "author_inst": "Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Juthamas Buahom", - "author_inst": "Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Supapat Visanpattanasin", - "author_inst": "Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Nootaree Niljianskul", - "author_inst": "PTT Public Company Limited, Bangkok, Thailand" - }, - { - "author_name": "Pimchai Chaiyen", - "author_inst": "School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand" - }, - { - "author_name": "Ruchanok Tinikul", - "author_inst": "Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Nuanjun Wichukchinda", - "author_inst": "Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand" - }, - { - "author_name": "Surakameth Mahasirimongkol", - "author_inst": "Division of Genomic Medicine and Innovation Support, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand" - }, - { - "author_name": "Rujipas Sirijatuphat", - "author_inst": "Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Nasikarn Angkasekwinai", - "author_inst": "Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Michael A Crone", - "author_inst": "London Biofoundry, Imperial College Translation and Innovation Hub; Department of Infectious Disease; UK Dementia Research Institute Centre for Care Research an" - }, - { - "author_name": "Paul S Freemont", - "author_inst": "London Biofoundry, Imperial College Translation and Innovation Hub; Department of Infectious Disease; UK Dementia Research Institute Centre for Care Research an" - }, - { - "author_name": "Julia Joung", - "author_inst": "Howard Hughes Medical Institute; Broad Institute of MIT and Harvard; McGovern Institute for Brain Research at MIT; Department of Biological Engineering; Departm" - }, - { - "author_name": "Alim Ladha", - "author_inst": "Howard Hughes Medical Institute; Broad Institute of MIT and Harvard; McGovern Institute for Brain Research at MIT; Department of Biological Engineering; Departm" - }, - { - "author_name": "Omar Abudayyeh", - "author_inst": "McGovern Institute for Brain Research at MIT, Cambridge, MA, USA" - }, - { - "author_name": "Jonathan Gootenberg", - "author_inst": "McGovern Institute for Brain Research at MIT, Cambridge, MA, USA" - }, - { - "author_name": "Feng Zhang", - "author_inst": "Howard Hughes Medical Institute; Broad Institute of MIT and Harvard; McGovern Institute for Brain Research at MIT; Department of Biological Engineering; Departm" - }, - { - "author_name": "Claire Chewapreecha", - "author_inst": "Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Wellcome Sanger Institute, Hinxton, UK" - }, - { - "author_name": "Sittinan Chanarat", - "author_inst": "Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Navin Horthongkham", - "author_inst": "Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Danaya Pakotiprapha", - "author_inst": "Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Chayasith Uttamapinant", - "author_inst": "School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.17.22272538", "rel_title": "From Delta to Omicron SARS-CoV-2 variant: switch to saliva sampling for higher detection rate", @@ -380129,6 +381637,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2022.03.16.22272521", + "rel_title": "The decay of coronavirus in sewage pipes and the development of a predictive model for the estimation of SARS-CoV-2 infection cases based on wastewater surveillance", + "rel_date": "2022-03-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.16.22272521", + "rel_abs": "Wastewater surveillance serves as a promising approach to elucidate the silent transmission of SARS-CoV-2 in a given community by detecting the virus in wastewater treatment facilities. This study monitored the viral RNA abundance at one WWTP and three communities during the COVID-19 outbreak in the Yanta district of Xian city from December 2021 to January 2022. To further understand the decay of the coronavirus in sewage pipes, avian infectious bronchitis virus (IBV) was seeded in two recirculating water systems and operated for 90 days. Based on the viral abundance in the wastewater of Xian and the above data regarding the decay of coronavirus in sewage pipes, Monte Carol simulations were performed to estimate the infectious cases in Xian. The results suggested that the delta variant was first detected on Dec-10, five days earlier than the reported date of clinical samples. SARS-CoV-2 was detected on December 18 in the monitored community two days earlier than the first case and was consecutively detected in the following two sampling times. In pipelines without biofilms, the results showed that high temperature significantly reduced the viral RNA abundance by 2.18 log10 GC/L after experiencing 20 km travel distance, while only a 1.68 log10 GC/L reduction was observed in the pipeline with a low water temperature. After 90 days of operation, the biofilm matured in the pipeline in both systems. Reductions of viral RNA abundance of 2.14 and 4.79 log10 GC/L were observed in low- and high-temperature systems with mature biofilms, respectively. Based on the above results, we adjusted the input parameters for Monte Carol simulation and estimated 23.3, 50.1, 127.3 and 524.2 infected persons in December 14, 18, 22 and 26, respectively, which is largely consistent with the clinical reports. This work highlights the viability of wastewater surveillance for the early warning of COVID-19 at both the community and city levels, which represents a valuable complement to clinical approaches.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Songzhe Fu", + "author_inst": "Dalian Ocean University" + }, + { + "author_name": "Qingyao Wang", + "author_inst": "Dalian Ocean University" + }, + { + "author_name": "Fenglan He", + "author_inst": "Nanchang Center for Disease Control and Prevention" + }, + { + "author_name": "Can Zhou", + "author_inst": "Dalian Ocean University" + }, + { + "author_name": "Jin Zhang", + "author_inst": "Dalian Ocean University" + }, + { + "author_name": "Wen Xia", + "author_inst": "Nanchang Center for Disease Control and Prevention" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.03.16.22272497", "rel_title": "Variant-specific burden of SARS-CoV-2 in Michigan: March 2020 through November 2021", @@ -380633,41 +382180,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.17.22272535", - "rel_title": "Comparison of the 2021 COVID-19 'Roadmap' Projections against Public Health Data", - "rel_date": "2022-03-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.17.22272535", - "rel_abs": "Control and mitigation of the COVID-19 pandemic in England has relied on a combination of vaccination and non-pharmaceutical interventions (NPIs). Some of these NPIs are extremely costly (economically and socially), so it was important to relax these promptly without overwhelming already burdened health services. The eventual policy was a Roadmap of four relaxation steps throughout 2021, taking England from lock-down to the cessation of all restrictions on social interaction. In a series of six Roadmap documents generated throughout 2021, models assessed the potential risk of each relaxation step. Here we show that the model projections generated a reliable estimation of medium-term hospital admission trends, with the data points up to September 2021 generally lying within our 95% prediction intervals. The greatest uncertainties in the modelled scenarios came from vaccine efficacy estimates against novel variants, and from assumptions about human behaviour in the face of changing restrictions and risk.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Matt J Keeling", - "author_inst": "University of Warwick" - }, - { - "author_name": "Louise J Dyson", - "author_inst": "University of Warwick" - }, - { - "author_name": "Michael Tildesley", - "author_inst": "University of Warwick" - }, - { - "author_name": "Edward M Hill", - "author_inst": "University of Warwick" - }, - { - "author_name": "Sam M Moore", - "author_inst": "University of Warwick" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.03.14.22272314", "rel_title": "COVID-19 Prediction using Genomic Footprint of SARS-CoV-2 in Air, Surface Swab and Wastewater", @@ -381899,6 +383411,93 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.03.15.484379", + "rel_title": "Hypoxia inducible factors regulate infectious SARS-CoV-2, epithelial damage and respiratory symptoms in a hamster COVID-19 model.", + "rel_date": "2022-03-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.15.484379", + "rel_abs": "Understanding the host pathways that define susceptibility to SARS-CoV-2 infection and disease are essential for the design of new therapies. Oxygen levels in the microenvironment define the transcriptional landscape, however the influence of hypoxia on virus replication and disease in animal models is not well understood. In this study, we identify a role for the hypoxic inducible factor (HIF) signalling axis to inhibit SARS-CoV-2 infection, epithelial damage and respiratory symptoms in Syrian hamsters. Pharmacological activation of HIF with the prolyl-hydroxylase inhibitor FG-4592 significantly reduced the levels of infectious virus in the upper and lower respiratory tract. Nasal and lung epithelia showed a reduction in SARS-CoV-2 RNA and nucleocapsid expression in treated animals. Transcriptomic and pathological analysis showed reduced epithelial damage and increased expression of ciliated cells. Our study provides new insights on the intrinsic antiviral properties of the HIF signalling pathway in SARS-CoV-2 replication that may be applicable to other respiratory pathogens and identifies new therapeutic opportunities.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Peter AC Wing", + "author_inst": "University of Oxford" + }, + { + "author_name": "Maria Prange-Barczynska", + "author_inst": "University of Oxford" + }, + { + "author_name": "Amy Cross", + "author_inst": "University of Oxford" + }, + { + "author_name": "Stefania Crotta", + "author_inst": "Francis Crick Institute" + }, + { + "author_name": "Claudia Orbegozo Rubio", + "author_inst": "University of Oxford" + }, + { + "author_name": "Xiaotong Cheng", + "author_inst": "University of Oxford" + }, + { + "author_name": "James M Harris", + "author_inst": "University of Oxford" + }, + { + "author_name": "Xiaodong Zhuang", + "author_inst": "University of Oxford" + }, + { + "author_name": "Rachel L Johnson", + "author_inst": "United Kingdom Health Security Agency" + }, + { + "author_name": "Kathryn A Ryan", + "author_inst": "United Kingdom Health Security Agency" + }, + { + "author_name": "Yper Hall", + "author_inst": "United Kingdom Health Security Agency" + }, + { + "author_name": "Miles W Carroll", + "author_inst": "University of Oxford" + }, + { + "author_name": "Fadi Issa", + "author_inst": "University of Oxford" + }, + { + "author_name": "Peter Balfe", + "author_inst": "University of Oxford" + }, + { + "author_name": "Andreas Wack", + "author_inst": "Francis Crick Institute" + }, + { + "author_name": "Tammie Bishop", + "author_inst": "University of Oxford" + }, + { + "author_name": "Francisco J Salguero", + "author_inst": "United Kingdom Health Security Agency" + }, + { + "author_name": "Jane A. McKeating", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.03.15.484404", "rel_title": "Omicron variant of SARS-COV-2 gains new mutations in New Zealand and Hong Kong", @@ -382283,81 +383882,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.03.14.22272359", - "rel_title": "Biomarkers Selection for Population Normalization in SARS-CoV-2 Wastewater-based Epidemiology", - "rel_date": "2022-03-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.14.22272359", - "rel_abs": "Wastewater-based epidemiology (WBE) has been one of the most cost-effective approaches to track the SARS-CoV-2 levels in the communities since the COVID-19 outbreak in 2020. Normalizing SARS-CoV-2 concentrations by the population biomarkers in wastewater can be critical for interpreting the viral loads, comparing the epidemiological trends among the sewersheds, and identifying the vulnerable communities. In this study, five population biomarkers, pepper mild mottle virus (pMMoV), creatinine (CRE), 5-hydroxyindoleacetic acid (5-HIAA), caffeine (CAF) and its metabolite paraxanthine (PARA) were investigated for their utility in normalizing the SARS-CoV-2 loads through developed direct and indirect approaches. Their utility in assessing the real-time population contributing to the wastewater was also evaluated. The best performed candidate was further tested for its capacity for improving correlation between normalized SARS-CoV-2 loads and the clinical cases reported in the City of Columbia, Missouri, a university town with a constantly fluctuated population. Our results showed that, except CRE, the direct and indirect normalization approaches using biomarkers allow accounting for the changes in wastewater dilution and differences in relative human waste input over time regardless flow volume and population at any given WWTP. Among selected biomarkers, PARA is the most reliable population biomarker in determining the SARS-CoV-2 load per capita due to its high accuracy, low variability, and high temporal consistency to reflect the change in population dynamics and dilution in wastewater. It also demonstrated its excellent utility for real-time assessment of the population contributing to the wastewater. In addition, the viral loads normalized by the PARA-estimated population significantly improved the correlation (rho=0.5878, p<0.05) between SARS-CoV-2 load per capita and case numbers per capita. This chemical biomarker offers an excellent alternative to the currently CDC-recommended pMMoV genetic biomarker to help us understand the size, distribution, and dynamics of local populations for forecasting the prevalence of SARS-CoV2 within each sewershed.\n\nHIGHLIGHT (bullet points)O_LIThe paraxanthine (PARA), the metabolite of the caffeine, is a more reliable population biomarker in SARS-CoV-2 wastewater-based epidemiology studies than the currently recommended pMMoV genetic marker.\nC_LIO_LISARS-CoV-2 load per capita could be directly normalized using the regression functions derived from correlation between paraxanthine and population without flowrate and population data.\nC_LIO_LINormalizing SARS-CoV-2 levels with the chemical marker PARA significantly improved the correlation between viral loads per capita and case numbers per capita.\nC_LIO_LIThe chemical marker PARA demonstrated its excellent utility for real-time assessment of the population contributing to the wastewater.\nC_LI", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Shu-Yu Hsu", - "author_inst": "University of Missouri" - }, - { - "author_name": "Mohamed B Bayati", - "author_inst": "University of Missouri Columbia" - }, - { - "author_name": "Chenhui Li", - "author_inst": "University of Missouri" - }, - { - "author_name": "Hsin-Yeh Hsieh", - "author_inst": "University of Missouri" - }, - { - "author_name": "Anthony Belenchia", - "author_inst": "Missouri Department of Health and Senior Services" - }, - { - "author_name": "Hweiyiing Johnson", - "author_inst": "Missouri Department of Health and Senior Services" - }, - { - "author_name": "Jessica Klutts", - "author_inst": "Missouri Department of Natural Resources" - }, - { - "author_name": "Melissa Reynolds", - "author_inst": "Missouri Department of Health and Senior Services" - }, - { - "author_name": "Elizabeth Semkiw", - "author_inst": "Missouri Department of Health and Senior Services" - }, - { - "author_name": "Jeff Wenzel", - "author_inst": "Missouri Department of Health and Senior Services" - }, - { - "author_name": "Chris Wieberg", - "author_inst": "Missouri Department of Natural Resources" - }, - { - "author_name": "Sally A Zemmer", - "author_inst": "Missouri Department of Natural Resources" - }, - { - "author_name": "Trevor Foley", - "author_inst": "Missouri Department of Corrections" - }, - { - "author_name": "Marc Johnson", - "author_inst": "University of Missouri" - }, - { - "author_name": "Chung-Ho Lin", - "author_inst": "University of Missouri" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.03.14.22271847", "rel_title": "Employer Requirements and COVID-19 Vaccination and Attitudes among Healthcare Personnel in the U.S.: Findings from National Immunization Survey Adult COVID Module, August - September 2021", @@ -383697,6 +385221,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.14.22272283", + "rel_title": "Migrants' primary care utilisation before and during the COVID-19 pandemic in England: An interrupted time series", + "rel_date": "2022-03-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.14.22272283", + "rel_abs": "BackgroundHow international migrants access and use primary care in England is poorly understood. We aimed to compare primary care consultation rates between international migrants and non-migrants in England before and during the COVID-19 pandemic (2015- 2020).\n\nMethodsUsing linked data from the Clinical Practice Research Datalink (CPRD) GOLD and the Office for National Statistics, we identified migrants using country-of-birth, visa-status or other codes indicating international migration. We ran a controlled interrupted time series (ITS) using negative binomial regression to compare rates before and during the pandemic.\n\nFindingsIn 262,644 individuals, pre-pandemic consultation rates per person-year were 4.35 (4.34-4.36) for migrants and 4.6 (4.59-4.6) for non-migrants (RR:0.94 [0.92-0.96]). Between 29 March and 26 December 2020, rates reduced to 3.54 (3.52-3.57) for migrants and 4.2 (4.17-4.23) for non-migrants (RR:0.84 [0.8-0.88]). Overall, this represents an 11% widening of the pre-pandemic difference in consultation rates between migrants and non-migrants during the first year of the pandemic (RR:0.89, 95%CI:0.84-0.94). This widening was greater for children, individuals whose first language was not English, and individuals of White British, White non-British and Black/African/Caribbean/Black British ethnicities.\n\nInterpretationMigrants were less likely to use primary care before the pandemic and the first year of the pandemic exacerbated this difference. As GP practices retain remote and hybrid models of service delivery, they must improve services and ensure they are accessible and responsive to migrants healthcare needs.\n\nFundingThis study was funded by the Medical Research Council (MR/V028375/1) and Wellcome Clinical Research Career Development Fellowship (206602).", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Claire X Zhang", + "author_inst": "UCL" + }, + { + "author_name": "Yamina Boukari", + "author_inst": "University College London" + }, + { + "author_name": "Neha Pathak", + "author_inst": "University College London" + }, + { + "author_name": "Rohini Mathur", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Srinivasa Vittal Katikireddi", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Parth Patel", + "author_inst": "University College London" + }, + { + "author_name": "In\u00eas Campos-Matos", + "author_inst": "Department of Health and Social Care" + }, + { + "author_name": "Dan Lewer", + "author_inst": "University College London" + }, + { + "author_name": "Vincent Nguyen", + "author_inst": "University College London" + }, + { + "author_name": "Greg Hugenholtz", + "author_inst": "University College London" + }, + { + "author_name": "Rachel Burns", + "author_inst": "University College London" + }, + { + "author_name": "Amy R Mulick", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Alasdair Henderson", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Robert W Aldridge", + "author_inst": "UCL" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "primary care research" + }, { "rel_doi": "10.1101/2022.03.11.484006", "rel_title": "Dual inhibition of vacuolar ATPase and TMPRSS2 is required for complete blockade of SARS-CoV-2 entry into cells", @@ -384081,53 +385676,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2022.03.10.22272237", - "rel_title": "Long COVID in Children and Adolescents: A Systematic Review and Meta-analyses.", - "rel_date": "2022-03-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.10.22272237", - "rel_abs": "The objective of this systematic review and meta-analyses is to estimate the prevalence of long-COVID in children and adolescents and to present the full spectrum of symptoms present after acute COVID-19. We have used PubMed and Embase to identify observational studies published before February 10th, 2022 that included a minimum of 30 patients with ages ranging from 0 to 18 years that met the National Institute for Healthcare Excellence (NICE) definition of long-COVID, which consists of both ongoing (4 to 12 weeks) and post-COVID-19 ([≥]12 weeks) symptoms. Random-effects meta-analyses were performed using the MetaXL software to estimate the pooled prevalence with a 95% confidence interval (CI). Heterogeneity was assessed using I2 statistics. The Preferred Reporting Items for Systematic Reviewers and Meta-analysis (PRISMA) reporting guideline was followed (registration PROSPERO CRD42021275408). The literature search yielded 8,373 publications, of which 21 studies met the inclusion criteria, and a total of 80,071 children and adolescents were included. The prevalence of long-COVID was 25.24%, and the most prevalent clinical manifestations were mood symptoms (16.50%), fatigue (9.66%), and sleep disorders (8.42%). Children infected by SARS-CoV-2 had a higher risk of persistent dyspnea, anosmia/ageusia, and/or fever compared to controls. Limitations of the studies analyzed include lack of standardized definitions, recall, selection, misclassification, nonresponse and/or loss of follow-up, and a high level of heterogeneity.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Sandra Lopez-Leon", - "author_inst": "Novartis Pharmaceuticals" - }, - { - "author_name": "Talia Wegman-Ostrosky", - "author_inst": "Instituto Nacional de Cancerologia" - }, - { - "author_name": "Norma Cipatli Ayuzo del Valle", - "author_inst": "Tecnologico de Monterrey, Mexico" - }, - { - "author_name": "Carol Perelman", - "author_inst": "Somedicyt, UNAM" - }, - { - "author_name": "Rosalinda Sepulveda", - "author_inst": "Harvard T.H. Chan School of Public Health Boston" - }, - { - "author_name": "Paulina Alejandra Rebolledo", - "author_inst": "Rollis School of Public Health, Emory University" - }, - { - "author_name": "Angelica Cuapio", - "author_inst": "Karolinska Institute, Stockholm, Sweden" - }, - { - "author_name": "Sonia Villapol", - "author_inst": "Houston Methodist Research Institute, Texas" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.10.22272236", "rel_title": "EMS prehospital response to the COVID-19 pandemic in the US: A brief literature review", @@ -385467,6 +387015,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.03.13.22272176", + "rel_title": "Vaccination against SARS-CoV-2 in UK school-aged children and young people decreases infection rates and reduces COVID-19 symptoms", + "rel_date": "2022-03-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.13.22272176", + "rel_abs": "BackgroundWe aimed to explore the effectiveness of one-dose BNT162b2 vaccination upon SARS-CoV-2 infection, its effect on COVID-19 presentation, and post-vaccination symptoms in children and young people (CYP) in the UK during periods of Delta and Omicron variant predominance.\n\nMethodsIn this prospective longitudinal cohort study, we analysed data from 115,775 CYP aged 12-17 years, proxy-reported through the Covid Symptom Study (CSS) smartphone application. We calculated post-vaccination infection risk after one dose of BNT162b2, and described the illness profile of CYP with post-vaccination SARS- CoV-2 infection, compared to unvaccinated CYP, and post-vaccination side-effects.\n\nFindingsBetween August 5, 2021 and February 14, 2022, 25,971 UK CYP aged 12-17 years received one dose of BNT162b2 vaccine. Vaccination reduced (proxy-reported) infection risk (-80{middle dot}4% and -53{middle dot}7% at 14-30 days with Delta and Omicron variants respectively, and -61{middle dot}5% and -63{middle dot}7% after 61-90 days). The probability of remaining infection-free diverged soon after vaccination, and was greater in CYP with prior SARS-CoV-2 infection. Vaccinated CYP who contracted SARS-CoV-2 during the Delta period had milder disease than unvaccinated CYP; during the Omicron period this was only evident in children aged 12-15 years. Overall disease profile was similar in both vaccinated and unvaccinated CYP. Post-vaccination local side-effects were common, systemic side-effects were uncommon, and both resolved quickly.\n\nInterpretationOne dose of BNT162b2 vaccine reduced risk of SARS-CoV-2 infection for at least 90 days in CYP aged 12-17 years. Vaccine protection varied for SARS-CoV-2 variant type (lower for Omicron than Delta variant), and was enhanced by pre-vaccination SARS-CoV-2 infection. Severity of COVID-19 presentation after vaccination was generally milder, although unvaccinated CYP also had generally mild disease. Overall, vaccination was well-tolerated.\n\nFundingUK Government Department of Health and Social Care, Chronic Disease Research Foundation, The Wellcome Trust, UK Engineering and Physical Sciences Research Council, UK Research and Innovation London Medical Imaging & Artificial Intelligence Centre for Value Based Healthcare, UK National Institute for Health Research, UK Medical Research Council, British Heart Foundation and Alzheimers Society, and ZOE Limited.\n\nResearch in context\n\nEvidence before this studyWe searched PubMed database for peer-reviewed articles and medRxiv for preprint papers, published between January 1, 2021 and February 15, 2022 using keywords (\"SARS-CoV-2\" OR \"COVID-19\") AND (child* OR p?ediatric* OR teenager*) AND (\"vaccin*\" OR \"immunization campaign\") AND (\"efficacy\" OR \"effectiveness\" OR \"symptoms\") AND (\"delta\" or \"omicron\" OR \"B.1.617.2\" OR \"B.1.1.529\"). The PubMed search retrieved 36 studies, of which fewer than 30% specifically investigated individuals <18 years.\n\nEleven studies explored SARS-CoV-2 viral transmission: seroprevalence in children (n=4), including age-dependency of susceptibility to SARS-CoV-2 infection (n=1), SARS-CoV-2 transmission in schools (n=5), and the effect of school closure on viral transmission (n=1).\n\nEighteen documents reported clinical aspects, including manifestation of infection (n=13), symptomatology, disease duration, and severity in children. Other studies estimated emergency department visits, hospitalization, need for intensive care, and/or deaths in children (n=4), and explored prognostic factors (n=1).\n\nThirteen studies explored vaccination-related aspects, including vaccination of children within specific paediatric co-morbidity groups (e.g., children with Down syndrome, inflammatory bowel disease, and cancer survivors, n=4), mRNA vaccine efficacy in children and adolescents from the general population (n=7), and the relation between vaccination and severity of disease and hospitalization cases (n=2). Four clinical trials were conducted using mRNA vaccines in minors, also exploring side effects. Sixty percent of children were found to have side effects after BNT162b2 vaccination, and especially after the second dose; however, most symptoms were mild and transient apart from rare uncomplicated skin ulcers. Two studies focused on severe adverse effects and safety of SARS-CoV-2 vaccines in children, reporting on myocarditis episodes and two cases of Guillain-Barre syndrome. All other studies were beyond the scope of our research.\n\nAdded value of this studyWe assessed multiple components of the UK vaccination campaign in a cohort of children and young people (CYP) aged 12-17 years drawn from a large UK community-based citizen-science study, who received a first dose of BNT162b2 vaccine. We describe a variant-dependent protective effect of the first dose against both Delta and Omicron, with additional protective effect of pre-vaccination SARS- CoV-2 infection on post-vaccination re-infection. We compare the illness profile in CYP infected post-vaccination with that of unvaccinated CYP, demonstrating overall milder disease with fewer symptoms for vaccinated CYP. We describe local and systemic side-effects during the first week following first-dose vaccination, confirming that local symptoms are common, systemic symptoms uncommon, and both usually transient.\n\nImplications of all the available evidenceOur data confirm that first dose BNT162b2 vaccination in CYP reduces risk of infection by SARS-CoV-2 variants, with generally local and brief side-effects. If infected after vaccination, COVID-19 is milder, if manifest at all. The study aims to contribute quantitative evidence to the risk-benefit evaluation of vaccination in CYP to inform discussion regarding rationale for their vaccination and the designing of national immunisation campaigns for this age group; and applies citizen-science approaches in the conduct of epidemiological surveillance and data collection in the UK community.\n\nImportantly, this study was conducted during Delta and Omicron predominance in UK; specificity of vaccine efficacy to variants is also illustrated; and results may not be generalizable to future SARS-CoV-2 strains.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Erika Molteni", + "author_inst": "King's College London" + }, + { + "author_name": "Liane S Canas", + "author_inst": "King's College London" + }, + { + "author_name": "Kerstin Klaser", + "author_inst": "King's College London" + }, + { + "author_name": "Jie Deng", + "author_inst": "King's College London" + }, + { + "author_name": "Sunil S Bhopal", + "author_inst": "Newcastle University" + }, + { + "author_name": "Robert C Hughes", + "author_inst": "London School of Hygiene & Tropical Medicine, London" + }, + { + "author_name": "Liyuan Chen", + "author_inst": "King's College London" + }, + { + "author_name": "Benjamin Murray", + "author_inst": "King's College London" + }, + { + "author_name": "Eric Kerfoot", + "author_inst": "King's College London" + }, + { + "author_name": "Michela Antonelli", + "author_inst": "King's College London" + }, + { + "author_name": "Carole Helene Sudre", + "author_inst": "King's College London" + }, + { + "author_name": "Joan Capdevila Pujol", + "author_inst": "Zoe Limited, London, UK" + }, + { + "author_name": "Lorenzo Polidori", + "author_inst": "Zoe Limited, London, UK" + }, + { + "author_name": "Anna May", + "author_inst": "Zoe Limited, London, UK" + }, + { + "author_name": "Alexander Hammers", + "author_inst": "King's College London" + }, + { + "author_name": "Jonathan Wolf", + "author_inst": "Zoe Limited, London, UK" + }, + { + "author_name": "Timothy Spector", + "author_inst": "King's College London" + }, + { + "author_name": "Claire J Steves", + "author_inst": "King's College London" + }, + { + "author_name": "Sebastien Ourselin", + "author_inst": "King's College London" + }, + { + "author_name": "Michael Absoud", + "author_inst": "King's College London" + }, + { + "author_name": "Marc Modat", + "author_inst": "King's College London" + }, + { + "author_name": "Emma L Duncan", + "author_inst": "King's College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.03.12.22272300", "rel_title": "Did COVID-19 Vaccines Go to the Whitest Neighborhoods First? Racial Inequities in Six Million Phase 1 Doses Shipped to Pennsylvania", @@ -385955,85 +387606,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.10.22272197", - "rel_title": "Blood group O and post-COVID-19 syndrome", - "rel_date": "2022-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.10.22272197", - "rel_abs": "ObjectiveThe ABO blood group system modulates the inflammatory response and has been involved in COVID-19. O-group protects against SARS-CoV-2 infection, but there are no data regarding post-COVID-19 syndrome (PCS). Our aim was to assess this possible association.\n\nSubjects and methodsCase-control study in a community setting, with subjects who had experienced mild COVID-19. Cases were PCS+, controls were PCS-, and the exposure variable, O-group. Epidemiological data (age, sex, BMI, smoking, comorbidities), laboratory parameters (inflammatory markers, IgG antibodies, blood type) and clinical data were collected. Composite inflammatory indices were developed. Multivariate analyses were performed.\n\nResultsWe analyzed 121 subjects (56.2% women), mean age 45.7 {+/-} 16 years. Blood group frequencies were 43.3%, 7.7%, 5.7%, and 43.3% for A, B, AB and O, respectively. Thirty-six patients were PCS+. There were no significant differences between cases and controls. Compared to non-O, a higher prevalence of PCS (p=0.036), number of symptoms (p=0.017) and myalgia (p=0.030) were noted in O-group. Concerning inflammatory markers, PCS+ and PCS-showed no differences in A, B, and AB groups. In contrast, O-group PCS+ patients had significantly higher lymphocyte count, higher levels of fibrinogen and CRP, and higher percentages of 3 composite indices, than PCS-subjects. The O-group showed a 4-fold increased risk of PCS compared to non-O (adjusted OR=4.20 [95%CI, 1.2-14]; p=0.023).\n\nConclusionAn increased risk of PCS has shown to be associated with O-group, after controlling for confounders. In O-group subjects with PCS, slightly albeit significant, raised levels of fibrinogen, CRP, and lymphocyte count, have been demonstrated.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Sara Diaz-Salazar", - "author_inst": "Camargo-Interior Primary Health Care Center. Servicio Cantabro de Salud. Camargo. Cantabria. Spain." - }, - { - "author_name": "Raquel Navas", - "author_inst": "Camargo-Costa Primary Health Care Center. Servicio Cantabro de Salud. Camargo. Cantabria. Spain." - }, - { - "author_name": "Laura Sainz-Maza", - "author_inst": "Camargo-Costa Primary Health Care Center. Servicio Cantabro de Salud. Camargo. Cantabria. Spain." - }, - { - "author_name": "Patricia Fierro", - "author_inst": "Camargo-Interior Primary Health Care Center. Servicio Cantabro de Salud. Camargo. Cantabria. Spain." - }, - { - "author_name": "Meryam Maamar", - "author_inst": "Emergency Service. Osakidetza, Servicio Vasco de Salud. Bilbao. Pais Vasco. Spain." - }, - { - "author_name": "Arancha Artime", - "author_inst": "El Llano - Primary Health Care Center. SESPA, Servicio de Salud del Principado de Asturias. Gijon. Asturias. Spain." - }, - { - "author_name": "Hector Basterrechea", - "author_inst": "Camargo-Interior Primary Health Care Center. Servicio Cantabro de Salud. Camargo. Cantabria. Spain." - }, - { - "author_name": "Benedetta Petitta", - "author_inst": "Camargo-Interior Primary Health Care Center. Servicio Cantabro de Salud. Camargo Cantabria. Spain." - }, - { - "author_name": "Carlota Lamadrid", - "author_inst": "Camargo-Interior Primary Health Care Center. Servicio Cantabro de Salud. Camargo. Cantabria. Spain." - }, - { - "author_name": "Lucia Pedraja", - "author_inst": "Camargo-Interior Primary Health Care Center. Servicio Cantabro de Salud. Camargo. Cantabria. Spain." - }, - { - "author_name": "Claudia Gandara-Samperio", - "author_inst": "Camargo-Interior Primary Health Care Center. Servicio Cantabro de Salud. Camargo. Cantabria. Spain." - }, - { - "author_name": "Stefanie Pini", - "author_inst": "Hospital-at-Home Service. Hospital Universitario Marques de Valdecilla. Santander. Cantabria. Spain." - }, - { - "author_name": "Jose M. Olmos", - "author_inst": "Servicio de Medicina Interna. Hospital Universitario Marques de Valdecilla. Instituto de Investigacion Valdecilla (IDIVAL). Depto de Medicina y Psiquiatria. Uni" - }, - { - "author_name": "Carmen Ramos-Barron", - "author_inst": "Camargo-Costa Primary Health Care Center. Servicio Cantabro de Salud. Depto de Medicina y Psiquiatria. Universidad de Cantabria. Santander. Cantabria. Spain." - }, - { - "author_name": "Emilio Pariente", - "author_inst": "Camargo-Interior Primary Health Care Center. Servicio Cantabro de Salud. Depto de Medicina y Psiquiatria. Universidad de Cantabria. Santander. Cantabria. Spain." - }, - { - "author_name": "Jose L Hernandez", - "author_inst": "Servicio de Medicina Interna. Hospital Universitario Marques de Valdecilla. Instituto de Investigacion Valdecilla (IDIVAL). Depto de Medicina y Psiquiatria. Uni" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.09.22272066", "rel_title": "Seroneutralization of Omicron BA.1 and BA.2 in patients receiving anti-SARS-CoV-2 monoclonal antibodies.", @@ -387641,6 +389213,173 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.03.07.22272026", + "rel_title": "Trends, regional variation and clinical characteristics of recipients of antivirals and neutralising monoclonal antibodies for non-hospitalised COVID-19: a descriptive cohort study of 23.4 million people in OpenSAFELY", + "rel_date": "2022-03-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.07.22272026", + "rel_abs": "ObjectivesAscertain patient eligibility status and describe coverage of antivirals and neutralising monoclonal antibodies (nMAB) as treatment for COVID-19 in community settings in England.\n\nDesignCohort study, approved by NHS England.\n\nSettingRoutine clinical data from 23.4m people linked to data on COVID-19 infection and treatment, within the OpenSAFELY-TPP database.\n\nParticipantsNon-hospitalised COVID-19 patients at high-risk of severe outcomes.\n\nInterventionsNirmatrelvir/ritonavir (Paxlovid), sotrovimab, molnupiravir, casirivimab or remdesivir, administered in the community by COVID-19 Medicine Delivery Units.\n\nResultsWe identified 102,170 non-hospitalised patients with COVID-19 between 11th December 2021 and 28th April 2022 at high-risk of severe outcomes and therefore potentially eligible for antiviral and/or nMAB treatment. Of these patients, 18,210 (18%) received treatment; sotrovimab, 9,340 (51%); molnupiravir, 4,500 (25%); Paxlovid, 4,290 (24%); casirivimab, 50 (<1%); and remdesivir, 20 (<1%). The proportion of patients treated increased from 8% (180/2,380) in the first week of treatment availability to 22% (420/1870) in the latest week. The proportion treated varied by high risk group, lowest in those with Liver disease (12%; 95% CI 11 to 13); by treatment type, with sotrovimab favoured over molnupiravir/Paxlovid in all but three high risk groups: Down syndrome (36%; 95% CI 31 to 40), Rare neurological conditions (46%; 95% CI 44 to 48), and Primary immune deficiencies (49%; 95% CI 48 to 51); by ethnicity, from Black (10%; 95% CI 9 to 11) to White (18%; 95% CI 18 to 19); by NHS Region, from 11% (95% CI 10 to 12) in Yorkshire and the Humber to 23% (95% CI 22 to 24) in the East of England); and by deprivation level, from 12% (95% CI 12 to 13) in the most deprived areas to 21% (95% CI 21 to 22) in the least deprived areas. There was also lower coverage among unvaccinated patients (5%; 95% CI 4 to 7), those with dementia (5%; 95% CI 4 to 6) and care home residents (6%; 95% CI 5 to 6).\n\nConclusionsUsing the OpenSAFELY platform we were able to identify patients who were potentially eligible to receive treatment and assess the coverage of these new treatments amongst these patients. Targeted activity may be needed to address apparent lower treatment coverage observed among certain groups, in particular (at present): different NHS regions, socioeconomically deprived areas, and care homes.\n\nWhat is already known about this topicSince the emergence of COVID-19, a number of approaches to treatment have been tried and evaluated. These have mainly consisted of treatments such as dexamethasone, which were used in UK hospitals,from early on in the pandemic to prevent progression to severe disease. Until recently (December 2021), no treatments have been widely used in community settings across England.\n\nWhat this study addsFollowing the rollout of antiviral medicines and neutralising monoclonal antibodies (nMABs) as treatment for patients with COVID-19, we were able to identify patients who were potentially eligible to receive antivirals or nMABs and assess the coverage of these new treatments amongst these patients, in as close to real-time as the available data flows would support. While the proportion of the potentially eligible patients receiving treatment increased over time, rising from 8% (180/2,380) in the first week of the roll out to 22% (420/1870) in the last week of April 2022, there were variations in coverage between key clinical, geographic, and demographic subgroup.\n\nHow this study might affect research, practice, or policyTargeted activity may therefore be needed to address lower treatment rates observed among certain geographic areas and key groups including ethnic minorities, people living in areas of higher deprivation, and in care homes.", + "rel_num_authors": 38, + "rel_authors": [ + { + "author_name": "Amelia CA Green", + "author_inst": "University of Oxford" + }, + { + "author_name": "Helen J Curtis", + "author_inst": "University of Oxford" + }, + { + "author_name": "Rose Higgins", + "author_inst": "University of Oxford" + }, + { + "author_name": "Rebecca Smith", + "author_inst": "University of Oxford" + }, + { + "author_name": "Amir Mehrkar", + "author_inst": "University of Oxford" + }, + { + "author_name": "Peter Inglesby", + "author_inst": "University of Oxford" + }, + { + "author_name": "Viyaasan Mahalingasivam", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Henry Drysdale", + "author_inst": "University of Oxford" + }, + { + "author_name": "Nicholas DeVito", + "author_inst": "University of Oxford" + }, + { + "author_name": "Richard Croker", + "author_inst": "University of Oxford" + }, + { + "author_name": "Christopher T Rentsch", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Krishnan Bhaskaran", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Colm D Andrews", + "author_inst": "University of Oxford" + }, + { + "author_name": "Sebastian CJ Bacon", + "author_inst": "University of Oxford" + }, + { + "author_name": "Simon Davy", + "author_inst": "University of Oxford" + }, + { + "author_name": "Iain Dillingham", + "author_inst": "University of Oxford" + }, + { + "author_name": "David Evans", + "author_inst": "University of Oxford" + }, + { + "author_name": "Louis Fisher", + "author_inst": "University of Oxford" + }, + { + "author_name": "George Hickman", + "author_inst": "University of Oxford" + }, + { + "author_name": "Lisa E M Hopcroft", + "author_inst": "University of Oxford" + }, + { + "author_name": "William J Hulme", + "author_inst": "University of Oxford" + }, + { + "author_name": "Jon Massey", + "author_inst": "University of Oxford" + }, + { + "author_name": "Jessica Morley", + "author_inst": "University of Oxford" + }, + { + "author_name": "Caroline E Morton", + "author_inst": "University of Oxford" + }, + { + "author_name": "Robin Y Park", + "author_inst": "University of Oxford" + }, + { + "author_name": "Alex J Walker", + "author_inst": "University of Oxford" + }, + { + "author_name": "Tom Ward", + "author_inst": "University of Oxford" + }, + { + "author_name": "Milan Wiedemann", + "author_inst": "University of Oxford" + }, + { + "author_name": "Christopher Bates", + "author_inst": "TPP" + }, + { + "author_name": "Jonathan Cockburn", + "author_inst": "TPP" + }, + { + "author_name": "John Parry", + "author_inst": "TPP" + }, + { + "author_name": "Frank Hester", + "author_inst": "TPP" + }, + { + "author_name": "Sam Harper", + "author_inst": "TPP" + }, + { + "author_name": "Ian J Douglas", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Stephen JW Evans", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Laurie Tomlinson", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Brian MacKenna", + "author_inst": "University of Oxford" + }, + { + "author_name": "Ben Goldacre", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "primary care research" + }, { "rel_doi": "10.1101/2022.03.07.22272028", "rel_title": "Short-term drop in antibody titer after the third dose of SARS-CoV-2 BNT162b2 vaccine in adults", @@ -388073,37 +389812,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2022.03.10.483652", - "rel_title": "Open modification searching of SARS-CoV-2-human protein interaction data reveals novel viral modification sites", - "rel_date": "2022-03-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.10.483652", - "rel_abs": "The outbreak of the SARS-CoV-2 coronavirus, the causative agent of the COVID-19 disease, has led to an ongoing global pandemic since 2019. Mass spectrometry can be used to understand the molecular mechanisms of viral infection by SARS-CoV-2, for example, by determining virus-host protein-protein interactions (PPIs) through which SARS-CoV-2 hijacks its human hosts during infection, and to study the role of post-translational modifications (PTMs). We have reanalyzed public affinity purification mass spectrometry data using open modification searching to investigate the presence of PTMs in the context of the SARS-CoV-2 virus-host PPI network. Based on an over two-fold increase in identified spectra, our detected protein interactions show a high overlap with independent mass spectrometry-based SARS-CoV-2 studies and virus-host interactions for alternative viruses, as well as previously unknown protein interactions. Additionally, we identified several novel modification sites on SARS-CoV-2 proteins that we investigated in relation to their interactions with host proteins. A detailed analysis of relevant modifications, including phosphorylation, ubiquitination, and S-nitrosylation, provides important hypotheses about the functional role of these modifications during viral infection by SARS-CoV-2.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Charlotte Adams", - "author_inst": "University of Antwerp, Antwerp, Belgium" - }, - { - "author_name": "Kurt Boonen", - "author_inst": "Flemish Institute for Technological Research (VITO), Mol, Belgium" - }, - { - "author_name": "Kris Laukens", - "author_inst": "University of Antwerp, Antwerp, Belgium" - }, - { - "author_name": "Wout Bittremieux", - "author_inst": "University of California San Diego, La Jolla, CA, USA" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2022.03.08.22271980", "rel_title": "Self-injury, suicidal ideation and -attempt and eating disorders in young people following the initial and second COVID-19 lockdown", @@ -389683,6 +391391,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2022.03.07.22271699", + "rel_title": "Severity of maternal SARS-CoV-2 infection and perinatal outcomes during the Omicron variant dominant period: UK Obstetric Surveillance System national cohort study.", + "rel_date": "2022-03-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.07.22271699", + "rel_abs": "ObjectivesTo describe the severity of maternal infection when the Omicron SARS-CoV-2 variant was dominant (15/12/21-14/01/22) and compare outcomes among groups with different vaccination status.\n\nDesignProspective cohort study\n\nSettingUK consultant-led maternity units\n\nParticipantsPregnant women hospitalised with a positive SARS-CoV-2 PCR test up to 7 days prior to admission and/or during admission up to 2 days after giving birth.\n\nMain outcome measuresSymptomatic or asymptomatic infection. Vaccination status. Severity of maternal infection (moderate or severe infection according to modified WHO criteria). Mode of birth and perinatal outcomes.\n\nResultsOut of 1561 women admitted to hospital with SARS-CoV-2 infection, 449 (28.8%) were symptomatic. Among symptomatic women admitted, 86 (19.2%) had moderate to severe infection; 51 (11.4%) had pneumonia on imaging, 62 (14.3%) received respiratory support, and 19 (4.2%) were admitted to the intensive care unit (ICU). Three women died (0.7%). Vaccination status was known for 383 symptomatic women (85.3%) women; 249 (65.0%) were unvaccinated, 45 (11.7%) had received one vaccine dose, 76 (19.8%) had received two doses and 13 (3.4%) had received three doses. 59/249 (23.7%) unvaccinated women had moderate to severe infection, compared to 10/45 (22.2%) who had one dose, 9/76 (11.8%) who had two doses and 0/13 (0%) who had three doses. Among the 19 symptomatic women admitted to ICU, 14 (73.7%) were unvaccinated, 3 (15.8%) had received one dose, 1 (5.3%) had received two doses, 0 (0%) had received 3 doses and 1 (5.3%) had unknown vaccination status.\n\nConclusionThe risk of severe respiratory disease amongst unvaccinated pregnant women admitted with symptomatic SARS-CoV-2 infection during the Omicron dominance period was comparable to that observed during the period the wildtype variant was dominant. Most women with severe disease were unvaccinated. Vaccine coverage among pregnant women admitted with SARS-CoV-2 was low compared to the overall pregnancy population and very low compared to the general population. Ongoing action to prioritise and advocate for vaccine uptake in pregnancy is essential.\n\nO_TEXTBOXSUMMARY BOX\n\nWhat is already known on this topic\n\nO_LIIn non-pregnant adults, growing evidence indicates a lower risk of severe respiratory disease with the Omicron SARS-CoV-2 Variant of Concern (VOC).\nC_LIO_LIPregnant women admitted during the periods in which the Alpha and Delta VOC were dominant were at increased risk of moderate to severe SARS-CoV-2 infection compared to the period when the original wildtype infection was dominant.\nC_LIO_LIMost women admitted to hospital with symptomatic SARS-CoV-2 infection have been unvaccinated.\nC_LI\n\nWhat this study adds\n\nO_LIOne in four women who had received no vaccine or a single dose had moderate to severe infection, compared with one in eight women who had received two doses and no women who had received three doses\nC_LIO_LIThe proportional rate of moderate to severe infection in unvaccinated pregnant women during the Omicron dominance period is similar to the rate observed during the wildtype dominance period\nC_LIO_LIOne in eight symptomatic admitted pregnant women needed respiratory support during the period when Omicron was dominant\nC_LI\n\nC_TEXTBOX", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Hilde Marie Engjom", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Rema Ramakrishnan", + "author_inst": "National Perinatal Epidemiology Unit, Nuffield Department of Population Health, University of Oxford" + }, + { + "author_name": "Nicola Vousden", + "author_inst": "National Perinatal Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, UK, OX3 7LF" + }, + { + "author_name": "Kathryn Bunch", + "author_inst": "National Perinatal Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, UK, OX3 7LF" + }, + { + "author_name": "Edvard P Morris", + "author_inst": "Royal College of Obstetricians and Gynaecologists, London, UK, SE1 1SZ" + }, + { + "author_name": "Nigel Simpson", + "author_inst": "Department of Women's and Children's Health, School of Medicine, University of Leeds, UK, LS2 9JT" + }, + { + "author_name": "Christopher Gale", + "author_inst": "Imperial College London" + }, + { + "author_name": "Pat OBrien", + "author_inst": "Institute for Womens Health, University College London, London, UK" + }, + { + "author_name": "Maria Quigley", + "author_inst": "National Perinatal Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, UK, OX3 7LF" + }, + { + "author_name": "Peter Brocklehurst", + "author_inst": "Birmingham Clinical Trials Unit, Institute of Applied Health Research, University of Birmingham, UK" + }, + { + "author_name": "Jennifer J Kurinczuk", + "author_inst": "National Perinatal Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, UK, OX3 7LF" + }, + { + "author_name": "Marian Knight", + "author_inst": "National Perinatal Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, UK, OX3 7LF" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.03.07.22272051", "rel_title": "Impact of long-term COVID on workers: a systematic review protocol", @@ -390215,25 +391986,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.03.01.22271721", - "rel_title": "The relative impact of vaccination momentum on COVID-19 rates of death in the USA in 2020/2021. The forgotten role of population wellness.", - "rel_date": "2022-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.01.22271721", - "rel_abs": "It is widely accepted that individual underlying health conditions contribute to morbidity and mortality associated with COVID-19; and by inference population wellness will also contribute to COVID-19 outcomes. In addition, over the last two years the predominant pharmaceutical public health response to COVID-19 has been vaccination momentum (i.e. mass and rapid inoculation campaigns).\n\nThis paper aims to compare vaccination momentum throughout 2021 and measures of population wellness to estimate the relative impact of each on deaths attributed to COVID-19 across the 50 States of America, plus Washington DC, during 2020 (i.e. the pre-vaccination period) and 2021 (i.e. the vaccination period).\n\nOur analysis shows that: (a) COVID-19 rates of death in 2020 are more important, and statistically more significant, at predicting rates of death in 2021 than vaccination momentum during 2021; (b) vaccination momentum does not predict the magnitude of change in COVID-19 rates of death between 2020 and 2021; and (c) for several underlying heath and risk factors vaccination momentum is significantly less important than population wellness at predicting COVID-19 rates of death.\n\nOf particular interest are our observations that exercise and fruit consumption are 10.1 times more significant at predicting COVID-19 deaths than vaccination momentum, obesity (BMI 30+) is 9.6 times more significant at predicting COVID-19 deaths than vaccination momentum, heart attacks are 4.37 times more significant at predicting COVID-19 deaths than vaccination momentum and smoking is 3.2 times more significant at predicting COVID-19 deaths than vaccination momentum.\n\nIf medical and health regulators are to deliver a quantum decrease in COVID-19 deaths they must move beyond the overwhelming focus on COVID-19 vaccination. They must have the courage to urge governments and private organisations to mandate greater exercise, weight loss, less junk food, and better nutrition. And a concerted effort at reducing chronic adverse health conditions.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Victor Keddis", - "author_inst": "University of Melbourne" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.02.23.22271045", "rel_title": "High frequency and persistence of Anti-DSG2 antibodies in post COVID-19 serum samples", @@ -391829,6 +393581,29 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.03.07.483258", + "rel_title": "Intragenomic rearrangements of SARS-CoV-2 and other \u03b2-coronaviruses", + "rel_date": "2022-03-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.07.483258", + "rel_abs": "Variation of the betacoronavirus SARS-CoV-2 has been the bane of COVID-19 control. Documented variation includes point mutations, deletions, insertions, and recombination among closely or distantly related coronaviruses. Here, we describe yet another aspect of genome variation by beta- and alphacoronaviruses. Specifically, we report numerous genomic insertions of 5-untranslated region sequences into coding regions of SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses. To our knowledge this is the first systematic description of such insertions. In many cases, these insertions change viral protein sequences and further foster genomic flexibility and viral adaptability through insertion of transcription regulatory sequences in novel positions within the genome. Among human Embecorivus betacoronaviruses, for instance, from 65% to all of the surveyed sequences in publicly available databases contain 5-UTR-derived inserted sequences. In limited instances, there is mounting evidence that these insertions alter the fundamental biological properties of mutant viruses. Intragenomic rearrangements add to our appreciation of how variants of SARS-CoV-2 and other beta- and alphacoronaviruses may arise.\n\nSignificanceUnderstanding mechanisms of variation in coronaviruses is vital to control of their associated diseases. Beyond point mutations, insertions, deletions and recombination, we here describe for the first time intragenomic rearrangements and their relevance to changes in transmissibility, immune escape and/or virulence documented during the SARS-CoV-2 pandemic.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Roberto Patarca", + "author_inst": "ACCESS Health International" + }, + { + "author_name": "William A Haseltine", + "author_inst": "ACCES Health International" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2022.03.05.483145", "rel_title": "Predicted binding interface between coronavirus nsp3 and nsp4", @@ -392201,73 +393976,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.04.22271540", - "rel_title": "The mutational steps of SARS-CoV-2 to become like Omicron within seven months: the story of immune escape in an immunocompromised patient.", - "rel_date": "2022-03-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.04.22271540", - "rel_abs": "We studied a unique case of prolonged viral shedding in an immunocompromised patient that generated a series of SARS-CoV-2 immune escape mutations over a period of seven months. During the persisting SARS-CoV-2 infection seventeen non-synonymous mutations were observed, thirteen (13/17; 76.5%) of which occurred in the genomic region coding for spike. Fifteen (15/17; 88.2%) of these mutations have already been described in the context of variants of concern and include the prominent immune escape mutations S:E484K, S:D950N, S:P681H, S:N501Y, S:del(9), N:S235F and S:H655Y. Fifty percent of all mutations acquired by the investigated strain (11/22) are found in similar form in the Omicron variant of concern. The study shows the chronology of the evolution of intra-host mutations, which can be seen as the straight mutational response of the virus to specific antibodies and should therefore be given special attention in the rating of immune escape mutations of SARS-CoV-2.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Sissy Therese Sonnleitner", - "author_inst": "Medical University Innsbruck" - }, - { - "author_name": "Martina Prelog", - "author_inst": "University Hospital Wuerzburg" - }, - { - "author_name": "Stefanie Sonnleitner", - "author_inst": "Dr. Gernot Walder GmbH" - }, - { - "author_name": "Eva Hinterbichler", - "author_inst": "Dr. Gernot Walder GmbH" - }, - { - "author_name": "Hannah Halbfurter", - "author_inst": "Dr. Gernot Walder GmbH" - }, - { - "author_name": "Dominik Kopecky", - "author_inst": "Dr. Gernot Walder GmbH" - }, - { - "author_name": "Giovanni Almanzar", - "author_inst": "University Hospital Wuerzburg" - }, - { - "author_name": "Stephan Koblmueller", - "author_inst": "University of Graz" - }, - { - "author_name": "Christian Sturmbauer", - "author_inst": "University of Graz" - }, - { - "author_name": "Leonard Feist", - "author_inst": "GenXPro GmbH, Frankfurt" - }, - { - "author_name": "Ralf Horres", - "author_inst": "GenXPro GmbH, Frankfurt" - }, - { - "author_name": "Wilfried Posch", - "author_inst": "Medical University Innsbruck" - }, - { - "author_name": "Gernot Walder", - "author_inst": "Dr. Gernot Walder GmbH" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.03.04.22271917", "rel_title": "Social capital, urbanization level, and COVID-19 vaccination uptake in the United States: A national level analysis", @@ -393207,6 +394915,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.03.02.22271106", + "rel_title": "Proteome reveals antiviral host response and NETosis during acute COVID-19 in high-risk patients", + "rel_date": "2022-03-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.02.22271106", + "rel_abs": "SARS-CoV-2 remains an acute threat to human health, endangering hospital capacities worldwide. Many studies have aimed at informing pathophysiologic understanding and identification of disease indicators for risk assessment, monitoring, and therapeutic guidance. While findings start to emerge in the general population, observations in high-risk patients with complex pre-existing conditions are limited.\n\nTo this end, we biomedically characterized quantitative proteomics in a hospitalized cohort of COVID-19 patients with mild to severe symptoms suffering from different (co)-morbidities in comparison to both healthy individuals and patients with non-COVID related inflammation. Deep clinical phenotyping enabled the identification of individual disease trajectories in COVID-19 patients. By the use of this specific disease phase assignment, proteome analysis revealed a severity dependent general type-2 centered host response side-by-side with a disease specific antiviral immune reaction in early disease. The identification of phenomena such as neutrophil extracellular trap (NET) formation and a pro-coagulatory response together with the regulation of proteins related to SARS-CoV-2-specific symptoms by unbiased proteome screening both confirms results from targeted approaches and provides novel information for biomarker and therapy development.\n\nGraphical AbstractSars-CoV-2 remains a challenging threat to our health care system with many pathophysiological mechanisms not fully understood, especially in high-risk patients. Therefore, we characterized a cohort of hospitalized COVID-19 patients with multiple comorbidities by quantitative plasma proteomics and deep clinical phenotyping. The individual patients disease progression was determined and the subsequently assigned proteome profiles compared with a healthy and a chronically inflamed control cohort. The identified disease phase and severity specific protein profiles revealed an antiviral immune response together with coagulation activation indicating the formation of NETosis side-by-side with tissue remodeling related to the inflammatory signature.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=197 HEIGHT=200 SRC=\"FIGDIR/small/22271106v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (50K):\norg.highwire.dtl.DTLVardef@1e791faorg.highwire.dtl.DTLVardef@20d3d6org.highwire.dtl.DTLVardef@1339e42org.highwire.dtl.DTLVardef@1db3710_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Alina Bauer", + "author_inst": "Helmholtz Zentrum Muenchen, Computational Health Department, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany" + }, + { + "author_name": "Elisabeth Pachl", + "author_inst": "Helmholtz Zentrum Muenchen, Computational Health Department, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany; Fraunhofer IKS, Fraunho" + }, + { + "author_name": "Johannes C. Hellmuth", + "author_inst": "Department of Medicine III, University Hospital, LMU Munich, Munich, Germany" + }, + { + "author_name": "Nikolaus Kneidinger", + "author_inst": "Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Muenchen, Member of the DZL, Munich, Germ" + }, + { + "author_name": "Marion Frankenberger", + "author_inst": "Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Muenchen, Member of the German Center for" + }, + { + "author_name": "Hans C. Stubbe", + "author_inst": "Department of Medicine II, University Hospital, LMU Munich, Munich, Germany; Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the " + }, + { + "author_name": "Bernhard Ryffel", + "author_inst": "Laboratory of Experimental and Molecular Immunology and Neurogenetics (INEM), UMR 7355 CNRS-University of Orleans and Artimmune, Orleans, France" + }, + { + "author_name": "Agnese Petrera", + "author_inst": "Metabolomics and Proteomics Core, Helmholtz Zentrum Muenchen, Munich, Germany" + }, + { + "author_name": "Stefanie M. Hauck", + "author_inst": "Metabolomics and Proteomics Core, Helmholtz Zentrum Muenchen, Munich, Germany" + }, + { + "author_name": "J\u00fcrgen Behr", + "author_inst": "Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Zentrum Muenchen, Germany" + }, + { + "author_name": "Rainer Kaiser", + "author_inst": "Medizinische Klinik und Poliklinik I, University Hospital, LMU Munich, Munich, Germany, DZHK (German Center for Cardiovascular Research), Partner Site Munich He" + }, + { + "author_name": "Clemens Scherer", + "author_inst": "Medizinische Klinik und Poliklinik I, University Hospital, LMU Munich, Munich, Germany, DZHK (German Center for Cardiovascular Research), Partner Site Munich He" + }, + { + "author_name": "Li Deng", + "author_inst": "Helmholtz Zentrum Muenchen, Computational Health Department, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany; Institute of Virology, " + }, + { + "author_name": "Daniel Teupser", + "author_inst": "Institute of Laboratory Medicine, University Hospital, LMU Munich, Munich, Germany" + }, + { + "author_name": "Narges Ahmidi", + "author_inst": "Fraunhofer IKS, Fraunhofer Institute for Cognitive Systems IKS, 80686 Munich, Germany" + }, + { + "author_name": "Maximilian Muenchhoff", + "author_inst": "Max von Pettenkofer Institute and Gene Center, Virology, National Reference Center for Retroviruses, LMU Muenchen, Munich, Germany; German Center for Infection " + }, + { + "author_name": "Benjamin Schubert", + "author_inst": "Helmholtz Zentrum Muenchen, Computational Health Department, Member of the German Center for Lung Research (DZL), 85764 Munich, Germany; Department of Mathemati" + }, + { + "author_name": "Anne Hilgendorff", + "author_inst": "Institute of Lung Biology and Disease and Comprehensive Pneumology Center with the CPC-M bioArchive, Helmholtz Ze; Center for Comprehensive Developmental Care (" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2022.03.03.22271860", "rel_title": "Sero-surveillance for IgG to SARS-CoV-2 at antenatal care clinics in three Kenyan referral hospitals: repeated cross-sectional surveys 2020-21", @@ -393867,57 +395662,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.03.03.22271836", - "rel_title": "The relationship between BMI and COVID-19: exploring misclassification and selection bias in a two-sample Mendelian randomisation study", - "rel_date": "2022-03-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.03.22271836", - "rel_abs": "ObjectiveTo use the example of the effect of body mass index (BMI) on COVID-19 susceptibility and severity to illustrate methods to explore potential selection and misclassification bias in Mendelian randomisation (MR) of COVID-19 determinants.\n\nDesignTwo-sample MR analysis.\n\nSettingSummary statistics from the Genetic Investigation of ANthropometric Traits (GIANT) and COVID-19 Host Genetics Initiative (HGI) consortia.\n\nParticipants681,275 participants in GIANT and more than 2.5 million people from the COVID-19 HGI consortia.\n\nExposureGenetically instrumented BMI.\n\nMain outcome measuresSeven case/control definitions for SARS-CoV-2 infection and COVID-19 severity: very severe respiratory confirmed COVID-19 vs not hospitalised COVID-19 (A1) and vs population (those who were never tested, tested negative or had unknown testing status (A2)); hospitalised COVID-19 vs not hospitalised COVID-19 (B1) and vs population (B2); COVID-19 vs lab/self-reported negative (C1) and vs population (C2); and predicted COVID-19 from self-reported symptoms vs predicted or self-reported non-COVID-19 (D1).\n\nResultsWith the exception of A1 comparison, genetically higher BMI was associated with higher odds of COVID-19 in all comparison groups, with odds ratios (OR) ranging from 1.11 (95%CI: 0.94, 1.32) for D1 to 1.57 (95%CI: 1.57 (1.39, 1.78) for A2. As a method to assess selection bias, we found no strong evidence of an effect of COVID-19 on BMI in a no-relevance analysis, in which COVID-19 was considered the exposure, although measured after BMI. We found evidence of genetic correlation between COVID-19 outcomes and potential predictors of selection determined a priori (smoking, education, and income), which could either indicate selection bias or a causal pathway to infection. Results from multivariable MR adjusting for these predictors of selection yielded similar results to the main analysis, suggesting the latter.\n\nConclusionsWe have proposed a set of analyses for exploring potential selection and misclassification bias in MR studies of risk factors for SARS-CoV-2 infection and COVID-19 and demonstrated this with an illustrative example. Although selection by socioeconomic position and arelated traits is present, MR results are not substantially affected by selection/misclassification bias in our example. We recommend the methods we demonstrate, and provide detailed analytic code for their use, are used in MR studies assessing risk factors for COVID-19, and other MR studies where such biases are likely in the available data.\n\nSummaryO_ST_ABSWhat is already known on this topicC_ST_ABS- Mendelian randomisation (MR) studies have been conducted to investigate the potential causal relationship between body mass index (BMI) and COVID-19 susceptibility and severity.\n- There are several sources of selection (e.g. when only subgroups with specific characteristics are tested or respond to study questionnaires) and misclassification (e.g. those not tested are assumed not to have COVID-19) that could bias MR studies of risk factors for COVID-19.\n- Previous MR studies have not explored how selection and misclassification bias in the underlying genome-wide association studies could bias MR results.\n\n\nWhat this study adds- Using the most recent release of the COVID-19 Host Genetics Initiative data (with data up to June 2021), we demonstrate a potential causal effect of BMI on susceptibility to detected SARS-CoV-2 infection and on severe COVID-19 disease, and that these results are unlikely to be substantially biased due to selection and misclassification.\n- This conclusion is based on no evidence of an effect of COVID-19 on BMI (a no-relevance control study, as BMI was measured before the COVID-19 pandemic) and finding genetic correlation between predictors of selection (e.g. socioeconomic position) and COVID-19 for which multivariable MR supported a role in causing susceptibility to infection.\n- We recommend studies use the set of analyses demonstrated here in future MR studies of COVID-19 risk factors, or other examples where selection bias is likely.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Gemma Louise Clayton", - "author_inst": "University of Bristol" - }, - { - "author_name": "Ana Goncalves Soares", - "author_inst": "University of Bristol" - }, - { - "author_name": "Neil Goulding", - "author_inst": "University of Bristol" - }, - { - "author_name": "Maria Carolina Goncalves Borges", - "author_inst": "University of Bristol" - }, - { - "author_name": "Michael Holmes", - "author_inst": "University of Oxford" - }, - { - "author_name": "George Davey Smith", - "author_inst": "University of Bristol" - }, - { - "author_name": "Kate Tilling", - "author_inst": "University of Bristol" - }, - { - "author_name": "Deborah A Lawlor", - "author_inst": "University of Bristol" - }, - { - "author_name": "Alice R Carter", - "author_inst": "Medical Research Council Integrative Epidemiology Unit, University of Bristol" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.03.01.482592", "rel_title": "Determining the optimal SARS-CoV-2 mRNA vaccine dosing interval for maximum immunogenicity", @@ -394993,6 +396737,41 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2022.03.03.22271835", + "rel_title": "Acute and long-term impacts of COVID-19 on economic vulnerability: a population-based longitudinal study (COVIDENCE UK)", + "rel_date": "2022-03-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.03.22271835", + "rel_abs": "BackgroundSocio-economic deprivation is well recognised as a risk factor for developing COVID-19. However, the impact of COVID-19 on economic vulnerability has not previously been characterised.\n\nObjectiveTo determine whether COVID-19 has a significant impact on adequacy of household income to meet basic needs (primary outcome) and work absence due to sickness (secondary outcome), both at the onset of illness (acutely) and subsequently (long-term).\n\nDesignMultivariate mixed regression analysis of self-reported data from monthly on-line questionnaires, completed 1st May 2020 to 28th October 2021, adjusting for baseline characteristics including age, sex, socioeconomic status and self-rated health.\n\nSetting and ParticipantsParticipants (n=16,910) were UK residents aged 16 years or over participating in a national longitudinal study of COVID-19 (COVIDENCE UK).\n\nResultsIncident COVID-19 was independently associated with increased odds of participants reporting household income as being inadequate to meet their basic needs, both acutely (adjusted odds ratio [aOR) 1.39, 95% confidence interval [CI] 1.12 to 1.73) and in the long-term (aOR 1.15, 95% CI 1.00 to 1.33). Exploratory analysis revealed the long-term association to be restricted to those who reported long COVID, defined as the presence of symptoms lasting more than 4 weeks after the acute episode (aOR 1.39, 95% CI 1.10 to 1.77). Incident COVID-19 associated with increased odds of reporting sickness absence from work in the long-term (aOR 5.29, 95% CI 2.76 to 10.10) but not acutely (aOR 1.34, 95% CI 0.52 to 3.49).\n\nConclusionsWe demonstrate an independent association between COVID-19 and increased risk of economic vulnerability, both acutely and in the long-term. Taking these findings together with pre-existing research showing that socio-economic disadvantage increases the risk of developing COVID-19, this may generate a vicious cycle of impaired health and poor economic outcomes.\n\nTrial registrationNCT04330599\n\nSummary BoxO_ST_ABSWhat is already known on this topicC_ST_ABSO_LISocioeconomic deprivation is recognised as a major risk factor for incidence and severity of COVID-19 disease, mediated via factors including increased occupational and household exposure to SARS-CoV-2 and greater physical vulnerability due to comorbidities\nC_LIO_LIThe potential for COVID-19 to act as a cause, rather than a consequence, of economic vulnerability has not previously been characterised.\nC_LI\n\nWhat this study addsO_LIWe demonstrate an independent association between incident COVID-19 and subsequent self-report of household income being inadequate to meet basic needs, both acutely and in the long term\nC_LIO_LIIncident COVID-19 was also associated with increased odds of subsequent self-report of sickness absence from work in the long-term.\nC_LI", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Anne E Williamson", + "author_inst": "Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London" + }, + { + "author_name": "Florence Tydeman", + "author_inst": "Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London" + }, + { + "author_name": "Alec Miners", + "author_inst": "Department of Health Services Research and Policy, London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Kate Pyper", + "author_inst": "Department of Mathematics and Statistics, University of Strathclyde" + }, + { + "author_name": "Adrian R Martineau", + "author_inst": "Institute of Population Health Sciences, Barts and The London School of Medicine and Dentistry, Queen Mary University of London" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2022.03.02.22271759", "rel_title": "SARS-CoV-2 IgG seroprevalence in the Okinawa Main Island and remote islands in Okinawa, Japan, 2020-2021.", @@ -395773,33 +397552,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.02.17.22270791", - "rel_title": "Vaccine effectiveness and duration of protection against symptomatic and severe Covid-19 during the first year of vaccination in France", - "rel_date": "2022-03-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.17.22270791", - "rel_abs": "BackgroundSARS-CoV-2 continues to spread despite fast vaccine rollout, which could be attributed to waning immunity or to a reduced protection against some variants. A thorough characterization of vaccine protection and its duration in time is needed to inform vaccination policies and enhance public trust.\n\nMethodsWe matched three national databases with exhaustive information on screening, vaccination and hospitalizations in France over the year 2021. We performed a two-step analysis to estimate vaccine effectiveness against severe forms of Covid-19 in people aged 50 years or over, combining: (i) a test-negative case-control design to assess vaccine effectiveness against symptomatic infections; and (ii) a survival analysis to assess the additional protection against severe outcomes (hospitalizations and inpatient deaths) in infected individuals.\n\nResultsWe found a high vaccine effectiveness in people aged 50 years or more, reaching 82% against symptomatic infections and 94% against severe outcomes, after a full vaccination scheme.\n\nVaccine effectiveness against symptomatic infections strongly decreased over time, dropping to 53% after six months, but remained high against severe forms (90% after six months). The booster dose allowed restoring high protection levels. Vaccine protection and its evolution in time, showed little difference against the variants that circulated prior to December 2021 in France, including the Delta variant.\n\nConclusionThough vaccine immunity decreases over time, vaccination remains crucial to provide individual protection against severe diseases. This decline can be reversed by the injection of a booster dose.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Milena Suarez Castillo", - "author_inst": "Insee" - }, - { - "author_name": "Hamid Khaoua", - "author_inst": "Drees" - }, - { - "author_name": "No\u00e9mie Courtejoie", - "author_inst": "Drees" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.03.02.482745", "rel_title": "Amplification of Olfactory Signals by Anoctamin 9 is Essential for Mammalian Olfaction: a Risk Factor for the Covid-19-associated Anosmia", @@ -397219,6 +398971,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.03.01.482536", + "rel_title": "Discovery of compounds that inhibit SARS-CoV-2 Mac1-ADP-ribose binding by high-throughput screening", + "rel_date": "2022-03-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.03.01.482536", + "rel_abs": "The emergence of several zoonotic viruses in the last twenty years, especially the pandemic outbreak of SARS-CoV-2, has exposed a dearth of antiviral drug therapies for viruses with pandemic potential. Developing a diverse drug portfolio will be critical for our ability to rapidly respond to novel coronaviruses (CoVs) and other viruses with pandemic potential. Here we focus on the SARS-CoV-2 conserved macrodomain (Mac1), a small domain of non-structural protein 3 (nsp3). Mac1 is an ADP-ribosylhydrolase that cleaves mono-ADP-ribose (MAR) from target proteins, protects the virus from the anti-viral effects of host ADP-ribosyltransferases, and is critical for the replication and pathogenesis of CoVs. In this study, a luminescent-based high-throughput assay was used to screen [~]38,000 small molecules for those that could inhibit Mac1-ADP-ribose binding. We identified 5 compounds amongst 3 chemotypes that inhibit SARS-CoV-2 Mac1-ADP-ribose binding in multiple assays with IC50 values less than 100{micro}M, inhibit ADP-ribosylhydrolase activity, and have evidence of direct Mac1 binding. These chemotypes are strong candidates for further derivatization into highly effective Mac1 inhibitors.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Anu Roy", + "author_inst": "University of Kansas" + }, + { + "author_name": "Yousef M Alhammad", + "author_inst": "University of Kansas" + }, + { + "author_name": "Peter McDonald", + "author_inst": "University of Kansas" + }, + { + "author_name": "David K Johnson", + "author_inst": "University of Kansas" + }, + { + "author_name": "Junlin Zhuo", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Sarah Wazir", + "author_inst": "Oulu University" + }, + { + "author_name": "Dana V Ferraris", + "author_inst": "McDaniel College" + }, + { + "author_name": "Lari Lehti\u00f6", + "author_inst": "University of Oulu" + }, + { + "author_name": "Anthony Leung", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Anthony R Fehr", + "author_inst": "University of Kansas" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2022.03.02.480688", "rel_title": "Flipped Over U: Structural Basis for dsRNA Cleavage by the SARS-CoV-2 Endoribonuclease", @@ -397643,101 +399450,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.03.01.22271735", - "rel_title": "Comparison of the reactogenicity and immunogenicity of a reduced and standard booster dose of the mRNA COVID-19 vaccine in healthy adults after two doses of inactivated vaccine.", - "rel_date": "2022-03-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.03.01.22271735", - "rel_abs": "The coronavirus disease 2019 (COVID-19) pandemic has been a serious healthcare problem worldwide since December 2019. The third dose of heterologous vaccine was recently approved by World Health Organization. The present study compared the reactogenicity and immunogenicity of the reduced and standard third booster dose of the BNT162b2 and mRNA-1273 vaccine in adults who previously received the two-dose CoronaVac vaccine. Results showed that headache, joint pain, and diarrhea were more frequent in the 15 g-than the 30 g-BNT162b2 groups, whereas joint pain and chilling were more frequent in the 100 g-than the 50 g-mRNA-1273 groups. No significant differences in immunogenicity were detected. These findings demonstrate that the reduced dose of the mRNA vaccines elicited antibody responses against the SARS-CoV-2 delta and omicron variants that were comparable to the standard dose. The reduced dose could be used to increase vaccine coverage in situations of limited global vaccine supply.\n\nHighlightsO_LIThe 15 g- and 30 g-BNT162b2, and 50 g- and 100 g-mRNA-1273 booster doses were compared\nC_LIO_LIBooster vaccination with the mRNA vaccine elicits high Ig and IgG anti-RBD in CoronaVac-vaccinated adults\nC_LIO_LINo differences were observed in antibody responses after the reduced or standard booster dose of the mRNA vaccine in CoronaVac-vaccinated adults\nC_LIO_LINeutralizing antibodies against the delta and omicron variants were significantly higher after the booster dose\nC_LIO_LINeutralizing antibody titers were lower against the omicron variant than the delta variant in all vaccinated adults\nC_LI", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Sitthichai Kanokudom", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.;Osteoarthritis and Musculoskeleton Research U" - }, - { - "author_name": "Suvichada Assawakosri", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.;Osteoarthritis and Musculoskeleton Research U" - }, - { - "author_name": "Nungruthai suntronwong", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand." - }, - { - "author_name": "Jira Chansaenroj", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand." - }, - { - "author_name": "Chompoonut Auphimai", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand." - }, - { - "author_name": "Pornjarim Nilyanimit", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand." - }, - { - "author_name": "Preeyaporn Vichaiwattana", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand." - }, - { - "author_name": "Thanunrat Thongmee", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand." - }, - { - "author_name": "Ritthideach Yorsaeng", - "author_inst": "Faculty of Medicine, Chulalongkorn University" - }, - { - "author_name": "Thaneeya Duangchinda", - "author_inst": "Division of Dengue Hemorrhagic Fever Research, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.;Siriraj Center of Research Ex" - }, - { - "author_name": "Warangkana Chantima", - "author_inst": "Division of Dengue Hemorrhagic Fever Research; Siriraj Center of Research Excellence in Dengue and Emerging Pathogens, Faculty of Medicine, Siriraj Hospital, Ma" - }, - { - "author_name": "Pattarakul Pakchotanon", - "author_inst": "Molecular Biology of Dengue and Flaviviruses Research Team, National Center for Genetic Engineering and Biotechnology, National Science and Development Agency, " - }, - { - "author_name": "Donchida Srimuan", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand." - }, - { - "author_name": "Thaksaporn Thatsanatorn", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand." - }, - { - "author_name": "Sirapa Klinfueng", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand." - }, - { - "author_name": "Juthathip Mongkolsapaya", - "author_inst": "Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7BN, UK.; Chinese Academy of Medical Science (CAMS) Oxfor" - }, - { - "author_name": "Natthinee Sudhinaraset", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand" - }, - { - "author_name": "Nasamon Wanlapakorn", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand." - }, - { - "author_name": "Sittisak Honsawek", - "author_inst": "Department of Biochemistry, Osteoarthritis and Musculoskeleton Research Unit, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospita" - }, - { - "author_name": "Yong Poovorawan", - "author_inst": "Center of Excellence in Clinical Virology, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.;The Royal Society of Thailand (FRS(T)), Sanam" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2022.03.01.22271717", "rel_title": "Prevalence of Chronic Diseases, Depression, and Stress among U.S. Child Care Professionals during the COVID-19 Pandemic", @@ -399069,6 +400781,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.02.28.22271643", + "rel_title": "Myocarditis and Pericarditis following COVID-19 Vaccination: Evidence Syntheses on Incidence, Risk Factors, Natural History, and Hypothesized Mechanisms", + "rel_date": "2022-03-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.28.22271643", + "rel_abs": "ObjectivesMyocarditis and pericarditis are adverse events of special interest after vaccination for COVID-19. Evidence syntheses were conducted on incidence rates, risk factors for myocarditis and pericarditis after COVID-19 mRNA vaccination, clinical presentation and short- and longer-term outcomes of cases, and proposed mechanisms and their supporting evidence.\n\nDesignSystematic reviews and evidence reviews.\n\nData sourcesMedline, Embase and the Cochrane Library were searched from October 2020 to January 10, 2022; reference lists and grey literature (to January 13, 2021).\n\nReview methodsLarge (>10,000) or population-based/multisite observational studies and surveillance data (incidence and risk factors) reporting on confirmed myocarditis or pericarditis after COVID-19 vaccination; case series (n[≥]5, presentation, short-term clinical course and longer-term outcomes); opinions/letters/reviews/primary studies focused on describing or supporting hypothesized mechanisms. A single reviewer completed screening and another verified 50% of exclusions, using a machine-learning program to prioritize records. A second reviewer verified all exclusions at full text, extracted data, and (for incidence and risk factors) risk of bias assessments using modified Joanna Briggs Institute tools. Team consensus determined certainty of evidence ratings for incidence and risk factors using GRADE.\n\nResults46 studies were included (14 on incidence, 7 on risk factors, 11 on characteristics and short-term course, 3 on longer term outcomes, and 21 on mechanisms). Incidence of myocarditis after mRNA vaccines is highest in male adolescents and young adults (12-17y: range 50-139 cases per million [low certainty] and 18-29y: range 28-147 per million [moderate certainty]). For 5-11 year-old males and females and females 18-29 years of age, incidence of myocarditis after vaccination with Pfizer may be fewer than 20 cases per million (low certainty). There was very low certainty evidence for incidence after a third dose of an mRNA vaccine. For 18-29 year-old males and females, incidence of myocarditis is probably higher after vaccination with Moderna compared to Pfizer (moderate certainty). Among 12-17, 18-29 and 18-39 year-olds, incidence of myocarditis/pericarditis after dose 2 of an mRNA vaccine may be lower when administered [≥]31 days compared to [≤]30 days after dose 1 (low certainty). Data specific to males aged 18-29 indicated that the dosing interval may need to increase to [≥]56 days to substantially drop incidence. For clinical course and short-term outcomes only one small series (n=8) was found for 5-11 year olds. In cases of adolescents and adults, the majority (>90%) of myocarditis cases involved 20-30 year-old males with symptom onset 2 to 4 days after second dose (71-100%). Most cases were hospitalized ([≥]84%) for a short duration (2-4 d). For pericarditis, data is limited but more variation has been reported in patient age, sex, onset timing and rate of hospitalization. Case series with longer-term (3 mo; n=38) follow-up suggest persistent ECG abnormalities, as well as ongoing symptoms and/or a need for medications or restriction from activities in >50% of patients. 16 hypothesized mechanisms are described, with little direct supporting or refuting evidence.\n\nConclusionsAdolescent and young adult males are at the highest risk of myocarditis after mRNA vaccination. Pfizer over Moderna and waiting more than 30 days between doses may be preferred for this population. Incidence of myocarditis in children aged 5-11 may be very rare but certainty was low. Data on clinical risk factors was very limited. Clinical course of mRNA related myocarditis appears to be benign although longer term follow-up data is limited. Prospective studies with appropriate testing (e.g., biopsy, tissue morphology) will enhance understanding of mechanism(s).\n\nFunding and Registration noThis project was funded in part by the Canadian Institutes of Health Research (CIHR) through the COVID-19 Evidence Network to support Decision-making (COVID-END) at McMaster University. Not registered.\n\nSummary boxWhat is already known about this topic?\n\nCase reports and surveillance signals of myocarditis (inflammation of the heart muscle) and pericarditis (inflammation of the two-layered sac surrounding the heart) after COVID-19 vaccination appeared as early as April 2021.\n\nThese have prompted ongoing surveillance and research of these complications to investigate their incidence, possible attribution to the vaccines, and clinical course.\n\nWhat this study adds\n\nThis review critically appraises and synthesizes the available evidence to-date on the incidence of and risk factors for myocarditis and pericarditis after COVID-19 vaccination in multiple countries. It summarizes the presentation and clinical course of over 8000 reported cases and describes some initial reports of longer term outcomes. Further, many possible mechanisms are outlined and discussed.\n\nThough low, the incidence of myocarditis is probably the highest in young males aged 12-29 years and is probably higher with Moderna than Pfizer mRNA vaccines. Longer dosing intervals may be beneficial. Most cases are mild and self-limiting, though data in 5-11 year-olds is very limited. Continued active surveillance with longer term follow-up is warranted.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Jennifer Pillay", + "author_inst": "University of Alberta" + }, + { + "author_name": "Lindsay Gaudet", + "author_inst": "University of Alberta" + }, + { + "author_name": "Aireen Wingert", + "author_inst": "University of Alberta" + }, + { + "author_name": "Liza Bialy", + "author_inst": "University of Alberta" + }, + { + "author_name": "Andrew S Mackie", + "author_inst": "University of Alberta" + }, + { + "author_name": "Ian Paterson", + "author_inst": "University of Alberta" + }, + { + "author_name": "Lisa Hartling", + "author_inst": "University of Alberta" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.27.482162", "rel_title": "Stable nebulization and muco-trapping properties of Regdanvimab/IN-006 support its development as a potent, dose-saving inhaled therapy for COVID-19", @@ -399525,93 +401280,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2022.02.25.481974", - "rel_title": "An immunoPET probe to SARS-CoV-2 reveals early infection of the male genital tract in rhesus macaques", - "rel_date": "2022-02-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.25.481974", - "rel_abs": "The systemic nature of SARS-CoV-2 infection is highly recognized, but poorly characterized. A non-invasive and unbiased method is needed to clarify whole body spatiotemporal dynamics of SARS-CoV-2 infection after transmission. We recently developed a probe based on the anti-SARS-CoV-2 spike antibody CR3022 to study SARS-CoV-2 pathogenesis in vivo. Herein, we describe its use in immunoPET to investigate SARS-CoV-2 infection of three rhesus macaques. Using PET/CT imaging of macaques at different times post-SARS-CoV-2 inoculation, we track the 64Cu-labelled CR3022-F(ab)2 probe targeting the spike protein of SARS-CoV-2 to study the dynamics of infection within the respiratory tract and uncover novel sites of infection. Using this method, we uncovered differences in lung pathology between infection with the WA1 isolate and the delta variant, which were readily corroborated through computed tomography scans. The 64Cu-CR3022-probe also demonstrated dynamic changes occurring between 1- and 2-weeks post-infection. Remarkably, a robust signal was seen in the male genital tract (MGT) of all three animals studied. Infection of the MGT was validated by immunofluorescence imaging of infected cells in the testicular and penile tissue and severe pathology was observed in the testes of one animal at 2-weeks post-infection. The results presented here underscore the utility of using immunoPET to study the dynamics of SARS-CoV-2 infection to understand its pathogenicity and discover new anatomical sites of viral replication. We provide direct evidence for SARS-CoV-2 infection of the MGT in rhesus macaques revealing the possible pathologic outcomes of viral replication at these sites.\n\nGraphic AbstractPET/CT detected SARS-CoV-2 infection of 4 different tissues in the male genital tract illuminates the cause of COVID-19 clinical sequalae of male sexual health and fertility\n\nO_FIG O_LINKSMALLFIG WIDTH=189 HEIGHT=200 SRC=\"FIGDIR/small/481974v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (74K):\norg.highwire.dtl.DTLVardef@188c53aorg.highwire.dtl.DTLVardef@4c639forg.highwire.dtl.DTLVardef@120799forg.highwire.dtl.DTLVardef@110edb1_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO Diagram shows schematic illustration of the male genital tract of the rhesus macaque. Virus icon shows sites of SARS-CoV-2 PET signal. Text highlighting the clinical sequalae associated with each sight of infection is shown in text adjacent to each infection site.\n\nC_FIG", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Patrick J Madden", - "author_inst": "Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA" - }, - { - "author_name": "Yanique Thomas", - "author_inst": "Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA" - }, - { - "author_name": "Robert V Blair", - "author_inst": "Division of Comparative Pathology, Tulane National Primate Research Center, Covington, Louisiana, USA" - }, - { - "author_name": "Sadia Samer", - "author_inst": "Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA" - }, - { - "author_name": "Mark Doyle", - "author_inst": "Division of Comparative Pathology, Tulane National Primate Research Center, Covington, Louisiana, USA" - }, - { - "author_name": "Cecily C Midkiff", - "author_inst": "Division of Comparative Pathology, Tulane National Primate Research Center, Covington, Louisiana, USA" - }, - { - "author_name": "Lara A. Doyle-Meyers", - "author_inst": "Tulane National Primate Research Center, Covington, Louisiana, USA." - }, - { - "author_name": "Mark E Becker", - "author_inst": "Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA" - }, - { - "author_name": "Muhammad S Arif", - "author_inst": "Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA" - }, - { - "author_name": "Michael D McRaven", - "author_inst": "Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA" - }, - { - "author_name": "Lacy M Simons", - "author_inst": "Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Chicago, IL, USA. Center for Pathogen Genomics and Microbial Evolution, Ha" - }, - { - "author_name": "Ann M Carias", - "author_inst": "Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA" - }, - { - "author_name": "Elena Martinelli", - "author_inst": "Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA" - }, - { - "author_name": "Ramon Lorenzo-Redondo", - "author_inst": "Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Chicago, IL, USA. Center for Pathogen Genomics and Microbial Evolution, Ha" - }, - { - "author_name": "Judd F Hultquist", - "author_inst": "Department of Medicine, Division of Infectious Diseases, Feinberg School of Medicine, Chicago, IL, USA. Center for Pathogen Genomics and Microbial Evolution, Ha" - }, - { - "author_name": "Francois J Villinger", - "author_inst": "New Iberia Research Center, University of Louisiana-Lafayette, New Iberia, Louisiana, USA" - }, - { - "author_name": "Ronald S Veazey", - "author_inst": "Division of Comparative Pathology, Tulane National Primate Research Center, Covington, Louisiana, USA" - }, - { - "author_name": "Thomas J Hope", - "author_inst": "Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2022.02.27.482147", "rel_title": "Different efficacies of neutralizing antibodies and antiviral drugs on SARS-CoV-2 Omicron subvariants, BA.1 and BA.2", @@ -401055,6 +402723,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.26.22271546", + "rel_title": "Genomics of Post-Vaccination SARS-CoV-2 Infections During the Delta Dominated Second Wave of COVID-19 Pandemic, from Mumbai Metropolitan Region (MMR), India", + "rel_date": "2022-02-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.26.22271546", + "rel_abs": "Vaccination against SARS-CoV-2 was launched in India in January 2021. Though vaccination reduced hospitalization and mortality due to COVID-19, vaccine breakthrough infections have become common. The present study was initiated in May 2021 to understand the proportion of predominant variants in post-vaccination infections during the Delta dominated second wave of COVID-19 in the Mumbai Metropolitan Region (MMR) in India and to understand any mutations selected in the post-vaccination infections or showing association with any patient demographics. We collected samples (n=166) from severe/moderate/mild COVID-19 patients who were either vaccinated (COVISHIELD/COVAXIN - partial/fully vaccinated) or unvaccinated, from a city hospital and from home isolation patients in MMR. A total of 150 viral genomes were sequenced by Oxford Nanopore sequencing (using MinION) and the data of 136 viral genomes were analyzed for clade/lineage and for identifying mutations in all the genomes. The sequences belonged to three clades (21A, 21I and 21J) and their lineage was identified as either Delta (B.1.617.2) or Delta+ (B.1.617.2 + K417N) or sub-lineages of Delta variant (AY.120/AY.38/AY.99). A total of 620 mutations were identified of which 10 mutations showed an increase in trend with time (May-Oct 2021). Associations of 6 mutations (2 in spike, 3 in orf1a and 1 in nucleocapsid) were shown with milder forms of the disease and one mutation (in orf1a) with partial vaccination status. The results indicate a trend towards reduction in disease severity as the wave progressed.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Kayzad S Nilgiriwala", + "author_inst": "The Foundation for Medical Research" + }, + { + "author_name": "Pratibha Kadam", + "author_inst": "The Foundation for Medical Research" + }, + { + "author_name": "Grishma Patel", + "author_inst": "The Foundation for Medical Research" + }, + { + "author_name": "Ambreen Shaikh", + "author_inst": "The Foundation for Medical Research" + }, + { + "author_name": "Tejal Mestry", + "author_inst": "The Foundation for Medical Research" + }, + { + "author_name": "Smriti Vaswani", + "author_inst": "The Foundation for Medical Research" + }, + { + "author_name": "Shalini Sakthivel", + "author_inst": "The Foundation for Medical Research" + }, + { + "author_name": "Aruna Poojary", + "author_inst": "Breach Candy Hospital" + }, + { + "author_name": "Bhavesh Gandhi", + "author_inst": "Breach Candy Hospital" + }, + { + "author_name": "Seema Rohra", + "author_inst": "Breach Candy Hospital" + }, + { + "author_name": "Zarir Udwadia", + "author_inst": "Breach Candy Hospital" + }, + { + "author_name": "Vikas Oswal", + "author_inst": "Vikas Nursing Home" + }, + { + "author_name": "Daksha Shah", + "author_inst": "Municipal Corporation of Greater Mumbai" + }, + { + "author_name": "Mangala Gomare", + "author_inst": "Municipal Corporation of Greater Mumbai" + }, + { + "author_name": "Kalpana Sriraman", + "author_inst": "The Foundation for Medical Research" + }, + { + "author_name": "Nerges Mistry", + "author_inst": "The Foundation for Medical Research" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.25.22271277", "rel_title": "Rapid genome surveillance of SARS-CoV-2 and study of risk factors using shipping container laboratories and portable DNA sequencing technology", @@ -401463,37 +403210,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2022.02.25.22271520", - "rel_title": "Late-Ensemble of Convolutional Neural Networks with Test Time Augmentation for Chest XR COVID-19 Detection", - "rel_date": "2022-02-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.25.22271520", - "rel_abs": "COVID-19, a severe acute respiratory syndrome aggressively spread among global populations in just a few months. Since then, it has had four dominant variants (Alpha, Beta, Gamma and Delta) that are far more contagious than original. Accurate and timely diagnosis of COVID-19 is critical for analysis of damage to lungs, treatment, as well as quarantine management [7]. CT, MRI or X-rays image analysis using deep learning provide an efficient and accurate diagnosis of COVID-19 that could help to counter its outbreak. With the aim to provide efficient multi-class COVID-19 detection, recently, COVID-19 Detection challenge using X-ray is organized [12]. In this paper, the late-fusion of features is extracted from pre-trained various convolutional neural networks and fine-tuned these models using the challenge dataset. The DensNet201 with Adam optimizer and EffecientNet-B3 are fine-tuned on the challenge dataset and ensembles the features to get the final prediction. Besides, we also considered the test time augmentation technique after the late-ensembling approach to further improve the performance of our proposed solution. Evaluation on Chest XR COVID-19 showed that our model achieved overall accuracy is 95.67%. We made the code is publicly available1. The proposed approach was ranked 6th in Chest XR COVID-19 detection Challenge [1].", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Abdul Qayyum", - "author_inst": "University of Burgundy, Dijon, France" - }, - { - "author_name": "Imran Razzak", - "author_inst": "Deakin University, Geelong, Australia" - }, - { - "author_name": "Moona Mazher", - "author_inst": "University Rovira i Virgili, Spain" - }, - { - "author_name": "Domenec Puig", - "author_inst": "University Rovira i Virgili, Spain" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2022.02.23.22271303", "rel_title": "Changes in the quality of cancer care as assessed through performance indicators during the first wave of the COVID-19 pandemic in 2020: a Scoping Review", @@ -402633,6 +404349,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.02.16.22271092", + "rel_title": "Presence of Symptoms 6 Weeks After COVID-19 Among Vaccinated and Unvaccinated U.S. Healthcare Personnel", + "rel_date": "2022-02-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.16.22271092", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSImportanceC_ST_ABSAlthough COVID-19 vaccines protect against infection and severe disease, the role of vaccination in preventing prolonged symptoms in those with subsequent infection is unclear.\n\nObjectiveTo determine differences in symptoms stratified by prior vaccination reported by healthcare personnel (HCP) 6 weeks after onset of COVID-19, and whether there were differences in timing of return to work.\n\nDesignNested cohort study within a multicenter vaccine effectiveness study. HCP with COVID-19 between December 2020 and August 2021 were followed up 6 weeks after illness onset.\n\nSettingHealth systems in 12 U.S. states.\n\nParticipantsHCP participating in a vaccine effectiveness study were eligible for inclusion if they had confirmed COVID-19 with either verified mRNA vaccination (symptom onset [≥]14 days after two doses) or no prior COVID-19 vaccination. Among 681 eligible participants, 419 (61%) completed a follow-up survey approximately 6 weeks after illness onset.\n\nExposuresTwo doses of a COVID-19 mRNA vaccine compared with no COVID-19 vaccine.\n\nMain outcomes and measuresPresence of symptoms 6 weeks after onset of COVID-19 illness and days to return to work after COVID-19 illness.\n\nResultsAmong 419 HCP with confirmed COVID-19, 298 (71%) reported one or more COVID-like symptoms 6 weeks after illness onset, with a lower prevalence among vaccinated participants (60.6%) compared with unvaccinated participants (60.6% vs. 79.1%; aRR 0.70, 95% CI 0.58-0.84). Vaccinated HCP returned to work a median 2.0 days (95% CI 1.0-3.0) sooner than unvaccinated HCP (aHR 1.37; 95% CI, 1.04-1.79).\n\nConclusionsA history of two doses of COVID-19 mRNA vaccine among HCP with COVID-19 illness was associated with decreased risk of COVID-like symptoms at 6 weeks and earlier to return to work. Vaccination is associated with improved recovery from COVID-19, in addition to preventing symptomatic infection.\n\nKEY POINTSO_ST_ABSQuestionC_ST_ABSDoes vaccination lead to improved recovery of symptoms and return to work following COVID-19?\n\nFindingsIn this nested cohort study of healthcare personnel, participants with COVID-19 who had received two doses of a COVID-19 mRNA vaccine were less likely to report symptoms 6 weeks after illness onset than participants with COVID-19 who were unvaccinated. Return to work was sooner if previously vaccinated.\n\nMeaningVaccination is associated with improved recovery from COVID-19, in addition to prevention of infection and disease.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Nicholas M. Mohr", + "author_inst": "University of Iowa Carver College of Medicine" + }, + { + "author_name": "Ian D Plumb", + "author_inst": "CDC/DDID/NCIRD/DVD" + }, + { + "author_name": "Karisa K Harland", + "author_inst": "University of Iowa" + }, + { + "author_name": "Tamara Pilishvili", + "author_inst": "CDC" + }, + { + "author_name": "Katherine E Flemming-Dutra", + "author_inst": "CDC/DDID/NCIRD/DBD" + }, + { + "author_name": "Anusha Krishnadasan", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Karin F Hoth", + "author_inst": "University of Iowa" + }, + { + "author_name": "Sharon H Saydah", + "author_inst": "CDC/DDI/NCIRD/DVD" + }, + { + "author_name": "Zachary Mankoff", + "author_inst": "Thomas Jefferson University Hospital" + }, + { + "author_name": "John P Haran", + "author_inst": "University of Massachusetts" + }, + { + "author_name": "Melissa Briggs-Hagen", + "author_inst": "CDC/DDI/NCIRD/DVD" + }, + { + "author_name": "Eliezer Santos Leon", + "author_inst": "University of Iowa" + }, + { + "author_name": "David A Talan", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "- Project PREVENT Network", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.22.481551", "rel_title": "Highly divergent white-tailed deer SARS-CoV-2 with potential deer-to-human transmission", @@ -403237,25 +405024,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.21.481324", - "rel_title": "A single-dose of the deactivated rabies virus vectored COVID-19 vaccine, CORAVAX, is highly efficacious and alleviates lung inflammation in the hamster model.", - "rel_date": "2022-02-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.21.481324", - "rel_abs": "Without sufficient herd immunity through either vaccination or natural infection, the Coronavirus Disease 2019 pandemic is unlikely to be controlled. Waning immunity with the currently approved vaccines suggests the need to evaluate vaccines causing the induction of long-term responses. Here we report the immunogenicity and efficacy of our adjuvanted single-dose Rabies vectored SARS CoV-2 S1 vaccine, CORAVAX, in hamsters. CORAVAX induces high SARS CoV-2 S1 specific and virus-neutralizing antibodies (VNA) that prevent weight loss, viral loads, disease, lung inflammation, and the cytokine storm in hamsters. We also observed high Rabies VNA titers. In summary, CORAVAX is a promising dual antigen vaccine candidate for clinical evaluation against SARS CoV-2 and Rabies virus.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Matthias Johannes Schnell", - "author_inst": "Thomas Jefferson University - Center City Campus: Thomas Jefferson University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.02.22.481436", "rel_title": "Characterization of various remdesivir-resistant mutations of SARS-CoV-2 by mathematical modeling and molecular dynamics simulation.", @@ -404375,6 +406143,105 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.02.23.481644", + "rel_title": "Omicron BA.1 and BA.2 are antigenically distinct SARS-CoV-2 variants", + "rel_date": "2022-02-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.23.481644", + "rel_abs": "The emergence and rapid spread of SARS-CoV-2 variants may impact vaccine efficacy significantly1. The Omicron variant termed BA.2, which differs genetically substantially from BA.1, is currently replacing BA.1 in several countries, but its antigenic characteristics have not yet been assessed2,3. Here, we used antigenic cartography to quantify and visualize antigenic differences between SARS-CoV-2 variants using hamster sera obtained after primary infection. Whereas early variants are antigenically similar, clustering relatively close to each other in antigenic space, Omicron BA.1 and BA.2 have evolved as two distinct antigenic outliers. Our data show that BA.1 and BA.2 both escape (vaccine-induced) antibody responses as a result of different antigenic characteristics. Close monitoring of the antigenic changes of SARS-CoV-2 using antigenic cartography can be helpful in the selection of future vaccine strains.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Anna Z Mykytyn", + "author_inst": "Erasmus Medical Centre" + }, + { + "author_name": "Melanie Rissmann", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Adinda Kok", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Miruna Rosu", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Debby Schipper", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Tim I Breugem", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Petra B van den Doel", + "author_inst": "Erasmus University Medical Center" + }, + { + "author_name": "Felicity Chandler", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Theo Bestebroer", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Maurice de Wit", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Martin E. van Royen", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Richard Molenkamp", + "author_inst": "Erasmus University Medical Center" + }, + { + "author_name": "Bas Oude Munnink", + "author_inst": "ErasmusMC" + }, + { + "author_name": "Rory Dylan de Vries", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Corine GeurtsvanKessel", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Derek J Smith", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Marion Koopmans", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Barry Rockx", + "author_inst": "Erasmus University Medical Center" + }, + { + "author_name": "Mart Matthias Lamers", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Ron Fouchier", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Bart Haagmans", + "author_inst": "Erasmus Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.02.23.481658", "rel_title": "Bacterial metatranscriptomes in wastewater can differentiate virally infected human populations", @@ -404739,57 +406606,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.23.22271372", - "rel_title": "Genomic surveillance of SARS-CoV-2 reveals emergence of Omicron BA.2 in Islamabad, Pakistan", - "rel_date": "2022-02-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.23.22271372", - "rel_abs": "The Omicron variant of SARS-CoV-2 has rapidly replace previous variants of SARS CoV2 around the globe and is now a major variant of concern. The genomic surveillance of Omicron variant also reveals spread of its subvariant BA.2 which has differing transmissibility in comparison to its other subvariant BA.1. BA.1 and BA.2 harbors different mutational profile. One of the important change in both the subvariants is the presence of 69-70 deletion in BA.1 and absence of this deletion in BA.2. This deletion can be used as tool for the detection of omicron sub variants using real time PCR. In the current study we have used the TaqPath COVID-19 PCR kit for the detection of 69-70 deletion followed by genotyping using SNPsig(R) SARS-CoV-2 (EscapePLEX) kit (PrimerDesign, UK) that target K417N, E484K, and P681R mutations. The samples with the amplification of spike gene and K417N were termed as probable BA.2 cases. A subset of samples (n=13) were further subjected to whole genome sequencing. The results showed all the 13 samples were of BA.2. Hence, this assay can be used as a cost effective method for the detection of omicron BA.2 variant using real time PCR in resource limiting settings. Moreover, the detection of BA.2 with highly transmissible mutations in Islamabad, Pakistan may potentially increase the number of positive cases. In that scenario, there has to be stringent genomic surveillance to understand the circulating lineages in the country.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Massab Umair", - "author_inst": "National Institute of Health" - }, - { - "author_name": "Aamer Ikram", - "author_inst": "National Institute of Health" - }, - { - "author_name": "Zaira Rehman", - "author_inst": "National Institute of Health" - }, - { - "author_name": "Syed Adnan Haider", - "author_inst": "National Institute of Health" - }, - { - "author_name": "Muhammad Ammar", - "author_inst": "National Institute of Health" - }, - { - "author_name": "Nazish Badar", - "author_inst": "National Institute of Health" - }, - { - "author_name": "Qasim Ali", - "author_inst": "National Institute of Health" - }, - { - "author_name": "Muhammad Suleman Rana", - "author_inst": "National Institute of Health" - }, - { - "author_name": "Muhammad Salman", - "author_inst": "National Institute of Health" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.02.23.22271411", "rel_title": "COVID-19 mortality in the United States: It's been two Americas from the start", @@ -405929,6 +407745,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2022.02.17.22271138", + "rel_title": "Influenza vaccination reveals and partly reverses sex dimorphic immune imprints associated with prior mild COVID-19", + "rel_date": "2022-02-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.17.22271138", + "rel_abs": "Viral infections can have profound and durable functional impacts on the immune system. There is an urgent need to characterize the long-term immune effects of SARS-CoV-2 infection given the persistence of symptoms in some individuals and the continued threat of novel variants. Here we use systems immunology, including longitudinal multimodal single cell analysis (surface proteins, transcriptome, and V(D)J sequences) from 33 previously healthy individuals after recovery from mild, non-hospitalized COVID-19 and 40 age- and sex-matched healthy controls with no history of COVID-19 to comparatively assess the post-infection immune status (mean: 151 days after diagnosis) and subsequent innate and adaptive responses to seasonal influenza vaccination. Identification of both sex-specific and -independent temporally stable changes, including signatures of T-cell activation and repression of innate defense/immune receptor genes (e.g., Toll-like receptors) in monocytes, suggest that mild COVID-19 can establish new post-recovery immunological set-points. COVID-19-recovered males had higher innate, influenza-specific plasmablast, and antibody responses after vaccination compared to healthy males and COVID-19-recovered females, partly attributable to elevated pre-vaccination frequencies of a GPR56 expressing CD8+ T-cell subset in male recoverees that are \"poised\" to produce higher levels of IFN{gamma} upon inflammatory stimulation. Intriguingly, by day 1 post-vaccination in COVID-19-recovered subjects, the expression of the repressed genes in monocytes increased and moved towards the pre-vaccination baseline of healthy controls, suggesting that the acute inflammation induced by vaccination could partly reset the immune states established by mild COVID-19. Our study reveals sex-dimorphic immune imprints and in vivo functional impacts of mild COVID-19 in humans, suggesting that prior COVID-19, and possibly respiratory viral infections in general, could change future responses to vaccination and in turn, vaccines could help reset the immune system after COVID-19, both in an antigen-agnostic manner.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Rachel Sparks", + "author_inst": "Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA" + }, + { + "author_name": "William W Lau", + "author_inst": "Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA" + }, + { + "author_name": "Can Liu", + "author_inst": "Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA; Graduate Program in Biological Sciences, University of M" + }, + { + "author_name": "Kyu Lee Han", + "author_inst": "NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA" + }, + { + "author_name": "Kiera L Vrindten", + "author_inst": "Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA" + }, + { + "author_name": "Guangping Sun", + "author_inst": "Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA; Division of Intramural Research, NIAID, NIH, Bethesda, M" + }, + { + "author_name": "Milann Cox", + "author_inst": "Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA" + }, + { + "author_name": "Sarah F Andrews", + "author_inst": "Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA" + }, + { + "author_name": "Neha Bansal", + "author_inst": "Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA" + }, + { + "author_name": "Laura E Failla", + "author_inst": "Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA" + }, + { + "author_name": "Jody Manischewitz", + "author_inst": "Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA" + }, + { + "author_name": "Gabrielle Grubbs", + "author_inst": "Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA" + }, + { + "author_name": "Lisa R King", + "author_inst": "Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA" + }, + { + "author_name": "Galina Koroleva", + "author_inst": "NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA" + }, + { + "author_name": "Stephanie Leimenstoll", + "author_inst": "Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA" + }, + { + "author_name": "LaQuita Snow", + "author_inst": "Laboratory of Clinical Immunology and Microbiology, NIAID, NIH, Bethesda, MD, USA" + }, + { + "author_name": "- OP11 Clinical Staff", + "author_inst": "" + }, + { + "author_name": "Jinguo Chen", + "author_inst": "NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA" + }, + { + "author_name": "Juanjie Tang", + "author_inst": "Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA" + }, + { + "author_name": "Amrita Mukherjee", + "author_inst": "NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA" + }, + { + "author_name": "Brain A Sellers", + "author_inst": "NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA" + }, + { + "author_name": "Richard Apps", + "author_inst": "NIH Center for Human Immunology, NIAID, NIH, Bethesda, MD, USA" + }, + { + "author_name": "Adrian B McDermott", + "author_inst": "Vaccine Research Center, NIAID, NIH, Bethesda, MD, USA" + }, + { + "author_name": "Andrew J Martins", + "author_inst": "Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA" + }, + { + "author_name": "Evan M Bloch", + "author_inst": "Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA" + }, + { + "author_name": "Hana Golding", + "author_inst": "Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA" + }, + { + "author_name": "Surender Khurana", + "author_inst": "Division of Viral Products, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, USA" + }, + { + "author_name": "John S Tsang", + "author_inst": "Multiscale Systems Biology Section, Laboratory of Immune System Biology, NIAID, NIH, Bethesda, MD, USA; NIH Center for Human Immunology, NIAID, NIH, Bethesda, M" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.19.22271112", "rel_title": "Occurrence and significance of Omicron BA.1 infection followed by BA.2 reinfection", @@ -406520,141 +408463,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.02.19.481089", - "rel_title": "Targeted Down Regulation Of Core Mitochondrial Genes During SARS-CoV-2 Infection", - "rel_date": "2022-02-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.19.481089", - "rel_abs": "Defects in mitochondrial oxidative phosphorylation (OXPHOS) have been reported in COVID-19 patients, but the timing and organs affected vary among reports. Here, we reveal the dynamics of COVID-19 through transcription profiles in nasopharyngeal and autopsy samples from patients and infected rodent models. While mitochondrial bioenergetics is repressed in the viral nasopharyngeal portal of entry, it is up regulated in autopsy lung tissues from deceased patients. In most disease stages and organs, discrete OXPHOS functions are blocked by the virus, and this is countered by the host broadly up regulating unblocked OXPHOS functions. No such rebound is seen in autopsy heart, results in severe repression of genes across all OXPHOS modules. Hence, targeted enhancement of mitochondrial gene expression may mitigate the pathogenesis of COVID-19.\n\nOne-Sentence SummaryCovid-19 is associated with targeted inhibition of mitochondrial gene transcription.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "Justin Frere", - "author_inst": "New York University" - }, - { - "author_name": "Sonja M Best", - "author_inst": "Rocky Mountain Laboratories NIAID, COVID-19 International Research Team" - }, - { - "author_name": "Henry Cope", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Viktorija Zaksas", - "author_inst": "University of Chicago" - }, - { - "author_name": "Amanda Saravia-Butler", - "author_inst": "NASA Ames Research Center, Logyx LLC" - }, - { - "author_name": "Cem Meydan", - "author_inst": "Weill Cornell Medicine, COVID-19 International Research Team" - }, - { - "author_name": "Jonathan Foox", - "author_inst": "Weill Cornell Medical College" - }, - { - "author_name": "Christopher Mozsary", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Yared H Kidane", - "author_inst": "Scottish Rite for Children, COVID-19 International Research Team" - }, - { - "author_name": "Waldemar Priebe", - "author_inst": "University of Texas MD Anderson Cancer Center, COVID-19 International Research Team" - }, - { - "author_name": "Mark Emmett", - "author_inst": "University of Texas Medical Branch, COVID-19 International Research Team" - }, - { - "author_name": "Robert Meller", - "author_inst": "Morehouse School of Medicine, COVID-19 International Research Team" - }, - { - "author_name": "Urminder Singh", - "author_inst": "Iowa State University, COVID-19 International Research Team." - }, - { - "author_name": "Yaron Bram", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Benjamin R. tenOever", - "author_inst": "New York University Langone Medical Center" - }, - { - "author_name": "Mark T. Heise", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Nathaniel J. Moorman", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Emily A. Madden", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Sharon A. Taft-Benz", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Elizabeth J. Anderson", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Wes A. Sanders", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Rebekah J. Dickmander", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Victoria K. Baxter", - "author_inst": "University of North Carolina" - }, - { - "author_name": "Stephen Baylin", - "author_inst": "Johns Hopkins University, School of Medicine, COVID-19 International Research Team." - }, - { - "author_name": "Eve Wurtele", - "author_inst": "Iowa State University, COVID-19 International Research Team." - }, - { - "author_name": "Pedro Moraes-vieira", - "author_inst": "University of Campinas, COVID-19 International Research Team." - }, - { - "author_name": "Christopher Mason", - "author_inst": "Weill Cornell Medical College, New York Genome Center, COVID-19 International Research Team." - }, - { - "author_name": "Jonathan C Schisler", - "author_inst": "The University of North Carolina at Chapel Hill, COVID-19 International Research Team." - }, - { - "author_name": "Robert E. Schwartz", - "author_inst": "Weill Cornell Graduate School of Medical Sciences, COVID-19 International Research Team." - }, - { - "author_name": "Afshin Beheshti", - "author_inst": "KBR, NASA Ames Research Center, Broad Institute of MIT and Harvard, Cambridge, COVID-19 International Research Team." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2022.02.21.481247", "rel_title": "A novel intranasal administration adenoviral vector-based platform for rapid COVID-19 vaccine development", @@ -407930,6 +409738,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rehabilitation medicine and physical therapy" }, + { + "rel_doi": "10.1101/2022.02.16.22271059", + "rel_title": "Genomic monitoring unveils a high prevalence of SARS-CoV 2 Omicron Variant in vaccine breakthrough cases in Bahia, Brazil", + "rel_date": "2022-02-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.16.22271059", + "rel_abs": "Genome sequencing proved to be an excellent tool to monitor the molecular epidemiology of the disease caused by SARS-CoV-2, i.e., coronavirus disease (COVID-19). Some reports of infected, vaccinated individuals have aroused great interest because they are primarily being infected with circulating variants of concern (VOCs). To investigate the cases of infected, vaccinated individuals in Salvador, Bahia, Brazil, we performed genomic monitoring to estimate the magnitude of the different VOCs in these cases. Nasopharyngeal swabs from infected (symptomatic and asymptomatic), fully vaccinated individuals (n=29) who were of varying age and had RT-qPCR Ct values of [≤]30 were subjected to viral sequencing using Nanopore technology. Our analysis revealed that the Omicron variant was found in 99% of cases and that only one case was due to the Delta variant. Infected, fully vaccinated patients have a favorable clinical prognosis; however, within the community, they become viral carriers with the aggravating factor of viral dissemination of VOCs not neutralized by the vaccines.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Gubio Soares Campos", + "author_inst": "Universidade Federal da Bahia" + }, + { + "author_name": "Marta Giovanetti", + "author_inst": "Fundacao Oswaldo Cruz" + }, + { + "author_name": "Laise de Moraes", + "author_inst": "Fundacao Oswaldo Cruz" + }, + { + "author_name": "Helena S da Hora", + "author_inst": "Universidade Federal da Bahia" + }, + { + "author_name": "Keila Motta Alcantara", + "author_inst": "Universidade Federal da Bahia" + }, + { + "author_name": "Silvia Ines Sardi", + "author_inst": "Universidade Federal da Bahia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.02.16.22271064", "rel_title": "An open-label randomized, controlled trial of the effect of lopinavir/ritonavir, lopinavir/ritonavir plus IFN-beta-1a and hydroxychloroquine in hospitalized patients with COVID-19 - Final results from the DisCoVeRy trial", @@ -408618,69 +410465,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, - { - "rel_doi": "10.1101/2022.02.17.22271142", - "rel_title": "Performance of three rapid antigen tests against the SARS-CoV-2 Omicron variant", - "rel_date": "2022-02-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.17.22271142", - "rel_abs": "Rapid antigen detection tests (RADTs) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are now in widespread use in the United States. RADTs play an important role in maintaining an open society but require periodic reassessment to ensure test performance remains intact as the virus evolves. The nucleocapsid (N) protein is the target for the majority of RADTs and the SARS-CoV-2 Omicron variant has several N protein mutations that are previously uncharacterized. We sought to assess the impact of these mutations by testing 30 Omicron variant samples across a wide range of viral loads on three widely used RADTs: the iHealth COVID-19 Antigen Rapid Test, the ACON Laboratories FlowFlex COVID-19 Antigen Home Test, and the Abbott BinaxNOW COVID-19 Antigen Card, using 30 Delta variant samples as a comparator. We found no change in the analytic sensitivity of all three RADTs for detection of Omicron versus Delta, but noted differences in performance between assays. No RADT was able to detect samples with a cycle threshold (Ct) value of [≥]27.5 for the envelope gene target on the Roche cobas RT-PCR assay. Epidemiologic studies are necessary to correlate these findings with their real-world performance.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Sanjat Kanjilal", - "author_inst": "Harvard Medical School & Harvard Pilgrim Healthcare Institute" - }, - { - "author_name": "Sujata Chalise", - "author_inst": "Brigham and Women's Hospital & Harvard Medical School" - }, - { - "author_name": "Adnan Shami Shah", - "author_inst": "Brigham and Women's Hospital & Harvard Medical School" - }, - { - "author_name": "Chi-An Cheng", - "author_inst": "Brigham and Women's Hospital & Harvard Medical School" - }, - { - "author_name": "Yasmeen Senussi", - "author_inst": "Brigham and Women's Hospital & Harvard Medical School" - }, - { - "author_name": "Rockib Uddin", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Vamsi Thiriveedhi", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Ha Eun Cho", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Seamus Carroll", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Jacob Lemieux", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Sarah Turbett", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "David R. Walt", - "author_inst": "Brigham and Women's Hospital & Harvard Medical School" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.16.22271042", "rel_title": "Performance of an artificial intelligence-based smartphone app for guided reading of SARS-CoV-2 lateral-flow immunoassays", @@ -409968,6 +411752,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.02.17.480819", + "rel_title": "Metagenomic analysis reveals the abundance and diversity of opportunistic fungal pathogens in the nasopharyngeal tract of COVID-19 patients", + "rel_date": "2022-02-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.17.480819", + "rel_abs": "The nasopharyngeal tract (NT) of human is a habitat of a diverse microbial community that work together with other gut microbes to maintain the host immunity. In our previous study, we reported that SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiome (bacteria, archaea and commensal respiratory viruses) but increases the abundance of pathobionts. This study aimed to assess the possible changes in the resident fungal diversity by the inclusion of opportunistic fungi due to the infection of SARS-CoV-2 in the NT of humans. Twenty-two (n = 22) nasopharyngeal swab samples (including COVID-19 = 8, Recovered = 7, and Healthy = 7) were collected for RNAseq-based metagenomics analyses. Our results indicate that SARS-CoV-2 infection significantly increased (p < 0.05, Wilcoxon test) the population and diversity of NT fungi with a high inclusion of opportunistic pathogens. We detected 863 fungal species including 533, 445, and 188 species in COVID-19, Recovered, and Healthy individuals, respectively that indicate a distinct microbiome dysbiosis due to the SARS-CoV-2 infection. Remarkably, 37% of the fungal species were exclusively associated with SARS-CoV-2 infection, where S. cerevisiae (88.62%) and Phaffia rhodozyma (10.30%) were two top abundant species in the NT of COVID-19 patients. Importantly, 16% commensal fungal species found in the Healthy control were not detected in either COVID-19 patients or when they were recovered from the COVID-19. Pairwise Spearmans correlation test showed that several altered metabolic pathways had significant positive correlations (r > 0.5, p < 0.01) with dominant fungal species detected in three metagenomes. Taken together, our results indicate that SARS-CoV-2 infection causes significant dysbiosis of fungal microbiome and alters some metabolic pathways and expression of genes in the NT of human. Findings of our study might be helpful for developing microbiome-based diagnostics, and also devising appropriate therapeutic regimens including antifungal drugs for prevention and control of concurrent fungal coinfections in COVID-19 patients.\n\nAuthor summaryThe SARS-CoV-2 is a highly transmissible and pathogenic betacoronavirus that primarily enters into the human body through NT to cause fearsome COVID-19 disease. Recent high throughput sequencing and downstream bioinformatic analyses revealed that microbiome dysbiosis associated with SARS-CoV-2 infection are not limited to bacteria, and fungi are also implicated in COVID-19 development in susceptible individuals. This study demonstrates that SARS-CoV-2 infection results in remarkable depletion of NT commensal fungal microbiomes with inclusion of various opportunistic fungal pathogens. We discussed the role of these altered fungal microbiomes in the pathophysiology of the SARS-CoV-2 infection. Our results suggest that dysbiosis in fungal microbiomes and associated altered metabolic functional pathways (or genes) possibly play a determining role in the progression of SARS-CoV-2 pathogenesis. Thus, the identifiable changes in the diversity and composition of the NT fungal population and their related genomic features demonstrated in this study might lay a foundation for better understanding of the underlying mechanism of co-pathogenesis, and the ongoing development of therapeutic agents including antifungal drugs for the resolution of COVID-19 pandemic.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "M. Nazmul Hoque", + "author_inst": "Bangabandhu Sheikh Mujibur Rahman Agricultural University" + }, + { + "author_name": "M. Shaminur Rahman", + "author_inst": "Jessore Science and Technology University: Jessore University of Science and Technology" + }, + { + "author_name": "Md. Murshed Hasan Sarkar", + "author_inst": "Bangladesh Council of Scientific and Industrial Research" + }, + { + "author_name": "Md Ahashan Habib", + "author_inst": "Bangladesh Council of Scientific and Industrial Research" + }, + { + "author_name": "M. Anwar Hossain", + "author_inst": "Jessore University of Science and Technology" + }, + { + "author_name": "M. Salim Khan", + "author_inst": "Bangladesh Council of Scientific and Industrial Research" + }, + { + "author_name": "Tofazzal Islam", + "author_inst": "Bangabandhu Sheikh Mujibur Rahman Agricultural University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.02.17.480826", "rel_title": "Genomic Characterization of Sars-Cov-2 from Islamabad Pakistan by Rapid Nanopore Sequencing", @@ -410604,33 +412431,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.16.22271093", - "rel_title": "A novel SEIR-e model for disease transmission and pathogen exposure", - "rel_date": "2022-02-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.16.22271093", - "rel_abs": "In this study, we couple compartment models for indoor air quality and disease transmission to develop a novel SEIR-e model for disease transmission and pathogen exposure. In doing so, we gain insight into the contribution of people-people and people-pathogen interactions to the spread of transmissible diseases. A general modelling framework is used to assess the risk of infection in indoor environments due to people-pathogen interactions via inhalation of viral airborne aerosols, and contact with contaminated surfaces. We couple the indoor environment model with a standard disease transmission model to investigate how both people-people and people-pathogen interactions result in disease transmission. The coupled model is referred to as the SEIR-e model. To demonstrate the applicability of the SEIR-e model and the novel insights it can provide into different exposure pathways, parameter values which describe exposure due to people-people and people-pathogen interactions are inferred using Bayesian techniques and case data relating to the 2020 outbreak of COVID-19 in Victoria (Australia).", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Tamara A Tambyah", - "author_inst": "Defence Science and Technology Group" - }, - { - "author_name": "Matthew J Testolin", - "author_inst": "Defence Science and Technology Group" - }, - { - "author_name": "Alexander M Hill", - "author_inst": "Defence Science and Technology Group" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.02.16.22271055", "rel_title": "The public health impact of poor sleep on severe COVID-19, influenza and upper respiratory infections", @@ -411874,6 +413674,93 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.02.16.480524", + "rel_title": "Experimental infection of mink with SARS-COV-2 Omicron (BA.1) variant leads to symptomatic disease with lung pathology and transmission", + "rel_date": "2022-02-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.16.480524", + "rel_abs": "We report an experimental infection of American mink with SARS-CoV-2 Omicron variant and show that minks remain virus RNA positive for days, develop clinical signs and histopathological changes, and transmit the virus to uninfected recipients warranting further studies and preparedness.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Jenni Virtanen", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Kirsi Aaltonen", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Kristel Kegler", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Vinaya Venkat", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Thanakorn Niamsap", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Lauri Kareinen", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Rasmus Malmgren", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Olga Kivela", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Nina Atanasova", + "author_inst": "University of Helsinki and Finnish Meteorological Institute" + }, + { + "author_name": "Pamela Osterlund", + "author_inst": "Finnish Institute for Health and Welfare" + }, + { + "author_name": "Teemu Smura", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Antti Sukura", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Tomas Strandin", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Lara Dutra", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Olli Vapalahti", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Heli Nordgren", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Ravi Kant", + "author_inst": "University of Helsinki" + }, + { + "author_name": "Tarja Sironen", + "author_inst": "Haartman Institute, University of Helsinki" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.02.11.22270848", "rel_title": "Strength and durability of antibody responses to BNT162b2 and CoronaVac", @@ -412334,81 +414221,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.10.22270733", - "rel_title": "Differential durability of humoral and T cell immunity after two and three BNT162b2 vaccinations in adults aged >80 years", - "rel_date": "2022-02-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.10.22270733", - "rel_abs": "A third mRNA-based \"booster\" vaccination is the favored strategy to maintain protection against SARS-CoV-2 infection. Yet, significant waning of specific immunity within six months after 2nd vaccination, along with higher incidence of breakthrough infections associated with the time elapsed since 2nd vaccination raises concerns regarding the durability of immunity also after 3rd vaccination. We assessed virus-specific serum antibody and T cell response in the blood after vaccination with the mRNA vaccine BNT162b2 in more than 50 individuals older than 80 years. All old adults demonstrated a strong humoral response to 3rd vaccination which was at average higher and waned slower than the response to 2nd vaccination, indicative of enhanced humoral immunity. In contrast, their respective T cell response quantitatively limited to the level obtained after 2nd vaccination, with similar waning over time and no evidence for enhanced IFNg production. Because BNT162b2-mediated protection from the Omicron variant relies more on T cells than antibodies, our findings raise concern on the durability of protection from the Omicron variant by BNT162b2 in the senior population.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Addi Josua Romero Olmedo", - "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Philipps-University Marburg" - }, - { - "author_name": "Axel Ronald Schulz", - "author_inst": "Deutsches Rheumaforschungszentrum Berlin, Leibniz Institute" - }, - { - "author_name": "Svenja Hochstaetter", - "author_inst": "Institute of Virology, Philipps-University, Marburg, Germany" - }, - { - "author_name": "Dennis Das Gupta", - "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Philipps-University Marburg" - }, - { - "author_name": "Heike Hirseland", - "author_inst": "Deutsches Rheumaforschungszentrum Berlin, Leibniz Institute" - }, - { - "author_name": "Daniel Staudenraus", - "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Philipps-University Marburg" - }, - { - "author_name": "Baerbel Camara", - "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Philipps-University Marburg" - }, - { - "author_name": "Kirsten Volland", - "author_inst": "Institute of Virology, Philipps-University, Marburg" - }, - { - "author_name": "Veronique Hefter", - "author_inst": "Institute of Virology, Philipps-University, Marburg" - }, - { - "author_name": "Siddhesh Sapre", - "author_inst": "Institute of Virology, Philipps-University, Marburg" - }, - { - "author_name": "Verena Kraehling", - "author_inst": "Institute of Virology, Philipps-University, Marburg" - }, - { - "author_name": "Helena Mueller-Kraeuter", - "author_inst": "Institute of Virology, Philipps-University, Marburg" - }, - { - "author_name": "Henrik Mei", - "author_inst": "Deutsches Rheumaforschungszentrum Berlin, Leibniz Institute" - }, - { - "author_name": "Christian Keller", - "author_inst": "Institute of Virology, Philipps-University, Marburg" - }, - { - "author_name": "Michael Lohoff", - "author_inst": "Institute of Medical Microbiology and Hospital Hygiene, Philipps-University Marburg" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.13.22270856", "rel_title": "Structural risk factors for SARS-CoV-2 infection in an urban slum: Age, gender and income", @@ -413980,6 +415792,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "transplantation" }, + { + "rel_doi": "10.1101/2022.02.14.480460", + "rel_title": "A live-attenuated SARS-CoV-2 vaccine candidate with accessory protein deletions", + "rel_date": "2022-02-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.14.480460", + "rel_abs": "We report a live-attenuated SARS-CoV-2 vaccine candidate with (i) re-engineered viral transcriptional regulator sequences and (ii) deleted open-reading-frames (ORF) 3, 6, 7, and 8 ({Delta}3678). The {Delta}3678 virus replicates about 7,500-fold lower than wild-type SARS-CoV-2 on primary human airway cultures, but restores its replication on interferon-deficient Vero-E6 cells that are approved for vaccine production. The {Delta}3678 virus is highly attenuated in both hamster and K18-hACE2 mouse models. A single-dose immunization of the {Delta}3678 virus protects hamsters from wild-type virus challenge and transmission. Among the deleted ORFs in the {Delta}3678 virus, ORF3a accounts for the most attenuation through antagonizing STAT1 phosphorylation during type-I interferon signaling. We also developed an mNeonGreen reporter {Delta}3678 virus for high-throughput neutralization and antiviral testing. Altogether, the results suggest that {Delta}3678 SARS-CoV-2 may serve as a live-attenuated vaccine candidate and a research tool for potential biosafety level-2 use.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Yang Liu", + "author_inst": "UTMB" + }, + { + "author_name": "Xianwen Zhang", + "author_inst": "UTMB" + }, + { + "author_name": "Jianying Liu", + "author_inst": "UTMB" + }, + { + "author_name": "Hongjie Xia", + "author_inst": "UTMB" + }, + { + "author_name": "Jing Zou", + "author_inst": "UTMB" + }, + { + "author_name": "Antonio E. Muruato", + "author_inst": "UTMB" + }, + { + "author_name": "Sivakumar Periasamy", + "author_inst": "UTMB" + }, + { + "author_name": "Jessica A. Plante", + "author_inst": "UTMB" + }, + { + "author_name": "Nathen E. Bopp", + "author_inst": "UTMB" + }, + { + "author_name": "Chaitanya Kurhade", + "author_inst": "UTMB" + }, + { + "author_name": "Alexander Bukreyev", + "author_inst": "UTMB" + }, + { + "author_name": "Ping Ren", + "author_inst": "UTMB" + }, + { + "author_name": "Tian Wang", + "author_inst": "UTMB" + }, + { + "author_name": "Vineet D. Menachery", + "author_inst": "UTMB" + }, + { + "author_name": "Kenneth S. Plante", + "author_inst": "UTMB" + }, + { + "author_name": "Xuping Xie", + "author_inst": "UTMB" + }, + { + "author_name": "Scott C. Weaver", + "author_inst": "UTMB" + }, + { + "author_name": "Pei-Yong Shi", + "author_inst": "UTMB" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.02.14.480430", "rel_title": "A global lipid map reveals host dependency factors conserved across SARS-CoV-2 variants", @@ -414580,57 +416479,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2022.02.11.22270859", - "rel_title": "Clinical and economic benefits of lenzilumab plus standard of care compared with standard of care alone for the treatment of hospitalized patients with Coronavirus Disease 19 (COVID-19) from the perspective of National Health Service England", - "rel_date": "2022-02-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.11.22270859", - "rel_abs": "PurposeEstimate the clinical and economic benefits of lenzilumab plus standard of care (SOC) compared with SOC alone in the treatment of hospitalized COVID-19 patients from the National Health Service (NHS) England perspective.\n\nMethodsA cost calculator was developed to estimate the clinical benefits and costs of adding lenzilumab to SOC in newly hospitalized COVID-19 patients over 28 days. The LIVE-AIR trial results informed the clinical inputs: failure to achieve survival without ventilation (SWOV), mortality, time to recovery, intensive care unit (ICU) admission, and invasive mechanical ventilation (IMV) use. Base case costs included drug acquisition and administration for lenzilumab and remdesivir and hospital resource costs based on level of care required. Clinical and economic benefits per weekly cohort of newly hospitalized patients were also estimated.\n\nResultsIn all populations examined, specified clinical outcomes were improved with lenzilumab plus SOC over SOC treatment alone. In a base case population aged <85 years with C-reactive protein (CRP) <150 mg/L, with or without remdesivir, adding lenzilumab to SOC was estimated to result in per-patient cost savings of {pound}1,162. In a weekly cohort of 4,754 newly hospitalized patients, addition of lenzilumab to SOC could result in 599 IMV uses avoided, 352 additional lives saved, and over {pound}5.5 million in cost savings. Scenario results for per-patient cost savings included: 1) aged <85 years, CRP <150 mg/L, and receiving remdesivir ({pound}3,127); 2) Black patients with CRP <150 mg/L ({pound}9,977); and 3) Black patients from the full population ({pound}2,369). Conversely, in the full mITT population, results estimated additional cost of {pound}4,005 per patient.\n\nConclusionFindings support clinical benefits for SWOV, mortality, time to recovery, time in ICU, time on IMV, and ventilator use, and an economic benefit from the NHS England perspective when adding lenzilumab to SOC for hospitalized COVID-19 patients.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Adrian Kilcoyne", - "author_inst": "Humanigen Inc" - }, - { - "author_name": "Edward Jordan", - "author_inst": "Humanigen Inc." - }, - { - "author_name": "Kimberly Thomas", - "author_inst": "EVERSANA" - }, - { - "author_name": "Alicia N. Pepper", - "author_inst": "EVERSANA" - }, - { - "author_name": "Allen Zhou", - "author_inst": "EVERSANA" - }, - { - "author_name": "Dale Chappell", - "author_inst": "Humanigen Inc." - }, - { - "author_name": "Miyuru Amarapala", - "author_inst": "Humanigen Inc." - }, - { - "author_name": "Rachel-Karson Theriault", - "author_inst": "EVERSANA" - }, - { - "author_name": "Melissa Thompson", - "author_inst": "EVERSANA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2022.02.11.22270504", "rel_title": "Assessing the Profile of Unvaccinated COVID-19 Individuals in African American and Latinx Communities in Eastern Pennsylvania", @@ -415882,6 +417730,145 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, + { + "rel_doi": "10.1101/2022.02.10.22270471", + "rel_title": "POST-ACUTE SEQUELAE AND ADAPTIVE IMMUNE RESPONSES IN PEOPLE LIVING WITH HIV RECOVERING FROM SARS-COV-2 INFECTION", + "rel_date": "2022-02-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.10.22270471", + "rel_abs": "BackgroundLimited data are available on the long-term clinical and immunologic consequences of SARS-CoV-2 infection in people with HIV (PWH).\n\nMethodsWe measured SARS-CoV-2 specific humoral and cellular responses in people with and without HIV recovering from COVID-19 (n=39 and n=43, respectively) using binding antibody, surrogate virus neutralization, intracellular cytokine staining, and inflammatory marker assays. We identified individuals experiencing post-acute sequelae of SARS-CoV-2 infection (PASC) and evaluated immunologic parameters. We used linear regression and generalized linear models to examine differences by HIV status in the magnitude of inflammatory and virus-specific antibody and T cell responses, as well as differences in the prevalence of PASC.\n\nResultsAmong PWH, we found broadly similar SARS-CoV-2-specific antibody and T cell responses as compared with a well-matched group of HIV-negative individuals. PWH had 70% lower relative levels of SARS-CoV-2 specific memory CD8+ T cells (p=0.007) and 53% higher relative levels of PD-1+ SARS-CoV-2 specific CD4+ T cells (p=0.007). Higher CD4/CD8 ratio was associated with lower PD-1 expression on SARS-CoV-2 specific CD8+ T cells (0.34-fold effect, p=0.02). HIV status was strongly associated with PASC (odds ratio 4.01, p=0.008), and levels of certain inflammatory markers (IL-6, TNF-alpha, and IP-10) were associated with persistent symptoms.\n\nConclusionsWe identified potentially important differences in SARS-CoV-2 specific CD4+ and CD8+ T cells in PWH and HIV-negative participants that might have implications for long-term immunity conferred by natural infection. HIV status strongly predicted the presence of PASC. Larger and more detailed studies of PASC in PWH are urgently needed.", + "rel_num_authors": 31, + "rel_authors": [ + { + "author_name": "Michael J Peluso", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Matthew A Spinelli", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Tyler-Marie Deveau", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Carrie A Forman", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Sadie E Munter", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Sujata Mathur", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Alex F Tang", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Scott Lu", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Sarah A Goldberg", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Mireya I Arreguin", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Rebecca Hoh", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Viva Tai", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Jessica Y Chen", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Enrique O. Martinez", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Ahmed Chenna", + "author_inst": "Monogram Biosciences" + }, + { + "author_name": "John W Winslow", + "author_inst": "Monogram Biosciences" + }, + { + "author_name": "Christos J Petropoulos", + "author_inst": "Monogram Biosciences" + }, + { + "author_name": "Alessandro Sette", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Daniella Weiskopf", + "author_inst": "University of California, San Diego" + }, + { + "author_name": "Nitasha Kumar", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Kara L Lynch", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Peter W Hunt", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Matthew S Durstenfeld", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Priscilla Y Hsue", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "J Daniel Kelly", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Jeffrey N Martin", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "David V Glidden", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Monica Gandhi", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Steven G Deeks", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Rachel L Rutishauser", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Timothy J Henrich", + "author_inst": "University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "hiv aids" + }, { "rel_doi": "10.1101/2022.02.13.22270896", "rel_title": "Comprehensive humoral and cellular immune responses to SARS-CoV-2 variants in diverse Chinese populations: A benefit perspective of national vaccination", @@ -416402,85 +418389,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.11.22270667", - "rel_title": "Correlation between post-vaccination titres of combined IgG, IgA, and IgM anti-Spike antibodies and protection against breakthrough SARS-CoV-2 infection: a population-based longitudinal study (COVIDENCE UK)", - "rel_date": "2022-02-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.11.22270667", - "rel_abs": "In this population-based cohort of 7530 adults, combined IgG/A/M anti-Spike titres measured after SARS-CoV-2 vaccination were predictive of protection against breakthrough SARS-CoV-2 infection. Discrimination was significantly improved by adjustment for factors influencing risk of SARS-CoV-2 exposure including household overcrowding, public transport use, and visits to indoor public places.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Giulia Vivaldi", - "author_inst": "Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "David A Jolliffe", - "author_inst": "Blizard Institute and the Wolfson Institute of Population Health, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London" - }, - { - "author_name": "Sian Faustini", - "author_inst": "Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK" - }, - { - "author_name": "Hayley Holt", - "author_inst": "Blizard Institute and the Wolfson Institute of Population Health, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London" - }, - { - "author_name": "Natalia Perdek", - "author_inst": "Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Mohammad Talaei", - "author_inst": "Wolfson Institute of Population Health, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Florence Tydeman", - "author_inst": "Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Emma S Chambers", - "author_inst": "Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Weigang Cai", - "author_inst": "Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Wenhao Li", - "author_inst": "Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Joseph M Gibbons", - "author_inst": "Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Corinna Pade", - "author_inst": "Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "\u00c1ine McKnight", - "author_inst": "Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Seif O Shaheen", - "author_inst": "Wolfson Institute of Population Health, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK" - }, - { - "author_name": "Alex G Richter", - "author_inst": "Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK" - }, - { - "author_name": "Adrian R Martineau", - "author_inst": "Blizard Institute and the Wolfson Institute of Population Health, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.02.11.22270876", "rel_title": "Food intake patterns, social determinants and emotions during COVID-19 confinement: an online survey among adults in Panama.", @@ -417772,6 +419680,33 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2022.02.11.480029", + "rel_title": "Omicron (BA.1) and Sub-Variants (BA.1, BA.2 and BA.3) of SARS-CoV-2 Spike Infectivity and Pathogenicity: A Comparative Sequence and Structural-based Computational Assessment", + "rel_date": "2022-02-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.11.480029", + "rel_abs": "The Omicron variant of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has now spread throughout the world. We used computational tools to assess the spike infectivity, transmission, and pathogenicity of Omicron (BA.1) and sub-variants (BA.1.1, BA.2, and BA.3) in this study. BA.1 has 39 mutations, BA.1.1 has 40 mutations, BA.2 has 31 mutations, and BA.3 has 34 mutations, with 21 shared mutations between all. We observed 11 common mutations in Omicrons receptor-binding domain and sub-variants. In pathogenicity analysis, the Y505H, N786K, T95I, N211I, N856K, and V213R mutations in omicron and sub-variants are predicted to be deleterious. Due to the major effect of the mutations characterising, in the receptor-binding domain (RBD), we found that Omicron and sub-variants had a higher positive electrostatic surface potential. This could increase interaction between RBD and electronegative human angiotensin-converting enzyme 2 (hACE2). Omicron and sub-variants had a higher affinity for hACE2 and the potential for increased transmission when compared to the wild type. Among Omicron sub-lineages, BA.2 and BA.3 have a higher transmission potential than BA.1 and BA.1.1. We predicted that mutated residues in BA.1.1 (K478), BA.2 (R400, R490, R495), and BA.3 (R397 and H499) formation of new salt bridges and hydrogen bonds. Omicron and sub-variant mutations at Receptor-binding Motif (RBM) residues such as Q493R, N501Y, Q498, T478K, and Y505H all contribute significantly to binding affinity with human ACE2. Interactions with Omicron variant mutations at residues 493, 496, 498, and 501 seem to restore ACE2 binding effectiveness lost due to other mutations like K417N and Y505H.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Suresh Kumar", + "author_inst": "Management & Science University" + }, + { + "author_name": "Kalimuthu Karuppanan", + "author_inst": "University of Oxford, UK" + }, + { + "author_name": "Gunasekaran Subramaniam", + "author_inst": "University of Oxford, Oxford, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.02.10.22270782", "rel_title": "Impact of COVID-19 pandemic and anti-pandemic measures on tuberculosis, viral hepatitis, HIV/AIDS and malaria - a systematic review", @@ -418247,29 +420182,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.02.10.22270783", - "rel_title": "Implementation and economic effects of local non-pharmaceutical interventions", - "rel_date": "2022-02-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.10.22270783", - "rel_abs": "In this paper, we analyze economic costs and consequences of local non-pharmaceutical interventions (NPIs) aimed at containing the COVID-19 pandemic. Using comprehensive data on municipal and regional policies in Norway, we implement a difference-in-differences framework identifying impacts of local NPIs from discontinuous differential shifts in outcomes following the implementation of new policies. In treated municipalities, local NPIs lead to persistent reductions in mobility, persistent increases in unemployment, and transient reductions in consumer spending. Analyses of spatial spillovers show that the implementation of local NPIs increases retail mobility in non-treated neighboring municipalities. Overall, our findings suggest that local NPIs have economic consequences for local economies and induce residents to shift their consumption of goods and services to neighboring municipalities.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Anna Aasen Godoy", - "author_inst": "The Norwegian Institute of Public Health" - }, - { - "author_name": "Maja Weemes Grotting", - "author_inst": "The Norwegian Institute of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2022.02.09.22269744", "rel_title": "Machine Learning Generalizability Across Healthcare Settings: Insights from multi-site COVID-19 screening", @@ -419569,6 +421481,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.02.07.22270640", + "rel_title": "The interaction effect between hemoglobin and hypoxemia on COVID-19 mortality in a sample from Bogota, Colombia: An exploratory study.", + "rel_date": "2022-02-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.07.22270640", + "rel_abs": "PurposeWe aimed to assess the effect of hemoglobin (Hb) concentration and oxygenation index on COVID-19 patients mortality risk.\n\nPatients and methodsWe retrospectively reviewed sociodemographic and clinical characteristics, laboratory findings, and clinical outcomes from patients admitted to a tertiary care hospital in Bogota, Colombia. We assessed exploratory associations between oxygenation index and Hb concentration at admission and clinical outcomes. We used a generalized additive model (GAM) to evaluate the nonlinear relations observed and the classification and regression trees (CART) algorithm to assess the interaction effects found.\n\nResultsFrom March to July 2020, 643 patients were admitted, of which 52% were male. The median age was 60 years old, and the most frequent comorbidity was hypertension (35.76%). The median value of SpO2/FiO2 was 419, and the median Hb concentration was 14.8 g/dL. The mortality was 19.1% (123 patients). Age, sex, and history of hypertension were independently associated with mortality. We described a nonlinear relationship between SpO2/FiO2, Hb concentration and neutrophil-to-lymphocyte ratio with mortality and an interaction effect between SpO2/FiO2 and Hb concentration. Patients with a similar oxygenation index had different mortality likelihoods based upon their Hb at admission. CART showed that patients with SpO2/FiO2 < 324, who were older than 62 years, and had an Hb of [≥] 16 g/dl had the highest mortality risk (96%). Additionally, patients with SpO2/FiO2 > 324 but Hb of < 12 and neutrophil-to-lymphocyte ratio of > 4 had a higher mortality likelihood (57%). In contrast, patients with SpO2/FiO2 > 324 and Hb of > 12 g/dl had the lowest mortality risk (10%).\n\nConclusionWe found that a decreased SpO2/FiO2 increased mortality risk. Extreme values of Hb, either low or high, showed an increase in likelihood of mortality. However, Hb concentration modified the SpO2/FiO2 effect on mortality; the likelihood of death in patients with low SpO2/FiO2 increased as Hb increased.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Andr\u00e9s Felipe Pati\u00f1o-Aldana", + "author_inst": "Universidad del Rosario: Universidad Del Rosario" + }, + { + "author_name": "\u00c1ngela Mar\u00eda Ru\u00edz Sternberg", + "author_inst": "Universidad Del Rosario Escuela de Medicina y Ciencias de la Salud" + }, + { + "author_name": "Angela Maria Pinzon-Rondon", + "author_inst": "Universidad Del Rosario" + }, + { + "author_name": "Nicolas Molano-Gonz\u00e1lez", + "author_inst": "Universidad del Rosario: Universidad Del Rosario" + }, + { + "author_name": "David Ren\u00e9 Rodr\u00edguez-Lima", + "author_inst": "M\u00e9deri: Hospital Universitario Mayor" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.08.22270666", "rel_title": "Monitoring SARS-CoV-2 in wastewater during New York City's second wave of COVID-19: Sewershed-level trends and relationships to publicly available clinical testing data", @@ -420153,69 +422100,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2022.02.07.479471", - "rel_title": "The mechanism of RNA capping by SARS-CoV-2", - "rel_date": "2022-02-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.07.479471", - "rel_abs": "The SARS-CoV-2 RNA genome contains a 5-cap that facilitates translation of viral proteins, protection from exonucleases and evasion of the host immune response1-4. How this cap is made is not completely understood. Here, we reconstitute the SARS-CoV-2 7MeGpppA2-O-Me-RNA cap using virally encoded non-structural proteins (nsps). We show that the kinase-like NiRAN domain5 of nsp12 transfers RNA to the amino terminus of nsp9, forming a covalent RNA-protein intermediate (a process termed RNAylation). Subsequently, the NiRAN domain transfers RNA to GDP, forming the cap core structure GpppA-RNA. The nsp146 and nsp167 methyltransferases then add methyl groups to form functional cap structures. Structural analyses of the replication-transcription complex bound to nsp9 identified key interactions that mediate the capping reaction. Furthermore, we demonstrate in a reverse genetics system8 that the N-terminus of nsp9 and the kinase-like active site residues in the NiRAN domain are required for successful SARS-CoV-2 replication. Collectively, our results reveal an unconventional mechanism by which SARS-CoV-2 caps its RNA genome, thus exposing a new target in the development of antivirals to treat COVID-19.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Gina J Park", - "author_inst": "UT Southwestern" - }, - { - "author_name": "Adam Osinski", - "author_inst": "UT Southwestern Medical Center" - }, - { - "author_name": "Genaro Hernandez", - "author_inst": "UT Southwestern" - }, - { - "author_name": "Jennifer Eitson", - "author_inst": "UT Southwestern" - }, - { - "author_name": "Abir Majumdar", - "author_inst": "UT Southwestern" - }, - { - "author_name": "Marco Tonelli", - "author_inst": "UW-Madison" - }, - { - "author_name": "Katherine Henzler-Wildman", - "author_inst": "University of Wisconsin - Madison" - }, - { - "author_name": "Krzysztof Pawlowski", - "author_inst": "UT Southwestern" - }, - { - "author_name": "Zhe Chen", - "author_inst": "UT Southwestern" - }, - { - "author_name": "Yang Li", - "author_inst": "University of Texas Southwestern Medical Center at Dallas" - }, - { - "author_name": "John Schoggins", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Vincent S. Tagliabracci", - "author_inst": "HHMI/UT Southwestern Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2022.02.08.479559", "rel_title": "Designing effective siRNAs to silence structural proteins associated genes of Indian SARS-CoV-2 strains: an in silico approach", @@ -421779,6 +423663,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.07.22270490", + "rel_title": "Effectiveness of Covid-19 Vaccines against the SARS-COV-2-Delta (B.1.617.2) in China-A Real World Study", + "rel_date": "2022-02-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.07.22270490", + "rel_abs": "AbstractsO_ST_ABSBackgroundC_ST_ABSSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) delta (B.1.617.2) variant is highly transmissible and has contributed to a surge in cases globally. This study aimed to explore the potential of vaccines against SARS-CoV-2 delta (B.1.617.2) variant in China.\n\nMethodsIn this real-world study, all data were extracted from Xian Chest Hospital. Confirmed cases infected with Delta VOC with exact date of positive viral testing were included for analysis. Patients meeting the study criteria were divided into unvaccinated and partially vaccinated (one dose), full vaccinated (two doses), and booster vaccination of COVID-19.\n\nResultsA total of 455 cases were enrolled in this study. Proportion of severe and critical cases in full vaccinated cases (1.82%) and cases with booster vaccination (1.35%) of COVID-19 were much lower than that of unvaccinated and partially vaccinated cases (8.16%). In addition, cases with booster vaccination (12.78 days) and full vaccinated cases (12.59 days) showed shorter duration of viral shedding than that in unvaccinated and partially vaccinated cases (13.87 days).\n\nConclusionThis is the first real world study indicating that Covid-19 vaccines showed much powerful effectiveness against the SARS-COV-2-Delta (B.1.617.2) in China, including lowing the proportion of severe illness and shorting the virus shedding time.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Xinge Ma", + "author_inst": "The First Affiliated Hospital of Xi'an Jiaotong University" + }, + { + "author_name": "Jianfeng Han", + "author_inst": "The First Affiliated Hospital of Xi'an Jiaotong University" + }, + { + "author_name": "Hongxia Li", + "author_inst": "The First Affiliated Hospital of Xi'an Jiaotong University" + }, + { + "author_name": "Chang Liu", + "author_inst": "The First Affiliated Hospital of Xi'an Jiaotong University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.05.22269707", "rel_title": "Acoustic Epidemiology in Pulmonary Tuberculosis & Covid19 leveraging Explainable AI/ML", @@ -422227,45 +424142,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.02.07.22270613", - "rel_title": "Time to reinfection and vaccine breakthrough SARS-CoV-2 infections: a retrospective cohort study", - "rel_date": "2022-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.07.22270613", - "rel_abs": "BackgroundIt is important to understand how BNT162b2, mRNA-1273, and JNJ-78436735 COVID-19 vaccines, as well as prior infection, protect against breakthrough cases and reinfections. Real world evidence on acquired immunity from vaccines, and from SARS-CoV-2 infection, can help public health decision-makers understand disease dynamics and viral escape to inform resource allocation for curbing the spread of pandemic.\n\nMethodsThis retrospective cohort study presents demographic information, survival functions, and probability distributions for 2,627,914 patients who received recommended doses of COVID-19 vaccines, and 63,691 patients who had a prior COVID-19 infection. In addition, patients receiving different vaccines were matched by age, sex, ethnic group, state of residency, and the quarter of the year in 2021 the COVID-19 vaccine was completed, to support survival analysis on pairwise matched cohorts.\n\nFindingsEach of the three vaccines and infection-induced immunity all showed a high probability of survival against breakthrough or reinfection cases (mRNA-1273: 0.997, BNT162b2: 0.997, JNJ-78436735: 0.992, previous infection: 0.965 at 180 days). The incidence rate of reinfection among those unvaccinated and previously infected was higher than that of breakthrough among the vaccinated population (reinfection: 0.9%; breakthrough:0.4%). In addition, 280 vaccinated patients died (0.01% all-cause mortality) within 21 days of the last vaccine dose, and 5898 (3.1 %) died within 21 days of a positive COVID-19 test.\n\nConclusionsDespite a gradual decline in vaccine-induced and infection-induced immunity, both acquired immunities were highly effective in preventing breakthrough and reinfection. In addition, for unvaccinated patients with COVID-19, those who did not die within 90 days of their initial infection (9565 deaths, 5.0% all-cause mortality rate), had a comparable asymptotic pattern of breakthrough infection as those who acquired immunity from a vaccine. Overall, the risks associated with COVID-19 infection are far greater than the marginal advantages of immunity acquired by prior infection.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Sevda Molani", - "author_inst": "Institute For Systems Biology" - }, - { - "author_name": "Andrew M Baumgartner", - "author_inst": "Institute for Systems Biology" - }, - { - "author_name": "Yeon Mi Hwang", - "author_inst": "Institute for Systems Biology" - }, - { - "author_name": "Venkata R Duvvuri", - "author_inst": "Institute for Systems Biology" - }, - { - "author_name": "Jason Goldman", - "author_inst": "Swedish Medical Center" - }, - { - "author_name": "Jennifer J Hadlock", - "author_inst": "Institute for System Biology" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.07.22270568", "rel_title": "Duration of protection of BNT162b2 and mRNA-1273 COVID-19 vaccines against symptomatic SARS-CoV-2 Omicron infection in Qatar", @@ -423797,6 +425673,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.07.22270614", + "rel_title": "Chronic Disease and Workforce Participation Among Medicaid Enrollees Over 50: The Potential Impact of Medicaid Work Requirements Post-COVID-19", + "rel_date": "2022-02-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.07.22270614", + "rel_abs": "As the COVID-19 pandemic wanes, states may reintroduce Medicaid work requirements to reduce enrollment. Using the Health and Retirement Study, we evaluated chronic disease burden among beneficiaries aged >50 (n=1460) who might be impacted by work requirements (i.e. working <20 hours per week). Seven of eight chronic conditions evaluated were associated with reduced workforce participation, including history of stroke (OR: 7.35; 95% CI: 2.98-18.14) and lung disease (OR: 4.39; 95% CI: 2.97-7.47). Those with more severe disease were also more likely to work fewer hours. Medicaid work requirements would likely have great impact on older beneficiaries with significant disease burden.\n\nKey PointsO_LIChronic disease linked to reduced work among older Medicaid beneficiaries.\nC_LIO_LIWork requirements would greatly impact those aged >50 with chronic conditions.\nC_LIO_LICoverage loss would have negative implications for long-term disease management.\nC_LI", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Rodlescia Sneed", + "author_inst": "Michigan State University" + }, + { + "author_name": "Alexander Stubblefield", + "author_inst": "Michigan State University" + }, + { + "author_name": "Graham Gardner", + "author_inst": "Michigan State University" + }, + { + "author_name": "Tamara Jordan", + "author_inst": "Michigan State University" + }, + { + "author_name": "Briana Mezuk", + "author_inst": "University of Michigan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2022.02.04.479209", "rel_title": "Comparative analysis of cell-cell communication at single-cell resolution", @@ -424257,165 +426168,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.02.06.479285", - "rel_title": "Vaccine Protection Against the SARS-CoV-2 Omicron Variant in Macaques", - "rel_date": "2022-02-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.06.479285", - "rel_abs": "BackgroundThe rapid spread of the SARS-CoV-2 Omicron (B.1.1.529) variant, including in highly vaccinated populations, has raised important questions about the efficacy of current vaccines. Immune correlates of vaccine protection against Omicron are not known.\n\nMethods30 cynomolgus macaques were immunized with homologous and heterologous prime-boost regimens with the mRNA-based BNT162b2 vaccine and the adenovirus vector-based Ad26.COV2.S vaccine. Following vaccination, animals were challenged with the SARS-CoV-2 Omicron variant by the intranasal and intratracheal routes.\n\nResultsOmicron neutralizing antibodies were observed following the boost immunization and were higher in animals that received BNT162b2, whereas Omicron CD8+ T cell responses were higher in animals that received Ad26.COV2.S. Following Omicron challenge, sham controls showed more prolonged virus in nasal swabs than in bronchoalveolar lavage. Vaccinated macaques demonstrated rapid control of virus in bronchoalveolar lavage, and most vaccinated animals also controlled virus in nasal swabs, showing that current vaccines provide substantial protection against Omicron in this model. However, vaccinated animals that had moderate levels of Omicron neutralizing antibodies but negligible Omicron CD8+ T cell responses failed to control virus in the upper respiratory tract. Virologic control correlated with both antibody and T cell responses.\n\nConclusionsBNT162b2 and Ad26.COV2.S provided robust protection against high-dose challenge with the SARS-CoV-2 Omicron variant in macaques. Protection against this highly mutated SARS-CoV-2 variant correlated with both humoral and cellular immune responses.", - "rel_num_authors": 36, - "rel_authors": [ - { - "author_name": "Abishek Chandrashekar", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Jingyou Yu", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Katherine McMahan", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Catherine Jacob-Dolan", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Jinyan Liu", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Xuan He", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "David Hope", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Tochi Anioke", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Julia Barrett", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Benjamin Chung", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Nicole Hachmann", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Michelle Lifton", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Jessica Miller", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Olivia Powers", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Michaela Sciacca", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Daniel Sellers", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Mazuba Siamatu", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Nehalee Surve", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Haley VanWyk", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Huahua Wan", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Cindy Wu", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Laurent Pessaint", - "author_inst": "Bioqual Inc" - }, - { - "author_name": "Daniel Valentin", - "author_inst": "Bioqual" - }, - { - "author_name": "Alex Van Ry", - "author_inst": "Bioqual" - }, - { - "author_name": "Jeanne Muench", - "author_inst": "Bioqual" - }, - { - "author_name": "Mona Boursiquot", - "author_inst": "Bioqual" - }, - { - "author_name": "Anthony Cook", - "author_inst": "Bioqual" - }, - { - "author_name": "Jason Velasco", - "author_inst": "Bioqual" - }, - { - "author_name": "Elyse Teow", - "author_inst": "Bioqual" - }, - { - "author_name": "Adrianus Boon", - "author_inst": "Washington University in St Louis" - }, - { - "author_name": "Mehul Suthar", - "author_inst": "Emory University" - }, - { - "author_name": "Neharika Jain", - "author_inst": "Tufts" - }, - { - "author_name": "Amanda J. Martinot", - "author_inst": "Tufts University Cummings School of Veterinary Medicine" - }, - { - "author_name": "Mark G. Lewis", - "author_inst": "Bioqual Inc" - }, - { - "author_name": "Hanne Andersen", - "author_inst": "Bioqual Inc" - }, - { - "author_name": "Dan H. Barouch", - "author_inst": "Beth Israel Deaconess Medical Center" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.02.07.479343", "rel_title": "Machine learning-based approach KEVOLVE efficiently identifies SARS-CoV-2 variant-specific genomic signatures", @@ -426091,6 +427843,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2022.02.07.22270575", + "rel_title": "COVID-19 outbreaks in Australia during a period of high epidemic control, 2020", + "rel_date": "2022-02-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.07.22270575", + "rel_abs": "To describe characteristics of COVID-19 outbreaks in Australia to guide policy development for mitigation of future outbreaks, we conducted a retrospective analysis of COVID-19 outbreaks affecting two or more people reported to COVID-Net--an Australian national surveillance network--from 28 January until 27 December 2020. The COVID-Net surveillance network covered all Australian states and territories, with an estimated population of 25,649,985 persons as at 31 June 2020. We reported the epidemiology of COVID-19 outbreaks in Australia, including the setting in which they occurred, size, and duration.\n\n853 outbreaks of COVID-19 were reported; associated with 13,957 confirmed cases, of whom 2,047 were hospitalised, and 800 died. The pattern of outbreaks followed a similar trend to the epidemic in Australia, defined by two distinct peaks in mid-March and July. Victoria reported the greatest number of outbreaks across all settings aligned with the second wave of infections. Outbreaks most commonly occurred in the workplace/industry setting (22%, 190/853), followed by education (14%, 122/853), residential aged care (13%, 114/853) and hospitals (10%, 83/853). The majority (40%, 340/853) of outbreaks had 6 to 24 cases, and the median outbreak duration increased in proportion with the number of associated cases.\n\nThis report summarising COVID-19 outbreaks in Australia identifies settings of highest risk. Surveillance of outbreaks informs our understanding of transmission dynamics in Australia relative to national and jurisdictional interventions. For settings that are high risk for COVID-19, it is important to prioritise planning, surveillance, and implementation of control measures.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Freya G Hogarth", + "author_inst": "Australian Government Department of Health" + }, + { + "author_name": "Rachel Nye", + "author_inst": "Australian Government Department of Health" + }, + { + "author_name": "Nevada Pingault", + "author_inst": "Western Australia Department of Health: Government of Western Australia Department of Health" + }, + { + "author_name": "Simon Crouch", + "author_inst": "Victorian Department of Health" + }, + { + "author_name": "Cushla Coffey", + "author_inst": "Queensland Health" + }, + { + "author_name": "Kylie Smith", + "author_inst": "Tasmanian Health Service THS: Tasmania Department of Health" + }, + { + "author_name": "Rowena Boyd", + "author_inst": "Northern Territory Department of Health and Community Services: Northern Territory Department of Health" + }, + { + "author_name": "Catherine Kelaher", + "author_inst": "Australian Government Department of Health" + }, + { + "author_name": "Tracie Reinten", + "author_inst": "NSW Health: New South Wales Ministry of Health" + }, + { + "author_name": "Moira C Hewitt", + "author_inst": "Australian Government Department of Health" + }, + { + "author_name": "Ben Polkinghorne", + "author_inst": "Australian National University" + }, + { + "author_name": "Martyn Kirk", + "author_inst": "Australian National University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.02.04.22270473", "rel_title": "Minimizing school disruption under high incidence conditions due to the Omicron variant in early 2022", @@ -426855,41 +428670,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.02.05.22270499", - "rel_title": "Comparative study of immunogenicity and safety of Gam-COVID-Vac and Sinopharm BBIBP-CorV vaccines in Belarus", - "rel_date": "2022-02-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.05.22270499", - "rel_abs": "IntroductionLack of comparative studies on efficiency of a broad range of COVID19 vaccines leads to lower levels of adoption and subsequent lower total immunity in several regions, including Republic of Belarus. This clinical study captures and transparently demonstrates varying immunogenic responses to Sputnik V and Sinopharm vaccines.\n\nAim of this study wasto compare the immunogenicity and reactogenicity of Sputnik V (Gam-COVID-Vac), RF and Sinopharm (BBIBP-CorV), PRC vaccines in vaccinated individuals.\n\nMaterials and MethodsA total of 60 adults participated the study. The immune response after vaccination was assessed using enzyme immunoassay. IgG levels measured in all participants at three time points: before the vaccination, 42 days after the first vaccine dose, and 6 months after the first vaccine dose. The results of the SARS-CoV-2 antibody test is quantified according to the WHO First International Standard (NIBSC code:20/136) and expressed in international units (BAU/ml).\n\nResultsThe study participants were divided into two groups, where 30 people (50%) were vaccinated with Sputnik V (Gam-COVID-Vac), and 30 people were vaccinated with Sinopharm (BBIBP-CorV), with no gender differences in the groups. The IgG levels at 42 days after the first vaccine dose were: Sputnik V (Gam-COVID-Vac)(42 days): Me=650.4 (642.2-669.4); Sinopharm (BBIBP-CorV)(42 days): Me=376.5 (290.9-526.4); p<0,001). The IgG levels at 6 months after the first vaccine dose were: Sputnik V (Gam-COVID-Vac)(6 months) Me=608.7 (574.6-647.1); Sinopharm (BBIBP-CorV)(6 months): Me=106.3 (78.21-332.4); p<0,001). Reactions after vaccination appeared in 27 vaccinated individuals (45%).\n\nConclusionThe study showed that Sputnik V (Gam-COVID-Vac) vaccine was more immunogenic than Sinopharm (BBIBP-CorV) vaccine. IgG levels in vaccinated individuals who previously recovered from SARS-CoV-2 infection (\"hybrid immunity\") were higher than in SARS-CoV-2 naive individuals. Reactions after vaccines administration were mild to moderate.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Igor Stoma", - "author_inst": "Gomel state medical university" - }, - { - "author_name": "Katsiaryna Korsak", - "author_inst": "Gomel state medical university" - }, - { - "author_name": "Evgenii Voropaev", - "author_inst": "Gomel state medical university" - }, - { - "author_name": "Olga Osipkina", - "author_inst": "Gomel state medical university" - }, - { - "author_name": "Aleksey Kovalev", - "author_inst": "Gomel state medical university" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.02.04.22270143", "rel_title": "Emulation of a target trial from observational data to compare effectiveness of Casirivimab/Imdevimab and Bamlanivimab/Etesevimab for early treatment of non-hospitalized patients with COVID-19", @@ -428133,6 +429913,285 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2022.02.03.479037", + "rel_title": "mRNA-1273 or mRNA-Omicron boost in vaccinated macaques elicits comparable B cell expansion, neutralizing antibodies and protection against Omicron", + "rel_date": "2022-02-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.03.479037", + "rel_abs": "SARS-CoV-2 Omicron is highly transmissible and has substantial resistance to antibody neutralization following immunization with ancestral spike-matched vaccines. It is unclear whether boosting with Omicron-specific vaccines would enhance immunity and protection. Here, nonhuman primates that received mRNA-1273 at weeks 0 and 4 were boosted at week 41 with mRNA-1273 or mRNA-Omicron. Neutralizing antibody titers against D614G were 4760 and 270 reciprocal ID50 at week 6 (peak) and week 41 (pre-boost), respectively, and 320 and 110 for Omicron. Two weeks after boost, titers against D614G and Omicron increased to 5360 and 2980, respectively, for mRNA-1273 and 2670 and 1930 for mRNA-Omicron. Following either boost, 70-80% of spike-specific B cells were cross-reactive against both WA1 and Omicron. Significant and equivalent control of virus replication in lower airways was observed following either boost. Therefore, an Omicron boost may not provide greater immunity or protection compared to a boost with the current mRNA-1273 vaccine.", + "rel_num_authors": 66, + "rel_authors": [ + { + "author_name": "Matthew Gagne", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Juan I. Moliva", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Kathryn E. Foulds", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Shayne F. Andrew", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Barbara J. Flynn", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Anne P. Werner", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Danielle A. Wagner", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "I-Ting Teng", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Bob C. Lin", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Christopher Moore", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Nazaire Jean-Baptiste", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Robin Carroll", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Stephanie L. Foster", + "author_inst": "Department of Pediatrics, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, Georgia, 30322, United St" + }, + { + "author_name": "Mit Patel", + "author_inst": "Department of Pediatrics, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, Georgia, 30322, United St" + }, + { + "author_name": "Madison Ellis", + "author_inst": "Department of Pediatrics, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, Georgia, 30322, United St" + }, + { + "author_name": "Venkata-Viswanadh Edara", + "author_inst": "Department of Pediatrics, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, Georgia, 30322, United St" + }, + { + "author_name": "Nahara Vargas Maldonado", + "author_inst": "Department of Pediatrics, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, Georgia, 30322, United St" + }, + { + "author_name": "Mahnaz Minai", + "author_inst": "Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rock" + }, + { + "author_name": "Lauren McCormick", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Christopher Cole Honeycutt", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Bianca M. Nagata", + "author_inst": "Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rock" + }, + { + "author_name": "Kevin W. Bock", + "author_inst": "Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rock" + }, + { + "author_name": "Caitlyn N. M. Dulan", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Jamilet Cordon", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "John-Paul M. Todd", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Elizabeth McCarthy", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Laurent Pessaint", + "author_inst": "Bioqual, Inc., Rockville, Maryland, 20850, United States of America" + }, + { + "author_name": "Alex Van Ry", + "author_inst": "Bioqual, Inc., Rockville, Maryland, 20850, United States of America" + }, + { + "author_name": "Brandon Narvaez", + "author_inst": "Bioqual, Inc., Rockville, Maryland, 20850, United States of America" + }, + { + "author_name": "Daniel Valentin", + "author_inst": "Bioqual, Inc., Rockville, Maryland, 20850, United States of America" + }, + { + "author_name": "Anthony Cook", + "author_inst": "Bioqual, Inc., Rockville, Maryland, 20850, United States of America" + }, + { + "author_name": "Alan Dodson", + "author_inst": "Bioqual, Inc., Rockville, Maryland, 20850, United States of America" + }, + { + "author_name": "Katelyn Steingrebe", + "author_inst": "Bioqual, Inc., Rockville, Maryland, 20850, United States of America" + }, + { + "author_name": "Dillon R. Flebbe", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Saule T. Nurmukhambetova", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Sucheta Godbole", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Amy R. Henry", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Farida Laboune", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Jesmine Roberts-Torres", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Cynthia G. Lorang", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Shivani Amin", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Jessica Trost", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Mursal Naisan", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Manjula Basappa", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Jacquelyn Willis", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Lingshu Wang", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Wei Shi", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Nicole A. Doria-Rose", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Adam S. Olia", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Cuiping Liu", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Darcy R. Harris", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Andrea Carfi", + "author_inst": "Moderna Inc., Cambridge, MA, 02139, United States of America" + }, + { + "author_name": "John R. Mascola", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Peter D. Kwong", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Darin K. Edwards", + "author_inst": "Moderna Inc., Cambridge, MA, 02139, United States of America" + }, + { + "author_name": "Hanne Andersen", + "author_inst": "Bioqual, Inc., Rockville, Maryland, 20850, United States of America" + }, + { + "author_name": "Mark G. Lewis", + "author_inst": "Bioqual, Inc., Rockville, Maryland, 20850, United States of America" + }, + { + "author_name": "Kizzmekia S. Corbett", + "author_inst": "Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, 02115, United States of America" + }, + { + "author_name": "Martha C. Nason", + "author_inst": "Biostatistics Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Ma" + }, + { + "author_name": "Adrian B. McDermott", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Mehul S. Suthar", + "author_inst": "Department of Pediatrics, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, Georgia, 30322, United St" + }, + { + "author_name": "Ian N. Moore", + "author_inst": "Division of Pathology, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, Georgia, 30329, United States of America" + }, + { + "author_name": "Mario Roederer", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Nancy J. Sullivan", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Daniel C. Douek", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + }, + { + "author_name": "Robert A. Seder", + "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.02.02.478897", "rel_title": "Primary human macrophages exhibit a modest inflammatory response early in SARS-CoV-2 infection", @@ -428709,61 +430768,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, - { - "rel_doi": "10.1101/2022.02.03.22270417", - "rel_title": "Fatality assessment and variant risk monitoring for COVID-19 using three new hospital occupancy related metrics", - "rel_date": "2022-02-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.03.22270417", - "rel_abs": "BackgroundThough case fatality rate (CFR) is widely used to reflect COVID-19 fatality risk, its use is limited by large temporal and spatial variation. Hospital mortality rate (HMR) is also used to assess the severity of COVID-19, but HMR data is not directly available except 35 states of USA. Alternative metrics are needed for COVID-19 severity and fatality assessment.\n\nMethodsNew metrics and their applications in fatality measurements and risk monitoring are proposed here. We also introduce a new mathematical model to estimate average hospital length of stay for death (Ldead) and discharges (Ldis). Multiple data sources were used for our analysis.\n\nFindingsWe propose three new metrics, hospital occupancy mortality rate (HOMR), ratio of total deaths to hospital occupancy (TDHOR) and ratio of hospital occupancy to cases (HOCR), for dynamic assessment of COVID-19 fatality risk. Estimated Ldead and Ldis for 501,079 COVID-19 hospitalizations in US 34 states between Aug 7, 2020 and Mar 1, 2021 were 14.0 and 18.2 days, respectively. We found that TDHOR values of 27 countries are less spatially and temporally variable and more capable of detecting changes in COVID-19 fatality risk. The dramatic changes in COVID-19 CFR observed in 27 countries during early stages of the pandemic were mostly caused by undiagnosed cases. Compared to the first week of November, 2021, the week mean HOCRs (mimics hospitalization-to-case ratio) for Omicron variant decreased 34.08% and 65.16% in the United Kingdom and USA respectively as of Jan 16, 2022.\n\nInterpretationThese new and reliable measurements for COVID-19 that could be expanded as a general index to other fatal infectious diseases for disease fatality risk and variant-associated risk monitoring.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed, medRxiv, and bioRxiv for peer-reviewed articles, preprints, and research reports on risk and health care evaluation for COVID-19 using the search terms \"hospital occupancy mortality rate\", \"ratio of total deaths to hospital occupancy\", \"ratio of hospital occupancy to case\" up to Jan 20, 2022. No similar concepts or studies were found. No similar mathematical models based on \"hospital occupancy mortality rate\" for the estimation of hospital length of stay for deaths and discharges have been identified to date.\n\nAdded value of the studyOur new metrics, HOMR and TDHOR, mimic HMR for COVID-19 fatality risk assessment but utilize readily available data for many US states and countries around the world. HOCR mimics hospitalization-to-case ratio for COVID-19. We also provide evidence that explains why COVID-19 CFR has such dramatic changes at the beginning of a COVID-19 outbreak. We have additionally provided new metrics for COVID-19 fatality risk dynamic monitoring including Omicron variant and showed that these metrics provided additional information.\n\nImplications of all the available evidenceThe results of this study, including average hospital length of stay for deaths and discharges for over 500,000 COVID-19 hospitalizations in the US, can aid county, state, and national leaders in making informed public health decisions related to the ongoing COVID-19 pandemic. This is the first study to provide quantitative evidence to address why CFR has a such a large variation at the beginning of the COVID-19 pandemic in most countries and will hopefully encourage more countries to release hospital occupancy data, which we show is both useful and easy information to collect. The new metrics introduced by our study are effective indicators for monitoring COVID-19 fatality risk, as well as potentially fatal COVID-19 variants, and could also be expanded to other fatal infectious diseases.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Ping-Wu Zhang", - "author_inst": "Wilmer Eye Institute, Johns Hopkins University School of Medicine; Baltimore, MD, 21231, USA" - }, - { - "author_name": "Steven H Zhang", - "author_inst": "Department of Computer Science, University of Maryland at College park, undergraduate student (present affiliation)" - }, - { - "author_name": "Wei-Feng Li", - "author_inst": "Wilmer Eye Institute, Johns Hopkins University School of Medicine; Baltimore, MD, 21231, USA" - }, - { - "author_name": "Casey J Keuthan", - "author_inst": "Wilmer Eye Institute, Johns Hopkins University School of Medicine; Baltimore, MD, 21231, USA" - }, - { - "author_name": "Shuaizhang Li", - "author_inst": "Wilmer Eye Institute, Johns Hopkins University School of Medicine; Baltimore, MD, 21231, USA" - }, - { - "author_name": "Felipe Takaesu", - "author_inst": "Wilmer Eye Institute, Johns Hopkins University School of Medicine; Baltimore, MD, 21231, USA" - }, - { - "author_name": "Cynthia A Berlinicke", - "author_inst": "Wilmer Eye Institute, Johns Hopkins University School of Medicine; Baltimore, MD, 21231, USA" - }, - { - "author_name": "Jun Wan", - "author_inst": "Department of Medical and Molecular Genetics, Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, 4620" - }, - { - "author_name": "Jing Sun", - "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, MD, 21113, USA" - }, - { - "author_name": "Donald J Zack", - "author_inst": "Wilmer Eye Institute, Johns Hopkins University School of Medicine; Baltimore, MD, 21231, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.02.02.22270353", "rel_title": "Modeling Vaccinations, Virus Variants and Lockdown: Early guidance for Sars-Cov-2 health policies in India", @@ -430031,6 +432035,29 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.02.02.478873", + "rel_title": "Unraveling the Enzymatic Mechanism of the SARS-CoV-2 RNA-Dependent-RNA-Polymerase. An Unusual Active Site Leading to High Replication Rates.", + "rel_date": "2022-02-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.02.478873", + "rel_abs": "Viral infection relies on the hijacking of cellular machineries to enforce the reproduction of the infecting virus and its subsequent diffusion. In this context the replication of the viral genome is a key step performed by specific enzymes, i.e. polymerases. The replication of SARS-CoV-2, the causative agent of the COVID-19 pandemics, is based on the duplication of its RNA genome, an action performed by the viral RNA-dependent-RNA polymerase. In this contribution, for the first time and by using two-dimensional enhanced sampling quantum mechanics/ molecular mechanics, we have determined the chemical mechanisms leading to the inclusion of a nucleotide in the nascent viral RNA strand. We prove the high efficiency of the polymerase, which lowers the activation free energy to less than 10 kcal/mol. Furthermore, the SARS-CoV-2 polymerase active site is slightly different from those found usually found in other similar enzymes, and particularly it lacks the possibility to enforce a proton shuttle via a nearby histidine. Our simulations show that this absence is partially compensate by lysine, whose proton assist the reaction opening up an alternative, but highly efficient, reactive channel. Our results present the first mechanistic resolution of SARS-CoV-2 genome replication and shed light on unusual enzymatic reactivity paving the way for future rational design of antivirals targeting emerging RNA viruses.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Emmanuelle Bignon", + "author_inst": "Universite de Lorraine" + }, + { + "author_name": "Antonio Monari", + "author_inst": "Universite de Paris and CNRS, ITODYS" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2022.02.03.22270390", "rel_title": "Private Equity Acquisition in Ophthalmology and Optometry: A Time Series Analysis of the Pre-COVID, COVID Pre-Vaccine, and COVID Post-Vaccine Eras", @@ -430623,25 +432650,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2022.02.03.22270396", - "rel_title": "COVID-19 Vaccination is Associated with Decreasing Cases, Hospitalizations, and Deaths Across Age Groups and Variants over 9 months in Switzerland", - "rel_date": "2022-02-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.03.22270396", - "rel_abs": "Recent studies assessing COVID-19 vaccine efficacy at the population level found counterintuitive results, such as positive associations between vaccination and infections or deaths. These ecological studies have limitations, including too short observation periods, focusing on infections, and not controlling for age groups and dominant variants. The current study addresses these limitations by investigating the relations between vaccination and COVID-19 cases, hospitalizations, and deaths over a longer period (9[1/2] months) while also considering age groups (from 10 to 80+ years old) and variants (Alpha and Delta), utilizing data from Switzerland. Results suggest that vaccination is negatively related to cases overall and in all cantons of Switzerland, and that vaccination is negatively related to hospitalizations and deaths from 50 years old. Furthermore, vaccination is a significant predictor of cases, hospitalizations, and deaths while holding the effects of age and dominant variant constant.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Jean-Luc Jucker", - "author_inst": "Currently none" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.02.03.22270306", "rel_title": "Mental health in a diverse sample of healthcare workers during the COVID-19 pandemic: cross-sectional analysis of the UK-REACH study", @@ -431989,6 +433997,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.02.02.22270302", + "rel_title": "Durability of Omicron-neutralizing serum activity following mRNA booster immunization in elderly individuals", + "rel_date": "2022-02-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.02.22270302", + "rel_abs": "Elderly individuals are at high risk for severe COVID-19. Due to modest vaccine responses compared to younger individuals and the time elapsed since prioritized vaccinations, the emerging immune-evasive Omicron variant of SARS-CoV-2 is a particular concern for the elderly. Here we longitudinally determined SARS-CoV-2-neutralizing serum activity against different variants in a cohort of 37 individuals with a median age of 82 years. Participants were followed for 10 months after an initial two-dose BNT162b2 vaccination and up to 4.5 months after a BNT162b2 booster. Detectable Omicron-neutralizing activity was nearly absent after two vaccinations but elicited in 89% of individuals by the booster immunization. Neutralizing titers against the Wu01, Delta, and Omicron variants showed similar post-boost declines and 81% of individuals maintained detectable activity against Omicron. Our study demonstrates the mRNA booster effectiveness in inducing Omicron neutralizing activity and provides critical information on vaccine response durability in the highly vulnerable elderly population.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Kanika Vanshylla", + "author_inst": "Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany" + }, + { + "author_name": "Pinkus Tober-Lau", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charite-Universitaetsmedizin Berlin, Freie Universitaet Berlin and Humboldt-Universitaet zu Berlin, " + }, + { + "author_name": "Henning Gruell", + "author_inst": "Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany" + }, + { + "author_name": "Friederike Muenn", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charite-Universitaetsmedizin Berlin, Freie Universitaet Berlin and Humboldt-Universitaet zu Berlin, " + }, + { + "author_name": "Ralf Eggeling", + "author_inst": "Methods in Medical Informatics, Department of Computer Science, University of Tuebingen, Tuebingen, Germany" + }, + { + "author_name": "Nico Pfeifer", + "author_inst": "Methods in Medical Informatics, Department of Computer Science, University of Tuebingen, Tuebingen, Germany" + }, + { + "author_name": "N. Han Le", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charite-Universitaetsmedizin Berlin, Freie Universitaet Berlin and Humboldt-Universitaet zu Berlin, " + }, + { + "author_name": "Irmgard Landgraf", + "author_inst": "Hausarztpraxis am Agaplesion Bethanien Sophienhaus, Berlin, Germany" + }, + { + "author_name": "Florian Kurth", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charite-Universitaetsmedizin Berlin, Freie Universitaet Berlin and Humboldt-Universitaet zu Berlin, " + }, + { + "author_name": "Leif Erik Sander", + "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charite-Universitaetsmedizin Berlin, Freie Universitaet Berlin and Humboldt-Universitaet zu Berlin, " + }, + { + "author_name": "Florian Klein", + "author_inst": "Laboratory of Experimental Immunology, Institute of Virology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.02.01.22270279", "rel_title": "Rapid, high throughput, automated detection of SARS-CoV-2 neutralizing antibodies against native-like vaccine and delta variant spike trimers", @@ -432429,61 +434496,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2022.02.01.478697", - "rel_title": "Patterns of Volatility Across the Spike Protein Accurately Predict the Emergence of Mutations within SARS-CoV-2 Lineages", - "rel_date": "2022-02-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.02.01.478697", - "rel_abs": "Mutations in the spike glycoprotein of SARS-CoV-2 allow the virus to probe the sequence space in search of higher-fitness states. New sublineages of SARS-CoV-2 variants-of-concern (VOCs) continuously emerge with such mutations. Interestingly, the sites of mutation in these sublineages vary between the VOCs. Whether such differences reflect the random nature of mutation appearance or distinct evolutionary spaces of spike in the VOCs is unclear. Here we show that each position of spike has a lineage-specific likelihood for mutations to appear and dominate descendent sublineages. This likelihood can be accurately estimated from the lineage-specific mutational profile of spike at a protein-wide level. The mutability environment of each position, including adjacent sites on the protein structure and neighboring sites on the network of comutability, accurately forecast changes in descendent sublineages. Mapping of imminent changes within the VOCs can contribute to the design of immunogens and therapeutics that address future forms of SARS-CoV-2.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Roberth Anthony Rojas Chavez", - "author_inst": "The University of Iowa" - }, - { - "author_name": "Mohammad Fili", - "author_inst": "Iowa State University" - }, - { - "author_name": "Changze Han", - "author_inst": "The University of Iowa" - }, - { - "author_name": "Syed A. Rahman", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Isaiah Guzman L Bicar", - "author_inst": "The University of Iowa" - }, - { - "author_name": "Sullivan Gregory", - "author_inst": "The University of Iowa" - }, - { - "author_name": "Guiping Hu", - "author_inst": "Rochester Institute of Technology" - }, - { - "author_name": "Jishnu Das", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Grant D. Brown", - "author_inst": "The University of Iowa" - }, - { - "author_name": "Hillel Haim", - "author_inst": "The University of Iowa" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2022.02.01.478685", "rel_title": "Chronic alcohol intake regulates expression of SARS-CoV2 infection-relevant genes in an organ-specific manner", @@ -433651,6 +435663,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.01.31.22270058", + "rel_title": "Analysis of COVID-19 infection amongst healthcare workers in Rivers State, Nigeria", + "rel_date": "2022-02-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.31.22270058", + "rel_abs": "Background/aimsHealthcare workers (HCWs) are at an increased risk of infection and mortality associated with the COVID-19 pandemic. This study determined the illness severity and mortality amongst COVID-19 infected healthcare workers.\n\nMethodsThe current study was a retrospective cohort study using population-level data. Secondary analysis was conducted on collated data from the Public Health Emergency Operations Centre (PHEOC) at the State Ministry of Health. The cohort included all documented healthcare workers with confirmed COVID-19 infection (diagnosed by Polymerase Chain Reaction). Data were gathered from the COVID-19 patient database of the PHEOC, on demographics, place of work, illness severity and outcome. Descriptive statistics were reported on the cohort characteristics. Adjusted odds ratio was used to report the measure of association between illness severity and risk factors.\n\nResultsThe mean age was 43 years and 50.5% of the cohort were female. Of the 301 healthcare workers, 187 patients were symptomatic with 32 requiring hospitalisation. From the available data, seven infected HCWs died of their COVID-19 infection, resulting in a case fatality ratio of 2.3%. A subgroup analysis was conducted on the health professionals infected -doctors (71.7%), nurses (27.3%), others (1%). Symptomatic cases were more inclined to progress to severe illness. Predictors of mortality assessed included age, sex, case class and illness severity. The logistic regression model was statistically significant,{chi} 2(9) = 16.965, = 0.049.\n\nConclusionFrontline healthcare workers are at an increased risk of exposure to COVID-19 infections. In Nigeria, there is a higher risk of experiencing a severe disease if symptomatic while infected with COVID-19. It is imperative that preventive strategies, proper education, and awareness are put in place to protect healthcare workers.\n\nSummary BoxHealthcare workers as first responders, are vulnerable to workplace infections. It is manifest in the COVID-19 pandemic where deaths of healthcare workers resulted in further shortage of the already compromised human resource; consequently compromising effective healthcare delivery. As the pandemic progresses, studies have been conducted globally on this topic and scientific evidence continues to show higher mortality and disease severity of COVID-19. Nevertheless, it is important to understand the effect of COVID-19 on healthcare workers in Nigeria-a developing country.\n\nThis study highlights the illness severity and mortality associated with COVID-19 among the study population; its results presented a higher case fatality rate than both national and subnational rates. The results also further emphasises the need to protect healthcare workers; ensure they are knowledgable in both infection prevention and control, and that the healthcare space is safe against nosocomial infections\n\nThe study adds to the scientific evidence on the severity and mortality associated with COVID-19 in Nigeria. A national research is needed to extrapolate the findings from this study to the nation. Hence, expatiate on the global fight against coronaviruses such as COVID-19.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Chidinma Eze-Emiri", + "author_inst": "University of Port Harcourt, River State, Nigeria" + }, + { + "author_name": "Foster Patrick", + "author_inst": "University of Port Harcourt, Rivers State, Nigeria" + }, + { + "author_name": "Ezinne Igwe", + "author_inst": "University of Wollongong, NSW, Australia" + }, + { + "author_name": "Golden Owhonda", + "author_inst": "Rivers State Ministry of Health, Port Harcourt, Rivers State, Nigeria" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.01.31.22270203", "rel_title": "Blood transcriptomes of SARS-CoV-2 infected kidney transplant recipients demonstrate immune insufficiency", @@ -434311,145 +436354,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2022.02.01.22270170", - "rel_title": "Detection of prevalent SARS-CoV-2 variant lineages in wastewater and clinical sequences from cities in Quebec, Canada", - "rel_date": "2022-02-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.02.01.22270170", - "rel_abs": "Wastewater-based epidemiology has emerged as a promising tool to monitor pathogens in a population, particularly when clinical diagnostic capacities become overwhelmed. During the ongoing COVID-19 pandemic caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), several jurisdictions have tracked viral concentrations in wastewater to inform public health authorities. While some studies have also sequenced SARS-CoV-2 genomes from wastewater, there have been relatively few direct comparisons between viral genetic diversity in wastewater and matched clinical samples from the same region and time period. Here we report sequencing and inference of SARS-CoV-2 mutations and variant lineages (including variants of concern) in 936 wastewater samples and thousands of matched clinical sequences collected between March 2020 and July 2021 in the cities of Montreal, Quebec City, and Laval, representing almost half the population of the Canadian province of Quebec. We benchmarked our sequencing and variant-calling methods on known viral genome sequences to establish thresholds for inferring variants in wastewater with confidence. We found that variant frequency estimates in wastewater and clinical samples are correlated over time in each city, with similar dates of first detection. Across all variant lineages, wastewater detection is more concordant with targeted outbreak sequencing than with semi-random clinical swab sampling. Most variants were first observed in clinical and outbreak data due to higher sequencing rate. However, wastewater sequencing is highly efficient, detecting more variants for a given sampling effort. This shows the potential for wastewater sequencing to provide useful public health data, especially at places or times when sufficient clinical sampling is infrequent or infeasible.", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Arnaud N'Guessan", - "author_inst": "Universite de Montreal" - }, - { - "author_name": "Alexandra Tsitouras", - "author_inst": "McGill University" - }, - { - "author_name": "Fernando Sanchez-Quete", - "author_inst": "McGill University" - }, - { - "author_name": "Eyerusalem Goitom", - "author_inst": "Polytechnique Montreal" - }, - { - "author_name": "Sarah Julia Reiling", - "author_inst": "McGill Genome Centre" - }, - { - "author_name": "Jose Hector Galvez", - "author_inst": "Canadian Centre for Computational Genomics" - }, - { - "author_name": "Thanh Luan Nguyen", - "author_inst": "Polytechnique Montreal" - }, - { - "author_name": "Ha Thanh Loan Nguyen", - "author_inst": "Polytechnique Montreal" - }, - { - "author_name": "Flavia Visentin", - "author_inst": "Polytechnique Montreal" - }, - { - "author_name": "Mounia Hachad", - "author_inst": "Polytechnique Montreal" - }, - { - "author_name": "Kateryna Krylova", - "author_inst": "Polytechnique Montreal" - }, - { - "author_name": "Sara Matthews", - "author_inst": "Polytechnique Montreal" - }, - { - "author_name": "Susanne A Kraemer", - "author_inst": "McGill University" - }, - { - "author_name": "Paul Stretenowich", - "author_inst": "Canadian Centre for Computational Genomics" - }, - { - "author_name": "Mathieu Bourgey", - "author_inst": "Canadian Centre for Computational Genomics" - }, - { - "author_name": "Haig Djambazian", - "author_inst": "McGill Genome Centre" - }, - { - "author_name": "Shu-Huang Chen", - "author_inst": "McGill University" - }, - { - "author_name": "Anne-Marie Roy", - "author_inst": "McGill University" - }, - { - "author_name": "Brent Brookes", - "author_inst": "McGill University" - }, - { - "author_name": "Sally Lee", - "author_inst": "McGill University" - }, - { - "author_name": "Marie-Michelle Simon", - "author_inst": "McGill University" - }, - { - "author_name": "Thomas Maere", - "author_inst": "Universite Laval" - }, - { - "author_name": "Peter Vanrolleghem", - "author_inst": "Universite Laval" - }, - { - "author_name": "Marc-Andre Labelle", - "author_inst": "Centre des technologies de l'eau" - }, - { - "author_name": "Sandrine Moreira", - "author_inst": "Laboratoire de Sante Publique du Quebec, Institut National de Sante Publique" - }, - { - "author_name": "Ines Levade", - "author_inst": "Laboratoire de Sante Publique du Quebec, Institut National de Sante Publique" - }, - { - "author_name": "Guillaume Bourque", - "author_inst": "Canadian Centre for Computational Genomics, McGill University" - }, - { - "author_name": "Jiannis Ragoussis", - "author_inst": "McGill Genome Centre" - }, - { - "author_name": "Sarah Dorner", - "author_inst": "Polytechnique Montreal" - }, - { - "author_name": "Dominic Frigon", - "author_inst": "McGill University" - }, - { - "author_name": "B. Jesse Shapiro", - "author_inst": "McGill University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.31.22270226", "rel_title": "SARS-CoV-2 Variant Surveillance Using Tandem Targeted RT-PCR-based Genotyping Assays and Whole Genome Sequencing", @@ -435509,6 +437413,93 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2022.01.30.478343", + "rel_title": "High Frequencies of PD-1+TIM3+TIGIT+CTLA4+ Functionally Exhausted SARS-CoV-2-Specific CD4+ and CD8+ T Cells Associated with Severe Disease in Critically ill COVID-19 Patients", + "rel_date": "2022-01-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.30.478343", + "rel_abs": "SARS-CoV-2-specific memory T cells that cross-react with common cold coronaviruses (CCCs) are present in both healthy donors and COVID-19 patients. However, whether these cross-reactive T cells play a role in COVID-19 pathogenesis versus protection remain to be fully elucidated. In this study, we characterized cross-reactive SARS-CoV-2-specific CD4+ and CD8+ T cells, targeting genome-wide conserved epitopes in a cohort of 147 non-vaccinated COVID-19 patients, divided into six groups based on the degrees of disease severity. We compared the frequency, phenotype, and function of these SARS-CoV-2-specific CD4+ and CD8+ T cells between severely ill and asymptomatic COVID-19 patients and correlated this with -CCCs and {beta}-CCCs co-infection status. Compared with asymptomatic COVID-19 patients, the severely ill COVID-19 patients and patients with fatal outcomes: (i) Presented a broad leukocytosis and a broad CD4+ and CD8+ T cell lymphopenia; (ii) Developed low frequencies of functional IFN-{gamma}-producing CD134+CD138+CD4+ and CD134+CD138+CD8+ T cells directed toward conserved epitopes from structural, non-structural and regulatory SARS-CoV-2 proteins; (iii) Displayed high frequencies of SARS-CoV-2-specific functionally exhausted PD-1+TIM3+TIGIT+CTLA4+CD4+ and PD-1+TIM3+TIGIT+CTLA4+CD8+ T cells; and (iv) Displayed similar frequencies of co-infections with {beta}-CCCs strains but significantly fewer co-infections with -CCCs strains. Interestingly, the cross-reactive SARS-CoV-2 epitopes that recalled the strongest CD4+ and CD8+ T cell responses in unexposed healthy donors (HD) were the most strongly associated with better disease outcome seen in asymptomatic COVID-19 patients. Our results demonstrate that, the critically ill COVID-19 patients displayed fewer co-infection with -CCCs strain, presented broad T cell lymphopenia and higher frequencies of cross-reactive exhausted SARS-CoV-2-specific CD4+ and CD8+ T cells. In contrast, the asymptomatic COVID-19 patients, appeared to present more co-infections with -CCCs strains, associated with higher frequencies of functional cross-reactive SARS-CoV-2-specific CD4+ and CD8+ T cells. These findings support the development of broadly protective, T-cell-based, multi-antigen universal pan-Coronavirus vaccines.\n\nKEY POINTSO_LIA broad lymphopenia and lower frequencies of SARS-CoV-2-specific CD4+ and CD8+ T-cells were associated with severe disease onset in COVID-19 patients.\nC_LIO_LIHigh frequencies of phenotypically and functionally exhausted SARS-CoV-2-specific CD4+ and CD8+ T cells, co-expressing multiple exhaustion markers, and targeting multiple structural, non-structural, and regulatory SARS-CoV-2 protein antigens, were detected in severely ill COVID-19 patients.\nC_LIO_LICompared to severely ill COVID-19 patients and to patients with fatal outcomes, the (non-vaccinated) asymptomatic COVID-19 patients presented more functional cross-reactive CD4+ and CD8+ T cells targeting conserved epitopes from structural, non-structural, and regulatory SARS-CoV-2 protein antigens.\nC_LIO_LIThe cross-reactive SARS-CoV-2 epitopes that recalled the strongest CD4+ and CD8+ T cell responses in unexposed healthy donors (HD) were the most strongly associated with better disease outcomes seen in asymptomatic COVID-19 patients.\nC_LIO_LICompared to severely ill COVID-19 patients and to patients with fatal outcomes, the (non-vaccinated) asymptomatic COVID-19 patients presented higher rates of co-infection with the -CCCs strains.\nC_LIO_LICompared to patients with mild or asymptomatic COVID-19, severely ill symptomatic patients and patients with fatal outcomes had more exhausted SARS-CoV-2-speccific CD4+ and CD8+ T cells that preferentially target cross-reactive epitopes that share high identity and similarity with the {beta}-CCCs strains.\nC_LI", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Pierre-Gregoire A Coulon", + "author_inst": "Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA 92697" + }, + { + "author_name": "Swayam Prakash", + "author_inst": "Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA 92697" + }, + { + "author_name": "Nisha R Dhanushkodi", + "author_inst": "Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA 92697" + }, + { + "author_name": "Ruchi Srivastava", + "author_inst": "Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA 92697" + }, + { + "author_name": "Latifa Zayou", + "author_inst": "Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA 92697" + }, + { + "author_name": "Delia F Tifrea", + "author_inst": "Department of Pathology and Laboratory Medicine, School of Medicine, Irvine, CA 92697" + }, + { + "author_name": "Robert A Edwards", + "author_inst": "Department of Pathology and Laboratory Medicine, School of Medicine, Irvine, CA 92697" + }, + { + "author_name": "Cesar J Figueroa", + "author_inst": "Department of Surgery, Divisions of Trauma, Burns & Critical Care, School of Medicine, Irvine, CA 92697" + }, + { + "author_name": "Sebastian D Schubl", + "author_inst": "Department of Surgery, Divisions of Trauma, Burns & Critical Care, School of Medicine, Irvine, CA 92697" + }, + { + "author_name": "Lanny Hsieh", + "author_inst": "Department of Medicine, Division of Infectious Diseases and Hospitalist Program, School of Medicine, Irvine, CA 92697" + }, + { + "author_name": "Anthony B Nesburn", + "author_inst": "Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA 92697" + }, + { + "author_name": "Baruch D Kuppermann", + "author_inst": "Laboratory of Cellular and Molecular Immunology, Gavin Herbert Eye Institute, University of California Irvine, School of Medicine, Irvine, CA 92697" + }, + { + "author_name": "Elmostafa BAHRAOUI", + "author_inst": "INFINITY, INSERM, University Toulouse III" + }, + { + "author_name": "Hawa Vahed", + "author_inst": "Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA 92660" + }, + { + "author_name": "Daniel Gil", + "author_inst": "Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA 92660" + }, + { + "author_name": "Trevor M Jones", + "author_inst": "Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA 92660" + }, + { + "author_name": "Jeffrey B Ulmer", + "author_inst": "Department of Vaccines and Immunotherapies, TechImmune, LLC, University Lab Partners, Irvine, CA 92660" + }, + { + "author_name": "LBACHIR BENMOHAMED", + "author_inst": "UC Irvine, School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2022.01.27.477964", "rel_title": "Virucidal activity and mechanism of action of cetylpyridinium chloride against SARS-CoV-2", @@ -435929,217 +437920,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.29.22270094", - "rel_title": "Polygenic predisposition to venous thromboembolism is associated with increased COVID-19 positive testing rates", - "rel_date": "2022-01-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.29.22270094", - "rel_abs": "Genetic predisposition to venous thrombosis may impact COVID-19 infection and its sequelae. Participants in the ongoing prospective cohort study, Million Veteran Program (MVP), who were tested for COVID-19, with European ancestry, were evaluated for associations with polygenic venous thromboembolic risk, Factor V Leiden mutation (FVL) (rs6025) and prothrombin gene 3 -UTR mutation (F2 G20210A)(rs1799963), and their interactions. Logistic regression models assessed genetic associations with VTE diagnosis, COVID-19 (positive) testing rates and outcome severity (modified WHO criteria), and post-test conditions, adjusting for outpatient anticoagulation medication usage, age, sex, and genetic principal components. 108,437 out of 464,961 European American MVP participants were tested for COVID-19 with 9786 (9%) positive. PRS(VTE), FVL, F2 G20210A were not significantly associated with the propensity of being tested for COVID-19. PRS(VTE) was significantly associated with a positive COVID-19 test in F5 wild type (WT) individuals (OR 1.05; 95% CI [1.02-1.07]), but not in FVL carriers (0.97, [0.91-1.94]). There was no association with severe outcome for FVL, F2 G20210A or PRS(VTE). Outpatient anticoagulation usage in the two years prior to testing was associated with worse clinical outcomes. PRS(VTE) was associated with prevalent VTE diagnosis among both FVL carriers or F5 wild type individuals as well as incident VTE in the two years prior to testing. Increased genetic propensity for VTE in the MVP was associated with increased COVID-19 positive testing rates, suggesting a role of coagulation in the initial steps of COVID-19 infection.\n\nKey PointsO_LIIncreased genetic predisposition to venous thrombosis is associated with increased COVID-19 positive testing rates.\nC_LIO_LIPRS for VTE further risk stratifies factor V Leiden carriers regarding their VTE risk.\nC_LI", - "rel_num_authors": 49, - "rel_authors": [ - { - "author_name": "Jessica Minnier", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Jennifer E Huffman", - "author_inst": "VA Boston Healthcare System" - }, - { - "author_name": "Lina Gao", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Jacob Joseph", - "author_inst": "VA Boston Healthcare System" - }, - { - "author_name": "Emily S Wan", - "author_inst": "VA Boston Healthcare System" - }, - { - "author_name": "Wen-Chih Wu", - "author_inst": "Providence VA Healthcare System" - }, - { - "author_name": "Ayako Suzuki", - "author_inst": "Durham VA Medical Center" - }, - { - "author_name": "Gita A Pathak", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Renato Polimanti", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Mehrdad Arjomandi", - "author_inst": "San Francisco VA Healthcare System; University of California San Francisco" - }, - { - "author_name": "Kyong-Mi Chang", - "author_inst": "Corporal Michael J Crescenz VA Medical Center" - }, - { - "author_name": "Helene Garcon", - "author_inst": "VA Boston Healthcare System" - }, - { - "author_name": "Anurag Verma", - "author_inst": "Corporal Michael J Crescenz VA Medical Center" - }, - { - "author_name": "Yuk-Lam Ho", - "author_inst": "VA Boston Healthcare System" - }, - { - "author_name": "James B Meigs", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Kelly Cho", - "author_inst": "VA Boston Healthcare System" - }, - { - "author_name": "Robert A Bonomo", - "author_inst": "Louis Stokes Cleveland VA" - }, - { - "author_name": "Bryan R Gorman", - "author_inst": "VA Boston Healthcare System" - }, - { - "author_name": "Saiju Pyarajan", - "author_inst": "VA Boston Healthcare System" - }, - { - "author_name": "Elise Gatsby", - "author_inst": "VA Informatics and Computing Infrastructure (VINCI), VA Salt Lake City Healthcare System" - }, - { - "author_name": "Nallakkandi Rajeevan", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Kristine E Lynch", - "author_inst": "VA Informatics and Computing Infrastructure (VINCI), VA Salt Lake City Healthcare System" - }, - { - "author_name": "Julie A Lynch", - "author_inst": "VA Salt Lake City Health Care System" - }, - { - "author_name": "Seyedeh Maryam Zekavat", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Pradeep Natarajan", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Cecelia J Madison", - "author_inst": "Portland VA Medical Center" - }, - { - "author_name": "Jin J Zhou", - "author_inst": "University of California, Los Angeles" - }, - { - "author_name": "Darshana N Jhala", - "author_inst": "Corporal Michael J Crescenz VA Medical Center" - }, - { - "author_name": "Curtis J Donskey", - "author_inst": "Louis Stokes Cleveland VA and Case Western Reserve University" - }, - { - "author_name": "John E McGeary", - "author_inst": "Providence VA Medical Center" - }, - { - "author_name": "Peter D Reaven", - "author_inst": "Phoenix VA Healthcare System" - }, - { - "author_name": "Yan V Sun", - "author_inst": "Emory University School of Public Health" - }, - { - "author_name": "Mat Freiberg", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Joel Gelernter", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Jeffrey M Petersen", - "author_inst": "Corporal Michael J Crescenz VA Medical Center" - }, - { - "author_name": "Adriana Hung", - "author_inst": "Tennesse Valley Healthcare System" - }, - { - "author_name": "Rose DL Huang", - "author_inst": "VA Boston Healthcare System" - }, - { - "author_name": "Ravi K Madduri", - "author_inst": "Argonne National Laboratory" - }, - { - "author_name": "Sharvari Dalal", - "author_inst": "Corporal Michael J Crescenz VA Medical Center" - }, - { - "author_name": "Quinn S Wells", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Katherine P Liao", - "author_inst": "VA Boston Healthcare System" - }, - { - "author_name": "Peter W.F. Wilson", - "author_inst": "Atlanta VA Health Care System" - }, - { - "author_name": "Philip S Tsao", - "author_inst": "VA Palo Alto Health Care System" - }, - { - "author_name": "Christopher J O'Donnell", - "author_inst": "VA Boston Healthcare System" - }, - { - "author_name": "John M Gaziano", - "author_inst": "VA Boston Healthcare System" - }, - { - "author_name": "- VA Million Veteran Program", - "author_inst": "" - }, - { - "author_name": "Richard L Hauger", - "author_inst": "VA San Diego Healthcare System" - }, - { - "author_name": "Sudha K. Iyengar", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Shiuh-Wen Luoh", - "author_inst": "VA Portland Health Care System" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "hematology" - }, { "rel_doi": "10.1101/2022.01.30.22269998", "rel_title": "An ML prediction model based on clinical parameters and automated CT scan features for COVID-19 patients", @@ -437415,6 +439195,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.01.28.22270006", + "rel_title": "A mixed methods analysis of participation in social contact surveys", + "rel_date": "2022-01-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.28.22270006", + "rel_abs": "BackgroundSocial contact survey data forms a core component of modern epidemic models: however, there has been little assessment of the potential biases in such data.\n\nMethodsWe conducted focus groups with university students who had (n=13) and had not (n=14) completed a social contact survey during the COVID-19 pandemic. Qualitative findings were explored quantitatively by analysing participation data.\n\nResultsThe opportunity to contribute to COVID-19 research, to be heard and feel useful were frequently reported motivators for participating in the contact survey. Reductions in survey engagement following lifting of COVID-19 restrictions may have occurred because the research was perceived to be less critical and/ or because the participants were busier and had more contacts. Having a high number of contacts to report, uncertainty around how to report each contact, and concerns around confidentiality were identified as factors leading to inaccurate reporting. Focus groups participants thought that financial incentives or provision of study results would encourage participation.\n\nConclusionsIncentives could improve engagement with social contact surveys. Qualitative research can inform the format, timing, and wording of surveys to optimise completion and accuracy.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC=\"FIGDIR/small/22270006v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (47K):\norg.highwire.dtl.DTLVardef@10a3dd4org.highwire.dtl.DTLVardef@1616032org.highwire.dtl.DTLVardef@1f2aab8org.highwire.dtl.DTLVardef@a62043_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Emily J Nixon", + "author_inst": "University of Bristol" + }, + { + "author_name": "Taru Silvonen", + "author_inst": "University of Bristol" + }, + { + "author_name": "Antoine Barreaux", + "author_inst": "CIRAD" + }, + { + "author_name": "Rachel Kwiatkowska", + "author_inst": "University of Bristol" + }, + { + "author_name": "Adam Trickey", + "author_inst": "University of Bristol" + }, + { + "author_name": "Amy C Thomas", + "author_inst": "University of Bristol" + }, + { + "author_name": "Becky Ali", + "author_inst": "University of Bristol" + }, + { + "author_name": "Georgia Treneman-evans", + "author_inst": "University of Bristol" + }, + { + "author_name": "Hannah Christensen", + "author_inst": "University of Bristol" + }, + { + "author_name": "Ellen Brooks Pollock", + "author_inst": "University of Bristol" + }, + { + "author_name": "Sarah Denford", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.01.27.22269965", "rel_title": "Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations", @@ -437975,41 +439814,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.28.22270022", - "rel_title": "Continuing inequalities in COVID-19 mortality in England and Wales, and the changing importance of regional, over local, deprivation", - "rel_date": "2022-01-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.28.22270022", - "rel_abs": "BackgroundObservational studies have highlighted that where individuals live is far more important for risk of dying with COVID-19, than for dying of other causes. Deprivation is commonly proposed as explaining such differences. During the period of localised restrictions in late 2020, areas with higher restrictions tended to be more deprived. We explore how this impacted the relationship between deprivation and mortality and see whether local or regional deprivation matters more for inequalities in COVID-19 mortality.\n\nMethodsWe use publicly available population data on deaths due to COVID-19 and all-cause mortality between March 2020 and April 2021 to investigate the scale of spatial inequalities. We use a multiscale approach to simultaneously consider three spatial scales through which processes driving inequalities may act. We go on to explore whether deprivation explains such inequalities.\n\nResultsAdjusting for population age structure and number of care homes, we find highest regional inequality in October 2020, with a COVID-19 mortality rate ratio of 5.86 (95% CI 3.31 to 19.00) for the median between-region comparison. We find spatial context is most important, and spatial inequalities higher, during periods of low mortality. Almost all unexplained spatial inequality in October 2020 is removed by adjusting for deprivation. During October 2020, one standard deviation increase in regional deprivation was associated with 2.45 times higher local mortality (95% CI, 1.75 to 3.48).\n\nConclusionsSpatial inequalities are greatest in periods of lowest overall mortality, implying that as mortality declines it does not do so equally. During the prolonged period of low restrictions and low mortality in summer 2020, spatial inequalities strongly increased. Contrary to previous months, we show that the strong spatial patterning during autumn 2020 is almost entirely explained by deprivation. As overall mortality declines, policymakers must be proactive in detecting areas where this is not happening, or risk worsening already strong health inequalities.\n\nKey messages- Spatial inequalities in local mortality are highest in periods of lower overall mortality.\n- Spatial inequality in COVID-19 mortality peaked in October 2020, before decreasing strongly in November and over the winter period.\n- Deprivation explains almost all inequality during October when inequality was at its highest.\n- Regional deprivation was far more strongly associated with local mortality than local deprivation during September to November 2020.\n- This is consistent with an overdispersed distribution of secondary infections governed by transmission heterogeneity structured by deprivation.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Gareth J Griffith", - "author_inst": "University of Bristol" - }, - { - "author_name": "Gwilym Owen", - "author_inst": "University of Liverpool" - }, - { - "author_name": "David Manley", - "author_inst": "University of Bristol" - }, - { - "author_name": "Laura D Howe", - "author_inst": "University of Bristol" - }, - { - "author_name": "George Davey Smith", - "author_inst": "University of Bristol" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.27.22269982", "rel_title": "Psychological Outcomes of Surgery Trainees in the Era of COVID-19 at a Tertiary Care Hospital of Karachi, Pakistan: A Cross-Sectional Study", @@ -439241,6 +441045,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.26.22269848", + "rel_title": "mRNA vaccine boosting enhances antibody responses against SARS-CoV-2 Omicron variant in patients with antibody deficiency syndromes", + "rel_date": "2022-01-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.26.22269848", + "rel_abs": "Patients with primary antibody deficiency syndromes (PAD) have poor humoral immune responses requiring immunoglobulin replacement therapy. We followed PAD patients after SARS-CoV-2 vaccination by evaluating their immunoglobulin replacement products and serum for anti-spike binding, Fc{gamma}R binding, and neutralizing activities. Immunoglobulin replacement products had low anti-spike and receptor binding domain (RBD) titers and neutralizing activity. In COVID-19-naive PAD patients, anti-spike and RBD titers increased after mRNA vaccination but decreased to pre-immunization levels by 90 days. Patients vaccinated after SARS-CoV-2 infection developed higher responses comparable to healthy donors. Most vaccinated PAD patients had serum neutralizing antibody titers above an estimated correlate of protection against ancestral SARS-CoV-2 and Delta virus but not against Omicron virus, although this was improved by boosting. Thus, currently used immunoglobulin replacement products likely have limited protective activity, and immunization and boosting of PAD patients with mRNA vaccines should confer at least short-term immunity against SARS-CoV-2 variants, including Omicron.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Ofer Zimmerman", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Alexa Michelle Altman Doss", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Paulina Kaplonek", + "author_inst": "Ragon Institute" + }, + { + "author_name": "Laura A. VanBlargan", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Chieh-Yu Liang", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Rita E. Chen", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Jennifer Marie Monroy", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "H. James Wedner", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Anthony Kulczycki", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Tarisa L. Mantia", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Caitlin C. O'Shaughnessy", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Hannah G. Davis-Adams", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Harry L. Bertera", + "author_inst": "Ragon Institute" + }, + { + "author_name": "Lucas J. Adams", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Saravanan Raju", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Fang R. Zhao", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Christopher J. Rigell", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Tiffany Biason Dy", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Andrew L. Kau", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Zhen Ren", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Jackson Turner", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Jane A. O'Halloran", + "author_inst": "Washington University in St. Louis School of Medicine" + }, + { + "author_name": "Rachel Presti", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Daved H. Fremont", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Peggy L. Kendall", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Ali H. Ellebedy", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Galit Alter", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Michael S. Diamond", + "author_inst": "Washington University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2022.01.27.22269787", "rel_title": "Early introduction and rise of the Omicron SARS-CoV-2 variant in highly vaccinated university populations", @@ -439677,149 +441608,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2022.01.26.22269856", - "rel_title": "Antibody and T cell responses to SARS-CoV-2 mRNA vaccines during maintenance therapy for immune-mediated inflammatory diseases", - "rel_date": "2022-01-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.26.22269856", - "rel_abs": "BackgroundLimited information is available on the impact of immunosuppressants on COVID-19 vaccination in patients with immune-mediated inflammatory diseases (IMID).\n\nMethodsThis observational cohort study examined the immunogenicity of SARS-CoV-2 mRNA vaccines in adult patients with inflammatory bowel disease, rheumatoid arthritis, ankylosing spondylitis, or psoriatic disease, with or without maintenance immunosuppressive therapies. Antibody and T cell responses to SARS-COV-2, including neutralization against SARS-CoV-2 variants were determined before and after 1 and 2 vaccine doses.\n\nResultsWe prospectively followed 150 subjects, 26 healthy controls, 9 IMID patients on no treatment, 44 on anti-TNF, 16 on anti-TNF with methotrexate/azathioprine (MTX/AZA), 10 on anti-IL-23, 28 on anti-IL-12/23, 9 on anti-IL-17, and 8 on MTX/AZA. Antibody and T cell responses to SARS-CoV-2 were detected in all participants, increasing from dose 1 to dose 2 and declining 3 months later, with greater attrition in IMID patients compared to healthy controls. Antibody levels and neutralization efficacy against variants of concern were substantially lower in anti-TNF treated patients than in healthy controls and were undetectable against Omicron by 3 months after dose 2.\n\nConclusionsOur findings support the need for a third dose of mRNA vaccine and for continued monitoring of immunity in these patient groups.\n\nFundingFunded by a donation from Juan and Stefania Speck and by Canadian Institutes of Health (CIHR) /COVID-Immunity Task Force (CITF) grants VR-1 172711 and VS1-175545 (T.H.W. and A.C.G); CIHR FDN-143250 (T.H.W.), GA2-177716 (V.C., A.C.G., T.W.), GA1-177703 (A.C.G.) and the CIHR rapid response network to SARS-CoV-2 variants, CoVaRR-Net (to A.C.G.).", - "rel_num_authors": 32, - "rel_authors": [ - { - "author_name": "Roya M Dayam", - "author_inst": "Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada" - }, - { - "author_name": "Jaclyn C Law", - "author_inst": "Department of Immunology, University of Toronto, Toronto, Ontario, Canada" - }, - { - "author_name": "Rogier L Goetgebuer", - "author_inst": "Zane Cohen Centre for Digestive Diseases, Division of Gastroenterology, Mount Sinai Hospital, Sinai Health System, University of Toronto, Toronto, Ontario, Cana" - }, - { - "author_name": "Gary YC Chao", - "author_inst": "Department of Immunology, University of Toronto, Toronto, Ontario, Canada" - }, - { - "author_name": "Kento T Abe", - "author_inst": "Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health " - }, - { - "author_name": "Mitchell Sutton", - "author_inst": "Schroeder Arthritis Institute, Krembil Research Institute, University Health Network; Division of Rheumatology, Department of Medicine, University of Toronto, T" - }, - { - "author_name": "Naomi Finkelstein", - "author_inst": "Schroeder Arthritis Institute, Krembil Research Institute, University Health Network; Division of Rheumatology, Department of Medicine, University of Toronto, T" - }, - { - "author_name": "Joanne M Stempak", - "author_inst": "Zane Cohen Centre for Digestive Diseases, Division of Gastroenterology, Mount Sinai Hospital, Sinai Health System, University of Toronto, Toronto, Ontario, Cana" - }, - { - "author_name": "Daniel Pereira", - "author_inst": "Schroeder Arthritis Institute, Krembil Research Institute, University Health Network; Division of Rheumatology, Department of Medicine, University of Toronto, T" - }, - { - "author_name": "David Croituru", - "author_inst": "Division of Dermatology, Department of Medicine, University of Toronto, Toronto, Canada" - }, - { - "author_name": "Lily Acheampong", - "author_inst": "Division of Dermatology, Department of Medicine, Womens College Hospital, Toronto, Canada" - }, - { - "author_name": "Saima Rizwan", - "author_inst": "Zane Cohen Centre for Digestive Diseases, Division of Gastroenterology, Mount Sinai Hospital, Sinai Health System, University of Toronto, Toronto, Ontario, Cana" - }, - { - "author_name": "Klaudia Rymaszewski", - "author_inst": "Zane Cohen Centre for Digestive Diseases, Division of Gastroenterology, Mount Sinai Hospital, Sinai Health System, University of Toronto, Toronto, Ontario, Cana" - }, - { - "author_name": "Raquel Milgrom", - "author_inst": "Zane Cohen Centre for Digestive Diseases, Division of Gastroenterology, Mount Sinai Hospital, Sinai Health System, University of Toronto, Toronto, Ontario, Cana" - }, - { - "author_name": "Darshini Ganatra", - "author_inst": "Schroeder Arthritis Institute, Krembil Research Institute, University Health Network; Division of Rheumatology, Department of Medicine, University of Toronto, T" - }, - { - "author_name": "Nathalia Vieira Batista", - "author_inst": "Department of Immunology, University of Toronto, Toronto, Ontario, Canada" - }, - { - "author_name": "Melanie Girard", - "author_inst": "Department of Immunology, University of Toronto, Toronto, Ontario, Canada" - }, - { - "author_name": "Irene Lau", - "author_inst": "Department of Immunology, University of Toronto, Toronto, Ontario, Canada" - }, - { - "author_name": "Ryan Law", - "author_inst": "Department of Immunology, University of Toronto, Toronto, Ontario, Canada" - }, - { - "author_name": "Michelle W Cheung", - "author_inst": "Department of Immunology, University of Toronto, Toronto, Ontario, Canada" - }, - { - "author_name": "Bhavisha Rathod", - "author_inst": "Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada" - }, - { - "author_name": "Julia Kitaygorodsky", - "author_inst": "Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada,Department of Molecular Genetics, University of To" - }, - { - "author_name": "Reuben Samson", - "author_inst": "Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada, Department of Molecular Genetics, University of T" - }, - { - "author_name": "Queenie Hu", - "author_inst": "Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada" - }, - { - "author_name": "W Rod Hardy", - "author_inst": "Sinai Health System" - }, - { - "author_name": "Nigil Haroon", - "author_inst": "Schroeder Arthritis Institute, Krembil Research Institute, University Health Network; Division of Rheumatology, Department of Medicine, University of Toronto, T" - }, - { - "author_name": "Robert D Inman", - "author_inst": "Schroeder Arthritis Institute, Krembil Research Institute, University Health Network; Division of Rheumatology, Department of Medicine, University of Toronto, T" - }, - { - "author_name": "Vincent Piguet", - "author_inst": "Division of Dermatology, Department of Medicine, University of Toronto, Toronto, Canada; Division of Dermatology, Department of Medicine, Womens College Hospi" - }, - { - "author_name": "Vinod Chandran", - "author_inst": "Schroeder Arthritis Institute, Krembil Research Institute, University Health Network; Division of Rheumatology, Department of Medicine, University of Toronto, T" - }, - { - "author_name": "Mark S Silverberg", - "author_inst": "Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital, Sinai Health System, Toronto, Ontario, Canada,Zane Cohen Centre for Digestive Diseases, Division" - }, - { - "author_name": "Anne-Claude Gingras", - "author_inst": "Lunenfeld-Tanenbaum Research Institute at Mount Sinai Hospital; Sinai Health System, Department of Molecular Genetics, University of Toronto, Toronto, Ontario, " - }, - { - "author_name": "Tania H Watts", - "author_inst": "Department of Immunology, University of Toronto, Toronto, Ontario, Canada" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.26.22269824", "rel_title": "SARS-CoV-2 in schools: genome analysis shows that concurrent cases in the second and third wave were often unconnected", @@ -441339,6 +443127,41 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2022.01.26.477969", + "rel_title": "Effect of SARS-CoV-2 spike mutations on its activation by TMPRSS2 and TMPRSS13", + "rel_date": "2022-01-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.26.477969", + "rel_abs": "The continuous emergence of new SARS-CoV-2 variants urges better understanding of the functional motifs in the spike (S) protein and their tolerance towards mutations. We here focus on the S2 motif which, during virus entry, requires cleavage by a cell surface protease to release the fusion peptide. Though belonging to an immunogenic region, the SARS-CoV-2 S2 motif (811-KPSKR-815) has shown hardly any variation, with its three basic (K/R) residues being >99.99% conserved thus far. By creating a series of mutant S-pseudotyped viruses, we show that K814, which precedes the scissile R815 residue, is dispensable for SARS-CoV-2 spike activation by TMPRSS2 but not TMPRSS13. The latter protease lost its activity towards SARS-CoV-2 S when the S2 motif was swapped with that of the low pathogenic 229E coronavirus (685-RVAGR-689) and also the reverse effect was seen. This swap had no impact on TMPRSS2 activation. Also in the MERS-CoV spike, introducing a dibasic scissile motif was fully accepted by TMPRSS13 but less so by TMPRSS2. Our findings are the first to demonstrate which S2 residues are important for SARS-CoV-2 spike activation by these two airway proteases, with TMPRSS13 exhibiting higher preference for K/R rich motifs than TMPRSS2. This preemptive insight can help to estimate the impact of S2 motif changes as they may appear in new SARS-CoV-2 variants.\n\nIMPORTANCESince the start of the COVID-19 pandemic, SARS-CoV-2 is undergoing worldwide selection with frequent appearance of new variants. The surveillance would benefit from proactive characterization of the functional motifs in the spike protein, the most variable viral factor. This is linked to immune evasion but also influences spike functioning in a direct manner. Remarkably, though located in a strong immunogenic region, the S2 cleavage motif has, thus far, remained highly conserved. This suggests that its amino acid sequence is critical for spike activation by airway proteases. To investigate this, we assessed which S2 site mutations affect processing by TMPRSS2 and TMPRSS13, two main activators of the SARS-CoV-2 spike. Being the first in its kind, our study will help to assess the biological impact of S2 site variations as soon as they are detected during variant surveillance.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Annelies Stevaert", + "author_inst": "Rega Institute for Medical Research, KU Leuven - University of Leuven" + }, + { + "author_name": "Ria Van Berwaer", + "author_inst": "Rega Institute for Medical Research, KU Leuven - University of Leuven" + }, + { + "author_name": "Valerie Raeymaekers", + "author_inst": "Rega Institute for Medical Research, KU Leuven - University of Leuven" + }, + { + "author_name": "Manon Laporte", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Lieve M.J. Naesens", + "author_inst": "Rega Institute for Medical Research, KU Leuven - University of Leuven" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.01.26.477774", "rel_title": "The P132H mutation in the main protease of Omicron SARS-CoV-2 decreases thermal stability without compromising catalysis or small-molecule drug inhibition", @@ -441907,53 +443730,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, - { - "rel_doi": "10.1101/2022.01.20.21267627", - "rel_title": "\"It affects every aspect of your life\": A qualitative study of the impact of delaying surgery during COVID-19", - "rel_date": "2022-01-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.20.21267627", - "rel_abs": "BackgroundThe COVID-19 pandemic has overwhelmed healthcare systems, leading many jurisdictions to reduce surgical services to create capacity (beds and staff) to care for the surge of patients with COVID-19. These decisions were made in haste, and little is known about the impact on patients whose surgery was delayed. This study explores the impact of delaying non-urgent surgeries on patients, from their perspective.\n\nMethodsUsing an interpretative description approach, we conducted interviews with adult patients and their caregivers who had their surgery delayed or cancelled during the COVID-19 pandemic in Alberta, Canada. Trained interviewers conducted semi-structured interviews. Interviews were iteratively analyzed by two independent reviewers using an inductive approach to thematic content analysis to understand key elements of the patient experience.\n\nResultsWe conducted 16 interviews with participants ranging from 27 to 75 years of age with a variety of surgical procedures delayed. We identified four interconnected themes: individual-level impacts (physical health, mental health, family and friends, work, quality of life), system-level factors (healthcare resources, communication, perceived accountability/responsibility), unique issues related to COVID-19, and uncertainty.\n\nInterpretationThe patient-reported impact of having a surgery delayed during the COVID-19 pandemic was diffuse and consequential. While the decision to delay non-urgent surgeries was made to manage the strain on healthcare systems, our study illustrates the consequences of these decisions. We advocate for the development and adoption of strategies to mitigate the burden of distress that waiting for surgery during and after COVID-19 has on patients and their family/caregivers.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Khara M Sauro", - "author_inst": "University of Calgary" - }, - { - "author_name": "Christine Smith", - "author_inst": "University of Calgary" - }, - { - "author_name": "Jaling Kersen", - "author_inst": "University of Calgary" - }, - { - "author_name": "Emma Schalm", - "author_inst": "University of Calgary" - }, - { - "author_name": "Natalia Jaworska", - "author_inst": "University of Calgary" - }, - { - "author_name": "Pamela Roach", - "author_inst": "University of Calgary" - }, - { - "author_name": "Sanjay Beesoon", - "author_inst": "Alberta Health Services" - }, - { - "author_name": "Mary Brindle", - "author_inst": "University of Calgary" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "surgery" - }, { "rel_doi": "10.1101/2022.01.26.22269659", "rel_title": "Mucosal immunity against SARS-CoV-2 variants of concern including Omicron following vaccination", @@ -443653,6 +445429,101 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.01.25.477673", + "rel_title": "Despite the odds: formation of the SARS-CoV-2 methylation complex.", + "rel_date": "2022-01-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.25.477673", + "rel_abs": "Coronaviruses protect their single-stranded RNA genome with a methylated cap during replication. The capping process is initiated by several nonstructural proteins (nsp) encoded in the viral genome. The methylation is performed by two methyltransferases, nsp14 and nsp16 where nsp10 acts as a co-factor to both. Aditionally, nsp14 carries an exonuclease domain, which operates in the proofreading system during RNA replication of the viral genome. Both nsp14 and nsp16 were reported to independently bind nsp10, but the available structural information suggests that the concomitant interaction between these three proteins should be impossible due to steric clashes. Here, we show that nsp14, nsp10, and nsp16 can form a heterotrimer complex. This interaction is expected to encourage formation of mature capped viral mRNA, modulating the nsp14s exonuclease activity, and protecting the viral RNA. Our findings show that nsp14 is amenable to allosteric regulation and may serve as a novel target for therapeutic approaches.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Alex Matsuda", + "author_inst": "Jagiellonian University" + }, + { + "author_name": "Jacek Plewka", + "author_inst": "Jagiellonian University" + }, + { + "author_name": "Yuliya Chykunova", + "author_inst": "Jagiellonian University" + }, + { + "author_name": "Alisha N. Jones", + "author_inst": "Helmholtz Zentrum Munchen" + }, + { + "author_name": "Magdalena Pachota", + "author_inst": "Jagiellonian University" + }, + { + "author_name": "Michal Rawski", + "author_inst": "Jagiellonian University" + }, + { + "author_name": "Andre Mourao", + "author_inst": "Helmholtz Zentrum Munchen" + }, + { + "author_name": "Abdulkarim Karim", + "author_inst": "Jagiellonian University" + }, + { + "author_name": "Leanid Kresik", + "author_inst": "Jagiellonian University" + }, + { + "author_name": "Kinga Lis", + "author_inst": "Jagiellonian University" + }, + { + "author_name": "Igor Minia", + "author_inst": "Berlin Institute for Medical Systems Biology" + }, + { + "author_name": "Kinga Hartman", + "author_inst": "AGH University of Science and Technology" + }, + { + "author_name": "Ravi Sonani", + "author_inst": "Jagiellonian University" + }, + { + "author_name": "Grzegorz Dubin", + "author_inst": "Jagiellonian University" + }, + { + "author_name": "Michael Sattler", + "author_inst": "Helmholtz Zentrum Munchen" + }, + { + "author_name": "Piotr Suder", + "author_inst": "AGH University of Science and Technology" + }, + { + "author_name": "Pawel Mak", + "author_inst": "Jagiellonian University" + }, + { + "author_name": "Grzegorz Popowicz", + "author_inst": "Helmholtz Zentrum Munchen" + }, + { + "author_name": "Krzysztof Pyrc", + "author_inst": "Jagiellonian University" + }, + { + "author_name": "Anna Czarna", + "author_inst": "Jagiellonian University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2022.01.25.477753", "rel_title": "The SARS-CoV-2 protein NSP2 impairs the microRNA-induced silencing capacity of human cells", @@ -444121,33 +445992,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "geriatric medicine" }, - { - "rel_doi": "10.1101/2022.01.23.22269626", - "rel_title": "Death review caused by Covid 19 in Bangladesh", - "rel_date": "2022-01-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.23.22269626", - "rel_abs": "IntroductionCOVID-19 pandemic had taken away lots of human life prematurely worldwide and death laid its icy hands also on Bangladesh. So, objectives of this study were to explore the monthly distributions, age, sex, co-morbidities, localities and duration of hospital stay among the COVID death cases.\n\nMethodsIn this observational study six months hospital death files were collected and explored for monthly distributions, age, sex, co-morbidities, localities and hospital stay. RT-PCR positive confirmed 113 COVID deaths were enrolled and suspected COVID deaths were excluded. Ethical clearance from the hospital authority was taken before hand. Data was compiled and analyzed by SPSS-20.\n\nResultsThere was a low frequency of death in May-2021 and October-2021(7.1% and 2.7% respectively) but more during June -2021 to September 2021 (12.4%, 16.8%, 42.5% and 18.6% respectively). Female deaths were little more than male deaths(53.1% vs 46.9%). Age more than 51 years were the most vulnerable where 26(23%) deaths were at age group 51-60 years, 39(34.5%) deaths were at 61-70 years and 22(19.4%) deaths were more than 71 years. Mean age of death was found 60.66 years and mean duration of hospital stay was found 9.45 days. Maximum duration of hospital stay was 45 days for one patient. Co-morbidities of death cases revealed 52(46.00%) patients had DM and HTN both, 17(15.0%) patients had HTN, 16(14.1%) had DM, 3(2.6%) had BA and COPD, 4(3.5%) had CKD, 2(1.7%) had cancer, 3(2.6%) had CVD, 19(16.8%) had IHD and 16(14.1%) patients had no co-morbidities. Locality of the death cases revealed 44(38.9%) came from rural areas and 69(61.1%) came from urban areas.\n\nConclusionHigher age group and multiple co-morbidities specially DM, HTN and IHD were related with COVID deaths mostly found in our study.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Rajat Sanker Roy Biswas", - "author_inst": "CMOSHMC" - }, - { - "author_name": "Jishu Deb Nath", - "author_inst": "CMOSHMC" - }, - { - "author_name": "Fatema Emrose Nisha", - "author_inst": "CMOSHMC" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.23.22269497", "rel_title": "T cell response to intact SARS-CoV-2 includes coronavirus cross-reactive and variant-specific components", @@ -445179,6 +447023,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.01.25.477671", + "rel_title": "Structural insight into antibody evasion of SARS-CoV-2 omicron variant", + "rel_date": "2022-01-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.25.477671", + "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to mutate and evolve with the emergence of omicron (B.1.1.529) as the new variant of concern. The rapid spread of this variant regionally and globally could be an allusion to increased infectivity, transmissibility, and antibody resistance. The omicron variant has a large set of mutations in its spike protein, specifically in the receptor binding domain (RBD), reflecting their significance in ACE2 interaction and antibody recognition. We have carried out the present study to understand how these mutations structurally impact the binding of the antibodies to their target epitope. We have computationally evaluated the binding of different classes of RBD targeted antibodies, namely, CB6 (etesevimab), REGN10933 (casirivimab), S309 (sotrovimab), and S2X259 to the omicron mutation-induced RBD. Molecular dynamics simulations and binding free energy calculations unveil the binding affinity and stability of the antibody-RBD complexes. All the four antibodies show reduced binding affinity towards the omicron RBD. The therapeutic antibody CB6 aka etesevimab was substantially affected due to numerous omicron mutations occurring in its target epitope. This study provides a structural insight into the reduced efficacy of RBD targeting antibodies against the SARS-CoV-2 omicron variant.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Jyoti Verma", + "author_inst": "Jawaharlal Nehru University" + }, + { + "author_name": "Naidu Subbarao", + "author_inst": "Jawaharlal Nehru University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.01.24.22269676", "rel_title": "Projection of Healthcare Demand in Germany and Switzerland Urged by Omicron Wave (January-March 2022)", @@ -445691,61 +447558,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.24.22269781", - "rel_title": "Effects of vaccination against COVID-19 on the emotional health of Peruvian older adults", - "rel_date": "2022-01-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.24.22269781", - "rel_abs": "BackgroundCOVID-19 vaccination may reduce anxiety and depression. However, the pandemic significantly impacted the elderly from low-middle-income countries. Therefore, we aimed to estimate the effect of vaccination against COVID-19 on the emotional health of older adults.\n\nMethodsWe selected a nationally stratified sample of non-hospitalized adults aged 60 to 79 years who intended to receive the COVID-19 vaccine or had already received it during recruitment. We assess the fear, anxiety, and worry about COVID-19, general anxiety, and depression at baseline and after a month. We estimated the adjusted odds ratios (aOR) and 95% confidence intervals (95% CI) for each altered emotional health outcomes in those who had one and two doses, compared with those who were not vaccinated using multilevel logistic regression with mixed effects.\n\nResultsWe recruited 861 older adults. Loss to follow-up was 20.8%. At baseline, 43.9% had only one dose of the vaccine, and 49.1% had two doses. In the analysis during follow-up, those who had two doses had less fear (ORa: 0.19; CI95%: 0.07 to 0.51) and anxiety to COVID-19 (ORa: 0.45; CI95%: 0.22 to 0.89), compared to non-vaccinated. We observed no effects in those with only one dose.\n\nLimitationsInability to obtain the planned sample size for primary analysis. There is a selection bias during recruitment and a measurement bias because of self-reported vaccination.\n\nConclusionsCOVID-19 vaccination with two doses in elders improves the perception of COVID-19 infection consequences. This information could be integrated into the vaccination campaign as its beneficial effect.\n\nHighlightsO_LIUp to 90% of elders in a Peruvian sample had at least one dose of COVID-19 vaccine\nC_LIO_LITwo doses of COVID-19 vaccine reduced the levels of fear and anxiety for COVID-19\nC_LIO_LIOnly one dose of vaccine didnt had effect in any emotional mental outcome\nC_LI", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Christoper A. Alarcon-Ruiz", - "author_inst": "Direccion de Investigacion en Salud, Instituto de Evaluacion de Tecnologias en Salud e Investigacion, IETSI, EsSalud, Lima, Peru" - }, - { - "author_name": "Zoila Romero-Albino", - "author_inst": "Gerencia de la Persona Adulta Mayor y Prestaciones Sociales, EsSalud, Lima, Peru" - }, - { - "author_name": "Percy Soto-Becerra Sr.", - "author_inst": "Direccion de Investigacion en Salud, Instituto de Evaluacion de Tecnologias en Salud e Investigacion, IETSI, EsSalud, Lima, Peru" - }, - { - "author_name": "Jeff Huarcaya-Victoria", - "author_inst": "Departamento de Psiquiatria, Unidad Funcional de Psiquiatria de Enlace, Hospital Nacional Guillermo Almenara Irigoyen, EsSalud, Lima, Peru" - }, - { - "author_name": "Fernando M. Runzer-Colmenares", - "author_inst": "Facultad de Ciencias de la Salud, Universidad Cientifica del Sur, Lima, Peru" - }, - { - "author_name": "Elisa Romani-Huacani", - "author_inst": "Asociacion benefica PRISMA, Lima Peru" - }, - { - "author_name": "David Villarreal-Zegarra", - "author_inst": "Instituto Peruano de Orientacion Psicologica, Lima, Peru" - }, - { - "author_name": "Jorge L. Maguina", - "author_inst": "Direccion de Investigacion en Salud, Instituto de Evaluacion de Tecnologias en Salud e Investigacion, IETSI, EsSalud, Lima, Peru" - }, - { - "author_name": "Moises Apolaya-Segura", - "author_inst": "Direccion de Investigacion en Salud, Instituto de Evaluacion de Tecnologias en Salud e Investigacion, IETSI, EsSalud, Lima, Peru" - }, - { - "author_name": "Sofia Cuba-Fuentes", - "author_inst": "Gerencia de la Persona Adulta Mayor y Prestaciones Sociales, EsSalud, Lima, Peru" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2022.01.24.22269542", "rel_title": "COVID-19 vaccination recruits and matures cross-reactive antibodies to conserved epitopes in endemic coronavirus Spike proteins", @@ -446961,6 +448773,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2022.01.22.22269701", + "rel_title": "Effectiveness of BBV152 vaccine against SARS-CoV-2 infections, hospitalizations, and deaths among healthcare workers in the setting of high delta variant transmission in New Delhi, India", + "rel_date": "2022-01-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.22.22269701", + "rel_abs": "BackgroundDelta variant transmission resulted in surge of SARS CoV-2 cases in New Delhi, India during the early half of year 2021. Health Care Workers (HCWs) received vaccines on priority for prevention of infection. Real life effectiveness of BBV152 vaccine against severe disease including hospitalization and death was not known.\n\nObjectiveTo estimate effectiveness of BBV152 vaccine among HCWs against SARS CoV-2 infection, hospitalization or death\n\nDesignObservational study\n\nSettinga multi -speciality tertiary care public funded hospital in New Delhi, India.\n\nParticipants12,237 HCWs\n\nInterventionsBBV152 vaccine (Covaxin, Bharat Biotech limited, Hyderabad, India); whole virion inactivated vaccine; two doses four weeks apart\n\nMeasurementsvaccine effectiveness after receipt of two doses of BBV152 protecting against any SARS CoV-2 infection, symptomatic infections or hospitalizations or deaths, and hospitalizations or deaths.\n\nResultsThe mean age of HCWs was 36({+/-}11) years, 66% were men and 16% had comorbidity. After adjusting for potential covariates viz age, sex, health worker type category, body mass index, and comorbidity, the vaccine effectiveness (95% Confidence Interval) in fully vaccinated HCWs and [≥]14 days elapsed after the receipt of second dose was 44% (37 to 51, p<0.001) against symptomatic infection, hospitalization or death due to SARS CoV-2, and 61% (37 to 76, p<0.001) against hospitalization or death, respectively.\n\nConclusionsBBV152 vaccine with complete two doses offer a modest response to SARS CoV-2 infection in real life situations against a backdrop of high delta variant community transmission. Efforts in maximizing receipt of full vaccines should be invested for HCWs, who are at higher occupational risk for infection.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Sumit Malhotra", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Kalaivani Mani", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Rakesh Lodha", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Sameer Bakhshi", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Vijay Prakash Mathur", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Pooja Gupta", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Saurabh Kedia", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Jeeva Sankar", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Parmeshwar Kumar", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Arvind Kumar", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Vineet Ahuja", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Subrata Sinha", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "Randeep Guleria", + "author_inst": "All India Institute of Medical Sciences, New Delhi" + }, + { + "author_name": "- COVID Reinfection AIIMS Consortium", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.01.23.22269719", "rel_title": "Should healthcare workers with SARS-CoV-2 household exposures work? A Cohort Study.", @@ -447321,169 +449204,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2022.01.24.22269734", - "rel_title": "SARS-CoV-2 viremia precedes an IL6 response in severe COVID-19 patients: results of a longitudinal prospective cohort", - "rel_date": "2022-01-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.24.22269734", - "rel_abs": "BackgroundInterleukin 6 (IL6) levels and SARS-CoV-2 viremia have been correlated with COVID-19 severity. The association over time between them has not been assessed in a prospective cohort. Our aim was to evaluate the relationship between SARS-CoV-2 viremia and time evolution of IL6 levels in a COVID-19 prospective cohort.\n\nMethodsSecondary analysis from a prospective cohort including COVID-19 hospitalized patients from Hospital Universitario La Princesa between November 2020 and January 2021. Serial plasma samples were collected from admission until discharge. Viral load was quantified by Real-Time Polymerase Chain Reaction and IL6 levels with an enzyme immunoassay. To represent the evolution over time of both variables we used the graphic command twoway of Stata.\n\nResultsA total of 57 patients were recruited, with median age of 63 years (IQR [53-81]), 61.4% male and 68.4% caucasian. The peak of viremia appeared shortly after symptom onset in patients with persistent viremia (more than 1 sample with >1.3 log10 copies/ml) and also in those with at least one IL6>30 pg/ml, followed by a progressive increase in IL6 around 10 days later. Persistent viremia in the first week of hospitalization was associated with higher levels of IL6. Both IL6 and SARS-CoV-2 viral load were higher in males, with a quicker increase with age.\n\nConclusionsIn those patients with worse outcomes, an early peak of SARS-CoV-2 viral load precedes an increase in IL6 levels. Monitoring SARS-CoV-2 viral load during the first week after symptom onset may be helpful to predict disease severity in COVID-19 patients.", - "rel_num_authors": 37, - "rel_authors": [ - { - "author_name": "Emilia Roy-Vallejo", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Laura Cardenoso", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Ana Triguero-Martinez", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Marta Chicot Llano", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Nelly D. Zurita Cruz", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Elena Avalos Perez-Urria", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Ana Barrios", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Julia Hernando Santos", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Javier Ortiz", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Sebastian C. Rodriguez-Garcia", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Marianela Ciudad Sanudo", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Celeste Marcos", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Elena Garcia Castillo", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Leticia Fontan Garcia-Rodrigo", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Begona Gonzalez", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Rosa Mendez", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Isabel Iturrate", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Ancor Sanz-Garcia", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Almudena Villa", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Ana Sanchez Azofra", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Begona Quicios", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "David Arribas", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Jesus Alvarez-Rodriguez", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Pablo Patino", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Marina Trigueros", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Miren Uriarte", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Alexandra Martin Ramirez", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Cristina Arevalo", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Jose Maria Galvan-Roman", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Rosario Garcia-Vicuna", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Julio Ancochea", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Cecilia Munoz-Calleja", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Elena Fernandez-Ruiz", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Rafael de la Camara", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Carmen Suarez Fernandez", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Isidoro Gonzalez-Alvaro", - "author_inst": "Hospital Universitario de La Princesa" - }, - { - "author_name": "Diego A. Rodriguez Serrano", - "author_inst": "Hospital Universitario de La Princesa" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.24.477479", "rel_title": "Forecasted trends of the new COVID-19 epidemic due to the Omicron variant in Thailand, 2022", @@ -448835,6 +450555,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.01.19.22269391", + "rel_title": "COVID-19 and its clinical severity are associated with alterations of plasma sphingolipids and enzyme activities of sphingomyelinase and ceramidase", + "rel_date": "2022-01-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.19.22269391", + "rel_abs": "In the current pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; COVID-19), a better understanding of the underlying mechanisms is essential to reduce morbidity and mortality and treat post-COVID-19 disease. Here, we analyzed alterations of sphingolipids and their metabolizing enzymes in 125 men and 74 women tested positive for SARS-CoV-2 and hospitalized with mild, moderate or severe symptoms or after convalescence.\n\nThe activities of acid and neutral sphingomyelinases (ASM, NSM), which hydrolyze sphingomyelin to ceramide, were significantly increased in COVID-19 patients, while the activity of neutral ceramidase (NC), which hydrolyzes ceramide to sphingosine, was reduced. These alterations could each contribute to elevated ceramide levels in patients. Accordingly, liquid chromatography tandem-mass spectrometry (LC-MS/MS) yielded increased levels of ceramides 16:0 and 18:0 with highest levels in severely affected patients and similar effects for dihydroceramides 16:0 and 18:0, whereas levels of (dihydro-)ceramides 24:0 were reduced. Furthermore, sphingomyelin 20:0; 22:0 and 24:0 as substrates of ASM and NSM as well as their dihydrosphingomyelin counterparts were reduced in patients as well as sphingosine-1-phosphate further downstream of NC activity. Effects of NSM, NC, ceramides and sphingomyelins remained significant after Bonferroni correction. SARS-CoV-2 antibody levels in convalescent patients were associated with age but none of the sphingolipid parameters. Based on our data, COVID-19 is associated with a dysregulation of sphingolipid homeostasis in a severity-dependent manner, particularly focused around a reduction of sphingomyelins and an accumulation of ceramides by increased enzyme activities leading to ceramide elevation (ASM, NSM) combined with a decreased activity of enzymes (NC) reducing ceramide levels. The potential of a combined sphingolipid/enzyme pattern as a diagnostic and prognostic marker and therapeutic target deserves further exploration.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Christiane M\u00fchle", + "author_inst": "Universit\u00e4tsklinikum Erlangen and Friedrich-Alexander University Erlangen-N\u00fcrnberg (FAU)" + }, + { + "author_name": "Andreas Kremer", + "author_inst": "Department of Medicine 1, Universit\u00e4tsklinikum Erlangen and Friedrich-Alexander University Erlangen-N\u00fcrnberg (FAU), Germany and Department of Gastroenterology a" + }, + { + "author_name": "Marcel Vetter", + "author_inst": "Department of Medicine 1, Universit\u00e4tsklinikum Erlangen and Friedrich-Alexander University Erlangen-N\u00fcrnberg (FAU)" + }, + { + "author_name": "Jonas Schmid", + "author_inst": "Department of Medicine 1, Universit\u00e4tsklinikum Erlangen and Friedrich-Alexander University Erlangen-N\u00fcrnberg (FAU)" + }, + { + "author_name": "Susanne Achenbach", + "author_inst": "Department of Transfusion Medicine, Universit\u00e4tsklinikum Erlangen and Friedrich-Alexander University Erlangen-N\u00fcrnberg (FAU), German" + }, + { + "author_name": "Fabian Schumacher", + "author_inst": "Freie Universit\u00e4t Berlin, Institute of Pharmacy, K\u00f6nigin-Luise-Str. 2+4, 14195 Berlin, Germany" + }, + { + "author_name": "Bernd Lenz", + "author_inst": "Department of Addictive Behavior and Addiction Medicine, Central Institute of Mental Health (CIMH), Medical Faculty Mannheim, Heidelberg University, Germany" + }, + { + "author_name": "C\u00e9line Cougoule", + "author_inst": "Institut de Pharmacologie et de Biologie Structurale, IPBS, Universit\u00e9 de Toulouse, Toulouse, France" + }, + { + "author_name": "Nicolas Hoertel", + "author_inst": "Universit\u00e9 de Paris, AP-HP, H\u00f4pital Corentin-Celton, DMU Psychiatrie et Addictologie, D\u00e9partement de Psychiatrie, INSERM, Institut de Psychiatrie et Neuroscienc" + }, + { + "author_name": "Alexander Carpinteiro", + "author_inst": "Department of Hematology and Stem Cell Transplantation, University Hospital Essen, University of Duisburg-Essen, Essen, Germany and Institute for Molecular Biol" + }, + { + "author_name": "Erich Gulbins", + "author_inst": "Institute for Molecular Biology, University Medicine Essen, University of Duisburg- Essen, Essen, Germany" + }, + { + "author_name": "Burkhard Kleuser", + "author_inst": "Freie Universit\u00e4t Berlin, Institute of Pharmacy, K\u00f6nigin-Luise-Str. 2+4, 14195 Berlin, Germany" + }, + { + "author_name": "Johannes Kornhuber", + "author_inst": "Department of Psychiatry and Psychotherapy, Universit\u00e4tsklinikum Erlangen and Friedrich-Alexander University Erlangen-N\u00fcrnberg (FAU), Germany" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.14.22269289", "rel_title": "Serological study of CoronaVac vaccine and booster doses in Chile: immunogenicity and persistence of anti-SARS-CoV-2 S antibodies", @@ -449507,41 +451294,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2022.01.20.477105", - "rel_title": "In Silico Analysis Of The Effects Of Omicron Spike Amino Acid Changes On The Interactions With Human ACE2 Receptor And Structurally Characterized Complexes With Human Antibodies", - "rel_date": "2022-01-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.20.477105", - "rel_abs": "The new SARS-CoV-2 variant Omicron is characterised, among others, by more than 30 amino acid changes (including 4 deletions and 1 insertion) occurring on the spike glycoprotein.\n\nWe report a comprehensive analysis of the effects of the Omicron spike amino acid changes in the interaction with human ACE2 receptor or with human antibodies, obtained by analysing the publicly available resolved 3D structures. Our analysis predicts that amino acid changes occurring on amino acids interacting with the ACE2 receptor may increase Omicron transmissibility. The interactions of Omicron spike with human antibodies can be both negatively and positively affected by amino acid changes, with a predicted total loss of interactions only in few complexes. We believe that such an approach can be used to better understand SARS-CoV-2 transmissibility, detectability, and epidemiology, especially when extended to other than spike proteins.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Deborah Giordano", - "author_inst": "National Research Council, Institute of Food Science" - }, - { - "author_name": "Bernardina Scafuri", - "author_inst": "Department of Chemistry and Biology \"A. Zambelli\", University of Salerno" - }, - { - "author_name": "Carmen Biancaniello", - "author_inst": "Department of Electrical Engineering and Information Technology, University of Naples \"Federico II\"" - }, - { - "author_name": "Mauro Petrillo", - "author_inst": "Seidor Italy srl" - }, - { - "author_name": "Angelo Facchiano", - "author_inst": "National Research Council, Institute of Food Science" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2022.01.20.477107", "rel_title": "Broadly-recognized, cross-reactive SARS-CoV-2 CD4 T cell epitopes are highly conserved across human coronaviruses and presented by common HLA alleles", @@ -450869,6 +452621,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.18.22269501", + "rel_title": "Seroprevalence of anti-SARS coronavirus 2 antibodies in Thai adults during the first three epidemic waves", + "rel_date": "2022-01-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.18.22269501", + "rel_abs": "This study sought to determine the anti-SARS-CoV-2 antibody status of 4111 Thai people from May 2020 to April 2021, a period which spanned the first two and part of the third epidemic wave of the COVID-19 in Thailand. Participants comprised 142 COVID-19 patients, 2113 individuals at risk due to their occupations [health personnel, airport officers, public transport drivers, and workers in entertainment venues (pubs, bars and massage parlors)], 1856 individuals at risk due to sharing workplaces or living communities with COVID-19 patients, and 553 Thai citizens returning after extended periods in countries with a high disease prevalence. All sera were tested in a microneutralization assay and a chemiluminescence immunoassay (CLIA) for IgG against the N protein. Furthermore, we performed an immunofluorescence assay to resolve discordant results between the two assays. Antibody responses developed in 88% (15 of 17) of COVID-19 patients at 8 days and in 94-100% between 15 and 60 days after disease onset. Neutralizing antibodies persisted for at least 8 months, longer than the IgG did, against the N protein. None of the health providers, airport officers, and public transport drivers were seropositive, while the antibodies were present in 0.44% of entertainment workers. This study showed the seropositivity of 1.9, 1.5, and 7.5% during the 3 epidemic waves, respectively, in Bangkok residents who were at risk due to sharing workplaces or communities with COVID-19 patients. Also, antibody prevalence was 1.3% in Chiang Mai people during the first epidemic wave, and varied between 6.5 and 47.0% in Thais returning from high-risk countries. This serosurveillance study found a low infection rate of SARS-CoV-2 in Thailand before the emergence of the Delta variant in late May 2021. The findings support the Ministry of Public Healths data, which are based on numbers of patients and contact tracing.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Hatairat Lerdsamran", + "author_inst": "Mahidol University" + }, + { + "author_name": "Anek Mungaomklang", + "author_inst": "Royal Thai Government Ministry of Public Health" + }, + { + "author_name": "Sopon Iamsirithaworn", + "author_inst": "Royal Thai Government Ministry of Public Health" + }, + { + "author_name": "Jarunee Prasertsopon", + "author_inst": "Mahidol University" + }, + { + "author_name": "Witthawat Wiriyarat", + "author_inst": "Mahidol University" + }, + { + "author_name": "Suthee Saritsiri", + "author_inst": "Bangkok Metropolitan Administration" + }, + { + "author_name": "Ratikorn Anusorntanawat", + "author_inst": "Royal Thai Government Ministry of Public Health" + }, + { + "author_name": "Nirada Siriyakorn", + "author_inst": "Royal Thai Government Ministry of Public Health" + }, + { + "author_name": "Poj Intalapaporn", + "author_inst": "Royal Thai Government Ministry of Public Health" + }, + { + "author_name": "Somrak Sirikhetkon", + "author_inst": "Royal Thai Government Ministry of Public Health" + }, + { + "author_name": "Kantima Sangsiriwut", + "author_inst": "Mahidol University" + }, + { + "author_name": "Worawat Dangsakul", + "author_inst": "Royal Thai Government Ministry of Public Health" + }, + { + "author_name": "Suteema Sawadpongpan", + "author_inst": "Mahidol University" + }, + { + "author_name": "Nattakan Thinpan", + "author_inst": "Mahidol University" + }, + { + "author_name": "Pilailuk Okada", + "author_inst": "Royal Thai Government Ministry of Public Health" + }, + { + "author_name": "Ranida Techasuwanna", + "author_inst": "Royal Thai Government Ministry of Public Health" + }, + { + "author_name": "Noparat Mongkalangoon", + "author_inst": "Royal Thai Government Ministry of Public Health" + }, + { + "author_name": "Kriengkrai Prasert", + "author_inst": "Royal Thai Government Ministry of Public Health" + }, + { + "author_name": "Pilaipan Puthavathana", + "author_inst": "Mahidol University Faculty of Medical Technology" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.18.22269330", "rel_title": "Effectiveness of COVID-19 Vaccines in preventing Infectiousness, Hospitalization and Mortality: A Historical Cohort Study Using Iranian Registration Data During Vaccination program", @@ -451225,49 +453068,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.20.22269618", - "rel_title": "Molecular diagnosis of SARS-CoV-2: a validation of saliva samples", - "rel_date": "2022-01-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.20.22269618", - "rel_abs": "Nasopharyngeal swabs are the most used in sample collecting for covid-19 tests in SARS-CoV-2 molecular diagnosis. However, this sampling method presents some disadvantages, since, in addition to being dependent on imported materials, it is invasive, causes discomfort in patients, and, presents the risk of contamination for the medical collection team. This study aimed at validating saliva samples to obtain viral RNA to be used in the molecular diagnostic test for SARS-CoV-2 using the RT-qPCR technique. Results presented 93,44% concordance in in comparison to nasopharyngeal swabs sampling. Therefore, saliva samples used in SARS-CoV-2 RT-qPCR detection tests presented consistent results.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Natalia V R da Silva", - "author_inst": "Laboratory of Molecular Diagnosis, Federal University of Vicosa, campus Rio Paranaiba." - }, - { - "author_name": "Samyra S N Pereira", - "author_inst": "Laboratory of Molecular Diagnosis, Federal University of Vicosa, campus Rio Paranaiba" - }, - { - "author_name": "Karine F Kavalco", - "author_inst": "Laboratory of Molecular Diagnosis, Federal University of Vicosa, campus Rio Paranaiba" - }, - { - "author_name": "Fabiano B Menegidio", - "author_inst": "University of Mogi das Cruzes" - }, - { - "author_name": "Luanda Medeiros-Santana", - "author_inst": "Laboratory of Molecular Diagnosis, Federal University of Vicosa, campus Rio Paranaiba" - }, - { - "author_name": "Liliane E Visotto", - "author_inst": "Laboratory of Molecular Diagnosis, Federal University of Vicosa, campus Rio Paranaiba" - }, - { - "author_name": "Rubens Pasa", - "author_inst": "Laboratory of Molecular Diagnosis, Federal University of Vicosa, campus Rio Paranaiba" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2022.01.20.22269617", "rel_title": "\"I feel like my body is broken\": Exploring the experiences of people living with long COVID", @@ -452691,6 +454491,69 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2022.01.19.477009", + "rel_title": "Computation of Antigenicity Predicts SARS-CoV-2 Vaccine Breakthrough Variants", + "rel_date": "2022-01-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.19.477009", + "rel_abs": "It has been reported that multiple SARS-CoV-2 variants of concerns (VOCs) including B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma), and B.1.617.2 (Delta) can reduce neutralisation by antibodies, resulting in vaccine breakthrough infections. Virus-antiserum neutralisation assays are typically performed to monitor potential vaccine breakthrough strains. However, such experimental-based methods are slow and cannot instantly validate whether newly emerging variants can break through current vaccines or therapeutic antibodies. To address this, we sought to establish a computational model to predict the antigenicity of SARS-CoV-2 variants by sequence alone and in real time. In this study, we firstly identified the relationship between the antigenic difference transformed from the amino acid sequence and the antigenic distance from the neutralisation titres. Based on this correlation, we obtained a computational model for the receptor binding domain (RBD) of the spike protein to predict the fold decrease in virus-antiserum neutralisation titres with high accuracy (~0.79). Our predicted results were comparable with experimental neutralisation titres of variants, including B.1.1.7 (Alpha), B.1.351 (Beta), B.1.617.2 (Delta), B.1.429 (Epsilon), P.1 (Gamma), B.1.526 (Iota), B.1.617.1 (Kappa), and C.37 (Lambda), as well as SARS-CoV. Here, we firstly predicted the fold of decrease of B.1.1.529 (Omicron) as 17.4-fold less susceptible to neutralisation. We visualised all 1521 SARS-CoV-2 lineages to indicate variants including B.1.621 (Mu), B.1.630, B.1.633, B.1.649, and C.1.2, which can induce vaccine breakthrough infections in addition to reported VOCs B.1.351 (Beta), P.1 (Gamma), B.1.617.2 (Delta), and B.1.1.529 (Omicron). Our study offers a quick approach to predict the antigenicity of SARS-CoV-2 variants as soon as they emerge. Furthermore, this approach can facilitate future vaccine updates to cover all major variants. An online version can be accessed at http://jdlab.online.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Ye-fan Hu", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Jing-chu Hu", + "author_inst": "Shenzhen Institutes of Advanced Technology" + }, + { + "author_name": "Hua-Rui Gong", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Antoine Danchin", + "author_inst": "CNRS / Institut Pasteur" + }, + { + "author_name": "Ren Sun", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Hin Chu", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Ivan Fan-Ngai Hung", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Kwok Yung Yuen", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Kelvin Kai-Wang To", + "author_inst": "University of Hong Kong" + }, + { + "author_name": "Bao-Zhong Zhang", + "author_inst": "Shenzhen Institutes of Advanced Technology" + }, + { + "author_name": "Thomas Yau", + "author_inst": "The University of Hong Kong" + }, + { + "author_name": "Jian-Dong Huang", + "author_inst": "The University of Hong Kong" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2022.01.18.476864", "rel_title": "Longitudinal Assessment of SARS-CoV-2 Specific T Cell Cytokine-Producing Responses for 1 Year Reveals Persistence of Multi-Cytokine Proliferative Responses, with Greater Immunity Associated with Disease Severity", @@ -453203,85 +455066,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.01.17.22269283", - "rel_title": "ELF5 is a respiratory epithelial cell-specific risk gene for severe COVID-19", - "rel_date": "2022-01-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.17.22269283", - "rel_abs": "Despite two years of intense global research activity, host genetic factors that predispose to a poorer prognosis and severe course of COVID-19 infection remain poorly understood. Here, we identified eight candidate protein mediators of COVID-19 outcomes by establishing a shared genetic architecture at protein-coding loci using large-scale human genetic studies. The transcription factor ELF5 (ELF5) showed robust and directionally consistent associations across different outcome definitions, including a >4-fold higher risk (odds ratio: 4.85; 95%-CI: 2.65-8.89; p-value<3.1x10-7) for severe COVID-19 per 1 s.d. higher genetically predicted plasma ELF5. We show that ELF5 is specifically expressed in epithelial cells of the respiratory system, such as secretory and alveolar type 2 cells, using single-cell RNA sequencing and immunohistochemistry. These cells are also likely targets of SARS-CoV-2 by colocalisation with key host factors, including ACE2 and TMPRSS2. We also observed a 25% reduced risk of severe COVID-19 per 1 s.d. higher genetically predicted plasma G-CSF, a finding corroborated by a clinical trial of recombinant human G-CSF in COVID-19 patients with lymphopenia reporting a lower number of patients developing critical illness and death. In summary, large-scale human genetic studies together with gene expression at single-cell resolution highlight ELF5 as a novel risk gene for COVID-19 prognosis, supporting a role of epithelial cells of the respiratory system in the adverse host response to SARS-CoV-2.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Maik Pietzner", - "author_inst": "Computational Medicine, Berlin Institute of Health (BIH) at Charit\u00e9 \u2013 Universit\u00e4tsmedizin Berlin, Germany" - }, - { - "author_name": "Robert Lorenz Chua", - "author_inst": "Center for Digital Health, Berlin Institute of Health (BIH) at Charit\u00e9 \u2013 Universit\u00e4tsmedizin Berlin, Germany" - }, - { - "author_name": "Eleanor Wheeler", - "author_inst": "MRC Epidemiology Unit, University of Cambridge, Cambridge, UK" - }, - { - "author_name": "Katharina Jechow", - "author_inst": "Center for Digital Health, Berlin Institute of Health (BIH) at Charit\u00e9 \u2013 Universit\u00e4tsmedizin Berlin, Germany" - }, - { - "author_name": "Helena Radbruch", - "author_inst": "Department of Neuropathology, Charit\u00e9 \u2013 Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin und Humboldt-Universit\u00e4t zu Berlin, Berlin, Ger" - }, - { - "author_name": "Saskia Trump", - "author_inst": "Molecular Epidemiology Unit, Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin and Berlin Insti" - }, - { - "author_name": "Bettina Heidecker", - "author_inst": "Department of Cardiology, Charit\u00e9 \u2013 Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin und Humboldt-Universit\u00e4t zu Berlin, Berlin, Germany" - }, - { - "author_name": "Frank Heppner", - "author_inst": "Department of Neuropathology, Charit\u00e9 \u2013 Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin und Humboldt-Universit\u00e4t zu Berlin, Berlin, Ger" - }, - { - "author_name": "Roland Eils", - "author_inst": "Center for Digital Health, Berlin Institute of Health (BIH) at Charit\u00e9 \u2013 Universit\u00e4tsmedizin Berlin, Germany" - }, - { - "author_name": "Marcus Mall", - "author_inst": "Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine, Charit\u00e9-Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t B" - }, - { - "author_name": "Leif Erik Sander", - "author_inst": "Department of Infectious Diseases and Respiratory Medicine, Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Univers" - }, - { - "author_name": "Irina Lehmann", - "author_inst": "Molecular Epidemiology Unit, Charit\u00e9 - Universit\u00e4tsmedizin Berlin, corporate member of Freie Universit\u00e4t Berlin, Humboldt-Universit\u00e4t zu Berlin and Berlin Insti" - }, - { - "author_name": "S\u00f6ren Lukassen", - "author_inst": "Center for Digital Health, Berlin Institute of Health (BIH) at Charit\u00e9 \u2013 Universit\u00e4tsmedizin Berlin, Germany" - }, - { - "author_name": "Nicholas J. Wareham", - "author_inst": "MRC Epidemiology Unit, University of Cambridge, Cambridge, UK" - }, - { - "author_name": "Christian Conrad", - "author_inst": "Center for Digital Health, Berlin Institute of Health (BIH) at Charit\u00e9 \u2013 Universit\u00e4tsmedizin Berlin, Germany" - }, - { - "author_name": "Claudia Langenberg", - "author_inst": "Computational Medicine, Berlin Institute of Health (BIH) at Charit\u00e9 \u2013 Universit\u00e4tsmedizin Berlin, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2022.01.19.22269529", "rel_title": "Serum extracellular vesicles trace COVID-19 progression and immune responses", @@ -454787,6 +456571,20 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.01.17.22269421", + "rel_title": "Estimation of the COVID-19 Average Incubation Time:Systematic Review, Meta-analysis and SensitivityAnalyses", + "rel_date": "2022-01-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.17.22269421", + "rel_abs": "ObjectivesWe aim to provide sensible estimates of the average incubation time of COVID-19 by capitalizing available estimates reported in the literature and explore different ways to accommodate heterogeneity involved with the reported studies.\n\nMethodsWe search through online databases to collect the studies about estimates of the average incubation time and conduct meta-analyses to accommodate heterogeneity of the studies and the publication bias. Cochrans heterogeneity statistic Q and Higgins & Thompsons I2 statistic are employed. Subgroup analyses are conducted using mixed effects models and publication bias is assessed using the funnel plot and Eggers test.\n\nResultsUsing all those reported mean incubation estimates, the average incubation time is estimated to be 6.43 days with a 95% confidence interval (CI) (5.90, 6.96), and using all those reported mean incubation estimates together with those transformed median incubation estimates, the estimated average incubation time is 6.07 days with a 95% CI (5.70,6.45).\n\nConclusionsProviding sensible estimates of the average incubation time for COVID-19 is important yet complex, and the available results vary considerably due to many factors including heterogeneity and publication bias. We take different angles to estimate the mean incubation time, and our analyses provide estimates to range from 5.68 days to 8.30 days.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.01.17.22269222", "rel_title": "The value of vaccine booster doses to mitigate the global impact of the Omicron SARS-CoV-2 variant", @@ -455181,45 +456979,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "addiction medicine" }, - { - "rel_doi": "10.1101/2022.01.16.22269377", - "rel_title": "The Impact of State Paid Sick Leave Policies on Longitudinal Weekday Workplace Mobility During the COVID-19 Pandemic", - "rel_date": "2022-01-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.16.22269377", - "rel_abs": "ObjectivesTo evaluate whether the Families First Coronavirus Response Act (FFCRA) modified the association between pre-existing state paid sick leave (PSL) and weekday workplace mobility between February 15 and July 7, 2020.\n\nMethodsThe 50 US states and Washington, D.C. were divided into exposure groups based on the presence or absence of pre-existing state PSL policies. Derived from Google COVID-19 Community Mobility Reports, the outcome was measured as the daily percent change in weekday workplace mobility. Mixed-effects, interrupted time series regression was performed to evaluate weekday workplace mobility after the implementation of the FFCRA on April 1st, 2020.\n\nResultsStates with pre-existing PSL policies exhibited a greater drop in mobility following the passage of the FFCRA ({beta}=-8.86,95%CI:-11.6,-6.10,P< 001). This remained significant after adjusting for state-level health, economic, and sociodemographic indicators ({beta}=-3.13,95%CI:-5.92,-0.34,P=.039).\n\nConclusionsPre-existing PSL policies contributed to a significant decline in weekday workplace mobility after the FFCRA, which may have influenced local health outcomes.\n\nPolicy implicationsThe presence of pre-existing state policies may differentially influence the impact of federal legislation enacted during emergencies.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Catherine C. Pollack", - "author_inst": "Geisel School of Medicine at Dartmouth" - }, - { - "author_name": "Akshay Deverakonda", - "author_inst": "COVID-19 Dispersed Volunteer Research Network" - }, - { - "author_name": "Fahim Hassan", - "author_inst": "University of Alberta" - }, - { - "author_name": "Syed Haque", - "author_inst": "Northeastern University" - }, - { - "author_name": "Angel N. Desai", - "author_inst": "University of California - Davis" - }, - { - "author_name": "Maimuna Majumder", - "author_inst": "Boston Children's Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2022.01.17.22269201", "rel_title": "SARS-CoV-2 vaccination of convalescents boosts neutralization capacity against SARS-CoV-2 Delta and Omicron that can be predicted by anti-S antibody concentrations in serological assays", @@ -456391,6 +458150,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.14.21267836", + "rel_title": "Generation of novel SARS-CoV-2 variants on B.1.1.7 lineage in three patients with advanced HIV disease", + "rel_date": "2022-01-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.14.21267836", + "rel_abs": "The emergence of new SARS-COV-2 variants is of public health concern in case of vaccine escape. Described are three patients with advanced HIV-1 and chronic SARS-CoV-2 infection in whom there is evidence of selection and persistence of novel mutations which are associated with increased transmissibility and immune escape.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Anna C Riddell", + "author_inst": "Barts Health NHS Trust" + }, + { + "author_name": "Beatrix Kele", + "author_inst": "Barts Health NHS Trust" + }, + { + "author_name": "Kathryn Harris", + "author_inst": "Barts Health NHS Trust" + }, + { + "author_name": "Jon Bible", + "author_inst": "Barts Health NHS Trust" + }, + { + "author_name": "Maurice Murphy", + "author_inst": "Barts Health NHS Trust" + }, + { + "author_name": "Subathira Dakshina", + "author_inst": "Barts Health NHS Trust" + }, + { + "author_name": "Nathaniel Storey", + "author_inst": "Great Ormond Street Hospital for Children NHS Foundation Trust" + }, + { + "author_name": "Dola Owoyemi", + "author_inst": "Barts Health NHS Trust" + }, + { + "author_name": "Corinna Pade", + "author_inst": "Barts and The London School of Medicine and Dentistry Blizard Institute" + }, + { + "author_name": "Joseph M Gibbons", + "author_inst": "Barts and The London School of Medicine and Dentistry Blizard Institute" + }, + { + "author_name": "David Harrington", + "author_inst": "Barts Health NHS Trust" + }, + { + "author_name": "Eliza Alexander", + "author_inst": "Barts Health NHS Trust" + }, + { + "author_name": "\u00c1ine McKnight", + "author_inst": "Barts and The London School of Medicine and Dentistry Blizard Institute" + }, + { + "author_name": "Teresa Cutino-Moguel", + "author_inst": "Barts Health NHS Trust" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.14.22269270", "rel_title": "Validation of a clinical and genetic model for predicting severe COVID-19", @@ -456819,29 +458649,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.13.476204", - "rel_title": "Covariance predicts conserved protein residue interactions important to the emergence and continued evolution of SARS-CoV-2 as a human pathogen", - "rel_date": "2022-01-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.13.476204", - "rel_abs": "SARS-CoV-2 is one of three recognized coronaviruses (CoVs) that have caused epidemics or pandemics in the 21st century and that likely emerged from animal reservoirs. Differences in nucleotide and protein sequence composition within related {beta}-coronaviruses are often used to better understand CoV evolution, host adaptation, and their emergence as human pathogens. Here we report the comprehensive analysis of amino acid residue changes that have occurred in lineage B {beta}-coronaviruses that show covariance with each other. This analysis revealed patterns of covariance within conserved viral proteins that potentially define conserved interactions within and between core proteins encoded by SARS-CoV-2 related {beta}-coranaviruses. We identified not only individual pairs but also networks of amino acid residues that exhibited statistically high frequencies of covariance with each other using an independent pair model followed by a tandem model approach. Using 149 different CoV genomes that vary in their relatedness, we identified networks of unique combinations of alleles that can be incrementally traced genome by genome within different phylogenic lineages. Remarkably, covariant residues and their respective regions most abundantly represented are implicated in the emergence of SARS-CoV-2 are also enriched in dominant SARS-CoV-2 variants.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "William P Robins", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "John J Mekalanos", - "author_inst": "Harvard Medical School" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.01.13.476223", "rel_title": "ATP6V1B2 and IFI27 and their intrinsic functional genomic characteristics associated with SARS-CoV-2", @@ -458165,6 +459972,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2022.01.13.22269198", + "rel_title": "Seasonal Prediction of Omicron Pandemic", + "rel_date": "2022-01-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.13.22269198", + "rel_abs": "The ongoing coronavirus disease 2019 (COVID-19) pandemic has pushed the world in the face of another huge outbreak. In order to have a better understanding on the fast transmission of Omicron variant, we made seasonal predictions on the development of Omicron pandemic globally, as well as 11 key countries. The results demonstrated that the pandemic has an exponential-like growth rate at the initial stage of the outbreak, and will have small resurgences around April and June in north hemisphere countries and south hemisphere countries, respectively.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Jianping Huang Sr.", + "author_inst": "Lanzhou University" + }, + { + "author_name": "Yingjie Zhao", + "author_inst": "Collaborative Innovation Centre for West Ecological Safety (CIWES), Lanzhou University" + }, + { + "author_name": "Li Zhang", + "author_inst": "College of Atmospheric Sciences, Lanzhou University" + }, + { + "author_name": "Xu Li", + "author_inst": "College of Atmospheric Sciences, Lanzhou University" + }, + { + "author_name": "Shuoyuan Gao", + "author_inst": "College of Atmospheric Sciences, Lanzhou University" + }, + { + "author_name": "Xiaodong Song", + "author_inst": "Collaborative Innovation Centre for West Ecological Safety (CIWES), Lanzhou University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.01.10.22269041", "rel_title": "Evidence of early community transmission of Omicron (B1.1.529) in Delhi- A city with very high seropositivity and past exposure!", @@ -458973,37 +460819,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2022.01.13.22269236", - "rel_title": "Estimating the relative proportions of SARS-CoV-2 strains from wastewater samples", - "rel_date": "2022-01-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.13.22269236", - "rel_abs": "Wastewater surveillance has become essential for monitoring the spread of SARS-CoV-2. The quantification of SARS-CoV-2 RNA in wastewater correlates with the Covid-19 caseload in a community. However, estimating the proportions of different SARS-CoV-2 strains has remained technically difficult. We present a method for estimating the relative proportions of SARS-CoV-2 strains from wastewater samples. The method uses an initial step to remove unlikely strains, imputation of missing nucleotides using the global SARS-CoV-2 phylogeny, and an Expectation-Maximization (EM) algorithm for obtaining maximum likelihood estimates of the proportions of different strains in a sample. Using simulations with a reference database of >3 million SARS-CoV-2 genomes, we show that the estimated proportions accurately reflect the true proportions given sufficiently high sequencing depth and that the phylogenetic imputation is highly accurate and substantially improves the reference database.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Lenore Pipes", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Zihao Chen", - "author_inst": "Peking University" - }, - { - "author_name": "Svetlana Afanaseva", - "author_inst": "University of California-Berkeley" - }, - { - "author_name": "Rasmus Nielsen", - "author_inst": "University of California, Berkeley" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.12.22269157", "rel_title": "Estimation of age-stratified contact rates during the COVID-19 pandemic using a novel inference algorithm", @@ -460459,6 +462274,29 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2022.01.11.475877", + "rel_title": "GenomeBits insight into omicron and delta variants of coronavirus pathogen", + "rel_date": "2022-01-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.11.475877", + "rel_abs": "We apply the new GenomeBits method to uncover underlying genomic features of omicron and delta coronavirus variants. This is a statistical algorithm whose salient feature is to map the nucleotide bases into a finite alternating ({+/-}) sum series of distributed terms of binary (0,1) indicators. We show how by this method, distinctive signals can be uncovered out of the intrinsic data organization of amino acid progressions along their base positions. Results reveal a sort of ordered (or constant) to disordered (or peaked) transition around the coronavirus S-spike protein region. Together with our previous results for past variants of coronavirus: Alpha, Beta, Gamma, Epsilon and Eta, we conclude that the mapping into GenomeBits strands of omicron and delta variants can help to characterize mutant pathogens.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Enrique Canessa Sr.", + "author_inst": "ICTP, Trieste" + }, + { + "author_name": "Livio Tenze Sr.", + "author_inst": "ICTP, Trieste" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2022.01.07.475397", "rel_title": "Investigation of the Effects of N-Linked Glycans on the Stability of the Spike Protein in SARS-CoV-2 by Molecular Dynamics Simulations", @@ -461127,73 +462965,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2022.01.11.475327", - "rel_title": "Systemic infection of SARS-CoV-2 in free ranging Leopard (Panthera pardus fusca) in India", - "rel_date": "2022-01-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.11.475327", - "rel_abs": "We report patho-morphological and virological characterization of SARS-CoV-2 in naturally infected, free ranging Indian Leopard (Panthera pardus fusca). Whole genome sequence analysis confirmed infection of Delta variant of SARS-CoV-2, possibly spill over from humans, but the case was detected when infection level had dropped significantly in human population. This report underlines the need for intensive screening of wild animals for keeping track of the virus evolution and development of carrier status of SARS-CoV-2 among wildlife species.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Sonalika Mahajan", - "author_inst": "ICAR Indian Veterinary Research Institute" - }, - { - "author_name": "Karikalan Mathesh", - "author_inst": "ICAR-Indian Veterinary Research Institute Izatnagar" - }, - { - "author_name": "Vishal Chander", - "author_inst": "ICAR-Indian Veterinary Research Institute Izatnagar Bareilly UP" - }, - { - "author_name": "Abhijit M Pawde", - "author_inst": "ICAR-Indian Veterinary Research Institute Izatnagar Bareilly UP" - }, - { - "author_name": "G Saikumar", - "author_inst": "ICAR Indian Veterinary Research Institute Izatnagar" - }, - { - "author_name": "M Semmaran", - "author_inst": "Divisional Director, Social forestry, Bijnor, Uttar Pradesh 246701" - }, - { - "author_name": "P Sree lakshmi", - "author_inst": "ICAR-Indian Veterinary Research Institute Izatnagar Bareilly Uttar Pradesh" - }, - { - "author_name": "Megha Sharma", - "author_inst": "ICAR-Indian Veterinary Research Institute Izatnagar Bareilly Uttar Pradesh" - }, - { - "author_name": "Sukdeb nandi", - "author_inst": "ICAR-Indian Veterinary Research Institute Izatnagar Bareilly Uttar Pradesh" - }, - { - "author_name": "Karam Pal Singh", - "author_inst": "ICAR-Indian Veterinary Research Institute Izatnagar Bareilly Uttar Pradesh" - }, - { - "author_name": "Vivek Kumar Gupta", - "author_inst": "ICAR-Indian Veterinary Research Institute Izatnagar Bareilly Uttar Pradesh" - }, - { - "author_name": "R. K. Singh", - "author_inst": "Division of Virology, Indian Veterinary Research Institute" - }, - { - "author_name": "Gaurav Sharma", - "author_inst": "ICAR-Indian Veterinary Research Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.01.11.475922", "rel_title": "Structural and functional impact by SARS-CoV-2 Omicron spike mutations", @@ -462381,6 +464152,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.11.22269068", + "rel_title": "The impact of post-hospital remote monitoring of COVID-19 patients using pulse oximetry: a national observational study using hospital activity data", + "rel_date": "2022-01-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.11.22269068", + "rel_abs": "BackgroundThere was a national roll out of COVID Virtual Wards (CVW) during Englands second COVID-19 wave (Autumn 2020 - Spring 2021). These services used remote pulse oximetry monitoring for COVID-19 patients following discharge from hospital. A key aim was to enable rapid detection of patient deterioration. It was anticipated that the services would support early discharge and avoid readmissions, reducing pressure on beds. This study is an evaluation of the impact of the CVW services on hospital activity.\n\nMethodsUsing retrospective patient-level hospital admissions data, we built multivariate models to analyse the relationship between the implementation of CVW services and hospital activity outcomes: length of COVID-19 related stays and subsequent COVID-19 readmissions within 28 days. We used data from more than 98% of recorded COVID-19 hospital stays in England, where the patient was discharged alive between mid-August 2020 and late February 2021.\n\nFindingsWe found a longer length of stay for COVID-19 patients discharged from hospitals where a CVW was available, when compared to patients discharged from hospitals where there was no CVW (adjusted IRR 1{middle dot}05, 95% CI 1{middle dot}01 to 1{middle dot}09). We found no evidence of a relationship between the availability of CVW and subsequent rates of readmission for COVID-19 (adjusted OR 0{middle dot}95, 95% CI 0{middle dot}89 to 1{middle dot}02).\n\nInterpretationWe found no evidence of early discharges or reduced readmissions associated with the roll out of COVID Virtual Wards across England. Our analysis made pragmatic use of national-scale hospital data, but it is possible that a lack of specific data (for example, on which patients were enrolled) may have meant that true impacts, especially at a local level, were not ultimately discernible.\n\nFundingThis is independent research funded by the National Institute for Health Research, Health Services & Delivery Research programme and NHSEI.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSPost-hospital virtual wards have been found to have a positive impact on patient outcomes when focussed on patients with specific diseases, for example those with heart disease. There has been less evidence of impact for more heterogenous groups of patients. While these services have been rolled out at scale in England, there has been little evidence thus far that post-hospital virtual wards (using pulse oximetry monitoring) have helped to reduce the length of stay of hospitalised COVID-19 patients, or rates of subsequent readmissions for COVID-19.\n\nAdded value of this studyThis national-scale study provides evidence that the rollout of post-hospital discharge virtual ward services for COVID-19 patients in England did not reduce lengths of stay in hospital, or rates of readmission.\n\nImplications of all the available evidenceWhile there is currently an absence of evidence of positive impacts for COVID-19 patients discharged to a virtual ward, our study emphasises the need for quality data to be collected as part of future service implementation.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Theo Georghiou", + "author_inst": "Nuffield Trust" + }, + { + "author_name": "Chris Sherlaw-Johnson", + "author_inst": "Nuffield Trust" + }, + { + "author_name": "Efthalia Massou", + "author_inst": "Department of Public Health and Primary Care, University of Cambridge" + }, + { + "author_name": "Stephen Morris", + "author_inst": "Department of Public Health & Primary Care, University of Cambridge" + }, + { + "author_name": "Nadia E Crellin", + "author_inst": "Nuffield Trust" + }, + { + "author_name": "Lauren Herlitz", + "author_inst": "Department of Applied Health Research, University College London" + }, + { + "author_name": "Manbinder S Sidhu", + "author_inst": "Health Services Management Centre, University of Birmingham" + }, + { + "author_name": "Sonila M Tomini", + "author_inst": "Department of Applied Health Research, University College London" + }, + { + "author_name": "Cecilia Vindrola-Padros", + "author_inst": "Department of Targeted Intervention, University College London" + }, + { + "author_name": "Holly Walton", + "author_inst": "Department of Applied Health Research, University College London" + }, + { + "author_name": "Naomi J Fulop", + "author_inst": "Department of Applied Health Research, University College London" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.10.475725", "rel_title": "A single-cell atlas reveals shared and distinct immune responses and metabolism during SARS-CoV-2 and HIV-1 infections", @@ -462893,109 +464723,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2022.01.08.22268953", - "rel_title": "Anti-PEG antibodies boosted in humans by SARS-CoV-2 lipid nanoparticle mRNA vaccine", - "rel_date": "2022-01-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.08.22268953", - "rel_abs": "Humans commonly have low level antibodies to poly(ethylene) glycol (PEG) due to environmental exposure. Lipid nanoparticle (LNP) mRNA vaccines for SARS-CoV-2 contain small amounts of PEG but it is not known whether PEG antibodies are enhanced by vaccination and what their impact is on particle-immune cell interactions in human blood. We studied plasma from 130 adults receiving either the BNT162b2 (Pfizer-BioNTech) or mRNA-1273 (Moderna) mRNA vaccines, or no SARS-CoV-2 vaccine for PEG-specific antibodies. Anti-PEG IgG was commonly detected prior to vaccination and was significantly boosted a mean of 13.1-fold (range 1.0 to 70.9) following mRNA-1273 vaccination and a mean of 1.78-fold (range 0.68 to 16.6) following BNT162b2 vaccination. Anti-PEG IgM increased 68.5-fold (range 0.9 to 377.1) and 2.64-fold (0.76 to 12.84) following mRNA-1273 and BNT162b2 vaccination, respectively. The rise in PEG-specific antibodies following mRNA-1273 vaccination was associated with a significant increase in the association of clinically relevant PEGylated LNPs with blood phagocytes ex vivo. PEG antibodies did not impact the SARS-CoV-2 specific neutralizing antibody response to vaccination. However, the elevated levels of vaccine-induced anti-PEG antibodies correlated with increased systemic reactogenicity following two doses of vaccination. We conclude that PEG-specific antibodies can be boosted by LNP mRNA-vaccination and that the rise in PEG-specific antibodies is associated with systemic reactogenicity and an increase of PEG particle-leukocyte association in human blood. The longer-term clinical impact of the increase in PEG-specific antibodies induced by lipid nanoparticle mRNA-vaccines should be monitored.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Yi Ju", - "author_inst": "RMIT University" - }, - { - "author_name": "Wen Shi Lee", - "author_inst": "The Peter Doherty Institute for Infection and Immunity, University of Melbourne" - }, - { - "author_name": "Emily H. Pilkington", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne" - }, - { - "author_name": "Hannah G. Kelly", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne" - }, - { - "author_name": "Shiyao Li", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Kevin J. Selva", - "author_inst": "The Peter Doherty Institute for Infection and Immunity" - }, - { - "author_name": "Kathleen M. Wragg", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne" - }, - { - "author_name": "Kanta Subbarao", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne" - }, - { - "author_name": "Thi H.O. Nguyen", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne" - }, - { - "author_name": "Louise C. Rowntree", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne" - }, - { - "author_name": "Lilith F. Allen", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne" - }, - { - "author_name": "Katherine Bond", - "author_inst": "Royal Melbourne Hospital" - }, - { - "author_name": "Deborah A. Williamson", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne" - }, - { - "author_name": "Nghia P. Truong", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne" - }, - { - "author_name": "Magdalena Plebanski", - "author_inst": "RMIT University" - }, - { - "author_name": "Katherine Kedzierska", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne" - }, - { - "author_name": "Siddhartha Mahanty", - "author_inst": "Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne" - }, - { - "author_name": "Amy W. Chung", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Frank Caruso", - "author_inst": "The University of Melbourne" - }, - { - "author_name": "Adam K. Wheatley", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Jennifer A Juno", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Stephen J. Kent", - "author_inst": "University of Melbourne" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2022.01.08.22268901", "rel_title": "Autoantibodies in COVID-19 correlate with anti-viral humoral responses and distinct immune signatures", @@ -464263,6 +465990,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.10.22268799", + "rel_title": "Quantifying behavior change during the first year of the COVID-19 pandemic in the United States", + "rel_date": "2022-01-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.10.22268799", + "rel_abs": "BackgroundDuring the first year of the COVID-19 pandemic, the most effective way to reduce transmission and to protect oneself was to reduce contact with others. However, it is unclear how behavior changed, despite numerous surveys about peoples attitudes and actions during the pandemic and public health efforts to influence behavior.\n\nMethodsWe used two sources of data to quantify changes in behavior at the county level during the first year of the pandemic in the United States: aggregated mobile device (smartphone) location data to approximate the fraction of people staying at home each day and digital invitation data to capture the number and size of social gatherings.\n\nResultsBetween mid-March to early April 2020, the number of events fell and the fraction of devices staying at home peaked, independently of when states issued emergency orders or stay-at-home recommendations. Activity began to recover in May or June, with later rebounds in counties that suffered an early spring wave of reported COVID-19 cases. Counties with high incidence in the summer had more events, higher mobility, and less stringent state-level COVID-related restrictions the month before than counties with low incidence. Counties with high incidence in early fall stayed at home less and had less stringent state-level COVID-related restrictions in October, when cases began to rise in some parts of the US. During the early months of the pandemic, the number of events was inversely correlated with the fraction of devices staying at home, but after the fall of 2020 mobility appeared to stay constant as the number of events fell. Greater changes in behavior were observed in counties where a larger fraction voted for Biden in the 2020 US Presidential election. The number of people invited per event dropped gradually throughout the first year of the pandemic.\n\nConclusionsThe mobility and events datasets uncovered different kinds of behavioral responses to the pandemic. Our results indicate that people did in fact change their behavior in ways that likely reduced COVID exposure and transmission, though the degree of change appeared to be affected by political views. Though the mobility data captured the initial massive behavior changes in the first months of the pandemic, the digital invitation data, presented here for the first time, continued to show large changes in behavior later in the first year of the pandemic.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Dennis L Chao", + "author_inst": "Bill & Melinda Gates Foundation" + }, + { + "author_name": "Victor Cho", + "author_inst": "Evite, Inc" + }, + { + "author_name": "Amanda S Izzo", + "author_inst": "Bill & Melinda Gates Foundation" + }, + { + "author_name": "Joshua L Proctor", + "author_inst": "Bill & Melinda Gates Foundation" + }, + { + "author_name": "Marita Zimmermann", + "author_inst": "Bill & Melinda Gates Foundation" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.01.07.475453", "rel_title": "Mild respiratory SARS-CoV-2 infection can cause multi-lineage cellular dysregulation and myelin loss in the brain", @@ -464726,65 +466488,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2022.01.10.475620", - "rel_title": "Strong SARS-CoV-2 N-specific CD8+ T immunity induced by engineered extracellular vesicles associates with protection from lethal infection in mice.", - "rel_date": "2022-01-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.10.475620", - "rel_abs": "SARS-CoV-2-specific CD8+ T cell immunity is expected to counteract viral variants in both efficient and durable ways. We recently described a way to induce a potent SARS-CoV-2 CD8+ T immune response through the generation of engineered extracellular vesicles (EVs) emerging from muscle cells. This method relies on intramuscular injection of DNA vectors expressing different SARS-CoV-2 antigens fused at their N-terminus with Nefmut protein, i.e., a very efficient EV-anchoring protein. However, quality, tissue distribution, and efficacy of these SARS-CoV-2-specific CD8+ T cells remained uninvestigated. To fill the gaps, antigen-specific CD8+ T lymphocytes induced by the immunization through the Nefmut-based method were characterized in terms of their polyfunctionality and localization at lung airways, i.e., the primary targets of SARS-CoV-2 infection. We found that injection of vectors expressing Nefmut/S1 and Nefmut/N generated polyfunctional CD8+ T lymphocytes in both spleens and bronchoalveolar lavage fluids (BALFs). When immunized mice were infected with 4.4 lethal doses 50% of SARS-CoV-2, all S1-immunized mice succumbed, whereas those developing the highest percentages of N-specific CD8+ T lymphocytes resisted the lethal challenge. We also provide evidence that the N-specific immunization coupled with the development of antigen-specific CD8+ T-resident memory cells in lungs, supporting the idea that the Nefmut- based immunization can confer a long-lasting, lung-specific immune memory. In view of the limitations of current anti-SARS-CoV-2 vaccines in terms of antibody waning and efficiency against variants, our CD8+ T cell-based platform could be considered for a new combination prophylactic strategy.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Flavia Ferrantelli", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Chiara Chiozzini", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Francesco Manfredi", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Patrizia Leone", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Massimo Spada", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Antonio DiVirgilio", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Andrea Giovannelli", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Massimo Sanchez", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Andrea Cara", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Zuleika Michelini", - "author_inst": "Istituto Superiore di Sanita" - }, - { - "author_name": "Maurizio Federico", - "author_inst": "Istituto Superiore di Sanita" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2022.01.07.22268918", "rel_title": "Identifying SARS-CoV-2 regional introductions and transmission clusters in real time", @@ -466316,6 +468019,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.07.22268891", + "rel_title": "COVID-19 impact on routine immunisations for vaccine-preventable diseases: Projecting the effect of different routes to recovery", + "rel_date": "2022-01-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.07.22268891", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSIntroductionC_ST_ABSOver the past two decades, vaccination programmes for vaccine-preventable diseases (VPDs) have expanded across low- and middle-income countries (LMICs). However, the rise of COVID-19 resulted in global disruption to routine immunisation (RI) activities. Such disruptions could have a detrimental effect on public health, leading to more deaths from VPDs, particularly without mitigation efforts. Hence, as RIs resume, it is important to estimate the effectiveness of different approaches for recovery.\n\nMethodsWe apply an impact extrapolation method developed by the Vaccine Impact Modelling Consortium to estimate the impact of COVID-19-related disruptions with different recovery scenarios for ten VPDs across 112 LMICs. We focus on deaths averted due to RIs occurring in the years 2020-2030 and investigate two recovery scenarios relative to a no-COVID-19 scenario. In the recovery scenarios, we assume a 10% COVID-19-related drop in RI coverage in the year 2020. We then linearly interpolate coverage to the year 2030 to investigate two routes to recovery, whereby the immunization agenda (IA2030) targets are reached by 2030 or fall short by 10%.\n\nResultsWe estimate that falling short of the IA2030 targets by 10% leads to 11.26% fewer fully vaccinated persons (FVPs) and 11.34% more deaths over the years 2020-2030 relative to the no-COVID-19 scenario, whereas, reaching the IA2030 targets reduces these proportions to 5% fewer FVPs and 5.22% more deaths. The impact of the disruption varies across the VPDs with diseases where coverage expands drastically in future years facing a smaller detrimental effect.\n\nConclusionOverall, our results show that drops in RI coverage could result in more deaths due to VPDs. As the impact of COVID-19-related disruptions is dependent on the vaccination coverage that is achieved over the coming years, the continued efforts of building up coverage and addressing gaps in immunity are vital in the road to recovery.\n\nSUMMARYO_ST_ABSWhat is already known?C_ST_ABSO_LIThe impact of vaccination programmes without COVID-19-related disruption has been assessed by the Vaccine Impact Modelling Consortium.\nC_LIO_LIThe COVID-19 pandemic has disrupted vaccination programmes resulting in a decline in coverage in the year 2020, the ramifications of this is unclear.\nC_LI\n\nWhat are the new findings?O_LIWe estimate the impact of disruptions to routine immunisation coverage and different routes to recovery. We compare to a scenario without COVID-19-related disruptions (assuming no drops in immunisation coverage).\nC_LIO_LIWe estimate that reaching the Immunization Agenda (IA2030) targets leads to 5% fewer FVPs and 5.22% more deaths over the years 2020 to 2030 relative to the scenario with no COVID-19-related disruptions, whereas falling short of the IA2030 targets by 10% leads to 11.26% fewer fully vaccinated persons (FVPs) and 11.34% more deaths.\nC_LIO_LIThe impact of the disruption varies across the vaccine-preventable diseases with those forecasted to have vast expansions in coverage post-2020 able to recover more.\nC_LI\n\nWhat do the new findings imply?O_LIA drop in vaccination coverage results in fewer vaccinated individuals and thus more deaths due to vaccine-preventable diseases. To mitigate this, building up coverage of routine immunisations and addressing immunity gaps with activities such as catch-up campaigns are vital in the road to recovery.\nC_LI", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Jaspreet Toor", + "author_inst": "Imperial College London" + }, + { + "author_name": "Xiang Li", + "author_inst": "Imperial College London" + }, + { + "author_name": "Mark Jit", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Caroline Trotter", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Susy Echeverria-Londono", + "author_inst": "Imperial College London" + }, + { + "author_name": "Anna-Maria Hartner", + "author_inst": "Imperial College London" + }, + { + "author_name": "Jeremy Roth", + "author_inst": "Imperial College London" + }, + { + "author_name": "Allison Portnoy", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Kaja Abbas", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Neil M Ferguson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Katy A M Gaythorpe", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2022.01.07.22268886", "rel_title": "Estimation of excess all-cause mortality due to COVID-19 in Thailand", @@ -466688,157 +468450,6 @@ "type": "new results", "category": "scientific communication and education" }, - { - "rel_doi": "10.1101/2022.01.05.21268323", - "rel_title": "Lineage replacement and evolution captured by the United Kingdom Covid Infection Survey", - "rel_date": "2022-01-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.05.21268323", - "rel_abs": "The Office for National Statistics COVID-19 Infection Survey (ONS-CIS) is the largest surveillance study of SARS-CoV-2 positivity in the community, and collected data on the United Kingdom (UK) epidemic from April 2020 until March 2023 before being paused. Here, we report on the epidemiological and evolutionary dynamics of SARS-CoV-2 determined by analysing the sequenced samples collected by the ONS-CIS during this period. We observed a series of sweeps or partial sweeps, with each sweeping lineage having a distinct growth advantage compared to their predecessors. The sweeps also generated an alternating pattern in which most samples had either S-gene target failure (SGTF) or non- SGTF over time. Evolution was characterised by steadily increasing divergence and diversity within lineages, but with step increases in divergence associated with each sweeping major lineage. This led to a faster overall rate of evolution when measured at the between-lineage level compared to within lineages, and fluctuating levels of diversity. These observations highlight the value of viral sequencing integrated into community surveillance studies to monitor the viral epidemiology and evolution of SARS-CoV-2, and potentially other pathogens, particularly in the current phase of the pandemic with routine RT-PCR testing now ended in the community.", - "rel_num_authors": 34, - "rel_authors": [ - { - "author_name": "Katrina A Lythgoe", - "author_inst": "University of Oxford" - }, - { - "author_name": "Tanya Golubchik", - "author_inst": "University of Oxford" - }, - { - "author_name": "Matthew Hall", - "author_inst": "University of Oxford" - }, - { - "author_name": "Thomas House", - "author_inst": "University of Manchester" - }, - { - "author_name": "Roberto Cahuantzi", - "author_inst": "University of Manchester" - }, - { - "author_name": "George MacIntyre-Cockett", - "author_inst": "University of Oxford" - }, - { - "author_name": "Helen Fryer", - "author_inst": "University of Oxford" - }, - { - "author_name": "Laura Thomson", - "author_inst": "University of Oxford" - }, - { - "author_name": "Anel Nurtay", - "author_inst": "University of Oxford" - }, - { - "author_name": "Mahan Ghafari", - "author_inst": "University of Oxford" - }, - { - "author_name": "David Buck", - "author_inst": "University of Oxford" - }, - { - "author_name": "Angie Green", - "author_inst": "University of Oxford" - }, - { - "author_name": "Amy Trebes", - "author_inst": "University of Oxford" - }, - { - "author_name": "Paolo Piazza", - "author_inst": "University of Oxford" - }, - { - "author_name": "Lorne J Lonie", - "author_inst": "University of Oxford" - }, - { - "author_name": "Ruth Studley", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Emma Rourke", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Darren Smith", - "author_inst": "Northumbria University" - }, - { - "author_name": "Matthew Bashton", - "author_inst": "Northumbria University" - }, - { - "author_name": "Andrew Nelson", - "author_inst": "Northumbria University" - }, - { - "author_name": "Matthew Crown", - "author_inst": "Northumbria University" - }, - { - "author_name": "Clare McCann", - "author_inst": "Northumbria University" - }, - { - "author_name": "Gregory R Young", - "author_inst": "Northumbria University" - }, - { - "author_name": "Rui Andre Nunes de Santos", - "author_inst": "Northumbria University" - }, - { - "author_name": "Zack Richards", - "author_inst": "Northumbria University" - }, - { - "author_name": "Adnan Tariq", - "author_inst": "Northumbria University" - }, - { - "author_name": "- Wellcome Sanger Institute COVID-19 Surveillance Team", - "author_inst": "Wellcome Sanger Institute" - }, - { - "author_name": "- COVID-19 Infection Survey Group", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "- The COVID-19 Genomics UK (COG-UK) consortium", - "author_inst": "" - }, - { - "author_name": "Christophe Fraser", - "author_inst": "University of Oxford" - }, - { - "author_name": "Ian Diamond", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Jeff Barrett", - "author_inst": "Wellcome Sanger Institute" - }, - { - "author_name": "Ann Sarah Walker", - "author_inst": "University of Oxford" - }, - { - "author_name": "David Bonsall", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.06.22268711", "rel_title": "Regulatory T-cells are central hubs for age-, sex- and severity-associated cellular networks during COVID-19", @@ -468177,6 +469788,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.04.22268721", + "rel_title": "Preliminary modeling estimates of the relative transmissibility and immune escape of the Omicron SARS-CoV-2 variant of concern in South Africa", + "rel_date": "2022-01-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.04.22268721", + "rel_abs": "We develop a stochastic, multi-strain, compartmental epidemic model to estimate the relative transmissibility and immune escape of the Omicron variant of concern (VOC) in South Africa. The model integrates population, non-pharmaceutical interventions, vaccines, and epidemiological data and it is calibrated in the period May 1st, 2021 - November 23rd, 2021. We explore a parameter space of relative transmissibility with respect to the Delta variant and immune escape for Omicron by assuming an initial seeding, from unknown origin, in the first week of October 2021. We identify a region of the parameter space where combinations of relative transmissibility and immune escape are compatible with the growth of the epidemic wave. We also find that changes in the generation time associated with Omicron infections strongly affect the results concerning its relative transmissibility. The presented results are informed by current knowledge of Omicron and subject to changes.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Nicol\u00f2 Gozzi", + "author_inst": "Networks and Urban Systems Centre, University of Greenwich, UK" + }, + { + "author_name": "Matteo Chinazzi", + "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA" + }, + { + "author_name": "Jessica T. Davis", + "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA" + }, + { + "author_name": "Kunpeng Mu", + "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA" + }, + { + "author_name": "Ana Pastore y Piontti", + "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA" + }, + { + "author_name": "Alessandro Vespignani", + "author_inst": "Laboratory for the Modeling of Biological and Socio-technical Systems, Northeastern University, Boston, MA USA" + }, + { + "author_name": "Nicola Perra", + "author_inst": "Networks and Urban Systems Centre, University of Greenwich, UK" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2022.01.01.21268131", "rel_title": "Bayesian Estimation of real-time Epidemic Growth Rates using Gaussian Processes: local dynamics of SARS-CoV-2 in England", @@ -468529,101 +470183,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2022.01.03.22268681", - "rel_title": "Reported Cases of Multisystem Inflammatory Syndrome in Children Aged 12 to 20 Years in the United States Who Received COVID-19 Vaccine, December 2020 through August 2021", - "rel_date": "2022-01-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.03.22268681", - "rel_abs": "BackgroundMultisystem inflammatory syndrome in children (MIS-C) is a hyperinflammatory condition associated with antecedent SARS-CoV-2 infection. In the United States, reporting of MIS-C after vaccination is required under COVID-19 vaccine emergency use authorizations. This case series describes persons aged 12-20 years with MIS-C following COVID-19 vaccination reported to passive surveillance systems or through clinician outreach to CDC.\n\nMethodsWe investigated potential cases of MIS-C after COVID-19 vaccination reported to CDCs health department-based national MIS-C surveillance, the Vaccine Adverse Event Reporting System (VAERS, co-administered by CDC and the U.S. FDA), and CDCs Clinical Immunization Safety Assessment Project (CISA) from December 14, 2020, to August 31, 2021. We describe cases meeting the CDC MIS-C case definition. Any positive SARS-CoV-2 serology test satisfied the case criteria although anti-nucleocapsid antibody indicates SARS-CoV-2 infection, while anti-spike protein antibody indicates either infection or COVID-19 vaccination.\n\nFindingsWe identified 21 persons with MIS-C after COVID-19 vaccination. Of these 21 persons, median age was 16 years (range, 12-20 years); 13 (62%) were male. All were hospitalized; 12 (57%) had intensive care unit admission, and all were discharged home. Fifteen (71%) of the 21 had laboratory evidence of past or recent SARS-CoV-2 infection, and six (29%) did not. Through August 2021, 21,335,331 persons aged 12-20 years had received [≥]1 dose of COVID-19 vaccine, making the overall reporting rate for MIS-C following vaccination 1{middle dot}0 case per million persons receiving [≥]1 vaccine dose in this age group. The reporting rate for those without evidence of SARS-CoV-2 infection was 0{middle dot}3 cases per million vaccinated persons.\n\nInterpretationIn our case series, we describe a small number of persons with MIS-C who had received [≥]1 COVID-19 vaccine dose before illness onset. Continued reporting of potential cases and surveillance for MIS-C illnesses after COVID-19 vaccination is warranted.\n\nFundingThis work was supported by the Centers for Disease Control and Prevention Clinical Immunization Safety Assessment (CISA] Project contracts 200-2012-50430-0005 to Vanderbilt University Medical Center and 200-2012-53661 to Cincinnati Childrens Hospital Medical Center.\n\nResearch in context panelO_ST_ABSEvidence before this studyC_ST_ABSMultisystem inflammatory syndrome in children (MIS-C), also known as paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS), is an uncommon, but serious, complication described after SARS-CoV-2 infection that is characterized by a generalized hyperinflammatory response. A review of the literature using PubMed identified reports of six persons aged 12-20 years who developed MIS-C following COVID-19 vaccination. Search terms used to identify these reports were: \"multisystem inflammatory syndrome in children\", \"MIS-C\", \"MISC\", \"multisystem inflammatory syndrome in adults\", \"MIS-A\", \"MISA\", \"paediatric inflammatory multisystem syndrome\", and \"PIMS-TS\" each with any COVID-19 vaccine type. There were no exclusion criteria (i.e., all ages and languages).\n\nAdded value of this studyWe conducted integrated surveillance for MIS-C after COVID-19 vaccination using two passive surveillance systems, CDCs MIS-C national surveillance and the Vaccine Adverse Event Reporting System (VAERS), and clinician or health department outreach to CDC, including through Clinical Immunization Safety Assessment (CISA) Project consultations. We investigated reports of potential MIS-C occurring from December 14, 2020, to August 31, 2021, in persons aged 12-20 years any time after receipt of COVID-19 vaccine to identify those that met the CDC MIS-C case definition. Any positive serology test was accepted as meeting the CDC MIS-C case definition, although anti- nucleocapsid antibody is indicative of SARS-CoV-2 infection, while anti-spike protein antibody may be induced either by SARS-CoV-2 infection or by COVID-19 vaccination. We investigated 47 reports and identified 21 persons with MIS-C after receipt of COVID-19 vaccine. Of the 21 persons with MIS-C, median age was 16 years (range 12-20 years), and 13 (62%) were male. Fifteen (71%) had laboratory evidence of past or recent SARS-CoV-2 infection (positive SARS-CoV-2 nucleic acid amplification test [NAAT], viral antigen, or serology test before or during MIS-C illness evaluation), and 5 (33%) of those 15 had illness onset after their second vaccine dose. Six (29%) of 21 persons had no laboratory evidence of past or recent SARS-CoV-2 infection, and five of those six (83%) had onset of MIS-C after the second vaccine dose.\n\nImplications of all the available evidenceDuring the first nine months of the COVID-19 vaccination program in the United States, >21 million persons aged 12 to 20 years received [≥]1 dose of COVID-19 vaccine as of August 31, 2021. This case series describes MIS-C in 21 persons following vaccine receipt during this time period; the majority of persons reported also had evidence of SARS-CoV-2 infection. The surveillance has limitations, but our findings suggest that MIS-C as identified in this report following COVID-19 vaccination is rare. In evaluating persons with a clinical presentation consistent with MIS-C after COVID-19 vaccination it is important to consider alternative diagnoses, and anti-nucleocapsid antibody testing may be helpful. Continued surveillance for MIS-C illness after COVID-19 vaccination is warranted, especially as pediatric COVID-19 vaccination expands. Providers are encouraged to report potential MIS-C cases after COVID-19 vaccination to VAERS.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Anna R. Yousaf", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Margaret Cortese", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Allan W. Taylor", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Karen R. Broder", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Matthew E. Oster", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Joshua M. Wong", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Alice Y. Guh", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "David W. McCormick", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Satoshi Kamidani", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Elizabeth Schlaudecker", - "author_inst": "Cincinnati Childrens Hospital Medical Center" - }, - { - "author_name": "Kathryn Edwards", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "C. Buddy Creech", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Mary A. Staat", - "author_inst": "Cincinnati Childrens Hospital Medical Center" - }, - { - "author_name": "Ermias D. Belay", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Paige Marquez", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "John R. Su", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Mark B. Salzman", - "author_inst": "Kaiser Permanente West Los Angeles Medical Center" - }, - { - "author_name": "Deborah Thompson", - "author_inst": "Food and Drug Administration" - }, - { - "author_name": "Angela P. Campbell", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "- MIS-C Investigation Authorship Group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2022.01.01.21268576", "rel_title": "COVID-19 vaccination status is associated with physical activity in German-speaking countries: the COR-PHYS-Q cohort study", @@ -469831,6 +471390,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2022.01.04.22268758", + "rel_title": "Containment of a multi-index B.1.1.7 outbreak on a university campus through a genomically-informed public health response", + "rel_date": "2022-01-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.04.22268758", + "rel_abs": "The first cluster of SARS-CoV-2 cases with lineage B.1.1.7 in the state of Michigan was identified through intensive university-led surveillance sampling and targeted sequencing. A collaborative investigation and response was conducted by the local and state health departments, and the campus and athletic medicine COVID-19 response teams, using S-gene target failure screening and rapid genomic sequencing to inform containment strategies. A total of 50 cases of B.1.1.7-lineage SARS-CoV-2 were identified in this outbreak, which was due to three coincident introductions of B.1.1.7-lineage SARS-CoV-2, all of which were genetically distinct from lineages which later circulated in the broader community. This investigation demonstrates the successful implementation of a genomically-informed outbreak response which can be extended to university campuses and other settings at high risk for rapid emergence of new variants.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Emily Toth Martin", + "author_inst": "University of Michigan-Ann Arbor" + }, + { + "author_name": "Adam S Lauring", + "author_inst": "Department of Internal Medicine, University of Michigan School of Medicine" + }, + { + "author_name": "JoLynn P Montgomery", + "author_inst": "EpiStudies, LLC" + }, + { + "author_name": "Andrew L Valesano", + "author_inst": "Department of Internal Medicine, University of Michigan School of Medicine" + }, + { + "author_name": "Marisa C Eisenberg", + "author_inst": "Department of Epidemiology, University of Michigan School of Public Health" + }, + { + "author_name": "Danielle Sheen", + "author_inst": "Environmental Health & Safety, University of Michigan" + }, + { + "author_name": "Jennifer Nord", + "author_inst": "Environmental Health & Safety, University of Michigan" + }, + { + "author_name": "Robert D Ernst", + "author_inst": "Department of Internal Medicine, University of Michigan School of Medicine" + }, + { + "author_name": "Lindsey Y Mortenson", + "author_inst": "University Health Service, University of Michigan;" + }, + { + "author_name": "Riccardo Valdez", + "author_inst": "Department of Pathology, University of Michigan Medical School" + }, + { + "author_name": "Yashar Niknafs", + "author_inst": "LynxDx, Inc." + }, + { + "author_name": "Darryl Conway", + "author_inst": "Athletics, University of Michigan" + }, + { + "author_name": "Sami F Rifat", + "author_inst": "Athletic Medicine, University of Michigan" + }, + { + "author_name": "Natasha Bagdasarian", + "author_inst": "Michigan Department of Health and Human Services" + }, + { + "author_name": "Sarah Lyon-Callo", + "author_inst": "Michigan Department of Health and Human Services" + }, + { + "author_name": "Jim Collins", + "author_inst": "Michigan Department of Health and Human Services" + }, + { + "author_name": "Heather Blakenship", + "author_inst": "Michigan Department of Health and Human Services" + }, + { + "author_name": "Marty Soehnlen", + "author_inst": "Michigan Department of Health and Human Services" + }, + { + "author_name": "Juan Marquez", + "author_inst": "Washtenaw County Health Department" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2022.01.04.22268760", "rel_title": "Differential Effects of Race/Ethnicity and Social Vulnerability on COVID-19 Positivity, Hospitalization, and Death in the San Francisco Bay Area", @@ -470215,109 +471865,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nursing" }, - { - "rel_doi": "10.1101/2022.01.05.22268646", - "rel_title": "SARS-CoV-2 Genetic diversity and lineage dynamics of in Egypt", - "rel_date": "2022-01-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2022.01.05.22268646", - "rel_abs": "COVID-19 was first diagnosed in Egypt on 14 February 2020. By the end of November 2021, over 333,840 cases and 18,832 deaths had been reported. As part of national genomic surveillance, 1,027 SARS-CoV-2 near whole-genomes had been generated and published by the end of May 2021. Here we describe the genomic epidemiology of SARS-CoV-2 in Egypt over this period using a subset of 976 high-quality Egyptian genomes analysed together with a representative set of global sequences within a phylogenetic framework. We show that a single lineage, C.36, introduced early in the pandemic was responsible for most cases in Egypt. Furthermore, we show that to remain dominant in the face of mounting immunity from previous infection and vaccination, this lineage evolved into various sub-lineages acquiring several mutations known to confer adaptive advantage and pathogenic properties. These results highlight the value of continuous genomic surveillance in regions where VOCs are not predominant and enforcement of public health measures to prevent expansion of existing lineages.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Wael Hamed Roshdy", - "author_inst": "Central Public Health Laboratory, Ministry of Health and Population, Cairo, Egypt." - }, - { - "author_name": "Mohamed K Khalifa", - "author_inst": "Omicsense, Cairo, Egypt." - }, - { - "author_name": "James Emmanuel San", - "author_inst": "Kwazulu Natal Research and Innovation Sequencing Platform" - }, - { - "author_name": "Houriiyah Tegally", - "author_inst": "Kwazulu Natal research and Innovation Sequencing Platform (KRISP)" - }, - { - "author_name": "Eduan Wilkinson", - "author_inst": "Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa" - }, - { - "author_name": "Shymaa Showky", - "author_inst": "Central Public Health Laboratory, Ministry of Health and Population, Cairo, Egypt" - }, - { - "author_name": "Darren P Martin", - "author_inst": "Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa." - }, - { - "author_name": "Monika Moir", - "author_inst": "Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa" - }, - { - "author_name": "Amel Naguib", - "author_inst": "Central Public Health Laboratory, Ministry of Health and Population, Cairo, Egypt." - }, - { - "author_name": "Nancy Elguindy", - "author_inst": "Central Public Health Laboratory, Ministry of Health and Population, Cairo, Egypt." - }, - { - "author_name": "Mokhtar R Gomaa", - "author_inst": "Centre of Scientific Excellence for Influenza Viruses, National Research Centre, 12622 Dokki, Giza, Egypt." - }, - { - "author_name": "Manal Fahim", - "author_inst": "Department of Surveillance and Epidemiology, Ministry of Health and Population, Cairo, Egypt." - }, - { - "author_name": "Hanaa Abu Elsood", - "author_inst": "Public Health Initiative, Cairo, Egypt." - }, - { - "author_name": "Amira A Mohsen", - "author_inst": "World Health Organization, Egypt Country Office, Cairo, Egypt." - }, - { - "author_name": "Ramy Galal", - "author_inst": "World Health Organization, Egypt Country Office, Cairo, Egypt." - }, - { - "author_name": "Mohamed Hassany", - "author_inst": "World Health Organization, Egypt Country Office, Cairo, Egypt." - }, - { - "author_name": "Richard J Lessells", - "author_inst": "Kwazulu Natal research and Innovation Sequencing Platform (KRISP)" - }, - { - "author_name": "Ahmed A Al Karmalawy", - "author_inst": "Department of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta 34518, Egypt." - }, - { - "author_name": "Rabeh EL Shesheny", - "author_inst": "Omicsense, Cairo, Egypt." - }, - { - "author_name": "Ahmed M Kandeil", - "author_inst": "Department of Pharmaceutical Medicinal Chemistry, Faculty of Pharmacy, Horus University-Egypt, New Damietta 34518, Egypt." - }, - { - "author_name": "Mohamed A Ali", - "author_inst": "Public Health Initiative, Cairo, Egypt." - }, - { - "author_name": "Tulio de Oliveira", - "author_inst": "Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2022.01.04.22268773", "rel_title": "Timing of Breakthrough Infection Risk After Vaccination Against SARS-CoV-2", @@ -471693,6 +473240,37 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2022.01.03.474721", + "rel_title": "Hydrodynamics of spike proteins dictate a transport-affinity competition for SARS-CoV-2 and other enveloped viruses", + "rel_date": "2022-01-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2022.01.03.474721", + "rel_abs": "Many viruses, such as SARS-CoV-2 or Influenza, possess spike-decorated envelopes. Depending on the virus type, a large variability is present in spikes number, morphology and reactivity, which remains generally unexplained. Since viruses transmissibility depend on features beyond their genetic sequence, new tools are required to discern the effects of spikes functionality, interaction, and morphology. Here, we postulate the relevance of hydrodynamic interactions in the viral infectivity of enveloped viruses and propose micro-rheological characterization as a platform for viruses differentiation. To understand how the spikes affect virion mobility and infectivity, we investigate the diffusivity of spike-decorate structures using mesoscopic-hydrodynamic simulations. Furthermore, we explored the interplay between affinity and passive viral transport. Our results revealed that the diffusional mechanism of SARS-CoV-2 is strongly influenced by the size and distribution of its spikes. We propose and validate a universal mechanism to explain the link between optimal virion structure and maximal infectivity for many virus families.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Nicolas Moreno", + "author_inst": "Basque Center for Applied Mathematics" + }, + { + "author_name": "Daniela Moreno-Chaparro", + "author_inst": "Basque Center for Applied Mathematics" + }, + { + "author_name": "Florencio Balboa Usabiaga", + "author_inst": "Basque Center for Applied Mathematics" + }, + { + "author_name": "Marco Ellero", + "author_inst": "Basque Center for Applied Mathematics" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.12.30.474602", "rel_title": "Integrated Autolysis, DNA Hydrolysis and Precipitation Enables an Improved Bioprocess for Q-Griffithsin, a Broad-Spectrum Antiviral and Clinical-Stage anti-COVID-19 Candidate", @@ -472341,33 +473919,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.12.30.21268571", - "rel_title": "Estimation the state of the Covid-19 epidemic curve in Mayotte", - "rel_date": "2022-01-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.30.21268571", - "rel_abs": "We study in this work some statistical methods to estimate the parameters resulting from the use of an age-structured contact mathematical epidemic model in order to analyze the evolution of the epidemic curve of Covid-19 in the French overseas department Mayotte from march 13, 2020 to february 26,2021. Using several statistic methods based on time dependent method, maximum likelihood, mixture method, we fit the probability distribution which underlines the serial interval distribution and we give an adapted version of the generation time distribution from Package R0. The best-fit model of the serial interval was given by a mixture of Weibull distribution. Furthermore this estimation allows to obtain the evolution of the time varying effective reproduction number and hence the temporal transmission rates. Finally based on others known estimates parameters we incorporate the estimated parameters in the model in order to give an approximation of the epidemic curve in Mayotte under the conditions of the model. We also discuss the limit of our study and the conclusion concerned a probable impact of non pharmacological interventions of the Covid-19 in Mayotte such us the re-infection cases and the introduction of the variants which probably affect the estimates.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Solym Mawaki MANOU-ABI", - "author_inst": "Institut Montpellierain Alexander Grothendieck" - }, - { - "author_name": "Yousri SLAOUI", - "author_inst": "LMA" - }, - { - "author_name": "Julien BALICCHI", - "author_inst": "Agence Regionale de Sante de Mayotte" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2022.01.02.22268622", "rel_title": "Estimating protection afforded by prior infection in preventing reinfection: Applying the test-negative study design", @@ -473699,6 +475250,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.30.21267140", + "rel_title": "EARLY LENZILUMAB TREATMENT OF COVID-19 PATIENTS USING C-REACTIVE PROTEIN AS A BIOMARKER IMPROVES EFFICACY: RESULTS FROM THE PHASE 3 LIVE-AIR TRIAL", + "rel_date": "2022-01-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.30.21267140", + "rel_abs": "ObjectiveThe LIVE-AIR trial demonstrated that the anti-GM-CSF monoclonal antibody, lenzilumab improved the likelihood of survival without invasive mechanical ventilation (SWOV) in COVID-19 patients; with greatest effect in those with baseline CRP below the median baseline value of 79 mg/L. Similar to GM-CSF, C-reactive protein (CRP) levels are correlated with COVID-19 severity. This current analysis assessed the utility of baseline CRP levels to guide treatment with lenzilumab.\n\nDesignLIVE-AIR was a phase 3, double-blind, placebo-controlled trial. Participants were randomized 1:1 and stratified according to age and disease severity, to receive lenzilumab or placebo on Day 0, were followed through Day 28.\n\nSettingSecondary and tertiary care hospitals in the US and Brazil.\n\nParticipants520 hospitalized COVID-19 participants with SpO2[≤] 94% on room air or required supplemental oxygen but not invasive mechanical ventilation were included.\n\nInterventionsLenzilumab (1800mg; divided as 3 doses, q8h) or placebo infusion alongside standard treatments including corticosteroids and remdesivir.\n\nMain outcome measuresA multi-variate logistic regression analysis assessed key baseline risk factors for progression to IMV or death. The primary endpoint, SWOV, and key secondary endpoints were analyzed according to baseline CRP levels in all participants with CRP values.\n\nResultsThe multi-variate analysis demonstrated that elevated baseline plasma CRP was the most predictive feature for progression to IMV or death. SWOV was achieved in 152 (90%; 95%CI: 85to 94) lenzilumab and 183 (79%; 72 to 84) placebo participants with baseline CRP<150 mg/L and its likelihood was greater with lenzilumab than placebo (HR: 2.54; 95%CI, 1.46 to 4.41; p=0.0009) but not in participants with CRP[≥]150 mg/L at baseline. CRP as a covariate in the overall analysis demonstrated a statistically significant interaction with lenzilumab treatment (p=0.044). Grade [≥] 3 adverse events in participants with baseline CRP<150 mg/L were reported in 18% and 28% in lenzilumab or placebo, respectively. No treatment-emergent serious adverse events were attributable to lenzilumab.\n\nConclusionThese finding suggest that COVID-19 participants with low baseline CRP levels achieve the greatest clinical benefit from lenzilumab and that baseline CRP levels may be a useful biomarker to guide therapeutic intervention.\n\nTrial RegistrationClinicalTrials.gov NCT04351152\n\nWHAT IS ALREADY KNOWN ON THIS TOPICGM-CSF is one of the early upstream mediators and orchestrators of the hyperinflammatory immune response following SARS-CoV-2 infection. Baseline levels of GM-CSF and CRP have each been shown to correlate with COVID-19 disease progression. Increases in CRP are driven by elevations of IL-6 during the hyperinflammatory response following SARS-CoV-2 infection. In the phase 3, randomized, double-blind, placebo-controlled LIVE-AIR study, GM-CSF neutralization with lenzilumab significantly improved the likelihood of survival without invasive mechanical ventilation (SWOV, primary endpoint, also referred to as ventilator-free survival) vs. placebo (HR:1.54; 95% CI, 1.02 to 2.32; p=0.0403), which included standard supportive care including corticosteroids and remdesivir. No treatment-emergent serious adverse events attributable to lenzilumab have been reported to date.\n\nWHAT THIS STUDY ADDSA comprehensive analysis of LIVE -AIR CRP data provides evidence for the utility of baseline CRP to predict progression to IMV and death. Baseline CRP was identified to be the strongest predictor of SWOV in this study. Patients with baseline CRP<150 mg/L represented 78% of the study population and demonstrated the greatest clinical benefit with lenzilumab, including SWOV through day 28 (HR: 2.54; 95%CI; 1.46-4.41; nominal p=0.0009). A biomarker-driven approach using baseline CRP levels to guide therapeutic intervention may improve outcomes in those hospitalized with COVID-19. Participants with baseline CRP levels above 150 mg/L were described as experiencing COVID-19-associated hyperinflammation and were at risk of imminent escalation of respiratory support or death. Elevated baseline plasma CRP was the most predictive feature for progression to IMV or death (OR, 0.15; 95%CI, 0.07-0.29; nominal p<0.001). These findings suggest that baseline CRP may be a useful biomarker in determining which participants may be most successfully treated with lenzilumab.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Zelalem Temesgen", + "author_inst": "Mayo Clinic, Division of Infectious Disease, Rochester, MN" + }, + { + "author_name": "Colleen F. Kelley", + "author_inst": "Division of Infectious Diseases, Emory University School of Medicine, Grady Memorial Hospital, Atlanta, GA" + }, + { + "author_name": "Frank Cerasoli", + "author_inst": "RxMedical Dynamics, New York, NY" + }, + { + "author_name": "Adrian Kilcoyne", + "author_inst": "Humanigen, Inc., Burlingame, CA" + }, + { + "author_name": "Dale Chappell", + "author_inst": "Humanigen, Inc., Burlingame, CA" + }, + { + "author_name": "Cameron Durrant", + "author_inst": "Humanigen, Inc., Burlingame, CA" + }, + { + "author_name": "Omar Ahmed", + "author_inst": "Humanigen, Inc., Burlingame, CA" + }, + { + "author_name": "Gabrielle Chappell", + "author_inst": "Humanigen, Inc., Burlingame, CA" + }, + { + "author_name": "Victoria Catterson", + "author_inst": "BioSymetrics, Inc., New York, NY" + }, + { + "author_name": "Christopher Polk", + "author_inst": "Atrium Health, Charlotte, NC" + }, + { + "author_name": "Andrew D. Badley", + "author_inst": "Mayo Clinic, Division of Infectious Disease and Department of Molecular Medicine, Rochester, MN" + }, + { + "author_name": "Vincent Marconi", + "author_inst": "Division of Infectious Diseases, Emory University School of Medicine, Rollins School of Public Health, and Emory Vaccine Center, Atlanta, GA" + }, + { + "author_name": "- the LIVE-AIR Study Group", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2021.12.30.21268308", "rel_title": "Cross reactivity of spike glycoprotein induced antibody against delta and omicron variants before and after third SARS-CoV-2 vaccine dose", @@ -474275,73 +475893,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "transplantation" }, - { - "rel_doi": "10.1101/2021.12.30.21268565", - "rel_title": "Effectiveness of COVID-19 vaccines against Omicron or Delta infection", - "rel_date": "2022-01-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.30.21268565", - "rel_abs": "BackgroundThe incidence of SARS-CoV-2 infection, including among those who have received 2 doses of COVID-19 vaccines, increased substantially following the emergence of Omicron in Ontario, Canada.\n\nMethodsApplying the test-negative study design to linked provincial databases, we estimated vaccine effectiveness (VE) against symptomatic infection and severe outcomes (hospitalization or death) caused by Omicron or Delta between December 6 and 26, 2021. We used multivariable logistic regression to estimate the effectiveness of 2 or 3 COVID-19 vaccine doses by time since the latest dose, compared to unvaccinated individuals.\n\nResultsWe included 16,087 Omicron-positive cases, 4,261 Delta-positive cases, and 114,087 test-negative controls. VE against symptomatic Delta infection declined from 89% (95%CI, 86-92%) 7-59 days after a second dose to 80% (95%CI, 74-84%) after [≥]240 days, but increased to 97% (95%CI, 96-98%) [≥]7 days after a third dose. VE against symptomatic Omicron infection was only 36% (95%CI, 24-45%) 7-59 days after a second dose and provided no protection after [≥]180 days, but increased to 61% (95%CI, 56-65%) [≥]7 days after a third dose. VE against severe outcomes was very high following a third dose for both Delta and Omicron (99% [95%CI, 98-99%] and 95% [95%CI, 87-98%], respectively).\n\nConclusionsIn contrast to high levels of protection against both symptomatic infection and severe outcomes caused by Delta, our results suggest that 2 doses of COVID-19 vaccines only offer modest and short-term protection against symptomatic Omicron infection. A third dose improves protection against symptomatic infection and provides excellent protection against severe outcomes for both variants.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Sarah A Buchan", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Hannah Chung", - "author_inst": "ICES" - }, - { - "author_name": "Kevin A Brown", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Peter C Austin", - "author_inst": "ICES" - }, - { - "author_name": "Deshayne B Fell", - "author_inst": "University of Ottawa" - }, - { - "author_name": "Jonathan Gubbay", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Sharifa Nasreen", - "author_inst": "University of Toronto" - }, - { - "author_name": "Kevin L Schwartz", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Maria E Sundaram", - "author_inst": "Marshfield Clinic Research Institute" - }, - { - "author_name": "Mina Tadrous", - "author_inst": "Womens College Hospital" - }, - { - "author_name": "Kumanan Wilson", - "author_inst": "University of Ottawa" - }, - { - "author_name": "Sarah E Wilson", - "author_inst": "Public Health Ontario" - }, - { - "author_name": "Jeff Kwong", - "author_inst": "ICES" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.31.21268580", "rel_title": "Global Perspective of COVID-19 Vaccine Nationalism", @@ -475857,6 +477408,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.29.21268511", + "rel_title": "COVID-19 vaccine effectiveness among immunocompromised populations: a targeted literature review of real-world studies", + "rel_date": "2021-12-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.29.21268511", + "rel_abs": "IntroductionFrom July through October of 2021, several countries issued recommendations for increased COVID-19 vaccine protection for individuals with one or more immunocompromised (IC) conditions. It is critically important to understand the vaccine effectiveness (VE) of COVID-19 vaccines among IC populations as recommendations are updated over time in response to the evolving COVID-19 pandemic.\n\nAreas coveredA targeted literature review was conducted to identify real-world studies that assessed COVID-19 VE in IC populations between December 2020 and September 2021. A total of 10 studies from four countries were identified and summarized in this review.\n\nExpert opinion/commentaryVE of the widely available COVID-19 vaccines, including BNT162b2 (Pfizer/BioNTech), mRNA-1273 (Moderna), Ad26.COV2.S (Janssen), and ChAdOx1 nCoV-19 (Oxford/AstraZeneca), ranged from 64%-90% against SARS-CoV-2 infection, 73%-84% against symptomatic illness, 70%-100% against severe illness, and 63%-100% against COVID-19-related hospitalization among the fully vaccinated IC populations included in the studies. COVID-19 VE for most outcomes in the IC populations included in these studies was lower than in the general populations. These findings provide preliminary evidence that the IC population requires greater protective measures to prevent COVID-19 infection and associated illness, hence should be prioritized while implementing recommendations of additional COVID-19 vaccine doses.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Manuela Di Fusco", + "author_inst": "Pfizer Inc." + }, + { + "author_name": "Jay Lin", + "author_inst": "Novosys Health" + }, + { + "author_name": "Shailja Vaghela", + "author_inst": "HealthEcon Consulting Inc." + }, + { + "author_name": "Melissa Lingohr-Smith", + "author_inst": "Novosys Health" + }, + { + "author_name": "Jennifer L Nguyen", + "author_inst": "Pfizer, Inc." + }, + { + "author_name": "Thomas Scassellati Sforzolini", + "author_inst": "Pfizer, Inc." + }, + { + "author_name": "Jennifer Judy", + "author_inst": "Pfizer, Inc." + }, + { + "author_name": "Alejandro Cane", + "author_inst": "Pfizer, Inc." + }, + { + "author_name": "Mary M Moran", + "author_inst": "Pfizer, Inc." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pharmacology and therapeutics" + }, { "rel_doi": "10.1101/2021.12.27.21268264", "rel_title": "Immunomodulation by intravenous omega-3 fatty acid treatment in older subjects hospitalized for COVID-19: a single-blind randomized controlled trial", @@ -476505,37 +478107,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.12.30.21268537", - "rel_title": "The rich-to-poor vaccine donation game: When will self-interested countries donate their surplus vaccines during pandemics?", - "rel_date": "2021-12-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.30.21268537", - "rel_abs": "When will self-interested vaccine-rich countries voluntarily donate their surplus vaccines to vaccine-poor countries during a pandemic? We develop a game-theoretic approach to address this question. We identify vaccine-rich countries optimal surplus donation strategies, and then examine whether these strategies are stable (Nash equilibrium or self-enforcing international agreement). We identify parameter ranges in which full or partial surplus stock donations are optimal for the donor countries. Within a more restrictive parameter region, these optimal strategies are also stable. This implies that, under certain conditions (notably a total amount of surplus vaccines that is sufficiently large), simple coordination can lead to significant donations by strictly self-interested vaccine-rich countries. On the other hand, if the total amount that the countries can donate is small, we expect no contribution from self-interested countries. The results of this analysis provide guidance to policy makers in identifying the circumstances in which coordination efforts are likely to be effective.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Adam Lampert", - "author_inst": "The Hebrew University" - }, - { - "author_name": "Raanan Sulitzeanu-Kenan", - "author_inst": "The Hebrew University" - }, - { - "author_name": "Pieter Vanhuysse", - "author_inst": "University of Southern Denmark" - }, - { - "author_name": "Markus Tepe", - "author_inst": "University of Oldenburg" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.12.30.21268307", "rel_title": "Short-term Projections based on Early Omicron Variant Dynamics in England.", @@ -477899,6 +479470,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.28.474336", + "rel_title": "A Novel CRISPR-Engineered, Stem Cell-Derived Cellular Vaccine", + "rel_date": "2021-12-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.28.474336", + "rel_abs": "COVID-19 has forced rapid clinical translation of novel vaccine technologies, principally mRNA vaccines, that have resulted in meaningful efficacy and adequate safety in response to the global pandemic. Notwithstanding this success, there remains an opportunity for innovation in vaccine technology to address current limitations and meet the challenges of inevitable future pandemics. We describe a universal vaccine cell (UVC) rationally designed to mimic the natural physiologic immunity induced post viral infection of host cells. Induced pluripotent stem cells were CRISPR engineered to delete MHC-I expression and simultaneously overexpress a NK Ligand adjuvant to increase rapid cellular apoptosis which was hypothesized to enhance viral antigen presentation in the resulting immune microenvironment leading to a protective immune response. Cells were further engineered to express the parental variant WA1/2020 SARS-CoV-2 spike protein as a representative viral antigen prior to irradiation and cryopreservation. The cellular vaccine was then used to immunize non-human primates in a standard 2-dose, IM injected prime + boost vaccination with 1e8 cells per 1 ml dose resulting in robust neutralizing antibody responses (1e3 nAb titers) with decreasing levels at 6 months duration. Similar titers generated in this established NHP model have translated into protective human neutralizing antibody levels in SARS-Cov-2 vaccinated individuals. Animals vaccinated with WA1/2020 spike antigens were subsequently challenged with 1.0 x 105 TCID50 infectious Delta (B.1.617.2) SARS-CoV-2 in a heterologous challenge which resulted in an approximately 3-log order decrease in viral RNA load in the lungs. These heterologous viral challenge results reflect the ongoing real-world experience of original variant WA1/2020 spike antigen vaccinated populations exposed to rapidly emerging variants like Delta and now Omicron. This cellular vaccine is designed to be a rapidly scalable cell line with a modular poly-antigenic payload to allow for practical, large-scale clinical manufacturing and use in an evolving viral variant environment. Human clinical translation of the UVC is being actively explored for this and potential future pandemics.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Krishnendu Chakraborty", + "author_inst": "Intima Bioscience" + }, + { + "author_name": "Abishek Chandrashekar", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Adam Sidaway", + "author_inst": "Intima Bioscience" + }, + { + "author_name": "Elizabeth Latta", + "author_inst": "Intima Bioscience" + }, + { + "author_name": "Jingyou Yu", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Katherine McMahan", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Cordelia Manickam", + "author_inst": "BIDMC/Harvard Medical School" + }, + { + "author_name": "Kyle Kroll", + "author_inst": "BIDMC/Harvard Medical School" + }, + { + "author_name": "Matthew Mosher", + "author_inst": "BIDMC/Harvard Medical School" + }, + { + "author_name": "R. Keith Reeves", + "author_inst": "BIDMC/Harvard Medical School" + }, + { + "author_name": "Rihab Gam", + "author_inst": "Intima Bioscience" + }, + { + "author_name": "Elisa Arthofer", + "author_inst": "Intima Bioscience" + }, + { + "author_name": "Modassir Choudhry", + "author_inst": "Intima Bioscience" + }, + { + "author_name": "Dan H. Barouch", + "author_inst": "Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Tom Henley", + "author_inst": "Intima Bioscience" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.12.29.474432", "rel_title": "mRNA-1273 and Ad26.COV2.S vaccines protect against the B.1.621 variant of SARS-CoV-2", @@ -478539,113 +480185,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.27.21268416", - "rel_title": "Divergent SARS CoV-2 Omicron-specific T- and B-cell responses in COVID-19 vaccine recipients", - "rel_date": "2021-12-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.27.21268416", - "rel_abs": "The severe acute respiratory distress syndrome coronavirus-2 (SARS-CoV-2) Omicron variant (B.1.1.529) is spreading rapidly, even in vaccinated individuals, raising concerns about immune escape. Here, we studied neutralizing antibodies and T-cell responses to SARS-CoV-2 D614G (wildtype, WT), and the B.1.351 (Beta), B.1.617.2 (Delta), and B.1.1.529 (Omicron) variants of concern (VOC) in a cohort of 60 health care workers (HCW) after immunization with ChAdOx-1 S, Ad26.COV2.S, mRNA-1273 or BNT162b2. High binding antibody levels against WT SARS-CoV-2 spike (S) were detected 28 days after vaccination with both mRNA vaccines (mRNA-1273 or BNT162b2), which significantly decreased after 6 months. In contrast, antibody levels were lower after Ad26.COV2.S vaccination but did not wane. Neutralization assays with authentic virus showed consistent cross-neutralization of the Beta and Delta variants in study participants, but Omicron-specific responses were significantly lower or absent (up to a 34-fold decrease compared to D614G). Notably, BNT162b2 booster vaccination after either two mRNA-1273 immunizations or Ad26.COV.2 priming partially restored neutralization of the Omicron variant, but responses were still up to-17-fold decreased compared to D614G. CD4+ T-cell responses were detected up to 6 months after all vaccination regimens; S-specific T-cell responses were highest after mRNA-1273 vaccination. No significant differences were detected between D614G- and variant-specific T-cell responses, including Omicron, indicating minimal escape at the T-cell level. This study shows that vaccinated individuals retain T-cell immunity to the SARS-CoV-2 Omicron variant, potentially balancing the lack of neutralizing antibodies in preventing or limiting severe COVID-19. Booster vaccinations may be needed to further restore Omicron cross-neutralization by antibodies.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Corine H. GeurtsvanKessel", - "author_inst": "Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands" - }, - { - "author_name": "Daryl Geers", - "author_inst": "Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands" - }, - { - "author_name": "Katharina S. Schmitz", - "author_inst": "Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands" - }, - { - "author_name": "Anna Z. Mykytyn", - "author_inst": "Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands" - }, - { - "author_name": "Mart M. Lamers", - "author_inst": "Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands" - }, - { - "author_name": "Susanne Bogers", - "author_inst": "Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands" - }, - { - "author_name": "Lennert Gommers", - "author_inst": "Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands" - }, - { - "author_name": "Roos S.G. Sablerolles", - "author_inst": "Department of Hospital Pharmacy, Erasmus MC, Rotterdam, Netherlands" - }, - { - "author_name": "Nella N. Nieuwkoop", - "author_inst": "Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands" - }, - { - "author_name": "Laurine C. Rijsbergen", - "author_inst": "Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands" - }, - { - "author_name": "Laura L.A. van Dijk", - "author_inst": "Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands" - }, - { - "author_name": "Janet de Wilde", - "author_inst": "Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands" - }, - { - "author_name": "Kimberly Alblas", - "author_inst": "Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands" - }, - { - "author_name": "Tim I. Breugem", - "author_inst": "Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands" - }, - { - "author_name": "Bart J.A. Rijnders", - "author_inst": "Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands" - }, - { - "author_name": "Herbert de Jager", - "author_inst": "Department of Occupational Health Services, Erasmus MC, Rotterdam, Netherlands" - }, - { - "author_name": "Daniela Weiskopf", - "author_inst": "Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA" - }, - { - "author_name": "P. Hugo M. van der Kuy", - "author_inst": "Department of Hospital Pharmacy, Erasmus MC, Rotterdam, Netherlands" - }, - { - "author_name": "Alessandro Sette", - "author_inst": "Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA" - }, - { - "author_name": "Marion P.G. Koopmans", - "author_inst": "Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands" - }, - { - "author_name": "Alba Grifoni", - "author_inst": "Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA" - }, - { - "author_name": "Bart L. Haagmans", - "author_inst": "Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands" - }, - { - "author_name": "Rory D. de Vries", - "author_inst": "Department of Viroscience, Erasmus MC, Rotterdam, the Netherlands" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.27.21268446", "rel_title": "Sociodemographic factors and self-restraint from social behaviors during the COVID-19 pandemic in Japan: a cross-sectional study", @@ -479921,6 +481460,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.12.27.21268456", + "rel_title": "Seroprevalence, waning, and correlates of anti-SARS-CoV-2 IgG antibodies in Tyrol, Austria: Large-scale study of 35,193 blood donors conducted between June 2020 and September 2021", + "rel_date": "2021-12-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.27.21268456", + "rel_abs": "BackgroundThere is uncertainty about the seroprevalence of anti-SARS-CoV-2 antibodies in the general population of Austria, and about the extent to which antibodies elicited by vaccination or infection wane over time.\n\nAimTo estimate seroprevalence, waning, and correlates of anti-SARS-CoV-2 IgG antibodies in the Federal State of Tyrol, Austria.\n\nMethodsWe conducted a seroepidemiological study between June 2020 and September 2021, enrolling blood donors aged 18-70 years across Tyrol, Austria (participation rate 84.0%). We analysed serum samples for antibodies against spike or nucleocapsid proteins of SARS-CoV-2 with Abbott SARS-CoV-2 IgG assays.\n\nResultsWe performed 47,363 serological tests among 35,193 individuals (median age 43.1 years [IQR: 29.3-53.7], 45.3% women, 10.0% with prior SARS-CoV-2 infection). Seroprevalence increased from 3.4% (95% CI: 2.8-4.2%) in June 2020 to 82.7% (95% CI: 81.4-83.8%) in September 2021, largely due to vaccination. Anti-spike IgG seroprevalence was 99.6% (99.4-99.7%) among fully vaccinated individuals, 90.4% (88.8-91.7%) among unvaccinated with prior infection, and 11.5% (10.8-12.3%) among unvaccinated without known prior infection. Anti-spike IgG levels were reduced by 44.0% (34.9-51.7%) at 5-6 months compared to 0-3 months after infection. In fully vaccinated individuals, they decreased by 31.7% (29.4-33.9%) per month. In multivariable adjusted analyses, both seropositivity among unvaccinated and antibody levels among fully vaccinated individuals were higher at young age (<25 years), higher with a known prior infection, and lower in current smokers.\n\nConclusionSeroprevalence in Tyrol increased to 82.7% in September 2021, with the bulk of seropositivity stemming from vaccination. Antibody levels substantially and gradually declined after vaccination or infection.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Anita Siller", + "author_inst": "Central Institute for Blood Transfusion and Immunology, Tirol Kliniken GmbH, Innsbruck, Austria" + }, + { + "author_name": "Lisa Seekircher", + "author_inst": "Clinical Epidemiology Team, Medical University of Innsbruck, Innsbruck, Austria" + }, + { + "author_name": "Gregor A Wachter", + "author_inst": "Central Institute for Blood Transfusion and Immunology, Tirol Kliniken GmbH, Innsbruck, Austria" + }, + { + "author_name": "Manfred Astl", + "author_inst": "Central Institute for Blood Transfusion and Immunology, Tirol Kliniken GmbH, Innsbruck, Austria" + }, + { + "author_name": "Lena Tschiderer", + "author_inst": "Clinical Epidemiology Team, Medical University of Innsbruck, Innsbruck, Austria" + }, + { + "author_name": "Bernhard Pfeifer", + "author_inst": "Department of Clinical Epidemiology, Tyrolean Federal Institute for Integrated Care, Tirol Kliniken GmbH, Innsbruck, Austria, and Division for Healthcare Networ" + }, + { + "author_name": "Manfred Gaber", + "author_inst": "Blood donor service Tyrol of the Austrian Red Cross, Rum, Austria" + }, + { + "author_name": "Harald Schennach", + "author_inst": "Central Institute for Blood Transfusion and Immunology, Tirol Kliniken GmbH, Innsbruck, Austria" + }, + { + "author_name": "Peter Willeit", + "author_inst": "Clinical Epidemiology Team, Medical University of Innsbruck, Innsbruck, Austria, and Department of Public Health and Primary Care, University of Cambridge, Camb" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.12.26.21268380", "rel_title": "SARS-CoV-2 spike T cell responses induced upon vaccination or infection remain robust against Omicron", @@ -480685,77 +482275,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.12.26.472655", - "rel_title": "Evaluation of maternal-infant dyad inflammatory cytokines in pregnancies affected by maternal SARS-CoV-2 infection in early and late gestation.", - "rel_date": "2021-12-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.26.472655", - "rel_abs": "ObjectiveSARS-CoV-2 infection induces significant inflammatory cytokine production in adults, but infant cytokine signatures in pregnancies affected by maternal SARS-CoV-2 are less well characterized. We aimed to evaluate cytokine profiles of mothers and their infants following COVID-19 in pregnancy.\n\nStudy DesignSerum samples at delivery from 31 mother-infant dyads with maternal SARS-CoV-2 infection in pregnancy (COVID) were examined in comparison to 29 control dyads (Control). Samples were evaluated using a 13-plex cytokine assay.\n\nResultsIn comparison with controls, interleukin (IL)-6 and interferon gamma-induced protein 10 (IP-10) were higher in COVID maternal and infant samples (p<0.05) and IL-8 uniquely elevated in COVID infant samples (p<0.05). Significant elevations in IL-6, IP-10 and IL-8 were found among both early (1st/2nd Trimester) and late (3rd Trimester) maternal SARS-CoV-2 infections.\n\nConclusionsMaternal SARS-CoV-2 infections throughout gestation are associated with increased maternal and infant inflammatory cytokines at birth with potential to impact long-term infant health.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Elizabeth Taglauer", - "author_inst": "Department of Pediatrics, Boston Medical Center" - }, - { - "author_name": "Yashoda Dhole", - "author_inst": "Boston University School of Medicine" - }, - { - "author_name": "Jeffery Boateng", - "author_inst": "Department of Pediatrics, Boston Medical Center" - }, - { - "author_name": "Jennifer E Snyder-Cappione", - "author_inst": "Department of Microbiology, Boston University School of Medicine" - }, - { - "author_name": "Samantha E Parker", - "author_inst": "Boston University School of Public Health" - }, - { - "author_name": "Katherine Clarke", - "author_inst": "Department of Microbiology, Boston University School of Medicine" - }, - { - "author_name": "Lillian Juttukonda", - "author_inst": "Department of Pediatrics, Boston Medical Center" - }, - { - "author_name": "Jean Devera", - "author_inst": "Boston University School of Medicine" - }, - { - "author_name": "Jessica Hunnewell", - "author_inst": "Boston University School of Public Health" - }, - { - "author_name": "Elizabeth Barnett", - "author_inst": "Department of Pediatrics, Boston Medical Center" - }, - { - "author_name": "Hongpeng Jia", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Christina Yarrington", - "author_inst": "Department of Obstetrics and Gynecology, Boston Medical Center" - }, - { - "author_name": "Vishakha Sabharwal", - "author_inst": "Department of Pediatrics, Boston Medical Center" - }, - { - "author_name": "Elisha Wachman", - "author_inst": "Department of Pediatrics, Boston Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.12.28.474344", "rel_title": "Effect of nebulised BromAc(R) on rheology of artificial sputum: relevance to muco-obstructive respiratory diseases including COVID-19", @@ -482267,6 +483786,33 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.12.21.21268173", + "rel_title": "Post COVID-19 1st Dose Vaccination Common Symptoms among SE Asia College Students", + "rel_date": "2021-12-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.21.21268173", + "rel_abs": "In the second year of the COVID-19 epidemic in the Southeast Asia (SE) regions, there is a plan to reopen the school, including the campus. Among students in Indonesia, college students have a population of almost 8.3 million. Considering the massive numbers of college students, school reopening should be supported by adequate COVID-19 vaccination. As a result, the first dose of the inactivated virus COVID-19 vaccine has been administered, including to college students aged over 18 years old. While COVID-19 vaccination is widely available, there is still a scarcity of information on post-vaccination symptoms. As reported from other locations, post vaccination has been reported. Then, this study aims to assess the common symptoms of COVID-19 1st dose vaccinations among the following groups: gender (male and female college students), age, body weight, and height. The observed symptoms include sore arms, fatigue, headache, fever with a body temperature above 38 {degrees}C, nausea, shivering, and muscle joint pain. Participants in this study were students at the university. They were considered eligible for this study if they were currently enrolled at university, were at least 19 years of age, and provided informed consent. The data was recorded using a standardized online questionnaire. The answers were collected in an online database. At the beginning of the questionnaire, subjects or students were informed that data would be collected anonymously. Based on the results, the symptoms were different between female and male students. In fact, female students have experienced more symptoms than male students. While male students only suffered sore arms (68%) followed by headache symptoms (32%). Similar to male students, sore arms are the most common symptom observed among female students. Among female students, from the most to the least common symptoms observed from 20 years of age in this study are sore arms at site reaction > headache > fatigue > fever > muscle joint pain > shivering > nausea. A higher risk of presenting fatigue and headache symptoms was found in those with a non-overweight status with weight ranges of 50-60 kg.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Andri Wibowo", + "author_inst": "Universitas Indonesia" + }, + { + "author_name": "Natasya O Yostyadiananda", + "author_inst": "Universitas Indonesia" + }, + { + "author_name": "Gabriella RA Gunawan", + "author_inst": "Universitas Indonesia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.12.27.21268278", "rel_title": "SARS-CoV-2 Omicron VOC Transmission in Danish Households", @@ -482923,489 +484469,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.12.21.21268143", - "rel_title": "Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission", - "rel_date": "2021-12-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.21.21268143", - "rel_abs": "As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also introduce biases. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here, we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We develop and deploy improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detect emerging variants of concern up to 14 days earlier in wastewater samples, and identify multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.", - "rel_num_authors": 117, - "rel_authors": [ - { - "author_name": "Smruthi Karthikeyan", - "author_inst": "Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Joshua I Levy", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Peter De Hoff", - "author_inst": "Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Greg Humphrey", - "author_inst": "Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Amanda Birmingham", - "author_inst": "Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Kristen Jepsen", - "author_inst": "Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Sawyer Farmer", - "author_inst": "Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Helena M. Tubb", - "author_inst": "Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Tommy Valles", - "author_inst": "Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Caitlin E Tribelhorn", - "author_inst": "Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Rebecca Tsai", - "author_inst": "Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Stefan Aigner", - "author_inst": "Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Shashank Sathe", - "author_inst": "Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Niema Moshiri", - "author_inst": "Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Benjamin Henson", - "author_inst": "Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Abbas Hakim", - "author_inst": "Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Nathan A Baer", - "author_inst": "Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Tom Barber", - "author_inst": "Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Pedro Belda-Ferre", - "author_inst": "Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Marisol Chacon", - "author_inst": "Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Willi Cheung", - "author_inst": "Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Evelyn S Crescini", - "author_inst": "Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Emily R Eisner", - "author_inst": "Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Alma L Lastrella", - "author_inst": "Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Elijah S Lawrence", - "author_inst": "Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Clarisse A Marotz", - "author_inst": "Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Toan T Ngo", - "author_inst": "Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Tyler Ostrander", - "author_inst": "Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Ashley Plascencia", - "author_inst": "Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Rodolfo A Salido", - "author_inst": "Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Phoebe Seaver", - "author_inst": "Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Elizabeth W Smoot", - "author_inst": "Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Daniel McDonald", - "author_inst": "Department of Pediatrics, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Robert M Neuhard", - "author_inst": "Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Angela L Scioscia", - "author_inst": "Student Health and Well-Being, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Alysson M. Satterlund", - "author_inst": "Student Affairs, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Elizabeth H Simmons", - "author_inst": "Academic Affairs, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Dismas B. Abelman", - "author_inst": "Return to Learn, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "David Brenner", - "author_inst": "Return to Learn, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Judith Carbone Bruner", - "author_inst": "Return to Learn, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Anne Buckley", - "author_inst": "Return to Learn, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Michael Ellison", - "author_inst": "Return to Learn, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Jeffrey Gattas", - "author_inst": "Return to Learn, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Steven L Gonias", - "author_inst": "Department of Pathology, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Matt Hale", - "author_inst": "Return to Learn, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Faith Kirkham Hawkins", - "author_inst": "Return to Learn, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Lydia Ikeda", - "author_inst": "Return to Learn, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Hemlata Jhaveri", - "author_inst": "Return to Learn, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Ted Johnson", - "author_inst": "Return to Learn, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Vince Kellen", - "author_inst": "Return to Learn, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Brendan Kremer", - "author_inst": "Return to Learn, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Gary C. Matthews", - "author_inst": "Return to Learn, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Ronald McLawhon", - "author_inst": "Return to Learn, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Pierre Ouillet", - "author_inst": "Return to Learn, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Daniel Park", - "author_inst": "Return to Learn, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Allorah Pradenas", - "author_inst": "Return to Learn, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Sharon Reed", - "author_inst": "Department of Pathology and Medicine, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Lindsay Riggs", - "author_inst": "Return to Learn, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Alison M. Sanders", - "author_inst": "Return to Learn, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Bradley Sollenberger", - "author_inst": "Return to Learn, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Angela Song", - "author_inst": "Return to Learn, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Benjamin White", - "author_inst": "Return to Learn, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Terri Winbush", - "author_inst": "Return to Learn, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Christine M Aceves", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Catelyn Anderson", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Karthik Gangavarapu", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Emory Hufbauer", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Ezra Kurzban", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Justin Lee", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Nathaniel L Matteson", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Edyth Parker", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Sarah A Perkins", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Karthik S Ramesh", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Refugio Robles-Sikisaka", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Madison A Schwab", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Emily Spencer", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Shirlee Wohl", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Laura Nicholson", - "author_inst": "Scripps Health" - }, - { - "author_name": "Ian H Mchardy", - "author_inst": "Scripps Health" - }, - { - "author_name": "David P Dimmock", - "author_inst": "Rady Children's Institute for Genomic Medicine, San Diego, CA, USA" - }, - { - "author_name": "Charlotte A Hobbs", - "author_inst": "Rady Children's Institute for Genomic Medicine, San Diego, CA, USA" - }, - { - "author_name": "Omid Bakhtar", - "author_inst": "Sharp Healthcare, San Diego, CA, USA" - }, - { - "author_name": "Aaron Harding", - "author_inst": "Sharp Healthcare, San Diego, CA, USA" - }, - { - "author_name": "Art Mendoza", - "author_inst": "Sharp Healthcare, San Diego, CA, USA" - }, - { - "author_name": "Alexandre Bolze", - "author_inst": "Helix, San Mateo, CA, USA" - }, - { - "author_name": "David Becker", - "author_inst": "Helix, San Mateo, CA, USA" - }, - { - "author_name": "Elizabeth T Cirulli", - "author_inst": "Helix, San Mateo, CA, USA" - }, - { - "author_name": "Magnus Isaksson", - "author_inst": "Helix, San Mateo, CA, USA" - }, - { - "author_name": "Kelly M Schiabor Barrett", - "author_inst": "Helix, San Mateo, CA, USA" - }, - { - "author_name": "Nicole L Washington", - "author_inst": "Helix, San Mateo, CA, USA" - }, - { - "author_name": "John D Malone", - "author_inst": "County of San Diego Health and Human Services Agency, San Diego, CA, USA" - }, - { - "author_name": "Ashleigh Murphy Schafer", - "author_inst": "County of San Diego Health and Human Services Agency, San Diego, CA, USA" - }, - { - "author_name": "Nikos Gurfield", - "author_inst": "County of San Diego Health and Human Services Agency, San Diego, CA, USA" - }, - { - "author_name": "Sarah Stous", - "author_inst": "County of San Diego Health and Human Services Agency, San Diego, CA, USA" - }, - { - "author_name": "Rebecca Fielding-Miller", - "author_inst": "Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA; Division of Infectious Disease and Globa" - }, - { - "author_name": "Tommi Gaines", - "author_inst": "Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Richard Garfein", - "author_inst": "Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Cheryl A. M. Anderson", - "author_inst": "Herbert Wertheim School of Public Health and Human Longevity Science , Division of Hypertension and Nephrology, University of California San Diego, La Jolla, CA" - }, - { - "author_name": "Natasha K. Martin", - "author_inst": "Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Robert T Schooley", - "author_inst": "Division of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Brett Austin", - "author_inst": "County of San Diego Health and Human Services Agency, San Diego, CA, USA" - }, - { - "author_name": "Duncan R. MacCannell", - "author_inst": "Office of Advanced Molecular Detection, Centers for Disease Control and Prevention, Atlanta, GA, USA" - }, - { - "author_name": "Stephen F Kingsmore", - "author_inst": "Rady Children's Institute for Genomic Medicine, San Diego, CA, USA" - }, - { - "author_name": "William Lee", - "author_inst": "Helix, San Mateo, CA, USA" - }, - { - "author_name": "Seema Shah", - "author_inst": "County of San Diego Health and Human Services Agency, San Diego, CA, USA" - }, - { - "author_name": "Eric McDonald", - "author_inst": "County of San Diego Health and Human Services Agency, San Diego, CA, USA" - }, - { - "author_name": "Alexander T. Yu", - "author_inst": "COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA" - }, - { - "author_name": "Mark Zeller", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA" - }, - { - "author_name": "Kathleen M Fisch", - "author_inst": "Center for Computational Biology and Bioinformatics, Department of Obstetrics, Gynecology, and Reproductive Science" - }, - { - "author_name": "Christopher A. Longhurst", - "author_inst": "Department of Pediatrics, University of California San Diego, La Jolla, CA, USA; Department of Biomedical Informatics, University of California, San Diego, La J" - }, - { - "author_name": "Patty Maysent", - "author_inst": "Office of the UC San Diego Health CEO, University of California, San Diego" - }, - { - "author_name": "David Pride", - "author_inst": "Departments of Pathology and Medicine, University of California, San Diego, La Jolla, CA" - }, - { - "author_name": "Pradeep K. Khosla", - "author_inst": "Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA" - }, - { - "author_name": "Louise C Laurent", - "author_inst": "Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, Department of Obstetrics, Gynecology, and Reproductive Sciences, " - }, - { - "author_name": "Gene W Yeo", - "author_inst": "Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, Department of Cellular and Molecular Medicine, University of Cali" - }, - { - "author_name": "Kristian G Andersen", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA, Scripps Research Translational Institute, La Jolla, CA, USA" - }, - { - "author_name": "Rob Knight", - "author_inst": "Department of Pediatrics, University of California San Diego, La Jolla, CA, USA; Department of Bioengineering, University of California San Diego, La Jolla, CA," - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.12.22.21268232", "rel_title": "Understanding the impact of the COVID-19 pandemic on a socially deprived UK coastal town: a preliminary exploratory analysis of health and socioeconomic data", @@ -484613,6 +485676,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.24.21268387", + "rel_title": "The Canadian COVID-19 Experiences Survey: Study Protocol", + "rel_date": "2021-12-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.24.21268387", + "rel_abs": "IntroductionVaccine hesitancy and inconsistent mitigation behavior performance have been significant challenges throughout the COVID-19 pandemic. In Canada, despite relatively high vaccine availability and uptake, willingness to accept booster shots and maintain mitigation behaviors in the post-acute phase of COVID-19 remain uncertain. The aim of the Canadian COVID-19 Experiences Project (CCEP) is two-fold: 1) to identify social-cognitive and neurocognitive correlates of vaccine hesitancy and mitigation behaviors, and 2) to identify optimal communication strategies to promote vaccination and mitigation behaviors into the post-acute phase of the pandemic.\n\nMethods and analysesThe CCEP is comprised of two components: a conventional population survey (Study 1) and a functionally interconnected laboratory study (Study 2). Study 1 will involve 3 waves of data collection. Wave 1, completed between 28 September and 21 October, 2021, recruited 1,958 vaccine-hesitant (49.8%) and fully vaccinated (50.2%) adults using quota sampling to ensure maximum statistical power. Measures included a variety of social cognitive (e.g., beliefs, intentions) and neurocognitive (e.g., delay discounting) measures, followed by an opportunity to view and rate a set of professionally produced COVID-19 public service announcement (PSA) videos for perceived efficacy. Study 2 employs the same survey items and PSAs but coupled with lab-based eye tracking and functional brain imaging to directly quantify neural indicators of attention capture and self-reflection in a smaller community sample. In the final phase of the project, subjective impressions and neural indicators of PSA efficacy will be compared and used to inform recommendations for construction of COVID-19 PSAs into the post-acute phase of the pandemic.\n\nEthics and disseminationThe CCEP has received ethical review and approval by the University of Waterloo Office of Research Ethics. Findings will be disseminated through peer-reviewed publications and presentations at scientific meetings.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Peter Hall", + "author_inst": "University of Waterloo" + }, + { + "author_name": "Geoffrey Fong", + "author_inst": "University of Waterloo" + }, + { + "author_name": "Sara Hitchman", + "author_inst": "University of Zurich" + }, + { + "author_name": "Anne Quah", + "author_inst": "University of Waterloo" + }, + { + "author_name": "Thomas Agar", + "author_inst": "University of Waterloo" + }, + { + "author_name": "Gang Meng", + "author_inst": "University of Waterloo" + }, + { + "author_name": "Hasan Ayaz", + "author_inst": "Drexel University" + }, + { + "author_name": "Bruce Dore", + "author_inst": "McGill University" + }, + { + "author_name": "Mohammad Nazmus Sakib", + "author_inst": "University of Waterloo" + }, + { + "author_name": "Anna Hudson", + "author_inst": "University of Waterloo" + }, + { + "author_name": "Christian Boudreau", + "author_inst": "University of Waterloo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.22.21268212", "rel_title": "Dying from COVID-19 or with COVID-19: a definitive answer through a retrospective analysis of mortality in Italy", @@ -485289,33 +486411,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.23.21268332", - "rel_title": "Extending upon: What effect might border screening have on preventing importation of COVID-19 compared with other infections? - Considering the additional effect of post-arrival isolation", - "rel_date": "2021-12-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.23.21268332", - "rel_abs": "We recently described a simple model through which we assessed what effect subjecting travellers to a single on-arrival test might have on reducing risk of importing disease cases during simulated outbreaks of COVID-19, Influenza, SARS, and Ebola. We build upon this work to allow for the additional requirement that inbound travellers also undergo a period of self-isolation upon arrival, where upon completion the traveller is again tested for signs of infection prior to admission across the border. Prior results indicated that a single on-arrival test has the potential to detect 9% of travellers infected with COVID-19, compared to 35%, 10% and 3% for travellers infected with influenza, SARS, and Ebola respectively. Our extended model shows that testing administered after a 2-day isolation period may be able to detect up to 41%, 97%, 44% and 15% of COVID-19, Influenza, SARS, and Ebola infected travellers respectively. Longer self-isolation periods increase detection rates further, with an 8-day self-isolation period suggesting detection rates of up to 94%, 100%, 98% and 62% for travellers infected with COVID-19, Influenza, SARS, and Ebola respectively. These results therefore suggest that testing arrivals after an enforced period of self-isolation may present a reasonable method of protecting against case importation during international outbreaks.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Declan Bays", - "author_inst": "United Kingdom Health Security Agency" - }, - { - "author_name": "Emma Bennett", - "author_inst": "United Kingdom Health Security Agency" - }, - { - "author_name": "Thomas James Ronald Finnie", - "author_inst": "United Kingdom Health Security Agency" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.12.22.21268253", "rel_title": "COVID-19 vaccination effectiveness rates by week and sources of bias", @@ -486547,6 +487642,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, + { + "rel_doi": "10.1101/2021.12.22.21268252", + "rel_title": "Rapid increase in Omicron infections in England during December 2021: REACT-1 study", + "rel_date": "2021-12-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.22.21268252", + "rel_abs": "BackgroundThe highest-ever recorded numbers of daily severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in England has been observed during December 2021 and have coincided with a rapid rise in the highly transmissible Omicron variant despite high levels of vaccination in the population. Although additional COVID-19 measures have been introduced in England and internationally to contain the epidemic, there remains uncertainty about the spread and severity of Omicron infections among the general population.\n\nMethodsThe REal-time Assessment of Community Transmission-1 (REACT-1) study has been monitoring the prevalence of SARS-CoV-2 infection in England since May 2020. REACT-1 obtains self-administered throat and nose swabs from a random sample of the population of England at ages 5 years and over. Swabs are tested for SARS-CoV-2 infection by reverse transcription polymerase chain reaction (RT-PCR) and samples testing positive are sent for viral genome sequencing. To date 16 rounds have been completed, each including [~]100,000 or more participants with data collected over a period of 2 to 3 weeks per month. Socio-demographic, lifestyle and clinical information (including previous history of COVID-19 and symptoms prior to swabbing) is collected by online or telephone questionnaire. Here we report results from round 14 (9-27 September 2021), round 15 (19 October - 05 November 2021) and round 16 (23 November - 14 December 2021) for a total of 297,728 participants with a valid RT-PCR test result, of whom 259,225 (87.1%) consented for linkage to their NHS records including detailed information on vaccination (vaccination status, date). We used these data to estimate community prevalence and trends by age and region, to evaluate vaccine effectiveness against infection in children ages 12 to 17 years, and effect of a third (booster) dose in adults, and to monitor the emergence of the Omicron variant in England.\n\nResultsWe observed a high overall prevalence of 1.41% (1.33%, 1.51%) in the community during round 16. We found strong evidence of an increase in prevalence during round 16 with an estimated reproduction number R of 1.13 (1.06, 1.09) for the whole of round 16 and 1.27 (1.14, 1.40) when restricting to observations from 1 December onwards. The reproduction number in those aged 18-54 years was estimated at 1.23 (1.14, 1.33) for the whole of round 16 and 1.41 (1.23, 1.61) from 1 December. Our data also provide strong evidence of a steep increase in prevalence in London with an estimated R of 1.62 (1.34, 1.93) from 1 December onwards and a daily prevalence reaching 6.07% (4.06%, 9.00%) on 14 December 2021. As of 1 to 11 December 2021, of the 275 lineages determined, 11 (4.0%) corresponded to the Omicron variant. The first Omicron infection was detected in London on 3 December, and subsequent infections mostly appeared in the South of England. The 11 Omicron cases were all aged 18 to 54 years, double-vaccinated (reflecting the large numbers of people who have received two doses of vaccine in this age group) but not boosted, 9 were men, 5 lived in London and 7 were symptomatic (5 with classic COVID-19 symptoms: loss or change of sense of smell or taste, fever, persistent cough), 2 were asymptomatic, and symptoms were unknown for 2 cases. The proportion of Omicron (vs Delta or Delta sub-lineages) was found to increase rapidly with a daily increase of 66.0% (32.7%, 127.3%) in the odds of Omicron (vs. Delta) infection, conditional on swab positivity. Highest prevalence of swab positivity by age was observed in (unvaccinated) children aged 5 to 11 years (4.74% [4.15%, 5.40%]) similar to the prevalence observed at these ages in round 15. In contrast, prevalence in children aged 12 to 17 years more than halved from 5.35% (4.78%, 5.99%) in round 15 to 2.31% (1.91%, 2.80%) in round 16. As of 14 December 2021, 76.6% children at ages 12 to 17 years had received at least one vaccine dose; we estimated that vaccine effectiveness against infection was 57.9% (44.1%, 68.3%) in this age group. In addition, the prevalence of swab positivity in adults aged 65 years and over fell by over 40% from 0.84% (0.72%, 0.99%) in round 15 to 0.48% (0.39%,0.59%) in round 16 and for those aged 75 years and over it fell by two-thirds from 0.63% (0.48%,0.82%) to 0.21% (0.13%,0.32%). At these ages a high proportion of participants (>90%) had received a third vaccine dose; we estimated that adults having received a third vaccine dose had a three- to four-fold lower risk of testing positive compared to those who had received two doses.\n\nConclusionA large fall in swab positivity from round 15 to round 16 among 12 to 17 year olds, most of whom have been vaccinated, contrasts with the continuing high prevalence among 5 to 11 year olds who have largely not been vaccinated. Likewise there were large falls in swab positivity among people aged 65 years and over, the vast majority of whom have had a third (booster) vaccine dose; these results reinforce the importance of the vaccine and booster campaign. However, the rapidly increasing prevalence of SARS-CoV-2 infections in England during December 2021, coincident with the rapid rise of Omicron infections, may lead to renewed pressure on health services. Additional measures beyond vaccination may be needed to control the current wave of infections and prevent health services (in England and other countries) from being overwhelmed.\n\nSummaryThe unprecedented rise in SARS-CoV-2 infections is concurrent with rapid spread of the Omicron variant in England and globally. We analysed prevalence of SARS-CoV-2 and its dynamics in England from end of November to mid-December 2021 among almost 100,000 participants from the REACT-1 study. Prevalence was high during December 2021 with rapid growth nationally and in London, and of the proportion of infections due to Omicron. We observed a large fall in swab positivity among mostly vaccinated older children (12-17 years) compared with unvaccinated younger children (5-11 years), and in adults who received a third vs. two doses of vaccine. Our results reiterate the importance of vaccination and booster campaigns; however, additional measures may be needed to control the rapid growth of the Omicron variant.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Paul Elliott", + "author_inst": "School of Public Health, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research" + }, + { + "author_name": "Barbara Bodinier", + "author_inst": "School of Public Health, Imperial College London, UK" + }, + { + "author_name": "Oliver Eales", + "author_inst": "School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency" + }, + { + "author_name": "Haowei Wang", + "author_inst": "School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency" + }, + { + "author_name": "David Haw", + "author_inst": "School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency" + }, + { + "author_name": "Joshua Elliott", + "author_inst": "Imperial College London" + }, + { + "author_name": "Matthew Whitaker", + "author_inst": "School of Public Health, Imperial College London, UK" + }, + { + "author_name": "Jakob Jonnerby", + "author_inst": "School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency" + }, + { + "author_name": "David Tang", + "author_inst": "Imperial College London" + }, + { + "author_name": "Caroline E. Walters", + "author_inst": "School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency" + }, + { + "author_name": "Christina Atchinson", + "author_inst": "School of Public Health, Imperial College London, UK" + }, + { + "author_name": "Peter J. Diggle", + "author_inst": "CHICAS, Lancaster Medical School, Lancaster University, UK and Health Data Research, UK" + }, + { + "author_name": "Andrew J. Page", + "author_inst": "Quadram Institute, Norwich, UK" + }, + { + "author_name": "Alex Trotter", + "author_inst": "Quadram Institute Bioscience" + }, + { + "author_name": "Deborah Ashby", + "author_inst": "School of Public Health, Imperial College London, UK" + }, + { + "author_name": "Wendy Barclay", + "author_inst": "Department of Infectious Disease, Imperial College London, UK" + }, + { + "author_name": "Graham Taylor", + "author_inst": "Department of Infectious Disease, Imperial College London, UK" + }, + { + "author_name": "Helen Ward", + "author_inst": "School of Public Health, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research" + }, + { + "author_name": "Ara Darzi", + "author_inst": "Imperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical Research Centre, UKInstitute of Global Health Innovation at " + }, + { + "author_name": "Graham Cooke", + "author_inst": "Department of Infectious Disease, Imperial College London, UKImperial College Healthcare NHS Trust, UKNational Institute for Health Research Imperial Biomedical" + }, + { + "author_name": "Marc Chadeau-Hyam", + "author_inst": "School of Public Health, Imperial College London, UK" + }, + { + "author_name": "Christl A Donnelly", + "author_inst": "School of Public Health, Imperial College London, UKMRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergency" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.12.21.470882", "rel_title": "COVID-19: Salient Aspects of Coronavirus Infection, Vaccines and Vaccination Testing and their Implications", @@ -487011,45 +488209,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.23.21267893", - "rel_title": "Echinacea as a Potential Force against Coronavirus Infections? A Mini-Review of Randomized Controlled Trials in Adults and Children", - "rel_date": "2021-12-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.23.21267893", - "rel_abs": "Echinacea purpurea was shown to broadly inhibit coronaviruses and SARS-CoV-2 in vitro. This review discusses the available clinical evidence from randomized, blinded and controlled human studies. Two RCTs with results on enveloped viruses, respectively coronavirus infections during prevention treatment were detected. Incidence and/or viral loads were measured by RT-PCR and symptom severity was recorded. Jawad et al. (2012) collected nasopharyngeal swabs from adults (N=755) over 4 months of continuous prevention. Overall, 24 and 47 enveloped virus infections occurred, including 21 and 33 coronavirus detections [229E; HKU1; OC43] with Echinaforce(R) extract [2400mg daily] and placebo, respectively (p=0.0114). Ogal et al. (2021) administered the same extract [1200mg] or control for 4 months to children (4 - 12 years) (N=203). Echinacea reduced the incidence of enveloped virus infections from 47 to 29 (p=0.0038) whereas 11 and 13 coronavirus detections [229E, OC43, NL63] were counted (p>0.05). Respiratory symptoms during coronavirus infections were significantly lower with area-under-curve AUC=75.8 (+/-50.24) versus 27.1 (+/-21.27) score points (p=0.0036). Importantly, viral loads in nasal secretions were significantly reduced by 98.5%, with Ct-values 31.1 [95% CI 26.3; 35.9] versus 25.0 [95% CI 20.5; 29.5] (p = 0.0479). Results from clinical studies confirm the antiviral activity found for Echinacea in vitro, embracing enveloped respiratory pathogens and therefore coronaviruses as well. Substantiating results from a new completed study seems to extrapolate these effects to the prevention of SARS-CoV-2 infection. As hypothesized, the testified broad antiviral activity of Echinacea extract appears to be inclusive for SARS-CoV-2.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Simon Nicolussi", - "author_inst": "iC-Cure scientific" - }, - { - "author_name": "Karin Ardjomand-Woelkart", - "author_inst": "Institute of Pharmaceutical Sciences, Department of Pharmacognosy, University Graz, Austria" - }, - { - "author_name": "Rainer Stange", - "author_inst": "Institute of Social Medicine, Epidemiology and Health Economics, Charite-Universitaetsmedizin Berlin, Corporate Member of Freie Universitaet Berlin, Humboldt-Un" - }, - { - "author_name": "Giuseppe Gancitano", - "author_inst": "1st \"Tuscania\" Paratrooper Regiment Carabinieri, Italian Ministry of Defence, Livorno, Italy" - }, - { - "author_name": "Peter Klein", - "author_inst": "d.s.h. statistical services GmbH, Rohrbach Germany" - }, - { - "author_name": "Mercedes Ogal", - "author_inst": "Pediatric clinic, Brunnen, Switzerland" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.23.21268316", "rel_title": "Three doses of the BNT162b2 vaccine confer neutralising antibody capacity against the SARS-CoV-2 B.1.1.529 (Omicron) variant of concern", @@ -488621,6 +489780,20 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2021.12.21.473702", + "rel_title": "Tutorial: Investigating SARS-CoV-2 evolution and phylogeny using MNHN-Tree-Tools", + "rel_date": "2021-12-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.21.473702", + "rel_abs": "The Covid-19 pandemic has caused at more than 3 million deaths by Mai this year [1]. It had a significant impact on the daily life and the global economy [2]. The virus has since its first recorded outbreak in China [3] mutated into new strains [4]. The Nextstrain [5] project has so far been monitoring the evolution of the virus. At the same time we were developing in our lab the MNHN-Tree-Tools [6] toolkit, primarily for the investigation of DNA repeat sequences. We have further extended MNHN-Tree-Tools [6] to guide phylogenetics. As such the toolkit has evolved into a high performance code, allowing for a fast investigation of millions of sequences. Given the context of the pandemic it became evident that we will use our versatile tool to investigate the evolution of SARS-CoV-2 sequences. Our efforts have cumulated in this tutorial that we share with the scientific community.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "cc_by_nd", + "type": "confirmatory results", + "category": "genetics" + }, { "rel_doi": "10.1101/2021.12.22.472458", "rel_title": "Computational Mapping of the Human-SARS-CoV-2 Protein-RNA Interactome", @@ -489033,57 +490206,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.22.21268274", - "rel_title": "SARS-CoV-2 Antigen Tests Predict Infectivity Based on Viral Culture: Comparison of Antigen, PCR Viral Load, and Viral Culture Testing on a Large Sample Cohort", - "rel_date": "2021-12-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.22.21268274", - "rel_abs": "The relationship of SARS-CoV-2 antigen testing results, viral load, and viral culture detection remains to be fully defined. Presumptively, viral culture can provide a surrogate measure for infectivity of sampled individuals, and thereby inform how and where to most appropriately deploy available diagnostic testing modalities. We therefore determined the relationship of antigen testing results from three lateral flow and one microfluidics assay to viral culture performed in parallel in 181 nasopharyngeal swab samples positive for SARS-CoV-2. Sample viral loads, determined by RT-qPCR, were distributed across the range of viral load values observed in our testing population. We found that antigen tests were predictive of viral culture positivity, with the LumiraDx method showing enhanced sensitivity (90%; 95% confidence interval (95% CI) 83-94%) compared with the BD Veritor (74%, 95% CI 65-81%), CareStart (74%, 95% CI 65-81%) and Oscar Corona (74%, 95% CI 65-82%) lateral flow antigen tests. Antigen and viral culture positivity were also highly correlated with sample viral load, with areas under the receiver-operator characteristic curves (ROCs) of 0.94-0.97 and 0.92, respectively. In particular, a viral load threshold of 100,000 copies/mL was 95% sensitive (95% CI, 90-98%) and 72% specific (95% CI, 60-81%) for predicting viral culture positivity. Taken together, the detection of SARS-CoV-2 antigen identified highly infectious individuals, some of whom may harbor 10,000-fold more virus in their samples than those with any detectable infectious virus. As such, our data support use of antigen testing in defining infectivity status at the time of sampling.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "James E Kirby", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Stefan Riedel", - "author_inst": "Beth Israel Deaconess Medical Center, Harvard Medical School" - }, - { - "author_name": "Sanjucta Dutta", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Ramy Arnaout", - "author_inst": "Beth Israel Deaconess Medical Center, Harvard Medical School" - }, - { - "author_name": "Annie Cheng", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Sarah Ditelberg", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Donald J Hamel", - "author_inst": "Harvard School of Public Health" - }, - { - "author_name": "Charlotte A. Chang", - "author_inst": "Harvard T.H.Chan School of Public Health" - }, - { - "author_name": "Phyllis J. Kanki", - "author_inst": "Harvard T. H. Chan School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.23.21268005", "rel_title": "TROPONIN IS INDEPENDENTLY ASSOCIATED WITH DEATH IN PATIENTS WITH COVID: A RETROSPECTIVE STUDY", @@ -490675,6 +491797,57 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.12.20.473447", + "rel_title": "Blockade of TMPRSS2-mediated priming of SARS-CoV-2 by the N-terminal peptide of lactoferrin", + "rel_date": "2021-12-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.20.473447", + "rel_abs": "In addition to vaccines, there is an urgent need for supplemental antiviral therapeutics to dampen the persistent COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). The transmembrane protease serine 2 (TMPRSS2), which is responsible for the proteolytic processing of the SARS-CoV-2 spike protein as virus priming for cell entry, appears as a rational therapeutic target for the clearance of SARS-CoV-2 infection. Accordingly, selective inhibitors of TMPRSS2 represent potential tools for prevention and treatment of COVID-19. Here, we tested the inhibitory capacities of the human milk glycoprotein lactoferrin and its N-terminal peptide pLF1, which we identified as inhibitors of plasminogen, a serine protease homologous to TMPRSS2. In vitro proteolysis assays revealed that, unlike full-length lactoferrin, pLF1 significantly inhibited the proteolytic activity of TMPRSS2. pLF1 inhibited both the proteolytic processing of the SARS-CoV-2 spike protein and the SARS-CoV-2 infection of simian Vero cells. Because lactoferrin is a natural product and several biologically active peptides, such as the N-terminally derived lactoferricins, are produced naturally by pepsin-mediated digestion, natural or synthetic peptides from lactoferrin represent well-achievable candidates for supporting prevention and treatment of COVID-19.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Anna Ohradanova-Repic", + "author_inst": "MUW" + }, + { + "author_name": "Laura Gebetsberger", + "author_inst": "MUW" + }, + { + "author_name": "Gabor Tajti", + "author_inst": "MUW" + }, + { + "author_name": "Gabriela Ondrovicova", + "author_inst": "SAS" + }, + { + "author_name": "Romana Prazenicova", + "author_inst": "SAS" + }, + { + "author_name": "Rostislav Skrabana", + "author_inst": "SAS" + }, + { + "author_name": "Peter Barath", + "author_inst": "SAS" + }, + { + "author_name": "Hannes Stockinger", + "author_inst": "MUW" + }, + { + "author_name": "Vladimir Leksa", + "author_inst": "SAS" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.12.20.473421", "rel_title": "Virus-like particles (VLPs) are efficient tools for boosting mRNA-induced antibodies", @@ -491287,37 +492460,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.12.17.473140", - "rel_title": "Human genetic variants associated with COVID-19 severity are enriched in immune and epithelium regulatory networks", - "rel_date": "2021-12-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.17.473140", - "rel_abs": "Human genetic variants can influence the severity of symptoms being infected with SARS-COV-2. Several genome-wide association studies have identified human genomic risk SNPs associated with COVID-19 severity. However, the causal tissues or cell types of COVID-19 severity are uncertain and candidate genes associated with these human risk SNPs were investigated in genomic proximity instead of their functional cellular contexts. Here, we compiled regulatory networks of 77 human contexts and revealed those risk SNPs enriched cellular contexts and associated transcript factors, regulatory elements, and target genes. Twenty-one human contexts were identified and grouped into two categories: immune cells and epithelium cells. We further aggregated the regulatory networks of immune cells, epithelium cells, and immune-epithelium crosstalk and investigated their association with risk SNPs regulation. Two genomic clusters, chemokine receptors cluster and OAS cluster, showed the strongest association with COVID-19 severity and different regulations in immune and epithelium contexts. Our findings were supported by analysis on both microarray and whole genome sequencing based GWAS summary statistics.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Zhanying Feng", - "author_inst": "Academy of Mathematics and System Science" - }, - { - "author_name": "Xianwen Ren", - "author_inst": "Peking University" - }, - { - "author_name": "Zhana Duren", - "author_inst": "Clemson University" - }, - { - "author_name": "Yong Wang", - "author_inst": "Academy of mathematics and systems science, Chinese Academy of Sciences." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2021.12.19.473380", "rel_title": "SARS-CoV-2 Omicron Variant: ACE2 Binding, Cryo-EM Structure of Spike Protein-ACE2 Complex and Antibody Evasion", @@ -493001,6 +494143,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.20.21267918", + "rel_title": "Keeping doors open: A cross-sectional survey of family physician practice patterns during COVID-19, needs, and intentions", + "rel_date": "2021-12-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.20.21267918", + "rel_abs": "ObjectiveTo determine the extent to which family physicians closed their doors altogether or for in-person visits during the pandemic, their future practice intentions, and related factors.\n\nMethodsBetween March and June 2021, we conducted a cross-sectional survey using email, fax, and phone of 1,186 family doctors practicing comprehensive family medicine in Toronto, Ontario. We asked about practice patterns in January 2021, use of virtual care, and practice intentions.\n\nResultsOf the 1,016 (86%) that responded to the survey, 99.7% (1001/1004) indicated their practice was open in January 2021 with 94.8% (928/979) seeing patients in-person and 30.8% (264/856) providing in-person care to patients reporting COVID-19 symptoms. Respondents estimated spending 58.2% of clinical care time on phone visits and an additional 5.8% on video and 7.5% on email. 17.2% (77/447) were planning to close their current practice in the next five years. There was a higher proportion of physicians who worked alone in a clinic among those who did not see patients in-person (27.6% no vs 12.4% yes, p<0.05), did not see symptomatic patients (15.6% no vs 6.5 % yes, p<0.001), and those who planned to close their practice in the next 5 years (28.9% yes vs 13.9% no, p<0.01).\n\nInterpretationThe vast majority of family physicians in Toronto were open to in-person care in January 2021 but almost one-fifth are considering closing their practice in the next five years. Policy-makers need to prepare for a growing family physician shortage and better understand factors that support recruitment and retention.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Tara Kiran", + "author_inst": "St. Michael's Hospital" + }, + { + "author_name": "Ri Wang", + "author_inst": "St. Michael's Hospital" + }, + { + "author_name": "Curtis Handford", + "author_inst": "St. Michael's Hospital" + }, + { + "author_name": "Nadine Laraya", + "author_inst": "University of Toronto" + }, + { + "author_name": "Azza Eissa", + "author_inst": "University of Toronto" + }, + { + "author_name": "Pauline Pariser", + "author_inst": "University of Toronto" + }, + { + "author_name": "Rebecca Brown", + "author_inst": "St. Michael's Hospital" + }, + { + "author_name": "Cheryl Pedersen", + "author_inst": "St. Michael's Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "primary care research" + }, { "rel_doi": "10.1101/2021.12.18.21268039", "rel_title": "Comparative effectiveness of the BNT162b2 vs ChAdOx1 vaccine against Covid-19", @@ -493572,53 +494761,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.20.21268124", - "rel_title": "SARS-CoV-2 vaccine effectiveness and breakthrough infections in maintenance dialysis patients", - "rel_date": "2021-12-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.20.21268124", - "rel_abs": "BackgroundSARS-CoV-2 vaccine effectiveness during the Delta period and immunogenicity threshold associated with protection against COVID-19 related hospitalization or death in the dialysis population is unknown.\n\nMethodsA retrospective, observational study assessed SARS-CoV-2 vaccine effectiveness and immunogenicity threshold in all adult maintenance dialysis patients without COVID-19 history treated between February 1 and October 2, 2021. All COVID-19 infections, composite of hospitalization or death following COVID-19 and available SARS-CoV-2 anti-spike immunoglobulin (Ig) G values were extracted from electronic medical record. COVID-19 cases per 10,000 days at risk and vaccine effectiveness during pre-Delta and Delta periods were determined.\n\nResultsOf 15,718 patients receiving dialysis during the study period, 11,191 (71%) were fully vaccinated, 733 (5%) were partially vaccinated and 3,794 (24%) were unvaccinated. 967 COVID-19 were cases identified: 511 (53%) occurred in unvaccinated patients and 579 (60%) occurred during the Delta period. COVID-19 related hospitalization or death was less likely among vaccinated versus unvaccinated patients for all vaccines (adjusted HR 0.19 [0.12, 0.30]) and for BNT162b2/Pfizer, mRNA-1273/Moderna, and Ad26.COV2.S/Janssen (adjusted HR=0.25 [0.16, 0.40], 0.14 [0.08, 0.22], and 0.34 [0.17, 0.68] respectively). Among those with anti-spike IgG levels, those with IgG level [≥] 7 had significantly lower risk of a COVID-19 diagnosis (HR=0.25 [0.15, 0.42]) and none experienced a COVID-related hospitalization or death.\n\nConclusionsAmong maintenance dialysis patients, SARS-CoV-2 vaccination was associated with a lower risk of COVID-19 diagnosis and associated hospitalization or death. Among vaccinated patients, low anti-spike IgG level is associated with worse COVID-19 related outcomes.\n\nSignificance StatementSARS-CoV-2 vaccine effectiveness and association between antibody levels and clinical outcomes in maintenance dialysis patients is not known. Between February 1 and October 2, 2021, vaccine effectiveness was 85% against COVID-19 infection and 81% against composite of COVID-related hospitalization or death. COVID-19 case rates and severe outcomes were higher during the Delta dominant period (June 27-October 2, 2021). Increasing time (weeks) since full vaccination status was associated with increased risk for COVID-19 related hospitalization or death. Anti-spike IgG level [≥] 7 had lower risk of a COVID-19 diagnosis and no COVID-related hospitalization or death. Our findings supports utilization of SARS-CoV-2 vaccination and suggests that monitoring SARS-CoV-2 antibody levels and administering additional vaccine doses to maintain adequate immunity will be beneficial.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Harold J Manley", - "author_inst": "Dialysis Clinic Inc" - }, - { - "author_name": "Gideon Aweh", - "author_inst": "dialysis clinic, inc" - }, - { - "author_name": "Caroline M Hsu", - "author_inst": "Tufts Medical Center" - }, - { - "author_name": "Daniel E Weiner", - "author_inst": "Tufts Medical Center" - }, - { - "author_name": "Dana Miskulin", - "author_inst": "Tufts Medical Center" - }, - { - "author_name": "Antonia M Harford", - "author_inst": "Dialysis Clinic, Inc" - }, - { - "author_name": "Doug Johnson", - "author_inst": "Dialysis Clinic, Inc." - }, - { - "author_name": "Eduardo K Lacson Jr.", - "author_inst": "Dialysis Clinic, Inc." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.19.473359", "rel_title": "Pentosan polysulfate inhibits attachment and infection by SARS-CoV-2 in vitro: insights into structural requirements for binding.", @@ -494974,6 +496116,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.12.21.21268155", + "rel_title": "Variability in physical inactivity responses of university students during COVID-19 pandemic: A monitoring of daily step counts using a smartphone application", + "rel_date": "2021-12-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.21.21268155", + "rel_abs": "This study investigated the changes in physical inactivity of university students during the COVID-19 pandemic, with reference to their academic calendar. We used the daily step counts recorded by a smartphone application (iPhone Health App) from April 2020 to January 2021 (287 days) for 603 students. The data for 287 days were divided into five periods based on their academic calendar. The median value of daily step counts across each period was calculated. A k-means clustering analysis was performed to classify the 603 participants into subgroups to demonstrate the variability in the physical inactivity responses. The median daily step counts, with a 7-days moving average, dramatically decreased from 5,000 to 2,000 steps/day in early April. It remained at a lower level (less than 2,000 steps/day) during the first semester, then increased to more than 5,000 steps/day at the start of summer vacation. The clustering analysis demonstrated the variability in physical inactivity responses. Independent of the academic calendar, many inactive students did not recover their original daily step counts after its dramatic decrement. Consequently, promoting physical activity is recommended for inactive university students over the course of the whole semester.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Shoji Konda", + "author_inst": "Osaka University" + }, + { + "author_name": "Issei Ogasawara", + "author_inst": "Osaka University" + }, + { + "author_name": "Kazuki Fujita", + "author_inst": "Osaka University" + }, + { + "author_name": "Chisa Aoyama", + "author_inst": "Osaka University" + }, + { + "author_name": "Teruki Yokoyama", + "author_inst": "Osaka University" + }, + { + "author_name": "Takuya Magome", + "author_inst": "Otemon Gakuin University, Osaka University" + }, + { + "author_name": "Chen Yulong", + "author_inst": "Osaka University" + }, + { + "author_name": "Ken Hashizume", + "author_inst": "Osaka University" + }, + { + "author_name": "Tomoyuki Matsuo", + "author_inst": "Osaka University" + }, + { + "author_name": "Ken Nakata", + "author_inst": "Osaka University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "sports medicine" + }, { "rel_doi": "10.1101/2021.12.20.21268081", "rel_title": "Economic burden and catastrophic health expenditure associated with COVID-19 hospitalisations in Kerala, South India", @@ -495426,413 +496623,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2021.12.19.21268028", - "rel_title": "Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa", - "rel_date": "2021-12-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.19.21268028", - "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic in southern Africa has been characterised by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, whilst the second and third waves were driven by the Beta and Delta variants respectively1-3. In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng Province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, predicted to influence antibody neutralization and spike function4. Here, we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.", - "rel_num_authors": 98, - "rel_authors": [ - { - "author_name": "Raquel Viana", - "author_inst": "Lancet Laboratories, Johannesburg, South Africa" - }, - { - "author_name": "Sikhulile Moyo", - "author_inst": "Botswana Harvard AIDS Institite Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana Harvard T.H. Chan School of Public health, Boston, Ma" - }, - { - "author_name": "Daniel Gyamfi Amoako", - "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa" - }, - { - "author_name": "Houriiyah Tegally", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa Centre" - }, - { - "author_name": "Cathrine Scheepers", - "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa" - }, - { - "author_name": "Richard J Lessells", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa Centre" - }, - { - "author_name": "Jennifer Giandhari", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa" - }, - { - "author_name": "Nicole Wolter", - "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa" - }, - { - "author_name": "Josie Everatt", - "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa" - }, - { - "author_name": "Andrew Rambaut", - "author_inst": "Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK" - }, - { - "author_name": "Christian Althaus", - "author_inst": "University of Bern" - }, - { - "author_name": "Eduan Wilkinson", - "author_inst": "Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University; Stellenbosch, South Africa" - }, - { - "author_name": "Adriano Mendes", - "author_inst": "Zoonotic arbo and Resiratory virus program, Department Medical Virology, University of Pretoria, Pretoria, South Africa" - }, - { - "author_name": "Amy Strydom", - "author_inst": "Zoonotic arbo and Resiratory virus program, Department Medical Virology, University of Pretoria, Pretoria, South Africa" - }, - { - "author_name": "Michaela Davids", - "author_inst": "Zoonotic arbo and Resiratory virus program, Department Medical Virology, University of Pretoria, Pretoria, South Africa" - }, - { - "author_name": "Simnikiwe Mayaphi", - "author_inst": "Department Medical Virology University of Pretoria, Pretoria, South Africa National Health Laboratory Services, Thswane Academic Devision, Pretoria, South Afric" - }, - { - "author_name": "Simani Gaseitsiwe", - "author_inst": "Botswana Harvard AIDS Institite Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana Department of Immunology and Infectious Diseases, Har" - }, - { - "author_name": "Wonderful T Choga", - "author_inst": "Botswana Harvard AIDS Institite Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana" - }, - { - "author_name": "Dorcas Maruapula", - "author_inst": "Botswana Harvard AIDS Institite Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana" - }, - { - "author_name": "Boitumelo Zuze", - "author_inst": "Botswana Harvard AIDS Institite Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana" - }, - { - "author_name": "Botshelo Radibe", - "author_inst": "Botswana Harvard AIDS Institite Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana" - }, - { - "author_name": "Legodile Koopile", - "author_inst": "Botswana Harvard AIDS Institite Partnership, Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana" - }, - { - "author_name": "Roger Shapiro", - "author_inst": "Botswana Harvard AIDS Institite Partnership, Gaborone, Botswana Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Bos" - }, - { - "author_name": "Shahin Lockman", - "author_inst": "Botswana Harvard AIDS Institite Partnership, Gaborone, Botswana Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Bos" - }, - { - "author_name": "Mpaphi B. Mbulawa", - "author_inst": "National Health Laboratory, Gaborone, Botswana" - }, - { - "author_name": "Thongbotho Mphoyakgosi", - "author_inst": "National Health Laboratory, Gaborone, Botswana" - }, - { - "author_name": "Pamela Smith-Lawrence", - "author_inst": "Health Services, Ministry of Health and Wellness, Gaborone, Botswana" - }, - { - "author_name": "Mosepele Mosepele", - "author_inst": "Department of Medicine, Faculty of Medicine, University of Botswana, Gaborone, Botswana Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana Botswana Pr" - }, - { - "author_name": "Mogomotsi Matshaba", - "author_inst": "Botswana-Baylor Children's Clinical Centre of E cellence Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana Botswana Presidential COVID-19 Taskforce" - }, - { - "author_name": "Kereng Masupu", - "author_inst": "Botswana Presidential COVID-19 Taskforce, Gaborone, Botswana" - }, - { - "author_name": "Mohammed Chand", - "author_inst": "Diagnofirm Medical Laboratories, Gaborone, Botswana" - }, - { - "author_name": "Charity Joseph", - "author_inst": "Diagnofirm Medical Laboratories, Gaborone, Botswana" - }, - { - "author_name": "Lesego Kuate-Lere", - "author_inst": "Ministry of Health and Wellness, Gaborone, Botswana" - }, - { - "author_name": "Onalethatha Lesetedi-Mafoko", - "author_inst": "Ministry of Health and Wellness, Gaborone, Botswana" - }, - { - "author_name": "Kgomotso Moruisi", - "author_inst": "Ministry of Health and Wellness, Gaborone, Botswana" - }, - { - "author_name": "Lesley Scott", - "author_inst": "University of the Witwatersrand" - }, - { - "author_name": "Wendy Stevens", - "author_inst": "University of the Witwatersrand" - }, - { - "author_name": "Constantinos Kurt Wibmer", - "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa" - }, - { - "author_name": "Anele Mnguni", - "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa" - }, - { - "author_name": "Arshad Ismail", - "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa" - }, - { - "author_name": "Boitshoko Mahlangu", - "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa" - }, - { - "author_name": "Darren P. Martin", - "author_inst": "Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; Wellcome Centre for Infectious Diseases Research in Af" - }, - { - "author_name": "Verity Hill", - "author_inst": "Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK" - }, - { - "author_name": "Rachel Colquhoun", - "author_inst": "Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK" - }, - { - "author_name": "Modisa S. Motswaledi", - "author_inst": "Department of Medical Laboratory Sciences, School of Allied Health Professions, Faculty of Health Sciences, University of Botswana,Gaborone, Botswana" - }, - { - "author_name": "James Emmanuel San", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa" - }, - { - "author_name": "Noxolo Ntuli", - "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa" - }, - { - "author_name": "Gerald Motsatsi", - "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa" - }, - { - "author_name": "Sureshnee Pillay", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa" - }, - { - "author_name": "Thabo Mohale", - "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa" - }, - { - "author_name": "Upasana Ramphal", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa" - }, - { - "author_name": "Yeshnee Naidoo", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa" - }, - { - "author_name": "Naume Tebeila", - "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa Department of Veterinary Tropic" - }, - { - "author_name": "Marta Giovanetti", - "author_inst": "FioCruz Foundation" - }, - { - "author_name": "Koleka Mlisana", - "author_inst": "National Health Laboratory Service (NHLS), Johannesburg, South Africa Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa" - }, - { - "author_name": "Carolyn Williamson", - "author_inst": "Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa; National Health Laboratory Service (NHLS),South Africa" - }, - { - "author_name": "Nei-yuan Hsiao", - "author_inst": "Division of Medical Virology, Faculty of Health Sciences, University of Cape Town and National Health Laboratory Service, Cape Town, South Africa National Healt" - }, - { - "author_name": "Nokukhanya Msomi", - "author_inst": "National Health Laboratory Service (NHLS), Johannesburg, South Africa Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa" - }, - { - "author_name": "Kamela Mahlakwane", - "author_inst": "National Health Laboratory Service (NHLS), Johannesburg, South Africa Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa" - }, - { - "author_name": "Susan Engelbrecht", - "author_inst": "Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa;" - }, - { - "author_name": "Tongai Maponga", - "author_inst": "Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa;" - }, - { - "author_name": "Wolfgang Preiser", - "author_inst": "Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa; National Health Laboratory S" - }, - { - "author_name": "Zinhle Makatini", - "author_inst": "National Health Laboratory Service (NHLS), Johannesburg, South Africa National Health Laboratory Service (NHLS), Johannesburg, South Africa" - }, - { - "author_name": "Oluwakemi Laguda-Akingba", - "author_inst": "National Health Laboratory Service (NHLS), Johannesburg, South Africa Faculty of Health Sciences, Walter Sisulu University, Eastern Cape, South Africa" - }, - { - "author_name": "Lavanya Singh", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa" - }, - { - "author_name": "Ugochukwu J. Anyaneji", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa" - }, - { - "author_name": "Monika Moir", - "author_inst": "Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University; Stellenbosch, South Africa" - }, - { - "author_name": "Stephanie van Wyk", - "author_inst": "Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University; Stellenbosch, South Africa" - }, - { - "author_name": "Derek Tshiabuila", - "author_inst": "Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University; Stellenbosch, South Africa" - }, - { - "author_name": "Yajna Ramphal", - "author_inst": "Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University; Stellenbosch, South Africa" - }, - { - "author_name": "Arisha Maharaj", - "author_inst": "Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University; Stellenbosch, South Africa" - }, - { - "author_name": "Sergei Pond", - "author_inst": "Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Pennsylvania, USA" - }, - { - "author_name": "Alexander G Lucaci", - "author_inst": "Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Pennsylvania, USA" - }, - { - "author_name": "Steven Weaver", - "author_inst": "Institute for Genomics and Evolutionary Medicine, Department of Biology, Temple University, Pennsylvania, USA" - }, - { - "author_name": "Maciej F Boni", - "author_inst": "Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA, USA" - }, - { - "author_name": "Koen Deforche", - "author_inst": "Emweb bv, Herent, Belgium" - }, - { - "author_name": "Kathleen Subramoney", - "author_inst": "National Health Laboratory Service (NHLS), Johannesburg, South Africa" - }, - { - "author_name": "Diana Hardie", - "author_inst": "Division of Medical Virology, Faculty of Health Sciences, University of Cape Town and National Health Laboratory Service, Cape Town, South Africa" - }, - { - "author_name": "Gert Marais", - "author_inst": "Division of Medical Virology, Faculty of Health Sciences, University of Cape Town and National Health Laboratory Service, Cape Town, South Africa" - }, - { - "author_name": "Deelan Doolabh", - "author_inst": "Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Rageema Joseph", - "author_inst": "Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Nokuzola Mbhele", - "author_inst": "Division of Medical Virology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa" - }, - { - "author_name": "Luicer Olubayo", - "author_inst": "Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa) Division of Computational Biology, Faculty of Health Sciences, Unversity of Cape Town" - }, - { - "author_name": "Arash Iranzadeh", - "author_inst": "Division of Computational Biology, Faculty of Health Sciences, Unversity of Cape Town" - }, - { - "author_name": "Alexander E Zarebski", - "author_inst": "Department of Zoology, University of Oxford, Mansfield Road, Oxford, Oxford OX1 3SZ, UK" - }, - { - "author_name": "Joseph Tsui", - "author_inst": "Department of Zoology, University of Oxford, Mansfield Road, Oxford, Oxford OX1 3SZ, UK" - }, - { - "author_name": "Moritz UG Kraemer", - "author_inst": "Department of Zoology, University of Oxford, Mansfield Road, Oxford, Oxford OX1 3SZ, UK" - }, - { - "author_name": "Oliver G Pybus", - "author_inst": "Department of Zoology, University of Oxford, Mansfield Road, Oxford, Oxford OX1 3SZ, UK" - }, - { - "author_name": "Dominique Goedhals", - "author_inst": "PathCare Vermaak, Pretoria, South Africa Division of Virology, University of the Free State, Bloemfontein, South Africa" - }, - { - "author_name": "Phillip Armand Bester", - "author_inst": "Division of Virology, National Health Laboratory Service, Bloemfontein, South Africa Division of Virology, University of the Free State, Bloemfontein, South Afr" - }, - { - "author_name": "Martin M Nyaga", - "author_inst": "Next Generation Sequencing Unit, University of the Free State, Bloemfontein, South Africa Division of Virology, University of the Free State, Bloemfontein, Sout" - }, - { - "author_name": "Peter N Mwangi", - "author_inst": "Next Generation Sequencing Unit, University of the Free State, Bloemfontein, South Africa Division of Virology, University of the Free State, Bloemfontein, Sout" - }, - { - "author_name": "Allison Glass", - "author_inst": "Lancet Laboratories, Johannesburg, South Africa; School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa" - }, - { - "author_name": "Florette Treurnicht", - "author_inst": "National Health Laboratory Service (NHLS), Johannesburg, South Africa" - }, - { - "author_name": "Marietjie Venter", - "author_inst": "Zoonotic arbo and Respiratory virus research programme, Department Medical Virology, University of Pretoria;" - }, - { - "author_name": "Jinal N. Bhiman", - "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa Faculty of Health Sciences, Uni" - }, - { - "author_name": "Anne von Gottberg", - "author_inst": "National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa Faculty of Health Sciences, Uni" - }, - { - "author_name": "Tulio de Oliveira", - "author_inst": "University of KwaZulu-Natal" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.20.21267966", "rel_title": "Vaccine effectiveness against SARS-CoV-2 infection with the Omicron or Delta variants following a two-dose or booster BNT162b2 or mRNA-1273 vaccination series: A Danish cohort study", @@ -497084,6 +497874,45 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2021.12.17.473260", + "rel_title": "A Computational Dissection of Spike protein of SARS-CoV-2 Omicron Variant", + "rel_date": "2021-12-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.17.473260", + "rel_abs": "The emergence of SARS-CoV-2 omicron variant in late November, 2021 and its rapid spread to different countries, warns the health authorities to take initiative to work on containing its spread. The omicron SARS-CoV-2 variant is unusual from the other variants of concerns reported earlier as it harbors many novel mutations in its genome particularly with >30 mutations in the spike glycoprotein alone. The current study investigated the variation in binding mechanism which it carries compared to the wild type. The study also explored the interaction profile of spike-omicron with human ACE2 receptor. The structure of omicron spike glycoprotein was determined though homology modeling. The interaction analysis was performed through docking using HADDOCK followed by binding affinity calculation. Finally, the comparison of interactions were performed among spike-ACE2 complex of wild type, delta and omicron variants. The interaction analysis has revealed the involvement of highly charged and polar residues (H505, Arg498, Ser446, Arg493, and Tyr501) in the interactions. The important novel interactions in the spike-ACE2-omicron complex was observed as S494:H34, S496:D38, R498:Y41, Y501:K353, and H505:R393 and R493:D38. Moreover, the binding affinity of spike-ACE2-omicron complex (-17.6Kcal/mol) is much higher than wild type-ACE2 (-13.2Kcal/mol) and delta-ACE2 complex (-13.3Kcal/mol). These results indicate that the involvement of polar and charged residues in the interactions with ACE2 may have an impact on increased transmissibility of omicron variant.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Zaira Rehman", + "author_inst": "National Institute of Health (Pakistan)" + }, + { + "author_name": "Massab Umair", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Aamer Ikram", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Muhammad Salman", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Syed Adnan Haider", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Muhmmad Ammar", + "author_inst": "National Institute of Health" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.12.17.473265", "rel_title": "Evidence for a Potential Pre-Pandemic SARS-like Coronavirus Among Animals in North America", @@ -497572,33 +498401,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.18.21268026", - "rel_title": "Measurement of the extent of Anxiety and Depression that has occurred in college students due to the COVID 19 pandemic: An Survey based cross-sectional study.", - "rel_date": "2021-12-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.18.21268026", - "rel_abs": "OVERVIEWThe ongoing Pandemic because of the Coronavirus disease 2019 (COVID-19) has caused all the educational institutes including colleges to be closed for a very long time. As a result the students are compelled to remain in their homes for this time. Prolonged stay at home along with excess use of social media and other modes to \"kill\" the time are quite famous to cause certain health issues in a person, specially the teenagers and adolescents. Mental wellbegin, being a dimension of health as per WHO should not be ignored at all specially in these situations.\n\nMETHOD OF STUDYAn Online Questionnaire is prepared based of the ZUNG Self Rating Anxiety and Self Rating Depression Scale (Pre-validated Scales). The Form is circulated digitally among the people and then we have collected the data in excel. Based on the result we have prepared our statistical chart.\n\nRESULTQuite a significant number of candidates were suffering due to the pandemic situation. 17.091% were suffering from mild to moderate anxiety, 1.785% had marked to severe anxiety levels(Constituting approximately 18.9% of the total). On the other hand, 8.673% of the students had mild depression, while 1 candidate (0.255%) had moderate depression and 1 (0.255%) had severe depression, (Constituting approximately 9.20% of the total). We found that candidates in the age group of 23-24 years had the maximum prevalence of depression, it was followed by candidates with age between 21-22 years. We found that the candidates with age between 23 to 24 years were having highest prevalence of significant anxiety levels which is closely followed by candidates having age which lies between 22 years to 23 years.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Shubham Goswami", - "author_inst": "Bankura Sammilani Medical College and Hospital" - }, - { - "author_name": "Soujanya Chakraborty", - "author_inst": "Bankura Sammilani Medical College and Hospital" - }, - { - "author_name": "Aritra Chakraborty", - "author_inst": "Bankura Sammilani Medical College and Hospital" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.12.17.21267987", "rel_title": "Carbon dioxide, COVID-19 and the importance of restaurant ventilation: a case study from Spain approaching Christmas 2021", @@ -498618,6 +499420,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2021.12.16.21267914", + "rel_title": "The impact of shielding during the COVID-19 pandemic on mental health: Evidence from the English Longitudinal Study of Ageing", + "rel_date": "2021-12-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.16.21267914", + "rel_abs": "BackgroundDuring the COVID-19 pandemic, older and clinically vulnerable people were instructed to shield or stay at home to save lives. Policies restricting social contact and human interaction pose a risk to mental health, but we know very little about the impact of shielding and stay at home orders on the mental health of older people.\n\nAimsUnderstand the extent to which shielding contributes to poorer mental health.\n\nMethodExploiting longitudinal data from Wave 9 (2018/19) and two COVID-19 sub-studies (June/July 2020; November/December 2020) of the English Longitudinal Study of Ageing we use logistic and linear regression models to investigate associations between patterns of shielding during the pandemic and mental health, controlling for socio-demographic characteristics, pre-pandemic physical and mental health, and social isolation measures.\n\nResultsBy December 2020, 70% of older people were still shielding or staying at home, with 5% shielding throughout the first 9 months of the pandemic. Respondents who shielded experienced worse mental health. Although prior characteristics and lack of social interactions explain some of this association, even controlling for all covariates, those shielding throughout had higher odds of reporting elevated depressive symptoms (OR=1.87, 95%CI=1.22;2.87) and reported lower quality of life (B=-1.28, 95%CI=-2.04;-0.52) than those who neither shielded nor stayed at home. Shielding was also associated with increased anxiety.\n\nConclusionsShielding itself seems associated with worse mental health among older people, highlighting the need for policymakers to address the mental health needs of those who shielded, both in emerging from the current pandemic and for the future.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Giorgio Di Gessa", + "author_inst": "University College London" + }, + { + "author_name": "Debora Price", + "author_inst": "University of Manchester" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.12.17.21267941", "rel_title": "Predictors of uncertainty and unwillingness to receive the COVID-19 booster vaccine in a sample of 22,139 fully vaccinated adults in the UK", @@ -499534,93 +500359,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2021.12.16.21267932", - "rel_title": "A Single Dose of COVID-19 mRNA Vaccine Induces Airway Immunity in COVID-19 Convalescent Patients", - "rel_date": "2021-12-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.16.21267932", - "rel_abs": "BackgroundMucosal antibodies can prevent virus entry and replication in mucosal epithelial cells and hence virus shedding. Preclinical and clinical studies have shown that a parenteral booster injection of a vaccine against a mucosal pathogen promotes stronger mucosal immune responses following prior infection compared to two injections of a parenteral vaccine. We investigated whether this was also the case for a COVID-19 mRNA vaccine.\n\nMethodsTwenty-three COVID-19 convalescent patients and 20 SARS-CoV-2-naive subjects were vaccinated with respectively one and two doses of the Pfizer-BioNTech COVID-19 RNA vaccine. Nasal Epithelial Lining Fluid (NELF) and plasma were collected before and after vaccination and assessed for Immunoglobulin (Ig)G and IgA to Spike and for their ability to inhibit the binding of Spike to its ACE-2 receptor. Blood was analyzed one week after vaccination for the number of Spike-specific Antibody Secreting Cells (ASCs) with a mucosal tropism.\n\nResultsIn COVID-19 convalescent patients, a single dose of vaccine amplified pre-existing Spike-specific IgG and IgA antibody responses in both NELF and blood against both vaccine homologous and variant strains, including delta. These responses were associated with Spike-specific IgG and IgA ASCs with a mucosal tropism in blood. Nasal IgA and IgG antibody responses were lower in magnitude in SARS-CoV-2-naive subjects after two vaccine doses\n\nConclusionThis study showed that a parenteral booster injection of a COVID-19 RNA vaccine promoted stronger mucosal immune responses in COVID-19 convalescent patients compared to SARS-CoV-2 naive subjects who had received a first vaccine dose.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Charles Hugo MARQUETTE", - "author_inst": "Universite Cote d'azur" - }, - { - "author_name": "Emanuela MARTINUZZI", - "author_inst": "Universite Cote d'Azur, CNRS, Institut de Pharmacologie Moleculaire et Cellulaire, Valbonne, France" - }, - { - "author_name": "Jonathan BENZAQUEN", - "author_inst": "Universite Cote d'Azur, Centre Hospitalier Universitaire de Nice, Department of Pulmonary Medicine, CNRS, INSERM, Institute of Research on Cancer and Aging, Nic" - }, - { - "author_name": "Olivier GUERIN", - "author_inst": "Universite Cote d'Azur, Centre Hospitalier Universitaire de Nice. Pole rehabilitation autonomie viellissement, Nice, France" - }, - { - "author_name": "Sylvie LEROY", - "author_inst": "Universite Cote d'Azur, Centre Hospitalier Universitaire de Nice, Department of Pulmonary Medicine, CNRS, Institut de Pharmacologie Moleculaire et Cellulaire, N" - }, - { - "author_name": "Thomas SIMON", - "author_inst": "Universite Cote d'Azur, CNRS, Institut de Pharmacologie Moleculaire et Cellulaire, Valbonne, France" - }, - { - "author_name": "Marius ILIE", - "author_inst": "Universite Cote d'Azur, CNRS, INSERM, Institute of Research on Cancer and Aging, Centre Hospitalier Universitaire de Nice, Laboratory of Clinical and Experiment" - }, - { - "author_name": "Veronique HOFMAN", - "author_inst": "Universite Cote d'Azur, CNRS, INSERM, Institute of Research on Cancer and Aging, Centre Hospitalier Universitaire de Nice, Laboratory of Clinical and Experiment" - }, - { - "author_name": "Maryline ALLEGRA", - "author_inst": "Universite Cote d'Azur, Centre Hospitalier Universitaire de Nice, Laboratory of Clinical and Experimental Pathology, Biobank (BB-0033-00025), FHU OncoAge, Centr" - }, - { - "author_name": "Virginie TANGA", - "author_inst": "Universite Cote d'Azur, Centre Hospitalier Universitaire de Nice, Laboratory of Clinical and Experimental Pathology, Biobank (BB-0033-00025), FHU OncoAge, Centr" - }, - { - "author_name": "Emeline MICHEL", - "author_inst": "Universite Cote d'Azur, Centre Hospitalier Universitaire de Nice. Pole rehabilitation autonomie viellissement, Nice, France" - }, - { - "author_name": "Jacques BOUTROS", - "author_inst": "Universite Cote d'Azur, Centre Hospitalier Universitaire de Nice, Department of Pulmonary Medicine, FHU OncoAge, Nice, France" - }, - { - "author_name": "Charlotte MANIEL", - "author_inst": "Universite Cote d'Azur, Centre Hospitalier Universitaire de Nice, Department of Pulmonary Medicine, FHU OncoAge, Nice, France" - }, - { - "author_name": "Antoine SICARD", - "author_inst": "Universite Cote d'Azur, Centre Hospitalier Universitaire de Nice, Clinical Research Unit, Nice, France" - }, - { - "author_name": "Nicolas GLAICHENHAUS", - "author_inst": "Universite Cote d'Azur, CNRS, Institut de Pharmacologie Moleculaire et Cellulaire, Valbonne, France" - }, - { - "author_name": "Cecil CZERKINSKY", - "author_inst": "Universite Cote d'Azur, CNRS, Institut de Pharmacologie Moleculaire et Cellulaire, Valbonne, France" - }, - { - "author_name": "Philippe BLANCOU", - "author_inst": "Universite Cote d'Azur, CNRS, Institut de Pharmacologie Moleculaire et Cellulaire, Valbonne, France" - }, - { - "author_name": "Paul HOFMAN", - "author_inst": "Universite Cote d'Azur, CNRS, INSERM, Institute of Research on Cancer and Aging, Centre Hospitalier Universitaire de Nice, Laboratory of Clinical and Experiment" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.17.21267925", "rel_title": "SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2", @@ -500832,6 +501570,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.12.15.21267849", + "rel_title": "Neurodevelopmental outcomes at one year in offspring of mothers who test positive for SARS-CoV-2 during pregnancy", + "rel_date": "2021-12-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.15.21267849", + "rel_abs": "ImportanceEpidemiologic studies suggest maternal immune activation during pregnancy may be associated with neurodevelopmental effects in offspring.\n\nObjectiveTo determine whether in utero exposure to the novel coronavirus SARS-CoV-2 is associated with risk for neurodevelopmental disorders in the first 12 months after birth.\n\nDesignRetrospective cohort\n\nParticipantsLive offspring of all mothers who delivered between March and September 2020 at one of six Massachusetts hospitals across two health systems.\n\nExposureSARS-CoV-2 infection confirmed by PCR during pregnancy\n\nMain Outcome and MeasuresNeurodevelopmental disorders determined from ICD-10 diagnostic codes over 12 months; sociodemographic and clinical features of mothers and offspring; all drawn from the electronic health record.\n\nResultsThe cohort included 7,772 live births (7,466 pregnancies, 96% singleton, 222 births to SARS-CoV-2 positive mothers), with mean maternal age of 32.9 years; offspring were 9.9% Asian, 8.4% Black, and 69.0% white; 15.1% were of Hispanic ethnicity. Preterm delivery was more likely among exposed mothers (14% versus 8.7%; p=.003). Maternal SARS-CoV-2 positivity during pregnancy was associated with greater rate of neurodevelopmental diagnoses (crude OR 2.17 [95% CI 1.24-3.79, p=0.006]) as well as models adjusted for race, ethnicity, insurance status, offspring sex, maternal age, and preterm status (adjusted OR 1.86 [95% CI 1.03-3.36, p=0.04]). Third-trimester infection was associated with effects of larger magnitude (adjusted OR 2.34, 95% CI 1.23-4.44, p=0.01)\n\nConclusion and RelevanceOur results provide preliminary evidence that maternal SARS-CoV-2 may be associated with neurodevelopmental sequelae in some offspring. Prospective studies with longer follow-up duration will be required to exclude confounding and confirm these effects.\n\nTrial RegistrationNA\n\nKey PointsO_ST_ABSQuestionC_ST_ABSDoes COVID-19 exposure in utero increase the risk for neurodevelopmental disorders in the first year of life?\n\nFindingsIn a cohort of babies delivered during COVID-19, those born to mothers with a positive SARS-CoV-2 PCR test during pregnancy were more likely to receive a neurodevelopmental diagnosis in the first 12 months after delivery, even after accounting for preterm delivery.\n\nMeaningThese preliminary findings suggest that COVID-19 exposure may impact neurodevelopment, and highlight the need for prospective investigation of outcomes in children exposed to COVID-19 in utero.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Andrea G. Edlow", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Victor M Castro", + "author_inst": "Mass General Brigham" + }, + { + "author_name": "Lydia Shook", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Anjali J Kaimal", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Roy H Perlis", + "author_inst": "Massachusetts General Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2021.12.14.21267778", "rel_title": "Efficient control of IL-6, CRP and Ferritin in Covid-19 patients with two variants of Beta-1,3-1,6 glucans in combination, within 15 days in an open-label prospective clinical trial", @@ -501284,77 +502057,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.12.16.21267703", - "rel_title": "Evaluation of SARS-CoV-2 Antibody Point of Care Devices in the Laboratory and Clinical Setting", - "rel_date": "2021-12-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.16.21267703", - "rel_abs": "SARS-CoV-2 Antibody tests have been marketed to diagnose previous SARS-CoV-2 infection and as a test of immune status. There is a lack of evidence on the performance and clinical utility of these tests. We aimed to carry out an evaluation of 14 point of care (POC) SARS-CoV-2 antibody tests.\n\nSerum from participants with previous RT-PCR (Real-Time Polymerase chain reaction) confirmed SARS-CoV-2 infection and pre-pandemic controls were used to determine specificity and sensitivity of each POC device. Changes in sensitivity with increasing time from infection were determined on a cohort of participants. Corresponding neutralising antibody status was measured to establish whether the detection of antibodies by the POC device correlated with immune status. Paired capillary and serum samples were collected to ascertain whether POC devices performed comparably on capillary samples.\n\nSensitivity and specificity varied between the POC devices and in general did not meet the manufacturers reported performance characteristics signifying the importance of independent evaluation of these tests. The sensitivity peaked at >20 days following symptoms onset however sensitivity of 3 POC devices evaluated at extended time points showed that sensitivity declined with time and this was particularly marked at >140 days post infection onset. This is relevant if the tests are to be used for sero-prevelence studies. Neutralising antibody data showed positive antibody results on POC devices did not necessarily confer high neutralising antibody titres and these POC devices cannot be used to determine immune status to the SARS-CoV-2 virus. Comparison of paired serum and capillary results showed that there was a decline in sensitivity using capillary blood. This has implications in the utility of the test as they are designed to be used on capillary blood by the general population.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Kirsty McCance", - "author_inst": "NHS Lothian" - }, - { - "author_name": "Helen Wise", - "author_inst": "NHS Lothian" - }, - { - "author_name": "Jennifer Simpson", - "author_inst": "NHS Lothian" - }, - { - "author_name": "Becky Bachelor", - "author_inst": "NHS Lothian" - }, - { - "author_name": "Harriet Hale", - "author_inst": "NHS Lothian" - }, - { - "author_name": "Linday McDonald", - "author_inst": "NHS Lothian" - }, - { - "author_name": "Azul Zorzoli", - "author_inst": "NHS Lothian" - }, - { - "author_name": "Elizabeth Furrie", - "author_inst": "NHS Tayside" - }, - { - "author_name": "Charu Chopra", - "author_inst": "NHS Lothian" - }, - { - "author_name": "Frauke Muecksch", - "author_inst": "Rocherfeller University" - }, - { - "author_name": "Theodora Hatziioannou", - "author_inst": "Rockerfeller University" - }, - { - "author_name": "Paul Bieniasz", - "author_inst": "Rockerfeller University" - }, - { - "author_name": "Kate Templeton", - "author_inst": "NHS Lothian" - }, - { - "author_name": "Sara Jenks", - "author_inst": "NHS Lothian" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2021.12.16.21267785", "rel_title": "Forecasting COVID-19 infection trends in the EU-27 countries, the UK and Switzerland due to SARS-CoV-2 Variant of Concern Omicron", @@ -502965,6 +503667,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.12.14.472547", + "rel_title": "From Deer-to-Deer: SARS-CoV-2 is efficiently transmitted and presents broad tissue tropism and replication sites in white-tailed deer", + "rel_date": "2021-12-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.14.472547", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19) in humans, has a broad host range, and is able to infect domestic and wild animal species. Notably, white-tailed deer (WTD, Odocoileus virginianus), the most widely distributed cervid species in the Americas, were shown to be highly susceptible to SARS-CoV-2 in challenge studies and reported natural infection rates approaching 40% in free-ranging WTD in the U.S. Thus, understanding the infection and transmission dynamics of SARS-CoV-2 in WTD is critical to prevent future zoonotic transmission to humans and for implementation of effective disease control measures. Here, we demonstrated that following intranasal inoculation with SARS-CoV-2, WTD fawns shed infectious virus up to day 5 post-inoculation (pi), with high viral loads shed in nasal and oral secretions. This resulted in efficient deer-to-deer transmission on day 3 pi. Consistent a with lack of infectious SARS-CoV-2 shedding after day 5 pi, no transmission was observed to contact animals added on days 6 and 9 pi. We have also investigated the tropism and sites of SARS-CoV-2 replication in adult WTD. Infectious virus was recovered from respiratory-, lymphoid-, and central nervous system tissues, indicating broad tissue tropism and multiple sites of virus replication. The study provides important insights on the infection and transmission dynamics of SARS-CoV-2 in WTD, a wild animal species that is highly susceptible to infection and with the potential to become a reservoir for the virus in the field.\n\nAuthor summaryThe high susceptibility of white-tailed deer (WTD) to SARS-CoV-2, their ability to transmit the virus to other deer, and the recent findings suggesting widespread SARS-CoV-2 infection in wild WTD populations in the U.S. underscore the need for a better understanding of the infection and transmission dynamics of SARS-CoV-2 in this potential reservoir species. Here we investigated the transmission dynamics of SARS-CoV-2 over time and defined the major sites of virus replication during the acute phase of infection. Additionally, we assessed the evolution of the virus as it replicated and transmitted between animals. The work provides important information on the infection dynamics of SARS-CoV-2 in WTD, an animal species that - if confirmed as a new reservoir of infection - may provide many opportunities for exposure and potential zoonotic transmission of the virus back to humans.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Mathias Martins", + "author_inst": "Cornell University College of Veterinary Medicine" + }, + { + "author_name": "Paola M. Boggiatto", + "author_inst": "USDA Agricultural Research Service" + }, + { + "author_name": "Alexandra Buckley", + "author_inst": "USDA Agricultural Research Service" + }, + { + "author_name": "Eric D. Cassmann", + "author_inst": "USDA Agricultural Research Service" + }, + { + "author_name": "Shollie Falkenberg", + "author_inst": "USDA Agricultural Research Service" + }, + { + "author_name": "Leonardo C. Caserta", + "author_inst": "Cornell University College of Veterinary Medicine" + }, + { + "author_name": "Maureen H.V. Fernandes", + "author_inst": "Cornell University College of Veterinary Medicine" + }, + { + "author_name": "Carly Kanipe", + "author_inst": "USDA Agricultural Research Service" + }, + { + "author_name": "Kelly Lager", + "author_inst": "USDA Agricultural Research Service" + }, + { + "author_name": "Mitchell V. Palmer", + "author_inst": "USDA Agricultural Research Service" + }, + { + "author_name": "Diego G. Diel", + "author_inst": "Cornell University College of Veterinary Medicine" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.12.14.472630", "rel_title": "Considerable escape of SARS-CoV-2 variant Omicron to antibody neutralization", @@ -503569,73 +504330,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.12.14.21267418", - "rel_title": "COVID-19 vaccination and Guillain-Barre syndrome: analyses using the National Immunoglobulin Database", - "rel_date": "2021-12-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.14.21267418", - "rel_abs": "Vaccination against viruses has rarely been associated with Guillain-Barre syndrome (GBS). An association with the COVID-19 vaccine is unknown. We performed a population-based study of National Health Service data in England and a multicentre surveillance study from UK hospitals, to investigate the relationship between COVID-19 vaccination and GBS.\n\nFirstly, case dates of GBS identified retrospectively in the National Immunoglobulin Database from 8 December 2021 to 8 July 2021 were linked to receipt dates of a COVID-19 vaccines using data from the National Immunisation Management System in England. For the linked dataset, GBS cases temporally associated with vaccination within a 6-week risk window of any COVID-19 vaccine were identified. Secondly, we prospectively collected incident UK-wide (four nations) GBS cases from 1 January 2021 to 7 November 2021 in a separate UK multicentre surveillance database. For this multicentre UK-wide surveillance dataset, we explored phenotypes of reported GBS cases to identify features of COVID-19 vaccine-associated GBS.\n\n996 GBS cases were recorded in the National Immunoglobulin Database from January to October 2021. A spike of GBS cases above the 2016-2020 average occurred in March-April 2021. 198 GBS cases occurred within 6 weeks of the first-dose COVID-19 vaccination in England (0.618 cases per 100,000 vaccinations, 176 ChAdOx1 nCoV-19 (AstraZeneca), 21 tozinameran (Pfizer), 1 mRNA-1273 (Moderna)). The 6-week excess of GBS (compared to the baseline rate of GBS cases 6-12 weeks after vaccination) occurs with a peak at 24 days post-vaccination; first-doses of ChAdOx1 nCoV-19 accounted for the excess. No excess was seen for second-dose vaccination. The absolute number of excess GBS cases from January-July 2021 was between 98-140 cases for first-dose ChAdOx1 nCoV-19 vaccination. First-dose tozinameran and second-dose of any vaccination showed no excess GBS risk. Detailed clinical data from 121 GBS patients were reported in the separate multicentre surveillance dataset during this timeframe. No phenotypic or demographic differences identified between vaccine-associated and non-vaccinated GBS cases occurring in the same timeframe.\n\nAnalysis of the linked NID/NIMS dataset suggests that first-dose ChAdOx1 nCoV-19 vaccination is associated with an excess GBS risk of 0.576 (95%CI 0.481-0.691) cases per 100,000 doses. However, examination of a multicentre surveillance dataset suggests that no specific clinical features, including facial weakness, are associated with vaccination-related GBS compared to non-vaccinated cases. The pathogenic cause of the ChAdOx1 nCoV-19 specific first dose link warrants further study.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Ryan Yann Shern Keh", - "author_inst": "National Hospital for Neurology and Neurosurgery" - }, - { - "author_name": "Sophie Scanlon", - "author_inst": "Medicines and Healthcare products Regulatory Agency, UK" - }, - { - "author_name": "Preeti Datta-Nemdharry", - "author_inst": "Medicines and Healthcare products Regulatory Agency, UK" - }, - { - "author_name": "Katherine Donegan", - "author_inst": "Medicines and Healthcare products Regulatory Agency, UK" - }, - { - "author_name": "Sally Cavanagh", - "author_inst": "NHS England & Improvement (NHSEI), National Health Service, UK" - }, - { - "author_name": "Mark Foster", - "author_inst": "Medical Data Solutions and Services (MDSAS) Ltd, data platform provider for the National Immunoglobulin Database" - }, - { - "author_name": "David Skelland", - "author_inst": "NHS Arden and Greater East Midlands (GEM) Commissioning Support Unit (CSU), UK" - }, - { - "author_name": "James Palmer", - "author_inst": "NHS England & Improvement (NHSEI), National Health Service, UK" - }, - { - "author_name": "Pedro Machado", - "author_inst": "MRC Centre for Neuromuscular Diseases, National Hospital of Neurology and Neurosurgery, Queen Square, University College London Hospitals NHS Foundation Trust, " - }, - { - "author_name": "Stephen Keddie", - "author_inst": "University College London" - }, - { - "author_name": "Aisling Carr", - "author_inst": "MRC Centre for Neuromuscular Diseases, National Hospital of Neurology and Neurosurgery, Queen Square, University College London Hospitals NHS Foundation Trust, " - }, - { - "author_name": "Michael Lunn", - "author_inst": "MRC Centre for Neuromuscular Diseases, National Hospital of Neurology and Neurosurgery, Queen Square, University College London Hospitals NHS Foundation Trust, " - }, - { - "author_name": "- BPNS/ABN COVID-19 Vaccine GBS Study Group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2021.12.14.21267773", "rel_title": "COVID-19 vaccine hesitancy in diverse groups in the UK - is the driver economic or cultural in student populations?", @@ -505331,6 +506025,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.13.21267509", + "rel_title": "Microarray-based detection of antibodies against SARS-CoV-2 proteins, common respiratory viruses and type I interferons", + "rel_date": "2021-12-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.13.21267509", + "rel_abs": "A microarray-based assay to detect IgG and IgM antibodies against betacoronaviruses (SARS-CoV-2, SARS, MERS, OC43, and HKU1), other respiratory viruses and type I interferons (IFN-Is) was developed. This multiplex assay was applied to track antibody cross-reactivity due to previous contact with similar viruses and to identify antibodies against IFN-Is as the markers for severe COVID-19. In total, 278 serum samples from convalescent plasma donors, COVID-19 patients in the intensive care unit (ICU) and patients who recovered from mild/moderate COVID-19, vaccine recipients, prepandemic and pandemic patients with autoimmune endocrine disorders, and a heterogeneous prepandemic cohort including healthy individuals and chronically ill patients were analyzed. The anti-SARS-CoV-2 microarray results agreed well with the ELISA results. Regarding ICU patients, autoantibodies against IFN-Is were detected in 10.5% of samples, and 10.5% of samples were found to simultaneously contain IgM antibodies against more than two different viruses. Cross-reactivity between IgG against the SARS-CoV-2 nucleocapsid and IgG against the OC43 and HKU1 spike proteins was observed, resulting in positive signals for the SARS-CoV-2 nucleocapsid in prepandemic samples from patients with autoimmune endocrine disorders. The presence of IgG against the SARS-CoV-2 nucleocapsid in the absence of IgG against the SARS-CoV-2 spike RBD should be interpreted with caution.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Elena Savvateeva", + "author_inst": "Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Ru" + }, + { + "author_name": "Marina Filippova", + "author_inst": "Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Ru" + }, + { + "author_name": "Vladimir Valuev-Elliston", + "author_inst": "Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Ru" + }, + { + "author_name": "Nurana Nuralieva", + "author_inst": "Endocrinology Research Centre, Ministry of Health of Russia, Moscow, Russia" + }, + { + "author_name": "Marina Yukina", + "author_inst": "Endocrinology Research Centre, Ministry of Health of Russia, Moscow, Russia" + }, + { + "author_name": "Ekaterina Troshina", + "author_inst": "Endocrinology Research Centre, Ministry of Health of Russia, Moscow, Russia" + }, + { + "author_name": "Vladimir Baklaushev", + "author_inst": "Federal Scientific and Clinical Center of Specialized Types of Medical Care and Medical Technologies of the Federal Medical and Biological Agency of Russia, Mos" + }, + { + "author_name": "Alexander Ivanov", + "author_inst": "Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Ru" + }, + { + "author_name": "Dmitry Gryadunov", + "author_inst": "Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Ru" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.09.21267566", "rel_title": "Oral antiviral clevudine compared with placebo in Korean COVID-19 patients with moderate severity", @@ -505651,57 +506396,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.12.10.21267582", - "rel_title": "Echinacea purpurea for the Long-term Prevention of Viral Respiratory Tract Infections during COVID-19 Pandemic: A Randomized, Open, Controlled, Exploratory Clinical Study", - "rel_date": "2021-12-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.10.21267582", - "rel_abs": "IntroductionSARS-CoV-2 vaccination is effective in preventing severe COVID-19, but efficacy in reducing viral load and transmission wanes over time. In addition, the emergence of novel SARS-CoV-2 variants increases the threat of uncontrolled dissemination and additional antiviral therapies are urgently needed for effective containment. In previous in vitro studies Echinacea purpurea demonstrated strong antiviral activity against enveloped viruses, including SARS-CoV-2. In this study, we examined the potential of Echinacea purpurea in preventing and treating respiratory tract infections (RTIs) and in particular, SARS-CoV-2 infections.\n\nMethods120 healthy volunteers (m,f, 18 - 75 years) were randomly assigned to Echinacea prevention or control group without any intervention. After a run-in week, participants went through 3 prevention cycles of 2, 2 and 1 months with daily 2400mg Echinacea purpurea extract (Echinaforce(R), EF). The prevention cycles were interrupted by breaks of 1 week. Acute respiratory symptoms were treated with 4000 mg EF for up to 10 days, and their severity assessed via a diary. Naso/oropharyngeal swabs and venous blood samples were routinely collected every month and during acute illnesses for detection and identification of respiratory viruses, including SARS-CoV-2 via RT-qPCR and serology.\n\nResultsSummarized over all phases of prevention, 21 and 29 samples tested positive for any virus in the EF and control group, of which 5 and 14 samples tested SARS-CoV-2 positive (RR=0.37, Chi-square test, p=0.03). Overall, 10 and 14 symptomatic episodes occurred, of which 5 and 8 were COVID-19 (RR=0.70, Chi-square test, p>0.05). EF treatment when applied during acute episodes significantly reduced the overall virus load by at least 2.12 log10 or approx. 99% (t-test, p<0.05), the time to virus clearance by 8.0 days for all viruses (Wilcoxon test, p=0.02) and by 4.8 days for SARS-CoV-2 (p>0.05) in comparison to control. Finally, EF treatment significantly reduced fever days (1 day vs 11 days, Chi-square test, p=0.003) but not the overall symptom severity. There were fewer COVID-19 related hospitalizations in the EF treatment group (N=0 vs N=2).\n\nDiscussion/ConclusionEF exhibited antiviral effects and reduced the risk of viral RTIs, including SARS-CoV-2. By substantially reducing virus loads in infected subjects, EF offers a supportive addition to existing mandated treatments like vaccinations. Future confirmatory studies are warranted.\n\nClinical Trials registration NrNCT05002179", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Emil Kolev", - "author_inst": "Clinical Research Center DCC Convex Ltd" - }, - { - "author_name": "Lilyana Mircheva", - "author_inst": "Convex ltd" - }, - { - "author_name": "Michael Edwards", - "author_inst": "National Heart Lung Institute, Imperial College London St Marys Campus" - }, - { - "author_name": "Sebastian L Johnston", - "author_inst": "Imperial College London" - }, - { - "author_name": "Krassimir Kalinov", - "author_inst": "Medistat Ltd. Statistical Services" - }, - { - "author_name": "Rainer Stange", - "author_inst": "Charite Universitaetsmedizin Berlin, Immanuel Hospital Berlin" - }, - { - "author_name": "Giuseppe Gancitano", - "author_inst": "1st \"Tuscania\" Paratrooper Regiment Carabinieri, Italian Ministry of Defence" - }, - { - "author_name": "Wim Vanden Berghe", - "author_inst": "Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES) and Integrated Personalized and Precision Oncology Network (IPPON), Department of " - }, - { - "author_name": "Samo Kreft", - "author_inst": "Faculty of Pharmacy, University of Ljubljana" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.13.21267698", "rel_title": "Development and external validation of the DOAT and DOATS scores: simple decision support tools to identify disease progression among nonelderly patients with mild/moderate COVID-19", @@ -507217,6 +507911,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.12.13.21267718", + "rel_title": "Mental Health During COVID-19: A Qualitative Study with Ethnically Diverse Healthcare Workers in the United Kingdom", + "rel_date": "2021-12-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.13.21267718", + "rel_abs": "IntroductionHealthcare workers are experiencing deterioration in their mental health due to COVID-19. Ethnic minority populations in the United Kingdom are disproportionately affected by COVID-19, with a higher death rate and poorer physical and mental health outcomes. It is important that healthcare organisations consider the specific context and mental, as well as physical, health needs of an ethnically diverse healthcare workforce in order to better support them during, and after, the COVID-19 pandemic.\n\nMethodsWe undertook a qualitative work package as part of the United Kingdom Research study into Ethnicity and COVID-19 outcomes among healthcare workers (UK-REACH). As part of the qualitative research, we conducted focus group discussions with healthcare workers between December 2020 and July 2021, and covered topics such as their experiences, fears and concerns, and perceptions about safety and protection, while working during the pandemic. The purposive sample included ancillary health workers, doctors, nurses, midwives and allied health professionals from diverse ethnic backgrounds. We conducted discussions using Microsoft Teams. Recordings were transcribed and thematically analysed.\n\nFindingsWe carried out 16 focus groups with a total of 61 participants. Several factors were identified which contributed to, and potentially exacerbated, the poor mental health of ethnic minority healthcare workers during this period including anxiety (due to inconsistent protocols and policy); fear (of infection); trauma (due to increased exposure to severe illness and death); guilt (of potentially infecting loved ones); and stress (due to longer working hours and increased workload).\n\nConclusionCOVID-19 has affected the mental health of healthcare workers. We identified a number of factors which may be contributing to a deterioration in mental health across diverse ethnic groups. Healthcare organisations should consider developing strategies to counter the negative impact of these factors. This paper will help employers of healthcare workers and other relevant policy makers better understand the wider implications and potential risks of COVID-19 and assist in developing strategies to safeguard the mental health of these healthcare workers going forward, and reduce ethnic disparities.\n\nKey messagesO_ST_ABSWhat is already known about this subjectC_ST_ABSO_LIHealthcare Workers (HCWs) are experiencing deterioration of their mental health due to COVID-19\nC_LIO_LIEthnic minority populations and HCWs are disproportionately affected by COVID-19\nC_LIO_LIMore research is needed on the specific factors influencing the mental health of ethnically diverse healthcare workforces\nC_LI\n\nWhat are the new findingsProminent factors influencing the mental health and emotional wellbeing of this population include:\n\nO_LIanxiety (due to inconsistent protocols and policy)\nC_LIO_LIfear (of infection)\nC_LIO_LItrauma (due to increased exposure to severe illness and death)\nC_LIO_LIguilt (of potentially infecting loved ones)\nC_LIO_LIstress (due to longer working hours and increased workload)\nC_LI\n\nHow might this impact on policy or clinical practice in the foreseeable futureO_LIHealthcare organisations should consider the specific circumstances of these staff and develop strategies to counter the negative impact of these factors and help safeguard the mental health of their staff\nC_LI", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Irtiza Qureshi", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Mayuri Gogoi", + "author_inst": "University of Leicester" + }, + { + "author_name": "Amani Al-Oraibi", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Fatimah Wobi", + "author_inst": "University of Leicester" + }, + { + "author_name": "Jonathan Chaloner", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Laura Gray", + "author_inst": "University of Leicester" + }, + { + "author_name": "Anna Louise Guyatt", + "author_inst": "University of Leicester" + }, + { + "author_name": "Laura Nellums", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Manish Pareek", + "author_inst": "University of Leicester" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2021.12.13.21267717", "rel_title": "Comparative efficacy of tocilizumab and baricitinib in COVID-19 treatment: a retrospective cohort study", @@ -507837,45 +508582,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.12.13.21267761", - "rel_title": "SARS-CoV-2 Omicron variant escapes neutralization by vaccinated and convalescent sera and therapeutic monoclonal antibodies", - "rel_date": "2021-12-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.13.21267761", - "rel_abs": "The novel SARS-CoV-2 variant, Omicron (B.1.1.529) contains about 30 mutations in the spike protein and the numerous mutations raise the concern of escape from vaccine, convalescent sera and therapeutic drugs. Here we analyze the alteration of their neutralizing titer with Omicron pseudovirus. Sera of 3 months after double BNT162b2 vaccination exhibite [~]27-fold lower neutralization titers against Omicron than D614G mutation. Neutralization titer is also reduced in convalescent sera from Alpha and Delta patients. However, some Delta patients have relatively preserved neutralization activity up to the level of 3-month double BNT162b2 vaccination. Omicron escapes from the cocktail of imdevimab and casirivimab, whereas sotrovimab that targets the conserved region to prevent viral escape is effective to Omicron similarly to the original SARS-CoV-2. The ACE2 decoy is another modality that neutralize the virus independently of mutational escape and Omicron is also sensitive to the engineered ACE2.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Nariko Ikemura", - "author_inst": "Kyoto Prefectural University of Medicine" - }, - { - "author_name": "Atsushi Hoshino", - "author_inst": "Kyoto Prefectural University of Medicine" - }, - { - "author_name": "Yusuke Higuchi", - "author_inst": "Kyoto Prefectural University of Medicine" - }, - { - "author_name": "Shunta Taminishi", - "author_inst": "Kyoto Prefectural University of Medicine" - }, - { - "author_name": "Tohru Inaba", - "author_inst": "Kyoto Prefectural University of Medicine" - }, - { - "author_name": "Satoaki Matoba", - "author_inst": "Kyoto Prefectural University of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.13.21267748", "rel_title": "Analysis: A meta-analysis of Early Results to predict Vaccine efficacy against Omicron", @@ -508971,6 +509677,41 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2021.12.10.472102", + "rel_title": "Mutations in RBD of SARS-CoV-2 Omicron variant result stronger binding to human ACE2 protein", + "rel_date": "2021-12-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.10.472102", + "rel_abs": "The COVID-19 pandemic caused by the SARS-CoV-2 virus has led to more than 270 million infections and 5.3 million of deaths worldwide. Several major variants of SARS-CoV-2 have emerged and posed challenges in controlling the pandemic. The recently occurred Omicron variant raised serious concerns about reducing the efficacy of vaccines and neutralization antibodies due to its vast mutations. We have modelled the complex structure of the human ACE2 protein and the receptor binding domain (RBD) of Omicron Spike protein (S-protein), and conducted atomistic molecular dynamics simulations to study the binding interactions. The analysis shows that the Omicron RBD binds more strongly to the human ACE2 protein than the original strain. The mutations at the ACE2-RBD interface enhance the tight binding by increasing hydrogen bonding interaction and enlarging buried solvent accessible surface area.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Cecylia Severin Lupala", + "author_inst": "Beijing Computational Science Research Center" + }, + { + "author_name": "Yongjin Ye", + "author_inst": "Beijing Computational Science Research Center" + }, + { + "author_name": "Hong Chen", + "author_inst": "Peking University" + }, + { + "author_name": "Xiaodong Su", + "author_inst": "Peking University" + }, + { + "author_name": "Haiguang Liu", + "author_inst": "Beijing Computational Science Research Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.12.10.472134", "rel_title": "SARS-CoV2 variant-specific replicating RNA vaccines protect from disease and pathology and reduce viral shedding following challenge with heterologous SARS-CoV2 variants of concern", @@ -509491,49 +510232,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.12.09.471735", - "rel_title": "The T cell receptor repertoire reflects the dynamics of the immune response to vaccination", - "rel_date": "2021-12-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.09.471735", - "rel_abs": "Early, high-resolution metrics are needed to ascertain the immune response to vaccinations. The T cell receptor (TCR), a heterodimer of one and one {beta} chain, is a promising target, with the complete TCR repertoire reflecting the T cells present in an individual. To this end, we developed Tseek, an unbiased and accurate method for profiling the TCR repertoire by sequencing the TCR and {beta} chains and developing a suite of tools for repertoire analysis. An added advantage is the ability to non-invasively analyze T cells in peripheral blood mononuclear cells (PBMCs). Tseek and the analytical suite were used to explore the T cell response to both the COVID-19 mRNA vaccine (n=9) and the seasonal inactivated Influenza vaccine (n=5) at several time points. Neutralizing antibody titers were also measured in the covid vaccine samples. The COVID-19 vaccine elicited a broad T cell response involving multiple expanded clones, whereas the Influenza vaccine elicited a narrower response involving fewer clones. Many distinct T cell clones responded at each time point, over a month, providing temporal details lacking in the antibody measurements, especially before the antibodies are detectable. In individuals recovered from a SARS-CoV-2 infection, the first vaccine dose elicited a robust T cell response, while the second dose elicited a comparatively weaker response, indicating a saturation of the response. The physical symptoms experienced by the recipients immediately following the vaccinations were not indicative of the TCR/antibody responses. The TCR responses broadly presaged the antibody responses. We also found that the TCR repertoire acts as an individual fingerprint: donors of blood samples taken years apart could be identified solely based upon their TCR repertoire, hinting at other surprising uses the TCR repertoire may have. These results demonstrate the promise of TCR repertoire sequencing as an early and sensitive measure of the adaptive immune response to vaccination, which can help improve immunogen selection and optimize vaccine dosage and spacing between doses.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Kevin Mohammed", - "author_inst": "Icahn School of Medicine at Mount Sinai, NY 10029" - }, - { - "author_name": "Austin Meadows", - "author_inst": "Girihlet Inc., 355 30th St., Oakland, CA 94609" - }, - { - "author_name": "Sandra Hatem", - "author_inst": "Icahn School of Medicine at Mount Sinai, NY 10029" - }, - { - "author_name": "Saboor Hekmaty", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Viviana Simon", - "author_inst": "Icahn School of Medicine at Mount Sinai, NY 10029" - }, - { - "author_name": "Anitha D Jayaprakash", - "author_inst": "Girihlet Inc., 355 30th St, Oakland, CA 94609" - }, - { - "author_name": "Ravi Sachidanandam", - "author_inst": "Icahn School of Medicine at Mount Sinai" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.12.10.21267590", "rel_title": "Real-life protection provided by vaccination, booster doses and previous infection against covid-19 infection, hospitalisation or death over time in the Czech Republic: a whole country retrospective view", @@ -510961,6 +511659,193 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.12.09.21267548", + "rel_title": "Proteomic Characterization of Acute Kidney Injury in Patients Hospitalized with SARS-CoV2 Infection", + "rel_date": "2021-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.09.21267548", + "rel_abs": "Acute kidney injury (AKI) is a known complication of COVID-19 and is associated with an increased risk of in-hospital mortality. Unbiased proteomics using biological specimens can lead to improved risk stratification and discover pathophysiological mechanisms. Using measurements of [~]4000 plasma proteins in two cohorts of patients hospitalized with COVID-19, we discovered and validated markers of COVID-associated AKI (stage 2 or 3) and long-term kidney dysfunction. In the discovery cohort (N= 437), we identified 413 higher plasma abundances of protein targets and 40 lower plasma abundances of protein targets associated with COVID-AKI (adjusted p <0.05). Of these, 62 proteins were validated in an external cohort (p <0.05, N =261). We demonstrate that COVID-AKI is associated with increased markers of tubular injury (NGAL) and myocardial injury. Using estimated glomerular filtration (eGFR) measurements taken after discharge, we also find that 25 of the 62 AKI-associated proteins are significantly associated with decreased post-discharge eGFR (adjusted p <0.05). Proteins most strongly associated with decreased post-discharge eGFR included desmocollin-2, trefoil factor 3, transmembrane emp24 domain-containing protein 10, and cystatin-C indicating tubular dysfunction and injury. Using clinical and proteomic data, our results suggest that while both acute and long-term COVID-associated kidney dysfunction are associated with markers of tubular dysfunction, AKI is driven by a largely multifactorial process involving hemodynamic instability and myocardial damage.", + "rel_num_authors": 43, + "rel_authors": [ + { + "author_name": "Ishan Paranjpe", + "author_inst": "The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Pushkala Jayaraman", + "author_inst": "Mount Sinai Clinical Intelligence Center(MSCIC), The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY," + }, + { + "author_name": "Chen-Yang Su", + "author_inst": "Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada" + }, + { + "author_name": "Sirui Zhou", + "author_inst": "Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada" + }, + { + "author_name": "Steven Chen", + "author_inst": "The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA." + }, + { + "author_name": "Ryan Thompson", + "author_inst": "The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Diane Marie Del Valle", + "author_inst": "The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Ephraim Kenigsberg", + "author_inst": "Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Shan Zhao", + "author_inst": "Department of Anesthesiology, Perioperative and Pain Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America" + }, + { + "author_name": "Suraj Jaladanki", + "author_inst": "The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Kumardeep Chaudhary", + "author_inst": "The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Steven Ascolillo", + "author_inst": "The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Akhil Vaid", + "author_inst": "The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Arvind Kumar", + "author_inst": "The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Edgar Gonzalez-Kozlova", + "author_inst": "The Mount Sinai Clinical Intelligence Center(MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Manish Paranjpe", + "author_inst": "Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, USA" + }, + { + "author_name": "Ross O Hagan", + "author_inst": "The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Samir Kamat", + "author_inst": "The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Faris F. Gulamali", + "author_inst": "The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Justin Kauffman", + "author_inst": "The Mount Sinai Clinical Intelligence Center(MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Hui Xie", + "author_inst": "Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Joceyln Harris", + "author_inst": "Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Manishkumar Patel", + "author_inst": "Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Kimberly Argueta", + "author_inst": "Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Craig Batchelor", + "author_inst": "Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Kai Nie", + "author_inst": "Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Sergio Dellepiane", + "author_inst": "Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America" + }, + { + "author_name": "Leisha Scott", + "author_inst": "Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Matthew A Levin", + "author_inst": "The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "John Cijiang He", + "author_inst": "Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America" + }, + { + "author_name": "Mayte Suarez-Farinas", + "author_inst": "Department of Biostatistics, Icahn School of Medicine, Mount Sinai, NY" + }, + { + "author_name": "Steven G Coca", + "author_inst": "Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America" + }, + { + "author_name": "Lili Chan", + "author_inst": "Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America" + }, + { + "author_name": "Evren U Azeloglu", + "author_inst": "Department of Medicine, Division of Nephrology, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America" + }, + { + "author_name": "Eric Schadt", + "author_inst": "Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Noam Beckmann", + "author_inst": "The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Sacha Gnjatic", + "author_inst": "Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA." + }, + { + "author_name": "Miram Merad", + "author_inst": "The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA." + }, + { + "author_name": "Seunghee Kim-Schulze", + "author_inst": "The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA." + }, + { + "author_name": "Brent Richards", + "author_inst": "Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada" + }, + { + "author_name": "Benjamin S Glicksberg", + "author_inst": "The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Alexander W Charney", + "author_inst": "The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA" + }, + { + "author_name": "Girish N Nadkarni", + "author_inst": "The Mount Sinai Clinical Intelligence Center (MSCIC), Icahn School of Medicine at Mount Sinai, New York, NY, USA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, { "rel_doi": "10.1101/2021.12.09.21267513", "rel_title": "Contribution of endogenous and exogenous antibodies to clearance of SARS-CoV-2 during convalescent plasma therapy", @@ -511605,49 +512490,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.12.09.21267349", - "rel_title": "Down-regulation of SARS-CoV-2 neutralizing antibodies in vaccinated smokers", - "rel_date": "2021-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.09.21267349", - "rel_abs": "Vaccination is an effective approach to help control coronavirus disease 2019 (COVID-19). However, since the vaccines produce a heterogenous immune response, the risk of breakthrough infection is increased in vaccinated individuals who generate low levels of neutralizing antibodies (NAbs). It is therefore paramount in the fight against COVID-19 to identify individuals who have a higher risk of breakthrough infection despite being vaccinated. Here we addressed the effect of cigarette smoking on the production of neutralizing antibodies (NAbs) following COVID-19 vaccination since smoking profoundly suppresses the adaptive immune response to pathogen infection and the association between vaccination and smoking remains unclear. The SARS-CoV-2 Spike antibodies and NAbs (days 0, 14, 42, and 90) were measured in 164 participants received two vaccine doses of an inactivated vaccine (Sinovac-CoronaVac) longitudinally. Anti-Spike antibodies was elevated 14 and 42 days after COVID-19 vaccination compared to baseline (i.e., \"Day 0\"). Notably, RBD antibodies showed significantly higher expression in the nonsmoking group (n=153) than the smoking (n=11) group on day 42 (p<0.0001, Students t-test). NAbs continually increased after the first and second vaccine dose, peaking on day 42. NAbs titers then significantly decreased until day 90. Compared to nonsmokers, the NAb levels in smokers remained low throughout the period of testing. The median NAb titers in the smoking group was 1.40-, 1.32-, or 3.00-fold lower than that of nonsmoking group on day 14, 42, or 90, respectively. Altogether, our results indicate that smoking is a specific risk factor for COVID-19 breakthrough infection following vaccination.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Jiahui Zhang", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom" - }, - { - "author_name": "Fei Teng", - "author_inst": "Emergency Medicine Clinical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, & Beijing Key Laboratory of Cardiopulmonary Cerebral Resusc" - }, - { - "author_name": "Xiaomei Zhang", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom" - }, - { - "author_name": "Hongye Wang", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom" - }, - { - "author_name": "Te Liang", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom" - }, - { - "author_name": "Shu-Bin Guo", - "author_inst": "Emergency Medicine Clinical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, & Beijing Key Laboratory of Cardiopulmonary Cerebral Resusc" - }, - { - "author_name": "xiaobo yu", - "author_inst": "State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeom" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.12.09.21267545", "rel_title": "COVID-19 booster vaccine attitudes and behaviors among university students and staff: the USC Trojan Pandemic Research Initiative", @@ -513027,6 +513869,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.12.07.471597", + "rel_title": "Deep Mutational Engineering of broadly-neutralizing and picomolar affinity nanobodies to accommodate SARS-CoV-1 & 2 antigenic polymorphism", + "rel_date": "2021-12-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.07.471597", + "rel_abs": "We report in this study the molecular engineering of nanobodies that bind with picomolar affinity to both SARS-CoV-1 and SARS-CoV-2 Receptor Binding Domains (RBD) and are highly neutralizing. We applied Deep Mutational Engineering to VHH72, a nanobody initially specific for SARS-CoV-1 RBD with little cross-reactivity to SARS-CoV-2 antigen. We first identified all the individual VHH substitutions that increase binding to SARS-CoV-2 RBD and then screened highly focused combinatorial libraries to isolate engineered nanobodies with improved properties. The corresponding VHH-Fc molecules show high affinities for SARS-CoV-2 antigens from various emerging variants and SARS-CoV-1, block the interaction between ACE2 and RBD and neutralize the virus with high efficiency. Its rare specificity across sarbecovirus relies on its peculiar epitope outside the immunodominant regions. The engineered nanobodies share a common motif of three amino acids, which contribute to the broad specificity of recognition. These nanobodies appears as promising therapeutic candidates to fight SARS-CoV-2 infection.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Adrien Laroche", + "author_inst": "Universite Paris-Saclay, CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Gif-sur-Yvette" + }, + { + "author_name": "Maria Lucia Orsini Delgado", + "author_inst": "Universite Paris-Saclay, CEA, INRAE, Medicines and Healthcare Technologies Department, SPI, Gif-sur-Yvette, France" + }, + { + "author_name": "Philippe Cuniasse", + "author_inst": "Universite Paris-Saclay, CNRS, CEA, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France" + }, + { + "author_name": "Steven Dubois", + "author_inst": "Universite Paris-Saclay, CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Gif-sur-Yvette" + }, + { + "author_name": "Raphael Sierocki", + "author_inst": "Deeptope SAS, Massy, France" + }, + { + "author_name": "Fabrice Gallais", + "author_inst": "Universite Paris Saclay, CEA, INRAE, Departement Medicaments et Technologies pour la Sante (DMTS), SPI, 30200 Bagnols-sur-Ceze, France" + }, + { + "author_name": "Stephanie Debroas", + "author_inst": "Universite Paris Saclay, CEA, INRAE, Departement Medicaments et Technologies pour la Sante (DMTS), SPI, 30200 Bagnols-sur-Ceze, France" + }, + { + "author_name": "Laurent Bellanger", + "author_inst": "Universite Paris Saclay, CEA, INRAE, Departement Medicaments et Technologies pour la Sante (DMTS), SPI, 30200 Bagnols-sur-Ceze, France" + }, + { + "author_name": "Stephanie Simon", + "author_inst": "Universite Paris-Saclay, CEA, INRAE, Medicines and Healthcare Technologies Department, SPI, Gif-sur-Yvette, France" + }, + { + "author_name": "Bernard Maillere", + "author_inst": "Universite Paris-Saclay, CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Gif-sur-Yvette, France" + }, + { + "author_name": "Herv\u00e9 Nozach", + "author_inst": "Universite Paris-Saclay, CEA, INRAE, Medicines and Healthcare Technologies Department, SIMoS, Gif-sur-Yvette" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.12.08.471688", "rel_title": "Mutations in the spike RBD of SARS-CoV-2 omicron variant may increase infectivity without dramatically altering the efficacy of current multi-dosage vaccinations", @@ -513435,125 +514336,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.12.08.471814", - "rel_title": "Nanotrap Particles Improve Nanopore Sequencing of SARS-CoV-2 and Other Respiratory Viruses", - "rel_date": "2021-12-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.08.471814", - "rel_abs": "Presented here is a magnetic hydrogel particle enabled workflow for capturing and concentrating SARS-CoV-2 from diagnostic remnant swab samples that significantly improves sequencing results using the Oxford Nanopore Technologies MinION sequencing platform. Our approach utilizes a novel affinity-based magnetic hydrogel particle, circumventing low input sample volumes and allowing for both rapid manual and automated high throughput workflows that are compatible with nanopore sequencing. This approach enhances standard RNA extraction protocols, providing up to 40x improvements in viral mapped reads, and improves sequencing coverage by 20-80% from lower titer diagnostic remnant samples. Furthermore, we demonstrate that this approach works for contrived influenza virus and respiratory syncytial virus samples, suggesting that it can be used to identify and improve sequencing results of multiple viruses in VTM samples. These methods can be performed manually or on a KingFisher Apex system.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Patrick Daniel Andersen", - "author_inst": "Ceres Nanosciences" - }, - { - "author_name": "Stephanie Barksdale", - "author_inst": "Ceres Nanosciences" - }, - { - "author_name": "Robert Alex Barclay", - "author_inst": "Ceres Nanosciences" - }, - { - "author_name": "Natalie Smith", - "author_inst": "Ceres Nanosciences" - }, - { - "author_name": "Justin Fernandes", - "author_inst": "Ceres Nanosciences" - }, - { - "author_name": "Daniel Goldfarb", - "author_inst": "Ceres Nanosciences" - }, - { - "author_name": "Robbie Barbero", - "author_inst": "Ceres Nanosciences" - }, - { - "author_name": "Tara Jones-Roe", - "author_inst": "Ceres Nanosciences" - }, - { - "author_name": "Katherine Besse", - "author_inst": "Ceres Nanosciences" - }, - { - "author_name": "Ross Dunlap", - "author_inst": "Ceres Nanosciences" - }, - { - "author_name": "Ross Kelly", - "author_inst": "Ceres Nanosciences" - }, - { - "author_name": "Shida Miao", - "author_inst": "Ceres Nanosciences" - }, - { - "author_name": "Chamodya Ruhunusiri", - "author_inst": "Ceres Nanosciences" - }, - { - "author_name": "Amy Munns", - "author_inst": "Ceres Nanosciences" - }, - { - "author_name": "Sayed Mosavi", - "author_inst": "Ceres Nanosciences" - }, - { - "author_name": "Denton Munns", - "author_inst": "Ceres Nanosciences" - }, - { - "author_name": "Laura Sanson", - "author_inst": "Ceres Nanosciences" - }, - { - "author_name": "Sahoo Saswata", - "author_inst": "Ceres Nanosciences" - }, - { - "author_name": "Olivia Swahn", - "author_inst": "Ceres Nanosciences" - }, - { - "author_name": "Killian Hull", - "author_inst": "Ceres Nanosciences" - }, - { - "author_name": "David White", - "author_inst": "Ceres Nanosciences" - }, - { - "author_name": "Kevin Kolb", - "author_inst": "Ceres Nanosciences" - }, - { - "author_name": "Fatemeh Noroozi", - "author_inst": "Ceres Nanosciences" - }, - { - "author_name": "Joshna Seelam", - "author_inst": "Ceres Nanosciences" - }, - { - "author_name": "Anurag Patnaik", - "author_inst": "Ceres Nanosciences" - }, - { - "author_name": "Ben Lepene", - "author_inst": "Ceres Nanosciences" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.12.08.21267496", "rel_title": "Vaccinating Children Against COVID-19 is Essential Prior to the Removal of Non-Pharmaceutical Interventions", @@ -514525,6 +515307,57 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.12.06.471421", + "rel_title": "Metabolic dysregulation induces impaired lymphocyte memory formation during severe SARS-CoV-2 infection", + "rel_date": "2021-12-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.06.471421", + "rel_abs": "Cellular metabolic dysregulation is a consequence of COVID-19 infection that is a key determinant of disease severity. To understand the mechanisms underlying these cellular changes, we performed high-dimensional immune cell profiling of PBMCs from COVID-19-infected patients, in combination with single cell transcriptomic analysis of COVID-19 BALFs. Hypoxia, a hallmark of COVID-19 ARDS, was found to elicit a global metabolic reprogramming in effector lymphocytes. In response to oxygen and nutrient-deprived microenvironments, these cells shift from aerobic respiration to increase their dependence on anaerobic processes including glycolysis, mitophagy, and glutaminolysis to fulfill their bioenergetic demands. We also demonstrate metabolic dysregulation of ciliated lung epithelial cells is linked to significant increase of proinflammatory cytokine secretion and upregulation of HLA class 1 machinery. Augmented HLA class-1 antigen stimulation by epithelial cells leads to cellular exhaustion of metabolically dysregulated CD8 and NK cells, impairing their memory cell differentiation. Unsupervised clustering techniques revealed multiple distinct, differentially abundant CD8 and NK memory cell states that are marked by high glycolytic flux, mitochondrial dysfunction, and cellular exhaustion, further highlighting the connection between disrupted metabolism and impaired memory cell function in COVID-19. Our findings provide novel insight on how SARS-CoV-2 infection affects host immunometabolism and anti-viral response during COVID-19.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC=\"FIGDIR/small/471421v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (32K):\norg.highwire.dtl.DTLVardef@18bff7borg.highwire.dtl.DTLVardef@31f46borg.highwire.dtl.DTLVardef@1a5ad50org.highwire.dtl.DTLVardef@1577a0_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIHypoxia and anaerobic glycolysis drive CD8, NK, NKT dysfunction\nC_LIO_LIHypoxia and anaerobic glycolysis impair memory differentiation in CD8 and NK cells\nC_LIO_LIHypoxia and anaerobic glycolysis cause mitochondrial dysfunction in CD8, NK, NKT cells\nC_LI", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Hung Nguyen", + "author_inst": "University of Central Florida" + }, + { + "author_name": "Sanjeev Gurshaney", + "author_inst": "University of Central Florida" + }, + { + "author_name": "Anamaria Morales Alvarez", + "author_inst": "University of Central Florida" + }, + { + "author_name": "Kevin Ezhakunnel", + "author_inst": "University of Central Florida" + }, + { + "author_name": "Andrew Manalo", + "author_inst": "University of Central Florida" + }, + { + "author_name": "Thien-Huong Huynh", + "author_inst": "University of Central Florida" + }, + { + "author_name": "Nhat -Tu Le", + "author_inst": "Houston Methodist" + }, + { + "author_name": "Daniel Lupu", + "author_inst": "AdventHealth" + }, + { + "author_name": "Stephen Gardell", + "author_inst": "AdventHealth" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.12.06.471528", "rel_title": "The cellular characterisation of SARS-CoV-2 spike protein in virus-infected cells using Receptor Binding Domain-binding specific human monoclonal antibodies.", @@ -514969,37 +515802,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.12.07.21267442", - "rel_title": "Dynamic analysis and evaluation of asymptomatic infection in the spread of COVID-19", - "rel_date": "2021-12-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.07.21267442", - "rel_abs": "COVID-19 has spread worldwide for nearly two years. Many countries have experienced repeated epidemics, that is, after the epidemic has been controlled for a period of time, the number of new cases per day is low, and the outbreak will occur again a few months later. In order to study the relationship between this low level of infection and the number of asymptomatic infections, and to evaluate the role of asymptomatic infections in the development of the epidemic, we have established an improved infectious disease dynamics model that can be used to evaluate the spread of the COVID-19 epidemic, and fitted the epidemic data in the three flat periods in England. According to the obtained parameters, according to the calculation of the model, the proportion of asymptomatic infections in these three flat periods are 41%, 53% and 58% respectively. After the first flat period, the number of daily newly confirmed cases predicted by the model began to increase around July 1, 2020. After more than four months of epidemic spread, it reached a peak on November 12, which is consistent with the actual case situation. Unanimous. After the second flat period, the model predicts that the number of new confirmed cases per day will increase from about May 7, 2021, and after about 73 days of epidemic development, it will reach a peak on July 20, showing the overall trend of the epidemic. In the above, the predicted results of the model are consistent with the actual cases. After the third flat period, the number of daily newly diagnosed cases predicted by the model began to increase around December 1, 2021, and reached a peak in December, and the number of cases will drop to a very low level after May 2022. According to our research results, due to the large number of asymptomatic infections, the spread of the epidemic is not easy to stop completely in a short time. However, when the epidemic enters a period of flat time, nucleic acid testing is performed, and asymptomatic infections are isolated at home for 14 days (the recovery period of symptomatic infection is about 10 days) may be an option that can be considered to interrupt the transmission of the case.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Chuan qing XU", - "author_inst": "Beijing University of Civil Engineering and Architecture" - }, - { - "author_name": "Zonghao Zhang", - "author_inst": "Beijing University of Civil Engineering and Architecture" - }, - { - "author_name": "Xiaotong Huang", - "author_inst": "Beijing University of Civil Engineering and Arcihtecture" - }, - { - "author_name": "Jingan Cui", - "author_inst": "Beijing University of Civil Engineering and Architecture" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.12.02.21266468", "rel_title": "Stochastic simulation of successive waves of COVID-19 in the province of Barcelona.", @@ -516427,6 +517229,33 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2021.11.29.21266774", + "rel_title": "Stressors, Manifestations and Course of COVID-19 Related Distress Among Nurses and Midwives in Tasmania", + "rel_date": "2021-12-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.29.21266774", + "rel_abs": "The deleterious effects relating to the COVID-19 pandemic on the mental health of healthcare workers has now been widely established. Understanding how COVID-19 affects their work and life is complex and multidimensional. This study describes the critical stressors and how they manifest within both the work and larger social environment for nurses and midwives in Tasmania, Australia.\n\nA longitudinal, descriptive survey was designed to explore the trajectory of the psychological health of Tasmanian public sector nurses and midwives during the COIVD-19 pandemic. The survey was distributed at 3 timepoints over a 12-month period and consisted of a battery of psychological tests which included the Patient Health Questionnaire, General Anxiety Disorder, Insomnia Severity Index, and the Impact of Events Scale-Revised, together with free text comments.\n\nThe associations between outcome and predictor variables were assessed using mixed effects linear regression and linear mixed model analyses. Free text comments were themed.\n\nHigh levels of stress and mental exhaustion were attributed to threatened workplace team culture; compromised quality of patient care; the impact on family, home, financial and economic domains; lack of clear communication; issues surrounding personal protective equipment; and female gender. Study data show younger nurses and midwives suffered higher levels of stress and mental exhaustion than older.\n\nThis study highlights the need for stable and functional relationships at home and at work for nurses and midwives.\n\nFactors which will help preserve the mental health of nurses and midwives include strong workplace culture with ongoing processes to monitor organisational burnout; building resilience, particularly among younger nurses and midwives; protection of healthcare worker safety; clear communication processes and supporting stable and functional relationships at home. The health service has an imperative to ensure optimum service delivery by safeguarding staff, despite the inevitable health stress imposed by the nature of the work.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Kathryn M Marsden", + "author_inst": "Tasmanian Health Service South" + }, + { + "author_name": "Julie M Porter", + "author_inst": "Tasmanian Health Service South" + }, + { + "author_name": "I.K. Robertson", + "author_inst": "University of Tasmania" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "nursing" + }, { "rel_doi": "10.1101/2021.11.30.21267096", "rel_title": "Statistical Inferences and Analysis based on the COVID-19 data from the United States", @@ -517011,57 +517840,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.12.05.471277", - "rel_title": "A zebrafish model of COVID-19-associated cytokine storm syndrome reveals differential proinflammatory activities of Spike proteins of SARS-CoV-2 variants of concern.", - "rel_date": "2021-12-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.12.05.471277", - "rel_abs": "The sudden and unexpected appearance of the COVID-19 pandemic turned the whole world upside down in a very short time. One of the main challenges faced has been to understand COVID-19 patient heterogeneity, as a minority develop life-threatening hyperinflammation, the so-called cytokine storm syndrome (CSS). Using the unique advantages of the zebrafish model we report here the proinflammatory role of Spike (S) proteins from different SARS-CoV-2 variants of concern after injection into the hindbrain ventricle, a cavity filled with cerebrospinal fluid to which immune cells can be easily recruited and that mimics the alveolar environment of the human lung. We found that wild type/Wuhan variant S1 (S1WT) protein promoted neutrophil and macrophage recruitment, local and systemic hyperinflammation, emergency myelopoiesis, and hemorrhages. In addition, S1{gamma} protein was more proinflammatory and S1{delta} was less proinflammatory than S1WT and, strikingly, S1{beta} promoted delayed and long-lasting inflammation. Pharmacological inhibition of the canonical inflammasome robustly alleviated S1 protein-induced inflammation and emergency myelopoiesis. In contrast, genetic inhibition of angiotensin-converting enzyme 2 strengthened the proinflammatory activity of S1, and the administration of angiopoietin (1-7) fully rescued S1-induced hyperinflammation and hemorrhages. These results shed light into the mechanisms orchestrating the COVID-19-associated CSS and the host immune response to different SARS-CoV-2 S protein variants.\n\nHighlightsO_LIS proteins of SARS-CoV-2 promote hyperinflammation, neutrophilia, monocytosis and hemorrhages in zebrafish.\nC_LIO_LIS protein effects in zebrafish are mediated via the canonical inflammasome and the Ace2/Angiopoietin (1-7) axis.\nC_LIO_LIDelta S1 is less proinflammatory than wild type S1 and fails to induce emergency myelopoiesis in zebrafish.\nC_LIO_LINaive and primed human white blood cells are unable to respond to S proteins.\nC_LI", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Sylwia D Tyrkalska", - "author_inst": "Universidad de Murcia" - }, - { - "author_name": "Alicia Martinez-Lopez", - "author_inst": "Universidad de Murcia" - }, - { - "author_name": "Ana B Arroyo", - "author_inst": "Universidad de Murcia" - }, - { - "author_name": "Francisco J Martinez-Morcillo", - "author_inst": "Universidad de Murcia" - }, - { - "author_name": "Sergio Candel", - "author_inst": "Universidad de Murcia" - }, - { - "author_name": "Pablo Mesa-del-Castillo", - "author_inst": "Hospital Clinico Universitario Virgen de la Arrixaca" - }, - { - "author_name": "Diana Garcia-Moreno", - "author_inst": "Universidad de Murcia" - }, - { - "author_name": "Maria L. Cayuela", - "author_inst": "University Hospital \"Virgen de la Arrixaca\"" - }, - { - "author_name": "Victoriano Mulero", - "author_inst": "Universidad de Murcia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.12.06.471377", "rel_title": "The Omicron Variant Increases the Interactions of SARS-CoV-2 Spike Glycoprotein with ACE2", @@ -518349,6 +519127,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.12.05.21267334", + "rel_title": "Association of regional Covid-19 mortality with indicators of indoor ventilation, including temperature and wind: insights into the upcoming winter: Update Dec. 5, 2021", + "rel_date": "2021-12-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.05.21267334", + "rel_abs": "BackgroundOutdoor environmental variables, such as cold temperatures and low wind speed, have been correlated with incidence and mortality from Covid-19 (caused by the SARS-CoV-2 virus). However, as Covid-19 predominantly spreads indoors, the degree to which outdoor environmental variables might directly cause disease spread is unclear.\n\nMethodsWorld regions were considered to have reliable data if the excess mortality did not greatly exceed reported Covid-19 mortality. The relative risk of Covid-19 mortality for 142 regions as a function of median weekly temperature and wind speed was determined. For instance, Covid-19 mortality following warm weeks in a country was compared with mortality following cold weeks in the same country.\n\nResultsCovid-19 mortality increases with cooling from 20 C to close to freezing (0 to 4 C, p<0.001). The relation of Covid-19 mortality with temperature demonstrates a maximum close to freezing. Below -5 C, the decrease in mortality with further cooling was statistically significant (p<0.01). With warming above room temperature (20 to 24 C), there is a nonsignificant trend for mortality to increase again. A literature review demonstrated that window opening and indoor ventilation tend to increase with warming in the range from freezing to room temperature.\n\nConclusionThe steep decline in Covid-19 mortality with warming in the range from freezing to room temperature may relate to window opening and less indoor crowding when it is comfortable outside. Below freezing, all windows are closed, and further cooling increases stack ventilation (secondary to indoor-outdoor temperature differences) and thereby tends to decrease Covid-19 mortality. Opening windows and other tools for improving indoor ventilation may decrease the spread of Covid-19.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Christopher T Leffler", + "author_inst": "Virginia Commonwealth University" + }, + { + "author_name": "Joseph D. Lykins V", + "author_inst": "Virginia Commonwealth University" + }, + { + "author_name": "Brandon I Fram", + "author_inst": "Virginia Commonwealth University" + }, + { + "author_name": "Edward Yang", + "author_inst": "Virginia Commonwealth University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.12.07.21267398", "rel_title": "In-hospital mortality due to breakthrough COVID-19 among recipients of COVISHIELD (ChAdOx nCoV-19) and COVAXIN (BBV152)", @@ -518697,181 +519506,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.12.06.21267101", - "rel_title": "SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia", - "rel_date": "2021-12-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.06.21267101", - "rel_abs": "Monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on surfaces is emerging as an important tool for identifying past exposure to individuals shedding viral RNA. Our past work has demonstrated that SARS-CoV-2 reverse transcription-quantitative PCR (RT-qPCR) signals from surfaces can identify when infected individuals have touched surfaces such as Halloween candy, and when they have been present in hospital rooms or schools. However, the sensitivity and specificity of surface sampling as a method for detecting the presence of a SARS-CoV-2 positive individual, as well as guidance about where to sample, has not been established. To address these questions, and to test whether our past observations linking SARS-CoV-2 abundance to Rothia spp. in hospitals also hold in a residential setting, we performed detailed spatial sampling of three isolation housing units, assessing each sample for SARS-CoV-2 abundance by RT-qPCR, linking the results to 16S rRNA gene amplicon sequences to assess the bacterial community at each location and to the Cq value of the contemporaneous clinical test. Our results show that the highest SARS-CoV-2 load in this setting is on touched surfaces such as light switches and faucets, but detectable signal is present in many non-touched surfaces that may be more relevant in settings such as schools where mask wearing is enforced. As in past studies, the bacterial community predicts which samples are positive for SARS-CoV-2, with Rothia sp. showing a positive association.\n\nImportanceSurface sampling for detecting SARS-CoV-2, the virus that causes coronavirus disease 2019 (COVID-19), is increasingly being used to locate infected individuals. We tested which indoor surfaces had high versus low viral loads by collecting 381 samples from three residential units where infected individuals resided, and interpreted the results in terms of whether SARS-CoV-2 was likely transmitted directly (e.g. touching a light switch) or indirectly (e.g. by droplets or aerosols settling). We found highest loads where the subject touched the surface directly, although enough virus was detected on indirectly contacted surfaces to make such locations useful for sampling (e.g. in schools, where students do not touch the light switches and also wear masks so they have no opportunity to touch their face and then the object). We also documented links between the bacteria present in a sample and the SARS-CoV-2 virus, consistent with earlier studies.", - "rel_num_authors": 40, - "rel_authors": [ - { - "author_name": "Victor J. Cant\u00fa", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Rodolfo A. Salido", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Shi Huang", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Gibraan Rahman", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Rebecca Tsai", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Holly D. Valentine", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Celestine G Magallanes", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Stefan Aigner", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Nathan A. Baer", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Tom Barber", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Pedro Belda-Ferre", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Maryan Betty", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "MacKenzie Bryant", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Mart\u00edn Casas Maya", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Anelizze Castro-Mart\u00ednez", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Marisol Chac\u00f3n", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Willi Cheung", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Evelyn S. Crescini", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Peter De Hoff", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Emily Eisner", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Sawyer Farmer", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Abbas Hakim", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Laura Kohn", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Alma L. Lastrella", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Elijah S. Lawrence", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Sydney C Morgan", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Toan T. Ngo", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Alhakam Nouri", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "R. Tyler Ostrander", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Ashley Plascencia", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Christopher A. Ruiz", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Shashank Sathe", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Phoebe Seaver", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Tara Schwartz", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Elizabeth W. Smoot", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Thomas Valles", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Gene W. Yeo", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Louise Laurent", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Rebecca Fielding-Miller", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Rob Knight", - "author_inst": "University of California, San Diego" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.12.07.21267364", "rel_title": "COVID-19 Prognostic Modeling Using CT Radiomic Features and Machine Learning Algorithms: Analysis of a Multi-Institutional Dataset of 14,339 Patients", @@ -520143,6 +520777,161 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2021.12.03.21266112", + "rel_title": "Brain Injury in COVID-19 is Associated with Autoinflammation and Autoimmunity", + "rel_date": "2021-12-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.03.21266112", + "rel_abs": "COVID-19 has been associated with many neurological complications including stroke, delirium and encephalitis. Furthermore, many individuals experience a protracted post-viral syndrome which is dominated by neuropsychiatric symptoms, and is seemingly unrelated to COVID-19 severity. The true frequency and underlying mechanisms of neurological injury are unknown, but exaggerated host inflammatory responses appear to be a key driver of severe COVID-19 more broadly.\n\nWe sought to investigate the dynamics of, and relationship between, serum markers of brain injury (neurofilament light [NfL], Glial Fibrillary Acidic Protein [GFAP] and total Tau) and markers of dysregulated host response including measures of autoinflammation (proinflammatory cytokines) and autoimmunity. Brain injury biomarkers were measured using the Quanterix Simoa HDx platform, cytokine profiling by Luminex (R&D) and autoantibodies by a custom protein microarray.\n\nDuring hospitalisation, patients with COVID-19 demonstrated elevations of NfL and GFAP in a severity-dependant manner, and there was evidence of ongoing active brain injury at follow-up 4 months later. Raised NfL and GFAP were associated with both elevations of pro-inflammatory cytokines and the presence of autoantibodies; autoantibodies were commonly seen against lung surfactant proteins as well as brain proteins such as myelin associated glycoprotein, but reactivity was seen to a large number of different antigens.\n\nFurthermore, a distinct process characterised by elevation of serum total Tau was seen in patients at follow-up, which appeared to be independent of initial disease severity and was not associated with dysregulated immune responses in the same manner as NfL and GFAP.", + "rel_num_authors": 35, + "rel_authors": [ + { + "author_name": "Edward J Needham", + "author_inst": "Department of Clinical Neurosciences, University of Cambridge, UK" + }, + { + "author_name": "Alex L Ren", + "author_inst": "Division of Anaesthesia, Department of Medicine, University of Cambridge, UK." + }, + { + "author_name": "Richard J Digby", + "author_inst": "Division of Anaesthesia, Department of Medicine, University of Cambridge, UK." + }, + { + "author_name": "Joanne G Outtrim", + "author_inst": "Division of Anaesthesia, Department of Medicine, University of Cambridge, UK." + }, + { + "author_name": "Dorothy A Chatfield", + "author_inst": "Division of Anaesthesia, Department of Medicine, University of Cambridge, UK." + }, + { + "author_name": "Virginia FJ Newcombe", + "author_inst": "Division of Anaesthesia, Department of Medicine, University of Cambridge, UK." + }, + { + "author_name": "Rainer Doffinger", + "author_inst": "Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK." + }, + { + "author_name": "Gabriela Barcenas-Morales", + "author_inst": "Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK." + }, + { + "author_name": "Claudia Fonseca", + "author_inst": "Cambridge Protein Arrays Ltd, Babraham Research Campus, Cambridge, UK" + }, + { + "author_name": "Michael J Taussig", + "author_inst": "Cambridge Protein Arrays Ltd, Babraham Research Campus, Cambridge, UK" + }, + { + "author_name": "Rowan M Burnstein", + "author_inst": "Division of Anaesthesia, Department of Medicine, University of Cambridge, UK." + }, + { + "author_name": "Cordelia Dunai", + "author_inst": "Clinical Infection Microbiology and Neuroimmunology, Institute of Infection, Veterinary and Ecological Science, Liverpool, UK." + }, + { + "author_name": "Nyarie Sithole", + "author_inst": "Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK." + }, + { + "author_name": "Nicholas J Ashton", + "author_inst": "Department of Psychiatry and Neurochemistry, Institute of Neuroscience & Physiology, the Sahlgrenska Academy at the University of Gothenburg, Molndal, Sweden." + }, + { + "author_name": "Henrik Zetterberg", + "author_inst": "Department of Psychiatry and Neurochemistry, Institute of Neuroscience & Physiology, the Sahlgrenska Academy at the University of Gothenburg, Molndal, Sweden; C" + }, + { + "author_name": "Magnus Gisslen", + "author_inst": "Department of Infectious Diseases, Institute of Biomedicine, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden; Region Vastra Gotaland" + }, + { + "author_name": "Eden Arvid", + "author_inst": "Department of Infectious Diseases, Institute of Biomedicine, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden; Region Vastra Gotaland" + }, + { + "author_name": "Emelie Marklund", + "author_inst": "Department of Infectious Diseases, Institute of Biomnedicine, the Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden; Region Vastra Gotalan" + }, + { + "author_name": "Michael J Griffiths", + "author_inst": "Institute of Infection, Veterinary & Ecological Sciences, University of Liverpool, Liverpool, UK." + }, + { + "author_name": "Jonathan Cavanagh", + "author_inst": "Centre for Immunobiology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, U" + }, + { + "author_name": "Gerome Breen", + "author_inst": "Department of Social Genetic and Developmental Psychiatry, King's College London, London, UK." + }, + { + "author_name": "Sarosh R Irani", + "author_inst": "Oxford Autoimmune Neurology Group, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK; Department of Neurology, Oxford University H" + }, + { + "author_name": "Anne Elmer", + "author_inst": "Cambridge Clinical Research Centre, NIHR Clinical Research Facility, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge, UK " + }, + { + "author_name": "Nathalie Kingston", + "author_inst": "NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge, UK." + }, + { + "author_name": "John R Bradley", + "author_inst": "NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge, UK; Department of Medicine, University of Cambridge, Ad" + }, + { + "author_name": "Leonie S Taams", + "author_inst": "Centre for Inflammation Biology and Cancer Immunology and Dept Inflammation Biology, School of Immunology and Microbial Sciences, Kings College London, Guys Cam" + }, + { + "author_name": "Benedict D michael", + "author_inst": "Clinical Infection Microbiology and Neuroimmunology, Institute of Infection, Veterinary and Ecological Science, Liverpool, UK." + }, + { + "author_name": "Edward T Bullmore", + "author_inst": "Department of Psychiatry, University of Cambridge, Herchel Smith Building for Brain and Mind Sciences, Cambridge Biomedical Campus, Cambridge, UK." + }, + { + "author_name": "Kenneth GC Smith", + "author_inst": "Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Je" + }, + { + "author_name": "Paul A Lyons", + "author_inst": "Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Je" + }, + { + "author_name": "Alasdair JC Coles", + "author_inst": "Department of Clinical Neurosciences, University of Cambridge, UK" + }, + { + "author_name": "David K Menon", + "author_inst": "Division of Anaesthesia, Department of Medicine, University of Cambridge, UK." + }, + { + "author_name": "- Cambridge NeuroCOVID Group", + "author_inst": "" + }, + { + "author_name": "- NIHR Cambridge Covid BioResource", + "author_inst": "" + }, + { + "author_name": "- NIHR Cambridge Clinical Research Facility", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2021.12.04.21267231", "rel_title": "A mixed-methods study of risk factors and experiences of healthcare workers tested for the novel coronavirus in Canada", @@ -520719,45 +521508,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.12.04.21267294", - "rel_title": "Characteristics of Patients Referred to a Cardiovascular Disease Clinic for Post-Acute Sequelae of SARS-CoV-2 Infection", - "rel_date": "2021-12-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.04.21267294", - "rel_abs": "There is limited literature on the cardiovascular manifestations of post-acute sequelae of SARS-CoV-2 infection (PASC). We aimed to describe the characteristics, diagnostic evaluations, and cardiac diagnoses in patients referred to a cardiovascular disease clinic designed for patients with PASC from May 2020 to September 2021. Of 126 patients, average age was 46 years (range 19-81 years), 43 (34%) were male. Patients presented on average five months after COVID-19 diagnosis. 30 (24%) patients were hospitalized for acute COVID-19. Severity of acute COVID-19 was mild in 37%, moderate in 41%, severe in 11%, and critical in 9%. Patients were also followed for PASC by pulmonology (53%), neurology (33%), otolaryngology (11%), and rheumatology (7%). Forty-three patients (34%) did not have significant comorbidities. The most common symptoms were dyspnea (52%), chest pain/pressure (48%), palpitations (44%), and fatigue (42%), commonly associated with exertion or exercise intolerance. The following cardiovascular diagnoses were identified: nonischemic cardiomyopathy (5%); new ischemia (3%); coronary vasospasm (2%); new atrial fibrillation (2%), new supraventricular tachycardia (2%); myocardial involvement (15%) by cardiac MRI, characterized by late gadolinium enhancement (LGE; 60%) or inflammation (48%). The remaining 97 patients (77%) exhibited common symptoms of fatigue, dyspnea on exertion, tachycardia, or chest pain, which we termed \"cardiovascular PASC syndrome.\" Three of these people met criteria for postural orthostatic tachycardia syndrome. Lower severity of acute COVID-19 was a significant predictor of cardiovascular PASC syndrome. In this cohort of patients referred to cardiology for PASC, 23% had a new diagnosis, but most displayed a pattern of symptoms associated with exercise intolerance.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Stephen Y Wang", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Philip Adejumo", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Claudia See", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Oyere K Onuma", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Edward J Miller", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Erica S Spatz", - "author_inst": "Yale School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2021.12.03.21267258", "rel_title": "Risk assessment of banknotes as a fomite of SARS-CoV-2 in cash payment transactions", @@ -522021,6 +522771,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2021.12.02.21267165", + "rel_title": "The Impact of COVID-19 on NO2 and PM2.5 Levels and Their Associations with Human Mobility Patterns in Singapore", + "rel_date": "2021-12-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.02.21267165", + "rel_abs": "The decline in NO2 and PM2.5 pollutant levels were observed during COVID-19 around the world, especially during lockdowns. Previous studies explained such observed decline with the decrease in human mobility, whilst overlooking the meteorological changes (e.g., rainfall, wind speed) that could mediate air pollution level simultaneously. This pitfall could potentially lead to over-or under-estimation of the effect of COVID-19 on air pollution. Consequently, this study aims to re-evaluate the impact of COVID-19 on NO2 and PM2.5 pollutant level in Singapore, by incorporating the effect of meteorological parameters in predicting NO2 and PM2.5 baseline in 2020 using machine learning methods. The results found that NO2 and PM2.5 declined by a maximum of 38% and 36%, respectively, during lockdown period. As two proxies for change in human mobility, taxi availability and carpark availability were found to increase and decrease by a maximum of 12.6% and 9.8%, respectively, in 2020 from 2019 during lockdown. To investigate how human mobility influenced air pollutant level, two correlation analyses were conducted: one between PM2.5 and carpark availability changes at regional scale and the other between NO2 and taxi availability changes at a spatial resolution of 0.01{degrees}. The NO2 variation was found to be more associated with the change in human mobility, with the correlation coefficients vary spatially across Singapore. A cluster of stronger correlations were found in the South and East Coast of Singapore. Contrarily, PM2.5 and carpark availability had a weak correlation, which could be due to the limit of regional analyses. Drawing to the wider context, the high association between human mobility and NO2 in the South and East Coast area can provide insights into future NO2 reduction policy in Singapore.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC=\"FIGDIR/small/21267165v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (29K):\norg.highwire.dtl.DTLVardef@1e0ea3aorg.highwire.dtl.DTLVardef@131be31org.highwire.dtl.DTLVardef@bda881org.highwire.dtl.DTLVardef@181dec5_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Yangyang Li", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Yihan Zhu", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Jia Yu Karen Tan", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Hoong Chen Teo", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Andrea Law", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Dezhan Qu", + "author_inst": "Northeast Normal University" + }, + { + "author_name": "Wei Luo", + "author_inst": "National University of Singapore" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.12.04.21267300", "rel_title": "Price-performance comparison of HEPA air purifiers and lower-cost MERV 13/14 filters with box fans for filtering out SARS-Cov-2 and other particulate aerosols in indoor community settings", @@ -522445,109 +523238,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.12.03.21267155", - "rel_title": "High viral loads: what drives fatal cases of COVID-19 in vaccinees? an autopsy study", - "rel_date": "2021-12-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.12.03.21267155", - "rel_abs": "BackgroundThe rate of SARS-CoV-2 breakthrough infections in vaccinees is becoming an increasingly serious issue.\n\nObjectiveTo determine the causes of death, histological organ alteration, and viral spread in relation to demographic, clinical-pathological, viral variants, and vaccine types.\n\nDesignComprehensive retrospective observational cohort study. Setting: Consecutive cases from four German academic medical centers.\n\nPatientsDeceased with proven SARS-CoV-2 infection after vaccination who died between January and November 2021. Collections of 29 vaccinees which were analyzed and compared to 141 nonvaccinated control cases.\n\nResultsAutopsies were performed on 16 partially and 13 fully vaccinated individuals. Most patients were elderly and suffered from several relevant comorbidities. Real-time RT-PCR (RT-qPCR) identified a significantly increased rate of generalized viral dissemination within the organism in vaccinated cases versus nonvaccinated cases (45% vs. 16%, respectively; P = 0.008). Vaccinated cases also showed high viral loads, reaching Ct values below 10, especially in the upper airways and lungs. This was accompanied by high rates of pulmonal bacterial or mycotic superinfections and the occurrence of immunocompromising factors such as malignancies, immunosuppressive drug intake, or decreased immunoglobulin levels. All these findings were particularly accentuated in partially vaccinated patients compared to fully vaccinated individuals. A fatal course after vaccination occurred in only 14% of all COVID-19 deceased in Augsburg.\n\nLimitationsRestricted number of cases\n\nConclusionsFatal cases of COVID-19 in vaccinees were rare and often associated with severe comorbidities or other immunosuppressive conditions. Interestingly, we observed striking virus dissemination in our case study, which may indicate a decreased ability to eliminate the virus in patients with an impaired immune system. However, the potential role of antibody-dependent enhancement must also be ruled out in future studies.\n\nFunding sourceThis work was supported by the German Registry of COVID-19 Autopsies (www.DeRegCOVID.ukaachen.de) and funded by the Federal Ministry of Health (ZMVI1-2520COR201), the Federal Ministry of Education and Research within the framework of the network of university medicine (DEFEAT PANDEMICs, 01KX2021), and the German Federal Ministry of Food and Agriculture through the Federal Office for Agriculture and Food (project ZooSeq, grant number 2819114019).", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Klaus Hirschbuehl", - "author_inst": "Hematology and Oncology, Medical Faculty, University of Augsburg, Augsburg, Germany" - }, - { - "author_name": "Tina Schaller", - "author_inst": "General Pathology and Molecular Diagnostics, Medical Faculty, University of Augsburg, Augsburg, Germany" - }, - { - "author_name": "Bruno Maerkl", - "author_inst": "General Pathology and Molecular Diagnostics, Medical Faculty, University of Augsburg, Augsburg, Germany" - }, - { - "author_name": "Rainer Claus", - "author_inst": "General Pathology and Molecular Diagnostics, Medical Faculty, University of Augsburg, Augsburg, Germany and Hematology and Oncology, Medical Faculty, University" - }, - { - "author_name": "Eva Sipos", - "author_inst": "General Pathology and Molecular Diagnostics, Medical Faculty, University of Augsburg, Augsburg, Germany" - }, - { - "author_name": "Lukas Rentschler", - "author_inst": "General Pathology and Molecular Diagnostics, Medical Faculty, University of Augsburg, Augsburg, Germany" - }, - { - "author_name": "Andrea Maccagno", - "author_inst": "General Pathology and Molecular Diagnostics, Medical Faculty, University of Augsburg, Augsburg, Germany" - }, - { - "author_name": "Bianca Grosser", - "author_inst": "General Pathology and Molecular Diagnostics, Medical Faculty, University of Augsburg, Augsburg, Germany" - }, - { - "author_name": "Elisabeth Kling", - "author_inst": "Microbiology, Medical Faculty, University of Augsburg, Augsburg, Germany" - }, - { - "author_name": "Michael Neidig", - "author_inst": "IV. Medical Clinic, University Hospital Augsburg, Augsburg, Germany" - }, - { - "author_name": "Thomas Kroencke", - "author_inst": "Diagnostic and Interventional Radiology, Medical Faculty, University of Augsburg, Augsburg, Germany" - }, - { - "author_name": "Oliver Spring", - "author_inst": "Anesthesiology and Operative Intensive Care Medicine, Medical Faculty, University of Augsburg, Augsburg, Germany" - }, - { - "author_name": "Georg Braun", - "author_inst": "Gastroenterology, Medical Faculty, University of Augsburg, Augsburg, Germany" - }, - { - "author_name": "Hans Boesmueller", - "author_inst": "Institute for Pathology and Neuropathology, University Hospital of Thuebingen, Thuebingen, Germany" - }, - { - "author_name": "Maximilian Seidl", - "author_inst": "Institute of Pathology, University of Duesseldorf, Duesseldorf, Germany" - }, - { - "author_name": "Irene Esposito", - "author_inst": "Institute of Pathology, University of Duesseldorf, Duesseldorf, Germany" - }, - { - "author_name": "Jessica Pablik", - "author_inst": "Department of Pathology, Technische Universitaet Dresden, Dresden, Germany" - }, - { - "author_name": "Julia Hilsenbeck", - "author_inst": "Department of Pathology, Technische Universitaet Dresden, Dresden, Germany" - }, - { - "author_name": "Peter Boor", - "author_inst": "Insitute of Pathology, RWTH Aachen University Hospital, Aachen, Germany" - }, - { - "author_name": "Martin Beer", - "author_inst": "Institute of Diagnostic Virology, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany" - }, - { - "author_name": "Sebastian Dintner", - "author_inst": "General Pathology and Molecular Diagnostics, Medical Faculty, University of Augsburg, Augsburg, Germany" - }, - { - "author_name": "Claudia Wylezich", - "author_inst": "Institute of Diagnostic Virology, Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Greifswald-Insel Riems, Germany" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.12.03.21267146", "rel_title": "Internal Tremors and Vibration Symptoms Among People with Post-Acute Sequelae of SARS-CoV-2: A narrative review of patient reports", @@ -523695,6 +524385,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.30.470550", + "rel_title": "Direct lysis RT-qPCR of SARS-CoV-2 in cell culture supernatant allows for fast and accurate quantification of virus, opening a vast array of applications", + "rel_date": "2021-12-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.30.470550", + "rel_abs": "An enormous global effort is being made to study SARS-CoV-2 and develop safe and effective treatments. Studying the entire virus replication cycle of SARS-CoV-2 is essential to identify host factors and treatments to combat the infection. However, quantification of released virus often requires lengthy procedures, such as endpoint dilution assays or reinfection with engineered reporter viruses. Quantification of viral RNA in cell supernatant is faster and can be performed on clinical isolates. However, viral RNA purification is expensive in time and resources and often unsuitable for high-throughput screening. Here, we show a direct lysis RT-qPCR method allowing sensitive, accurate, fast, and cheap quantification of SARS-CoV-2 in culture supernatant. During lysis, the virus is completely inactivated, allowing further processing in low containment areas. This protocol facilitates a wide array of high- and low-throughput applications from basic quantification to studying the biology of SARS-CoV-2 and to identify novel antiviral treatments in vitro.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Nicky Craig", + "author_inst": "The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK" + }, + { + "author_name": "Sarah Louise Fletcher", + "author_inst": "The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK" + }, + { + "author_name": "Alison Daniels", + "author_inst": "The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK & Division of Infection Medicine, Unive" + }, + { + "author_name": "Caitlin Newman", + "author_inst": "The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK" + }, + { + "author_name": "Amanda Warr", + "author_inst": "The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK" + }, + { + "author_name": "Christine Tait-Burkard", + "author_inst": "The University Of Edinburgh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.11.30.470521", "rel_title": "SARS-CoV-2 Delta derivatives impact on neutralization of Covishield recipient sera", @@ -524227,65 +524956,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.30.21267071", - "rel_title": "Increased risk of psychiatric sequelae of COVID-19 is highest early in the clinical course", - "rel_date": "2021-12-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.30.21267071", - "rel_abs": "BackgroundCOVID-19 has been shown to increase the risk of adverse mental health consequences. A recent electronic health record (EHR)-based observational study showed an almost two-fold increased risk of new-onset mental illness in the first 90 days following a diagnosis of acute COVID-19.\n\nMethodsWe used the National COVID Cohort Collaborative, a harmonized EHR repository with 2,965,506 COVID-19 positive patients, and compared cohorts of COVID-19 patients with comparable controls. Patients were propensity score-matched to control for confounding factors. We estimated the hazard ratio (COVID-19:control) for new-onset of mental illness for the first year following diagnosis. We additionally estimated the change in risk for new-onset mental illness between the periods of 21-120 and 121-365 days following infection.\n\nFindingsWe find a significant increase in incidence of new-onset mental disorders in the period of 21-120 days following COVID-19 (3.8%, 3.6-4.0) compared to patients with respiratory tract infections (3%, 2.8-3.2). We further show that the risk for new-onset mental illness decreases over the first year following COVID-19 diagnosis compared to other respiratory tract infections and demonstrate a reduced (non-significant) hazard ratio over the period of 121-365 days following diagnosis. Similar findings are seen for new-onset anxiety disorders but not for mood disorders.\n\nInterpretationPatients who have recovered from COVID-19 are at an increased risk for developing new-onset mental illness, especially anxiety disorders. This risk is most prominent in the first 120 days following infection.\n\nFundingNational Center for Advancing Translational Sciences (NCATS).", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Ben Coleman", - "author_inst": "The Jackson Laboratory, Genomic Medicine, Farmington 6032, CT, USA" - }, - { - "author_name": "Elena Casiraghi", - "author_inst": "AnacletoLab, Dipartimento di Informatica, Universita degli Studi di Milano, Italy" - }, - { - "author_name": "Hannah Blau", - "author_inst": "The Jackson Laboratory, Genomic Medicine, Farmington 6032, CT, USA" - }, - { - "author_name": "Lauren Chan", - "author_inst": "College of Public Health and Human Sciences, Oregon State University, Corvallis, OR, USA" - }, - { - "author_name": "Melissa A Haendel", - "author_inst": "University of Colorado Anschutz Medical Campus, Center for Health AI, Aurora 80045, CO, USA" - }, - { - "author_name": "Bryan Laraway", - "author_inst": "University of Colorado Anschutz Medical Campus, Center for Health AI, Aurora 80045, CO, USA" - }, - { - "author_name": "Tiffany J Callahan", - "author_inst": "University of Colorado Anschutz Medical Campus, Center for Health AI, Aurora 80045, CO, USA" - }, - { - "author_name": "Rachel R Deer", - "author_inst": "University of Texas Medical Branch, Galveston, TX, 77550 USA" - }, - { - "author_name": "Ken Wilkins", - "author_inst": "Biostatistics Program, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland" - }, - { - "author_name": "Justin Reese", - "author_inst": "Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA" - }, - { - "author_name": "Peter N Robinson", - "author_inst": "The Jackson Laboratory, Genomic Medicine, Farmington 6032, CT, USA" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.11.30.21267074", "rel_title": "SARS-COV-2 INFECTION IN PRIMARY CARE: A SINGLE-CENTERED, RETROSPECTIVE, OBSERVATIONAL STUDY", @@ -525225,6 +525895,129 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.11.30.21266756", + "rel_title": "Association of subcutaneous or intravenous route of administration of casirivimab and imdevimab monoclonal antibodies with clinical outcomes in COVID-19.", + "rel_date": "2021-12-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.30.21266756", + "rel_abs": "ImportanceMonoclonal antibody (mAb) treatment decreases hospitalization and death in outpatients with mild to moderate COVID-19; however, only intravenous administration has been evaluated in randomized clinical trials of treatment. Subcutaneous administration may expand outpatient treatment capacity and qualified staff available to administer treatment, but association with patient outcomes is understudied.\n\nObjectiveTo evaluate whether or not, i.) subcutaneous casirivimab and imdevimab treatment is associated with reduced 28-day hospitalization/death than non-treatment among mAb-eligible patients, and ii.) subcutaneous casirivimab and imdevimab treatment is clinically and statistically similar to intravenous casirivimab and imdevimab treatment.\n\nDesign, Setting, and ParticipantsProspective cohort study of outpatients in a learning health system in the United States with mild to moderate COVID-19 symptoms from July 14 to October 26, 2021 who were eligible for mAb treatment under emergency use authorization. A nontreated control group of eligible patients was also selected.\n\nInterventionSubcutaneous injection or intravenous administration of the combined single dose of casirivimab 600mg and imdevimab 600mg.\n\nMain Outcomes and MeasuresThe primary outcome was the 28-day adjusted risk ratio or adjusted risk difference for hospitalization or death. Secondary outcomes included 28-day adjusted risk ratios/differences of hospitalization, death, composite endpoint of ED admission and hospitalization, and rates of adverse events.\n\nResultsAmong 1,956 matched adults with mild to moderate COVID-19, patients who received casirivimab and imdevimab subcutaneously had a 28-day rate of hospitalization/death of 3.4% (n=652) compared to 7.8% (n=1,304) in nontreated controls [risk ratio 0.44 (95% confidence interval: 0.28 to 0.68, p < .001)]. Among 2,185 patients treated with subcutaneous (n=969) or intravenous (n=1,216) casirivimab and imdevimab, the 28-day rate of hospitalization/death was 2.8% vs. 1.7%, respectively which resulted in an adjusted risk difference of 1.5% (95% confidence interval: -0.5% to 3.5%, p=.14). The 28-day adjusted risk differences (subcutaneous - intravenous) for death, ICU admission, and mechanical ventilation were 0.3% or less, although the 95% confidence intervals were wide.\n\nConclusions and RelevanceSubcutaneously administered casirivimab-imdevimab is associated with reduced risk-adjusted hospitalization or death amongst outpatients with mild to moderate COVID-19 compared to no treatment and indicates low adjusted risk difference compared to patients treated intravenously.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSAmong outpatients with mild to moderate COVID-19, is subcutaneously administered casirivimab and imdevimab associated with improved risk-adjusted 28-day clinical outcomes compared to non-treatment with monoclonal antibodies, and clinically similar association compared to intravenously administered casirivimab and imdevimab?\n\nFindingsAmong 1,956 propensity-matched adults, outpatients who received casirivimab and imdevimab subcutaneously had a 28-day rate of hospitalization or death of 3.4% (n=652) compared to 7.8% (n=1,304) in non-treated controls [risk ratio 0.44 (95% confidence interval: 0.28 to 0.68, p < .001)]. Among 2,185 outpatients who received subcutaneous (n=969) or intravenous (n=1,216) casirivimab and imdevimab, the 28-day rate of hospitalization/death was 2.8% vs. 1.7%, respectively, which resulted in an adjusted risk difference of 1.5% (95% confidence interval: -0.5% to 3.5%, p=.14). The 28-day adjusted risk differences comparing subcutaneous to intravenous route for death, ICU admission, and mechanical ventilation were 0.3% or less, although the 95% confidence intervals were wide.\n\nMeaningSubcutaneously administered casirivimab and imdevimab is associated with reduced hospitalization or death amongst outpatients with mild to moderate COVID-19 compared to no treatment, and has a small, adjusted risk difference compared to patients treated intravenously.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Erin K. McCreary", + "author_inst": "University of Pittsburgh School of Medicine" + }, + { + "author_name": "J. Ryan Bariola", + "author_inst": "University of Pittsburgh School of Medicine" + }, + { + "author_name": "Richard J. Wadas", + "author_inst": "University of Pittsburgh School of Medicine" + }, + { + "author_name": "Judith A. Shovel", + "author_inst": "University of Pittsburgh Medical Center" + }, + { + "author_name": "Mary K. Wisniewski", + "author_inst": "University of Pittsburgh Medical Center" + }, + { + "author_name": "Michelle Adam", + "author_inst": "University of Pittsburgh Medical Center" + }, + { + "author_name": "Debbie Albin", + "author_inst": "University of Pittsburgh Medical Center" + }, + { + "author_name": "Tami E. Minnier", + "author_inst": "University of Pittsburgh Medical Center" + }, + { + "author_name": "Mark Schmidhofer", + "author_inst": "University of Pittsburgh School of Medicine" + }, + { + "author_name": "Russell Meyers", + "author_inst": "University of Pittsburgh School of Medicine" + }, + { + "author_name": "Oscar C. Marroquin", + "author_inst": "University of Pittsburgh Medical Center" + }, + { + "author_name": "Kevin Collins", + "author_inst": "University of Pittsburgh Medical Center" + }, + { + "author_name": "William Garrard", + "author_inst": "University of Pittsburgh Medical Center" + }, + { + "author_name": "Lindsay R. Berrry", + "author_inst": "Berry Consultants, LLC" + }, + { + "author_name": "Scott Berry", + "author_inst": "Berry Consultants, LLC" + }, + { + "author_name": "Amy M. Crawford", + "author_inst": "Berry Consultants, LLC" + }, + { + "author_name": "Anna McGlothlin", + "author_inst": "Berry Consultants, LLC" + }, + { + "author_name": "Kelsey Linstrum", + "author_inst": "University of Pittsburgh Medical Center" + }, + { + "author_name": "Anna Nakayama", + "author_inst": "University of Pittsburgh Medical Center" + }, + { + "author_name": "Stephanie K. Montgomery", + "author_inst": "University of Pittsburgh Medical Center" + }, + { + "author_name": "Graham M. Snyder", + "author_inst": "University of Pittsburgh Medical Center" + }, + { + "author_name": "Donald M. Yealy", + "author_inst": "University of Pittsburgh School of Medicine" + }, + { + "author_name": "Derek C. Angus", + "author_inst": "University of Pittsburgh Medical Center" + }, + { + "author_name": "Paula L. Kip", + "author_inst": "University of Pittsburgh Medical Center" + }, + { + "author_name": "Christopher W. Seymour", + "author_inst": "University of Pittsburgh School of Medicine" + }, + { + "author_name": "David T. Huang", + "author_inst": "University of Pittsburgh School of Medicine" + }, + { + "author_name": "Kevin E. Kip", + "author_inst": "University of Pittsburgh Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.30.470470", "rel_title": "SARS-CoV-2 variants impact RBD conformational dynamics and ACE2 accessibility", @@ -525905,121 +526698,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.29.21267042", - "rel_title": "Favipiravir for the Treatment of Coronavirus Disease 2019; a propensity score-matched cohort study", - "rel_date": "2021-11-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.29.21267042", - "rel_abs": "BackgroundWe investigated clinical outcomes of favipiravir in patients with COVID-19 pneumonia.\n\nMethodsPatients who between 23 May 2020 and 18 July 2020 received [≥]24 hours of favipiravir were assigned to the favipiravir group, while those who did not formed the non-favipiravir group. The primary outcome was 28-day clinical improvement, defined as two-category improvement from baseline on an 8-point ordinal scale. Propensity scores (PS) for favipiravir therapy were used for 1:1 matching. Cox regression was used to examine associations with the primary endpoint.\n\nResultsThe unmatched cohort included 1,493 patients, of which 51.7% were in the favipiravir group, and 48.3% were not receiving supplemental oxygen at baseline. Favipiravir was started within a median of 5 days from symptoms onset. Significant baseline differences between the two unmatched groups existed, but not between the PS-matched groups (N = 774). After PS-matching, there were no significant differences between the two groups in the proportion with 28-day clinical improvement (93.3% versus 92.8%, P 0.780), or 28-day all-cause mortality (2.1% versus 3.1%, P 0.360). Favipiravir was associated with more viral clearance by day 28 (79.8% versus 64.1%, P <0.001). In the adjusted Cox proportional hazards model, favipiravir therapy was not associated 28-day clinical improvement (adjusted hazard ratio 0.978, 95% confidence interval 0.862 -1.109, P 0.726). Adverse events were common in both groups, but the 93.9% were Grades 1-3.\n\nConclusionFavipiravir therapy for COVID-19 pneumonia is well tolerated but is not associated with an increased likelihood of clinical improvement or reduced all-cause mortality by 28 days.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Rand A ALATTAR", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Shiema ABDALLA", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Tasneem AK ABDALLAH", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Rashid KAZMAN", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Aseelah QADMOUR", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Tawheeda BH IBRAHIM", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Bassem ALHARIRI", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Shahd SHAAR", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Abeer BAJWA", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Abeir BH ALIMAM", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Rabia QAZI", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Fatma BEN ABID", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Joanne DAGHFAL", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Ali M ELDEEB", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Kinda SHUKRI", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Ahmed ELSAYED", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Fatima RUSTOM", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Musaed ALSAMAWI", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Alaaeldin ABDELMAJID", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Miguel AP BASULTO", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Armando AR COBIAN", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Mohamed ABUKHATTAB", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Muna A ALMASLAMANI", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Abdullatif ALKHAL", - "author_inst": "Hamad Medical Corporation" - }, - { - "author_name": "Ali S OMRANI", - "author_inst": "Hamad Medical Corporation" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.29.21266947", "rel_title": "The immunogenicity and safety of different COVID-19 booster vaccination following CoronaVac or ChAdOx1 nCoV-19 primary series", @@ -527507,6 +528185,61 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.11.30.21266889", + "rel_title": "Normalisation of SARS-CoV-2 concentrations in wastewater: the use of flow, conductivity and CrAssphages", + "rel_date": "2021-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.30.21266889", + "rel_abs": "Over the course of the COVID-19 pandemic in 2020-2021, monitoring of SARS-CoV-2 RNA in wastewater has rapidly evolved into a supplementary surveillance instrument for public health. Short term trends (2 weeks) are used as a basis for policy and decision making on measures for dealing with the pandemic. Normalization is required to account for the varying dilution rates of the domestic wastewater, that contains the shedded virus RNA. The dilution rate varies due to runoff, industrial discharges and extraneous waters. Three normalization methods using flow, conductivity and CrAssphage, have been investigated on 9 monitoring locations between Sep 2020 and Aug 2021, rendering 1071 24-hour flow-proportional samples. In addition, 221 stool samples have been analyzed to determine the daily CrAssphage load per person. Results show that flow normalization supported by a quality check using conductivity monitoring is the advocated normalization method in case flow monitoring is or can be made available. Although Crassphage shedding rates per person vary greatly, the CrAssphage loads were very consistent over time and space and direct CrAssphage based normalization can be applied reliably for populations of 5600 and above.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Jeroen Langeveld", + "author_inst": "TU Delft" + }, + { + "author_name": "Remy Schilperoort", + "author_inst": "partners4urbanwater" + }, + { + "author_name": "Leo Heijnen", + "author_inst": "KWR, Water Research Institute" + }, + { + "author_name": "goffe elsinga", + "author_inst": "kwr water research institute" + }, + { + "author_name": "claudia schapendonk", + "author_inst": "Erasmus MC" + }, + { + "author_name": "ewout fanoy", + "author_inst": "GGD Rotterdam" + }, + { + "author_name": "evelien de schepper", + "author_inst": "erasmus MC" + }, + { + "author_name": "Marion Koopmans", + "author_inst": "Erasmus Medical Center" + }, + { + "author_name": "Miranda de Graaf", + "author_inst": "Erasmus MC" + }, + { + "author_name": "Gertjan Medema", + "author_inst": "KWR Water Research Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.29.21267004", "rel_title": "Phase Shift Between Age-Specific COVID-19 Incidence Curves Points to a Potential Epidemic Driver Function of Kids and Juveniles in Germany", @@ -527771,53 +528504,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.29.21266976", - "rel_title": "Impact of the COVID-19 pandemic on the malaria burden in northern Ghana: Analysis of routine surveillance data", - "rel_date": "2021-11-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.29.21266976", - "rel_abs": "IntroductionThe COVID-19 pandemic and its collateral damage severely impact health systems globally and risk to worsen the malaria situation in endemic countries. Malaria is a leading cause of morbidity and mortality in Ghana. This study aims to analyze routine surveillance data to assess possible effects on the malaria burden in the first year of the COVID-19 pandemic in the Northern Region of Ghana.\n\nMethodsMonthly routine data from the District Health Information Management System II (DHIMS2) of the Northern Region of Ghana were analyzed. Overall outpatient department visits and malaria incidence rates from the years 2015 to 2019 were compared to the corresponding data of the year 2020.\n\nResultsCompared to the corresponding periods of the years 2015 to 2019, overall visits and malaria incidence in pediatric and adult outpatient departments in northern Ghana decreased in March and April 2020, when major movement and social restrictions were implemented in response to the pandemic. Incidence slightly rebounded afterwards in 2020 but stayed below the average of the previous years. Data from inpatient departments showed a similar but more pronounced trend when compared to outpatient departments. In pregnant women, however, malaria incidence in outpatient departments increased after the first COVID-19 wave.\n\nDiscussionThe findings from this study show that the COVID-19 pandemic affects the malaria burden in health facilities of Ghana, with declines in in- and outpatient rates. Pregnant women may experience reduced access to intermittent preventive malaria treatment and insecticide treated nets, resulting in subsequent higher malaria morbidity. Further data from other African countries, particularly on community-based studies, are needed to fully determine the impact of the pandemic on the malaria situation.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Anna-Katharina Heuschen", - "author_inst": "Institute of Global Health, Medical School, Ruprecht-Karls-University Heidelberg, Germany" - }, - { - "author_name": "Alhassan Abdul-Mumin", - "author_inst": "University for Development Studies, School of Medicine, Department of Pediatrics and Child Health, Tamale, Ghana" - }, - { - "author_name": "Martin Nyaaba Adokiya", - "author_inst": "University for Development Studies, School of Public Health, Department of Epidemiology, Biostatistics and Disease Control, Tamale, Ghana" - }, - { - "author_name": "Guangyu Lu", - "author_inst": "School of Public Health, Medical School, Yangzhou University, China" - }, - { - "author_name": "Albrecht Jahn", - "author_inst": "Institute of Global Health, Medical School, Ruprecht-Karls-University Heidelberg, Germany" - }, - { - "author_name": "Oliver Razum", - "author_inst": "Department of Epidemiology and International Public Health, School of Public Health, Bielefeld University, Germany" - }, - { - "author_name": "Volker Winkler", - "author_inst": "Institute of Global Health, Medical School, Ruprecht-Karls-University Heidelberg, Germany" - }, - { - "author_name": "Olaf Mueller", - "author_inst": "Institute of Global Health, Medical School, Ruprecht-Karls-University Heidelberg, Germany" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.11.23.469709", "rel_title": "Genetic alteration of human MYH6 is mimicked by SARS-CoV-2 polyprotein: mapping viral variants of cardiac interest", @@ -529105,6 +529791,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2021.11.26.21266918", + "rel_title": "DEVELOPMENT AND TESTING OF A LOW-COST INACTIVATION BUFFER THAT ALLOWS DIRECT SARS-COV-2 DETECTION IN SALIVA", + "rel_date": "2021-11-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.26.21266918", + "rel_abs": "Massive testing is a cornerstone in efforts to effectively track infections and stop COVID-19 transmission, including places where good vaccination coverage has been achieved. However, SARS-CoV-2 testing by RT-qPCR requires specialized personnel, protection equipment, commercial kits, and dedicated facilities, which represent significant challenges for massive testing implementation in resource-limited settings. It is therefore important to develop testing protocols that facilitate implementation and are inexpensive, fast, and sufficiently sensitive. In this work, we optimized the composition of a buffer (PKTP) containing a protease, a detergent, and an RNase inhibitor, that is compatible with the RT-qPCR chemistry, allowing for direct testing of SARS-CoV-2 from saliva in an RNA extraction-independent manner. This buffer is compatible with heat-inactivation reducing the biohazard risk of handling the samples. We assessed the PKTP buffer performance in comparison to the RNA-extraction-based protocol of the US Centers for Disease Control and Prevention in saliva samples from 70 COVID-19 patients finding a good sensitivity (82.2% for the N1 and 84.4% for the N2 target, respectively) and correlations (R=0.77, p<0.001 for N1, and R=0.78, p<0.001 for N2). We also propose an auto-collection protocol for saliva samples and a multiplex reaction to reduce the number of PCR reactions per patient and further reduce overall costs while maintaining diagnostic standards in favor of massive testing.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Brandon Bustos-Garcia", + "author_inst": "Institute of Cellular Physiology (IFC), National Autonomous University of Mexico (UNAM)" + }, + { + "author_name": "Sylvia Garza-Manero", + "author_inst": "Institute of Cellular Physiology (IFC), National Autonomous University of Mexico (UNAM)" + }, + { + "author_name": "Nallely Cano-Dominguez", + "author_inst": "Institute of Cellular Physiology (IFC), National Autonomous University of Mexico" + }, + { + "author_name": "Dulce Maria Lopez Sanchez", + "author_inst": "Centre for Research in Infectious Diseases of the National Institute of Respiratory Diseases (CIENI/INER)" + }, + { + "author_name": "Gonzalo Salgado-Montes de Oca", + "author_inst": "Centre for Research in Infectious Diseases of the National Institute of Respiratory Diseases (CIENI/INER)" + }, + { + "author_name": "Alfonso Salgado-Aguayo", + "author_inst": "Centre for Research in Infectious Diseases of the National Institute of Respiratory Diseases (CIENI/INER)" + }, + { + "author_name": "Felix Recillas-Targa", + "author_inst": "Institute of Cellular Physiology (IFC), National Autonomous University of Mexico" + }, + { + "author_name": "Santiago Avila-Rios", + "author_inst": "National Institute of Respiratory Diseases" + }, + { + "author_name": "Julian Valdes", + "author_inst": "Institute of Cellular Physiology (IFC), National Autonomous University of Mexico" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.25.21266298", "rel_title": "Management and containment of a SARS-CoV-2 Beta variant outbreak at the Malawi University of Science and Technology", @@ -529661,41 +530398,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.21.21266633", - "rel_title": "SARS-CoV-2 vaccination predicts COVID-19 progression and outcomes in hospitalized patients", - "rel_date": "2021-11-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.21.21266633", - "rel_abs": "BackgroundSARS-CoV-2 vaccination might impact on clinical progression of cases with breakthrough COVID-19 disease.\n\nObjectiveto evaluate the impact of SARS-CoV-2 vaccination on disease progression in COVID-19 hospitalized patient\n\nMethods and FindingsTwo-hundred eighty-four consecutive COVID-19 hospitalized patients, including 50 vaccinated cases entered the study. Compared to unvaccinated cases, vaccinated patients were older, exhibited more comorbidities and did not differ for COVID-19 severity at admission. During hospitalisation, unvaccinated patients showed worse disease progression, including higher need of oxygen and higher risk of death compared to vaccinated patients (OR 3.3; 1.05-10.7 95% CI in the whole cohort and OR 54.8; 3.5-852 in the ventilated cases).\n\nDiscussionThese findings argue for an important reduction in severity among vaccine breakthrough infection compared to unvaccinated cases in COVID-19 disease.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "alessandro padovani", - "author_inst": "University of Brescia and ASST Spedalicivili of Brescia" - }, - { - "author_name": "Viviana Cristillo", - "author_inst": "University of Brescia and ASST Spedali Civili of Brescia" - }, - { - "author_name": "daniela tomasoni", - "author_inst": "University of Brescia and ASST Spedali CIvili of Brescia" - }, - { - "author_name": "stefano gipponi", - "author_inst": "University of Brescia and ASST Spedali CIvili of Brescia" - }, - { - "author_name": "Andrea Pilotto", - "author_inst": "University of Brescia and ASST Spedali CIvili of Brescia" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.24.21266834", "rel_title": "Role of antibodies, inflammatory markers, and echocardiographic findings in post-acute cardiopulmonary symptoms after SARS-CoV-2 infection", @@ -530975,6 +531677,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2021.11.23.21266761", + "rel_title": "Higher Limbic and Basal Ganglia volumes in surviving COVID-negative patients and the relations to fatigue.", + "rel_date": "2021-11-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.23.21266761", + "rel_abs": "BackgroundAmong systemic abnormalities caused by the novel coronavirus, little is known about the critical attack on the central nervous system (CNS). Few studies have shown cerebrovascular pathologies that indicate CNS involvement in acute patients. However, replication studies are necessary to verify if these effects persist in COVID-19 survivors more conclusively. Furthermore, recent studies indicate fatigue is highly prevalent among long-COVID patients. How morphometry in each group relate to work-related fatigue need to be investigated.\n\nMethodCOVID survivors were MRI scanned two weeks after hospital discharge. We hypothesized, these survivors will demonstrate altered gray matter volume (GMV) and experience higher fatigue levels when compared to healthy controls, leading to stronger correlation of GMV with fatigue. Voxel-based morphometry was performed on T1-weighted MRI images between 46 survivors and 30 controls. Unpaired two-sample t-test and multiple linear regression were performed to observe group differences and correlation of fatigue with GMV.\n\nResultsThe COVID group experienced significantly higher fatigue levels and GMV of this group was significantly higher within the Limbic System and Basal Ganglia when compared to healthy controls. Moreover, while a significant positive correlation was observed across the whole group between GMV and self-reported fatigue, COVID subjects showed stronger effects within the Posterior Cingulate, Precuneus and Superior Parietal Lobule.\n\nConclusionBrain regions with GMV alterations in our analysis align with both single case acute patient reports and current group level neuroimaging findings. We also newly report a stronger positive correlation of GMV with fatigue among COVID survivors within brain regions associated with fatigue, indicating a link between structural abnormality and brain function in this cohort.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Rakibul Hafiz", + "author_inst": "New Jersey Institute of Technology" + }, + { + "author_name": "Tapan Kumar Gandhi", + "author_inst": "Indian Institute of Technology (IIT), Delhi, India" + }, + { + "author_name": "Sapna Mishra", + "author_inst": "Indian Institute of Technology (IIT), Delhi, India" + }, + { + "author_name": "Alok Prasad", + "author_inst": "Metro Heart Institute With Multispecialty" + }, + { + "author_name": "Vidur Mahajan", + "author_inst": "Indian Institute of Technology (IIT), Delhi, India" + }, + { + "author_name": "Xin Di", + "author_inst": "New Jersey Institute of Technology (NJIT)" + }, + { + "author_name": "Benjamin H. Natelson", + "author_inst": "Icahn School of Medicine at Mount Sinai, Mount Sinai Hospital" + }, + { + "author_name": "Bharat B. Biswal", + "author_inst": "New Jersey Institute of Technology (NJIT)" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2021.11.22.21266712", "rel_title": "Human phospho-signaling networks of SARS-CoV-2 infection are rewired by population genetic variants", @@ -531595,57 +532344,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.22.21266713", - "rel_title": "In Vitro Nasal Tissue Model for the Validation of Nasopharyngeal and Mid-turbinate Swabs for SARS-CoV-2 Testing", - "rel_date": "2021-11-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.22.21266713", - "rel_abs": "Large-scale population testing is a key tool to mitigate the spread of respiratory pathogens, as in the current COVID-19 pandemic, where swabs are used to collect samples in the upper airways (e.g. nasopharyngeal and mid-turbinate nasal cavities) for diagnostics. However, the high volume of supplies required to achieve large-scale population testing has posed unprecedented challenges for swab manufacturing and distribution, resulting in a global shortage that has heavily impacted testing capacity world-wide and prompted the development of new swabs suitable for large-scale production. Newly designed swabs require rigorous pre-clinical and clinical validation studies that are costly and time consuming (i.e. months to years long); reducing the risks associated with swab validation is therefore paramount for their rapid deployment. To address these shortages, we developed a 3D-printed tissue model that mimics the nasopharyngeal and mid-turbinate nasal cavities, and we validated its use as a new tool to rapidly test swab performance. In addition to the nasal architecture, the tissue model mimics the soft nasal tissue with a silk-based sponge lining, and the physiological nasal fluid with asymptomatic and symptomatic viscosities of synthetic mucus. We performed several assays comparing standard flocked and injection-molded swabs. We quantified the swab pick-up and release, and determined the effect of viral load and mucus viscosity on swab efficacy by spiking the synthetic mucus with heat-inactivated SARS-CoV-2 virus. By molecular assays, we found that injected molded swabs performed similarly or superiorly in comparison to standard flocked swabs and we underscored a viscosity-dependent difference in cycle threshold values between the asymptomatic and symptomatic mucus for both swabs. To conclude, we developed an in vitro nasal tissue model, that corroborated previous swab performance data from clinical studies, with the potential of providing researchers with a clinically relevant, reproducible, safe, and cost-effective validation tool for the rapid development of newly designed swabs.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Devon R Hartigan", - "author_inst": "University of Massachusetts Lowell" - }, - { - "author_name": "Miryam Adelfio", - "author_inst": "University of Massachusetts Lowell" - }, - { - "author_name": "Molly E Shutt", - "author_inst": "University of Massachusetts Lowell" - }, - { - "author_name": "Stephanie M Jones", - "author_inst": "University of Massachusetts Lowell" - }, - { - "author_name": "Shreya Patel", - "author_inst": "University of Massachusetts Lowell" - }, - { - "author_name": "Joshua T Marchand", - "author_inst": "University of Massachusetts Lowell" - }, - { - "author_name": "Pamela D McGuinness", - "author_inst": "University of Massachusetts Lowell" - }, - { - "author_name": "Bryan O Buchholz", - "author_inst": "University of Massachusetts Lowell" - }, - { - "author_name": "Chiara Elia Ghezzi", - "author_inst": "University of Massachusetts Lowell" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.22.21266540", "rel_title": "The role of multi-generational household clusters in COVID-19 in England", @@ -532869,6 +533567,37 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.11.24.21266779", + "rel_title": "Severe COVID-19 induces molecular signatures of aging in the human brain", + "rel_date": "2021-11-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.24.21266779", + "rel_abs": "Coronavirus disease 2019 (COVID-19) is predominantly an acute respiratory disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and remains a significant threat to public health. COVID-19 is accompanied by neurological symptoms and cognitive decline, but the molecular mechanisms underlying this effect remain unclear. As aging induces distinct molecular signatures in the brain associated with cognitive decline in healthy populations, we hypothesized that COVID-19 may induce molecular signatures of aging. Here, we performed whole transcriptomic analysis of human frontal cortex, a critical area for cognitive function, in 12 COVID-19 cases and age- and sex-matched uninfected controls. COVID-19 induces profound changes in gene expression, despite the absence of detectable virus in brain tissue. Pathway analysis shows downregulation of genes involved in synaptic function and cognition and upregulation of genes involved in immune processes. Comparison with five independent transcriptomic datasets of aging human frontal cortex reveals striking similarities between aged individuals and severe COVID-19 patients. Critically, individuals below 65 years of age exhibit profound transcriptomic changes not observed among older individuals in our patient cohort. Our data indicate that severe COVID-19 induces molecular signatures of aging in the human brain and emphasize the value of neurological follow-up in recovered individuals.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Maria Mavrikaki", + "author_inst": "Beth Israel Deaconess Medical Center, Harvard Medical School" + }, + { + "author_name": "Jonathan D. Lee", + "author_inst": "Beth Israel Deaconess Medical Center, Harvard Medical School" + }, + { + "author_name": "Isaac H. Solomon", + "author_inst": "Brigham and Women's Hospital, Harvard Medical School" + }, + { + "author_name": "Frank J. Slack", + "author_inst": "Beth Israel Deaconess Medical Center, Harvard Medical School" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2021.11.24.21266741", "rel_title": "A genome-wide association study of COVID-19 related hospitalization in Spain reveals genetic disparities among sexes", @@ -533341,37 +534070,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.22.21266599", - "rel_title": "Modeling on Wastewater Treatment Process in Saudi Arabia: a perspective of Covid-19", - "rel_date": "2021-11-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.22.21266599", - "rel_abs": "The novel coronavirus disease (COVID-19) pandemic has had devastating effects on healthcare systems and the global economy. Moreover, coronavirus has been found in human feces, sewage, and in wastewater treatment plants. In this paper, we highlight the transmission behavior, occurrence, and persistence of the virus in sewage and wastewater treatment plants. Our approach follows the process of identifying a coronavirus hotspot through existing wastewater plants in major cities of Saudi Arabia. The mathematical distributions, including the log-normal distribution, Gaussian model, and susceptible exposed infected recovery (SEIR) model, are adopted to predict the coronavirus load in wastewater plants. We highlight not only the potential virus removal techniques from wastewater treatment plants, but also methods of tracing SARS-CoV-2 in humans through wastewater treatment plants.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Abdullah A Ahmadini", - "author_inst": "Jazan University" - }, - { - "author_name": "Ahmed Msmali Hussein", - "author_inst": "Jazan University" - }, - { - "author_name": "Zico Meetei Mutum", - "author_inst": "Jazan University" - }, - { - "author_name": "Yaspal Raghav Singh", - "author_inst": "Jazan University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.11.24.21266735", "rel_title": "Increased risk of infection with SARS-CoV-2 Beta, Gamma, and Delta variant compared to Alpha variant in vaccinated individuals", @@ -534831,6 +535529,37 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.11.18.469065", + "rel_title": "Immune escape facilitation by mutations of epitope residues in RdRp of SARS-CoV-2", + "rel_date": "2021-11-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.18.469065", + "rel_abs": "SARS-CoV-2 has considerably higher mutation rate. SARS-CoV-2 possesses a RNA dependent RNA polymerase (RdRp) which helps to replicate its genome. The mutation P323L in RdRp is associated with the loss of a particular epitope (321-327) from this protein which may influence the pathogenesis of the concern SARS-CoV-2 through the development of antibody escape variants. We consider the effect of mutations in some of the epitope regions including the naturally occurring mutation P323L on the structure of the epitope and their interface with paratope using all-atom molecular dynamics (MD) simulation studies. P323L mutations cause conformational changes in the epitope region by opening up the region associated with increase in the radius of gyration and intramolecular hydrogen bonds, making the region less accessible. Moreover, the fluctuations in the dihedral angles in the epitope:paratope (IgG) interface increase which destabilize the interface. Such mutations may help in escaping antibody mediated immunity of the host.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Aayatti Mallick Gupta", + "author_inst": "S N Bose National Centre for Basic Sciences" + }, + { + "author_name": "Sasthi Charan Mandal", + "author_inst": "S N Bose National Centre for Basic Sciences" + }, + { + "author_name": "Jaydeb Chakrabarti", + "author_inst": "S N Bose National Centre for Basic Sciences" + }, + { + "author_name": "Sukhendu Mandal", + "author_inst": "University of Calcutta" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.11.19.469335", "rel_title": "Acute SARS-CoV-2 infection in pregnancy is associated with placental ACE-2 shedding", @@ -535191,57 +535920,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.11.19.21266581", - "rel_title": "Baseline hypocapnia is associated with intubation in COVID-19 diagnosed patients", - "rel_date": "2021-11-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.19.21266581", - "rel_abs": "IntroductionHypocapnia may be one of the several factors predefining the need for intubation of patients needing hospitalization for COVID-19 pneumonia.\n\nMethodsA retrospective evaluation of patient files hospitalized for COVID-19 pneumonia from October 2020 until January 2021. Univariate and multivariate regression was used, as well as a multinomial regression to account for multiple endpoints (discharge, intubation, death).\n\nResultsHypocapnia was strongly associated with intubation (OR: 0.86, 95% CI: 0.76, 0.97). Additionally, last pCO2 (OR: 1.08, 95% CI: 1.01, 1.16), baseline FiO2 (OR: 1.05, 95% CI: 1.03, 1.07) as well as last FiO2 (OR: 1.21, 95% CI: 1.11, 1.46), total severity score on admission (OR: 1.18, 95% CI: 1.03, 1.37) and last pO2 (OR: 0.89, 95% CI: 0.85, 0.92) were found to have a significant impact on intubation. Incorporation of deceased patients withheld the negative association with pCO2 levels (OR: 0.88, 95% CI: 0.78, 0.98).\n\nConclusionThe dissociation between respiratory failure and a clinically comfortable patient is partly due to decreased carbon dioxide levels and clinicians should bare it in mind when handling patients with COVID-19 pneumonia. Hypocapnia seems to be a determinant factor of intubation in patients with COVID-19 pneumonia in this study.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Athanasios Gounidis Dr", - "author_inst": "Department of Internal Medicine, Agios Pavlos General Hospital of Thessaloniki" - }, - { - "author_name": "Alexandros Evangeliou Dr", - "author_inst": "Department of Internal Medicine, Agios Pavlos General Hospital of Thessaloniki" - }, - { - "author_name": "Christina Kloura Dr", - "author_inst": "Department of Internal Medicine, Agios Pavlos General Hospital of Thessaloniki" - }, - { - "author_name": "Evangelia Magganari Dr", - "author_inst": "Department of Internal Medicine, Agios Pavlos General Hospital of Thessaloniki" - }, - { - "author_name": "Christiana Parisi Dr", - "author_inst": "Department of Internal Medicine, Agios Pavlos General Hospital of Thessaloniki" - }, - { - "author_name": "Michail Kourtidis Dr", - "author_inst": "Department of Internal Medicine, Agios Pavlos General Hospital of Thessaloniki" - }, - { - "author_name": "Martha Apostolopoulou Dr", - "author_inst": "Department of Internal Medicine, Agios Pavlos General Hospital of Thessaloniki" - }, - { - "author_name": "Georgios Kotronis Dr", - "author_inst": "Department of Internal Medicine, Agios Pavlos General Hospital of Thessaloniki" - }, - { - "author_name": "Fani Apostolidou Kiouti MD", - "author_inst": "Laboratory of Hygiene, Social & Preventive Medicine and Medical Statistics, Medical Faculty, Aristotle University of Thessaloniki" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2021.11.18.21266489", "rel_title": "Causal Inference and COVID-19 Nursing Home Patients: Identifying Factors That Reduced Mortality Risk", @@ -536397,6 +537075,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.17.21266473", + "rel_title": "ROLE OF BODY MASS AND PHYSICAL ACTIVITY IN AUTONOMIC FUNCTION MODULATION ON POST-COVID-19 CONDITION: AN OBSERVATIONAL SUBANALYSIS OF FIT-COVID STUDY", + "rel_date": "2021-11-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.17.21266473", + "rel_abs": "The harmful effects of coronavirus disease 2019 (COVID-19) can reach the autonomic nervous system (ANS) and endothelial function. Therefore, the detrimental multiorgan effects of COVID-19 could be induced by deregulations in ANS that may persist after the acute SARS-CoV-2 infection. Additionally, investigating the differences in ANS response in overweight/obese, and physically inactive participants who had COVID-19 compared to those who did not have the disease is necessary. The aim of the study was to analyze the autonomic function of young adults after mild-to-moderate infection with COVID-19 and to assess whether body mass index (BMI) and levels of physical activity modulates autonomic function in participants with and without COVID-19. Patients previously infected with COVID-19 and healthy controls were recruited for this cross-sectional observational study. A general anamnesis was taken and BMI and physical activity levels were assessed. The ANS was evaluated through heart rate variability. A total of 57 subjects were evaluated. Sympathetic nervous system activity in post-COVID-19 group was increased (stress index; p=0.0273). They also presented lower values of parasympathetic activity (p<0.05). Overweight/obese subjects in the post-COVID-19 group presented significantly lower parasympathetic activity and reduced global variability compared to non-obese in control group (p<0.05). Physically inactive subjects in post-COVID-19 group presented significantly higher sympathetic activity than active subjects in control group. Parasympathetic activity was significantly increased in physically active subjects in control group compared to the physically inactive post-COVID-19 group (p<0.05). COVID-19 promotes changes in the ANS of young adults, and these changes are modulated by Overweight/obesity and physical activity levels.\n\nKey Points- Our main finding is that even in mild and moderate infections, young adults who had COVID-19 had greater sympathetic activity, less parasympathetic activity, and global variability when compared to uninfected individuals.\n- In participants who were overweight and obese and/or physically inactive, cardiac autonomic modulation showed worse indices.\n- Our study provides new insights regarding the role of body mass index and physical activity status on post-COVID-19 infection autonomic deregulation that may contribute to the understand of pathophysiology and treatment of of post-acute sequelae SARS-CoV-2 infection.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Ana Paula Figueira Freire", + "author_inst": "Universidade do Oeste Paulista" + }, + { + "author_name": "Fabio Santos de Lira", + "author_inst": "Universidade Estadual Paulista" + }, + { + "author_name": "Ana Elisa von Ah Morano", + "author_inst": "Universidade Estadual Paulista" + }, + { + "author_name": "Telmo Pereira", + "author_inst": "University of Coimbra" + }, + { + "author_name": "Manuel-Joao Coelho Silva", + "author_inst": "University of Coimbra" + }, + { + "author_name": "Armando Caseiro", + "author_inst": "University of Coimbra" + }, + { + "author_name": "Diego Giulliano Destro Christofaro", + "author_inst": "Universidade Estadual Paulista" + }, + { + "author_name": "Osmar Marchioto Jr.", + "author_inst": "Universidade Estadual Paulista" + }, + { + "author_name": "Gilson Pires Dorneles", + "author_inst": "Universidade Federal de Ciencias da Saude de Porto Alegre" + }, + { + "author_name": "Ricardo Aurino Pinho", + "author_inst": "Pontificia Universidade Catolica Do Parana" + }, + { + "author_name": "Bruna Spolador de Alencar Silva", + "author_inst": "Universidade Estadual Paulista" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2021.11.19.468693", "rel_title": "The Effect of COVID-19 on the Postdoctoral Experience: a comparison of pre-pandemic and pandemic surveys.", @@ -536913,89 +537650,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.17.21266367", - "rel_title": "A prospective study of asymptomatic SARS-CoV-2 infection among individuals involved in academic research under limited operations during the COVID-19 pandemic", - "rel_date": "2021-11-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.17.21266367", - "rel_abs": "BackgroundEarly in the pandemic, transmission risk from asymptomatic infection was unclear making it imperative to monitor infection in workplace settings. Further, data on SARS-CoV-2 seroprevalence within university populations has been limited.\n\nMethodsWe performed a longitudinal study of University research employees on campus July-December 2020. We conducted questionnaires on COVID-19 risk factors, RT-PCR testing, and SARS-CoV-2 serology using an in-house spike RBD assay, laboratory-based Spike NTD assay, and standard nucleocapsid platform assay. We estimated prevalence and cumulative incidence of seroconversion with 95% confidence intervals using the inverse of the Kaplan-Meier estimator.\n\nResults910 individuals were included in this analysis. At baseline, 6.2% (95% CI 4.29-8.19) were seropositive using the spike RBD assay; four (0.4%) were seropositive using the nucleocapsid assay, and 44 (4.8%) using the Spike NTD assay. Cumulative incidence was 3.61% (95% CI: 2.04-5.16). Six asymptomatic individuals had positive RT-PCR results.\n\nConclusionsPrevalence and incidence of SARS-CoV-2 infections was low; however differences in target antigens of serological tests provided different estimates. Future research on appropriate methods of serological testing in unvaccinated and vaccinated populations is needed. Frequent RT-PCR testing of asymptomatic individuals is required to detect acute infections, and repeated serosurveys are beneficial for monitoring subclinical infection.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Audrey Pettifor", - "author_inst": "Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599" - }, - { - "author_name": "Bethany L DiPrete", - "author_inst": "Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599; Injury Prevention Rese" - }, - { - "author_name": "Bonnie E Shook-Sa", - "author_inst": "Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599" - }, - { - "author_name": "Lakshmanane Premkumar", - "author_inst": "Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599" - }, - { - "author_name": "Kriste Kuczynski", - "author_inst": "Department of Social Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599" - }, - { - "author_name": "Dirk Dittmer", - "author_inst": "Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599" - }, - { - "author_name": "Allison Aiello", - "author_inst": "Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599" - }, - { - "author_name": "Shannon Wallet", - "author_inst": "Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599; Division of Oral and Craniofa" - }, - { - "author_name": "Robert Maile", - "author_inst": "Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599; Department of Surgery, School" - }, - { - "author_name": "Joyce Tan", - "author_inst": "Department of Genetics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599" - }, - { - "author_name": "Ramesh Jadi", - "author_inst": "Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599" - }, - { - "author_name": "Linda Pluta", - "author_inst": "Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599" - }, - { - "author_name": "Aravinda M de Silva", - "author_inst": "Department of Microbiology and Immunology, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599" - }, - { - "author_name": "David J Weber", - "author_inst": "Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599; Division of Infectious " - }, - { - "author_name": "Min Kim", - "author_inst": "Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599" - }, - { - "author_name": "Arlene C Se\u00f1a", - "author_inst": "Division of Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599" - }, - { - "author_name": "Corbin D Jones", - "author_inst": "Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.11.16.21266265", "rel_title": "Strategy for a rapid screening and surveillance of SARS-CoV-2 variants by real time RT-PCR: a key tool that allowed control and delay in Delta spread in Cordoba, Argentina", @@ -538107,6 +538761,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.11.19.21266532", + "rel_title": "Monitoring of SARS-CoV-2 Antibodies Using Dried Blood Spot for At-Home Collection", + "rel_date": "2021-11-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.19.21266532", + "rel_abs": "The utilization of vaccines to fight the spread of SARS-CoV-2 has led to a growing need for expansive serological testing. To address this, an EUA approved immunoassay for detection of antibodies to SARS-CoV-2 in venous serum samples was investigated for use with dried blood spot (DBS) samples. Results from self-collected DBS samples demonstrated a 98.1% categorical agreement to venous serum with a correlation (R) of 0.9600 while professionally collected DBS samples demonstrated a categorical agreement of 100.0% with a correlation of 0.9888 to venous serum. Additional studies were performed to stress aspects of at-home DBS collection, including shipping stability, interference effects, and other sample-specific robustness studies. These studies demonstrated a categorical agreement of at least 95.0% and a mean bias less than {+/-}20.0%. Furthermore, the ability to track antibody levels following vaccination with the BioNTech/Pfizer vaccine was demonstrated with self-collected DBS samples from pre-dose (Day 0) out to 19 weeks.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Peyton K Miesse", + "author_inst": "Laboratory Corporation of America Holdings" + }, + { + "author_name": "Bradley B Collier", + "author_inst": "Laboratory Corporation of America Holdings" + }, + { + "author_name": "Russell P Grant", + "author_inst": "Laboratory Corporation of America Holdings" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.19.21266552", "rel_title": "Low neutralizing antibody titers against the Mu variant of SARS-CoV-2 in BNT162b2 vaccinated individuals", @@ -538523,29 +539204,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.16.21266414", - "rel_title": "Unraveling the spatiotemporal spread of COVID-19 in Brazil through spatial network connectivity", - "rel_date": "2021-11-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.16.21266414", - "rel_abs": "BackgroundDescribing and understanding the process of diffusion can allow local managers better plan emergence scenarios. Thus, the main aim of this study was to describe and unveil the spatiotemporal patterns of diffusion of the COVID-19 in Brazil from February 2020 until April 2021.\n\nMethodsThis is a retrospective purely observational ecologic study including all notified cases and deaths. We used satellite-derived night light imagery and spatiotemporal Empirical Orthogonal Function analysis to quantify the spatial network structure of lighted development and the spatiotemporal transmission of the pathogen through the network.\n\nResultsThe more populous state capitals within the largest network components presented higher frequency of deaths and earlier onset compared to the increasing numbers of smaller, less populous municipalities trending toward lower frequency of deaths and later onset. By week 48 2020, the full network was almost completely affected. Cases and deaths showed a distinct second wave of wider geographic expansion beginning in early November 2020.\n\nConclusionsThe spatiotemporal diffusion in Brazil was characterized by an intertwined process of overseas relocation, hierarchical network transmission and contagious effects. A rapid response as the immediate control of all ports, airports and borders combined with mandatory quarantine are critical to retard disease diffusion.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ligia V Barrozo", - "author_inst": "Universidade de Sao Paulo" - }, - { - "author_name": "Christopher Small", - "author_inst": "Columbia University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.11.16.21266350", "rel_title": "A booster dose of an inactivated vaccine increases neutralizing antibodies and T cell responses against SARS-CoV-2", @@ -539845,6 +540503,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2021.11.15.21266264", + "rel_title": "Association of COVID-19 employment disruption with mental and social wellbeing: evidence from nine UK longitudinal studies", + "rel_date": "2021-11-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.15.21266264", + "rel_abs": "BackgroundThe COVID-19 pandemic has led to major economic disruptions. In March 2020, the UK implemented the Coronavirus Job Retention Scheme - known as furlough - to minimize the impact of job losses. We investigate associations between change in employment status and mental and social wellbeing during the early stages of the pandemic.\n\nMethodsData were from 25,670 respondents, aged 17 to 66, across nine UK longitudinal studies. Furlough and other employment changes were defined using employment status pre-pandemic and during the first lockdown (April-June 2020). Mental and social wellbeing outcomes included psychological distress, life satisfaction, self-rated health, social contact, and loneliness. Study-specific modified Poisson regression estimates, adjusting for socio-demographic characteristics and pre-pandemic mental and social wellbeing measures, were pooled using meta-analysis.\n\nResultsCompared to those who remained working, furloughed workers were at greater risk of psychological distress (adjusted risk ratio, ARR=1.12; 95% CI: 0.97, 1.29), low life satisfaction (ARR=1.14; 95% CI: 1.07, 1.22), loneliness (ARR=1.12; 95% CI: 1.01, 1.23), and poor self-rated health (ARR=1.26; 95% CI: 1.05, 1.50), but excess risk was less pronounced than that of those no longer employed (e.g., ARR for psychological distress=1.39; 95% CI: 1.21, 1.59) or in stable unemployment (ARR=1.33; 95% CI: 1.09, 1.62).\n\nConclusionsDuring the early stages of the pandemic, those furloughed had increased risk for poor mental and social wellbeing. However, their excess risk was lower in magnitude than that of those who became or remained unemployed, suggesting that furlough may have partly mitigated poorer outcomes.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Jacques Wels", + "author_inst": "University College London" + }, + { + "author_name": "Charlotte Booth", + "author_inst": "University College London" + }, + { + "author_name": "Bozena Wielgoszewska", + "author_inst": "University College London" + }, + { + "author_name": "Michael J Green", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Giorgio Di Gessa", + "author_inst": "University College London" + }, + { + "author_name": "Charlotte F Huggins", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Gareth J Griffith", + "author_inst": "University of Bristol" + }, + { + "author_name": "Alex Siu Fung Kwong", + "author_inst": "University of Bristol" + }, + { + "author_name": "Ruth C E Bowyer", + "author_inst": "King's College London" + }, + { + "author_name": "Jane Maddock", + "author_inst": "University College London" + }, + { + "author_name": "Praveetha Patalay", + "author_inst": "University College London" + }, + { + "author_name": "Richard J Silverwood", + "author_inst": "University College London" + }, + { + "author_name": "Emla Fitzsimons", + "author_inst": "University College London" + }, + { + "author_name": "Richard John Shaw", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Ellen J Thompson", + "author_inst": "Kings College London" + }, + { + "author_name": "Andrew Steptoe", + "author_inst": "University College London" + }, + { + "author_name": "Alun Hughes", + "author_inst": "University College London" + }, + { + "author_name": "Nishi Chaturvedi", + "author_inst": "University College London" + }, + { + "author_name": "Claire J Steves", + "author_inst": "King's College London" + }, + { + "author_name": "Srinivasa Vittal Katikireddi", + "author_inst": "University of Glasgow" + }, + { + "author_name": "George B Ploubidis", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.11.16.21266383", "rel_title": "High COVID-19 vaccine coverage allows for a re-opening of European universities", @@ -540177,81 +540934,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.16.21266391", - "rel_title": "From online data collection to identification of disease mechanisms: The IL-1beta, IL-6 and TNF-alpha; cytokine triad is associated with post-acute sequelae of COVID-19 in a digital research cohort", - "rel_date": "2021-11-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.16.21266391", - "rel_abs": "Post-acute sequelae of COVID-19 (PASC) emerge as a global problem with unknown molecular drivers. In a digital epidemiology approach, we rapidly recruited 8,077 individuals out of 129,733 households in Halle (Saale) to the cohort study for digital health research in Germany (DigiHero). These responded to a basic questionnaire followed by a PASC-focused survey and blood sampling in case of prior positive SARS-CoV-2 testing in their household. The presented analysis is based on the first 318 DigiHero participants, the majority thereof after mild infections. PASC were reported in 67.8% of cases, consisted predominantly in fatigue, dyspnea and concentration deficit, persisted in 60% over the follow-up period of on average eight months and their resolution was unaffected by post-infection vaccination. PASC was not associated with post-COVID-19 autoantibodies, but with elevated levels of IL-1{beta}, IL-6 and TNF-. Blood profiling and single-cell data from validation cohorts with early infection suggested the induction of these cytokines in COVID-19 lung pro-inflammatory macrophages creating a self-sustaining feedback loop. Our data indicate a long-lasting cytokine triad -potentially underlying PASC symptoms - to be driven by macrophage primed during infection. We demonstrate how the combination of digital epidemiology with selective biobanking can rapidly generate hints towards disease mechanisms.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Christoph Schultheiss", - "author_inst": "Martin-Luther-University Halle-Wittenberg, Internal Medicine IV" - }, - { - "author_name": "Edith Willscher", - "author_inst": "Martin-Luther-University Halle-Wittenberg, Internal Medicine IV" - }, - { - "author_name": "Lisa Paschold", - "author_inst": "Martin-Luther-University Halle-Wittenberg, Internal Medicine IV" - }, - { - "author_name": "Cornelia Gottschick", - "author_inst": "Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin-Luther Univer" - }, - { - "author_name": "Bianca Klee", - "author_inst": "Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin-Luther Univer" - }, - { - "author_name": "Svenja-Sibylla Henkes", - "author_inst": "Martin-Luther-University Halle-Wittenberg, Internal Medicine IV" - }, - { - "author_name": "Lidia Bosurgi", - "author_inst": "Department of Medicine, University Medical Center Hamburg-Eppendorf" - }, - { - "author_name": "Jochen Dutzmann", - "author_inst": "Mid-German Heart Center, Department of Cardiology and Intensive Care Medicine, University Hospital, Martin-Luther-University Halle-Wittenberg" - }, - { - "author_name": "Daniel Sedding", - "author_inst": "Mid-German Heart Center, Department of Cardiology and Intensive Care Medicine, University Hospital, Martin-Luther-University Halle-Wittenberg" - }, - { - "author_name": "Thomas Frese", - "author_inst": "Institute of General Practice and Family Medicine, Martin-Luther-University Halle-Wittenberg" - }, - { - "author_name": "Matthias Girndt", - "author_inst": "Department of Internal Medicine II, Martin-Luther-University Halle-Wittenberg" - }, - { - "author_name": "Jessica I. Hoell", - "author_inst": "Pediatric Hematology and Oncology, Martin-Luther-University Halle-Wittenberg" - }, - { - "author_name": "Michael Gekle", - "author_inst": "Julius Bernstein-Institute of Physiology, Faculty of Medicine, Martin-Luther-University Halle-Wittenberg" - }, - { - "author_name": "Rafael Mikolajczyk", - "author_inst": "Institute for Medical Epidemiology, Biometrics and Informatics (IMEBI), Interdisciplinary Center for Health Sciences, Medical School of the Martin-Luther Univer" - }, - { - "author_name": "Mascha Binder", - "author_inst": "Martin-Luther-University Halle-Wittenberg, Internal Medicine IV" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.14.21266214", "rel_title": "Pulmonary thromboembolism in COVID-19 Patients on CT Pulmonary Angiography - A Single-Centre Retrospective Cohort Study in the United Arab Emirates", @@ -541787,6 +542469,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.11.14.21266294", + "rel_title": "Inactivated virus vaccine BBV152/Covaxin elicits robust cellular immune memory to SARS-CoV-2 and variants of concern", + "rel_date": "2021-11-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.14.21266294", + "rel_abs": "The characteristics of immune memory established in response to inactivated SARS-CoV-2 vaccines remains unclear. We determined the magnitude, quality and persistence of cellular and humoral memory responses up to 6 months after vaccination with BBV152/Covaxin. Here, we show that the quantity of vaccine-induced spike- and nucleoprotein-antibodies is comparable to that following natural infection and the antibodies are detectable up to 6 months. The RBD-specific antibodies decline in the range of 3 to 10-fold against the SARS-CoV-2 variants in the order of alpha (B.1.1.7) > delta (B.1.617.2) > beta (B.1.351), with no observed impact of gamma (P.1) and kappa (B.1.617.1) variant. We found that the vaccine induces memory B cells, similar to natural infection, which are impacted by virus variants in the same order as antibodies. The vaccine further induced antigen-specific functionally potent multi-cytokine expressing CD4+ T cells in [~]85% of the subjects, targeting spike and nucleoprotein of SARS-CoV-2. Marginal [~]1.3 fold-reduction was observed in vaccine-induced CD4+ T cells against the beta variant, with no significant impact of the alpha and the delta variants. The antigen-specific CD4+ T cells were populated in the central memory compartment and persisted up to 6 months of vaccination. Importantly the vaccine generated Tfh cells that are endowed with B cell help potential, similar to the Tfh cells induced after natural infection. Altogether, these findings establish that the inactivated virus vaccine BBV152 induces robust immune memory to SARS-CoV-2 and variants of concern, which persist for at least 6 months after vaccination. This study provides insight into the attributes of BBV152-elicited immune memory, and has implication for future vaccine development, guidance for use of inactivated virus vaccine, and booster immunization.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Rajesh Vikkurthi", + "author_inst": "Vaccine Immunology Laboratory, National Institute of Immunology, New Delhi, 110067, India" + }, + { + "author_name": "Asgar Ansari", + "author_inst": "Vaccine Immunology Laboratory, National Institute of Immunology, New Delhi, 110067, India" + }, + { + "author_name": "Anupama R Pai", + "author_inst": "Vaccine Immunology Laboratory, National Institute of Immunology, New Delhi, 110067, India" + }, + { + "author_name": "Someshwar Nath Jha", + "author_inst": "Vaccine Immunology Laboratory, National Institute of Immunology, New Delhi, 110067, India" + }, + { + "author_name": "Shilpa Sachan", + "author_inst": "Vaccine Immunology Laboratory, National Institute of Immunology, New Delhi, 110067, India" + }, + { + "author_name": "Suvechchha Pandit", + "author_inst": "Vaccine Immunology Laboratory, National Institute of Immunology, New Delhi, 110067, India" + }, + { + "author_name": "Bhushan Nikam", + "author_inst": "Vaccine Immunology Laboratory, National Institute of Immunology, New Delhi, 110067, India" + }, + { + "author_name": "Anurag Kalia", + "author_inst": "Vaccine Immunology Laboratory, National Institute of Immunology, New Delhi, 110067, India" + }, + { + "author_name": "Bimal Prasad Jit", + "author_inst": "Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029, India" + }, + { + "author_name": "Hilal Ahmad Parray", + "author_inst": "Translational Health Science and Technology Institute, Faridabad, 121001, India" + }, + { + "author_name": "Savita Singh", + "author_inst": "Translational Health Science and Technology Institute, Faridabad, 121001, India" + }, + { + "author_name": "Pallavi Kshetrapal", + "author_inst": "Translational Health Science and Technology Institute, Faridabad, 121001, India" + }, + { + "author_name": "Nitya Wadhwa", + "author_inst": "Translational Health Science and Technology Institute, Faridabad, 121001, India" + }, + { + "author_name": "Tripti Shrivastava", + "author_inst": "Translational Health Science and Technology Institute, Faridabad, 121001, India" + }, + { + "author_name": "Poonam Coshic", + "author_inst": "Department of Transfusion Medicine, All India Institute of Medical Sciences, New Delhi, 110029, India" + }, + { + "author_name": "Suresh Kumar", + "author_inst": "Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, 110002, India" + }, + { + "author_name": "Pragya Sharma", + "author_inst": "Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, 110002, India" + }, + { + "author_name": "Nandini Sharma", + "author_inst": "Maulana Azad Medical College and Lok Nayak Hospital, New Delhi, 110002, India" + }, + { + "author_name": "Juhi Taneja", + "author_inst": "ESIC Medical College and Hospital, Faridabad, 121012, India" + }, + { + "author_name": "Anil K Pandey", + "author_inst": "ESIC Medical College and Hospital, Faridabad, 121012, India" + }, + { + "author_name": "Ashok Sharma", + "author_inst": "Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029, India" + }, + { + "author_name": "Ramachandran Thiruvengadam", + "author_inst": "Translational Health Science and Technology Institute, Faridabad, 121001, India" + }, + { + "author_name": "Alba Grifoni", + "author_inst": "Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA" + }, + { + "author_name": "Shinjini Bhatnagar", + "author_inst": "Translational Health Science and Technology Institute, Faridabad, 121001, India" + }, + { + "author_name": "Daniela Weiskopf", + "author_inst": "Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA" + }, + { + "author_name": "Alessandro Sette", + "author_inst": "Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA" + }, + { + "author_name": "Pramod Kumar Garg", + "author_inst": "Translational Health Science and Technology Institute, Faridabad, 121001, India" + }, + { + "author_name": "Nimesh Gupta", + "author_inst": "Vaccine Immunology Laboratory, National Institute of Immunology, New Delhi, 110067, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.14.21266309", "rel_title": "Safety and Immunogenicity of anti-SARS CoV-2 vaccine SOBERANA 02 in homologous or heterologous scheme.", @@ -542299,113 +543108,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.11.10.21266063", - "rel_title": "Case Series of Thrombosis with Thrombocytopenia Syndrome following COVID-19 vaccination--United States, December 2020-August 2021", - "rel_date": "2021-11-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.10.21266063", - "rel_abs": "BackgroundThrombosis with thrombocytopenia syndrome (TTS) is a potentially life-threatening condition associated with adenoviral-vectored COVID-19 vaccination. TTS presents similarly to autoimmune heparin-induced thrombocytopenia. Twelve cases of cerebral venous sinus thrombosis following Janssen/Johnson & Johnson (Ad26.COV2.S) COVID-19 vaccination have been described.\n\nObjectiveDescribe surveillance data and reporting rates of TTS cases following COVID-19 vaccination.\n\nDesignCase series.\n\nSettingUnited States\n\nPatientsCase-patients reported to the Vaccine Adverse Event Reporting System (VAERS) receiving COVID-19 vaccine from December 14, 2020 through August 31, 2021, with thrombocytopenia and thrombosis (excluding isolated ischemic stroke or myocardial infarction). If thrombosis was only in an extremity vein or pulmonary embolism, a positive enzyme-linked immunosorbent assay for anti-platelet factor 4 antibody was required.\n\nMeasurementsReporting rates (cases/million vaccine doses) and descriptive epidemiology.\n\nResults52 TTS cases were confirmed following Ad26.COV2.S (n=50) or mRNA-based COVID-19 (n=2) vaccination. TTS reporting rates were 3.55 per million (Ad26.COV2.S) and 0.0057 per million (mRNA-based COVID-19 vaccines). Median age of patients with TTS following Ad26.COV2.S vaccination was 43.5 years (range: 18-70); 70% were female. Both TTS cases following mRNA-based COVID-19 vaccination occurred in males aged >50 years. All cases following Ad26.COV2.S vaccination involved hospitalization including 32 (64%) with intensive care unit admission. Outcomes of hospitalizations following Ad26.COV2.S vaccination included death (12%), discharge to post-acute care (16%), and discharge home (72%).\n\nLimitationsUnder-reporting and incomplete case follow-up.\n\nConclusionTTS is a rare but serious adverse event associated with Ad26.COV2.S vaccination. The different demographic characteristics of the two cases reported after mRNA-based COVID-19 vaccines and the much lower reporting rate suggest that these cases represent a background rate.\n\nFunding SourceCDC", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Isaac See", - "author_inst": "CDC" - }, - { - "author_name": "Allison Lale", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Paige Marquez", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Michael B Streiff", - "author_inst": "The Johns Hopkins University" - }, - { - "author_name": "Allison P Wheeler", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Naomi K Tepper", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Emily Jane Woo", - "author_inst": "Food and Drug Administration" - }, - { - "author_name": "Karen R Broder", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Kathryn M Edwards", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Ruth Gallego", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Andrew I Geller", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Kelly A Jackson", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Shashi Sharma", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Kawsar R Talaat", - "author_inst": "The Johns Hopkins University" - }, - { - "author_name": "Emmanuel B Walter", - "author_inst": "Duke University School of Medicine" - }, - { - "author_name": "Imo J Akpan", - "author_inst": "Columbia University Irving Medical Center" - }, - { - "author_name": "Thomas L Ortel", - "author_inst": "Duke University School of Medicine" - }, - { - "author_name": "Shannon Walker", - "author_inst": "Vanderbilt University Medicine Center" - }, - { - "author_name": "Jennifer C Yui", - "author_inst": "The Johns Hopkins University" - }, - { - "author_name": "Tom T Shimabukuro", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Adamma Mba-Jonas", - "author_inst": "Food and Drug Administration" - }, - { - "author_name": "John R Su", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "David K Shay", - "author_inst": "Centers for Disease Control and Prevention" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.11.12.21266183", "rel_title": "Using high-resolution contact networks to evaluate SARS-CoV-2 transmission and control in large-scale multi-day events", @@ -543653,6 +544355,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.11.21266237", + "rel_title": "An outbreak inside an outbreak: rising incidence of carbapenem-resistant isolates during the COVID-19 pandemic. Report from a tertiary care center in Argentina.", + "rel_date": "2021-11-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.11.21266237", + "rel_abs": "IntroductionCOVID-19 outbreaks have left us to deal with an aftermath on many fronts. In particular, disproportionate use of antibiotics, high ICU burden and longer in-hospital stays during the pandemic have been proposed to aggravate the emergency posed by carbapenem-resistant isolates (CRI), specially through carbapenemase production. However, there have been few reports worldwide regarding changes in CRI incidence and little latinamerican literature.\n\nObjectiveWe set out to determine whether the incidence of CRI rose in a tertiary care center in Santa Fe, Argentina during the time period with active cases of COVID-19.\n\nMethodsAnalytic epidemiologic study retrospectively designed. Two time periods were defined: P1 (without active cases of COVID-19) from September, 2019 to August, 2020 and P2 (starting at the onset of the first wave of COVID-19 in this institution) from September, 2020 to June 2021. All clinically-relevant microbiological samples -those meant for diagnostic purposes-taken during the study period from patients in the Internal Medicine and Surgical wards as well as the Intensive Care Units were included. Incidence was calculated by dividing the number of CRI during each time frame by the count of patient-day during that same period, multiplied by a hundred.\n\nResults9,135 hospitalizations, 50,145 patient-days of analysis. A total of 7285 clinical samples were taken, with an overall positivity for CRI of 12.1% (n=883). Overall CRI incidence during P2 was 2.5 times higher than in P1 (2.52 vs 0.955/100 patient-days, p <0.001). ICU CRI incidence raised from 6.78 to 8.69/100 patient-days in P2 (p=0.006).\n\nConclusionWe found alarming rates of CRI in our center, 2.5 times higher than previous to the first COVID-19 wave, similar to other reports worldwide. To our knowledge, this is one of the few Latin-American reports on the effect of the COVID-19 pandemic on CRI incidence.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Maximiliano Gabriel Castro", + "author_inst": "Hospital Dr. JB Iturraspe (Sta Fe, Arg)" + }, + { + "author_name": "Lucia Ines Ubiergo", + "author_inst": "Dr. JB Iturraspe Hospital" + }, + { + "author_name": "Macarena Vicino", + "author_inst": "Dr. JB Iturraspe Hospital" + }, + { + "author_name": "Gisel Cuevas", + "author_inst": "Dr. JB Iturraspe Hospital" + }, + { + "author_name": "Fernanda Argarana", + "author_inst": "Dr. JB Iturraspe Hospital" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.09.21265517", "rel_title": "Ultrafast RNA extraction-free SARS-CoV-2 detection by direct RT-PCR using a rapid thermal cycling approach", @@ -544197,53 +544934,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.11.10.21266124", - "rel_title": "Differences in COVID-19 vaccination coverage by occupation in England: a national linked data study", - "rel_date": "2021-11-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.10.21266124", - "rel_abs": "BackgroundMonitoring differences in COVID-19 vaccination uptake in different groups is crucial to help inform the policy response to the pandemic. A key gap is the absence of data on uptake by occupation.\n\nMethodsUsing nationwide population-level data, we calculated the proportion of people who had received two doses of a COVID-19 vaccine (assessed on 31 August 2021) by detailed occupational categories in adults aged 40-64 and estimated adjusted odds ratios to examine whether these differences were driven by occupation or other factors, such as education. We also examined whether vaccination rates differed by ability to work from home.\n\nResultsOur study population included 14,298,147 adults 40-64. Vaccination rates differed markedly by occupation, being higher in administrative and secretarial occupations (90.8%); professional occupations (90.7%); and managers, directors and senior officials (90.6%); and lowest (83.1%) in people working in elementary occupations. We found substantial differences in vaccination rates looking at finer occupational groups even after adjusting for confounding factors, such as education. Vaccination rates were higher in occupations which can be done from home and lower in those which cannot. Many occupations with low vaccination rates also involved contact with the public or with vulnerable people\n\nConclusionsIncreasing vaccination coverage in occupations with low vaccination rates is crucial to help protecting the public and control infection, especially in occupations that cannot be done from home and involve contacts with the public. Policies such as work from home if you can may only have limited future impact on hospitalisations and deaths\n\nWhat is already known on this subject?Whilst several studies highlight differences in vaccination coverage by ethnicity, religion, socio-demographic factors and certain underlying health conditions, there is very little evidence on how vaccination coverage varies by occupation, in the UK and elsewhere. The few study looking at occupational differences in vaccine hesitancy focus on healthcare workers or only examined broad occupational groups. There is currently no large-scale study on occupational differences in COVID-19 vaccination coverage in the UK.\n\nWhat this study adds?Using population-level linked data combining the 2011 Census, primary care records, mortality and vaccination data, we found that the vaccination rates of adults aged 40 to 64 years in England differed markedly by occupation. Vaccination rates were high in administrative and secretarial occupations, professional occupations and managers, directors and senior officials and low in people working in elementary occupations. Adjusting for other factors likely to be linked to occupation and vaccination, such as education, did not substantially alter the results. Vaccination rates were also associated with the ability to work from home, with the vaccination rate being higher in occupations which can be done performed from home. Policies aiming to increase vaccination rates in occupations that cannot be done from home and involve contacts with the public should be priorities", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Vahe Nafilyan", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Ted Dolby", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Katie Finning", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Jasper Morgan", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Rhiannon Edge", - "author_inst": "Lancaster University" - }, - { - "author_name": "Myer Glickman", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Neil Pearce", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Martie Van Tongeren", - "author_inst": "University of Manchester" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.11.07.21266018", "rel_title": "Quantifying changes in vaccine coverage in mainstream media as a result of COVID-19 outbreak", @@ -545639,6 +546329,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.11.09.21264627", + "rel_title": "ChAdOx1 n-COV-19 Vaccine Side Effects Among Health Care Workers in Trinidad and Tobago", + "rel_date": "2021-11-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.09.21264627", + "rel_abs": "BackgroundThe pharmaceutical firms have been lauded for the swift development, trial, approval, and rollout of various Covid-19 vaccines. However, a key issue in the vaccination campaign relates to vaccine hesitancy due to concerns on Covid-19 vaccines safety.\n\nMethodA retrospective longitudinal study was carried out via a telephone validated questionnaire. The questionnaire domains included demographic data, medical and COVID-19 related anamneses, and local and systemic side effects 48 hours after receiving the first dose of the vaccine and 48 hours after receiving the second dose of the vaccine.\n\nResultsThe questionnaire was administered to a sample of 687 healthcare workers (Male = 275; Female = 412). The results indicated that the incidence of reported fever, body pain, chills, nausea, myalgia, headache, malaise, fatigue and other systemic symptoms declined significantly 48 hours after administration of the second dose compared to the first dose. The Chi-square test and multiple logistics regression results were consistent in demonstrating that younger vaccine recipients were more likely to report fever, body pain, chills, nausea, myalgia, headache, fatigue and other symptoms compared to older vaccine recipients. The multiple logistics regression indicate that female vaccine recipients had greater odds of reporting headache, fatigue, discomfort and less likely to report no symptoms compared to male vaccine recipients, 48 hours after receiving both doses.\n\nConclusionsThe findings indicate that on average, vaccine recipients reported fewer number of local and systemic side effects within 48 hours after receiving the second dose compared to 48 hours after receiving the first dose. The findings have implications on public health policy efforts to lower vaccine hesitancy.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Chavin D Gopaul", + "author_inst": "The North Central Regional Health Authority" + }, + { + "author_name": "Dale Ventour", + "author_inst": "The University of the West Indies Trinidad and Tobago" + }, + { + "author_name": "Davlin Thomas", + "author_inst": "The North Central Regional Health Authority" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.11.09.467862", "rel_title": "Mice infected with Mycobacterium tuberculosis are resistant to secondary infection with SARS-CoV-2", @@ -546159,37 +546876,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.09.467827", - "rel_title": "A novel histone deacetylase inhibitor-based approach to eliminate microglia and retain astrocyte properties in glial cell culture.", - "rel_date": "2021-11-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.11.09.467827", - "rel_abs": "The close association between astrocytes and microglia causes great difficulties to distinguish their individual roles in innate immune responses in central nervous system. Current chemical-based methods to eliminate microglia in glial cell culture introduce various molecular and functional alterations to astrocytes. Here, we describe a novel two-step approach to achieve a complete elimination of microglia without affecting the biological properties of co-cultured astrocytes by temporal treatment of histone deacetylase inhibitor trichostatin A (TSA). We verify TSA as a potent inducer for microglial-specific cell death, which also causes comprehensive gene expression changes in astrocytes. However, withdrawal of TSA not only ensures no microglia repopulation, but also restores all the gene expression changes in terms of astrocyte functions, including neurotrophic factors, glutamate and potassium transporters, and reactive astrocyte subtypes. By contrast, withdrawal of PLX5622, the commonly used colony-stimulating factor 1 receptor inhibitor neither prevents microglia repopulation nor restores the gene expression changes mentioned above. Using this method, we are able to discriminate differential roles of microglia and astrocytes in the induced expression of antiviral and pro-inflammatory cytokines upon various pathological stimuli including the spike protein of SARS-CoV-2. This simple and efficient method can be customized for the understanding of microglia-astrocyte interaction and the development of epigenetic therapies that target over-activated microglia in neuroinflammation-related diseases.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Xi-Biao He", - "author_inst": "Shanghai University of Medicine & Health Sciences" - }, - { - "author_name": "Yi Wu", - "author_inst": "Speech Therapy Department, The Second Rehabilitation Hospital of Shanghai, Shanghai, China" - }, - { - "author_name": "Haozhi Huang", - "author_inst": "Department of Orthopaedic Surgery, Shanghai Tenth Peoples Hospital Affiliated to Tongji University, Shanghai, China" - }, - { - "author_name": "Fang Guo", - "author_inst": "Shanghai University of Medicine & Health Sciences, Shanghai, China." - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "neuroscience" - }, { "rel_doi": "10.1101/2021.11.09.467693", "rel_title": "The P681H mutation in the Spike glycoprotein confers Type I interferon resistance in the SARS-CoV-2 alpha (B.1.1.7) variant", @@ -547372,6 +548058,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2021.11.08.21266069", + "rel_title": "De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: A case report", + "rel_date": "2021-11-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.08.21266069", + "rel_abs": "SARS-CoV-2 remdesivir resistance mutations have been generated in vitro but have not been reported in patients receiving treatment with the antiviral agent. We present a case of an immunocompromised patient with acquired B-cell deficiency who developed an indolent, protracted course of SARS-CoV-2 infection. Remdesivir therapy alleviated symptoms and produced a transient virologic response, but her course was complicated by recrudescence of high-grade viral shedding. Whole genome sequencing identified a mutation, E802D, in the nsp12 RNA-dependent RNA polymerase, which was not present in pre-treatment specimens. In vitro experiments demonstrated that the mutation conferred a [~]6-fold increase in remdesivir IC50 but resulted in a fitness cost in the absence of remdesivir. Sustained clinical and virologic response was achieved after treatment with casirivimab-imdevimab. Although the fitness cost observed in vitro may limit the risk posed by E802D, this case illustrates the importance of monitoring for remdesivir resistance and the potential benefit of combinatorial therapies in immunocompromised patients with SARS-CoV-2 infection.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Shiv Gandhi", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Jonathan Klein", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Alexander Robertson", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Mario A. Pena-Hernandez", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Michelle J Lin", + "author_inst": "University of Washington School of Medicine" + }, + { + "author_name": "Pavitra Roychoudhury", + "author_inst": "University of Washington School of Medicine" + }, + { + "author_name": "Peiwen Lu", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "John Fournier", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "David Ferguson", + "author_inst": "Yale New Haven Hospital" + }, + { + "author_name": "Shah A. Mohamed Bakhash", + "author_inst": "University of Washington School of Medicine" + }, + { + "author_name": "M. Catherine Muenker", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Ariktha Srivathsan", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Elsio A. Wunder Jr.", + "author_inst": "Yale School of Public Health" + }, + { + "author_name": "Nicholas Kerantzas", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Wenshuai Wang", + "author_inst": "Yale University" + }, + { + "author_name": "Brett Lindenbach", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Anna Pyle", + "author_inst": "Yale University" + }, + { + "author_name": "Craig B. Wilen", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Onyema Ogbuagu", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Alexander L. Greninger", + "author_inst": "University of Washington School of Medicine" + }, + { + "author_name": "Akiko Iwasaki", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Wade L. Schulz", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Albert I. Ko", + "author_inst": "Yale School of Public Health" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.05.21265911", "rel_title": "Compassionate Use of REGEN-COV(R) in Patients with COVID-19 and Immunodeficiency-Associated Antibody Disorders", @@ -547672,57 +548465,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.08.21266055", - "rel_title": "Immunity to COVID-19 in India through vaccination and natural infection", - "rel_date": "2021-11-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.08.21266055", - "rel_abs": "In India, Corona Virus-2 Disease-2019 (COVID-19) continues to this day, although with subdued intensity, following two major waves of viral infection. Despite ongoing vaccination drives to curb the spread of COVID-19, the potential of the administered vaccines to render immune protection to the general population, and how this compares with the immune potential of natural infection remain unclear. In this study we examined correlates of immune protection (humoral and cell mediated) induced by the two vaccines Covishield and Covaxin, in individuals living in and around Kolkata, India. Additionally, we compared the vaccination induced immune response profile with that of natural infection, evaluating thereby if individuals infected during the first wave retained virus specific immunity. Our results indicate that while Covaxin generates better cell-mediated immunity toward the Delta variant of SARS-CoV-2 than Covishield, Covishield is more effective than Covaxin in inducing humoral immunity. Both Covishield and Covaxin, however, are more effective toward the wild type virus than the Delta variant. Moreover, the overall immune response resulting from natural infection in and around Kolkata is not only to a certain degree better than that generated by vaccination, especially in the case of the Delta variant, but cell mediated immunity to SARS-CoV-2 also lasts for at least ten months after the viral infection.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Tresa Rani Sarraf", - "author_inst": "CSIR-IICB" - }, - { - "author_name": "Shreyasi Maity", - "author_inst": "CSIR-IICB" - }, - { - "author_name": "Arjun Ghosh", - "author_inst": "Biobharati Life Science" - }, - { - "author_name": "Suchandan Bhattacharjee", - "author_inst": "Biobharati Life Science" - }, - { - "author_name": "Arijit Pani", - "author_inst": "Biobharati Life Science" - }, - { - "author_name": "Kaushik Saha", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Dhrubajyoti Chattopadhyay", - "author_inst": "Sister Nivedita University, Kolkata" - }, - { - "author_name": "Gourisankar Ghosh", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Malini Sen", - "author_inst": "CSIR-Indian Institute of Chemical Biology, Kolkata" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.11.09.21266054", "rel_title": "Time varying association between deprivation, ethnicity and SARS-CoV-2 infections in England: a space-time study", @@ -548818,6 +549560,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.06.21265632", + "rel_title": "SARS-CoV-2 specific T cell and humoral immune responses upon vaccination with BNT162b2", + "rel_date": "2021-11-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.06.21265632", + "rel_abs": "IntroductionThe humoral and cellular immune responses against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) upon coronavirus disease 2019 (COVID-19) vaccination remain to be clarified. Hence, we aimed to investigate the long-term chronological changes in SARS-CoV-2 specific IgG antibody, neutralizing antibody, and T cell responses during and after receiving the BNT162b2 vaccine.\n\nMethodsWe performed serological, neutralization, and T cell assays among 100 hospital workers aged 22-73 years who received the vaccine. We conducted seven surveys up to eight months after the second vaccination dose.\n\nResultsSARS-CoV-2 spike protein-specific IgG (IgG-S) titers and T cell responses increased significantly following the first vaccination dose. The highest titers were observed on day 29 and decreased gradually until the end of the follow-up period. There was no correlation between IgG-S and T cell responses. Notably, T cell responses were detected on day 15, earlier than the onset of neutralizing activity.\n\nConclusionsThis study demonstrated that both IgG-S and T cell responses were detected before acquiring sufficient levels of SARS-CoV-2 neutralizing antibodies. These immune responses are sustained for approximately six-ten weeks but not for seven months or later following the second vaccination, indicating the need for the booster dose (i.e., third vaccination).", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Junko S Takeuchi", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Ami Fukunaga", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Shohei Yamamoto", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Akihito Tanaka", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Kouki Matsuda", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Moto Kimura", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Azusa Kamikawa", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Yumiko Kito", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Kenji Maeda", + "author_inst": "National Center For Global Health and Medicine" + }, + { + "author_name": "Gohzoh Ueda", + "author_inst": "Abbott Japan LLC" + }, + { + "author_name": "Tetsuya Mizoue", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Mugen Ujiie", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Hiroaki Mitsuya", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Norio Ohmagari", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Wataru Sugiura", + "author_inst": "National Center for Global Health and Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.05.21265712", "rel_title": "A need of COVID19 vaccination for children aged <12 years: Comparative evidence from the clinical characteristics in patients during a recent Delta surge (B.1.617.2)", @@ -549594,45 +550411,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.05.21265763", - "rel_title": "Surveillance of COVID-19 in a Vaccinated Population: A Rapid Literature Review", - "rel_date": "2021-11-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.05.21265763", - "rel_abs": "ObjectivesWith the availability of COVID-19 vaccines, public health focus is shifting to post-vaccination surveillance to identify breakthrough infections in vaccinated populations. Therefore, the objectives of these reviews are to identify scientific evidence and international guidance on surveillance and testing approaches to monitor the presence of the virus in a vaccinated population.\n\nMethodWe searched Ovid MEDLINE(R), including Epub Ahead of Print, In-Process & Other Non-Indexed Citations, Embase, EBM Reviews - Cochrane Central Register of Controlled Trials, and EBM Reviews - Cochrane Database of Systematic Reviews. We also searched the Web of Science Core Collection. A grey literature search was also conducted. This search was limited to studies conducted since December 2020 and current to June 13th, 2021. There were no language limitations. COVID-19 surveillance studies that were published after December 2020 but did not specify whether they tested a vaccinated population were also considered for inclusion.\n\nFor the international guidance review, a grey literature search was conducted, including a thorough search of Google, websites of international government organizations (e.g., Center for Disease Control and Prevention [CDC], World Health Organization [WHO]), and McMaster Health Forum (CoVID-END). This search was primarily examining surveillance guidance published since December 2020 (to capture guidance specific to vaccinations) and any relevant pre-December 2020 guidance.\n\nResultsThirty-three studies were included for data synthesis of scientific evidence on surveillance of COVID-19. All the studies were published between April and June 2021. Twenty-one studies were from peer-reviewed journals. Five approaches to monitoring post-vaccination COVID-19 cases and emerging variants of concern were identified, including screening with reverse transcriptase polymerase chain reaction (RT-PCR) and/or a rapid antigen test, genomic surveillance, wastewater surveillance, metagenomics, and testing of air filters on public buses. For population surveillance, the following considerations and limitations were observed: variability in person-to-person testing frequency; lower sensitivity of antigen tests; timing of infections relative to PCR testing can result in missed infections; large studies may fail to identify local variations; and loss of interest in testing by participants in long follow-up studies.\n\nThrough comprehensive grey literature searching, 68 international guidance documents were captured for full-text review. A total of 26 documents met the inclusion criteria and were included in our synthesis. Seven overarching surveillance methods emerged in the literature. PCR-testing was the most recommended surveillance method, followed by genomic screening, serosurveillance, wastewater surveillance, antigen testing, health record screening, and syndromic surveillance.\n\nConclusionEvidence for post-vaccination COVID-19 surveillance was derived from studies in partially or fully vaccinated populations. Population PCR screening, supplemented by rapid antigen tests, was the most frequently used surveillance method and also the most commonly recommended across jurisdictions. Most recent guidance on COVID-19 surveillance is not specific to vaccinated individuals, or it is in effect but has not yet been updated to reflect that. Therefore, more evidence-informed guidance on testing and surveillance approaches in a vaccinated population that incorporates all testing modalities is required.\n\nEXECUTIVE SUMMARYO_ST_ABSObjectivesC_ST_ABSWith the availability of COVID-19 vaccines, public health focus is shifting to post-vaccination surveillance to identify breakthrough infections in vaccinated populations. Therefore, the objectives of these reviews are to: 1) identify scientific evidence on surveillance and testing approaches to monitor the presence of the virus in a vaccinated population and determine how these influence testing strategies; 2) identify international guidance on testing and surveillance for COVID-19 and its variants of concern in a vaccinated population; and 3) identify emerging technologies for surveillance.\n\nDesignA rapid review was conducted to identify scientific evidence on COVID-19 surveillance and testing approaches, and a targeted literature review was conducted on international guidance.\n\nMethodWe searched Ovid MEDLINE(R), including Epub Ahead of Print, In-Process & Other Non-Indexed Citations, Embase, EBM Reviews - Cochrane Central Register of Controlled Trials, and EBM Reviews - Cochrane Database of Systematic Reviews. We also searched the Web of Science Core Collection. We performed all searches on June 13, 2021. A grey literature search was also conducted, including: MedRxiv, Google, McMaster Health Forum (COVID-END), and websites of international government organizations (e.g., Center for Disease Control and Prevention [CDC], World Health Organization [WHO]). This search was limited to studies conducted since December 2020 and current to June 13th, 2021. There were no language limitations. COVID-19 surveillance studies that were published after December 2020 but did not specify whether they tested a vaccinated population were also considered for inclusion.\n\nFor the international guidance review, a grey literature search was conducted, including a thorough search of Google, websites of international government organizations (e.g., Center for Disease Control and Prevention [CDC], World Health Organization [WHO]), and McMaster Health Forum (CoVID-END). This search was primarily examining surveillance guidance published since December 2020 (to capture guidance specific to vaccinations) and any relevant pre-December 2020 guidance. Although the primary focus was on surveillance guidance in a vaccinated population, guidance that was published after December 2020 but was not vaccine-specific was also considered for inclusion; it was assumed that this guidance was still in effect and was not yet updated. There were no language limitations. A patient partner was engaged during the co-production of a plain language summary for both the rapid review of primary literature and the review of international guidance.\n\nResultsThirty-three studies were included for data synthesis of scientific evidence on surveillance of COVID-19. All the studies were published between April and June 2021. Twenty-one studies were from peer-reviewed journals. Five approaches to monitoring post-vaccination COVID-19 cases and emerging variants of concern were identified including, screening with reverse transcriptase polymerase chain reaction (RT-PCR) and/or a rapid antigen test, genomic surveillance, wastewater surveillance, metagenomics, and testing of air filters on public buses. Population surveillance with RT-PCR testing and/or rapid antigen testing was utilized in 22 studies, mostly in healthcare settings, but also in long-term care facilities (LTCFs) and in the community. The frequency of testing varied depending on whether there was an outbreak.\n\nFor population surveillance, the following considerations and limitations were observed: studies with discretionary access to testing have highly variable person-to-person testing frequency; antigen tests have lower sensitivity, therefore some positive cases may be missed; timing of infections relative to PCR testing as well as the sensitivity of the tests can result in missed infections; large sample sizes from multicentre studies increase generalizability, but fail to identify local variations from individual centres; with electronic database surveillance, it is difficult to confirm whether patients with a breakthrough infection and a previous positive SARS-CoV-2 test result had a true reinfection or had prolonged shedding from the previous infection; and participants lose interest in studies with long follow-up, with decrease in testing rates over time.\n\nSix wastewater surveillance and three genomic surveillance studies were identified in this review. A number of benefits such as, good correlation with clinical data, ability to predict major outbreaks, and rapid turnaround time were observed with wastewater surveillance. However, challenges such as, inconsistencies in variant representation depending on where the samples were taken within the community, differences in the capacity of wastewater to predict case numbers based on the size of the wastewater treatment plants, and cost, were noted. Emerging technologies like viral detection in public transport filters, novel sampling, and assay platforms were also identified.\n\nThrough comprehensive grey literature searching, 68 international guidance documents were captured for full-text review. A total of 26 documents met the inclusion criteria and were included in our synthesis. Most were not specific to vaccinated populations but reported on a surveillance method of COVID-19 and were therefore included in the review; it was assumed that they were still in effect but have not yet been updated. Eleven countries/regions were represented, including Australia, Brazil, France, Germany, India, New Zealand, Spain, United Kingdom, United States, Europe, and International. All of the guidance documents included surveillance methods appropriate for community settings. Other settings of interest were healthcare settings, including hospitals and primary care centres, long-term care facilities, points of entry for travel, schools, and other sentinel sites (e.g., prisons and closed settings). Seven overarching surveillance methods emerged in the literature. PCR-testing was the most recommended surveillance method, followed by genomic screening, serosurveillance, wastewater surveillance, antigen testing, health record screening, and syndromic surveillance.\n\nOnly one document (published by Public Health England) was identified that provided guidance on surveillance specific to vaccinated populations. The document outlined a plan to surveil and monitor COVID-19 in vaccinated populations through a series of targeted longitudinal studies, routine surveillance, enhanced surveillance, use of electronic health records, surveillance of vaccine failure (including follow-up with viral whole genome sequencing), and sero-surveillance (including blood donor samples, routine blood tests, and residual sera).\n\nConclusionEvidence for post-vaccination COVID-19 surveillance was derived from studies in partially or fully vaccinated populations. Population PCR screening, supplemented by rapid antigen tests, was the most frequently used surveillance method and also the most commonly recommended across jurisdictions. The selection of testing method and the frequency of testing was determined by the intensity of the disease and the scale of testing. Other common testing methods included wastewater surveillance and genomic surveillance. A few novel technologies are emerging, however, many of these are yet to be utilized in the real-world setting. There is limited evidence-based guidance on surveillance in a vaccinated population. Most recent guidance on COVID-19 surveillance is not specific to vaccinated individuals, or it is in effect but has not yet been updated to reflect that. Therefore, more evidence-informed guidance on testing and surveillance approaches in a vaccinated population that incorporates all testing modalities is required.\n\nProtocol/Topic RegistrationPROSPERO-CRD42021261215.\n\nKey DefinitionsAntigen: a foreign protein which induces an immune response in the body, especially the production of antibodies\n\nFully vaccinated: refers to individuals who have received complete dosage of a given vaccine\n\nPartially vaccinated: refers to individuals who have received an incomplete dosage of a given vaccine\n\nSero-surveillance: estimation of antibody levels against infectious diseases\n\nSurveillance: ongoing systematic collection, analysis, and interpretation of health data that are essential to the planning, implementation, and evaluation of public health practice\n\nVariants of Concern: a variant for which there is evidence of an increase in transmissibility and/or more severe disease\n\nVariants: virus with a permanent change in its genetic sequence", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Oluwaseun Egunsola", - "author_inst": "University of Calgary" - }, - { - "author_name": "Brenlea Farkas", - "author_inst": "University of Calgary" - }, - { - "author_name": "Jordyn Flanagan", - "author_inst": "University of Calgary" - }, - { - "author_name": "Charleen Salmon", - "author_inst": "University of Calgary" - }, - { - "author_name": "Liza Mastikhina", - "author_inst": "University of Calgary" - }, - { - "author_name": "Fiona Clement", - "author_inst": "University of Calgary" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.11.05.21265656", "rel_title": "REGEN-COV for the Treatment of Hospitalized Patients with Covid-19", @@ -550940,6 +551718,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.11.03.21265201", + "rel_title": "Optimising the quarantining and response sequence towards SARS-CoV-2 outbreaks on board cargo vessels", + "rel_date": "2021-11-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.03.21265201", + "rel_abs": "The Coronavirus Disease (COVID-19) pandemic has brought significant impact onto the maritime activities worldwide, including disruption to global trade and supply chains. The ability to predict the evolution and duration of a COVID-19 outbreak on cargo vessels would inform a more nuanced response to the event and provide a more precise return-to-trade date. A SEIQ(H)R (Susceptibility--Exposed-Infected--Quarantine--(Hospitalisation)--Removed/Recovered) model is developed and fit-tested to simulate the transmission dynamics of COVID-19 on board cargo vessels of up to 60 crew. Due to specific living and working circumstances on board cargo vessels, instead of utilising the reproduction number, we consider the highest fraction of crew members who share the same nationality to quantify the transmissibility of the disease. The performance of the model is verified using case studies based on data collected during COVID-19 outbreaks on three cargo vessels in Western Australia during 2020. The simulations show that the model can forecast the time taken for the transmission dynamics on each vessel to reach their equilibriums, providing informed predictions on the evolution of the outbreak, including hospitalisation rates and duration. The model demonstrates that (a) all crew members are susceptible to infection; (b) their roles on board is a determining factor in the evolution of the outbreak; (c) an unmitigated outbreak could affect the entire crew and continue on for many weeks. The ability to model the evolution of an outbreak, both in duration and severity, is essential to predict outcomes and to plan for the best response strategy. At the same time, it offers a higher degree of certainty regarding the return to trade, which is of significant importance to multiple stakeholders.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Kok Yew Ng", + "author_inst": "Ulster University" + }, + { + "author_name": "Tudor A Codreanu", + "author_inst": "State Health Incident Coordination Centre, Department of Health Western Australia, Perth, Western Australia, Australia." + }, + { + "author_name": "Meei Mei Gui", + "author_inst": "Queen's University Belfast" + }, + { + "author_name": "Pardis Biglarbeigi", + "author_inst": "Flowminder Foundation" + }, + { + "author_name": "Dewar Finlay", + "author_inst": "Ulster University" + }, + { + "author_name": "James McLaughlin", + "author_inst": "Ulster University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.11.05.21265569", "rel_title": "Evaluation of patients treated by telemedicine in the COVID-19 pandemic by a private clinic in Sao Paulo, Brazil: A non-randomized clinical trial preliminary study", @@ -551400,45 +552217,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.11.04.21265910", - "rel_title": "SARS-CoV-2 Aerosol Transmission Indoors: A Closer Look at Viral Load, Infectivity, the Effectiveness of Preventive Measures and a Simple Approach for Practical Recommendations", - "rel_date": "2021-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.04.21265910", - "rel_abs": "Currently, airborne transmission is seen as the most important transmission path for SARS-CoV-2. In this investigation, a classic dose-response model is used on the one hand to find out retrospectively the probable viral load of the infectious source patient at the time of transmission in 25 documented outbreaks. We showed that an infection due to airborne transmission at a distance from the infectious person was probably only possible in the 25 outbreaks examined, with attack rates of 4-100%, if the viral load had been higher than 1E+08 viral copies/ml. This demonstrates that the viral load estimated from the swab might overestimate a persons infectivity via aerosol, because a person is generally considered infectious, independent of the transmission way, when the viral load from the swab is 1E+06 viral copies/ml.\n\nOn the other hand, a possible approach is presented to predict the probable situational Attack Rate (PARs) of a group of persons in a room through aerosol particles emitted by an infectious source patient. Four main categories of influence on the risk of infection are formed: First the emitted viruses, depending on the viral load and the amount of respiratory particles, and necessary number of reproducible viruses for infection, second the room-specific data and duration of stay of the group of people, third the activity of the exposed persons, and fourth the effect of personal protection (e.g. wearing masks from infectious and/or susceptible person).\n\nFurthermore, a simplified method is presented to calculate either the maximum possible number of persons in a room, so that probably a maximum of one person becomes infected when an infectious person is in the room, or the PARs,simple for a given number of persons, ventilation rate and time of occupancy. We additionally show, taking into account organizational preventive measures, which person-related virus-free supply air flow rates are necessary to keep the number of newly infected persons to less than 1. The simple approach makes it easy to derive preventive organizational and ventilation measures. Our results show that the volume flow rate or a person-related flow rate is a much more effective parameter to evaluate ventilation for infection prevention than the air change rate. We suggest to monitor the CO2 concentration as an easy to implement and valid measurement system for indoor spaces.\n\nFinally, we show that of the three measures, besides of wearing masks and increasing ventilation, testing contributes the most to the joint protective effect. This corresponds to the classic approach to implement protection concepts: preventing the source from entering the room and emitting viruses at all. In summary, a layered approach of different measures is recommended to mutually compensate for possible failures of any one measure (e.g. incorrect execution of tests, incorrect fit of masks or irregular window opening), to increase the degree of protection and thus reduce the risk of transmission of SARS-CoV-2.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Martin Kriegel", - "author_inst": "Technical University of Berlin, Hermann-Rietschel-Institut" - }, - { - "author_name": "Anne Hartmann", - "author_inst": "Technical University of Berlin, Hermann-Rietschel-Institut" - }, - { - "author_name": "Udo Buchholz", - "author_inst": "Robert-Koch-Institute, Department for Infectious Disease Epidemiology" - }, - { - "author_name": "Janna Seifried", - "author_inst": "Robert-Koch-Institute, Department for Infectious Disease Epidemiology" - }, - { - "author_name": "Sigrid Baumgarte", - "author_inst": "Local health authority Hamburg-Nord" - }, - { - "author_name": "Petra Gastmeier", - "author_inst": "Charite-University Medicine Berlin, Institute for Hygiene and Environmental Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.11.04.21265916", "rel_title": "Severity and inpatient mortality of COVID-19 pneumonia from Beta variant infection: a clinical cohort study in Cape Town, South Africa", @@ -552606,6 +553384,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.11.03.21265819", + "rel_title": "Effectiveness of COVID-19 Vaccines and Post-vaccination SARS-COV 2 Infection, Hospitalization, and Mortality: a Systematic Review and Meta-analysis of Observational Studies", + "rel_date": "2021-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.03.21265819", + "rel_abs": "Introduction & ObjectiveVaccination is one of the most important and effective ways of preventing infectious diseases, and has recently been used in the COVID-19 epidemic and pandemic. The present meta-analysis study aimed to evaluate the effectiveness of COVID-19 vaccines in reducing the incidence of infection, hospitalization, and mortality in observational studies.\n\nMaterials and MethodsA systematic search was performed independently in Scopus, PubMed, ProQuest, and Google Scholar electronic databases as well as Preprint servers using the keywords under study. The heterogeneity of the studies was assessed using I2 and {chi}2 statistics, according to which the I2 of > 50% and P -value <0.1 was reported as heterogeneity of the studies. In addition, the Pooled Vaccine Effectiveness (PVE) obtained from the studies was calculated by converting (1-Pooled estimate x 100%) based on the type of outcome.\n\nResultsA total of 54 records were included in this meta-analysis. The rate of PVE against SARS-COV 2 infection was about 71% (OR = 0.29, 95% CI: 0.23-0.36) in the first dose and 87% (OR = 0.13, 95% CI: 0.08-0.21) in the second, and the highest effectiveness in the first and second doses was that of BNT162b2 mRNA and combined studies. The PVE versus COVID-19-associated hospitalization was 73% (OR = 0.27, 95% CI: 0.18-0.41) in the first dose and 89% (OR = 0.11, 95% CI: 0.07-0.17) in the second. mRNA-1273 and combined studies in the first dose and ChAdOx1 and mRNA-1273 in the second dose had the highest effectiveness. Regarding the COVID-19-related mortality, PVE was about 28% (HR = 0.39, 95% CI: 0.23-0.45) in the first dose and 89% (HR = 0.11, 95% CI: 0.03-0.43) in the second.\n\nConclusionThe evidence obtained from this study showed that the effectiveness of BNT162b2 mRNA, mRNA-1273, and ChAdOx1 in the first and second doses, and even combined studies were associated with increased effectiveness against SARS-COV2 infection, hospitalization, and death from COVID-19. In addition, considering that the second dose was significantly more efficient than the first one, a booster dose injection could be effective in high-risk individuals. On the other hand, it was important to observe other prevention considerations in the first days after taking the first dose.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Kazem Rahmani", + "author_inst": "Iran Unoversity of medical sciences" + }, + { + "author_name": "Rasoul Shavaleh", + "author_inst": "Iran University of Medical Sciences" + }, + { + "author_name": "Mahtab Forouhi", + "author_inst": "Shahid Beheshti University of Medical Sciences" + }, + { + "author_name": "Hamideh Feiz Disfani", + "author_inst": "Mashhad University of Medical Sciences" + }, + { + "author_name": "Mostafa Kamandi", + "author_inst": "Mashhad Universityof Medical Sciences" + }, + { + "author_name": "Aram Asareh Zadegan Dezfuli", + "author_inst": "Ahvaz Jundishapour University of Medical Sciences" + }, + { + "author_name": "Rozita Khatamian Oskooi", + "author_inst": "Birjand University of Medical Sciences" + }, + { + "author_name": "Molood Foogerdi", + "author_inst": "Birjand University of Medical Sciences" + }, + { + "author_name": "Moslem Soltani", + "author_inst": "Mashhad University of Medical sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.11.02.21265826", "rel_title": "The basic reproduction number of COVID-19 across Africa", @@ -553270,57 +554099,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.11.03.21265876", - "rel_title": "Investigating the relationship between interventions, contact patterns, and SARS-CoV-2 transmissibility", - "rel_date": "2021-11-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.03.21265876", - "rel_abs": "BackgroundAfter a rapid upsurge of COVID-19 cases in Italy during the fall of 2020, the government introduced a three-tiered restriction system aimed at increasing physical distancing. The Ministry of Health, after periodic epidemiological risk assessments, assigned a tier to each of the 21 Italian regions and autonomous provinces (AP). It is still unclear to what extent these different measures altered mixing patterns and how quickly the population adapted their social interactions to continuous changes in restrictions.\n\nMethods and findingsWe conducted a survey between July 2020 and March 2021 to monitor changes in social contact patterns among individuals in the metropolitan city of Milan, Italy, which was hardly hit by the second wave of COVID-19 pandemic. The number of contacts during periods characterized by different levels of restrictions was analyzed through negative binomial regression models and age-specific contact matrices were estimated under the different tiers. Relying on the empirically estimated mixing patterns, we quantified relative changes in SARS-CoV-2 transmission potential associated with the different tiers.\n\nAs tighter restrictions were implemented during the fall of 2020, a progressive reduction in the mean number of contacts recorded by study participants was observed: from 16.4% under mild restrictions (yellow tier), to 45.6% under strong restrictions (red tier). Higher restrictions levels were also found to increase the relative contribution of contacts occurring within the household. The SARS-CoV-2 reproduction number was estimated to decrease by 18.7% (95%CI: 4.6-30.8), 33.4% (95%CI: 22.7-43.2), and 50.2% (95%CI: 40.9-57.7) under the yellow, orange, and red tiers, respectively.\n\nConclusionsOur results give an important quantification of the expected contribution of different restriction levels in shaping social contacts and decreasing the transmission potential of SARS-CoV-2. These estimates can find an operational use in anticipating the effect that the implementation of these tiered restriction can have on SARS-CoV-2 reproduction number under an evolving epidemiological situation.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Filippo Trentini", - "author_inst": "Dondena Centre, Bocconi University" - }, - { - "author_name": "Adriana Manna", - "author_inst": "Department of Network and Data Science, Central European University, Wien, Austria" - }, - { - "author_name": "Nicoletta Balbo", - "author_inst": "Department of Social and Political Sciences, Bocconi University, Milan, Italy" - }, - { - "author_name": "Valentina Marziano", - "author_inst": "Fondazione Bruno Kessler" - }, - { - "author_name": "Giorgio Guzzetta", - "author_inst": "Fondazione Bruno Kessler" - }, - { - "author_name": "Stefano Merler", - "author_inst": "Fondazione Bruno Kessler" - }, - { - "author_name": "Marco Ajelli", - "author_inst": "Department of Epidemiology and Biostatistics, Indiana University School of Public Health" - }, - { - "author_name": "Piero Poletti", - "author_inst": "Bruno Kessler Foundation" - }, - { - "author_name": "Alessia Melegaro", - "author_inst": "Bocconi University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.11.03.21265861", "rel_title": "The impact of the initial and 2nd national COVID-19 lockdown on mental health in young people with and without pre-existing depressive symptoms", @@ -555116,6 +555894,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.10.31.21265672", + "rel_title": "Chest X-ray Severity and its Association with Outcomes in Patients with COVID-19 Presenting to the Emergency Department", + "rel_date": "2021-11-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.31.21265672", + "rel_abs": "BackgroundSeverity of radiographic abnormalities on chest X-ray (CXR) in patients with COVID-19 has been shown to be associated with worse outcomes, but studies are limited by different scoring systems, sample size, patient age and study duration. Data regarding the longitudinal evolution of radiographic abnormalities and its association with outcomes is scarce. We sought to evaluate these questions using a well-validated scoring system (the Radiographic Assessment of Lung Edema [RALE] score) using data over 6 months from a large, multi-hospital healthcare system.\n\nMethodsWe collected clinical and demographic data and quantified radiographic edema on CXRs obtained in the emergency department (ED) as well as on days 1-2 and 3-5 (in those admitted) in patients with a nasopharyngeal swab positive for SARS-CoV-2 PCR visiting the ED for COVID-19-related complaints between March and September 2020. We examined the association of baseline and longitudinal evolution of radiographic edema with severity of hypoxemia and clinical outcomes.\n\nResults870 patients were included (median age 53.6, 50.8% female). Inter-rate agreement for RALE scores was excellent (ICC = 0.84, 95% CI 0.82 - 0.87, p < 0.0001). RALE scores correlated with hypoxemia as quantified by SpO2-FiO2 ratio (r = -0.42, p < 0.001). Admitted patients had higher RALE scores than those discharged (6 [2, 11] vs 0 [0, 3], p < 0.001). An increase of RALE score of 4 or more was associated with worse 30-day survival (p < 0.01). Larger increases in the RALE score were associated with worse survival.\n\nConclusionsThe RALE score is reproducible and easily implementable in adult patients presenting to the ED with COVID-19. Its association with physiologic parameters and outcomes at baseline and longitudinally makes it a readily available tool for prognostication and early ICU triage, particularly in patients with worsening radiographic edema.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Daniel Kotok", + "author_inst": "Cleveland Clinic Florida" + }, + { + "author_name": "Jose Rivera Robles", + "author_inst": "Cleveland Clinic Florida" + }, + { + "author_name": "Christine Girard", + "author_inst": "Cleveland Clinic Florida" + }, + { + "author_name": "Shruti Shettigar", + "author_inst": "Cleveland Clinic Florida" + }, + { + "author_name": "Allen Lavina", + "author_inst": "Cleveland Clinic Florida" + }, + { + "author_name": "Samantha Gillenwater", + "author_inst": "Cleveland Clinic Florida" + }, + { + "author_name": "Andrew Kim", + "author_inst": "Cleveland Clinic Florida" + }, + { + "author_name": "Anas Hadeh", + "author_inst": "Cleveland Clinic Florida" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2021.10.31.21265711", "rel_title": "Cross-border transmissions of delta substrain AY.29 during Olympic and Paralympic Games", @@ -555624,49 +556449,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.11.01.21265729", - "rel_title": "Quantifying the effects of non-pharmaceutical and pharmaceutical interventions against COVID-19 epidemic in the Republic of Korea: Mathematical model-based approach considering age groups and the Delta variant", - "rel_date": "2021-11-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.11.01.21265729", - "rel_abs": "BackgroundEarly vaccination efforts and non-pharmaceutical interventions were insufficient to prevent a surge of coronavirus disease 2019 (COVID-19) cases triggered by the Delta variant. This study aims to understand how vaccination and variants contribute to the spread of COVID-19 so that appropriate measures are implemented.\n\nMethodsA compartment model that includes age, vaccination, and infection with the Delta or non-Delta variants was developed. We estimated the transmission rates using maximum likelihood estimation and phase-dependent reduction effect of non-pharmaceutical interventions (NPIs) according to government policies from 26 February to 8 October 2021. We extended our model simulation until 31 December considering the initiation of eased NPIs. Furthermore, we also performed simulations to examine the effect of NPIs, arrival timing of Delta variant, and speed of vaccine administration.\n\nResultsThe estimated transmission rate matrices show distinct pattern, with the transmission rates of younger age groups (0 39 years) much larger than non-Delta. Social distancing (SD) level 2 and SD4 in Korea were associated with transmission reduction factors of 0.64 to 0.69 and 0.70 to 0.78, respectively. The easing of NPIs to a level comparable to SD2 should be initiated not earlier than 16 October to keep the number of severe cases below the capacity of Koreas healthcare system. Simulation results also showed that a surge prompted by the spread of the Delta variant can be prevented if the number of people vaccinated daily was larger.\n\nConclusionsSimulations showed that the timing of easing and intensity of NPIs, vaccination speed, and screening measures are key factors in preventing another epidemic wave.\n\n2 Key MessagesO_LIMaximum likelihood estimation can be utilized to determine the transmission rates of the Delta and non-Delta variants.\nC_LIO_LIThe phase-dependent NPIs implemented by the Korean government were effectively quantified in the modelling study.\nC_LIO_LIEven with fast vaccination, resurgence of cases is still possible if NPIs are eased too early or screening measures are relaxed.\nC_LIO_LIThe model can be used as a guide for policy makers on deciding appropriate SD level that considers not only disease control, but also the socio-economic impact of maintaining strict measures.\nC_LI", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Youngsuk Ko", - "author_inst": "Konkuk University" - }, - { - "author_name": "Victoria May P Mendoza", - "author_inst": "Konkuk University" - }, - { - "author_name": "Yubin Seo", - "author_inst": "Hallym University College of Medicine" - }, - { - "author_name": "Jacob Lee", - "author_inst": "Hallym University College of Medicine" - }, - { - "author_name": "Yeonju Kim", - "author_inst": "Korea Disease Control and Prevention Agency" - }, - { - "author_name": "Donghyok Kwon", - "author_inst": "Korea Disease Control and Prevention Agency" - }, - { - "author_name": "Eunok Jung", - "author_inst": "Konkuk University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.10.31.21265627", "rel_title": "Predictors of COVID testing among Australian youth: Insights from the Longitudinal Study of Australian Children", @@ -556914,6 +557696,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2021.10.29.21265691", + "rel_title": "Assessment of the fatality rate and transmissibility taking account of undetected cases during an unprecedented COVID-19 surge in Taiwan", + "rel_date": "2021-10-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.29.21265691", + "rel_abs": "BackgroundDuring the COVID-19 outbreak in Taiwan between May 11 and June 20, 2021, the observed fatality rate (FR) was 5.3%, higher than the global average at 2.1%. The high number of reported deaths suggests that hospital capacity was insufficient. However, many unexplained deaths were subsequently identified as cases, indicating that there were a few undetected cases, hence resulting in a higher estimate of FR. Estimating the number of total infected cases or knowing how to reduce the undetected cases can allow an accurate estimation of the fatality rate (FR) and effective reproduction number (Rt).\n\nMethodsAfter adjusting for reporting delays, we estimated the number of undetected cases using reported deaths that were and were not previously detected. The daily FR and Rt were calculated using the number of total cases (i.e. including undetected cases). A logistic regression model was developed to predict the detection ratio among deaths using selected predictors from daily testing and tracing data.\n\nResultsThe estimated true daily case number at the peak of the outbreak on May 22 was 897, which was 24.3% higher than the reported number, but the difference became less than 4% on June 9 and afterward. After taking account of undetected cases, our estimated mean FR (4.7%) was still high but the daily rate showed a large decrease from 6.5% on May 19 to 2.8% on June 6. Rt reached a maximum value of 6.4 on May 11, compared to 6.0 estimated using the reported case number. The decreasing proportion of undetected cases was associated with the increases in the ratio of the number of tests conducted to reported cases, and the proportion of cases that are contact-traced before symptom onset.\n\nConclusionsIncreasing testing capacity and tracing efficiency can lead to a reduction of hidden cases and hence improvement in epidemiological parameter estimation.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Hsiang-Yu Yuan", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "M. Pear Hossain", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Tzai-Hung Wen", + "author_inst": "National Taiwan University" + }, + { + "author_name": "Ming-Jiuh Wang", + "author_inst": "National Taiwan University Hospital" + } + ], + "version": "1", + "license": "cc0_ng", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.29.21265628", "rel_title": "Contributions of occupation characteristics and educational attainment to racial/ethnic inequities in COVID-19 mortality", @@ -557326,57 +558139,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.28.21265544", - "rel_title": "In vitro characterisation and clinical evaluation of the diagnostic accuracy of a new antigen test for SARS-CoV-2 detection.", - "rel_date": "2021-10-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.28.21265544", - "rel_abs": "Background and aimsQuick, user-friendly and sensitive diagnostic tools are the key to controlling the spread of the SARS-CoV-2 pandemic in the new epidemiologic landscape. The aim of this work is to characterise a new Covid-19 antigen test that uses an innovative chromatographic Affimer(R)-based technology designed for the qualitative detection of SARS-CoV-2 antigen. As rapid technology to detect Covid-19, the test was extensively characterised in vitro. Once the analytical parameters of performance were set, the test system was challenged in a test field study. The aim of this study was to evaluate its diagnostic accuracy, as compared by the gold standard RT-PCR and other existing lateral flow tests.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "J.J. Montoya", - "author_inst": "Departamento de Radiologia, Rehabilitacion y Fisioterapia. Facultad de Medicina, Universidad Complutense de Madrid." - }, - { - "author_name": "J.M. Rubio", - "author_inst": "Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Ctra. de Pozuelo, 28, 28222 Majadahonda, Madrid." - }, - { - "author_name": "Y. Ouahid", - "author_inst": "Unidad de Desarrollo de Herramientas Moleculares para Diagnostico e Investigacion Clinica (UDHM-DC), MiRNAX Biosens (Avda. Industria no 4, Edificio 1) en colabo" - }, - { - "author_name": "A. Lopez-Lopez", - "author_inst": "Unidad de Desarrollo de Herramientas Moleculares para Diagnostico e Investigacion Clinica (UDHM-DC), MiRNAX Biosens (Avda. Industria no 4, Edificio 1) en colabo" - }, - { - "author_name": "A. Madejon", - "author_inst": "Centro de Investigacion Biomedica en Red, C/ Sinesio Delgado 10, 28029-MADRID, Hospital La Paz, Madrid, Spain." - }, - { - "author_name": "A.I. Gil-Garcia", - "author_inst": "Unidad de Desarrollo de Herramientas Moleculares para Diagnostico e Investigacion Clinica (UDHM-DC), MiRNAX Biosens (Avda. Industria no 4, Edificio 1) en colabo" - }, - { - "author_name": "R.J. Hannam", - "author_inst": "Avacta Life Sciences, Unit 20, Thorp Arch Estate, Wetherby, LS23 7FA, UK." - }, - { - "author_name": "H.R.E. Butler", - "author_inst": "Avacta Life Sciences, Unit 20, Thorp Arch Estate, Wetherby, LS23 7FA, UK." - }, - { - "author_name": "P. Castan", - "author_inst": "Unidad de Desarrollo de Herramientas Moleculares para Diagnostico e Investigacion Clinica (UDHM-DC), MiRNAX Biosens (Avda. Industria no 4, Edificio 1) en colabo" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.28.21265610", "rel_title": "COVID-19 Patients Symptoms: Gastrointestinal Presentations, Comorbidities and Outcome in a Canadian Hospital setting", @@ -558808,6 +559570,37 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.10.27.466182", + "rel_title": "Efficacy of anti-microbial gel vapours against aerosolised coronavirus, bacteria, and fungi", + "rel_date": "2021-10-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.27.466182", + "rel_abs": "BackgroundThe urban population spends up to 90% of their time indoors. The indoor environment harbours a diverse microbial population including viruses, bacteria, and fungi. Pathogens present in the indoor environment can be transmitted to humans through aerosols.\n\nAimThis study evaluated the efficacy of an antimicrobial gel containing a mix of essential oils against aerosols of bacteria, fungi, and coronavirus.\n\nMethodsThe antimicrobial gel was allowed to vapourize inside a glass chamber for 10 or 20 minutes. Microbial aerosols of Escerichia coli, Aspergillus flavus spores or murine hepatitis virus MHV 1, a surrogate of SARS CoV-2 was passed through the gel vapours and then collected on a 6-stage Andersen sampler. The number of viable microbes present in the aerosols collected in the different stages were enumerated and compared to number of viable microbes in control microbial aerosols that were not exposed to the gel vapours.\n\nResultsVaporizing the antimicrobial gel for 10 and 20 minutes resulted in a 48% (p = 0.002 Vs. control) and 53% (p = 0.001 Vs. control) reduction in the number of MHV-1 in the aerosols, respectively. The antimicrobial gel vaporised for 10 minutes, reduced the number of viable E. coli by 51% (p = 0.032 Vs. control) and Aspergillus flavus spores by 72% (p=0.008 Vs. control) in the aerosols.\n\nConclusionsThe antimicrobial gel may be able to reduce aerosol transmission of microbes.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Parthasarathi Kalaiselvan", + "author_inst": "University of New South Wales" + }, + { + "author_name": "Muhammad Yasir", + "author_inst": "University of New South Wales" + }, + { + "author_name": "Mark D. P. Willcox", + "author_inst": "University of New South Wales" + }, + { + "author_name": "Ajay Kumar Vijay", + "author_inst": "University of New South Wales" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.10.28.466298", "rel_title": "Identification of COVID-19 and COPD common key genes and pathways using a protein-protein interaction approach", @@ -559244,37 +560037,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.27.21265591", - "rel_title": "How many lives do COVID vaccines save? Evidence from Israel.", - "rel_date": "2021-10-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.27.21265591", - "rel_abs": "BackgroundIn December 2020, Israel began a mass vaccination program with the rapid rollout of the Pfizer-BioNTech COVID-19 BNT162b2 vaccine for adults in Israel. The campaign vaccinated fewer people than necessary for herd immunity. However, at the same time, government stringency measures in terms of closing public life were decreased. Real-world observational data were used to examine the effect of mass vaccination on Covid-19 mortality.\n\nMethodsThe study period to examine the effect of vaccination on mortality was chosen to capture when at least 90% of the population over age 70 were vaccinated for less than seven months. Projected deaths as expected from vaccine efficacy and actual mortality data were compared for the study population with examination of potential confounding effects of government stringency. Average government stringency (Oxford Stringency Index) was calculated in the study period and the preceding period of the pandemic. Potential confounding effects of an age shift in the distribution of deaths were examined by analyzing the distributions of deaths and cases before and after the study period.\n\nResultsConfirmed deaths from COVID-19 in the population over 70 after mass vaccination were recorded as 370, versus 408 expected from applying person-days of vaccine efficacy, and 5,120 estimated without vaccinations.\n\nConclusionsVaccines against COVID-19 saved more lives than expected by simply applying individual vaccine efficacy to the vaccinated population in Israel, despite a loosening of government stringency.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Ronen Arbel", - "author_inst": "Maximizing Health Outcomes Research Lab, Sapir College, Sderot, Israel" - }, - { - "author_name": "Candace Makeda Moore", - "author_inst": "Maximizing Health Outcomes Research Lab, Sapir College, Sderot, Israel" - }, - { - "author_name": "Ruslan Sergienko", - "author_inst": "Department of Health Policy and Management, Ben-Gurion University of the Negev, Beer Sheva, Israel" - }, - { - "author_name": "Joseph Pliskin", - "author_inst": "Department of Health Policy and Management, Harvard T. H. Chan School of Public Health, Boston, MA, USA" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.26.465846", "rel_title": "Deep autoencoder enables interpretable tissue-adaptive deconvolution and cell-type-specific gene analysis", @@ -560554,6 +561316,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2021.10.20.21265103", + "rel_title": "The Relationship Between Food Security and Dietary Patterns Status with COVID-19 in Northeastern Iran: Protocol for a Case-Control Study", + "rel_date": "2021-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.20.21265103", + "rel_abs": "BackgroundFood insecurity is defined as the limited or uncertain availability of enough food for a consistently active and healthy life. COVID-19 is a highly transmissible viral infection with high mortality due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and, or the uncommon severe pneumonia. This study assesses the relationship between food security and dietary patterns status with COVID-19 in the North Khorasan province, Iran.\n\nMethodsThis case-control study will be conducted in the men and women aged 20-60 years improved from COVID-19 infection. The cases (n=124) and controls (n=124) were selected according to the eligibility criteria, including recently improved COVID-19 according to the positive COVID-19 PCR test. People referred to public and private laboratories or employees of public and private factories, offices, and departments of hospitals and universities (for the cases) and negative PCR tests without any clinical signs of COVID-19 infection (for the controls). The North Khorasan province was the target place. The groups are matched for age, sex, and body mass index (BMI). The assessments will include anthropometric measurements and general demographic, USDA 18-item food security (18item-FSSM), and 147-item food frequency (FFQ) questionnaires. Finally, the determination of the relationship between food security and dietary patterns status and associated socioeconomic factors with COVID-19 is done. P-value will be <0.05.\n\nDiscussionThis study would be the first assessment of the relationship between food security and dietary patterns status with COVID-19 disease. It may help planners and policymakers to manage food insecurity and unhealthy dietary patterns and later increasing the immune system and decreasing the incidence of COVID-19. Further studies are suggested.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Sepideh Badri-Fariman", + "author_inst": "Tabriz University of Medical Sciences" + }, + { + "author_name": "Bahram Pourghassem-Gargari", + "author_inst": "Tabriz University of Medical Sciences, Tabriz" + }, + { + "author_name": "Mahtab Badri-Fariman", + "author_inst": "Tehran University of Medical Sciences" + }, + { + "author_name": "Mohammad Pourfridoni", + "author_inst": "Jiroft University of Medical Sciences" + }, + { + "author_name": "Milad Daneshi-Maskooni", + "author_inst": "Jiroft University of Medical Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "nutrition" + }, { "rel_doi": "10.1101/2021.10.19.21265200", "rel_title": "Preclinical and clinical validation of a novel injected molded swab for molecular assay detection of SARS-CoV-2 virus", @@ -561078,49 +561875,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.10.22.21265188", - "rel_title": "Response to the coronavirus disease 2019 (COVID-19) pandemic at private retail pharmacies in Kenya: a mixed methods study", - "rel_date": "2021-10-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.22.21265188", - "rel_abs": "BackgroundPrivate retail pharmacies in developing countries present a unique channel for COVID-19 prevention. We assessed the response to the COVID-19 pandemic by pharmacies in Kenya, aiming to identify strategies for maximising their contribution to the national response.\n\nMethodsWe conducted a prospective mixed-methods study, consisting of a questionnaire survey (n=195), a simulated client survey (n=103), and in-depth interviews (n=18). Data collection started approximately seven months after the pandemic reached Kenya. Quantitative data were summarized using measures of central tendency and multivariable modelling done using logistic regression. Qualitative analysis followed a thematic approach.\n\nResultsThe initial weeks of the pandemic were characterized by fear and panic among service providers and a surge in client flow. Subsequently, 61% of pharmacies experienced a dip in demand to below pre-pandemic levels and 31% reported challenges with unavailability, high price, and poor-quality of products. Almost all pharmacies were actively providing preventive materials and therapies; educating clients on prevention measures; counselling anxious clients; and handling and referring suspect cases. Fifty-nine pharmacies (55% [95% CI 45-65%]) reported ever receiving a client asking for COVID-19 testing and a similar proportion supported pharmacy-based testing. For treatment, most pharmacies (71%) recommended alternative therapies and nutritional supplements such as vitamin C; only 27% recommended conventional therapies such as antibiotics. While 48% had at least one staff member trained on COVID-19, a general feeling of disconnection from the national program prevailed.\n\nConclusionsPrivate pharmacies in Kenya were actively contributing to the COVID-19 response, but more deliberate engagement, support and linkages are required. Notably, there is an urgent need to develop guidelines for pharmacy-based COVID-19 testing, a service that is clearly needed and which could greatly increase test coverage. Roll-out of this and other pharmacy-based COVID-19 programs should be accompanied with implementation research in order to inform current and future pandemic responses.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Peter Mwangi Mugo", - "author_inst": "KEMRI Wellcome Trust Research Programme" - }, - { - "author_name": "Audrey Nyawira Mumbi", - "author_inst": "KEMRI Wellcome trust Research Programme" - }, - { - "author_name": "Daniella Munene", - "author_inst": "Pharmaceutical Society of Kenya" - }, - { - "author_name": "Jacinta Nzinga", - "author_inst": "KEMRI Wellcome Trust Research Programme" - }, - { - "author_name": "Sassy Molyneux", - "author_inst": "University of Oxford" - }, - { - "author_name": "Edwine Barasa", - "author_inst": "KEMRI-Wellcome Trust Research Programme" - }, - { - "author_name": "- Pharmaceutical Society of Kenya (PSK) COVID-19 Response Taskforce (CRT)", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2021.10.19.21265195", "rel_title": "ABO blood group type does not influence the level of SARS-CoV-2 antibody response in convalescent plasma donors", @@ -562400,6 +563154,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, + { + "rel_doi": "10.1101/2021.10.25.21265422", + "rel_title": "Limited impact of Delta variants mutations in the effectiveness of neutralization conferred by natural infection or COVID-19 vaccines in a Latino population", + "rel_date": "2021-10-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.25.21265422", + "rel_abs": "The SARS-CoV-2 pandemic has impacted public health systems all over the world. The Delta variant seems to possess enhanced transmissibility, but no clear evidence suggests it has increased virulence. Our data shows that pre-exposed individuals had similar neutralizing activity against the authentic COVID-19 strain and the Delta and Epsilon variants. After one vaccine dose, the neutralization capacity expands to all tested variants. Healthy vaccinated individuals showed a limited breadth of neutralization. One vaccine dose induced similar neutralizing antibodies against the Delta compared to the authentic strain. However, even after two doses, this capacity only expanded to the Epsilon variant.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Carlos A Sariol", + "author_inst": "Unit of Comparative Medicine, Medical Sciences Campus, University of Puerto Rico," + }, + { + "author_name": "Crisanta Serrano", + "author_inst": "UPR-MSC" + }, + { + "author_name": "Edwin J. Ortiz", + "author_inst": "Unit of Comparative Medicine, School of Medicine, University of Puerto Rico" + }, + { + "author_name": "Petraleigh Pantoja", + "author_inst": "Unit of Comparative Medicine, School of Medicine, University of Puerto Rico" + }, + { + "author_name": "Lorna Cruz", + "author_inst": "University of Puerto Rico, Medical Sciences Campus" + }, + { + "author_name": "Teresa Arana", + "author_inst": "Department of Microbiology, School of Medicine, University of Puerto Rico" + }, + { + "author_name": "Dianne Atehortua", + "author_inst": "Puerto Rico Science, Technology and Research Trust" + }, + { + "author_name": "Christina Pabon-Carrero", + "author_inst": "Puerto Rico Science, Technology and Research Trust" + }, + { + "author_name": "Ana M Espino", + "author_inst": "University of Puerto Rico Medical Sciences Campus" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.26.21265525", "rel_title": "COVCOG 1: Factors predicting Cognitive Symptoms in Long COVID. A First Publication from the COVID and Cognition Study.", @@ -563136,93 +563941,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.24.465626", - "rel_title": "SARS-CoV-2 infects human adipose tissue and elicits an inflammatory response consistent with severe COVID-19", - "rel_date": "2021-10-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.24.465626", - "rel_abs": "The COVID-19 pandemic, caused by the viral pathogen SARS-CoV-2, has taken the lives of millions of individuals around the world. Obesity is associated with adverse COVID-19 outcomes, but the underlying mechanism is unknown. In this report, we demonstrate that human adipose tissue from multiple depots is permissive to SARS-CoV-2 infection and that infection elicits an inflammatory response, including the secretion of known inflammatory mediators of severe COVID-19. We identify two cellular targets of SARS-CoV-2 infection in adipose tissue: mature adipocytes and adipose tissue macrophages. Adipose tissue macrophage infection is largely restricted to a highly inflammatory subpopulation of macrophages, present at baseline, that is further activated in response to SARS-CoV-2 infection. Preadipocytes, while not infected, adopt a proinflammatory phenotype. We further demonstrate that SARS-CoV-2 RNA is detectable in adipocytes in COVID-19 autopsy cases and is associated with an inflammatory infiltrate. Collectively, our findings indicate that adipose tissue supports SARS-CoV-2 infection and pathogenic inflammation and may explain the link between obesity and severe COVID-19.\n\nOne sentence summaryOur work provides the first in vivo evidence of SARS-CoV-2 infection in human adipose tissue and describes the associated inflammation.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Giovanny J Mart\u00ednez-Col\u00f3n", - "author_inst": "Stanford University" - }, - { - "author_name": "Kalani Ratnasiri", - "author_inst": "Stanford University" - }, - { - "author_name": "Heping Chen", - "author_inst": "Stanford University" - }, - { - "author_name": "Sizun Jiang", - "author_inst": "Stanford University" - }, - { - "author_name": "Elizabeth Zanley", - "author_inst": "Stanford University" - }, - { - "author_name": "Arjun Rustagi", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Renu Verma", - "author_inst": "Stanford University" - }, - { - "author_name": "Han Chen", - "author_inst": "Stanford University" - }, - { - "author_name": "Jason R Andrews", - "author_inst": "Stanford University" - }, - { - "author_name": "Kirsten Mertz", - "author_inst": "Cantonal Hospital Baselland" - }, - { - "author_name": "Alexandar Tzankov", - "author_inst": "University Hospital of Basel" - }, - { - "author_name": "Dan Azagury", - "author_inst": "Stanford University" - }, - { - "author_name": "Jack Boyd", - "author_inst": "Stanford University" - }, - { - "author_name": "Garry P Nolan", - "author_inst": "Stanford University" - }, - { - "author_name": "Christian M. Sch\u00fcrch", - "author_inst": "University Hospital and Comprehensive Cancer Center T\u00fcbingen" - }, - { - "author_name": "Matthias S Matter", - "author_inst": "University Hospital of Basel" - }, - { - "author_name": "Catherine A Blish", - "author_inst": "Stanford University" - }, - { - "author_name": "Tracey L McLaughlin", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.10.21.21265272", "rel_title": "Factors affecting nurses' duty to care during the COVID-19 pandemic", @@ -564430,6 +565148,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.10.25.21265324", + "rel_title": "Safety and Immunogenicity of the COVID-19 Vaccine BNT162b2 in Patients Undergoing Chemotherapy for Solid Cancer", + "rel_date": "2021-10-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.25.21265324", + "rel_abs": "BackgroundAlthough COVID-19 severity in cancer patients is high, the safety and immunogenicity of the BNT162b2 mRNA COVID-19 vaccine in patients undergoing chemotherapy for solid cancers in Japan have not been reported.\n\nMethodsWe investigated the safety and immunogenicity of BNT162b2 in 41 patients undergoing chemotherapy for solid cancers and in healthy volunteers who received 2 doses of BNT162b2. We evaluated serum IgG antibody titers for S1 protein by ELISA at pre-vaccination, prior to the second dose and 14 days after the second vaccination in 24 cancer patients undergoing cytotoxic chemotherapy (CC group), 17 cancer patients undergoing immune checkpoint inhibitor therapy (ICI group) and 12 age-matched healthy volunteers (HV group). Additionally, inflammatory cytokine levels were compared between the HV and ICI groups at pre and the next day of each vaccination.\n\nResultsAnti-S1 antibody levels were significantly lower in the ICI and CC groups than in the HV group after the second dose (median optimal density: 0.241 [0.063-1.205] and 0.161 [0.07-0.857] vs 0.644 [0.259-1.498], p = 0.0024 and p < 0.0001, respectively). Adverse effect profile did not differ among the three groups, and no serious adverse event occurred. There were no differences in vaccine-induced inflammatory cytokines between the HV and ICI groups.\n\nConclusionAlthough there were no significant differences in adverse events in three groups, antibody titers were significantly lower in the ICI and CC groups than in the HV group. Further protection strategies should be considered in cancer patients undergoing CC or ICI.\n\nMini abstractTiters of anti-S1 antibody after the second dose of BNT162b2 were significantly lower in patients with solid tumors undergoing active anticancer treatment than in the healthy volunteers.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Yohei Funakoshi", + "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan" + }, + { + "author_name": "Kimikazu Yakushijin", + "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan" + }, + { + "author_name": "Goh Ohji", + "author_inst": "Division of Infection Disease Therapeutics, Department of Microbiology and Infectious Diseases, Kobe University Hospital and Graduate School of Medicine, Kobe, " + }, + { + "author_name": "Wataru Hojo", + "author_inst": "R&D, Cellspect Co., Ltd., Morioka, Japan" + }, + { + "author_name": "Hironori Sakai", + "author_inst": "R&D, Cellspect Co., Ltd., Morioka, Japan" + }, + { + "author_name": "Ryo Takai", + "author_inst": "Division of Gastrointestinal Surgery, Department of Surgery, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan" + }, + { + "author_name": "Taku Nose", + "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan" + }, + { + "author_name": "Shinya Ohata", + "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan" + }, + { + "author_name": "Yoshiaki Nagatani", + "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan" + }, + { + "author_name": "Taiji Koyama", + "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan" + }, + { + "author_name": "Akihito Kitao", + "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan" + }, + { + "author_name": "Meiko Nishimura", + "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan" + }, + { + "author_name": "Yoshinori Imamura", + "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan" + }, + { + "author_name": "Naomi Kiyota", + "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan" + }, + { + "author_name": "Kenichi Harada", + "author_inst": "Division of Urology, Department of Surgery, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan" + }, + { + "author_name": "Yugo Tanaka", + "author_inst": "Division of Thoracic Surgery, Department of Surgery, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan" + }, + { + "author_name": "Yasuko Mori", + "author_inst": "Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan" + }, + { + "author_name": "Hironobu Minami", + "author_inst": "Division of Medical Oncology/Hematology, Department of Medicine, Kobe University Hospital and Graduate School of Medicine, Kobe, Japan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "oncology" + }, { "rel_doi": "10.1101/2021.10.24.21265455", "rel_title": "Vaccine hesitancy for coronavirus SARS-CoV-2 in North India", @@ -565166,213 +565971,6 @@ "type": "new results", "category": "synthetic biology" }, - { - "rel_doi": "10.1101/2021.10.23.465542", - "rel_title": "Protection from SARS-CoV-2 Delta one year after mRNA-1273 vaccination in nonhuman primates is coincident with an anamnestic antibody response in the lower airway", - "rel_date": "2021-10-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.23.465542", - "rel_abs": "mRNA-1273 vaccine efficacy against SARS-CoV-2 Delta wanes over time; however, there are limited data on the impact of durability of immune responses on protection. We immunized rhesus macaques at weeks 0 and 4 and assessed immune responses over one year in blood, upper and lower airways. Serum neutralizing titers to Delta were 280 and 34 reciprocal ID50 at weeks 6 (peak) and 48 (challenge), respectively. Antibody binding titers also decreased in bronchoalveolar lavage (BAL). Four days after challenge, virus was unculturable in BAL and subgenomic RNA declined [~]3-log10 compared to control animals. In nasal swabs, sgRNA declined 1-log10 and virus remained culturable. Anamnestic antibody responses (590-fold increase) but not T cell responses were detected in BAL by day 4 post-challenge. mRNA-1273-mediated protection in the lungs is durable but delayed and potentially dependent on anamnestic antibody responses. Rapid and sustained protection in upper and lower airways may eventually require a boost.", - "rel_num_authors": 48, - "rel_authors": [ - { - "author_name": "Matthew Gagne", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Kizzmekia S. Corbett", - "author_inst": "Vaccine Research Center, NIAID, NIH, Bethesda, Maryland, 20892, United States of America Department of Microbiology and Immunology, Harvard T.H. Chan School of" - }, - { - "author_name": "Barbara J. Flynn", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Kathryn E. Foulds", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Danielle A. Wagner", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Shayne F. Andrew", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "John-Paul M. Todd", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Christopher Cole Honeycutt", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Lauren McCormick", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Saule T. Nurmukhambetova", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Meredith E. Davis-Gardner", - "author_inst": "Department of Pediatrics, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, Georgia, 30322, United St" - }, - { - "author_name": "Laurent Pessaint", - "author_inst": "Bioqual, Inc., Rockville, Maryland, 20850, United States of America" - }, - { - "author_name": "Kevin W. Bock", - "author_inst": "Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rock" - }, - { - "author_name": "Bianca M. Nagata", - "author_inst": "Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rock" - }, - { - "author_name": "Mahnaz Minai", - "author_inst": "Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rock" - }, - { - "author_name": "Anne P. Werner", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Juan I. Moliva", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Courtney Tucker", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Cynthia G. Lorang", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Bingchun Zhao", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Elizabeth McCarthy", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Anthony Cook", - "author_inst": "Bioqual, Inc., Rockville, Maryland, 20850, United States of America" - }, - { - "author_name": "Alan Dodson", - "author_inst": "Bioqual, Inc., Rockville, Maryland, 20850, United States of America" - }, - { - "author_name": "Prakriti Mudvari", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Jesmine Roberts-Torres", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Farida Laboune", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Lingshu Wang", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Adrienne Goode", - "author_inst": "Bioqual, Inc., Rockville, Maryland, 20850, United States of America" - }, - { - "author_name": "Swagata Kar", - "author_inst": "Bioqual, Inc., Rockville, Maryland, 20850, United States of America" - }, - { - "author_name": "Seyhan Boyoglu-Barnum", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Eun Sung Yang", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Wei Shi", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Aur\u00e9lie Ploquin", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Nicole Doria-Rose", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Andrea Carfi", - "author_inst": "Moderna Inc., Cambridge, MA, 02139, United States of America" - }, - { - "author_name": "John R. Mascola", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Eli A. Boritz", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Darin K. Edwards", - "author_inst": "Moderna Inc., Cambridge, MA, 02139, United States of America" - }, - { - "author_name": "Hanne Andersen", - "author_inst": "Bioqual, Inc., Rockville, Maryland, 20850, United States of America" - }, - { - "author_name": "Mark G. Lewis", - "author_inst": "Bioqual, Inc., Rockville, Maryland, 20850, United States of America" - }, - { - "author_name": "Mehul S. Suthar", - "author_inst": "Department of Pediatrics, Emory Vaccine Center, Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, Georgia, 30322, United St" - }, - { - "author_name": "Barney S. Graham", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Mario Roederer", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Ian N. Moore", - "author_inst": "Infectious Disease Pathogenesis Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rock" - }, - { - "author_name": "Martha C. Nason", - "author_inst": "Biostatistics Research Branch, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Ma" - }, - { - "author_name": "Nancy J. Sullivan", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Daniel C. Douek", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - }, - { - "author_name": "Robert A. Seder", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of Ameri" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.10.23.465567", "rel_title": "SARS-CoV-2 Infection Impacts Carbon Metabolism and Depends on Glutamine for Replication in Syrian Hamster Astrocytes", @@ -566652,6 +567250,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2021.10.19.21265193", + "rel_title": "Use and impact of virtual primary care on quality and safety: public perspectives during the COVID-19 pandemic", + "rel_date": "2021-10-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.19.21265193", + "rel_abs": "BackgroundWith the onset of COVID-19, primary care has swiftly transitioned from face-to-face to virtual care, yet it remains largely unknown how this has impacted on the quality and safety of care.\n\nAimTo evaluate patient use of virtual primary care models during COVID-19 in terms of change in uptake, perceived impact on the quality and safety of care, and willingness of future use.\n\nDesign and settingAn online cross-sectional survey was administered to the public across the United Kingdom, Sweden, Italy and Germany.\n\nMethodsMcNemar tests were conducted to test pre- and post pandemic differences in uptake for each technology. One-way analysis of variance was conducted to examine patient experience ratings and perceived impacts on healthcare quality and safety across demographic characteristics.\n\nResultsRespondents (N=6,326) reported an increased use of telephone consultations (+6.3%, P<.001), patient-initiated services (+1.5%, n=98, p<0.001), video consultations (+1.4%, P<.001), remote triage (+1.3, p<0.001), and secure messaging systems (+0.9%, P=.019). Experience rates using virtual care technologies were higher for men (2.39{+/-}0.96 vs 2.29{+/-}0.92, P<.001), those with higher literacy (2.75{+/-}1.02 vs 2.29{+/-}0.92, P<.001), and participants from Germany (2.54{+/-}0.91, P<.001). Healthcare timeliness and efficiency were the quality dimensions most often reported as being positively impacted by virtual technologies (60.2%, n=2,793 and 55.7%, n=2,401, respectively), followed by effectiveness (46.5%, n=1,802), safety (45.5%, n=1,822), patient-centredness (45.2%, n=45.2) and equity (42.9%, n=1,726). Interest in future use was highest for telephone consultations (55.9%), followed by patient-initiated digital services (56.1%), secure messaging systems (43.4%), online triage (35.1%), video consultations (37.0%), and chat consultations (30.1%), although significant variation was observed between countries and patient characteristics.\n\nConclusionFuture work must examine the drivers and determinants of positive experiences using remote care to co-create a supportive environment that ensures equitable adoption and use across different patient groups. Comparative analysis between countries and health systems offers the opportunity for policymakers to learn from best practices internationally.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Ana Luisa Neves", + "author_inst": "NIHR Patient Safety Translational Research Centre, Imperial College" + }, + { + "author_name": "Jackie van Dael", + "author_inst": "NIHR Patient Safety Translational Research Centre, Imperial College" + }, + { + "author_name": "Niki O'Brien", + "author_inst": "Institute of Global Health Innovation, Imperial College" + }, + { + "author_name": "Kelsey Flott", + "author_inst": "NIHR Patient Safety Translational Research Centre, Imperial College" + }, + { + "author_name": "Saira Ghafur", + "author_inst": "Institute of Global Health Innovation, Imperial College" + }, + { + "author_name": "Ara Darzi", + "author_inst": "Institute of Global Health Innovation, Imperial College" + }, + { + "author_name": "Erik Mayer", + "author_inst": "NIHR Patient Safety Translational Research Centre, Imperial College" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2021.10.19.21265190", "rel_title": "Can the Rapid Antigen Test for COVID-19 Replace RT-PCR: A Meta-analysis of Test Agreement", @@ -567107,149 +567748,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.21.21265133", - "rel_title": "Post COVID-19 in children, adolescents, and adults: results of a matched cohort study including more than 150,000 individuals with COVID-19", - "rel_date": "2021-10-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.21.21265133", - "rel_abs": "BackgroundLong-term health sequelae of the coronavirus disease 2019 (COVID-19) are a major public health concern. However, evidence on post-acute COVID-19 syndrome (post COVID-19) is still limited, particularly for children and adolescents. Utilizing comprehensive healthcare data on more than 45 percent of the German population from January 2019 through December 2020, we investigated post COVID-19 in children/adolescents and adults.\n\nMethodsFrom a total of 38 million individuals, we identified all patients with laboratory confirmed diagnosis of COVID-19 through June 30, 2020. A control cohort was assigned using 1:5 exact matching on age, sex, and propensity score matching on prevalent medical conditions. COVID-19 and control cohorts were followed for incident morbidity outcomes documented at least three months after the date of COVID-19 diagnosis, which was used as the index date for both groups. Overall, 96 pre-defined outcomes were aggregated into 13 diagnosis/symptom complexes and three domains (physical health, mental health, physical/mental overlap domain). We used Poisson regression to estimate incidence rate ratios (IRRs) with 95%-confidence intervals (95%-CI).\n\nResultsThe study population included 157,134 individuals (11,950 children/adolescents and 145,184 adults) with confirmed COVID-19. COVID-19 and control cohort were well-balanced regarding covariates. For all health outcomes combined, incidence rates (IRs) in the COVID-19 cohort were significantly higher than those in the control cohort in both children/adolescents (IRR=1.30, 95%-CI=[1.25-1.35], IR COVID-19=436.91, IR Control=335.98) and adults (IRR=1.33, 95%-CI=[1.31-1.34], IR COVID-19=615.82, IR Control=464.15). The relative magnitude of increased documented morbidity was similar for the physical, mental, and physical/mental overlap domain. In the COVID-19 cohort, incidence rates were significantly higher in all 13 diagnosis/symptom complexes in adults and in ten diagnosis/symptom complexes in children/adolescents. IRR estimates were similar for the age groups 0-11 and 12-17. Incidence rates in children/adolescents were consistently lower than those in adults. Among the specific outcomes with the highest IRR and an incidence rate of at least 1/100 person-years in the COVID-19 cohort in children and adolescents were malaise/fatigue/exhaustion (IRR=2.28, 95%-CI=[1.71-3.06], IR COVID-19=12.58, IR Control=5.51), cough (IRR=1.74, 95%-CI=[1.48-2.04], IR COVID-19=36.56, IR Control=21.06), and throat/chest pain (IRR=1.72, 95%-CI=[1.39-2.12], IR COVID-19=20.01, IR Control=11.66). In adults, these included dysgeusia (IRR=6.69, 95%-CI=[5.88-7.60], IR COVID-19=12.42, IR Control=1.86), fever (IRR=3.33, 95%-CI=[3.01-3.68], IR COVID-19=11.53, IR Control=3.46), and dyspnea (IRR=2.88, 95%-CI=[2.74-3.02], IR COVID-19=43.91, IR Control=15.27).\n\nConclusionsThis large, matched cohort study indicates substantial new-onset post COVID-19 morbidity in pediatric and adult populations based on routine health care documentation. Further investigation is required to assess the persistence and long-term health impact of post COVID-19 conditions, especially in children and adolescents.", - "rel_num_authors": 32, - "rel_authors": [ - { - "author_name": "Martin Roessler", - "author_inst": "Center for Evidence-Based Healthcare (ZEGV), University Hospital Carl Gustav Carus and Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany" - }, - { - "author_name": "Falko Tesch", - "author_inst": "Center for Evidence-Based Healthcare (ZEGV), University Hospital Carl Gustav Carus and Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany" - }, - { - "author_name": "Manuel Batram", - "author_inst": "Vandage GmbH, Bielefeld, Germany and Faculty for Business Administration and Economics, Bielefeld University, Bielefeld, Germany" - }, - { - "author_name": "Josephine Jacob", - "author_inst": "InGef - Institute for Applied Health Research Berlin, Berlin, Germany" - }, - { - "author_name": "Friedrich Loser", - "author_inst": "Techniker Krankenkasse, Hamburg, Germany" - }, - { - "author_name": "Oliver Weidinger", - "author_inst": "AOK Bayern - Die Gesundheitskasse, Regensburg, Germany" - }, - { - "author_name": "Danny Wende", - "author_inst": "BARMER Institut f\u00fcr Gesundheitssystemforschung (bifg), Berlin, Germany" - }, - { - "author_name": "Annika Vivirito", - "author_inst": "InGef - Institute for Applied Health Research Berlin, Berlin, Germany" - }, - { - "author_name": "Nicole Toepfner", - "author_inst": "Department of Pediatrics, University Hospital Carl Gustav Carus and Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany" - }, - { - "author_name": "Martin Seifert", - "author_inst": "Center for Evidence-Based Healthcare (ZEGV), University Hospital Carl Gustav Carus and Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany" - }, - { - "author_name": "Oliver Nagel", - "author_inst": "InGef - Institute for Applied Health Research Berlin, Berlin, Germany" - }, - { - "author_name": "Christina K\u00f6nig", - "author_inst": "Techniker Krankenkasse, Hamburg, Germany" - }, - { - "author_name": "Roland Jucknewitz", - "author_inst": "AOK Bayern - Die Gesundheitskasse, Regensburg, Germany" - }, - { - "author_name": "Jakob Peter Armann", - "author_inst": "Department of Pediatrics, University Hospital Carl Gustav Carus and Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany" - }, - { - "author_name": "Reinhard Berner", - "author_inst": "Department of Pediatrics, University Hospital Carl Gustav Carus and Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany" - }, - { - "author_name": "Marina Treskova-Schwarzbach", - "author_inst": "Robert Koch-Institut, Berlin, Germany" - }, - { - "author_name": "Dagmar Hertle", - "author_inst": "BARMER Institut f\u00fcr Gesundheitssystemforschung (bifg), Berlin, Germany" - }, - { - "author_name": "Stefan Scholz", - "author_inst": "Robert Koch-Institut, Berlin, Germany" - }, - { - "author_name": "Stefan Stern", - "author_inst": "AOK Bayern - Die Gesundheitskasse, Regensburg, Germany" - }, - { - "author_name": "Pedro Ballesteros", - "author_inst": "BARMER Institut f\u00fcr Gesundheitssystemforschung (bifg), Berlin, Germany" - }, - { - "author_name": "Stefan Ba\u00dfler", - "author_inst": "AOK PLUS, Dresden, Germany" - }, - { - "author_name": "Barbara Bertele", - "author_inst": "Techniker Krankenkasse, Hamburg, Germany" - }, - { - "author_name": "Uwe Repschl\u00e4ger", - "author_inst": "BARMER Institut f\u00fcr Gesundheitssystemforschung (bifg), Berlin, Germany" - }, - { - "author_name": "Nico Richter", - "author_inst": "DAK-Gesundheit, Hamburg, Germany" - }, - { - "author_name": "Cordula Riederer", - "author_inst": "DAK-Gesundheit, Hamburg, Germany" - }, - { - "author_name": "Franziska Sobik", - "author_inst": "DAK-Gesundheit, Hamburg, Germany" - }, - { - "author_name": "Anja Schramm", - "author_inst": "AOK Bayern - Die Gesundheitskasse, Regensburg, Germany" - }, - { - "author_name": "Claudia Schulte", - "author_inst": "BARMER Institut f\u00fcr Gesundheitssystemforschung (bifg), Berlin, Germany" - }, - { - "author_name": "Lothar Wieler", - "author_inst": "Robert Koch-Institut, Berlin, Germany" - }, - { - "author_name": "Jochen Walker", - "author_inst": "InGef - Institute for Applied Health Research Berlin, Berlin, Germany" - }, - { - "author_name": "Christa Scheidt-Nave", - "author_inst": "Robert Koch-Institut, Berlin, Germany" - }, - { - "author_name": "Jochen Schmitt", - "author_inst": "Center for Evidence-Based Healthcare (ZEGV), University Hospital Carl Gustav Carus and Carl Gustav Carus Faculty of Medicine, TU Dresden, Dresden, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.10.21.465252", "rel_title": "Nasal prevention of SARS-CoV-2 infection by intranasal influenza-based boost vaccination", @@ -568737,6 +569235,45 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2021.10.19.464951", + "rel_title": "Preparation of ingestible antibodies to neutralize the binding of SarsCoV2 RBD (receptor binding domain) to human ACE2 Receptor", + "rel_date": "2021-10-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.19.464951", + "rel_abs": "COVID19 continues to be a serious threat to human health and mortality. There is dire need for new solutions to combat this pandemic especially for those individuals who are not vaccinated or unable to be vaccinated and continue to be exposed to the SARSCoV2. In addition, the emergence of new more transmissible variants such as delta pose additional threat from this virus.\n\nTo explore another solution for prevention and treatment of COVID 19, we have produced chicken egg derived IgY antibodies against the Receptor binding domain (RBD) of SARSCoV2 spike protein which is involved in binding to human cell ACE2 receptors. The - RBD IgY effectively neutralize the binding of RBD to ACE2 and prevent pseudovirus entry in a PRNT assay. Importantly our anti-RBD IgY also neutralize the binding of Sars CoV2 delta variant RBD to ACE2. Given that chicken egg derived IgY are safe and permissible for human consumption, we plan to develop these ingestible antibodies for prevention of viral entry in the oropharyngeal and digestive tract in humans as passive immunotherapy.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Gopi Kadiyala", + "author_inst": "Kyntox Bio Private Limited" + }, + { + "author_name": "Subramanian Iyer", + "author_inst": "ProdIgY Bio" + }, + { + "author_name": "Kranti Meher", + "author_inst": "Reagene Biosciences Private Limited" + }, + { + "author_name": "Subhramanyam Vangala", + "author_inst": "Reagene Biosciences Private Limited" + }, + { + "author_name": "Satish Chandran", + "author_inst": "ProdIgY Bio" + }, + { + "author_name": "Uday Saxena", + "author_inst": "Reagene Biosciences Private Limited" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.10.19.463727", "rel_title": "Neutralization of Mu and C.1.2 SARS-CoV-2 Variants by Vaccine-elicited Antibodies in Individuals With and Without Previous History of Infection", @@ -569261,29 +569798,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.15.21265037", - "rel_title": "Extreme COVID-19 waves reveal hyperexponential growth and finite-time singularity", - "rel_date": "2021-10-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.15.21265037", - "rel_abs": "Coronavirus disease 2019 (COVID-19) has rapidly spread throughout our planet, bringing human lives to a standstill. Understanding the early transmission dynamics helps plan intervention strategies such as lockdowns that mitigate further spread, minimizing the adverse impact on humanity and the economy1-3. Exponential growth of infections was thought to be the defining feature of an epidemic in its initial growth phase4-7; any variation from an exponential growth was described by adjusting the parameters of the exponential model7,8. Here, we show that, contrary to common belief, early stages of extreme COVID-19 waves display an unbounded growth and finite-time singularity accompanying a hyperexponential power-law. The faster than exponential growth phase is hazardous and would entail stricter regulations. Such a power-law description allows us to characterize COVID-19 waves with single power-law exponents, better than piece-wise exponentials. Furthermore, we identify the presence of log-periodic patterns decorating the power-law growth. These log-periodic oscillations may enable better prediction of the finite-time singularity. We anticipate that our findings of hyperexponential growth and log-periodicity will help model the COVID-19 transmission more accurately.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Induja Pavithran", - "author_inst": "Indian Institue of technology Madras" - }, - { - "author_name": "R. I. Sujith", - "author_inst": "Indian Institue of technology Madras" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.10.19.21265230", "rel_title": "Psychological, social and financial impact of COVID-19 on culturally and linguistically diverse communities: a cross-sectional Australian study", @@ -570515,6 +571029,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.18.464882", + "rel_title": "Rapid and Effective Inactivation of SARS-CoV-2 by a Cationic Conjugated Oligomer with Visible Light: Studies of Antiviral Activity in Solutions and on Supports", + "rel_date": "2021-10-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.18.464882", + "rel_abs": "This paper presents results of a study of a new cationic oligomer that contains end groups and a chromophore affording inactivation of SARS-Cov-2 by visible light irradiation in solution or as a solid coating on wipes paper and glass fiber filtration substrates. A key finding of this study is that the cationic oligomer with a central thiophene ring and imidazolium charged groups give outstanding performance in both killing of E. coli bacterial cells and inactivation of the virus at very short times. Our introduction of cationic N-Methyl Imidazolium groups enhances the light-activation process for both E. coli and SARS-Cov-2 but dampens the dark killing of the bacteria and eliminates the dark inactivation of the virus. For the studies with this oligomer in solution at concentration of 1 g/mL and E. coli we obtain 3 log killing of the bacteria with 10 min irradiation with LuzChem cool white lights (mimicking indoor illumination). With the oligomer in solution at a concentration of 10 g/mL, we observe 4 logs inactivation (99.99 %) in 5 minutes of irradiation and total inactivation after 10 min. The oligomer is quite active against E. coli on oligomer-coated wipes papers and glass fiber filter supports. The SARS-Cov-2 is also inactivated by the oligomer coated glass fiber filter papers. This study indicates that these oligomer-coated materials may be very useful as wipes and filtration materials.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Kemal Kaya", + "author_inst": "University of New Mexico" + }, + { + "author_name": "Mohammed I Khalil", + "author_inst": "University of New Mexico" + }, + { + "author_name": "Benjamin Fetrow", + "author_inst": "University of New Mexico" + }, + { + "author_name": "Hugh Fritz", + "author_inst": "University of New Mexico" + }, + { + "author_name": "Pradeepkumar Jagadesan", + "author_inst": "University of Texas at San Antonio" + }, + { + "author_name": "Virginie Bondu", + "author_inst": "University of New Mexico" + }, + { + "author_name": "Linea Ista", + "author_inst": "University of New Mexico" + }, + { + "author_name": "Eva Y Chi", + "author_inst": "University of New Mexico" + }, + { + "author_name": "David Whitten", + "author_inst": "University of New Mexico" + }, + { + "author_name": "Kirk S Schanze", + "author_inst": "University of Texas at San Antonio" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.10.18.21265128", "rel_title": "The effect of circulating zinc, selenium, copper and vitamin K1 on COVID-19 outcomes: a Mendelian randomization study", @@ -571074,49 +571643,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.14.21265010", - "rel_title": "How frequent are acute reactions to COVID-19 vaccination and who is at risk?", - "rel_date": "2021-10-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.14.21265010", - "rel_abs": "IntroductionOur objective was to describe and compare self-reported side effects of COVID-19 vaccines in the USA.\n\nMethodsA web-based registry enrolled volunteers who received a COVID-19 vaccine between March 19 -July 15, 2021. We collected self-reported short-term side effects, medical consultation, hospitalization, and quality of life impact following completed vaccination regimens (Pfizer, Moderna, J&J).\n\nResultsWe recruited 6,966 volunteers who completed their full course of vaccination (median age 48 years, IQR 35.0-62.0; 83.6% female): Pfizer 3,486; Moderna 2,857; J&J 623. Few (3.1%) sought medical care for post-vaccination side effects. Hospitalization (n=17; 0.3%) and severe allergic reactions (n=39; 0.6%) also were rare. Those with autoimmune disease or lung disease were approximately twice as likely to seek medical care (adjusted odds ratio (aOR) 2.01 [95% CI: 1.39;2.92] and 1.70 [95% CI: 1.12;2.58] respectively). 92.4% of participants reported [≥]1 side effect (median 3), with injection site reactions (78.9%), fatigue (70.3%), headache (49.0%) reported most frequently. More side effects were reported after the second dose of two-dose vaccines (medians: 1 vs. 2 for Pfizer and 1 vs. 3 for Moderna for first and second doses respectively) versus 3 for J&Js single-dose vaccine. For the employed, the median number of workdays missed was one. Diabetics and those vaccinated against influenza were substantially less likely to report [≥]3 symptoms (aOR 0.68, 95% CI 0.56,0.82 and aOR 0.82, 95% CI 0.73,0.93, respectively.)\n\nDiscussionThe total side effect burden was, not unexpectedly, greater with two-dose regimens but all three vaccines appear relatively safe. Very few subjects reported side effects serious enough to warrant medical care or reported post-vaccination hospitalization. While these findings do not address possible long-term effects, they do inform on their short-term safety and tolerability and will hopefully provide some reassurance and positively inform the benefit-risk and pharmacoeconomic assessment for all three vaccines.\n\nClinicaltrials.gov NCT04368065", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Nancy A Dreyer", - "author_inst": "IQVIA" - }, - { - "author_name": "Matthew W Reynolds", - "author_inst": "IQVIA" - }, - { - "author_name": "Lisa M Albert", - "author_inst": "IQVIA" - }, - { - "author_name": "Emma Brinkley", - "author_inst": "IQVIA" - }, - { - "author_name": "Tom Kwon", - "author_inst": "IQVIA" - }, - { - "author_name": "Christina D Mack", - "author_inst": "IQVIA" - }, - { - "author_name": "Stephen Toovey", - "author_inst": "Pegasus Research" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.15.21265021", "rel_title": "COVID-19 Likelihood Meter: a machine learning approach to COVID-19 screening for Indonesian health workers", @@ -572080,6 +572606,149 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, + { + "rel_doi": "10.1101/2021.10.16.21265087", + "rel_title": "Durability of antibody responses and frequency of clinical and subclinical SARS-CoV-2 infection six months after BNT162b2 COVID-19 vaccination in healthcare workers", + "rel_date": "2021-10-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.16.21265087", + "rel_abs": "Antibodies against SARS-CoV-2 decay but persist six months post-vaccination, with lower levels of neutralizing titers against Delta than wild-type. Only 2 of 227 vaccinated healthcare workers experienced outpatient symptomatic breakthrough infections despite 59 of 227 exhibiting serological evidence of exposure to SARS-CoV-2 as defined by development of anti-nucleocapsid protein antibodies.", + "rel_num_authors": 32, + "rel_authors": [ + { + "author_name": "Eric D Laing", + "author_inst": "Uniformed Services University, Bethesda, MD, USA" + }, + { + "author_name": "Carol D Weiss", + "author_inst": "US Food and Drug Administration, Silver Spring, MD, USA" + }, + { + "author_name": "Emily C Samuels", + "author_inst": "Uniformed Services University, Bethesda, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA" + }, + { + "author_name": "Si'Ana A Coggins", + "author_inst": "Uniformed Services University, Bethesda, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA" + }, + { + "author_name": "Wei Wang", + "author_inst": "US Food and Drug Administration, Silver Spring, MD, USA" + }, + { + "author_name": "Richard Wang", + "author_inst": "US Food and Drug Administration, Silver Spring, MD, USA" + }, + { + "author_name": "Russell Vassell", + "author_inst": "US Food and Drug Administration, Silver Spring, MD, USA" + }, + { + "author_name": "Spencer L Sterling", + "author_inst": "Uniformed Services University, Bethesda, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA" + }, + { + "author_name": "Marana A Tso", + "author_inst": "Uniformed Services University, Bethesda, MD, USA" + }, + { + "author_name": "Tonia Conner", + "author_inst": "Uniformed Services University, Bethesda, MD, USA" + }, + { + "author_name": "Emilie Goguet", + "author_inst": "Uniformed Services University, Bethesda, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA" + }, + { + "author_name": "Belinda M Jackson-Thompson", + "author_inst": "Uniformed Services University, Bethesda, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA" + }, + { + "author_name": "Luca Illinik", + "author_inst": "Naval Medical Research Center, Silver Spring, MD; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA" + }, + { + "author_name": "Julian Davies", + "author_inst": "Naval Medical Research Center, Silver Spring, MD; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA" + }, + { + "author_name": "Orlando Ortega", + "author_inst": "Naval Medical Research Center, Silver Spring, MD; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA" + }, + { + "author_name": "Edward Parmelee", + "author_inst": "Uniformed Services University, Bethesda, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA" + }, + { + "author_name": "Monique Hollis-Perry", + "author_inst": "Naval Medical Research Center, Silver Spring, MD" + }, + { + "author_name": "Santina E Maiolatesi", + "author_inst": "Naval Medical Research Center, Silver Spring, MD; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA" + }, + { + "author_name": "Gregory Wang", + "author_inst": "Naval Medical Research Center, Silver Spring, MD; General Dynamics Information Technology, Falls Church, VA" + }, + { + "author_name": "Kathleen F Ramsey", + "author_inst": "Naval Medical Research Center, Silver Spring, MD; General Dynamics Information Technology, Falls Church, VA" + }, + { + "author_name": "Anatalio E Reyes", + "author_inst": "Naval Medical Research Center, Silver Spring, MD; General Dynamics Information Technology, Falls Church, VA" + }, + { + "author_name": "Yolanda Alcorta", + "author_inst": "Naval Medical Research Center, Silver Spring, MD; General Dynamics Information Technology, Falls Church, VA" + }, + { + "author_name": "Mimi A Wong", + "author_inst": "Naval Medical Research Center, Silver Spring, MD; General Dynamics Information Technology, Falls Church, VA" + }, + { + "author_name": "Alyssa R Lindrose", + "author_inst": "Uniformed Services University, Bethesda, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA" + }, + { + "author_name": "Christopher A Duplessis", + "author_inst": "Naval Medical Research Center, Silver Spring, MD" + }, + { + "author_name": "David R Tribble", + "author_inst": "Uniformed Services University, Bethesda, MD, USA" + }, + { + "author_name": "Allison MW Malloy", + "author_inst": "Uniformed Services University, Bethesda, MD, USA" + }, + { + "author_name": "Timothy H Burgess", + "author_inst": "Uniformed Services University, Bethesda, MD, USA" + }, + { + "author_name": "Simon D Pollett", + "author_inst": "Uniformed Services University, Bethesda, MD, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA" + }, + { + "author_name": "Cara H Olsen", + "author_inst": "Uniformed Services University, Bethesda, MD, USA" + }, + { + "author_name": "Christopher C Broder", + "author_inst": "Uniformed Services University, Bethesda, MD, USA" + }, + { + "author_name": "Edward Mitre", + "author_inst": "Uniformed Services University, Bethesda, MD, USA" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.15.21264137", "rel_title": "COVID-19 is associated with higher risk of venous thrombosis, but not arterial thrombosis, compared with influenza: Insights from a large US cohort", @@ -572532,57 +573201,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.18.21265046", - "rel_title": "Comparative assessment of methods for short-term forecasts of COVID-19 admissions in England at the local level", - "rel_date": "2021-10-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.18.21265046", - "rel_abs": "BackgroundForecasting healthcare demand is essential in epidemic settings, both to inform situational awareness and facilitate resource planning. Ideally, forecasts should be robust across time and locations. During the COVID-19 pandemic in England, it is an ongoing concern that demand for hospital care for COVID-19 patients in England will exceed available resources.\n\nMethodsWe made weekly forecasts of daily COVID-19 hospital admissions for National Health Service (NHS) Trusts in England between August 2020 and April 2021 using three disease-agnostic forecasting models: a mean ensemble of autoregressive time series models, a linear regression model with 7-day-lagged local cases as a predictor, and a scaled convolution of local cases and a delay distribution. We compared their point and probabilistic accuracy to a mean-ensemble of them all, and to a simple baseline model of no change from the last day of admissions. We measured predictive performance using the Weighted Interval Score (WIS) and considered how this changed in different scenarios (the length of the predictive horizon, the date on which the forecast was made, and by location), as well as how much admissions forecasts improved when future cases were known.\n\nResultsAll models outperformed the baseline in the majority of scenarios. Forecasting accuracy varied by forecast date and location, depending on the trajectory of the outbreak, and all individual models had instances where they were the top- or bottom-ranked model. Forecasts produced by the mean-ensemble were both the most accurate and most consistently accurate forecasts amongst all the models considered. Forecasting accuracy was improved when using future observed, rather than forecast, cases, especially at longer forecast horizons.\n\nConclusionsAssuming no change in current admissions is rarely better than including at least a trend. Using confirmed COVID-19 cases as a predictor can improve admissions forecasts in some scenarios, but this is variable and depends on the ability to make consistently good case forecasts. However, ensemble forecasts can make forecasts that make consistently more accurate forecasts across time and locations. Given minimal requirements on data and computation, our admissions forecasting ensemble could be used to anticipate healthcare needs in future epidemic or pandemic settings.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Sophie Meakin", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Sam Abbott", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Nikos I Bosse", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "James D Munday", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Hugo Gruson", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Joel Hellewell", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "Katharine Sherratt", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "- CMMID COVID-19 Working Group", - "author_inst": "" - }, - { - "author_name": "Sebastian Funk", - "author_inst": "London School of Hygiene & Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.10.17.21265117", "rel_title": "Reductions in US life expectancy from COVID-19 by Race and Ethnicity: Is 2021 a repetition of 2020?", @@ -573829,6 +574447,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.11.21264845", + "rel_title": "Willingness to take the Covid-19 vaccines and associated factors at a tertiary institution community in Johannesburg, South Africa", + "rel_date": "2021-10-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.11.21264845", + "rel_abs": "BackgroundSA is aiming to achieve herd immunity against Covid-19 by the first quarter of 2022. The success of the Covid-19 vaccination roll-out depends primarily on the willingness of the population to take the vaccines.\n\nAimThis study examined the willingness to take the Covid-19 vaccine, along with the factors of concern, efficacy, and preferences of the individual which may increase the willingness to be vaccinated.\n\nSettingThis study was conducted at the University of the Witwatersrand, Johannesburg, amongst adult students and academic and professional staff.\n\nMethodsWe conducted a cross-sectional online study from 27 July - 14 August 2021. We performed descriptive and inferential analysis to determine the factors associated with willingness to take the Covid-19 vaccine.\n\nResults2364 participants responded to a survey link and 82% were students, 66.8% were in the 18-29 years age band, females represented 64.0% and 49.2% were black people. 1965 (83.3%) were willing to receive a Covid-19 vaccine, the most preferred vaccines were Pfizer (41%) and J&J (23%), local pharmacy (29%) and GP (17%) were the preferred places for vaccination and the trusted sources of information on Covid-19 vaccines were the general practitioners (40.6%) and specialists (19,2%). Perceptions that vaccines are safe (aOR=31.56, 95%CI: 16.02-62.12 for affirmative agreement) and effective (aOR=5.92, 95%CI: 2.87-12.19 for affirmative agreement) were the main determinants for willingness to taking a COVID-19 vaccine\n\nConclusionIt is imperative to reinforce the message of Covid-19 vaccine safety and efficacy and to include the GPs and the community pharmacies in the vaccination roll-out in SA.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Bhadrashil H Modi", + "author_inst": "University of Witwatersrand" + }, + { + "author_name": "Deidre Pretorius", + "author_inst": "University of Witwatersrand" + }, + { + "author_name": "Joel M Francis", + "author_inst": "University of Witwatersrand" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.10.10.21264809", "rel_title": "A novel framework based on deep learning and ANOVA feature selection method for diagnosis of COVID-19 cases from chest X-ray Images", @@ -574609,49 +575254,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2021.10.12.21264890", - "rel_title": "Breastfeeding infants receive neutralizing antibodies and cytokines from mothers immunized with a COVID-19 mRNA vaccine", - "rel_date": "2021-10-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.12.21264890", - "rel_abs": "ObjectiveTo evaluate the immune response to COVID-19 mRNA-based vaccines present in breastmilk and the transfer of the immune response to the breastfeeding child.\n\nMethodsA prospective cohort study enrolled 30 lactating women who received an mRNA-based COVID-19 vaccine between January and April 2021. Women provided serial milk samples, which included milk expressed before vaccination, milk expressed across 2-3 weeks after the first dose, and milk expressed across 3 weeks after the second dose. Women also were asked to provide their blood, spotted on cards (dried blood spots; DBS) 19 days after the first dose and 21 days after the second dose. Stool samples from the breastfed infants were collected 21 days after mothers received their second dose. Pre-pandemic samples of milk, DBS cards, and infant stool from prior studies were also utilized. Milk and infant stool samples were tested by ELISA for receptor-binding domain (RBD)-specific IgA and IgG. Milk samples were tested for the presence of neutralizing antibodies against the spike and four variants of concern (VOCs): D614G, B.1.1.7 (alpha), B.1.351 (beta), and P.1 (gamma). Milk samples were also tested by electrochemiluminescence assay for levels of 10 cytokines.\n\nResultsMilk from COVID-19-immunized women neutralized the spike and four VOCs and this response is primarily IgG-driven. The immune response in milk also included significantly elevated levels of interferon-{gamma} (IFN-{gamma}). The immune response to maternal vaccination was reflected in breastfed babies; anti-RBD IgG and anti-RBD IgA was detected in 33% and 30% of infant stool samples, respectively. Levels of anti-RBD antibodies in infant stool correlated with maternal vaccine side-effects.\n\nConclusionHumoral and cellular immune responses to mRNA-based COVID-19 vaccination are present in the breastmilk of most women. The milk anti-RBD antibodies can neutralize SARS-CoV-2 spike and VOCs. Importantly, we describe for the first time the transfer of anti-RBD antibodies to breastfed infants, with the potential to confer passive immunity against SARS-CoV-2.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Vignesh Narayanaswamy", - "author_inst": "University of Massachusetts Amherst" - }, - { - "author_name": "Brian Pentecost", - "author_inst": "University of Massachusetts Amherst" - }, - { - "author_name": "Corina N Schoen", - "author_inst": "Baystate Medical Center" - }, - { - "author_name": "Dominique Alfandari", - "author_inst": "University of Massachusetts Amherst" - }, - { - "author_name": "Sallie S Schneider", - "author_inst": "Baystate Medical Center" - }, - { - "author_name": "Ryan Baker", - "author_inst": "University of Massachusetts Amherst" - }, - { - "author_name": "Kathleen F Arcaro", - "author_inst": "University of Massachusetts Amherst" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2021.10.11.21264831", "rel_title": "SPECIFIC DETECTION OF SARS-COV-2 VARIANTS B.1.1.7 (ALPHA) AND B.1.617.2 (DELTA) USING A ONE-STEP QUANTITATIVE PCR ASSAY", @@ -576055,6 +576657,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.14.21264474", + "rel_title": "Deep phylogenetic-based clustering analysis uncovers new and shared mutations in SARS-CoV-2 variants as a result of directional and convergent evolution", + "rel_date": "2021-10-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.14.21264474", + "rel_abs": "Nearly two decades after the last epidemic caused by a severe acute respiratory syndrome coronavirus (SARS-CoV), newly emerged SARS-CoV-2 quickly spread in 2020 and precipitated an ongoing global public health crisis. Both the continuous accumulation of point mutations, owed to the naturally imposed genomic plasticity of SARS-CoV-2 evolutionary processes, as well as viral spread over time, allow this RNA virus to gain new genetic identities, spawn novel variants and enhance its potential for immune evasion. Here, through an in-depth phylogenetic clustering analysis of upwards of 200,000 whole-genome sequences, we reveal the presence of not previously reported and hitherto unidentified mutations and recombination breakpoints in Variants of Concern (VOC) and Variants of Interest (VOI) from Brazil, India (Beta, Eta and Kappa) and the USA (Beta, Eta and Lambda). Additionally, we identify sites with shared mutations under directional evolution in the SARS-CoV-2 Spike-encoding protein of VOC and VOI, tracing a heretofore-undescribed correlation with viral spread in South America, India and the USA. Our evidence-based analysis provides well-supported evidence of similar pathways of evolution for such mutations in all SARS-CoV-2 variants and sub-lineages. This raises two pivotal points: the co-circulation of variants and sub-lineages in close evolutionary environments, which sheds light onto their trajectories into convergent and directional evolution (i), and a linear perspective into the prospective vaccine efficacy against different SARS-CoV-2 strains (ii).\n\nAuthor summaryIn this study, through analysis of very robust and comprehensive datasets, we identify a plethora of mutations in the SARS-CoV-2 Spike cell surface protein of several variants of concern and multiple variants of interest. We trace an association of such mutations with viral spread in different countries. We further infer the presence of new SARS-CoV-2 sublineages and show that the vast majority of mutations identified in the SARS-CoV-2 Spike protein are under convergent evolution. If we consider every color of a Rubiks cubes face to represent a different mutation of a particular variant, evolutionary convergence can be achieved only when all composite pieces of a single face are of the same color and every face has one unique color. Overall, this raises two important points: we provide insight into the presence of SARS-CoV-2 variants and sub-lineages circulating in very close evolutionary environments and our analyses can serve to facilitate an outlook into the prospective vaccine efficacy against different SARS-CoV-2 strains.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Danilo Rosa Nunes", + "author_inst": "Federal University of Sao Paulo (UNIFESP)" + }, + { + "author_name": "Carla Torres Braconi", + "author_inst": "Federal University of Sao Paulo (UNIFESP)" + }, + { + "author_name": "Louisa Ludwig-Begall", + "author_inst": "University of Liege" + }, + { + "author_name": "Clarice Weis Arns", + "author_inst": "University of Campinas (UNICAMP)" + }, + { + "author_name": "Ricardo Duraes-Carvalho", + "author_inst": "University of Campinas" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.14.21264988", "rel_title": "Modelling airborne transmission of SARS-CoV-2 using CARA: Risk assessment for enclosed spaces", @@ -576483,65 +577120,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.13.21264901", - "rel_title": "Soluble angiotensin-converting enzyme 2 as a prognostic biomarker for disease progression in patients infected with SARS-CoV-2", - "rel_date": "2021-10-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.13.21264901", - "rel_abs": "BackgroundThere is a need for better prediction of disease severity in patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Soluble angiotensin-converting enzyme 2 (sACE2) arises from shedding of membrane ACE2 (mACE2) that is known to be a receptor for the spike protein of SARS-CoV-2; however, its value as a biomarker for disease severity is unknown. This study evaluated the predictive value of sACE2 in the context of other known biomarkers of inflammation and tissue damage (C-reactive protein [CRP], growth/differentiation factor-15 [GDF-15], interleukin-6 [IL-6], and soluble fms-like tyrosine kinase-1 [sFlt-1]) in patients with and without SARS-CoV-2 with different clinical outcomes.\n\nMethodsFor univariate analyses, median differences between biomarker levels were calculated for the following patient groups classified according to clinical outcome: reverse transcription polymerase chain reaction (RT-PCR)-confirmed SARS-CoV-2 positive (Groups 1-4); RT-PCR-confirmed SARS-CoV-2 negative following previous SARS-CoV-2 infection (Groups 5 and 6); and RT-PCR-confirmed SARS-CoV-2 negative controls (Group 7).\n\nResultsMedian levels of CRP, GDF-15, IL-6, and sFlt-1 were significantly higher in patients with SARS-CoV-2 who were admitted to hospital compared with patients who were discharged (all p<0.001), whereas levels of sACE2 were significantly lower (p<0.001). Receiver operating characteristic curve analysis of sACE2 provided cut-offs for the prediction of hospital admission of [≤]0.05 ng/mL (positive predictive value: 89.1%) and [≥]0.42 ng/mL (negative predictive value: 84.0%).\n\nConclusionThese findings support further investigation of sACE2, either as a single biomarker or as part of a panel, to predict hospitalisation risk and disease severity in patients infected with SARS-CoV-2.\n\nHIGHLIGHTSNoelia Diaz Troyano: Noy-Lee-ah Dee-az Tro-yah-no\n\nBetter prediction of disease severity in patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is needed. We measured soluble angiotensin-converting enzyme 2 (soluble ACE2) and other biomarkers of inflammation and tissue damage in patients recruited from Vall dHebron University Hospital, with and without SARS-CoV-2 and with different clinical outcomes. Levels of soluble ACE2 were significantly lower in patients with SARS-CoV-2 who had the most severe clinical outcome in all comparisons. These findings support a protective role for soluble ACE2 in SARS-CoV-2 infection and warrant further investigation of soluble ACE2 as a biomarker for disease severity in patients with SARS-CoV-2.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Noelia Diaz Troyano", - "author_inst": "Vall d'Hebron University Hospital" - }, - { - "author_name": "Pablo Gabriel Medina", - "author_inst": "Vall d'Hebron University Hospital" - }, - { - "author_name": "Stephen Weber", - "author_inst": "Roche Diagnostics GmbH" - }, - { - "author_name": "Martin Klammer", - "author_inst": "Roche Diagnostics GmbH" - }, - { - "author_name": "Raquel Barquin-DelPino", - "author_inst": "Vall d'Hebron University Hospital" - }, - { - "author_name": "Laura Castillo-Ribelles", - "author_inst": "Vall d'Hebron University Hospital" - }, - { - "author_name": "Angels Esteban", - "author_inst": "Vall d'Hebron University Hospital" - }, - { - "author_name": "Manuel Hern\u00e1ndez-Gonz\u00e1lez", - "author_inst": "Vall d'Hebron University Hospital" - }, - { - "author_name": "Roser Ferrer-Costa", - "author_inst": "Vall d'Hebron University Hospital" - }, - { - "author_name": "Tomas Pumarola", - "author_inst": "Vall d'Hebron University Hospital" - }, - { - "author_name": "Francisco Rodriguez Frias", - "author_inst": "Vall d'Hebron University Hospital" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.10.13.464050", "rel_title": "A Rapid Bead-Based Assay For Screening Of SARS-CoV-2 Neutralising Antibodies", @@ -577933,6 +578511,41 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.10.09.21264758", + "rel_title": "The military as a neglected pathogen transmitter and its implications for COVID-19: A systematic review", + "rel_date": "2021-10-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.09.21264758", + "rel_abs": "BackgroundThe risk of outbreaks escalating into pandemics has soared with globalization. Therefore, understanding transmission mechanisms of infectious diseases has become critical to formulating global public health policy. This systematic review assessed evidence in the medical and public health literature for the military as a disease vector.\n\nMethodsWe searched 3 electronic databases without temporal restrictions. Two researchers independently extracted study data using a standardized form. Through team discussions, studies were grouped according to their type of transmission mechanism and direct quotes were extracted to generate themes and sub-themes. A content analysis was later performed and frequency distributions for each theme were generated.\n\nResultsOf 6477 studies, 210 met our inclusion criteria and provided evidence, spanning over two centuries (1810 - 2020), for the military as a pathogen transmitter, within itself or between it and civilians. Biological mechanisms driving transmission included person-to-person transmission, contaminated food and water, vector-borne, and airborne routes. Contaminated food and/or water were the most common biological transmission route. Social mechanisms facilitating transmission included crowded living spaces, unhygienic conditions, strenuous working, training conditions, absent or inadequate vaccination programs, pressure from military leadership, poor compliance with public health advice, contractor mismanagement, high-risk behaviours, and occupation-specific freedom of movement. Living conditions were the most common social transmission mechanism, with young, low ranking military personnel repeatedly reported as the most affected group. Selected social mechanisms, such as employment-related freedom of movement, were unique to the military as a social institution. While few studies explicitly studied civilian populations, considerably more contained information that implied that civilians were likely impacted by outbreaks described in the military.\n\nConclusionsThis study identified features of the military that pose a significant threat to global health, especially to civilian health in countries with substantial military presence or underdeveloped health systems. While biological transmission mechanisms are shared by other social groups, selected social transmission mechanisms are unique to the military. As an increasingly interconnected world faces the challenges of COVID-19 and future infectious diseases, the identified features of the military may exacerbate current and similar challenges and impair attempts to implement successful and equitable global public health policies.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Claudia Chaufan", + "author_inst": "Faculty of Health, York University, Canada" + }, + { + "author_name": "Ilinca A. Dutescu", + "author_inst": "Faculty of Health, York University, Canada" + }, + { + "author_name": "Hanah Fekre", + "author_inst": "Faculty of Health, York University, Canada" + }, + { + "author_name": "Saba Marzabadi", + "author_inst": "Faculty of Health, York University, Canada" + }, + { + "author_name": "K.J. Noh", + "author_inst": "Independent Scholar, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.10.11.463956", "rel_title": "SARS-CoV-2 variants exhibit increased kinetic stability of open spike conformations as an evolutionary strategy", @@ -578249,33 +578862,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.11.463917", - "rel_title": "Secondary structure of subgenomic RNA M of SARS-CoV-2", - "rel_date": "2021-10-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.11.463917", - "rel_abs": "SARS-CoV-2 belongs the Coronavirinae family. As other coronaviruses, SARS-CoV-2 is enveloped and possesses positive-sense, single-stranded RNA genome of [~] 30 kb. Genome RNA is used as the template for replication and transcription. During these processes, positive-sense genomic RNA (gRNA) and subgenomic RNAs (sgRNAs) are created. Several studies showed importance of genomic RNA secondary structure in SARS-CoV-2 replication. However, the structure of sgRNAs have remained largely unsolved so far. In this study, we performed probing of sgRNA M of SARS-CoV-2 in vitro. This is the first experimentally informed secondary structure model of sgRNA M, which presents features likely to be important in sgRNA M function. The knowledge about sgRNA M provides insights to better understand virus biology and could be used for designing new therapeutics.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Marta Soszynska-Jozwiak", - "author_inst": "Institute of Bioorganic Chemistry, Polish Academy of Sciences" - }, - { - "author_name": "Ryszard Kierzek", - "author_inst": "Institute of Bioorganic Chemistry, Polish Academy of Sciences" - }, - { - "author_name": "Elzbieta Kierzek", - "author_inst": "Institute of Bioorganic Chemistry, Polish Academy of Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2021.10.09.463779", "rel_title": "Intelligent Resolution: Integrating Cryo-EM with AI-driven Multi-resolution Simulations to Observe the SARS-CoV-2 Replication-Transcription Machinery in Action", @@ -579402,6 +579988,117 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.10.08.21264519", + "rel_title": "Immunogenicity of the Ad26.CoV2.S vaccine in people living with HIV", + "rel_date": "2021-10-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.08.21264519", + "rel_abs": "BackgroundPeople living with HIV (PLWH) have been reported to have an increased risk of more severe COVID-19 disease outcome and an increased risk of death relative to HIV-uninfected individuals. Here we assessed the ability of the Johnson and Johnson Ad26.CoV2.S vaccine to elicit neutralizing antibodies to the Delta variant in PLWH relative to HIV-uninfected individuals. We also compared the neutralization after vaccination to neutralization elicited by SARS-CoV-2 infection only in HIV-uninfected, suppressed HIV PLWH, and PLWH with detectable HIV viremia.\n\nMethodsWe enrolled 26 PLWH and 73 HIV-uninfected participants from the SISONKE phase 3b open label South African clinical trial of the Ad26.CoV2.S vaccine in health care workers (HCW). Enrollment was a median 56 days (range 19-98 days) post-vaccination and PLWH in this group had well controlled HIV infection. We also enrolled unvaccinated participants previously infected with SARS-CoV-2. This group consisted of 34 PLWH and 28 HIV-uninfected individuals. 10 of the 34 (29%) SARS-CoV-2 infected only PLWH had detectable HIV viremia. We used records of a positive SARS-CoV-2 qPCR result, or when a positive result was absent, testing for SARS-CoV-2 nucleocapsid antibodies, to determine which vaccinated participants were SARS-CoV-2 infected prior to vaccination. Neutralization capacity was assessed using participant plasma in a live virus neutralization assay of the Delta SARS-CoV-2 variant currently dominating infections in South Africa. This study was approved by the Biomedical Research Ethics Committee at the University of KwaZulu-Natal (reference BREC/00001275/2020).\n\nFindingsThe majority (68%) of Ad26.CoV2.S vaccinated HCW were found to be previously infected with SARS-CoV-2. In this group, Delta variant neutralization was 9-fold higher compared to the infected only group (GMT=306 versus 36, p<0.0001) and 26-fold higher relative to the vaccinated only group (GMT=12, p<0.0001). No significant difference in Delta variant neutralization capacity was observed in vaccinated and previously SARS-CoV-2 infected PLWH relative to vaccinated and previously SARS-CoV-2 infected, HIV-uninfected participants (GMT=307 for HIV-uninfected, 300 for PLWH, p=0.95). SARS-CoV-2 infected, unvaccinated PLWH showed 7-fold reduced neutralization of the Delta variant relative to HIV-uninfected participants (GMT=105 for HIV-uninfected, 15 for PLWH, p=0.001). There was a higher frequency of non-responders in PLWH relative to HIV-uninfected participants in the SARS-CoV-2 infected unvaccinated group (27% versus 0%, p=0.0029) and 60% of HIV viremic versus 13% of HIV suppressed PLWH were non-responders (p=0.0088). In contrast, the frequency of non-responders was low in the vaccinated/infected group, and similar between HIV-uninfected and PLWH. Vaccinated only participants showed a low neutralization of the Delta variant, with a stronger response in PLWH (GMT=6 for HIV-uninfected, 73 for PLWH, p=0.02).\n\nInterpretationThe neutralization response of the Delta variant following Ad26.CoV2.S vaccination in PLWH with well controlled HIV was not inferior to HIV-uninfected study participants. In SARS-CoV-2 infected and non-vaccinated participants, the presence of HIV infection reduced the neutralization response to SARS-CoV-2 infection, and this effect was strongest in PLWH with detectable HIV viremia\n\nFundingSouth African Medical Research Council, The Bill & Melinda Gates Foundation.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Khadija Khan", + "author_inst": "Africa Health Research Institute; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal" + }, + { + "author_name": "Gila Lustig", + "author_inst": "Centre for the AIDS Programme of Research in South Africa" + }, + { + "author_name": "Mallory Bernstein", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Derseree Archary", + "author_inst": "Centre for the AIDS Programme of Research in South Africa; Department of Medical Microbiology, University of KwaZulu-Natal" + }, + { + "author_name": "Sandile Cele", + "author_inst": "Africa Health Research Institute; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal" + }, + { + "author_name": "Farina Karim", + "author_inst": "Africa Health Research Institute; School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal" + }, + { + "author_name": "Muneerah Smith", + "author_inst": "Department of Integrative Biomedical Sciences" + }, + { + "author_name": "Yashica Ganga", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Zesuliwe Jule", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Kajal Reedoy", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Yoliswa Miya", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "Ntombifuthi Mthabela", + "author_inst": "Africa Health Research Institute" + }, + { + "author_name": "- COMMIT-KZN Team", + "author_inst": "" + }, + { + "author_name": "Richard Lessells", + "author_inst": "School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; Centre for the AIDS Programme of Research in South Africa" + }, + { + "author_name": "Tulio de Oliveira", + "author_inst": "School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; Centre for the AIDS Programme of Research in South Africa" + }, + { + "author_name": "Bernadett Gosnell", + "author_inst": "Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal" + }, + { + "author_name": "Salim Abdool Karim", + "author_inst": "Centre for the AIDS Programme of Research in South Africa" + }, + { + "author_name": "Nigel Garrett", + "author_inst": "Centre for the AIDS Programme of Research in South Africa; Discipline of Public Health Medicine, School of Nursing and Public Health, University of KwaZulu-Nata" + }, + { + "author_name": "Willem Hanekom", + "author_inst": "Africa Health Research Institute; Division of Infection and Immunity, University College London" + }, + { + "author_name": "Linda Gail Bekker", + "author_inst": "Institute of Infectious Disease and Molecular Medicine; Desmond Tutu HIV Centre" + }, + { + "author_name": "Glenda Gray", + "author_inst": "South African Medical Research Council" + }, + { + "author_name": "Jonathan M Blackburn", + "author_inst": "Department of Integrative Biomedical Sciences; Institute of Infectious Disease and Molecular Medicine; Sengenics Corporation, Kuala Lumpur, Malaysia" + }, + { + "author_name": "Mahomed-Yunus S Moosa", + "author_inst": "Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal" + }, + { + "author_name": "Alex Sigal", + "author_inst": "Africa Health Research Institute" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "hiv aids" + }, { "rel_doi": "10.1101/2021.10.08.21264302", "rel_title": "Safety and immunogenicity of a SARS-CoV-2 recombinant protein vaccine with AS03 adjuvant in healthy adults: interim findings from a phase 2, randomised, dose-finding, multi-centre study", @@ -580134,33 +580831,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.08.21264749", - "rel_title": "Longitudinal changes in home confinement and mental health implications: A 17-month follow-up study in England during the COVID-19 pandemic", - "rel_date": "2021-10-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.08.21264749", - "rel_abs": "BackgroundThe COVID-19 pandemic has brought about significant behavioural changes, one of which is increased time spent at home. Although official lockdowns were typically short-term and allowed people to leave their homes for exercise and essential activities, some individuals did not leave their home for prolonged periods due to a range of factors including clinical vulnerability. This study aimed to explore longitudinal patterns of such home confinement across different stages of the COVID-19 pandemic in the UK, and its associated predictors and mental health outcomes.\n\nMethodsData were from the UCL COVID -19 Social Study. The analytical sample consisted of 25,390 adults in England who were followed up for 17 months from March 2020 to July 2021. Data were analysed using growth mixture models.\n\nResultsOur analyses identified three classes of growth trajectories, including one class showing a high level of persistent home confinement (24.8%), one changing class with clear alignment with national containment policy/advice (32.0%), and one class with a persistently low level of confinement (43.1%). A range of factors were found to be associated the class membership of home confinement trajectories, such as age, gender, income, employment status, social relationships and health. The class with a high level of confinement had the highest number of depressive and anxiety symptoms at the end of the follow-up independent of potential confounders.\n\nConclusionsThere was substantial heterogeneity in longitudinal patterns of home confinement during the COVID-19 pandemic. However, a striking proportion of our sample maintained a high level of home confinement over the course of 17 months, even during periods when containment measures were eased or removed and when infection rates were low. They also had the worst mental health outcomes. This group warrants special attention in addressing the mental health impact of the COVID-19 pandemic.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Feifei Bu", - "author_inst": "University College London" - }, - { - "author_name": "Andrew Steptoe", - "author_inst": "University College London" - }, - { - "author_name": "Daisy Fancourt", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.10.07.463592", "rel_title": "Comprehensive antibody profiling of mRNA vaccination in children", @@ -581268,6 +581938,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.04.21264542", + "rel_title": "Postvaccination SARS-CoV-2 infection among healthcare workers: A Systematic Review and meta-analysis", + "rel_date": "2021-10-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.04.21264542", + "rel_abs": "INTRODUCTIONHealthcare workers (HCWs) remain on the front line of the battle against SARS-CoV-2 and COVID-19 infection, and are among the highest groups at risk of infection during this raging pandemic. We conducted a systematic review and meta-analysis to assess incidence of postvaccination SARS-CoV-2 infection among vaccinated HCWs.\n\nMETHODSWe searched multiple databases from inception through August 2021 to identify studies that reported on incidence of postvaccination SARS-CoV-2 infection among HCWs. Meta-analysis was performed to determine pooled proportions of COVID-19 infection in partially and fully vaccinated individuals.\n\nRESULTSEighteen studies with 228,873 HCWs were included in the final analysis. Total number of partially vaccinated, fully vaccinated, and unvaccinated HCWs were 132,922, 155,673 and 17505, respectively. Overall pooled proportion of COVID-19 infections among partially/fully vaccinated and unvaccinated HCWs was 2.1% (95% CI 1.2-3.5). Among partially vaccinated, fully vaccinated and unvaccinated HCWs, pooled proportion of COVID-19 infections was 3.7% (95% CI 1.8-7.3), 1.3% (95% CI 0.6-2.9), and 10.1% (95% CI 4.5-19.5), respectively.\n\nDISCUSSIONOur analysis shows the risk of COVID-19 infection in both partially and fully vaccinated HCWs remains exceedingly low when compared to unvaccinated individuals. There remains an urgent need for all frontline HCWs to be vaccinated against SARS-CoV-2 infection.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Saurabh Chandan", + "author_inst": "CHI Health Creighton University Medical Center" + }, + { + "author_name": "Shahab R. Khan", + "author_inst": "Brigham and Womens Hospital, Harvard Medical School" + }, + { + "author_name": "Smit Deliwala", + "author_inst": "Hurley Medical Center" + }, + { + "author_name": "Babu P. Mohan", + "author_inst": "University of Utah Health" + }, + { + "author_name": "Daryl Ramai", + "author_inst": "University of Utah Health" + }, + { + "author_name": "Ojasvini C. Chandan", + "author_inst": "Childrens Hospital of Omaha" + }, + { + "author_name": "Antonio Facciorusso", + "author_inst": "University of Foggia" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.10.05.21262783", "rel_title": "Is the infection of the SARS-CoV-2 Delta variant associated with the outcomes of COVID-19 patients?", @@ -582032,33 +582745,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.06.21264645", - "rel_title": "A joint hierarchical model for the number of cases and deaths due to COVID-19 across the boroughs of Montreal", - "rel_date": "2021-10-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.06.21264645", - "rel_abs": "Montreal is the epicentre of the COVID-19 pandemic in Canada with highest number of deaths. The cumulative numbers of cases and deaths in the 33 areas of Montreal are modelled through bivariate hierarchical Bayesian models using Poisson distributions. The Poisson means are decomposed in the log scale as the sums of fixed effects and latent effects. The areal median age, the educational level, and the number of beds in long-term care homes are included in the fixed effects. To explore the correlation between cases and deaths inside and across areas, three bivariate models are considered for the latent effects, namely an independent one, a conditional autoregressive model, and one that allows for both spatially structured and unstructured sources of variability. As the inclusion of spatial effects change some of the fixed effects, we extend the Spatial+ approach to a Bayesian areal set up to investigate the presence of spatial confounding.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Victoire Michal", - "author_inst": "McGill University" - }, - { - "author_name": "Leo Vanciu", - "author_inst": "Marianapolis College" - }, - { - "author_name": "Alexandra M. Schmidt", - "author_inst": "McGill University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.10.05.21264462", "rel_title": "Detection and quantification of SARS-CoV-2 RNA in wastewater influent in relation to reported COVID-19 incidence in Finland", @@ -583690,6 +584376,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.10.07.463234", + "rel_title": "High-throughput Activity Assay for Screening Inhibitors of the SARS-CoV-2 Mac1 Macrodomain", + "rel_date": "2021-10-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.07.463234", + "rel_abs": "Macrodomains are a class of conserved ADP-ribosylhydrolases expressed by viruses of pandemic concern, including coronaviruses and alphaviruses. Viral macrodomains are critical for replication and virus-induced pathogenesis; therefore, these enzymes are a promising target for antiviral therapy. However, no potent or selective viral macrodomain inhibitors currently exist, in part due to the lack of a high-throughput assay for this class of enzymes. Here, we developed a high-throughput ADP-ribosylhydrolase assay using the SARS-CoV-2 macrodomain Mac1. We performed a pilot screen which identified dasatinib and dihydralazine as ADP-ribosylhydrolase inhibitors. Importantly, dasatinib does not inhibit MacroD2, the closest Mac1 homolog in humans. Our study demonstrates the feasibility of identifying selective inhibitors based on ADP-ribosylhydrolase activity, paving the way for screening large compound libraries to identify improved macrodomain inhibitors and explore their potential as antiviral therapies for SARS-CoV-2 and future viral threats.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Morgan A Dasovich", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Junlin Zhuo", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Ajit G Thomas", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Jack A Goodman", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Robert Lyle McPherson", + "author_inst": "Massachusetts Institute of Technology" + }, + { + "author_name": "Aravinth Kumar Jayabalan", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Veronica F. Busa", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Shang-Jung Cheng", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Brennan Murphy", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Karli R Redinger", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Takashi Tsukamoto", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Barbara S Slusher", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Jurgen Bosch", + "author_inst": "Case Western Reserve University" + }, + { + "author_name": "Jack Wei", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Anthony Leung", + "author_inst": "Johns Hopkins University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.10.03.21264490", "rel_title": "Assessment of Post COVID-19 Health Problems and its Determinants in North India: A descriptive cross section study", @@ -584162,77 +584923,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.10.05.463205", - "rel_title": "SARS-CoV-2 causes human BBB injury and neuroinflammation indirectly in a linked organ chip platform", - "rel_date": "2021-10-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.05.463205", - "rel_abs": "COVID-19 is a multi-system disease affecting many organs outside of the lungs, and patients generally develop varying degrees of neurological symptoms. Whereas, the pathogenesis underlying these neurological manifestations remains elusive. Although in vitro models and animal models are widely used in studies of SARS-CoV-2 infection, human organ models that can reflect the pathological alterations in a multi-organ context are still lacking. In this study, we propose a new strategy to probe the effects of SARS-CoV-2 on human brains in a linked alveolus-BBB organ chip platform. The new multi-organ platform allows to recapitulate the essential features of human alveolar-capillary barrier and blood-brain barrier in a microfluidic condition by co-culturing the organ-specific cells. The results reveal direct SARS-CoV-2 exposure has no obvious effects on BBB chip alone. While, infusion of endothelial medium from infected alveolus chips can cause BBB dysfunction and neuroinflammation on the linked chip platform, including brain endothelium disruption, glial cell activation and inflammatory cytokines release. These new findings suggest that SARS-CoV-2 could induce neuropathological alterations, which might not result from direct viral infection through hematogenous route, but rather likely from systemic inflammation following lung infection. This work provides a new strategy to study the virus-host interaction and neuropathology at an organ-organ context, which is not easily obtained by other in vitro models. This will facilitate to understand the neurological pathogenesis in SARS-CoV-2 and accelerate the development of new therapeutics.\n\nSUMMARYO_LIA linked human alveolus-BBB chip platform is established to explore the influences of SARS-CoV-2 on human brains in an organ-organ context.\nC_LIO_LISARS-CoV-2 infection could induce BBB injury and neuroinflammation.\nC_LIO_LIThe neuropathological changes are caused by SARS-CoV-2 indirectly, which might be mediated by systemic inflammation following lung infection, but probably not by direct viral neuroinvasion.\nC_LI", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Peng Wang", - "author_inst": "Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China" - }, - { - "author_name": "Lin Jin", - "author_inst": "Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences, , Kunming Institute of Zoology, Chinese Academy of Sciences, Kunmin" - }, - { - "author_name": "Min Zhang", - "author_inst": "Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China" - }, - { - "author_name": "Yunsong Wu", - "author_inst": "Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China" - }, - { - "author_name": "Zilei Duan", - "author_inst": "Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences, , Kunming Institute of Zoology, Chinese Academy of Sciences, Kunmin" - }, - { - "author_name": "Wenwen Chen", - "author_inst": "Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China" - }, - { - "author_name": "Chaoming Wang", - "author_inst": "Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences, , Kunming Institute of Zoology, Chinese Academy of Sciences, Kunmin" - }, - { - "author_name": "Zhiyi Liao", - "author_inst": "Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences, , Kunming Institute of Zoology, Chinese Academy of Sciences, Kunmin" - }, - { - "author_name": "Jianbao Han", - "author_inst": "Kunming National High-level Bio-safety Research Center for Non-human Primates, Center for Biosafety Mega-Science, Kunming Institute of Zoology, Chinese Academy " - }, - { - "author_name": "Yingqi Guo", - "author_inst": "Core Technology Facility of Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, Yunnan, China" - }, - { - "author_name": "Yaqiong Guo", - "author_inst": "Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China" - }, - { - "author_name": "Yaqing Wang", - "author_inst": "Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China" - }, - { - "author_name": "Ren Lai", - "author_inst": "Kunming Institute of Zoology, Chinese Academy of Sciences" - }, - { - "author_name": "Jianhua Qin", - "author_inst": "Dalian Insititute of Chemistry Physics, Chinese Academy of Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2021.10.05.463008", "rel_title": "How does temperature affect the dynamics of SARS-CoV-2 M proteins? Insights from Molecular Dynamics Simulations", @@ -586080,6 +586770,37 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.10.04.463014", + "rel_title": "Genetic association of TMPRSS2 rs2070788 polymorphism with COVID-19 Case Fatality Rate among Indian populations", + "rel_date": "2021-10-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.04.463014", + "rel_abs": "SARS-CoV2, the causative agent for COVID-19, an ongoing pandemic, engages the ACE2 receptor to enter the host cell through S protein priming by a serine protease, TMPRSS2. Variation in the TMPRSS2 gene may account for the difference in population disease susceptibility. The haplotype-based genetic sharing and structure of TMPRSS2 among global populations have not been studied so far. Therefore, in the present work, we used this approach with a focus on South Asia to study the haplotypes and their sharing among various populations worldwide. We have used next-generation sequencing data of 393 individuals and analysed the TMPRSS2 gene. Our analysis of genetic relatedness for this gene showed a closer affinity of South Asians with the West Eurasian populations therefore, host disease susceptibility and severity particularly in the context of TMPRSS2 will be more akin to West Eurasian instead of East Eurasian. This is in contrast to our prior study on ACE2 gene which shows South Asian haplotypes have a strong affinity towards West Eurasians. Thus ACE2 and TMPRSS2 have an antagonistic genetic relatedness among South Asians. We have also tested the SNPs frequencies of this gene among various Indian state populations with respect to the case fatality rate. Interestingly, we found a significant positive association between the rs2070788 SNP (G Allele) and the case fatality rate in India. It has been shown that the GG genotype of rs2070788 allele tends to have a higher expression of TMPRSS2 in the lung compared to the AG and AA genotypes, thus it might play a vital part in determining differential disease vulnerability. We trust that this information will be useful in underscoring the role of the TMPRSS2 variant in COVID-19 susceptibility and using it as a biomarker may help to predict populations at risk.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "RUDRA KUMAR PANDEY", + "author_inst": "BANARAS HINDU UNIVERSITY" + }, + { + "author_name": "Anshika Srivastava", + "author_inst": "BANARAS HINDU UNIVERSITY" + }, + { + "author_name": "Prajjval Pratap Singh", + "author_inst": "BANARAS HINDU UNIVERSITY" + }, + { + "author_name": "Gyaneshwer Chaubey", + "author_inst": "BANARAS HINDU UNIVERSITY" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genetics" + }, { "rel_doi": "10.1101/2021.10.05.463212", "rel_title": "TREM2+ and interstitial macrophages orchestrate airway inflammation in SARS-CoV-2 infection in rhesus macaques", @@ -586640,33 +587361,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.10.01.452232", - "rel_title": "Characterization and Structural Prediction of ORF10, ORF7b, ORF7a, ORF6, Membrane Glycoprotein, and Envelope Protein in SARS-CoV-2 Bangladeshi Variant through Bioinformatics Approach", - "rel_date": "2021-10-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.01.452232", - "rel_abs": "The acute respiratory disease induced by the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has become a global epidemic in just less than a year by the first half of 2020. The subsequent efficient human-to-human transmission of this virus eventually affected millions of people worldwide. The most devastating thing is that the infection rate is continuously uprising and resulting in significant mortality especially among the older age population and those with health co-morbidities. This enveloped, positive-sense RNA virus is chiefly responsible for the infection of the upper respiratory system. The virulence of the SARS-CoV-2 is mostly regulated by its proteins like entry to the host cell through fusion mechanism, fusion of infected cells with neighboring uninfected cells to spread the virus, inhibition of host gene expression, cellular differentiation, apoptosis, mitochondrial biogenesis, etc. But very little is known about the protein structures and functionalities. Therefore, the main purpose of this study is to learn more about these proteins through bioinformatics approaches. In this study, ORF10, ORF7b, ORF7a, ORF6, membrane glycoprotein, and envelope protein have been selected from a Bangladeshi Corona-virus strain G039392 and a number of bioinformatics tools (MEGA-X-V10.1.7, PONDR(R), ProtScale, ProtParam, SCRIBER, NetSurfP v2.0, IntFOLD, UCSF Chimera, and PyMol) and strategies were implemented for multiple sequence alignment and phylogeny analysis with 9 different variants, predicting hydropathicity, amino acid compositions, protein-binding propensity, protein disorders, 2D and 3D protein modeling. Selected proteins were characterized as highly flexible, structurally and electrostatically extremely stable, ordered, biologically active, hydrophobic, and closely related to the proteins of different variants. This detailed information regarding the characterization and structure of proteins of SARS-CoV-2 Bangladeshi variant was performed for the first time ever to unveil the deep mechanism behind the virulence features and also, this robust appraisal paves the future way for molecular docking, vaccine development targeting these characterized proteins.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Pinky Debnath", - "author_inst": "Research Assistant, Chemical Biotechnology Department, Technical University of Munich , Schuigasse 22, D 94315 Straubing , Germany" - }, - { - "author_name": "Umama Khan", - "author_inst": "Research Assistant, Biotechnology and Genetic Engineering Discipline, Khulna University, Khulna 9208, Bangladesh." - }, - { - "author_name": "Md. Salauddin Khan", - "author_inst": "Assistant Professor, Statistics Discipline, Khulna University, Khulna 9208, Bangladesh" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.10.01.462821", "rel_title": "Hierarchical Gaussian Processes and Mixtures of Experts to Model COVID-19 Patient Trajectories", @@ -587690,6 +588384,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.09.30.21264343", + "rel_title": "Genomic diversity of SARS-CoV-2 in Pakistan during fourth wave of pandemic", + "rel_date": "2021-10-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.30.21264343", + "rel_abs": "The emergence of different variants of concern of SARS-CoV-2 has resulted in upsurges of COVID positive cases around the globe. Pakistan is also experiencing fourth wave of COVID-19 with increasing number of positive cases. In order to understand the genomic diversity of circulating SARS-CoV-2 strains during fourth wave of pandemic in Pakistan, the current study was designed. The samples from 89 COVID-19 positive patients were subjected to whole genome sequencing using GeneStudio S5. The results showed that 99% (n=88) of isolates belonged to delta variant and only one isolate belonged to alpha variant. Among delta variant cases 26.1% (n=23) isolates were showing B.1.617.2 while 74% of isolates showing AY.4 lineage. Islamabad was found to be the most affected city with 54% (n=48) of cases, followed by Karachi (28%, n=25), and Rawalpindi (10%, n=9). AY.4 has slight difference in mutation profile compared to B.1.617.2. E156del, G142D and V26I mutations in spike and T181I in NSP6 were present in B.1.617.2 but not in AY.4. Interestingly, A446V mutation in NSP4 has been only observed in AY.4. The current study highlights the circulation of primarily delta variant (B.1.617.2 and AY.4) during fourth wave of pandemic in Pakistan.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Massab Umair", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Aamer Ikram", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Zaira Rehman", + "author_inst": "National Institute of Health (Pakistan)" + }, + { + "author_name": "Adnan Haider", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Nazish Badar", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Muhammad Ammar", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Abdul Ahad", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Rana Suleman", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Muhammad Salman", + "author_inst": "National Institute of Health" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.10.01.21264349", "rel_title": "Humoral cross-reactivity towards SARS-CoV-2 in young children with acute respiratory infection with low-pathogenicity coronaviruses", @@ -588242,129 +588987,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.10.01.21264428", - "rel_title": "Risk factors for infection, predictors of severe disease and antibody response to COVID-19 in patients with rheumatic diseases in Portugal - a multicentre, nationwide study", - "rel_date": "2021-10-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.01.21264428", - "rel_abs": "In order to identify risk factors for SARS-CoV-2 infection as well as for severe/critical COVID-19 in rheumatic and musculoskeletal diseases (RMDs) patients, we conducted a multicentre observational nationwide study of adult patients prospectively-followed in the Rheumatic Diseases Portuguese Register - Reuma.pt - during the first 6 months of the pandemic. We further evaluated the development of IgG antibodies against the receptor-binding domain (RBD) of SARS-CoV-2 in patients with RMDs. We used multivariate logistic regression to compare patients with COVID-19 (COVID-19+) with those who did not develop the disease (COVID-19-) and patients with mild/moderate disease with those exhibiting severe/critical COVID-19. COVID-19+ patients were asked to collect a blood sample for IgG testing [≥] 3 months after infection and results were compared with age-, sex- and sampling date-matched controls. Overall, 179 cases of COVID-19 were registered in Reuma.pt in the period of interest (median age 55 (IQR 20); 76.5% females) in a total of 6404 registered appointments. We found that patients treated with TNF inhibitors had reduced odds of infection (OR=0.16, 95%CI 0.10-0.26, p<0.001), severe disease (OR 0.11, 95%CI 0.01-0.84, p=0.010) and seroconversion rates (OR 0.13, 95%CI 0.02-0.91, p=0.040). Tocilizumab was also associated with a reduced risk of COVID-19 (OR 0.15, 95%CI 0.05-0.41, p<0.001). Older age, major comorbidities (diabetes, hypertension, obesity, cardiovascular disease, chronic pulmonary and kidney disease) and rituximab were associated with an increased risk of infection and worse prognosis, in line with previous reports. Importantly, most patients with inflammatory RMDs (86.2%) were able to develop a robust antibody response after SARS-CoV-2 infection, which was linked with disease severity.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Ana Rita Cruz-Machado", - "author_inst": "Rheumatology Department, Hospital de Santa Maria, Centro Hospitalar Universitario Lisboa Norte, Lisbon Academic Medical Center and European Reference Network on" - }, - { - "author_name": "Sofia C. Barreira", - "author_inst": "Rheumatology Department, Hospital de Santa Maria, Centro Hospitalar Universitario Lisboa Norte, Lisbon Academic Medical Center and European Reference Network on" - }, - { - "author_name": "Matilde Bandeira", - "author_inst": "Rheumatology Department, Hospital de Santa Maria, Centro Hospitalar Universitario Lisboa Norte, Lisbon Academic Medical Center and European Reference Network on" - }, - { - "author_name": "Marc Veldhoen", - "author_inst": "Instituto de Medicina Molecular Joao Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal." - }, - { - "author_name": "Andreia Gomes", - "author_inst": "Instituto de Medicina Molecular Joao Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal." - }, - { - "author_name": "Marta Serrano", - "author_inst": "Instituto de Medicina Molecular Joao Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal." - }, - { - "author_name": "Catarina Duarte", - "author_inst": "Rheumatology Department, Hospital de Santa Maria, Centro Hospitalar Universitario Lisboa Norte, Lisbon Academic Medical Center and European Reference Network on" - }, - { - "author_name": "Maria Rato", - "author_inst": "Rheumatology Department, Centro Hospitalar Universitario de Sao Joao EPE, Porto, Portugal." - }, - { - "author_name": "Bruno Miguel Fernandes", - "author_inst": "Rheumatology Department, Centro Hospitalar Universitario de Sao Joao EPE, Porto, Portugal." - }, - { - "author_name": "Salom\u00e9 Garcia", - "author_inst": "Rheumatology Department, Centro Hospitalar Universitario de Sao Joao EPE, Porto, Portugal." - }, - { - "author_name": "Filipe Pinheiro", - "author_inst": "Rheumatology Department, Centro Hospitalar Universitario de Sao Joao EPE, Porto, Portugal." - }, - { - "author_name": "Miguel Bernardes", - "author_inst": "Rheumatology Department, Centro Hospitalar Universitario de Sao Joao EPE, Porto, Portugal." - }, - { - "author_name": "Nathalie Madeira", - "author_inst": "Rheumatology Department, Instituto Portugues de Reumatologia, Lisbon, Portugal." - }, - { - "author_name": "Cl\u00e1udia Miguel", - "author_inst": "Rheumatology Department, Instituto Portugues de Reumatologia, Lisbon, Portugal." - }, - { - "author_name": "Rita Torres", - "author_inst": "Rheumatology Department, Hospital de Egas Moniz, Centro Hospitalar Lisboa Ocidental, Lisbon, Portugal." - }, - { - "author_name": "Ana Bento Silva", - "author_inst": "Rheumatology Department, Hospital de Egas Moniz, Centro Hospitalar Lisboa Ocidental, Lisbon, Portugal." - }, - { - "author_name": "Jorge Pestana", - "author_inst": "Rheumatology Department, Hospital Garcia de Orta, Almada, Portugal." - }, - { - "author_name": "Diogo Almeida", - "author_inst": "Rheumatology Department, Hospital de Braga, Braga, Portugal." - }, - { - "author_name": "Carolina Mazeda", - "author_inst": "Rheumatology Department, Centro Hospitalar do Baixo Vouga and Ibimed, Institute for Biomedicine, University of Aveiro, Aveiro, Portugal." - }, - { - "author_name": "Filipe Cunha Santos", - "author_inst": "Rheumatology Department, Local Health Unit of Guarda, Guarda, Portugal." - }, - { - "author_name": "Patr\u00edcia Pinto", - "author_inst": "Rheumatology Department, Centro Hospitalar de Vila Nova de Gaia/Espinho, Gaia, Portugal." - }, - { - "author_name": "Marlene Sousa", - "author_inst": "Rheumatology Department, Centro Hospitalar e Universitario de Coimbra, Coimbra, Portugal." - }, - { - "author_name": "Hugo Parente", - "author_inst": "Rheumatology Department, Unidade Local de Saude do Alto Minho, Ponte de Lima, Portugal." - }, - { - "author_name": "Gra\u00e7a Sequeira", - "author_inst": "Rheumatology Department, Centro Hospitalar Universitario do Algarve, Faro, Portugal." - }, - { - "author_name": "Maria Jos\u00e9 Santos", - "author_inst": "Rheumatology Department, Hospital Garcia de Orta, Almada, Portugal." - }, - { - "author_name": "Jo\u00e3o Eurico Fonseca", - "author_inst": "Rheumatology Department, Hospital de Santa Maria, Centro Hospitalar Universitario Lisboa Norte, Lisbon Academic Medical Center and European Reference Network on" - }, - { - "author_name": "Vasco C. Rom\u00e3o", - "author_inst": "Rheumatology Department, Hospital de Santa Maria, Centro Hospitalar Universitario Lisboa Norte, Lisbon Academic Medical Center and European Reference Network on" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "rheumatology" - }, { "rel_doi": "10.1101/2021.09.29.21263145", "rel_title": "COVID-19 in twins: What can we learn from them", @@ -589508,6 +590130,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.10.01.21264373", + "rel_title": "Longitudinal SARS-CoV-2 testing is punctuated by intermittent positivity and variable rates of cycle-threshold decline", + "rel_date": "2021-10-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.10.01.21264373", + "rel_abs": "The COVID-19 pandemic is complicated by cases of vaccine-breakthrough, re-infection, and widespread transmission of variants of concern (VOC). Consequently, the need to interpret longitudinal positive SARS-CoV-2 (SCV-2) tests is crucial in guiding clinical decisions regarding infection control precautions and treatment. Although quantitative tests are not routinely used diagnostically, standard diagnostic RT-PCR tests yield Ct values that are inversely correlated with RNA quantity. In this study, we performed a retrospective review of 72,217 SCV-2 PCR positive tests and identified 264 patients with longitudinal positivity prior to vaccination and VOC circulation. Patients with longitudinal positivity fell into two categories: short-term (207, 78%) or prolonged (57, 22%) positivity, defined as <= 28 (range 1-28, median 16) days and >28 (range 29-152, median 41) days, respectively. In general, Ct values declined over time in both groups; however, 11 short-term positive patients had greater amounts of RNA detected at their terminal test compared to the first positive, and 5 patients had RNA detected at Ct < 35 at least 40 days after initial infection. Oscillating positive and negative results occurred in both groups, although oscillation was seen three times more frequently in prolonged-positive patients. Patients with prolonged positivity had diverse clinical characteristics but were often critically ill and were discharged to high-level care or deceased (22%). Overall, this study demonstrates that caution must be emphasized when interpreting Ct values as a proxy for infectivity, predictor of severity, or a guide for patient care decisions in the absence of additional clinical context.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Shawn E. Hawken", + "author_inst": "UNC Medical Center" + }, + { + "author_name": "Subhashini A. Sellers", + "author_inst": "UNC School of Medicine" + }, + { + "author_name": "Jason R. Smedberg", + "author_inst": "UNC Medical Center" + }, + { + "author_name": "Jeremy D. Ward", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Herbert C. Whinna", + "author_inst": "UNC School of Medicine" + }, + { + "author_name": "William A. Fischer II", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Melissa B. Miller", + "author_inst": "UNC School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.29.21264089", "rel_title": "Immune Memory Response After a Booster Injection of mRNA-1273 for Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2)", @@ -589972,77 +590637,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.10.01.462460", - "rel_title": "ZBP1 induces inflammatory signaling via RIPK3 and promotes SARS-CoV-2-induced cytokine expression", - "rel_date": "2021-10-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.10.01.462460", - "rel_abs": "COVID-19 caused by the SARS-CoV-2 virus remains a threat to global health. The disease severity is mediated by cell death and inflammation, which regulate both the antiviral and the pathological innate immune responses. ZBP1, an interferon-induced cytosolic nucleic acid sensor, facilitates antiviral responses via RIPK3. Although ZBP1-mediated cell death is widely described, whether and how it promotes inflammatory signaling is unclear. Here, we report a ZBP1-induced inflammatory signaling pathway that depends on ubiquitination and RIPK3s scaffolding ability independently of cell death. In human cells, ZBP1 associates with RIPK1 and RIPK3 as well as ubiquitin ligases cIAP1 and LUBAC. RIPK1 and ZBP1 are ubiquitinated to promote TAK1- and IKK-mediated inflammatory signaling. Additionally, RIPK1 recruits the p43/41-caspase-8-p43-FLIP heterodimer to suppress RIPK3 kinase activity, which otherwise promotes inflammatory signaling in a kinase activity-dependent manner. Lastly, we show that ZBP1 contributes to SARS-CoV-2-induced cytokine production. Taken together, we describe a ZBP1-RIPK1-RIPK3-mediated inflammatory signaling pathway relayed by the scaffolding role of RIPKs and regulated by caspase-8. Our results suggest the ZBP1 pathway contributes to inflammation in response to SARS-CoV-2 infection.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Ruoshi Peng", - "author_inst": "University of Oxford" - }, - { - "author_name": "Xuan Wang-Kan", - "author_inst": "University of Oxford" - }, - { - "author_name": "Manja Idorn", - "author_inst": "Aarhus University" - }, - { - "author_name": "Felix Y Zhou", - "author_inst": "University of Oxford" - }, - { - "author_name": "Susana L Orozco", - "author_inst": "University of Washington" - }, - { - "author_name": "Julia McCarthy", - "author_inst": "University of Oxford" - }, - { - "author_name": "Carol S Leung", - "author_inst": "University of Oxford" - }, - { - "author_name": "Xin Lu", - "author_inst": "University of Oxford" - }, - { - "author_name": "Katrin Bagola", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jan Rehwinkel", - "author_inst": "University of Oxford" - }, - { - "author_name": "Andrew Oberst", - "author_inst": "University of Washington" - }, - { - "author_name": "Jonathan Maelfait", - "author_inst": "VIB-Ugent IRC" - }, - { - "author_name": "Soren R. Paludan", - "author_inst": "Aarhus University" - }, - { - "author_name": "Mads Gyrd-Hansen", - "author_inst": "University of Copenhagen" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.09.30.462687", "rel_title": "Comparison of Plaque Size, Thermal Stability, and Replication Rate among SARS-CoV-2 Variants of Concern", @@ -591846,6 +592440,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.28.21264066", + "rel_title": "How well does SARS-CoV-2 spread in hospitals?", + "rel_date": "2021-09-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.28.21264066", + "rel_abs": "Covid-19 poses significant risk of nosocomial transmission, and preventing this requires good estimates of the basic reproduction number R0 in hospitals and care facilities, but these are currently lacking. Such estimates are challenging due to small population sizes in these facilities and inconsistent testing practices.\n\nWe estimate the patient-to-patient R0 and daily transmission rate of SARS-CoV-2 using data from a closely monitored hospital outbreak in Paris 2020 during the first wave. We use a realistic epidemic model which accounts for progressive stages of infection, stochastic effects and a large proportion of asymptomatic infections. Innovatively, we explicitly include changes in testing capacity over time, as well as the evolving sensitivity of PCR testing at different stages of infection. We conduct rigorous statistical inference using iterative particle filtering to fit the model to the observed patient data and validate this methodology using simulation.\n\nWe provide estimates for R0 across the entire hospital (2.6) and in individual wards (from 3 to 15), possibly reflecting heterogeneity in contact patterns or control measures. An obligatory mask-wearing policy introduced during the outbreak is likely to have changed the R0, and we estimate values before (8.7) and after (1.3) its introduction, corresponding to a policy efficacy of 85%.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "George Shirreff", + "author_inst": "Laboratoire MESuRS, Conservatoire National des Arts et M\u00e9tiers, Paris, France ; Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion unit, P" + }, + { + "author_name": "Jean-Ralph Zahar", + "author_inst": "Infection Control Unit, H\u00f4pital Avicenne, Groupe Hospitalier Paris Seine Saint Denis, AP-HP, 93000 Bobigny, France" + }, + { + "author_name": "Simon Cauchemez", + "author_inst": "Mathematical Modelling of Infectious Diseases Unit, Institut Pasteur, UMR2000, CNRS, Paris, France." + }, + { + "author_name": "Laura Temime", + "author_inst": "Laboratoire MESuRS, Conservatoire National des Arts et M\u00e9tiers, Paris, France ; PACRI Unit, Institut Pasteur, Conservatoire national des Arts et M\u00e9tiers, Paris," + }, + { + "author_name": "Lulla Opatowski", + "author_inst": "Institut Pasteur, Epidemiology and Modelling of Antibiotic Evasion unit, Paris, France ; University of Versailles Saint-Quentin-en-Yvelines, Montigny-le-Bretonn" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.28.21264259", "rel_title": "Persistence of neuropsychiatric symptoms associated with SARS-CoV-2 positivity among a cohort of children and adolescents", @@ -592222,25 +592851,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.29.21264261", - "rel_title": "World Science against COVID-19: Gender and Geographical Distribution of Research.", - "rel_date": "2021-09-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.29.21264261", - "rel_abs": "In just a year and a half, an enormous volume of scientific research has been generated throughout the world to study a virus/disease that turned into a pandemic. All the articles on COVID-19 or SARS-CoV-2 included in the SCI-EXPANDED database (Web of Science), signed by more than a third of a million of authorships, were analyzed. Gender could be identified in 92% of the authorships. Women represent 40% of all authors, a similar proportion as first authors, but just 30% as last/senior authors. The pattern of collaboration shows an interesting finding: when a woman signs as a first or last/senior author, the article byline approximates gender parity\n\nAccording to the corresponding address, the USA shares 22.8% of all world articles, followed by China (14.4%), Italy (7.8%), the UK (5.8%), India (4.2%), Spain (3.8%), Germany (3.6%), France (2.9%), Turkey (2.5%), and Canada (2.4%).\n\nDespite their short lives, the papers received an average of 11 citations. The high impact of papers from China is striking (25.1 citations; the UK, 12.4 citations; the USA, 11.3 citations), presumably because the disease emerged in China, and the first publications (very cited) came from there.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "JULIO GONZALEZ-ALVAREZ Sr.", - "author_inst": "UNIVERSITY JAUME I" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.09.27.21264211", "rel_title": "Linguistic fairness in the U.S.: The case of multilingual public health information about COVID-19", @@ -593864,6 +594474,65 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.09.29.462326", + "rel_title": "Metabolic snapshot of plasma samples reveals new pathways implicated in SARS-CoV-2 pathogenesis", + "rel_date": "2021-09-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.29.462326", + "rel_abs": "Despite of the scientific and human efforts to understand COVID-19, there are questions still unanswered. Variations in the metabolic reaction to SARS-CoV-2 infection could explain the striking differences in the susceptibility to infection and the risk of severe disease. Here, we used untargeted metabolomics to examine novel metabolic pathways related to SARS-CoV-2 susceptibility and COVID-19 clinical severity using capillary electrophoresis coupled to a time-of-flight mass spectrometer (CE-TOF-MS) in plasma samples. We included 27 patients with confirmed COVID-19 early after symptom onset who were prospectively followed and 29 healthcare workers heavily exposed to SARS-CoV-2 but with low susceptibility to infection ( nonsusceptible). We found that the metabolite profile was predictive of the study group. We identified a total of 55 metabolites as biomarkers of SARS-CoV-2 susceptibility or COVID-19 clinical severity. We report the discovery of new plasma biomarkers for COVID-19 that provide mechanistic explanations for the clinical consequences of SARS-CoV-2, including mitochondrial and liver dysfunction as a consequence of hypoxemia (citrulline, citrate, and BAIBA), energy production and amino acid catabolism (L-glycine, L-alanine, L-serine, L-proline, L-aspartic acid and L-histidine), endothelial dysfunction and thrombosis (citrulline, L-ADMA, 2-AB, and Neu5Ac), and we found interconnections between these pathways. In summary, in this first report of the metabolomic profile of individuals with severe COVID-19 and SARS-CoV-2 susceptibility by CE-MS, we define several metabolic pathways implicated in SARS-CoV-2 susceptibility and COVID-19 clinical progression that could be developed as biomarkers of COVID-19.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Oihane E. Alb\u00f3niga", + "author_inst": "CEU San Pablo University: Universidad CEU San Pablo" + }, + { + "author_name": "Daniel Jim\u00e9nez", + "author_inst": "IRYCIS: Instituto Ramon y Cajal de Investigacion Sanitaria" + }, + { + "author_name": "Matilde S\u00e1nchez-Conde", + "author_inst": "IRYCIS: Instituto Ramon y Cajal de Investigacion Sanitaria" + }, + { + "author_name": "Pilar Vizcarra", + "author_inst": "IRYCIS: Instituto Ramon y Cajal de Investigacion Sanitaria" + }, + { + "author_name": "Raquel Ron", + "author_inst": "IRYCIS: Instituto Ramon y Cajal de Investigacion Sanitaria" + }, + { + "author_name": "Sabina Herrera", + "author_inst": "IRYCIS: Instituto Ramon y Cajal de Investigacion Sanitaria" + }, + { + "author_name": "Javier Mart\u00ednez-Sanz", + "author_inst": "IRYCIS: Instituto Ramon y Cajal de Investigacion Sanitaria" + }, + { + "author_name": "Elena Moreno", + "author_inst": "IRYCIS: Instituto Ramon y Cajal de Investigacion Sanitaria" + }, + { + "author_name": "Santiago Moreno", + "author_inst": "IRYCIS: Instituto Ramon y Cajal de Investigacion Sanitaria" + }, + { + "author_name": "Coral Barbas", + "author_inst": "CEU San Pablo University: Universidad CEU San Pablo" + }, + { + "author_name": "Sergio Serrano-Villar", + "author_inst": "University Hospital Ram\u00f3n y Cajal and IRYCIS" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.09.28.462270", "rel_title": "Data-driven approaches for genetic characterization of SARS-CoV-2 lineages", @@ -594328,25 +594997,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.27.21264130", - "rel_title": "Effectiveness of the mRNA BNT162b2 vaccine against SARS-CoV-2 severe infections in the Israeli over 60 population: a temporal analysis done by using the national surveillance data.", - "rel_date": "2021-09-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.27.21264130", - "rel_abs": "Last August, when the delta variant became the dominant infection strain, Israel, one of the countries with the highest levels of vaccination in the world, faced a scary pandemic wave. The frighteningly increasing number of infections was seen as the perfect storm to test the effectiveness of the mRNA BNT162b2 vaccine. The new surge forced the government to use a booster shot to protect the most vulnerable age groups. Starting from the August national surveillance data, we analysed the temporal effectiveness of vaccination against severe infections in the Israeli over 60 population. The study shows that the two-dose vaccine still works in preventing people from getting seriously sick but not with the same effectiveness observed in the first months of 2021. However, the observed temporal increase of the vaccine effectiveness in Israel, during August, suggests a correlation with the increase of the population protected by the booster shot.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Stefano De Leo", - "author_inst": "State University of Campinas" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.09.21.21263825", "rel_title": "Global Burden of Covid-19 Restrictions: National, Regional and Global Estimates", @@ -595386,6 +596036,77 @@ "type": "new results", "category": "systems biology" }, + { + "rel_doi": "10.1101/2021.09.21.21258385", + "rel_title": "Using genomic epidemiology of SARS-CoV-2 to support contact tracing and public health surveillance in rural Humboldt County, California.", + "rel_date": "2021-09-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.21.21258385", + "rel_abs": "During the COVID-19 pandemic within the United States, much of the responsibility for diagnostic testing and epidemiologic response has relied on the action of county-level departments of public health. Here we describe the integration of genomic surveillance into epidemiologic response within Humboldt County, a rural county in northwest California. Through a collaborative effort, 853 whole SARS-CoV-2 genomes were generated, representing [~]58% of the 1,449 SARS-CoV-2-positive cases detected in Humboldt County as of mid-March 2021. Phylogenetic analysis of these data was used to develop a comprehensive understanding of SARS-CoV-2 introductions to the county and to support contact tracing and epidemiologic investigations of all large outbreaks in the county. In the case of an outbreak on a commercial farm, viral genomic data were used to validate reported epidemiologic links and link additional cases within the community who did not report a farm exposure to the outbreak. During a separate outbreak within a skilled nursing facility, genomic surveillance data were used to rule out the putative index case, detect the emergence of an independent Spike:N501Y substitution, and verify that the outbreak had been brought under control. These use cases demonstrate how developing genomic surveillance capacity within local public health departments can support timely and responsive deployment of genomic epidemiology for surveillance and outbreak response based on local needs and priorities.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Gunnar Stoddard", + "author_inst": "Humboldt County Department of Health and Human Services - Public Health, Eureka, California, USA" + }, + { + "author_name": "Allison Black", + "author_inst": "Chan Zuckerberg Initiative" + }, + { + "author_name": "Patrick Ayscue", + "author_inst": "Chan Zuckerberg Biohub" + }, + { + "author_name": "Dan Lu", + "author_inst": "Chan Zuckerberg Initiative" + }, + { + "author_name": "Jack Kamm", + "author_inst": "Chan Zuckerberg Biohub" + }, + { + "author_name": "Karan Bhatt", + "author_inst": "Chan Zuckerberg Biohub" + }, + { + "author_name": "Lienna Chan", + "author_inst": "Chan Zuckerberg Biohub" + }, + { + "author_name": "Amy L Kistler", + "author_inst": "Chan Zuckerberg Biohub" + }, + { + "author_name": "Joshua Batson", + "author_inst": "Public Health Company" + }, + { + "author_name": "Angela Detweiler", + "author_inst": "Chan Zuckerberg Biohub" + }, + { + "author_name": "Michelle Tan", + "author_inst": "Chan Zuckerberg Biohub" + }, + { + "author_name": "Norma Neff", + "author_inst": "Chan Zuckerberg Biohub" + }, + { + "author_name": "Joseph L DeRisi", + "author_inst": "Chan Zuckerberg Biohub" + }, + { + "author_name": "Jeremy Corrigan", + "author_inst": "Humboldt County Public Health Laboratory, Eureka, California, USA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.21.21263740", "rel_title": "The Pandemic Brain: neuroinflammation in healthy, non-infected individuals during the COVID-19 pandemic", @@ -595838,37 +596559,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.26.21264145", - "rel_title": "Racial and ethnic inequalities in COVID-19 mortality within carceral settings: An analysis of Texas prisons and jails", - "rel_date": "2021-09-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.26.21264145", - "rel_abs": "Several analyses have highlighted racial and ethnic disparities related to COVID-19 health outcomes across the United States. Less focus has been placed on more localized contexts, such as carceral settings, where racial and ethnic inequities in COVID-19 health outcomes also exist, but the proximal drivers of inequality are different. In this study, we analyzed mortality rates among incarcerated people in the Texas Department of Criminal Justice (TDCJ) to assess racial and ethnic differences in COVID-19 mortality. We obtained monthly demographic and mortality information of the TDCJ population from April 1, 2019 to March 31, 2021 from TDCJ monthly reports and open record requests filed by the Texas Justice Initiative. We estimated the risk of COVID-19 mortality for the Hispanic and Black population relative to the White population using a Bayesian regression framework, adjusting for sex and age. In the first 12 months of the pandemic, Hispanic and Black all-cause mortality rates were higher than that of the White population, reversing the pattern observed the 12 months prior. Adjusted risk of COVID-19 mortality relative to the White population was 1.96 (CI 1.32-2.93) for the Hispanic population and 1.66 (CI 1.10-2.52) for the Black population. We find that COVID-19 mortality has disproportionately impacted Hispanic and Black individuals within the TDCJ population. As the proximal mechanisms which drive these inequalities are likely different than those which lead to racial inequalities in the non-incarcerated populations, future studies should look to assess and address the specific drivers of COVID-19 related disparities in carceral settings.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Neal Marquez", - "author_inst": "University of Washington" - }, - { - "author_name": "Destiny Moreno", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "Amanda Klonsky", - "author_inst": "University of Chicago" - }, - { - "author_name": "Sharon Dolovich", - "author_inst": "University of California Los Angeles" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.09.25.21264120", "rel_title": "Household Density and Influences from Family and Friends Shape Vaccine Intent Among Latino Families in the San Francisco Bay Area", @@ -597500,6 +598190,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.18.21263550", + "rel_title": "Persistent while declined neutralizing antibody responses in the convalescents of COVID-19 across clinical spectrum during the 16 months follow up", + "rel_date": "2021-09-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.18.21263550", + "rel_abs": "Elucidation the kinetics of neutralizing antibody response in the coronavirus disease 2019 (COVID-19) convalescents is crucial for the future control of the COVID-19 pandemic and vaccination strategies. Here we tested 411 sequential plasma samples collected up to 480 days post symptoms onset (d.a.o) from 214 convalescents of COVID-19 across clinical spectrum without re-exposure history after recovery and vaccination of SARS-CoV-2, using authentic SARS-CoV-2 microneutralization (MN) assays. COVID-19 convalescents free of re-exposure and vaccination could maintain relatively stable anti-RBD IgG and MN titers during 400[~]480 d.a.o after the peak at around 120 d.a.o and the subsequent decrease. Undetectable neutralizing activity started to occur in mild and asymptomatic infections during 330 to 480 d.a.o with an overall rate of 14.29% and up to 50% for the asymptomatic infections. Significant decline in MN titers was found in 91.67% COVID-19 convalescents with [≥] 50% decrease in MN titers when comparing the available peak and current MN titers ([≥] 300 d.a.o). Antibody-dependent immunity could also provide protection against most of circulating variants after one year, while significantly decreased neutralizing activities against the Beta, Delta and Lambda variants were found in most of individuals. In summary, our results indicated that neutralizing antibody responses could last at least 480 days in most COVID-19 convalescents despite of the obvious decline of neutralizing activity, while the up to 50% undetectable neutralizing activity in the asymptomatic infections is of great concern.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Yang Yang", + "author_inst": "Shenzhen Third People's Hospital" + }, + { + "author_name": "Minghui Yang", + "author_inst": "Shenzhen third people's hospital" + }, + { + "author_name": "Yun Peng", + "author_inst": "Shenzhen Third People's Hospital" + }, + { + "author_name": "Yanhua Liang", + "author_inst": "Shenzhen Third People's Hospital" + }, + { + "author_name": "Jinli Wei", + "author_inst": "Shenzhen Third People's Hospital" + }, + { + "author_name": "Li Xing", + "author_inst": "Shenzhen Third People's Hospital" + }, + { + "author_name": "Liping Guo", + "author_inst": "Shenzhen Third People's Hospital" + }, + { + "author_name": "Xiaohe Li", + "author_inst": "Shenzhen Third People's Hospital" + }, + { + "author_name": "Jie Li", + "author_inst": "Shenzhen Third People's Hospital" + }, + { + "author_name": "Jun Wang", + "author_inst": "Shenzhen Third People's Hospital" + }, + { + "author_name": "Mianhuan Li", + "author_inst": "Shenzhen Third People's Hospital" + }, + { + "author_name": "Zhixiang Xu", + "author_inst": "Shenzhen Third People's Hospital" + }, + { + "author_name": "Mingxia Zhang", + "author_inst": "Shenzhen Third People's Hospital" + }, + { + "author_name": "Fuxiang Wang", + "author_inst": "Shenzhen Third People's Hospital" + }, + { + "author_name": "Yi Shi", + "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of 12 Microbiology, Chinese Academy of Sciences, Beijing, China" + }, + { + "author_name": "Jing Yuan", + "author_inst": "Shenzhen Third People's Hospital" + }, + { + "author_name": "Yingxia Liu", + "author_inst": "Shenzhen Third People's Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.23.21263948", "rel_title": "Demographic characteristics of SARS-CoV-2 B.1.617.2 (Delta) variant infections in Indian population", @@ -597920,97 +598693,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.21.21263902", - "rel_title": "Quantification and prognostic significance of interferon-\u03b3 secreting SARS-CoV-2 responsive T cells in hospitalised patients with acute COVID-19", - "rel_date": "2021-09-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.21.21263902", - "rel_abs": "Little is known about T-cell responses during acute coronavirus disease-2019 (COVID-19). We measured T-cell interferon gamma (IFN-{gamma}) responses to spike 1 (S1), spike 2 (S2), nucleocapsid (N) and membrane (M) SARS-CoV-2 antigens using the T-SPOT(R) Discovery SARS-CoV-2 assay, a proven EliSPOT technology, in 114 hospitalised adult COVID-19 patients and assessed their association with clinical disease phenotype. T-SPOT(R) Discovery SARS-CoV-2 responses were detectable within 2 days of a positive PCR and did not correlate with vaccination status or symptom duration. Higher responses to S1 protein associated with a higher symptom burden, and serum IL-6 levels. Despite treatment with dexamethasone this subgroup was also at greater risk of requiring continuous positive airway pressure (CPAP) in the days following sampling. Higher T-cell responses measured using T-SPOT(R) Discovery SARS-CoV-2 associate with progressive disease in acute COVID-19 disease and may have utility as a prognostic biomarker that should be evaluated in larger cohorts.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Daniel Pan", - "author_inst": "University of Leicester" - }, - { - "author_name": "Jee Whang Kim", - "author_inst": "University of Leicester" - }, - { - "author_name": "Joshua Nazareth", - "author_inst": "University of Leicester" - }, - { - "author_name": "Sara Assadi", - "author_inst": "University of Leicester" - }, - { - "author_name": "Adam Bellass", - "author_inst": "University of Leicester" - }, - { - "author_name": "Jack Leach", - "author_inst": "University of Leicester" - }, - { - "author_name": "James G Brosnan", - "author_inst": "University of Leicester" - }, - { - "author_name": "Adam Ahmed", - "author_inst": "University of Leicester" - }, - { - "author_name": "Fleur Starcevic", - "author_inst": "University of Leicester" - }, - { - "author_name": "Shirley Sze", - "author_inst": "University of Leicester" - }, - { - "author_name": "Christopher A Martin", - "author_inst": "University of Leicester" - }, - { - "author_name": "Caroline M Williams", - "author_inst": "University of Leicester" - }, - { - "author_name": "Michael R Barer", - "author_inst": "University of Leicester" - }, - { - "author_name": "Amandip Sahota", - "author_inst": "University of Leicester" - }, - { - "author_name": "Prashanth Patel", - "author_inst": "University of Leicester" - }, - { - "author_name": "Andrea Tattersall", - "author_inst": "Oxford Immunotec" - }, - { - "author_name": "Andrea Cooper", - "author_inst": "University of Leicester" - }, - { - "author_name": "Manish Pareek", - "author_inst": "University of Leicester" - }, - { - "author_name": "Pranabashis Haldar", - "author_inst": "University of Leicester" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.23.21263649", "rel_title": "Social contacts and transmission of COVID-19 in British Columbia, Canada", @@ -599238,6 +599920,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.22.21263977", + "rel_title": "COVID-19 mortality risk correlates inversely with vitamin D3 status, and a mortality rate close to zero could theoretically be achieved at 50 ng/ml 25(OH)D3: Results of a systematic review and meta-analysis", + "rel_date": "2021-09-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.22.21263977", + "rel_abs": "BackgroundMuch research shows that blood calcidiol (25(OH)D3) levels correlate strongly with SARS-CoV-2 infection severity. There is open discussion regarding whether low D3 is caused by the infection or if deficiency negatively affects immune defense. The aim of this study was to collect further evidence on this topic.\n\nMethodsSystematic literature search was performed to identify retrospective cohort as well as clinical studies on COVID-19 mortality rates versus D3 blood levels. Mortality rates from clinical studies were corrected for age, sex and diabetes. Data were analyzed using correlation and linear regression.\n\nResultsOne population study and seven clinical studies were identified, which reported D3 blood levels pre-infection or on the day of hospital admission. They independently showed a negative Pearson correlation of D3 levels and mortality risk (r(17)=-.4154, p=.0770/r(13)=-.4886, p=.0646). For the combined data, median (IQR) D3 levels were 23.2 ng/ml (17.4 - 26.8), and a significant Pearson correlation was observed (r(32)=-.3989, p=.0194). Regression suggested a theoretical point of zero mortality at approximately 50 ng/ml D3.\n\nConclusionsThe two datasets provide strong evidence that low D3 is a predictor rather than a side effect of the infection. Despite ongoing vaccinations, we recommend raising serum 25(OH)D levels to above 50 ng/ml to prevent or mitigate new outbreaks due to escape mutations or decreasing antibody activity.\n\nTrial registrationNot applicable.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Lorenz Borsche", + "author_inst": "Independent Researcher" + }, + { + "author_name": "Bernd Glauner", + "author_inst": "Independent Researcher" + }, + { + "author_name": "Julian von Mendel", + "author_inst": "IU International University of Applied Sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.24.461759", "rel_title": "Protein Vaccine Induces a Durable, More Broadly Neutralizing Antibody Response in Macaques than Natural Infection with SARS-CoV-2 P.1", @@ -599670,57 +600379,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.09.23.21262822", - "rel_title": "Plasma S-Adenosylmethionine is Associated with Lung Injury in COVID-19", - "rel_date": "2021-09-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.23.21262822", - "rel_abs": "ObjectiveS-Adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) are indicators of global transmethylation and may play an important role as markers of severity of COVID-19.\n\nMethodsThe levels of plasma SAM and SAH were determined in patients admitted with COVID-19 (n = 56, mean age = 61). Lung injury was identified by computed tomography (CT) in accordance with the CT0-4 classification.\n\nResultsSAM was found to be a potential marker of lung damage risk in COVID-19 patients (SAM > 80 nM; CT3,4 vs. CT 0-2: relative ratio (RR) was 3.0; p = 0.0029). SAM/SAH > 6.0 was also found to be a marker of lung injury (CT2-4 vs. CT0,1: RR = 3.47, p = 0.0004). Interleukin-6 (IL-6) levels were associated with SAM ({rho} = 0.44, p = 0.01) and SAH ({rho} = 0.534, p = 0.001) levels.\n\nConclusionsHigh SAM levels and high methylation index are associated with the risk of lung injury in COVID-19 patients. The association of SAM and SAH with IL-6 indicates an important role of transmethylation in the development of cytokine imbalance in COVID-19 cases.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Evgeny Kryukov", - "author_inst": "Burdenko Main Military Clinical Hospital" - }, - { - "author_name": "Alexander Ivanov", - "author_inst": "Institute of General Pathology and Pathophysiology" - }, - { - "author_name": "Vladimir Karpov", - "author_inst": "Burdenko Main Military Clinical Hospital" - }, - { - "author_name": "Valery Alexandrin", - "author_inst": "Institute of General Pathology and Pathophysiology" - }, - { - "author_name": "Alexander Dygai", - "author_inst": "Institute of General Pathology and Pathophysiology" - }, - { - "author_name": "Maria Kruglova", - "author_inst": "Sechenov First Moscow State Medical University" - }, - { - "author_name": "Gennady Kostiuchenko", - "author_inst": "Regional Clinical Hospital" - }, - { - "author_name": "Sergei Kazakov", - "author_inst": "Burdenko Main Military Clinical Hospital" - }, - { - "author_name": "Aslan Kubatiev", - "author_inst": "Institute of General Pathology and Pathophysiology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2021.09.21.21262927", "rel_title": "Comparative analysis of human immune responses following SARS-CoV-2 vaccination with BNT162b2, mRNA-1273, or Ad26.COV2.S", @@ -600976,6 +601634,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, + { + "rel_doi": "10.1101/2021.09.22.21263984", + "rel_title": "Consequences of COVID-19 vaccine allocation inequity in Chicago", + "rel_date": "2021-09-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.22.21263984", + "rel_abs": "During Chicagos initial COVID-19 vaccine rollout, the city disproportionately allocated vaccines to zip codes with high incomes and predominantly White populations. However, the impact of this inequitable distribution on COVID-19 outcomes is unknown. This observational study determined the association between zip-code level vaccination rate and COVID-19 mortality in residents of 52 Chicago zip codes. After controlling for age distribution and recovery from infection, a 10% higher vaccination rate by March 28, 2021, was associated with a 39% lower relative risk of death during the peak of the spring wave of COVID-19. Using a difference-in-difference analysis, Chicago could have prevented an estimated 72% of deaths in the least vaccinated quartile of the city (vaccination rates of 17.8 - 26.9%) if it had had the same vaccination rate as the most vaccinated quartile (39.9 - 49.3%). Inequitable vaccine allocation in Chicago likely exacerbated existing racial disparities in COVID-19 mortality.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Sharon Zeng", + "author_inst": "University of Chicago" + }, + { + "author_name": "Kenley M Pelzer", + "author_inst": "University of Chicago" + }, + { + "author_name": "Robert D Gibbons", + "author_inst": "University of Chicago" + }, + { + "author_name": "Monica E Peek", + "author_inst": "University of Chicago" + }, + { + "author_name": "William Fiske Parker", + "author_inst": "University of Chicago" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.09.22.21263488", "rel_title": "Monoclonal antibodies therapy for Covid-19 - Experiences at a regional hospital.", @@ -601380,109 +602073,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.09.19.21262487", - "rel_title": "Genomic analysis of SARS-CoV-2 breakthrough infections from Varanasi, India", - "rel_date": "2021-09-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.19.21262487", - "rel_abs": "Studies worldwide have shown that the available vaccines are highly effective against SARS-CoV-2. However, there are growing laboratory reports that the newer variants of concerns (VOCs e.g. Alpha, Beta, Delta etc) may evade vaccine induced defense. In addition to that, there are few ground reports on health workers having breakthrough infections. In order to understand VOC driven breakthrough infection we investigated 14 individuals who tested positive for SARS-CoV-2 after being administered a single or double dose of Covishield (ChAdOx1, Serum Institute of India) from the city of Varanasi, which is located in the Indian state of Uttar Pradesh. Genomic analysis revealed that 78.6% (11/14) of the patients were infected with the B.1.617.2 (Delta) variant. Notably, the frequency (37%) of this variant in the region was significantly lower (p<0.01), suggesting that the vaccinated people were asymmetrically infected with the Delta variant. Most of the patients tested displayed mild symptoms, indicating that even a single dose of the vaccine can help in reducing the severity of the disease. However, more comprehensive epidemiological studies are required to understand the effectiveness of vaccines against the newer VOCs.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Lamuk Zaveri", - "author_inst": "CSIR - Centre for Cellular and Molecular Biology" - }, - { - "author_name": "Royana Singh", - "author_inst": "Banaras Hindu University" - }, - { - "author_name": "Priyoneel Basu", - "author_inst": "Banaras Hindu University" - }, - { - "author_name": "Sofia Banu", - "author_inst": "CSIR - Centre for Cellular and Molecular Biology" - }, - { - "author_name": "Payel Mukherjee", - "author_inst": "CSIR - Centre for Cellular and Molecular Biology" - }, - { - "author_name": "Shani Vishwakarma", - "author_inst": "Banaras Hindu University" - }, - { - "author_name": "Chetan Sahni", - "author_inst": "Banaras Hindu University" - }, - { - "author_name": "Manpreet Kaur", - "author_inst": "Banaras Hindu University" - }, - { - "author_name": "Nitish Kumar Singh", - "author_inst": "Banaras Hindu University" - }, - { - "author_name": "Abhay Kumar Yadav", - "author_inst": "Banaras Hindu University" - }, - { - "author_name": "Ajay Kumar Yadav", - "author_inst": "Banaras Hindu University" - }, - { - "author_name": "Ashish Ashish", - "author_inst": "Banaras Hindu University" - }, - { - "author_name": "Shivani Mishra", - "author_inst": "Banaras Hindu University" - }, - { - "author_name": "Shivam Tiwari", - "author_inst": "Banaras Hindu University" - }, - { - "author_name": "Surendra Pratap Mishra", - "author_inst": "Banaras Hindu University" - }, - { - "author_name": "Amareshwar Vodapalli", - "author_inst": "CSIR - Centre for Cellular and Molecular Biology" - }, - { - "author_name": "Himasri Bollu", - "author_inst": "CSIR - Centre for Cellular and Molecular Biology" - }, - { - "author_name": "Debashruti Das", - "author_inst": "Banaras Hindu University" - }, - { - "author_name": "Prajjval Pratap Singh", - "author_inst": "Banaras Hindu University" - }, - { - "author_name": "Gyaneshwer Chaubey", - "author_inst": "Banaras Hindu University" - }, - { - "author_name": "Divya Tej Sowpati", - "author_inst": "CSIR - Centre for Cellular and Molecular Biology" - }, - { - "author_name": "Karthik Bharadwaj Tallapaka", - "author_inst": "CSIR - Centre for Cellular and Molecular Biology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.18.21263782", "rel_title": "Alterations in CD39/CD73 Axis of T cells associated with COVID-19 severity", @@ -602990,6 +603580,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.20.21263865", + "rel_title": "Vitamin D and socioeconomic deprivation mediate COVID-19 ethnic health disparities", + "rel_date": "2021-09-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.20.21263865", + "rel_abs": "Ethnic minorities in developed countries suffer a disproportionately high burden of COVID-19 morbidity and mortality, and COVID-19 ethnic disparities have been attributed to social determinants of health. Vitamin D has been proposed as a modifiable risk factor that could mitigate COVID-19 health disparities. We investigated the relationship between vitamin D and COVID-19 susceptibility and severity using the UK Biobank, a large progressive cohort study of the United Kingdom population. Structural equation modelling was used to evaluate the ability of vitamin D, socioeconomic deprivation, and other known risk factors to mediate COVID-19 ethnic health disparities. Asian ethnicity is associated with higher COVID-19 susceptibility, compared to the majority White population, and Asian and Black ethnicity are both associated with higher COVID-19 severity. Socioeconomic deprivation mediates all three ethnic disparities and shows the highest overall signal of mediation for any COVID-19 risk factor. Vitamin supplements, including vitamin D, mediate the Asian disparity in COVID-19 susceptibility, and serum 25-hydroxyvitamin D (calcifediol) levels mediate Asian and Black COVID-19 severity disparities. Several measures of overall health also mediate COVID-19 ethnic disparities, underscoring the importance of comorbidities. Our results support ethnic minorities use of vitamin D as both a prophylactic and a supplemental therapeutic for COVID-19.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Leonardo Marino-Ramirez", + "author_inst": "National Institute on Minority Health and Health Disparities, National Institutes of Health" + }, + { + "author_name": "Maria Ahmad", + "author_inst": "National Institute on Minority Health and Health Disparities, National Institutes of Health" + }, + { + "author_name": "Lavanya Rishishwar", + "author_inst": "National Institute on Minority Health and Health Disparities, National Institutes of Health" + }, + { + "author_name": "Shashwat Deepali Nagar", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Kara K. Lee", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Emily T. Norris", + "author_inst": "National Institute on Minority Health and Health Disparities, National Institutes of Health" + }, + { + "author_name": "I. King King Jordan", + "author_inst": "Georgia Institute of Technology" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.20.21263509", "rel_title": "Real-world clinical performance of SARS-CoV-2 point-of-care diagnostic tests: a systematic review of available trials as per April, 4, 2021", @@ -603346,93 +603979,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.20.21263875", - "rel_title": "Comparative single-dose mRNA and ChAdOx1 vaccine effectiveness against SARS-CoV-2, including early variants of concern: a test-negative design, British Columbia, Canada", - "rel_date": "2021-09-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.20.21263875", - "rel_abs": "IntroductionIn randomized controlled trials, single-dose efficacy against SARS-CoV-2 illness exceeded 90% for mRNA vaccines (BNT162b2 and mRNA-1273), and 75% for ChAdOx1. In British Columbia (BC), Canada second doses were deferred up to 16 weeks and ChAdOx1 was only initially recommended for adults 55 years of age and older. We compared single-dose vaccine effectiveness (VE) during the spring 2021 wave in BC when Alpha and Gamma variants of concern (VOC) predominated.\n\nMethodsVE was estimated against infection and hospitalization by test-negative design: cases were RT-PCR test-positive for SARS-CoV-2 and controls were test-negative. Adults 50-69 years old with specimen collection between April 4 and May 22 (weeks 14-20) were included. Variant-specific VE was estimated between weeks 17-20 when genetic characterization of all case viruses was performed, primarily through whole genome sequencing.\n\nResultsVE analyses included 7,116 (10%) cases and 60,958 controls. Three-quarters of vaccinated participants received mRNA vaccine (60% BNT162b2, 15% mRNA-1273) and 25% received ChAdOx1. Half of genetically characterized viruses were Alpha, with 38% Gamma, 4% Delta and 8% non-VOCs. Single-dose VE against any infection was 75% (95%CI: 72-78) for BNT162b2, 82% (95%CI: 76-87) for mRNA-1273 and 61% (95%CI: 54-66) for ChAdOx1. VE against hospitalization was 83% (95%CI: 76-89), 85% (95%CI: 63-94) and 96% (95%CI: 86-99), respectively. VE against Alpha vs. Gamma infections did not differ among mRNA (78%;95%CI: 73-82 and 80%;95%CI: 74-85) or ChAdOx1 (66%;95%CI: 57-74 and 60%;95%CI: 48-69) recipients.\n\nConclusionsA single dose of mRNA vaccine reduced the SARS-CoV-2 infection risk by at least 75%, including infections due to early VOC. Although effectiveness of a single dose of ChAdOx1 was lower at 60% against infection, just one dose of any vaccine reduced the hospitalization risk by more than 80%. In the context of constrained vaccine supplies, these findings have implications for global vaccine deployment to reduce the overall burden of infections and hospitalizations due to SARS-CoV-2.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Danuta M Skowronski", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Solmaz Setayeshgar", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Macy Zou", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Natalie Prystajecky", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "John R Tyson", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Hind Sbihi", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Chris D Fjell", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Eleni Galanis", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Monika Naus", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "David M Patrick", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Shiraz El Adam", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "May Ahmed", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Shinhye Kim", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Bonnie Henry", - "author_inst": "Office of the Provincial Health Officer, Ministry of Health" - }, - { - "author_name": "Linda Hoang", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Manish Sadarangani", - "author_inst": "Vaccine Evaluation Center, BC Children's Hospital Research Institute" - }, - { - "author_name": "Agathat N Jassem", - "author_inst": "BC Centre for Disease Control" - }, - { - "author_name": "Mel Krajden", - "author_inst": "BC Centre for Disease Control" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.21.461301", "rel_title": "Design of Peptide Vaccine for COVID19: CD8+ and CD4+ T cell epitopes from SARS-CoV-2 open-reading-frame protein variants", @@ -604445,6 +604991,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2021.09.16.21263693", + "rel_title": "The longitudinal kinetics of antibodies in COVID-19 recovered patients over 14 months", + "rel_date": "2021-09-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.16.21263693", + "rel_abs": "Here, we describe the longitudinal kinetics of the serological response in COVID-19 recovered patients over the period of 14 months. The antibody kinetics in a cohort of 200 recovered patients with 89 follow up samples at 2-4 visits reveal that RBD-specific antibodies decay over the period of 14 month following the onset of symptoms. The decay rate is associated with the robustness of the response thus, recovered patients that exhibit elevated antibody levels at the first visit, experience faster decay. We further explored the longitudinal kinetics differences between recovered patients and naive BNT162b2 vaccinees. We found a significantly faster decay in naive vaccinees compared to recovered patients suggesting that the serological memory following natural infection is more robust compared to vaccination. Our data highlights the differences between serological memory induced by natural infection vs. vaccination, facilitating the decision making in Israel regarding the 3rd dose vaccination.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Tsuf Eyran", + "author_inst": "Tel-Aviv university" + }, + { + "author_name": "Anna Vaisman-Mentesh", + "author_inst": "Tel-Aviv University" + }, + { + "author_name": "Yeal Dror", + "author_inst": "Tel-Aviv University" + }, + { + "author_name": "Ligal Aizik", + "author_inst": "Tel-Aviv University" + }, + { + "author_name": "Aya Kigel", + "author_inst": "Tel-Aviv University" + }, + { + "author_name": "Shai Rosenstein", + "author_inst": "Tel-Aviv University" + }, + { + "author_name": "Yeal Bahar", + "author_inst": "Tel-Aviv University" + }, + { + "author_name": "David Taussig", + "author_inst": "Tel-Aviv University" + }, + { + "author_name": "Ran Tur-Kaspa", + "author_inst": "Department of Medicine D and the Liver Institute, Rabin Medical Center, Beilinson Hospital, Molecular Hepatology Research Laboratory, Felsenstein Medical Resear" + }, + { + "author_name": "Tatiana Kournos", + "author_inst": "Internal Medicine D, Hasharon Hospital-Rabin Medical Center, Petach Tikva, Israel" + }, + { + "author_name": "Dana Markovitch", + "author_inst": "Internal Medicine D, Hasharon Hospital-Rabin Medical Center, Petach Tikva, Israel" + }, + { + "author_name": "Dror Dicker", + "author_inst": "Internal Medicine D, Hasharon Hospital-Rabin Medical Center, Petach Tikva, Israel" + }, + { + "author_name": "Yariv Wine", + "author_inst": "Tel Aviv University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.16.21263692", "rel_title": "Immunogenicity of a third dose viral-vectored COVID-19 vaccine after receiving two-dose inactivated vaccines in healthy adults", @@ -604785,33 +605398,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2021.09.16.21263714", - "rel_title": "The Relationship of Vaccine Uptake and COVID-19 Infections among Nursing Home Staff and Residents in Missouri", - "rel_date": "2021-09-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.16.21263714", - "rel_abs": "Nursing homes (NH) continue to struggle with COVID-19 morbidity and mortality with older adult residents at greater risk of infection due to proximity to other residents, advanced aging-related chronic illnesses, and contact with staff. While many states have prioritized COVID-19 vaccinations among older adults, vaccinations among NH staff vary. The purpose of this study was to quantify the relationship between nursing home staff vaccination uptake and COVID-19 infections among residents. A zero-inflated Poisson regression model was constructed to predict the weekly number of COVID-19 cases among Missouri nursing home residents using data from the Centers for Medicaid and Medicare Services. A total of 1,124 COVID-19 infections were reported among 504 NH residents between January 1, 2021 and August 22, 2021. After adjusting for number of total residents, resident vaccine rate, staff quality rating, and respective county COVID-19 rate, for every percent increase in nursing home staff vaccine rate the risk of COVID-19 infections significantly decreased by 13% (IRR 0.87, 95% CI 0.81, 0.93). This study identified that NH staff, likely due to greater mobility, are important to prioritize in vaccination efforts to protect themselves and residents of their facilities from COVID-19 infections. Further, the CMS staff ratings were significant predictors of infection as well, which highlight the structural challenges that exist within and outside the context of a highly infectious and deadly pandemic. These results also provide insights to optimizing vaccination roll-out to best protect our communities most vulnerable residents.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Stephen Scroggins", - "author_inst": "Saint Louis University" - }, - { - "author_name": "Matthew Ellis", - "author_inst": "Washington University St. Louis" - }, - { - "author_name": "Enbal Shacham", - "author_inst": "Saint Louis University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.17.21263743", "rel_title": "Long Term Physical, Mental and Social Health Effects of COVID-19 in the Pediatric Population: A Scoping Review", @@ -605847,6 +606433,65 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2021.09.21.21263880", + "rel_title": "Prior Covid-19 and high RBD-IgG levels correlate with protection against VOC-delta SARS-CoV-2 infection in vaccinated Nursing Home Residents", + "rel_date": "2021-09-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.21.21263880", + "rel_abs": "BackgroundNursing Home (NH) residents are at high risk of serious illness and death from coronavirus disease 2019 (Covid-19), especially with the SARS-CoV-2 variants of concerns (VOC). It is unknown as to whether a history of Covid-19 prior to the vaccine and post-vaccine RBD-IgG levels are predictors of BNT162b2 vaccine effectiveness against VOC-{delta} in nursing home residents.\n\nMethodsWe analyzed the data from two NHs that faced a VOC-{delta} outbreak in July-August 2021. These NHs had suffered prior Covid-19 outbreaks in 2020 and 2021. In many of the residents, RBD-IgG levels were measured 6 weeks after the second vaccine dose, i.e. 3 to 5 months before the VOC-{delta} outbreak onset, and again during the outbreak (SARS-CoV-2 IgG II Quant assay, Abbott Diagnostics). We compared residents with vs without prior Covid-19 for (i) VOC-{delta} incidence, (ii) the correlation between post-vaccine RBD-IgG levels and VOC-{delta} incidence, and (iii) the time-related change in RBD-IgG levels.\n\nResultsAmong the 140 analyzed residents (58 to 101 years; 94 females, 46 men, mean age: 84.6 yr {+/-} 9.5 yr), one resident among the 44 with prior Covid-19 before vaccination developed a VOC-{delta} infection during the outbreak (1.3%) vs 55 of the 96 without Covid-19 prior to vaccination (57.3 %)(p<0.0001). The median value for RBD-IgG 6 weeks after the vaccine and during the outbreak was higher in residents with prior Covid-19 (31,553 AU/mL and 22,880 AU/mL) than in those without (1,050 AU/mL and 260 AU/mL)(p<0.0001). In residents without Covid-19 prior to vaccination, post-vaccination RDB-IgG levels did not predict protection against VOC-{delta} infection.\n\nConclusionsIn contrary to residents with prior SARS-CoV-2 infection, those without a history of Covid-19 before two BNT162b2 doses are not protected against VOC-{delta} infection and their RBD-Ig-G levels are low 3 to 5 months after vaccination. This suggests that a booster vaccine dose should be considered in this group of residents for a better protection against VOC-{delta} infection.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Hubert Blain", + "author_inst": "University hospital of Montpellier" + }, + { + "author_name": "Edouard TUAILLON", + "author_inst": "Montpellier University" + }, + { + "author_name": "Amandine Pisoni", + "author_inst": "Montpellier university" + }, + { + "author_name": "Laure Soriteau", + "author_inst": "Montpellier university" + }, + { + "author_name": "Elodie Million", + "author_inst": "Montpellier University" + }, + { + "author_name": "Marie-Suzanne Leglise", + "author_inst": "Montpellier University" + }, + { + "author_name": "Isabelle Bussereau", + "author_inst": "Montpellier university hospital" + }, + { + "author_name": "Stephanie Miot", + "author_inst": "Montpellier University" + }, + { + "author_name": "Yves Rolland", + "author_inst": "Toulouse university" + }, + { + "author_name": "Marie-Christine Picot", + "author_inst": "Montpellier University" + }, + { + "author_name": "Jean J Bousquet", + "author_inst": "CHU" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.17.21263670", "rel_title": "Effectiveness of vaccination in preventing severe SARS CoV-2 infection in South India-a hospital based cross sectional study", @@ -606379,157 +607024,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.14.21263153", - "rel_title": "Evolution of COVID-19 mortality over time: results from the Swiss hospital surveillance system (CH-SUR)", - "rel_date": "2021-09-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.14.21263153", - "rel_abs": "BackgroundWhen comparing the periods of time during and after the first wave of the ongoing SARS-CoV-2/COVID-19 pandemic in Europe, the associated COVID-19 mortality seems to have decreased substantially. Various factors could explain this trend, including changes in demographic characteristics of infected persons, and the improvement of case management. To date, no study has been performed to investigate the evolution of COVID-19 in-hospital mortality in Switzerland, while also accounting for risk factors.\n\nMethodsWe investigated the trends in COVID-19 related mortality (in-hospital and in-intermediate/intensive-care) over time in Switzerland, from February 2020 to May 2021, comparing in particular the first and the second wave. We used data from the COVID-19 Hospital-based Surveillance (CH-SUR) database. We performed survival analyses adjusting for well-known risk factors of COVID-19 mortality (age, sex and comorbidities) and accounting for competing risk.\n\nResultsOur analysis included 16,030 episodes recorded in CH-SUR, with 2,320 reported deaths due to COVID-19 (13.0% of included episodes). We found that overall in-hospital mortality was lower during the second wave of COVID-19 compared to the first wave (HR 0.71, 95% CI 0.69 - 0.72, p-value < 0.001), a decrease apparently not explained by changes in demographic characteristics of patients. In contrast, mortality in intermediate and intensive care significantly increased in the second wave compared to the first wave (HR 1.48, 95% CI 1.42 - 1.55, p-value < 0.001), with significant changes in the course of hospitalisation between the first and the second wave.\n\nConclusionWe found that, in Switzerland, COVID-19 mortality decreased among hospitalised persons, whereas it increased among patients admitted to intermediate or intensive care, when comparing the second wave to the first wave. We put our findings in perspective with changes over time in case management, treatment strategy, hospital burden and non-pharmaceutical interventions. Further analyses of the potential effect of virus variants and of vaccination on mortality would be crucial to have a complete overview of COVID-19 mortality trends throughout the different phases of the pandemic.", - "rel_num_authors": 34, - "rel_authors": [ - { - "author_name": "Maroussia Roelens", - "author_inst": "Institute of Global Health, Faculty of Medicine, University of Geneva, Geneva, Switzerland" - }, - { - "author_name": "Alexis Martin", - "author_inst": "Swiss Tropical and Public Health Institute, Basel, Switzerland ; University of Basel, Basel, Switzerland" - }, - { - "author_name": "Brian Friker", - "author_inst": "Veterinary Public Health Institute, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Filipe Maximiano Sousa", - "author_inst": "Veterinary Public Health Institute, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Amaury Thiabaud", - "author_inst": "Institute of Global Health, Faculty of Medicine, University of Geneva, Geneva, Switzerland" - }, - { - "author_name": "Beatriz Vidondo", - "author_inst": "Veterinary Public Health Institute, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Valentin Buchter", - "author_inst": "Swiss Federal Office of Public Health, Bern, Switzerland" - }, - { - "author_name": "C\u00e9line Gardiol", - "author_inst": "Swiss Federal Office of Public Health, Bern, Switzerland" - }, - { - "author_name": "Jasmin Vonlanthen", - "author_inst": "Swiss Federal Office of Public Health, Bern, Switzerland" - }, - { - "author_name": "Carlo Balmelli", - "author_inst": "Infection Control Programme, EOC Hospitals, Ticino, Switzerland" - }, - { - "author_name": "Manuel Battegay", - "author_inst": "Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland" - }, - { - "author_name": "Christoph Berger", - "author_inst": "Division of Infectious Diseases, and Children's Research Centre, University Children's Hospital Zurich, Zurich, Switzerland" - }, - { - "author_name": "Michael Buettcher", - "author_inst": "Paediatric Infectious Diseases, Department of Paediatrics, Children's Hospital, Cantonal Hospital Lucerne, Lucerne, Switzerland" - }, - { - "author_name": "Alexia Cusini", - "author_inst": "Department of Infectious Diseases, Cantonal Hospital Graubuenden, Chur, Switzerland" - }, - { - "author_name": "Domenica Flury", - "author_inst": "Division of Infectious Diseases and Hospital Epidemiology, Cantonal Hospital St Gallen, St Gallen, Switzerland" - }, - { - "author_name": "Ulrich Heininger", - "author_inst": "Infectious Diseases and Vaccinology, University of Basel Children's Hospital, Basel, Switzerland" - }, - { - "author_name": "Anita Niederer-Loher", - "author_inst": "Children's Hospital of Eastern Switzerland, St Gallen, Switzerland" - }, - { - "author_name": "Thomas Riedel", - "author_inst": "Department of Paediatrics, Cantonal Hospital Graubuenden, Chur, Switzerland" - }, - { - "author_name": "Peter W. Schreiber", - "author_inst": "Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich and University of Zurich, Zurich, Switzerland" - }, - { - "author_name": "Rami Sommerstein", - "author_inst": "Department of Infectious Diseases, Bern University Hospital (Inselspital), Bern, Switzerland ; Infectious Diseases and Hospital Hygiene, Hirslanden Central Swit" - }, - { - "author_name": "Nicolas Troillet", - "author_inst": "Service of Infectious Diseases, Central Institute, Valais Hospitals, Sion, Switzerland" - }, - { - "author_name": "Sara Tschudin-Sutter", - "author_inst": "Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland" - }, - { - "author_name": "Pauline Vetter", - "author_inst": "Geneva Center for Emerging Viral Diseases, Geneva University Hospitals, Geneva, Switzerland" - }, - { - "author_name": "Sara Bernhard-Stirnemann", - "author_inst": "Children's Hospital Aarau, Aarau, Switzerland" - }, - { - "author_name": "Natascia Corti", - "author_inst": "Unit of General Internal Medicine, Hirslanden Clinic, Zurich, Switzerland" - }, - { - "author_name": "Roman Gaudenz", - "author_inst": "Internal Medicine and Infectiology, Cantonal Hospital Nidwalden, Stans, Switzerland" - }, - { - "author_name": "Jonas Marschall", - "author_inst": "Department of Infectious Diseases, Bern University Hospital (Inselspital), Bern, Switzerland" - }, - { - "author_name": "Yvonne Nussbaumer-Ochsner", - "author_inst": "Clinic for Internal Medicine, Cantonal Hospital, Hospitals Schaffhausen, Switzerland" - }, - { - "author_name": "Laurence Senn", - "author_inst": "Service of Preventive Medicine, Lausanne University Hospital, CHUV, Lausanne, Switzerland" - }, - { - "author_name": "Danielle Vuichard-Gysin", - "author_inst": "Division of Infectious Diseases and Hospital Hygiene, Thurgau Hospital Group Munsterlingen and Frauenfeld, Switzerland" - }, - { - "author_name": "Petra Zimmermann", - "author_inst": "Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland ; Department of Paediatrics, Fribourg Hospital HFR, Fribourg, Switzerland" - }, - { - "author_name": "Franziska Zucol", - "author_inst": "Paediatric Infectious Diseases, Department of Paediatrics, Cantonal Hospital Winterthur, Winterthur, Switzerland" - }, - { - "author_name": "Anne Iten", - "author_inst": "Service of Prevention and Infection Control, Directorate of Medicine and Quality, University Hospital Geneva, HUG, Geneva, Switzerland" - }, - { - "author_name": "Olivia Keiser", - "author_inst": "Institute of Global Health, Faculty of Medicine, University of Geneva, Geneva, Switzerland" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.14.21263588", "rel_title": "Correlates of COVID-19 vaccine acceptance, hesitancy and refusal among employees of a safety net California county health system with an early and aggressive vaccination program: Results from a cross-sectional survey", @@ -608241,6 +608735,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.15.21263613", + "rel_title": "COVID-19 vaccine effectiveness against hospitalizations and ICU admissions in the Netherlands, April- August 2021", + "rel_date": "2021-09-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.15.21263613", + "rel_abs": "The objective of this study was to estimate vaccine effectiveness (VE) against COVID-19 hospitalization and ICU admission, per period according to dominating SARS-CoV-2 variant (Alpha and Delta), per vaccine and per time since vaccination. To this end, data from the national COVID-19 vaccination register was added to the national register of COVID-19 hospitalizations. For the study period 4 April - 29 August 2021, 15,571 hospitalized people with COVID-19 were included in the analysis, of whom 887 (5.7%) were fully vaccinated. Incidence rates of hospitalizations and ICU admissions per age group and vaccination status were calculated, and VE was estimated as 1-incidence rate ratio, adjusted for calendar date and age group in a negative binomial regression model. VE against hospitalization for full vaccination was 94% (95%CI 93-95%) in the Alpha period and 95% (95%CI 94-95%) in the Delta period. The VE for full vaccination against ICU admission was 93% (95%CI 87-96%) in the Alpha period and 97% (95%CI 97-98%) in the Delta period. VE was high in all age groups and did not show waning with time since vaccination up to 20 weeks after full vaccination.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Brechje de Gier", + "author_inst": "Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands" + }, + { + "author_name": "Marjolein Kooijman", + "author_inst": "Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands" + }, + { + "author_name": "Jeanet Kemmeren", + "author_inst": "Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands" + }, + { + "author_name": "Nicolette de Keizer", + "author_inst": "Amsterdam UMC, University of Amsterdam, Department of Medical Informatics, Amsterdam Public Health research institute, Amsterdam, The Netherlands; National Inte" + }, + { + "author_name": "Dave Dongelmans", + "author_inst": "National Intensive Care Evaluation (NICE) foundation, Amsterdam, the Netherlands; Amsterdam UMC, location AMC, University of Amsterdam, Department of Intensive " + }, + { + "author_name": "Senna C.J.L. van Iersel", + "author_inst": "Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands" + }, + { + "author_name": "Jan van de Kassteele", + "author_inst": "Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands" + }, + { + "author_name": "Stijn P. Andeweg", + "author_inst": "Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands" + }, + { + "author_name": "- the RIVM COVID-19 epidemiology and surveillance team", + "author_inst": "" + }, + { + "author_name": "Hester E. de Melker", + "author_inst": "Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands" + }, + { + "author_name": "Susan J.M. Hahn\u00e9", + "author_inst": "Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands" + }, + { + "author_name": "Mirjam J. Knol", + "author_inst": "Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands" + }, + { + "author_name": "Susan van den Hof", + "author_inst": "Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.14.21263567", "rel_title": "Comparison of children and young people admitted with SARS-CoV-2 across the UK in the first and second pandemic waves: prospective multicentre observational cohort study", @@ -608809,125 +609370,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.09.21263348", - "rel_title": "Robust clinical detection of SARS-CoV-2 variants by RT-PCR/MALDI-TOF multi-target approach", - "rel_date": "2021-09-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.09.21263348", - "rel_abs": "The COVID-19 pandemic sparked rapid development of SARS-CoV-2 diagnostics. However, emerging variants pose the risk for target dropout and false-negative results secondary to primer/probe binding site (PBS) mismatches. The Agena MassARRAY(R) SARS-CoV-2 Panel combines RT-PCR and MALDI-TOF mass-spectrometry to probe for five targets across N and ORF1ab genes, which provides a robust platform to accommodate PBS mismatches in divergent viruses. Herein, we utilize a deidentified dataset of 1,262 SARS-CoV-2-positive specimens from Mount Sinai Health System (New York City) from December 2020 through April 2021 to evaluate target results and corresponding sequencing data. Overall, the level of PBS mismatches was greater in specimens with target dropout. Of specimens with N3 target dropout, 57% harbored an A28095T substitution that is highly-specific for the alpha (B.1.1.7) variant of concern. These data highlight the benefit of redundancy in target design and the potential for target performance to illuminate the dynamics of circulating SARS-CoV-2 variants.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Matthew M. Hernandez", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Radhika Banu", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Ana S. Gonzalez-Reiche", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Adriana van de Guchte", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Zenab Khan", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Paras Shrestha", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Liyong Cao", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Feng Chen", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Huanzhi Shi", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Ayman Hanna", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Hala Alshammary", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Shelcie Fabre", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Angela Amoako", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Ajay Obla", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Bremy Alburquerque", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Luz Helena Pati\u00f1o", - "author_inst": "Universidad del Rosario" - }, - { - "author_name": "Juan David Ram\u00edrez", - "author_inst": "Universidad del Rosario" - }, - { - "author_name": "Robert Sebra", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Melissa R. Gitman", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Michael D. Nowak", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Carlos Cordon-Cardo", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Ted E. Schutzbank", - "author_inst": "Agena Bioscience" - }, - { - "author_name": "Viviana Simon", - "author_inst": "Icahn School of Medicine" - }, - { - "author_name": "Harm van Bakel", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Emilia M. Sordillo", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Alberto E. Paniz Mondolfi", - "author_inst": "Icahn School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.09.14.460411", "rel_title": "A genetic trap in yeast for inhibitors of SARS-CoV-2 main protease", @@ -610287,6 +610729,129 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.03.21263105", + "rel_title": "Emergence of SARS-CoV-2 Resistance with Monoclonal Antibody Therapy", + "rel_date": "2021-09-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.03.21263105", + "rel_abs": "Resistance mutations to monoclonal antibody (mAb) therapy has been reported, but in the non-immunosuppressed population, it is unclear if in vivo emergence of SARS-CoV-2 resistance mutations alters either viral replication dynamics or therapeutic efficacy. In ACTIV-2/A5401, non-hospitalized participants with symptomatic SARS-CoV-2 infection were randomized to bamlanivimab (700mg or 7000mg) or placebo. Treatment-emergent resistance mutations were significantly more likely detected after bamlanivimab 700mg treatment than placebo (7% of 111 vs 0% of 112 participants, P=0.003). There were no treatment-emergent resistance mutations among the 48 participants who received bamlanivimab 7000mg. Participants with emerging mAb resistant virus had significantly higher pre-treatment nasopharyngeal and anterior nasal viral load. Intensive respiratory tract viral sampling revealed the dynamic nature of SARS-CoV-2 evolution, with evidence of rapid and sustained viral rebound after emergence of resistance mutations, and worsened symptom severity. Participants with emerging bamlanivimab resistance often accumulated additional polymorphisms found in current variants of concern/interest and associated with immune escape. These results highlight the potential for rapid emergence of resistance during mAb monotherapy treatment, resulting in prolonged high level respiratory tract viral loads and clinical worsening. Careful virologic assessment should be prioritized during the development and clinical implementation of antiviral treatments for COVID-19.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Manish Chandra Choudhary", + "author_inst": "Brigham and Women's Hospital, Harvard Medical School, Boston, MA" + }, + { + "author_name": "Kara W Chew", + "author_inst": "University of California, Los Angeles, Los Angeles, CA" + }, + { + "author_name": "Rinki Deo", + "author_inst": "Brigham and Women's Hospital, Harvard Medical School, Boston, MA" + }, + { + "author_name": "James P Flynn", + "author_inst": "Brigham and Women's Hospital, Harvard Medical School, Boston, MA" + }, + { + "author_name": "James Regan", + "author_inst": "Brigham and Women's Hospital, Harvard Medical School, Boston, MA" + }, + { + "author_name": "Charles R Crain", + "author_inst": "Brigham and Women's Hospital, Harvard Medical School, Boston, MA" + }, + { + "author_name": "Carlee Moser", + "author_inst": "Harvard T.H. Chan School of Public Health, Boston, MA" + }, + { + "author_name": "Michael Hughes", + "author_inst": "Harvard T.H. Chan School of Public Health, Boston, MA" + }, + { + "author_name": "Justin Ritz", + "author_inst": "Harvard T.H. Chan School of Public Health, Boston, MA" + }, + { + "author_name": "Ruy M Ribeiro", + "author_inst": "Los Alamos National Laboratory, Los Alamos, NM" + }, + { + "author_name": "Ruian Ke", + "author_inst": "Los Alamos National Laboratory, Los Alamos, NM" + }, + { + "author_name": "Joan A Dragavon", + "author_inst": "University of Washington, Seattle, WA" + }, + { + "author_name": "Arzhang C Javan", + "author_inst": "National Institutes of Health, Bethesda, MD" + }, + { + "author_name": "Ajay Nirula", + "author_inst": "Lilly Research Laboratories, San Diego, CA" + }, + { + "author_name": "Paul Klekotka", + "author_inst": "Lilly Research Laboratories, San Diego, CA" + }, + { + "author_name": "Alexander L Greninger", + "author_inst": "University of Washington, Seattle, WA" + }, + { + "author_name": "Courtney V Fletcher", + "author_inst": "University of Nebraska Medical Center, Omaha, NE" + }, + { + "author_name": "Eric S Daar", + "author_inst": "University of California, Los Angeles, Los Angeles, CA" + }, + { + "author_name": "David A Wohl", + "author_inst": "University of North Carolina, Chapel Hill, NC" + }, + { + "author_name": "Joseph J Eron", + "author_inst": "University of North Carolina, Chapel Hill, NC" + }, + { + "author_name": "Judith S Currier", + "author_inst": "University of California, Los Angeles, Los Angeles, CA" + }, + { + "author_name": "Urvi M Parikh", + "author_inst": "University of Pittsburgh, Pittsburgh, PA" + }, + { + "author_name": "Scott F Sieg", + "author_inst": "Case Western Reserve University, Cleveland, OH" + }, + { + "author_name": "Alan S Perelson", + "author_inst": "Los Alamos National Laboratory, Los Alamos, NM" + }, + { + "author_name": "Robert W Coombs", + "author_inst": "University of Washington, Seattle, WA" + }, + { + "author_name": "Davey M Smith", + "author_inst": "University of California, San Diego, San Diego, CA" + }, + { + "author_name": "Jonathan Z Li", + "author_inst": "Brigham and Women's Hospital, Harvard Medical School, Boston, MA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.04.21262414", "rel_title": "Evaluation of commercially available high-throughput SARS-CoV-2 serological assays for serosurveillance and related applications", @@ -610803,81 +611368,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.09.14.460356", - "rel_title": "Rapid Identification of Neutralizing Antibodies against SARS-CoV-2 Variants by mRNA Display", - "rel_date": "2021-09-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.14.460356", - "rel_abs": "The increasing prevalence of SARS-CoV-2 variants with the ability to escape existing humoral protection conferred by previous infection and/or immunization necessitates the discovery of broadly-reactive neutralizing antibodies (nAbs). Utilizing mRNA display, we identified a set of antibodies against SARS-CoV-2 spike (S) proteins and characterized the structures of nAbs that recognized epitopes in the S1 subunit of the S glycoprotein. These structural studies revealed distinct binding modes for several antibodies, including targeting of rare cryptic epitopes in the receptor-binding domain (RBD) of S that interacts with angiotensin- converting enzyme 2 (ACE2) to initiate infection, as well as the S1 subdomain 1. A potent ACE2-blocking nAb was further engineered to sustain binding to S RBD with the E484K and L452R substitutions found in multiple SARS-CoV-2 variants. We demonstrate that mRNA display is a promising approach for the rapid identification of nAbs that can be used in combination to combat emerging SARS-CoV-2 variants.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Shiho Tanaka", - "author_inst": "ImmunityBio, Inc." - }, - { - "author_name": "C. Anders Olson", - "author_inst": "ImmunityBio, Inc." - }, - { - "author_name": "Christopher O. Barnes", - "author_inst": "Division of Biology and Biological Engineering, California Institute of Technology" - }, - { - "author_name": "Wendy Higashide", - "author_inst": "ImmunityBio, Inc." - }, - { - "author_name": "Marcos Gonzales", - "author_inst": "ImmunityBio, Inc." - }, - { - "author_name": "Justin Taft", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Ashley Richardson", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Marta Martin-Fernandez", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Dusan Bogunovic", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Priyanthi N. P. Gnanapragasam", - "author_inst": "CalTech" - }, - { - "author_name": "Pamela Bjorkman", - "author_inst": "Caltech" - }, - { - "author_name": "Patricia R Spilman", - "author_inst": "ImmunityBio, Inc." - }, - { - "author_name": "Kayvan Niazi", - "author_inst": "ImmunityBio, Inc." - }, - { - "author_name": "Shahrooz Rabizadeh", - "author_inst": "ImmunityBio, Inc." - }, - { - "author_name": "Patrick Soon-Shiong", - "author_inst": "ImmunityBio, Inc." - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.09.12.21263456", "rel_title": "Predictors of real-world parents acceptance to vaccinate their children against the COVID-19", @@ -612025,6 +612515,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.11.21263428", + "rel_title": "Interrogating COVID-19 Vaccine Hesitancy in the Philippines with a Nationwide Open-Access Online Survey", + "rel_date": "2021-09-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.11.21263428", + "rel_abs": "To mitigate the unprecedented health, social, and economic damage of COVID-19, the Philippines is undertaking a nationwide vaccination program to mitigate the effects of the global pandemic. In this study, we interrogated COVID-19 vaccine hesitancy in the country by deploying a nationwide open-access online survey, two months before the rollout of the national vaccination program. The Health Belief Model (HBM) posits that people are likely to adopt disease prevention behaviors and to accept medical interventions like vaccines if there is sufficient motivation and cues to action. A majority of our 7,193 respondents (62.5%) indicated that they were willing to be vaccinated against COVID-19. Moreover, multivariable analysis revealed that HBM constructs were associated with vaccination intention in the Philippines. Perceptions of high susceptibility, high severity, and significant benefits were all good predictors for vaccination intent. We also found that external cues to action were important. Large majorities of our respondents would only receive the COVID-19 vaccines after many others had received it (72.8%) or after politicians had received it (68.2%). Finally, our study revealed that most (21%) were willing to pay an amount of PHP1,000 [USD20] for the COVID-19 vaccines with an average willing-to-pay amount of PHP1,892 [USD38].", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Alexandria Caple", + "author_inst": "Providence College" + }, + { + "author_name": "Arnie Dimaano", + "author_inst": "University of Santo Tomas" + }, + { + "author_name": "Marc Martin Sagolili", + "author_inst": "University of Santo Tomas" + }, + { + "author_name": "April Anne Uy", + "author_inst": "University of Santo Tomas" + }, + { + "author_name": "Panjee Mariel Aguirre", + "author_inst": "University of Santo Tomas" + }, + { + "author_name": "Dean Lotus Alano", + "author_inst": "University of Santo Tomas" + }, + { + "author_name": "Giselle Sophia Camaya", + "author_inst": "University of Santo Tomas" + }, + { + "author_name": "Brent John Ciriaco", + "author_inst": "University of Santo Tomas" + }, + { + "author_name": "Princess Jerah Clavo", + "author_inst": "University of Santo Tomas" + }, + { + "author_name": "Dominic Cuyugan", + "author_inst": "University of Santo Tomas" + }, + { + "author_name": "Cleinne Florence Geesler Fermo", + "author_inst": "University of Santo Tomas" + }, + { + "author_name": "Paul Jeremy Lanete", + "author_inst": "University of Santo Tomas" + }, + { + "author_name": "Ardwayne Jurel La Torre", + "author_inst": "University of Santo Tomas" + }, + { + "author_name": "Thomas Albert Loteyro", + "author_inst": "University of Santo Tomas" + }, + { + "author_name": "Raisa Mikaela Lua", + "author_inst": "University of Santo Tomas" + }, + { + "author_name": "Nicole Gayle Manansala", + "author_inst": "University of Santo Tomas" + }, + { + "author_name": "Raphael Willard Mosquito", + "author_inst": "University of Santo Tomas" + }, + { + "author_name": "Alexa Marie Octaviano", + "author_inst": "University of Santo Tomas" + }, + { + "author_name": "Alexandra Erika Orfanel", + "author_inst": "University of Santo Tomas" + }, + { + "author_name": "Gheyanna Merly Pascual", + "author_inst": "University of Santo Tomas" + }, + { + "author_name": "Aubrey Joy Sale", + "author_inst": "University of Santo Tomas" + }, + { + "author_name": "Sophia Lorraine Tendenilla", + "author_inst": "University of Santo Tomas" + }, + { + "author_name": "Maria Sophia Trinidad", + "author_inst": "University of Santo Tomas" + }, + { + "author_name": "Nicole Jan Trinidad", + "author_inst": "University of Santo Tomas" + }, + { + "author_name": "Daphne Louise Verano", + "author_inst": "University of Santo Tomas" + }, + { + "author_name": "Nicanor Austriaco", + "author_inst": "Providence College" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.09.15.460506", "rel_title": "Phylodynamic Pattern of Genetic Clusters, Paradigm Shift on Spatio-temporal Distribution of Clades, and Impact of Spike Glycoprotein Mutations of SARS-CoV-2 Isolates from India", @@ -612437,121 +613046,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.09.10.21262710", - "rel_title": "Antibody responses to BNT162b2 mRNA vaccine: infection-naive individuals with abdominal obesity warrant attention", - "rel_date": "2021-09-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.10.21262710", - "rel_abs": "ObjectiveThe excess of visceral adipose tissue might hinder and delay the immune response. How people with abdominal obesity will respond to mRNA vaccines against SARS-CoV-2 is yet to be established. We evaluated SARS-CoV-2-specific antibody responses after the first and second dose of the BNT162b2 mRNA vaccine comparing the response of individuals affected by abdominal obesity (AO) to those without, discerning between individuals with or without prior infection.\n\nMethodsIgG neutralizing antibodies against the Trimeric complex (IgG-TrimericS) were measured at four time points: at baseline, at day 21 after vaccine dose-1, at one month and three months after dose-2. Nucleocapsid antibodies were assessed to detect prior SARS-CoV-2 infection. Waist circumference was measured to determine abdominal obesity.\n\nResultsBetween the first and third month after vaccine dose-2, the drop in IgG-TrimericS levels was more remarkable in individuals with AO compared to those without AO (2.44 fold [95%CI: 2.22-2.63] vs 1.82 fold [95%CI: 1.69-1.92], respectively, p<0.001). Multiple linear regression confirmed this result even when adjusting for possible confounders (p<0.001).\n\nConclusionsOur findings highlight the need to extend the duration of serological monitoring of antibody levels in infection-naive individuals with abdominal obesity, a higher-risk population category in terms of possible weaker antibody response.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "ALEXIS ELIAS MALAVAZOS", - "author_inst": "Endocrinology Unit, Clinical Nutrition and Cardiovascular Prevention Service, IRCCS Policlinico San Donato, San Donato Milanese, Milan, Italy; Department of Bio" - }, - { - "author_name": "Sara Basilico", - "author_inst": "Endocrinology Unit, Clinical Nutrition and Cardiovascular Prevention Service, IRCCS Policlinico San Donato, San Donato Milanese, Milan, Italy;" - }, - { - "author_name": "Gianluca Iacobellis", - "author_inst": "Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, University of Miami, FL, USA" - }, - { - "author_name": "Valentina Milani", - "author_inst": "Scientific Directorate, IRCCS Policlinico San Donato, San Donato Milanese, Milan, Italy" - }, - { - "author_name": "Rosanna Cardani", - "author_inst": "Biobank BioCor, Service of Laboratory Medicine1-Clinical Pathology, IRCCS Policlinico San Donato, San Donato Milanese, Milan, Italy." - }, - { - "author_name": "Federico Boniardi", - "author_inst": "Endocrinology Unit, Clinical Nutrition and Cardiovascular Prevention Service, IRCCS Policlinico San Donato, San Donato Milanese, Milan, Italy." - }, - { - "author_name": "Carola Dubini", - "author_inst": "Endocrinology Unit, Clinical Nutrition and Cardiovascular Prevention Service, IRCCS Policlinico San Donato, San Donato Milanese, Milan, Italy." - }, - { - "author_name": "Ilaria Prandoni", - "author_inst": "Endocrinology Unit, Clinical Nutrition and Cardiovascular Prevention Service, IRCCS Policlinico San Donato, San Donato Milanese, Milan, Italy." - }, - { - "author_name": "Gloria Capitanio", - "author_inst": "Endocrinology Unit, Clinical Nutrition and Cardiovascular Prevention Service, IRCCS Policlinico San Donato, San Donato Milanese, Milan, Italy." - }, - { - "author_name": "Laura Valentina Renna", - "author_inst": "Biobank BioCor, Service of Laboratory Medicine1-Clinical Pathology, IRCCS Policlinico San Donato, San Donato Milanese, Milan, Italy." - }, - { - "author_name": "Sara Boveri", - "author_inst": "Scientific Directorate, IRCCS Policlinico San Donato, San Donato Milanese, Milan, Italy" - }, - { - "author_name": "Matteo Carrara", - "author_inst": "Residency program in Clinical Pathology and Clinical Biochemistry, University of Milano, Milan, Italy." - }, - { - "author_name": "Giovanni Spuria", - "author_inst": "Residency program in Clinical Pathology and Clinical Biochemistry, University of Milano, Milan, Italy." - }, - { - "author_name": "Maria Teresa Cuppone", - "author_inst": "Scientific Directorate, IRCCS Policlinico San Donato, San Donato Milanese, Milan, Italy." - }, - { - "author_name": "Aurelia D'Acquisto", - "author_inst": "Scientific Directorate, IRCCS Policlinico San Donato, San Donato Milanese, Milan, Italy." - }, - { - "author_name": "Luca Carpinelli", - "author_inst": "Scientific Directorate, IRCCS Policlinico San Donato, San Donato Milanese, Milan, Italy." - }, - { - "author_name": "Marta Sacchi", - "author_inst": "Service of Laboratory Medicine, IRCCS Policlinico San Donato, San Donato Milanese, Milan, Italy." - }, - { - "author_name": "Lelio Morricone", - "author_inst": "Endocrinology Unit, Clinical Nutrition and Cardiovascular Prevention Service, IRCCS Policlinico San Donato, San Donato Milanese, Milan, Italy." - }, - { - "author_name": "Francesco Secchi", - "author_inst": "Department of Biomedical Sciences for Health, University of Milano, Milan, Italy." - }, - { - "author_name": "Elena Costa", - "author_inst": "Service of Laboratory Medicine, IRCCS Policlinico San Donato, San Donato Milanese, Milan, Italy." - }, - { - "author_name": "Lorenzo Menicanti", - "author_inst": "Scientific Directorate, IRCCS Policlinico San Donato, San Donato Milanese, Milan, Italy." - }, - { - "author_name": "Enzo Nisoli", - "author_inst": "Department of Medical Biotechnology and Translational Medicine, Centre for Study and Research on Obesity, University of Milan, Milan, Italy" - }, - { - "author_name": "Michele Olivo Carruba", - "author_inst": "Department of Medical Biotechnology and Translational Medicine, Centre for Study and Research on Obesity, University of Milan, Milan, Italy" - }, - { - "author_name": "Federico Ambrogi", - "author_inst": "Department of Clinical Sciences and Community Health, University of Milano, Milan, Italy." - }, - { - "author_name": "Massimiliano Marco Corsi Romanelli", - "author_inst": "Operative Unit of Laboratory Medicine1-Clinical Pathology, Department of Pathology and Laboratory Medicine, IRCCS Policlinico San Donato, San Donato Milanese, M" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "endocrinology" - }, { "rel_doi": "10.1101/2021.09.09.21263355", "rel_title": "CHARACTERIZING AND MANAGING AN EPIDEMIC: A FIRST PRINCIPLES MODEL AND A CLOSED FORM SOLUTION TO THE KERMACK AND MCKENDRICK EQUATIONS", @@ -614171,6 +614665,29 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2021.09.13.21262971", + "rel_title": "Low dose hydroxychloroquine prophylaxis for COVID-19 - a prospective study", + "rel_date": "2021-09-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.13.21262971", + "rel_abs": "BackgroundSince the outbreak of COVID-19 pandemic, the world began a frantic search for possible prophylactic options. While trials on hydroxychloroquine (HCQ) prophylaxis are ongoing, concrete evidence is lacking. The study aimed to determine the relative efficacy of various doses of oral HCQ in prophylaxis and mitigating the severity of COVID-19 in healthcare workers.\n\nMethodsThis was a prospective cohort with four arms (high, medium, low dose, and control) of HCQ prophylaxis, used by healthcare workers at a tertiary care center in India. Participants were grouped as per their opting for any one arm on a voluntary basis as per institute policy under the Government guidance. The outcomes studied were COVID-19 positivity by RT-PCR and its severity assessed by WHO COVID-19 severity scale.\n\nResultsTotal 486 participants were enrolled, of which 29 (6%) opted for low dose, 2 (<1%) medium dose, and none for high dose HCQ while 455 (93.6%) were in the control arm. Of the 164 participants who underwent RT-PCR, 96 (58.2%) tested positive. Out of these 96 positive cases, the majority of them (79 of 96 [82.3%]) were ambulatory and were managed conservatively at home. Only 17.7% (17 of 96) participants, all of them from the control group, required hospitalization with the mild-moderate disease. None of the participants had severe disease, COVID-related complications, ICU stay, or death. The difference in the outcome assessed amongst the various arms was statistically insignificant (p value >0.05).\n\nConclusionThis single-center study demonstrated that HCQ prophylaxis in healthcare workers does not cause a significant reduction in COVID-19 as well as mitigating its severity in those infected. At present, most of the trials have not shown any benefit. The debate continues to rage, should HCQ prophylaxis be given to healthcare workers for chemoprophylaxis?", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "- RE-HCP2 study group", + "author_inst": "" + }, + { + "author_name": "Prasan Kumar Panda", + "author_inst": "AIIMS Rishikesh" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.09.21263359", "rel_title": "A strategy to assess spillover risk of bat SARS-related coronaviruses in Southeast Asia", @@ -614703,29 +615220,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.09.13.460130", - "rel_title": "Elucidation of the interactions between SARS-CoV-2 Spike protein and wild and mutant types of IFITM proteins by in silico methods", - "rel_date": "2021-09-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.13.460130", - "rel_abs": "COVID-19 is a viral disease that has been a threat to the whole world since 2019. Although effective vaccines against the disease have been developed, there are still points to be clarified about the mechanism of SARS-CoV-2, which is the causative agent of COVID-19. In this study, we determined the binding energies and the bond types of complexes formed by open (6VYB) and closed (6VXX) forms of the Spike protein of SARS-CoV-2 and wild and mutant forms of IFITM1, IFITM2, and IFITM3 proteins using the molecular docking approach. First, all missense SNPs were found in the NCBI Single Nucleotide Polymorphism database (dbSNP) for IFITM1, IFITM2, and IFITM3 and analyzed with SIFT, PROVEAN, PolyPhen-2, SNAP2, Mutation Assessor, and PANTHER cSNP web-based tools to determine their pathogenicity. When at least four of these analysis tools showed that the SNP had a pathogenic effect on the protein product, this SNP was saved for further analysis. Delta delta G (DDG) and protein stability analysis for amino acid changes were performed in the web-based tools I-Mutant, MUpro, and SAAFEC-SEQ. The structural effect of amino acid change on the protein product was made using the HOPE web-based tool. HawkDock server was used for molecular docking and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) analysis and binding energies of all complexes were calculated. BIOVIA Discovery Studio program was utilized to visualize the complexes. Hydrogen bonds, salt bridges, and non-bonded contacts between Spike and IFITM protein chains in the complexes were detected with the PDBsum web-based tool. The best binding energy among the 6VYB-IFITM wild protein complexes belong to 6VYB-IFITM1 (-46.16 kcal/mol). Likewise, among the 6VXX-IFITM wild protein complexes, the most negative binding energy belongs to 6VXX-IFITM1 (-52.42 kcal/mol). An interesting result found in the study is the presence of hydrogen bonds between the cytoplasmic domain of the IFITM1 wild protein and the S2 domain of 6VYB. Among the Spike-IFITM mutant protein complexes, the best binding energy belongs to the 6VXX-IFITM2 N63S complex (-50.77 kcal/mol) and the worst binding energy belongs to the 6VXX-IFITM3 S50T complex (4.86 kcal/mol).\n\nThe study suggests that IFITM1 protein may act as a receptor for SARS-CoV-2 Spike protein. Assays must be advanced from in silico to in vitro for the determination of the receptor-ligand interactions between IFITM proteins and SARS-CoV-2.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Nazli Irmak Giritlioglu", - "author_inst": "Yildiz Technical University, Graduate Schools of Science and Engineering" - }, - { - "author_name": "Gizem Koprululu Kucuk", - "author_inst": "Yeditepe University, Graduate School of Natural and Applied Sciences" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.09.13.459777", "rel_title": "Real-time monitoring and analysis of SARS-CoV-2 nanopore sequencing with minoTour.", @@ -615949,6 +616443,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.07.21261811", + "rel_title": "A randomized controlled trial of inhaled ciclesonide for outpatient treatment of symptomatic COVID-19 infections", + "rel_date": "2021-09-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.07.21261811", + "rel_abs": "ImportanceSystemic corticosteroids are commonly used in the treatment of severe COVID-19. However, their role in the treatment of patients with mild to moderate disease is less clear. The inhaled corticosteroid ciclesonide has shown early promise as a potential treatment for COVID-19.\n\nObjectiveTo determine whether the inhaled steroid ciclesonide is efficacious in patients with high risk for disease progression and can reduce the incidence of long-term COVID-19 symptoms or post-acute sequelae of SARS-CoV-2.\n\nDesignThis was a phase III, multicenter, double-blind, randomized controlled trial to assess the safety and efficacy of ciclesonide metered-dose inhaler (MDI) for the treatment of non-hospitalized participants with symptomatic COVID-19 infection. Patients were screened from June 11, 2020 to November 3, 2020.\n\nSettingThe study was conducted at 10 centers throughout the U.S. public and private, academic and non-academic sites were represented among the centers.\n\nParticipantsParticipants were randomly assigned to ciclesonide MDI 160 {micro}g per actuation, two actuations twice a day (total daily dose 640 {micro}g) or placebo for 30 days.\n\nMain Outcomes and MeasuresThe primary endpoint was time to alleviation of all COVID-19 related symptoms (cough, dyspnea, chills, feeling feverish, repeated shaking with chills, muscle pain, headache, sore throat, and new loss of taste or smell) by Day 30. Secondary endpoints included subsequent emergency department visits or hospital admissions for reasons attributable to COVID-19.\n\nResults413 participants were screened and 400 (96.9%) were enrolled and randomized (197 in the ciclesonide arm and 203 in the placebo arm). The median time to alleviation of all COVID-19-related symptoms was 19.0 days (95% CI: 14.0, 21.0) in the ciclesonide arm and 19.0 days (95% CI: 16.0, 23.0) in the placebo arm. There was no difference in resolution of all symptoms by Day 30 (odds ratio [OR] 1.28, 95% CI: 0.84, 1.97). Participants treated with ciclesonide had fewer subsequent emergency department visits or hospital admissions for reasons attributable to COVID-19 (OR 0.18, 95% CI: 0.04 - 0.85). No subjects died during the study.\n\nConclusions and RelevanceCiclesonide did not achieve the primary efficacy endpoint of time to alleviation of all COVID-19-related symptoms. Future studies of inhaled steroids are needed to explore their efficacy in patients with high risk for disease progression and in reducing the incidence of long-term COVID-19 symptoms or post-acute sequelae of SARS-CoV-2.\n\nTrial RegistrationClinicalTrials.gov\n\nNCT04377711\n\nhttps://clinicaltrials.gov/ct2/show/NCT04377711\n\nKey PointsO_ST_ABSQuestionC_ST_ABSCan the inhaled steroid ciclesonide be efficacious in patients with high risk for disease progression and reduce the incidence of long-term COVID-19 symptoms or post-acute sequelae of SARS-CoV-2?\n\nFindingsIn this randomized clinical trial of 413 patients, ciclesonide did not reduce the time to alleviation of all COVID-19-related symptoms. However, patients treated with ciclesonide had fewer subsequent emergency department visits or hospital admissions for reasons attributable to COVID-19.\n\nMeaningFuture studies of inhaled steroids are needed to explore their efficacy in patients with high risk for disease progression and in reducing the incidence of long-term COVID-19 symptoms or post-acute sequelae of SARS-CoV-2.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Brian M Clemency", + "author_inst": "University at Buffalo" + }, + { + "author_name": "Renoj Varughese", + "author_inst": "University at Buffalo" + }, + { + "author_name": "Yaneicy Gonzalez-Rojas", + "author_inst": "Verus Clinical Research Corporation" + }, + { + "author_name": "Caryn G. Morse", + "author_inst": "Wake Forest School of Medicine" + }, + { + "author_name": "Wanda Phipatanakul", + "author_inst": "Boston Children's Hospital, Harvard Medical School" + }, + { + "author_name": "David J. Koster", + "author_inst": "Instat Clinical Research" + }, + { + "author_name": "Michael S. Blaiss", + "author_inst": "Medical College of Georgia at Augusta University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.08.21263279", "rel_title": "Enhanced Detection of Recently Emerged SARS-CoV-2 Variants of Concern in Wastewater", @@ -616293,89 +616830,6 @@ "type": "new results", "category": "genetics" }, - { - "rel_doi": "10.1101/2021.09.06.21263168", - "rel_title": "Coronavirus disease (COVID-19) associated Mucormycosis: An Anaesthesiologist's Perspective", - "rel_date": "2021-09-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.06.21263168", - "rel_abs": "PurposeAlthough unexpected airway difficulties are reported in patients with mucormycosis, the literature on airway management in patients with mucormycosis associated with Coronavirus disease is sparse.\n\nMethodsIn this retrospective case record review of 57 patients who underwent surgery for mucormycosis associated with coronavirus disease, we aimed to evaluate the demographics, airway management, procedural data, and mortality records.\n\nResultsForty-one (71.9%) patients had a diagnosis of sino-nasal mucormycosis, fourteen (24.6%) patients had a diagnosis of rhino-orbital mucormycosis, and 2 (3.5%) patients had a diagnosis of palatal mucormycosis. A total of 44 (77.2%) patients had co-morbidities. The most common co-morbidities were diabetes mellitus in 42 (73.6%) patients, followed by hypertension in 21 (36.8%) patients, and acute kidney injury in 14 (28.1%) patients. We used the intubation difficulty scale score to assess intubating conditions. Intubation was easy to slightly difficult in 53 (92.9%) patients. In our study, mortality occurred in 7 (12.3%) patients. The median (range) mortality time was 60 (27-74) days. The median (range) time to hospital discharge was 53.5 (10-85) days. The median [interquartile range] age of discharged versus expired patients was 47.5 [41,57.5] versus 64 [47,70] years (P = 0.04), and median (interquartile range) D-dimer levels in discharged versus expired patients was 364 [213, 638] versus 2448 [408,3301] ng/mL (P = 0.03).\n\nConclusionIn patients undergoing surgery for mucormycosis associated with the coronavirus disease, airway management was easy to slightly difficult in most patients. Perioperative complications can be minimized by taking timely and precautionary measures.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Prashant Sirohiya", - "author_inst": "National Cancer Institute, All India Institute of Medical Sciences, New Delhi" - }, - { - "author_name": "Saurabh Vig", - "author_inst": "AIIMS" - }, - { - "author_name": "Tanmay Mathur", - "author_inst": "AIIMS" - }, - { - "author_name": "Jitendra Kumar Meena", - "author_inst": "AIIMS" - }, - { - "author_name": "Smriti Panda", - "author_inst": "AIIMS" - }, - { - "author_name": "Gitartha Goswami", - "author_inst": "AIIMS" - }, - { - "author_name": "Raghav Gupta", - "author_inst": "AIIMS" - }, - { - "author_name": "Abhilash Konkimalla", - "author_inst": "AIIMS" - }, - { - "author_name": "Dheeraj Kondamudi", - "author_inst": "AIIMS" - }, - { - "author_name": "Nishkarsh Gupta", - "author_inst": "AIIMS" - }, - { - "author_name": "Brajesh Kumar Ratre", - "author_inst": "AIIMS" - }, - { - "author_name": "Ram Singh", - "author_inst": "AIIMS" - }, - { - "author_name": "Balbir Kumar", - "author_inst": "AIIMS" - }, - { - "author_name": "Anuja Pandit", - "author_inst": "AIIMS" - }, - { - "author_name": "Kapil Sikka", - "author_inst": "AIIMS" - }, - { - "author_name": "Alok Thakar", - "author_inst": "AIIMS" - }, - { - "author_name": "Sushma Bhatnagar", - "author_inst": "AIIMS" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "anesthesia" - }, { "rel_doi": "10.1101/2021.09.06.21263173", "rel_title": "Analysis of the prediction of the 2021 time-evolution of the COVID-19 Pandemic in Italy using a Planck's distribution", @@ -617539,6 +617993,149 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.09.10.21263376", + "rel_title": "An open label, adaptive, phase 1 trial of high-dose oral nitazoxanide in healthy volunteers: an antiviral candidate for SARS-CoV-2", + "rel_date": "2021-09-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.10.21263376", + "rel_abs": "Repurposing approved drugs may rapidly establish effective interventions during a public health crisis. This has yielded immunomodulatory treatments for severe COVID-19, but repurposed antivirals have not been successful to date because of redundancy of the target in vivo or suboptimal exposures at studied doses. Nitazoxanide is an FDA approved antiparasitic medicine, that physiologically-based pharmacokinetic (PBPK) modelling has indicated may provide antiviral concentrations across the dosing interval, when repurposed at higher than approved doses. Within the AGILE trial platform (NCT04746183) an open label, adaptive, phase 1 trial in healthy adult participants was undertaken with high dose nitazoxanide. Participants received 1500mg nitazoxanide orally twice-daily with food for 7 days. Primary outcomes were safety, tolerability, optimum dose and schedule. Intensive pharmacokinetic sampling was undertaken day 1 and 5 with Cmin sampling on day 3 and 7. Fourteen healthy participants were enrolled between 18th February and 11th May 2021. All 14 doses were completed by 10/14 participants. Nitazoxanide was safe and well tolerated with no significant adverse events. Moderate gastrointestinal disturbance (loose stools) occurred in 8 participants (57.1%), with urine and sclera discolouration in 12 (85.7%) and 9 (64.3%) participants, respectively, without clinically significant bilirubin elevation. This was self-limiting and resolved upon drug discontinuation. PBPK predictions were confirmed on day 1 but with underprediction at day 5. Median Cmin was above the in vitro target concentration on first dose and maintained throughout. Nitazoxanide administered at 1500mg BID with food was safe and well tolerated and a phase 1b/2a study is now being initiated in COVID-19 patients.", + "rel_num_authors": 32, + "rel_authors": [ + { + "author_name": "Lauren E Walker", + "author_inst": "University of Liverpool, 2 Liverpool University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Richard FitzGerald", + "author_inst": "Liverpool University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Geoffrey Saunders", + "author_inst": "Southampton Clinical Trials Unit, University of Southampton, Southampton UK" + }, + { + "author_name": "Rebecca Lyon", + "author_inst": "Liverpool University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Michael Fisher", + "author_inst": "University of Liverpool, 2 Liverpool University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Karen Martin", + "author_inst": "Southampton Clinical Trials Unit, University of Southampton, Southampton UK" + }, + { + "author_name": "Izabela Eberhart", + "author_inst": "Southampton Clinical Trials Unit, University of Southampton, Southampton UK" + }, + { + "author_name": "Christie Woods", + "author_inst": "Liverpool University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Sean Ewings", + "author_inst": "Southampton Clinical Trials Unit, University of Southampton, Southampton UK" + }, + { + "author_name": "Colin Hale", + "author_inst": "Liverpool University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Rajith KR Rajoli", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Laura Else", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Sujan Dilly-Penchala", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Alieu Amara", + "author_inst": "University of Liverpool" + }, + { + "author_name": "David G Lalloo", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Michael Jacobs", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Henry Pertinez", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Parys Hatchard", + "author_inst": "Southampton Clinical Trials Unit, University of Southampton, Southampton UK" + }, + { + "author_name": "Robert Waugh", + "author_inst": "Southampton Clinical Trials Unit, University of Southampton, Southampton UK" + }, + { + "author_name": "Megan Lawrence", + "author_inst": "Southampton Clinical Trials Unit, University of Southampton, Southampton UK" + }, + { + "author_name": "Lucy Johnson", + "author_inst": "Southampton Clinical Trials Unit, University of Southampton, Southampton UK" + }, + { + "author_name": "Keira Fines", + "author_inst": "Southampton Clinical Trials Unit, University of Southampton, Southampton UK" + }, + { + "author_name": "Helen Reynolds", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Timothy Rowland", + "author_inst": "Liverpool University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Rebecca Crook", + "author_inst": "Liverpool University Hospitals NHS Foundation Trust" + }, + { + "author_name": "Kelly Byrne", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Pavel Mozgunov", + "author_inst": "MRC Biostatistics Unit, University of Cambridge" + }, + { + "author_name": "Thomas Jaki", + "author_inst": "MRC Biostatistics Unit, University of Cambridge" + }, + { + "author_name": "Saye Khoo", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Andrew Owen", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Gareth Griffiths", + "author_inst": "Southampton Clinical Trials Unit, University of Southampton, Southampton UK" + }, + { + "author_name": "Thomas E Fletcher", + "author_inst": "Liverpool University Hospitals NHS Foundation Trust. Liverpool School of Tropical Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "pharmacology and therapeutics" + }, { "rel_doi": "10.1101/2021.09.02.21262480", "rel_title": "The contribution of hospital-acquired infections to the COVID-19 epidemic in England in the first half of 2020", @@ -618283,53 +618880,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.09.21263328", - "rel_title": "COVID-19 Vaccine Concerns about Safety, Effectiveness and Policies in the United States, Canada, Sweden, and Italy among Unvaccinated Individuals", - "rel_date": "2021-09-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.09.21263328", - "rel_abs": "Despite the effectiveness of the COVID-19 vaccine, global vaccination distribution efforts have thus far had varying levels of success. Vaccine hesitancy remains a threat to vaccine uptake. This study has four objectives: 1) describe and compare vaccine hesitancy proportions by country; 2) categorize vaccine-related concerns; 3) rank vaccine-related concerns; and 4) compare vaccine-related concerns by country and hesitancy status in four countries- the United States, Canada, Sweden, and Italy. Using the Pollfish survey platform, we sampled 1000 respondents in Canada, Sweden, and Italy and 750 respondents in the United States between May 21-28, 2021. Results showed vaccine related concerns varied across three topical areas- vaccine safety and government control, vaccine effectiveness and population control, and freedom. For each thematic area, the top concern was statistically significantly different in each country and among the hesitant and non-hesitant subsamples within each county. Understanding the specific concerns among individuals when it comes to the COVID-19 vaccine can help to inform public communications and identify which, if any, salient narratives, are global.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Rachael Piltch-Loeb", - "author_inst": "Harvard TH Chan School of Public Health" - }, - { - "author_name": "Nigel Harriman", - "author_inst": "Harvard TH Chan School of Public Health" - }, - { - "author_name": "Julia Healey", - "author_inst": "Harvard TH Chan School of Public Health" - }, - { - "author_name": "Marco Bonetti", - "author_inst": "Carlo F. Dondena Research Center and Bocconi Institute for Data Science and Analytics, Bocconi University" - }, - { - "author_name": "Veronica Toffolutti", - "author_inst": "Imperial College London" - }, - { - "author_name": "Marcia Testa", - "author_inst": "Harvard TH Chan School of Public Health" - }, - { - "author_name": "Max Su", - "author_inst": "Harvard TH Chan School of Public Health" - }, - { - "author_name": "Elena Savoia", - "author_inst": "Harvard TH Chan School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.09.10.459800", "rel_title": "pH-dependent polymorphism of the structure of SARS-CoV-2 nsp7", @@ -619817,6 +620367,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.09.04.21263123", + "rel_title": "Assessment of COVID-19 intervention strategies in the Nordic countries using genomic epidemiology", + "rel_date": "2021-09-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.04.21263123", + "rel_abs": "The Nordic countries, defined here as Norway, Sweden, Denmark, Finland and Iceland, are known for their comparable demographics and political systems. Since these countries implemented different COVID-19 intervention strategies, they provide a natural laboratory for examining how COVID-19 policies and mitigation strategies affected the propagation, evolution and spread of the SARS-CoV-2 virus. We explored how the duration, the size and number of transmission clusters, defined as country-specific monophyletic groups in a SARS-CoV-2 phylogenetic tree, differed between the Nordic countries. We found that Sweden had the largest number of COVID-19 transmission clusters followed by Denmark, Norway, Finland and Iceland. Moreover, Sweden and Denmark had the largest, and most enduring, transmission clusters followed by Norway, Finland and Iceland. In addition, there was a significant positive association between transmission cluster size and duration, suggesting that the size of transmission clusters could be reduced by rapid and effective contact tracing. Thus, these data indicate that to reduce the general burden of COVID-19 there should be a focus on limiting dense gatherings and their subsequent contacts to keep the number, size and duration of transmission clusters to a minimum. Our results further suggest that although geographical connectivity, population density and openness influence the spread and the size of SARS-CoV-2 transmission clusters, country-specific intervention strategies had the largest single impact.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Sebastian Duchene", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Leo Featherstone", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Birgitte Freiesleben de Blasio", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Edward C Holmes", + "author_inst": "University of Sydney" + }, + { + "author_name": "Jon Bohlin", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "John H.-O. Pettersson", + "author_inst": "Uppsala university" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.09.08.459398", "rel_title": "No substantial pre-existing B cell immunity against SARS-CoV-2 in healthy adults", @@ -620485,41 +621074,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.09.08.459260", - "rel_title": "Artemisia annua hot-water extracts show potent activity in vitro against Covid-19 variants including delta", - "rel_date": "2021-09-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.08.459260", - "rel_abs": "Ethnopharmacological relevanceFor millennia in Southeast Asia, Artemisia annua L. was used to treat \"fever\". This medicinal plant is effective against numerous infectious microbial and viral diseases and is used by many global communities as a source of artemisinin derivatives that are first-line drugs to treat malaria.\n\nAim of the StudyThe SARS-CoV-2 (Covid-19) global pandemic has killed millions and evolved numerous variants, with delta being the most transmissible to date and causing break-through infections of vaccinated individuals. We further queried the efficacy of A. annua cultivars against new variants.\n\nMaterials and MethodsUsing Vero E6 cells, we measured anti-SARS-CoV-2 activity of dried-leaf hot-water A. annua extracts of four cultivars, A3, BUR, MED, and SAM, to determine their efficacy against five fully infectious variants of the virus: alpha (B.1.1.7), beta (B.1.351), gamma (P.1), delta (B.1.617.2), and kappa (B.1.617.1).\n\nResultsIn addition to being effective against the original wild type WA1, A. annua cultivars A3, BUR, MED and SAM were also potent against all five variants. IC50 and IC90 values based on measured artemisinin content ranged from 0.3-8.4 M and 1.4-25.0 M, respectively. The IC50 and IC90 values based on dried leaf weight (DW) used to make the tea infusions ranged from 11.0-67.7 g DW and 59.5-160.6 g DW, respectively. Cell toxicity was insignificant at a leaf dry weight of [≤]50 g in the extract of any cultivar.\n\nConclusionsResults suggest that oral consumption of A. annua hot-water extracts (tea infusions), could provide a cost-effective therapy to help stave off the rapid global spread of these variants, buying time for broader implementation of vaccines.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Manoj S Nair", - "author_inst": "Columbia University" - }, - { - "author_name": "Yaoxing Huang", - "author_inst": "Columbia University" - }, - { - "author_name": "David A Fidock", - "author_inst": "Columbia University" - }, - { - "author_name": "Melissa Towler", - "author_inst": "Worcester Polytechnic Institute" - }, - { - "author_name": "Pamela Weathers", - "author_inst": "Worcester Polytechnic Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.09.08.459464", "rel_title": "SARS-CoV-2 expresses a microRNA-like small RNA able to selectively repress host genes", @@ -621819,6 +622373,93 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.09.06.459055", + "rel_title": "Increased neutralization of SARS-CoV-2 Delta variant by nanobody (Nb22) and the structural basis", + "rel_date": "2021-09-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.06.459055", + "rel_abs": "Current COVID-19 vaccines need to take at least one month to complete inoculation and then become effective. Around 51% global population are still not fully vaccinated. Instantaneous protection is an unmet need among those who are not fully vaccinated. In addition, breakthrough infections caused by SARS-CoV-2 are widely reported. All these highlight the unmet needing for short-term instantaneous prophylaxis (STIP) in the communities where SARS-CoV-2 is circulating. Previously, we reported nanobodies isolated from an alpaca immunized with the spike protein, exhibiting ultrahigh potency against SARS-CoV-2 and its variants. Herein, we found that Nb22, among our previously reported nanobodies, exhibited ultrapotent neutralization against Delta variant with an IC50 value of 0.41 ng/ml (5.13 pM). Furthermore, the crystal structural analysis revealed that the binding of Nb22 to WH01 and Delta RBDs both effectively blocked the binding of RBD to hACE2. Additionally, intranasal Nb22 exhibited protection against SARS-CoV-2 Delta variant in the post-exposure prophylaxis (PEP) and pre-exposure prophylaxis (PrEP). Of note, intranasal Nb22 also demonstrated high efficacy against SARS-CoV-2 Delta variant in STIP for seven days administered by single dose and exhibited long-lasting retention in the respiratory system for at least one month administered by four doses, providing a means of instantaneous short-term prophylaxis against SARS-CoV-2. Thus, ultrahigh potency, long-lasting retention in the respiratory system as well as stability at room-temperature make the intranasal or inhaled Nb22 to be a potential therapeutic or STIP agent against SARS-CoV-2.\n\nBrief summaryNb22 exhibits ultrahigh potency against Delta variant in vitro and is exploited by crystal structural analysis; furthermore, animal study demonstrates high effectiveness in the treatment and short-term instantaneous prophylaxis in hACE2 mice via intranasal administration.\n\nHighlightsO_LINb22 exhibits ultrapotent neutralization against Delta variant with an IC50 value of 0.41 ng/ml (5.13 pM).\nC_LIO_LIStructural analysis elucidates the ultrapotent neutralization of Nb22 against Delta variant.\nC_LIO_LINb22 demonstrates complete protection in the treatment of Delta variant infection in hACE2 transgenic mice.\nC_LIO_LIWe complete the proof of concept of STIP against SARS-CoV-2 using intranasal Nb22 with ultrahigh potency and long-lasting retention in respiratory system.\nC_LI\n\nGraphic Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC=\"FIGDIR/small/459055v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (44K):\norg.highwire.dtl.DTLVardef@144516corg.highwire.dtl.DTLVardef@3dc17forg.highwire.dtl.DTLVardef@6a8962org.highwire.dtl.DTLVardef@619cd7_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Xilin Wu", + "author_inst": "Medical School, Nanjing University" + }, + { + "author_name": "Yaxing Wang", + "author_inst": "Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University" + }, + { + "author_name": "Lin Cheng", + "author_inst": "Shenzhen Third People Hospital" + }, + { + "author_name": "Fengfeng Ni", + "author_inst": "Wuhan Institute of Virology, Wuhan" + }, + { + "author_name": "Linjing Zhu", + "author_inst": "Abrev Biotechnology Co., Ltd." + }, + { + "author_name": "Sen Ma", + "author_inst": "Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University" + }, + { + "author_name": "Bilian Huang", + "author_inst": "Center for Public Health Research, Medical School, Nanjing University, Nanjing, P.R. China." + }, + { + "author_name": "Mengmeng Ji", + "author_inst": "School of Life Sciences, Ningxia University, Yinchuan, P.R. China." + }, + { + "author_name": "Huimin Hu", + "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, P.R.China" + }, + { + "author_name": "Yuncheng Li", + "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan,China" + }, + { + "author_name": "Shijie Xu", + "author_inst": "Department of Antibody, Y-clone Medical Science Co. Ltd. Suzhou, P.R. China." + }, + { + "author_name": "Haixia Shi", + "author_inst": "Department of Antibody, Y-clone Medical Science Co. Ltd. Suzhou, P.R. China" + }, + { + "author_name": "Linshuo Liu", + "author_inst": "Department of Antibody, Y-clone Medical Science Co. Ltd. Suzhou, P.R. China." + }, + { + "author_name": "Waqas Nawaz", + "author_inst": "Center for Public Health Research, Medical School, Nanjing University" + }, + { + "author_name": "Qinxue Hu", + "author_inst": "State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China" + }, + { + "author_name": "Sheng Ye", + "author_inst": "Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University" + }, + { + "author_name": "Yalan Liu", + "author_inst": "tate Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China" + }, + { + "author_name": "Zhiwei Wu", + "author_inst": "School of Life Sciences, Ningxia University, Yinchuan, P.R. China." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.09.06.459005", "rel_title": "Ineffective neutralization of the SARS-CoV-2 Mu variant by convalescent and vaccine sera", @@ -622115,61 +622756,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.09.02.21263038", - "rel_title": "COVID-19 Vaccine Efficacy in a Diverse Urban Healthcare Worker Population", - "rel_date": "2021-09-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.09.02.21263038", - "rel_abs": "ObjectiveTo investigate COVID-19 vaccine efficacy (VE) among healthcare workers (HCWs) in an ethnically diverse community healthcare system, during its initial immunization campaign.\n\nMethodsHCWs of the system were retrospectively included from the beginning of a COVID-19 vaccination program (December 16, 2020) until March 31, 2021. Those with a prior COVID-19 infection before December 15 were excluded. The Occupational Health department of the system ran a COVID-19 screening and testing referral program for workers, consistently throughout the study period. A master database had been established and updated comprising of the demographics, COVID-19 PCR assays, and vaccinations of each HCW. Andersen-Gill extension of the Cox models were built to estimate the VE of fully/partially vaccinated person-days at risk.\n\nResultsAmong the 4317 eligible HCWs, 3249 (75%) received any vaccination during the study period. Vaccinated HCWs were older, less likely to be Black/African American, Hispanic/Latino or identify as two or more races, and more likely to be medical providers. After adjusting for age, sex, race, and the statewide background incidence at the time of vaccination, we observed a VE of 80.2% (95% CI: 57.5-90.8%) for [greater double equals]14 days after the first dose of Pfizer/Moderna, and 95.5% (95% CI: 88.2-98.3%) among those fully vaccinated (i.e. [greater double equals]14 days after the second dose of Pfizer/Moderna or the single dose of J&J/Janssen).\n\nConclusionCOVID-19 vaccine effectiveness in the real world is promising, and these data in concert with culturally appropriate may decrease vaccine hesitancy.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Eirini Iliaki", - "author_inst": "Occupational Medicine, Cambridge Health Alliance, Harvard Medical School, Cambridge MA, USA" - }, - { - "author_name": "Fan-Yun Lan", - "author_inst": "Occupational Medicine, Cambridge Health Alliance, Harvard Medical School, Cambridge MA, USA" - }, - { - "author_name": "Costas A. Christophi", - "author_inst": "Cyprus International Institute for Environmental and Public Health, Cyprus University of Technology, Limassol, Cyprus" - }, - { - "author_name": "Guido Guidotti", - "author_inst": "Department of Environmental Health, Harvard University T.H. Chan School of Public Health, Boston, MA, USA" - }, - { - "author_name": "Alexander D. Jobrack", - "author_inst": "Department of Environmental Health, Harvard University T.H. Chan School of Public Health, Boston, MA, USA" - }, - { - "author_name": "Jane Buley", - "author_inst": "Occupational Medicine, Cambridge Health Alliance, Harvard Medical School, Cambridge MA, USA" - }, - { - "author_name": "Neetha Nathan", - "author_inst": "Occupational Medicine, Cambridge Health Alliance, Harvard Medical School, Cambridge MA, USA" - }, - { - "author_name": "Rebecca Osgood", - "author_inst": "Pathology, Cambridge Health Alliance, Harvard Medical School, Cambridge MA, USA" - }, - { - "author_name": "Lou Ann Bruno-Murtha", - "author_inst": "Infection Prevention and Infectious Diseases, Cambridge Health Alliance, Harvard Medical School, Cambridge MA, USA" - }, - { - "author_name": "Stefanos N. Kales", - "author_inst": "Occupational Medicine, Cambridge Health Alliance, Harvard Medical School, Cambridge MA, USA" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.09.03.21263076", "rel_title": "Functional respiratory capacity in the elderly after COVID-19 -- a pilot study", @@ -623193,6 +623779,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.26.21262426", + "rel_title": "The comparability of Anti-Spike SARS-CoV-2 antibody tests is time-dependent: a prospective observational study", + "rel_date": "2021-09-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.26.21262426", + "rel_abs": "ObjectivesVarious commercial anti-Spike SARS-CoV-2 antibody tests are used for studies and in clinical settings after vaccination. An international standard for SARS-CoV-2 antibodies has been established to achieve comparability of such tests, allowing conversions to BAU/ml. This study aimed to investigate the comparability of antibody tests regarding the timing of blood collection after vaccination.\n\nMethodsFor this prospective observational study, antibody levels of 50 participants with homologous AZD1222 vaccination were evaluated at 3 and 11 weeks after the first dose and 3 weeks after the second dose using two commercial anti-Spike binding antibody assays (Roche and Abbott) and a surrogate neutralization assay.\n\nResultsThe correlation between Roche and Abbott changed significantly depending on the time point studied. Although 3 weeks after the first dose, Abbott provided values three times higher than Roche, 11 weeks after the first dose, the values for Roche were twice as high as for Abbott, and 3 weeks after the second dose even 5-6 times higher.\n\nConclusionsThe comparability of quantitative anti-Spike SARS-CoV-2 antibody tests is highly dependent on the timing of blood collection after vaccination. Therefore, standardization of the timing of blood collection might be necessary for the comparability of different quantitative SARS-COV-2 antibody assays.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=175 SRC=\"FIGDIR/small/21262426v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (27K):\norg.highwire.dtl.DTLVardef@1e789daorg.highwire.dtl.DTLVardef@b83aforg.highwire.dtl.DTLVardef@1f270daorg.highwire.dtl.DTLVardef@1cf296c_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Thomas Perkmann", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Patrick Mucher", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Nicole Perkmann-Nagele", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Astrid Radakovics", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Manuela Repl", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Thomas Koller", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Klaus G Schmetterer", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Johannes W Bigenzahn", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Florentina Leitner", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Galateja Jordakieva", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Oswald F Wagner", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Christoph J Binder", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Helmuth Haslacher", + "author_inst": "Medical University of Vienna" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.09.02.21263014", "rel_title": "No difference in risk of hospitalisation between reported cases of the SARS-CoV-2 Delta variant and Alpha variant in Norway", @@ -623617,89 +624270,6 @@ "type": "new results", "category": "genetics" }, - { - "rel_doi": "10.1101/2021.08.27.21262422", - "rel_title": "Characteristics associated with COVID-19 vaccine uptake among adults in England (08 December to 17 May 2021)", - "rel_date": "2021-09-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.27.21262422", - "rel_abs": "ObjectiveTo determine characteristics associated with COVID-19 vaccine coverage among individuals aged 50 years and above in England since the beginning of the programme.\n\nDesignObservational cross-sectional study assessed by logistic regression and mean prevalence margins.\n\nSettingCOVID-19 vaccinations delivered in England from 08 December 2020 - 17 May 2021.\n\nParticipants30,624,257/ 61,967,781 (49.4%) and 17,360,045/ 61,967,781 (28.1%) individuals in England were recorded as vaccinated in the National Immunisation Management System with a first dose and a second dose of a COVID-19 vaccine, respectively.\n\nInterventionsVaccination status with COVID-19 vaccinations.\n\nMain Outcome MeasuresProportion, adjusted odds ratios and mean prevalence margins for individuals not vaccinated with dose 1 among those aged 50-69 years old and dose 1 and 2 among those aged 70 years old and above.\n\nResultsAmong individuals aged 50 years and above, Black/African/Caribbean ethnic group was the least likely of all ethnic groups to be vaccinated with dose 1 of the COVID-19 vaccine. However, among those aged 70 years and above, the odds of not having dose 2 was 5.53 (95% CI 5.42 to 5.63) and 5.36 (90% CI 5.29 to 5.43) greater among Pakistani and Black/African/Caribbean compared to White British ethnicity, respectively. The odds of not receiving dose 2 was 1.18 (95% CI 1.16 to 1.20) higher among individuals who lived in a care home compared to those who did not. This was the opposite to that observed for dose 1, where the odds of not being vaccinated was significantly higher among those not living in a care home (0.89 (95% CI 0.87 to 0.91)).\n\nConclusionsWe found that there are characteristics associated with low COVID-19 vaccine coverage. Inequalities, such as ethnicity are a major contributor to suboptimal coverage and tailored interventions are required to improve coverage and protect the population from SARS-CoV-2.\n\nArticle summaryO_ST_ABSStrengths and Limitations of this studyC_ST_ABSO_LIThis is the is the first study assessing characteristics associated with COVID-19 vaccine coverage for all individuals aged 50 years and above in England.\nC_LIO_LIThis study uses data from the National Immunisation Management System (NIMS) which is based on all individuals in England with a registered NHS number.\nC_LIO_LIThis centralised national system captures individual level data for both vaccination status and demographic characteristics and allows for linkage to other datasets such as health care worker and care home resident status.\nC_LIO_LIThis study does not include those without an NHS number and, therefore, it is possible we have underestimated the number of vaccines delivered and odds of not being vaccinated for characteristics such as ethnic groups where we have seen the greatest impact.\nC_LIO_LIResidual errors in data entry on the point of care apps at the vaccination sites may have also occurred, though these errors are not likely to be widespread.\nC_LI", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Elise Tessier", - "author_inst": "Public Health England" - }, - { - "author_name": "Yuma Rai", - "author_inst": "Public Health England" - }, - { - "author_name": "Eleanor Clarke", - "author_inst": "Public Health England" - }, - { - "author_name": "Anissa Lakhani", - "author_inst": "Public Health England" - }, - { - "author_name": "Camille Tsang", - "author_inst": "Public Health England" - }, - { - "author_name": "Ashley Makwana", - "author_inst": "Public Health England" - }, - { - "author_name": "Heather Heard", - "author_inst": "Public Health England" - }, - { - "author_name": "Tim Rickeard", - "author_inst": "Public Health England" - }, - { - "author_name": "Shreya Lakhani", - "author_inst": "Public Health England" - }, - { - "author_name": "Partho Roy", - "author_inst": "Public Health England" - }, - { - "author_name": "Michael Edelstein", - "author_inst": "Bar Ilan University" - }, - { - "author_name": "Mary Ramsay", - "author_inst": "Public Health England" - }, - { - "author_name": "Jamie Lopez Bernal", - "author_inst": "Public Health England" - }, - { - "author_name": "Joanne White", - "author_inst": "Public Health England" - }, - { - "author_name": "Nick Andrews", - "author_inst": "Public Health England" - }, - { - "author_name": "Colin Campbell", - "author_inst": "Public Health England" - }, - { - "author_name": "Julia Stowe", - "author_inst": "Public Health England" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.09.03.458951", "rel_title": "Genomic evidence for divergent co-infections of SARS-CoV-2 lineages", @@ -624967,6 +625537,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.08.31.21262897", + "rel_title": "How control and relaxation interventions and virus mutations influence the resurgence of COVID-19", + "rel_date": "2021-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.31.21262897", + "rel_abs": "After a year of the unprecedented COVID-19 pandemic in 2020, the world has been overwhelmed by COVID-19 resurgences and virus mutations up to today. Here we develop a dynamic intervention, vaccination and mutation-driven epidemiological model with sequential interventions influencing epidemiological compartments and their state transition. We quantify epidemiological differences between waves under fatal viral mutations, the impacts of control or relaxation interventions and fatal virus mutations on resurgence under vaccinated or unvaccinated conditions, and estimate potential trends under varying interventions and mutations. Comprehensive analyses - between waves, with or without vaccinations, across representative countries with distinct ethnic and cultural backgrounds, what-if scenario simulations on second waves, and future 30-day trend - in two COVID-19 waves in Germany, France, Italy, Israel and Japan over 2020 and 2021 obtain quantitative empirical indication of the influence of strong vs. weak interventions, various combinations of control vs. relaxation strategies, and different transmissibility levels of coronavirus mutants on the behaviors and patterns of different waves and resurgences and future infection trends. The analyses quantify that (1) virus mutations, intervention fatigue, early relaxations, and lagging interventions, etc. may be common reasons for the resurgences observed in many countries; (2) timely strong interventions such as full lockdown will contain resurgence; (3) some resurgences relating to fatal mutants could have been better contained by either carrying forward the effective interventions from their early waves or implementing better controls and timing; (4) insufficient evidence is found on distinguishing the infection between unvaccinated and vaccinated countries while substantial vaccinations ensure much low mortality rate and high recovery rate; (5) resurgences with substantial vaccination have a much lower mortality rate and a higher recovery rate than those without vaccination; and (6) in the absence of sufficient vaccination, herd immunity and effective antiviral pharmaceutical treatments and with more infectious mutations, the widespread early or fast relaxation of interventions including public activity restrictions likely result in a COVID-19 resurgence. We also find the severity, number and timing of control and relaxation interventions determines a protection-deconfinement tradeoff, which can be used to evaluate the containment effect and the opportunity of resurgence and reopening under vaccination and fatal mutations.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Longbing Cao", + "author_inst": "University of Technology Sydney" + }, + { + "author_name": "Qing Liu", + "author_inst": "University of Technology Sydney" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.31.21262917", "rel_title": "Psychological antecedents towards COVID-19 vaccination using the Arabic 5C validated tool: An online study in 13 Arab countries", @@ -625619,41 +626212,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.09.01.458644", - "rel_title": "Co-expression analysis to identify key modules and hub genes associated with COVID19 in Platelets", - "rel_date": "2021-09-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.09.01.458644", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWThe severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is a highly contagious virus that causes a severe respiratory disease known as Corona virus disease 2019 (COVID19). Indeed, COVID19 increases the risk of cardiovascular occlusive/thrombotic events and is linked to poor outcomes. The pathophysiological processes underlying COVID19-induced thrombosis are complex, and remain poorly understood. To this end, platelets play important roles in regulating our cardiovascular system, including via contributions to coagulation and inflammation. There is an ample of evidence that circulating platelets are activated in COVID19 patients, which is a primary driver of the thrombotic outcome observed in these patients. However, the comprehensive molecular basis of platelet activation in COVID19 disease remains elusive, which warrants more investigation. Hence, we employed gene co-expression network analysis combined with pathways enrichment analysis to further investigate the aforementioned issues. Our study revealed three important gene clusters/modules that were closely related to COVID19. Furthermore, enrichment analysis showed that these three modules were mostly related to platelet metabolism, protein translation, mitochondrial activity, and oxidative phosphorylation, as well as regulation of megakaryocyte differentiation, and apoptosis, suggesting a hyperactivation status of platelets in COVID19. We identified the three hub genes from each of three key modules according to their intramodular connectivity value ranking, namely: COPE, CDC37, CAPNS1, AURKAIP1, LAMTOR2, GABARAP MT-ND1, MT-ND5, and MTRNR2L12. Collectively, our results offer a new and interesting insight into platelet involvement in COVID19 disease at the molecular level, which might aid in defining new targets for treatment of COVID19-induced thrombosis.\n\nkey pointsO_LICo-expression analysis of platelet RNAseq from COVID19 patients show distinct clusters of genes (modules) that are highly correlated to COVID19 disease.\nC_LIO_LIIdentifying these modules might help in understanding the mechanism of thrombosis in COVID19 patients\nC_LI", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Ahmed B. Alarabi", - "author_inst": "Department of Pharmacy Practice, Irma Lerma Rangel College of Pharmacy, Texas A&M University, Kingsville, Texas, USA" - }, - { - "author_name": "Attayeb Mohsen", - "author_inst": "Laboratory of Bioinformatics, Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health a" - }, - { - "author_name": "Kenji Mizuguchi", - "author_inst": "Laboratory of Bioinformatics, Artificial Intelligence Center for Health and Biomedical Research (ArCHER), National Institutes of Biomedical Innovation, Health a" - }, - { - "author_name": "Fatima Z. Alshbool", - "author_inst": "Department of Pharmacy Practice, Irma Lerma Rangel College of Pharmacy, Texas A&M University, Kingsville, Texas, USA." - }, - { - "author_name": "Fadi T. Khasawneh", - "author_inst": "Department of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, Kingsville, Texas, USA." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "systems biology" - }, { "rel_doi": "10.1101/2021.09.01.458475", "rel_title": "Azacytidine targeting SARS-CoV-2 viral RNA as a potential treatment for COVID-19", @@ -627193,6 +627751,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.30.458225", + "rel_title": "Epistasis at the SARS-CoV-2 RBD Interface and the Propitiously Boring Implications for Vaccine Escape", + "rel_date": "2021-08-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.30.458225", + "rel_abs": "At the time of this writing, December 2021, potential emergence of vaccine escape variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a grave global concern. The interface between the receptor-binding domain (RBD) of SARS-CoV-2 spike (S) protein and the host receptor (ACE2) overlap with the binding site of principal neutralizing antibodies (NAb), limiting the repertoire of viable mutations. Nonetheless, variants with multiple mutations in the RBD have rose to dominance. Non-additive, epistatic relationships among RBD mutations are apparent, and assessing the impact of such epistasis on the mutational landscape is crucial. Epistasis can substantially increase the risk of vaccine escape and cannot be completely characterized through the study of the wild type (WT) alone. We employed protein structure modeling using Rosetta to compare the effects of all single mutants at the RBD-NAb and RBD-ACE2 interfaces for the WT, Delta, Gamma, and Omicron variants. Overall, epistasis at the RBD interface appears to be limited and the effects of most multiple mutations are additive. Epistasis at the Delta variant interface weakly stabilizes NAb interaction relative to ACE2 interaction, whereas in the Gamma variant, epistasis more substantially destabilizes NAb interaction. Although a small, systematic trend towards NAb destabilization not observed for Delta or Gamma was detected for Omicron, and despite bearing significantly more RBD mutations, the epistatic landscape of the Omicron variant closely resembles that of Gamma. These results suggest that, although Omicron poses new risks not observed with Delta, structural constraints on the RBD hamper continued evolution towards more complete vaccine escape. The modest ensemble of mutations relative to the WT that are currently known to reduce vaccine efficacy is likely to comprise the majority of all possible escape mutations for future variants, predicting continued efficacy of the existing vaccines.\n\nSignificanceEmergence of vaccine escape variants of SARS-CoV-2 is arguably the most pressing problem during the COVID-19 pandemic as vaccines are distributed worldwide. We employed a computational approach to assess the risk of antibody escape resulting from mutations in the receptor-binding domain of the spike protein of the wild type SARS-CoV-2 virus as well as the Delta, Gamma, and Omicron variants. At the time of writing, December, 2021, Omicron is poised to replace Delta as the dominant variant worldwide. The efficacy of the existing vaccines against Omicron could be substantially reduced relative to the WT and the potential for vaccine escape is of grave concern. Our results suggest that although Omicron poses new evolutionary risks not observed for the Delta variant, structural constraints on the RBD make continued evolution towards more complete vaccine escape unlikely. The modest set of escape-enhancing mutations already identified for the wild type likely include the majority of all possible mutations with this effect.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Nash Delta Rochman", + "author_inst": "NIH" + }, + { + "author_name": "Guilhem Faure", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Yuri I. Wolf", + "author_inst": "NCBI/NLM/NIH" + }, + { + "author_name": "Peter Freddolino", + "author_inst": "University of Michigan" + }, + { + "author_name": "Feng Zhang", + "author_inst": "Broad Institute of MIT and Harvard; McGovern Institute for Brain Research at MIT" + }, + { + "author_name": "Eugene V. Koonin", + "author_inst": "NIH" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.08.27.457969", "rel_title": "May a Strain Chlamydia Isolated From SARS Patient's Autopsy Issues Inhibit the Proliferation of SARS-CoV? An Early Observation in Vitro.", @@ -627581,25 +628178,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.23.21262413", - "rel_title": "Towards the global equilibrium of COVID-19: statistical analysis of country-level data", - "rel_date": "2021-08-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.23.21262413", - "rel_abs": "ObjectivesThe time-varying effect of COVID-19 on a population of a given country or territory can be measured by the Reproduction Number (R) and the Case Fatality Rate (CFR). In our study, we explore the dynamics of these two measures to test whether the virus has reached its equilibrium point and to identify the main factors explaining the current R and CFR variability across countries.\n\nDesignA retrospective study of publicly available country-level data.\n\nSettingFifty countries having the highest number of confirmed COVID-19 cases at the end of September 2021.\n\nParticipantsAggregated data including 213 976 306 COVID-19 cases confirmed in the selected fifty countries from the start of the epidemic to September 30, 2021.\n\nPrimary and secondary outcome measuresThe daily values of COVID-19 R and CFR measures were estimated using country-level data from the Our World in Data website.\n\nResultsThe mean values of country-level moving averages of R and CFR went down from 1.118 and 6.3%, respectively, on June 30, 2020 to 1.083 and 3.6% on September 30, 2020 and to 1.015 and 1.8% by September 30, 2021. In parallel, the 10% to 90% inter-percentile range of R and CFR moving averages decreased from 0.288 and 13.3%, respectively, on June 30, 2020, to 0.151 and 7.7% on September 30, 2020, and to 0.107 and 3.3% by September 30, 2021. According to a comparison of the country-level 180-day moving averages of R and CFR calculated on September 30, 2021, an increase of 1% in the Delta variant share is associated with an increase of 0.0009 (95% CI 0.000 to 0.002) in the average Reproduction Number R, while an increase of 1% in the total percentage of confirmed COVID-19 cases per countrys population is associated with a decrease of 0.005 (95% CI 0.000 to 0.010) in the average R. Also, an increase of 1% in the total percentage of fully vaccinated people per countrys population is associated with a decrease of 0.04% (95% CI 0.01% to 0.06%) in the average CFR. Other virological, demographic, economic, immunization, or stringency factors were not statistically significantly associated with either R or CFR across the explored countries.\n\nConclusionsThe slow decrease in the country-level moving averages of R, approaching the level of 1.0 and accompanied by repeated outbreaks (\"waves\") in various countries, may indicate that COVID-19 has reached its point of a stable endemic equilibrium. A regression analysis implies that only a prohibitively high level of herd immunity (about 63%) may stop the endemic by reaching a stable disease-free equilibrium. It also appears that fully vaccinating about 70% of a countrys population should be sufficient for bringing the CFR close to the level of a seasonal flu (about 0.1%). Thus, while the currently available vaccines prove to be effective in reducing the mortality from the existing COVID-19 variants, they are unlikely to stop the spread of the virus in the foreseeable future. It is noteworthy that no statistically significant effects of government measures restricting the peoples behavior (such as lockdowns) were found in the analyzed data.\n\nStrengths and limitations of this studyO_LIIn this study, we have explored the long-term trends in country-level Reproduction Number and the Case Fatality Rate of COVID-19.\nC_LIO_LIOur study also investigated the long-term statistical dependence of the COVID-19 Reproduction Number and the Case Fatality Rate on epidemiological, demographic, economic, immunization, and government policy factors in each country.\nC_LIO_LIThe findings of this study may have important implications for the health policy-makers worldwide.\nC_LIO_LIThe officially reported numbers of daily COVID-19 confirmed cases depend on the local testing policy and usually underestimate the true number of carriers in the population.\nC_LIO_LIThe officially reported numbers of daily COVID-19 deaths in some countries may include all deceased individuals who tested positive for COVID-19, disregarding their actual cause of death, and exclude victims who were not tested for COVID-19.\nC_LI", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Mark Last", - "author_inst": "Ben-Gurion University of the Negev" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.08.26.21262699", "rel_title": "Prediction of vaccine efficacy of the Delta variant", @@ -629135,6 +629713,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.27.21262754", + "rel_title": "Trajectory of viral load in a prospective population-based cohort with incident SARS-CoV-2 G614 infection", + "rel_date": "2021-08-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.27.21262754", + "rel_abs": "ImportanceSARS-CoV-2 viral trajectory has not been well-characterized in documented incident infections. These data will inform SARS-CoV-2 natural history, transmission dynamics, prevention practices, and therapeutic development.\n\nObjectiveTo prospectively characterize early SARS-CoV-2 viral shedding in persons with incident infection.\n\nDesignProspective cohort study.\n\nSettingSecondary data analysis from a multicenter study in the U.S.\n\nParticipantsThe samples derived from a randomized controlled trial of 829 community-based asymptomatic participants recently exposed (<96 hours) to persons with SARS-CoV-2. Participants collected daily mid-turbinate swabs for SARS-CoV-2 detection by polymerase-chain-reaction and symptom diaries for 14-days. Persons with negative swab for SARS-CoV-2 at baseline who developed infection during the study were included in the analysis.\n\nExposureLaboratory-confirmed SARS-CoV-2 infection.\n\nMain outcomes and measuresThe observed SARS-CoV-2 viral shedding characteristics were summarized and shedding trajectories were examined using a piece-wise linear mixed-effects modeling. Whole viral genome sequencing was performed on samples with cycle threshold (Ct)<34.\n\nResultsNinety-seven persons (57% women, median age 37-years) developed incident infections during 14-days of follow-up. Two-hundred fifteen sequenced samples were assigned to 15 lineages that belonged to the G614 variant. Forty-two (43%), 18(19%), and 31(32%) participants had viral shedding for 1 day, 2-6 days, and [≥]7 days, with median peak viral load Ct of 38.5, 36.7, and 18.3, respectively. Six (6%) participants had 1-6 days of observed viral shedding with censored duration. The peak average viral load was observed on day 3 of viral shedding. The average Ct value was lower, indicating higher viral load, in persons reporting COVID-19 symptoms than asymptomatic. Using the statistical model, the median time from shedding onset to peak viral load was 1.4 days followed by a median of 9.7 days before clearance.\n\nConclusions and RelevanceIncident SARS-CoV-2 G614 infection resulted in a rapid viral load peak followed by slower decay and positive correlation between peak viral load and shedding duration; duration of shedding was heterogeneous. This longitudinal evaluation of the SARS-CoV-2 G614 variant with frequent molecular testing may serve as a reference for comparing emergent viral lineages to inform clinical trial designs and public health strategies to contain the spread of the virus.\n\nKEY POINTSO_ST_ABSQuestionC_ST_ABSWhat are the early SARS-CoV-2 G614 viral shedding characteristics in persons with incident infection?\n\nFindingsIn this prospective cohort of 97 community-based participants who collected daily mid-turbinate swabs for SARS-CoV-2 detection after recent exposure to SARS-CoV-2, viral trajectory was characterized by a rapid peak followed by slower decay. Peak viral load correlated positively with symptoms. The duration of shedding was heterogeneous.\n\nMeaningA detailed description of the SARS-CoV-2 G614 viral shedding trajectory serves as baseline for comparison to new viral variants of concern and inform models for the planning of clinical trials and transmission dynamics to end this pandemic.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Helen C Stankiewicz Karita", + "author_inst": "University of Washington" + }, + { + "author_name": "Tracy Q Dong", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Christine Johnston", + "author_inst": "University of Washington" + }, + { + "author_name": "Kathleen M Neuzil", + "author_inst": "University of Maryland" + }, + { + "author_name": "Michael K Paasche-Orlow", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Patricia J Kissinger", + "author_inst": "Tulane University" + }, + { + "author_name": "Anna Bershteyn", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "Lorna Thorpe", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "Meagan Deming", + "author_inst": "University of Maryland" + }, + { + "author_name": "Angelica Kottkamp", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "Miriam Laufer", + "author_inst": "University of Maryland" + }, + { + "author_name": "Raphael Landovitz", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Alfred Luk", + "author_inst": "Tulane University" + }, + { + "author_name": "Risa Hoffman", + "author_inst": "University of California Los Angeles" + }, + { + "author_name": "Pavitra Roychoudhury", + "author_inst": "University of Washington" + }, + { + "author_name": "Craig Magaret", + "author_inst": "University of Washington" + }, + { + "author_name": "Alex Greninger", + "author_inst": "University of Washington" + }, + { + "author_name": "Meeili Huang", + "author_inst": "University of Washington" + }, + { + "author_name": "Keith Jerome", + "author_inst": "University of Washington" + }, + { + "author_name": "Mark Wener", + "author_inst": "University of Washington" + }, + { + "author_name": "Connie L Celum", + "author_inst": "University of Washington" + }, + { + "author_name": "Helen Y Chu", + "author_inst": "University of Washington" + }, + { + "author_name": "Jared Baeten", + "author_inst": "University of Washington" + }, + { + "author_name": "Anna Wald", + "author_inst": "University of Washington" + }, + { + "author_name": "Ruanne V Barnabas", + "author_inst": "University of Washington" + }, + { + "author_name": "Elizabeth R Brown", + "author_inst": "Fred Hutchinson Cancer Research Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.28.21262778", "rel_title": "COVID-19 OUTCOMES IN PREGNANCY: A REVIEW OF 275 SCREENED STUDIES", @@ -629639,37 +630336,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.29.458083", - "rel_title": "Allosteric regulation of 3CL protease of SARS-CoV-2 and SARS-CoV observed in the crystal structure ensemble", - "rel_date": "2021-08-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.29.458083", - "rel_abs": "The 3C-like protease (3CLpro) of SARS-CoV-2 is a potential therapeutic target for COVID-19. Importantly, it has an abundance of structural information solved as a complex with various drug candidate compounds. Collecting these crystal structures (83 Protein Data Bank (PDB) entries) together with those of the highly homologous 3CLpro of SARS-CoV (101 PDB entries), we constructed the crystal structure ensemble of 3CLpro to analyze the dynamic regulation of its catalytic function. The structural dynamics of the 3CLpro dimer observed in the ensemble were characterized by the motions of four separate loops (the C-loop, E-loop, H-loop, and Linker) and the C-terminal domain III on the rigid core of the chymotrypsin fold. Among the four moving loops, the C-loop (also known as the oxyanion binding loop) causes the order (active)-disorder (collapsed) transition, which is regulated cooperatively by five hydrogen bonds made with the surrounding residues. The C-loop, E-loop, and Linker constitute the major ligand binding sites, which consist of a limited variety of binding residues including the substrate binding subsites. Ligand binding causes a ligand size dependent conformational change to the E-loop and Linker, which further stabilize the C-loop via the hydrogen bond between the C-loop and E-loop. The T285A mutation from SARS-CoV 3CLpro to SARS-CoV-2 3CLpro significantly closes the interface of the domain III dimer and allosterically stabilizes the active conformation of the C-loop via hydrogen bonds with Ser1 and Gly2; thus, SARS-CoV-2 3CLpro seems to have increased activity relative to that of SARS-CoV 3CLpro.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Akinori Kidera", - "author_inst": "Yokohama City University" - }, - { - "author_name": "Kei Moritsugu", - "author_inst": "Yokohama City University" - }, - { - "author_name": "Toru Ekimoto", - "author_inst": "Yokohama City University" - }, - { - "author_name": "Mitsunori Ikeguchi", - "author_inst": "Yokohama City University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.08.29.21262789", "rel_title": "Vaccines alone are no silver bullets: a modeling study on the impact of efficient contact tracing on COVID-19 infection and transmission", @@ -630861,6 +631527,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.27.21262731", + "rel_title": "mRNA vaccines effectiveness against COVID-19 hospitalizations and deaths in older adults: a cohort study based on data-linkage of national health registries in Portugal", + "rel_date": "2021-08-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.27.21262731", + "rel_abs": "BackgroundWe used electronic health registries to estimate the mRNA vaccine effectiveness (VE) against COVID-19 hospitalizations and deaths in older adults.\n\nMethodsWe established a cohort of individuals aged 65 and more years, resident in Portugal mainland through data linkage of eight national health registries. For each outcome, VE was computed as one minus the confounder-adjusted hazard ratio, estimated by time-dependent Cox regression.\n\nResultsVE against COVID-19 hospitalization [≥]14 days after the second dose was 94% (95%CI 88 to 97) for age-group 65-79 years old (yo) and 82% (95%CI 72 to 89) for [≥]80 yo. VE against COVID-19 related deaths [≥] 14 days after second dose was 96% (95%CI 92 to 98) for age-group 65-79 yo and 81% (95%CI 74 to 87), for [≥]80 yo individuals. No evidence of VE waning was observed after 98 days of second dose uptake.\n\nConclusionsmRNA vaccine effectiveness was high for the prevention of hospitalizations and deaths in age-group 65-79 yo and [≥]80 yo with a complete vaccination scheme, even after 98 days of second dose uptake.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Baltazar Nunes", + "author_inst": "Department of Epidemiology, Instituto Nacional de Saude Dr. Ricardo Jorge, Lisbon, Portugal" + }, + { + "author_name": "Ana Rodrigues", + "author_inst": "Department of Epidemiology, Instituto Nacional de Saude Dr. Ricardo Jorge, Lisbon, Portugal" + }, + { + "author_name": "Irina Kislaya", + "author_inst": "Department of Epidemiology, Instituto Nacional de Saude Dr. Ricardo Jorge, Lisbon, Portugal" + }, + { + "author_name": "Camila Cruz", + "author_inst": "Servicos Partilhados do Ministerio da Saude, Lisbon, Portugal" + }, + { + "author_name": "Andre Peralta-Santos", + "author_inst": "Direcao de Servicos de Informacao e Analise, Direcao-Geral da Saude, Lisbon, Portugal" + }, + { + "author_name": "Joao Lima", + "author_inst": "Servicos Partilhados do Ministerio da Saude, Lisbon, Portugal" + }, + { + "author_name": "Pedro Pinto Leite", + "author_inst": "Direcao de Servicos de Informacao e Analise, Direcao-Geral da Saude, Lisbon, Portugal" + }, + { + "author_name": "Duarte Sequeira", + "author_inst": "Servicos Partilhados do Ministerio da Saude, Lisbon, Portugal" + }, + { + "author_name": "Carlos Matias Dias", + "author_inst": "Department of Epidemiology, Instituto Nacional de Saude Dr. Ricardo Jorge, Lisbon, Portugal" + }, + { + "author_name": "Ausenda Machado", + "author_inst": "Department of Epidemiology, Instituto Nacional de Saude Dr. Ricardo Jorge, Lisbon, Portugal" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.27.21262744", "rel_title": "Previous Infection Combined with Vaccination Produces Neutralizing Antibodies With Potency Against SARS-CoV-2 Variants", @@ -631321,33 +632042,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.08.25.21262614", - "rel_title": "Democratic governance and excess mortality during the COVID-19 pandemic", - "rel_date": "2021-08-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.25.21262614", - "rel_abs": "BackgroundExcess mortality has been used to assess the health impact of COVID-19 across countries. Democracies aim to build trust in government and enable checks and balances on decision-making, which may be useful in a pandemic. On the other hand, democratic governments have been criticised as slow to enforce restrictive policies and being overly influenced by public opinion. This study sought to understand whether strength of democratic governance is associated with the variation in excess mortality observed across countries during the pandemic.\n\nMethodsThrough linking open-access datasets we constructed univariable and multivariable linear regression models investigating the association between country EIU Democracy Index (representing strength of democratic governance on a scale of 0 to 10) and excess mortality rates, from February 2020 to May 2021. We stratified our analysis into high-income and low and middle-income country groups and adjusted for several important confounders.\n\nResultsAcross 78 countries, the mean EIU democracy index was 6.74 (range 1.94 to 9.81) and the mean excess mortality rate was 128 per 100,000 (range -55 to 503 per 100,000). A one-point increase in EIU Democracy Index was associated with a decrease in excess mortality of 26.3 per 100,000 (p=0.002), after accounting for COVID-19 cases, age [≥] 65, gender, prevalence of cardiovascular disease, universal health coverage and the strength of early government restrictions. This association was particularly strong in high-income countries ({beta} -47.5, p<0.001) but non-significant in low and middle-income countries ({beta} -10.8, p=0.40).\n\nConclusionsSocio-political factors related to the way societies are governed have played an important role in mitigating the overall health impact of COVID-19. Given the omission of such considerations from outbreak risk assessment tools, and their particular significance in high-income countries rated most highly by such tools, this study strengthens the case to broaden the scope of traditional pandemic risk assessment.\n\nKey MessagesO_ST_ABSWhat is already known?C_ST_ABSO_LIPrevious studies have found that as countries become more democratic they experience a decline in rates of infant and child mortality, infections such as tuberculosis, and non-communicable diseases.\nC_LIO_LIIn Europe, more democratic countries were initially more reluctant to adopt restrictive COVID-19 measures that could conflict with democratic principles, including lockdowns.\nC_LI\n\nWhat are the new findings?O_LIWe found that a one-point increase in EIU Democracy Index was associated with a decrease in excess mortality of 26.3 per 100,000 (p=0.002), after accounting for several confounders including demographics, numbers of cases and the strength of early government responses.\nC_LIO_LIThis association was particularly significant in high-income countries ({beta} - 47.5, p<0.001), suggesting that way societies are governed has played an important role in mitigating the impact of COVID-19.\nC_LI\n\nWhat do the new findings imply?O_LIGiven the omission of social, political and cultural considerations from outbreak risk assessment tools, and criticisms of such tools that have failed to accurately reflect the observed impact of the pandemic across high-income countries, this study builds on the case to broaden of the scope of traditional pandemic risk assessment.\nC_LIO_LIFuture research into the mechanisms underlying our findings will help to understand and address the complex and deep-rooted vulnerabilities countries face in a protracted and large-scale public health emergency.\nC_LI", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Vageesh Jain", - "author_inst": "University College London" - }, - { - "author_name": "Jonathan Clarke", - "author_inst": "Imperial College London" - }, - { - "author_name": "Thomas Beaney", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.08.26.21262668", "rel_title": "Silent Hypoxia in Coronavirus disease-2019: Is it more dangerous?-A retrospective cohort study", @@ -632983,6 +633677,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.08.24.21262524", + "rel_title": "COVID-19 in Scottish care homes: A metapopulation model of spread among residents and staff", + "rel_date": "2021-08-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.24.21262524", + "rel_abs": "Care homes in the UK were disproportionately affected by the first wave of the COVID-19 pandemic, accounting for almost half of COVID-19 deaths over the course of the period from 6th March - 15th June 2020. Understanding how infectious diseases establish themselves throughout vulnerable communities is crucial for minimising deaths and lowering the total stress on the National Health Service (NHS Scotland). We model the spread of COVID-19 in the health-board of NHS Lothian, Scotland over the course of the first wave of the pandemic with a compartmental Susceptible - Exposed - Infected reported - Infected unreported - Recovered - Dead (SEIARD), metapopulation model. Care home residents, care home workers and the rest of the population are modelled as subpopulations, interacting on a network describing their mixing habits. We explicitly model the outbreaks reproduction rate and care home visitation level over time for each subpopulation, and execute a data fit and sensitivity analysis, focusing on parameters responsible for intra-subpopulation mixing: staff sharing, staff shift patterns and visitation. The results suggest that hospital discharges were not predominantly responsible for the early outbreak in care homes, and that only a few such cases led to infection seeding in care homes by the 6th of March Sensitivity analysis show the main mode of entry into care homes are infections by staff interacting with the general population. Visitation (before cancellation) and staff sharing were less significant in affecting outbreak size. Our model suggests that focusing on the protection and monitoring of staff, followed by reductions in staff sharing and quick cancellations of visitation can significantly reduce future infection attack rates of COVID-19 in care homes.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Matthew John Baister", + "author_inst": "University of Strathclyde" + }, + { + "author_name": "Ewan McTaggart", + "author_inst": "University of Strathclyde" + }, + { + "author_name": "Paul McMenemy", + "author_inst": "University of Stirling" + }, + { + "author_name": "Itamar Megiddo", + "author_inst": "University of Strathclyde" + }, + { + "author_name": "Adam Kleczkowski", + "author_inst": "University of Strathclyde" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.25.21262584", "rel_title": "Waning of BNT162b2 vaccine protection against SARS-CoV-2 infection in Qatar", @@ -633583,69 +634312,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.08.23.21262499", - "rel_title": "Comparative analyses of all FDA EUA-approved rapid antigen tests and RT-PCR for COVID-19 quarantine and surveillance-based isolation", - "rel_date": "2021-08-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.23.21262499", - "rel_abs": "BackgroundRapid antigen (RA) tests are being increasingly employed to detect SARS-CoV-2 infections in quarantine and surveillance. Prior research has focused on RT-PCR testing, a single RA test, or generic diagnostic characteristics of RA tests in assessing testing strategies.\n\nMethodsFor 18 RA tests with emergency use authorization from the United States of America FDA and an RT-PCR test, we conducted a comparative analysis of the post-quarantine transmission, the effective reproduction number during serial testing, and the false-positive rates. To quantify the extent of transmission, we developed an analytical mathematical framework informed by COVID-19 infectiousness, test specificity, and temporal diagnostic sensitivity data.\n\nResultsWe demonstrate that the relative effectiveness of RA and RT-PCR tests in reducing post-quarantine transmission depends on the quarantine duration and the turnaround time of testing results. For quarantines of two days or shorter, conducting a RA test on exit from quarantine reduces onward transmission more than a single RT-PCR test (with a 24-h delay) conducted upon exit. Applied to a complementary approach of performing serial testing at a specified frequency paired with isolation of positives, we have shown that RA tests outperform RT-PCR with a 24-h delay. The results from our modeling framework are consistent with quarantine and serial testing data collected from a remote industry setting.\n\nConclusionsThese RA test-specific results are an important component of the tool set for policy decision-making, and demonstrate that judicious selection of an appropriate RA test can supply a viable alternative to RT-PCR in efforts to control the spread of disease.\n\nPlain language summaryPrevious research has determined optimal timing for testing in quarantine and the utility of different frequencies of testing for disease surveillance using RT-PCR and generalized rapid antigen tests.\n\nHowever, these strategies can depend on the specific rapid antigen test used. By examining 18 rapid antigen tests, we demonstrate that a single rapid antigen test performs better than RT-PCR when quarantines are two days or less in duration. In the context of disease surveillance, the ability of a rapid antigen test to provide results quickly counteracts its lower sensitivity with potentially more false positives. These analytical results based on highly controlled test validation were consistent with real-world data obtained from quarantine and serial testing in an industrial setting.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Chad R Wells", - "author_inst": "CIDMA" - }, - { - "author_name": "Abhishek Pandey", - "author_inst": "Yale University" - }, - { - "author_name": "Seyed Moghadas", - "author_inst": "York University" - }, - { - "author_name": "Burton H. Singer", - "author_inst": "University of Florida" - }, - { - "author_name": "Gary Krieger", - "author_inst": "NewFields E&E" - }, - { - "author_name": "Richard J.L. Heron", - "author_inst": "BP" - }, - { - "author_name": "David E. Turner", - "author_inst": "BP" - }, - { - "author_name": "Justin P. Abshire", - "author_inst": "HSE Specialties, BHP Petroleum" - }, - { - "author_name": "Kimberly M. Phillips", - "author_inst": "BHP" - }, - { - "author_name": "A. Michael Donoghue", - "author_inst": "BHP" - }, - { - "author_name": "Alison P. Galvani", - "author_inst": "Center for Infectious Disease Modeling and Analysis" - }, - { - "author_name": "Jeffrey P. Townsend", - "author_inst": "Yale University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.08.22.21262449", "rel_title": "Country-level Association of Socioeconomic, Environmental and Healthcare-Related Factors with the Disease-Burden and Mortality Rate of COVID-19", @@ -634997,6 +635663,153 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.24.21262385", + "rel_title": "The relationship between autoantibodies targeting GPCRs and the renin-angiotensin system associates with COVID-19 severity", + "rel_date": "2021-08-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.24.21262385", + "rel_abs": "The coronavirus disease 2019 (COVID-19) can evolve to clinical manifestations resembling systemic autoimmune diseases, with the presence of autoantibodies that are still poorly characterized. To address this issue, we performed a cross-sectional study of 246 individuals to determine whether autoantibodies targeting G protein-coupled receptors (GPCRs) and renin-angiotensin system (RAS)-related molecules were associated with COVID-19-related clinical outcomes. Moderate and severe patients exhibited the highest autoantibody levels, relative to both healthy controls and patients with mild COVID-19 symptoms. Random Forest, a machine learning model, ranked anti-GPCR autoantibodies targeting downstream molecules in the RAS signaling pathway such as the angiotensin II type 1 and Mas receptor, and the chemokine receptor CXCR3 as the three strongest predictors of severe disease. Moreover, while the autoantibody network signatures were relatively conserved in patients with mild COVID-19 compared to healthy controls, they were disrupted in moderate and most perturbed in severe patients. Our data indicate that the relationship between autoantibodies targeting GPCRs and RAS-related molecules associates with the clinical severity of COVID-19, suggesting novel molecular pathways for therapeutic interventions.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Otavio Cabral Marques", + "author_inst": "Department of Immunology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, SP, Brazil" + }, + { + "author_name": "Gilad Halpert", + "author_inst": "Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Aviv University, Tel-Hashomer, Israel" + }, + { + "author_name": "Lena F Schimke", + "author_inst": "Department of Immunology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, SP, Brazil" + }, + { + "author_name": "Yuri Ostrinski", + "author_inst": "Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Aviv University, Tel-Hashomer, Israel" + }, + { + "author_name": "Israel Zyskind", + "author_inst": "Department of Pediatrics, NYU Langone Medical Center, New York, NY, USA" + }, + { + "author_name": "Miriam T Lattin", + "author_inst": "Department of Biology, Yeshiva University, Manhatten, NY, USA" + }, + { + "author_name": "Florian Tran", + "author_inst": "Department of Internal Medicine I, University Medical Center Schleswig-Holstein Campus Kiel, Kiel, Germany" + }, + { + "author_name": "Stefan Schreiber", + "author_inst": "Department of Internal Medicine I, University Medical Center Schleswig-Holstein Campus Kiel, Kiel, Germany" + }, + { + "author_name": "Alexandre H.C. Marques", + "author_inst": "Department of Immunology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, SP, Brazil." + }, + { + "author_name": "Igor Salerno Filgueiras", + "author_inst": "Department of Immunology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, SP, Brazil." + }, + { + "author_name": "Desiree Rodrigues Placa", + "author_inst": "Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, SP, Brazil." + }, + { + "author_name": "Gabriela Crispim Baiocchi", + "author_inst": "Department of Immunology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, SP, Brazil" + }, + { + "author_name": "Paula P Freire", + "author_inst": "Department of Immunology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, SP, Brazil." + }, + { + "author_name": "Dennyson Leandro M. Fonseca", + "author_inst": "Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, Sao Paulo, SP, Brazil" + }, + { + "author_name": "Jens Y. Humrich", + "author_inst": "Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lubeck, Lubeck, Germany" + }, + { + "author_name": "Tanja Lange", + "author_inst": "Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lubeck, Lubeck, Germany" + }, + { + "author_name": "Antje Muller", + "author_inst": "Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lubeck, Lubeck, Germany" + }, + { + "author_name": "Lasse M. Giil", + "author_inst": "Department of Internal Medicine, Haraldsplass Deaconess Hospital, Bergen, Norway" + }, + { + "author_name": "Hanna Grasshoff", + "author_inst": "Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lubeck, Lubeck, Germany" + }, + { + "author_name": "Anja Schumann", + "author_inst": "Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lubeck, Lubeck, Germany" + }, + { + "author_name": "Alexander Maximilian Hackel", + "author_inst": "Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lubeck, Lubeck, Germany" + }, + { + "author_name": "Juliane Junker", + "author_inst": "CellTrend Gesellschaft mit beschrankter Haftung (GmbH), Luckenwalde, Germany" + }, + { + "author_name": "Carlotta Meyer", + "author_inst": "CellTrend Gesellschaft mit beschrankter Haftung (GmbH), Luckenwalde, Germany" + }, + { + "author_name": "Hans D. Ochs", + "author_inst": "Department of Pediatrics, University of Washington School of Medicine, and Seattle Children's Research Institute, Seattle, WA, USA" + }, + { + "author_name": "Yael Bublil Lavi", + "author_inst": "Department of Chemistry Ben Gurion University Beer-Sheva, 84105, Israel" + }, + { + "author_name": "Kai Schulze-Forster", + "author_inst": "CellTrend Gesellschaft mit beschrankter Haftung (GmbH), Luckenwalde, Germany" + }, + { + "author_name": "Jonathan I. Silvergerg", + "author_inst": "Department of Dermatology, George Washington University, Washington, DC, USA" + }, + { + "author_name": "Howard Amital", + "author_inst": "Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Affiliated with the Sackler Faculty of Medicine, Tel-Aviv University, Tel-Hashomer, Israel" + }, + { + "author_name": "Jason Zimmerman", + "author_inst": "Maimonides Medical Center, Brooklyn, NY, USA" + }, + { + "author_name": "Harry Heidecke", + "author_inst": "CellTrend Gesellschaft mit beschrankter Haftung (GmbH), Luckenwalde, Germany" + }, + { + "author_name": "Avi Z Rosenberg", + "author_inst": "Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA" + }, + { + "author_name": "Gabriela Riemekasten", + "author_inst": "Department of Rheumatology, University Medical Center Schleswig-Holstein Campus Lubeck, Lubeck, Germany" + }, + { + "author_name": "Yehuda Shoenfeld", + "author_inst": "Zabludowicz Center for Autoimmune Diseases, Sheba Medical Center, Tel-Aviv University, Tel-Hashomer, Israel" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.24.21258577", "rel_title": "Sensitivity of wastewater-based epidemiology for detection of SARS-CoV-2 RNA in a low prevalence setting", @@ -635633,61 +636446,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.24.21262415", - "rel_title": "Comparing SARS-CoV-2 natural immunity to vaccine-induced immunity: reinfections versus breakthrough infections", - "rel_date": "2021-08-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.24.21262415", - "rel_abs": "BackgroundReports of waning vaccine-induced immunity against COVID-19 have begun to surface. With that, the comparable long-term protection conferred by previous infection with SARS-CoV-2 remains unclear.\n\nMethodsWe conducted a retrospective observational study comparing three groups: (1)SARS-CoV-2-naive individuals who received a two-dose regimen of the BioNTech/Pfizer mRNA BNT162b2 vaccine, (2)previously infected individuals who have not been vaccinated, and (3)previously infected and single dose vaccinated individuals. Three multivariate logistic regression models were applied. In all models we evaluated four outcomes: SARS-CoV-2 infection, symptomatic disease, COVID-19-related hospitalization and death. The follow-up period of June 1 to August 14, 2021, when the Delta variant was dominant in Israel.\n\nResultsSARS-CoV-2-naive vaccinees had a 13.06-fold (95% CI, 8.08 to 21.11) increased risk for breakthrough infection with the Delta variant compared to those previously infected, when the first event (infection or vaccination) occurred during January and February of 2021. The increased risk was significant (P<0.001) for symptomatic disease as well. When allowing the infection to occur at any time before vaccination (from March 2020 to February 2021), evidence of waning natural immunity was demonstrated, though SARS-CoV-2 naive vaccinees had a 5.96-fold (95% CI, 4.85 to 7.33) increased risk for breakthrough infection and a 7.13-fold (95% CI, 5.51 to 9.21) increased risk for symptomatic disease. SARS-CoV-2-naive vaccinees were also at a greater risk for COVID-19-related-hospitalizations compared to those that were previously infected.\n\nConclusionsThis study demonstrated that natural immunity confers longer lasting and stronger protection against infection, symptomatic disease and hospitalization caused by the Delta variant of SARS-CoV-2, compared to the BNT162b2 two-dose vaccine-induced immunity. Individuals who were both previously infected with SARS-CoV-2 and given a single dose of the vaccine gained additional protection against the Delta variant.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Sivan Gazit", - "author_inst": "Maccabi Healthcare Services" - }, - { - "author_name": "Roei Shlezinger", - "author_inst": "Kahn Sagol Maccabi (KSM) Research & Innovation Center, Maccabi Healthcare Services, Tel Aviv, 68125, Israel." - }, - { - "author_name": "Galit Perez", - "author_inst": "Kahn Sagol Maccabi (KSM) Research & Innovation Center, Maccabi Healthcare Services, Tel Aviv, 68125, Israel." - }, - { - "author_name": "Roni Lotan", - "author_inst": "Kahn Sagol Maccabi (KSM) Research & Innovation Center, Maccabi Healthcare Services, Tel Aviv, 68125, Israel." - }, - { - "author_name": "Asaf Peretz", - "author_inst": "Internal Medicine COVID-19 Ward, Samson Assuta Ashdod University Hospital, Ashdod Israel" - }, - { - "author_name": "Amir Ben-Tov", - "author_inst": "Kahn Sagol Maccabi (KSM) Research & Innovation Center, Maccabi Healthcare Services, Tel Aviv, 68125, Israel" - }, - { - "author_name": "Dani Cohen", - "author_inst": "Sackler Faculty of Medicine, School of Public Health, Tel Aviv University, Tel Aviv, Israel" - }, - { - "author_name": "Khitam Muhsen", - "author_inst": "Sackler Faculty of Medicine, School of Public Health, Tel Aviv University, Tel Aviv, Israel" - }, - { - "author_name": "Gabriel Chodick", - "author_inst": "Maccabitech Institute for Research and Innovation, Maccabi Healthcare Services, Israel" - }, - { - "author_name": "Tal Patalon", - "author_inst": "Kahn Sagol Maccabi (KSM) Research & Innovation Center, Maccabi Healthcare Services, Tel Aviv, 68125, Israel" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.22.21262216", "rel_title": "COVID-19 and Vitamin D (Co-VIVID Study): a systematic review and meta-analysis of randomized controlled trials", @@ -636950,6 +637708,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.23.21261779", + "rel_title": "Association of cerebral venous thrombosis with recent COVID-19 vaccination: case-crossover study using ascertainment through neuroimaging in Scotland.", + "rel_date": "2021-08-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.23.21261779", + "rel_abs": "ObjectivesTo investigate the association of primary acute cerebral venous thrombosis (CVT) with COVID-19 vaccination through complete ascertainment of all diagnosed CVT in the population of Scotland.\n\nDesignCase-crossover study comparing recent (1-14 days after vaccination) with less recent exposure to vaccination among cases of CVT.\n\nSettingNational data for Scotland from 1 December 2020, with diagnosed CVT case ascertainment through neuroimaging studies up to 17 May 2021 and diagnostic coding of hospital discharges up to 28 April 2021 and with linkage to vaccination records.\n\nMain outcome measurePrimary acute cerebral venous thrombosis\n\nResultsOf 50 primary acute CVT cases, 29 were ascertained only from neuroimaging studies, 2 were ascertained only from hospital discharges, and 19 were ascertained from both sources. Of these 50 cases, 14 had received the Astra-Zeneca ChAdOx1 vaccine and 3 the Pfizer BNT162b2 vaccine. The incidence of CVT per million doses in the first 14 days after vaccination was 2.2 (95% credible interval 0.9 to 4.1) for ChAdOx1 and 1 (95% credible interval 0.1 to 2.9) for BNT162b2. The rate ratio for CVT associated with exposure to ChAdOx1 in the first 14 days compared with exposure 15-84 days after vaccination was 3.2 (95% credible interval 1.1 to 9.5). The 95% credible interval for the rate ratio associated with recent versus less recent exposure to BNT162b2 (0.6 to 95.8) was too wide for useful inference.\n\nConclusionsThese findings support a causal association between CVT and the AstraZeneca vaccine. The absolute risk of post-vaccination CVT in this population-wide study in Scotland was lower than has been reported for populations in Scandinavia and Germany; the explanation for this is not clear.\n\nWhat is already known on this topicThe risk of cerebral venous thrombosis (CVT) within 28 days of receiving the AstraZeneca ChAdOx1 vaccine has been estimated as 18 to 25 per million doses in Germany and Scandinavia, but only 5 per million doses in the UK based on the Yellow Card reporting scheme. Risk estimates based on adverse event reporting systems are subject to under-ascertainment and other biases.\n\nWhat this study addsAll diagnosed cases of CVT in Scotland were ascertained by searching neuroimaging studies from December 2020 to May 2021 and linked to national vaccination records. The risk of CVT within 28 days of vaccination with ChAdOx1 was estimated as 3.5 per million doses with an upper bound of 6 per million doses, against a background incidence of about 12 per million adults per year. This indicates that the Yellow Card system has not seriously underestimated the risk in the UK; the explanation for higher risk in other European countries is not clear.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Paul M McKeigue", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Raj Burgul", + "author_inst": "Forth Valley Royal Hospital" + }, + { + "author_name": "Jennifer Bishop", + "author_inst": "Public Health Scotland" + }, + { + "author_name": "Chris Robertson", + "author_inst": "Department of Mathematics and Statistics, University of Strathclyde" + }, + { + "author_name": "Jim McMenamin", + "author_inst": "Public Health Scotland" + }, + { + "author_name": "Maureen O'Leary", + "author_inst": "Public Health Scotland" + }, + { + "author_name": "David A. McAllister", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Helen M Colhoun", + "author_inst": "University of Edinburgh" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.18.21262187", "rel_title": "Men are the main COVID-19 transmitters: lessons from couples", @@ -637358,97 +638163,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.18.21262061", - "rel_title": "Closed Doors: Predictors of Stress, Anxiety, Depression, and PTSD During the Onset of COVID-19 Pandemic in Brazil", - "rel_date": "2021-08-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.18.21262061", - "rel_abs": "BackgroundThe rise of mental health problems in the population directly or indirectly by the COVID-19 pandemic is a major concern. The aim of this study was to investigate and compare independent predictors of symptoms of stress, anxiety, depression, and post-traumatic stress disorder (PTSD) in Brazilians, one month after the implementation of measures of social distancing.\n\nMethodsIt was a cross-sectional study, performed through a web-based survey. Depression, Anxiety, and Stress Scale (DASS-21) and PTSD Checklist for DSM-5 (PCL-5) were the outcomes. Data were gathered regarding demographics, social distancing, economic problems, exposure to the news of the pandemic, psychiatric history, sleep disturbances, traumatic situations, and substance use. The Alcohol Use Disorders Identification Test - Consumption (AUDIT-C) was also included. Predictors of symptoms were investigated through hierarchical multiple linear regression.\n\nResultOf a sample of 3,587 participants, approximately two-thirds considered that their mental health worsened after the beginning of the social restriction measures. The most important predictors of the symptoms investigated were the intensity of the distress related to pandemic news, younger age, current psychiatric diagnosis, trouble sleeping, emotional abuse or violence, and economic problems.\n\nLimitationsThe convenience sample assessed online may have limited external validity. It does not represent the northern regions of the country and most participants was white wealthier females.\n\nConclusionsThese results confirm the hypothesis that a pandemic would have important impacts on the mental health of the population and indicate the level of distress related to the media as an important predictor of psychological suffering.\n\nHighlightsO_LIDistress triggered by news was the main predictor of psychological symptoms\nC_LIO_LISleeping problems were strong indicators of mental health problems\nC_LIO_LIPeople with ongoing psychiatric disorders are especially vulnerable\nC_LIO_LIMeasures to prevent interpersonal trauma and financial loss are crucial\nC_LIO_LIYoung people may experience great suffering at the onset of the pandemic\nC_LI", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Vitor Crestani Calegaro", - "author_inst": "Universidade Federal de Santa Maria" - }, - { - "author_name": "Luis F Ramos-Lima", - "author_inst": "Universidade Federal do Rio Grande do Sul" - }, - { - "author_name": "Mauricio Scopel Hoffmann", - "author_inst": "Universidade Federal de Santa Maria" - }, - { - "author_name": "Gustavo Zoratto", - "author_inst": "Universidade Federal de Santa Maria" - }, - { - "author_name": "Natalia Kerber", - "author_inst": "Universidade Federal de Santa Maria" - }, - { - "author_name": "Fernanda C Dala Costa", - "author_inst": "Universidade Federal de Santa Maria" - }, - { - "author_name": "Vitor Daniel Picinin", - "author_inst": "Universidade Federal de Santa Maria" - }, - { - "author_name": "Julia Kochler", - "author_inst": "Universidade Federal de Santa Maria" - }, - { - "author_name": "Leonardo Rodrigues", - "author_inst": "Universidade Federal de Santa Maria" - }, - { - "author_name": "Luisa Maciel", - "author_inst": "Universidade Federal de Santa Maria" - }, - { - "author_name": "Luiza Elizabete Braun", - "author_inst": "Universidade Federal de Santa Maria" - }, - { - "author_name": "Fernando Leite Girardi", - "author_inst": "Universidade Federal de Santa Maria" - }, - { - "author_name": "Gabriel O Cecatto", - "author_inst": "Universidade Federal de Santa Maria" - }, - { - "author_name": "Leopoldo Pompeo Weber", - "author_inst": "Universidade Federal de Santa Maria" - }, - { - "author_name": "Bruna Fragoso Rodrigues", - "author_inst": "Universidade Federal de Santa Maria" - }, - { - "author_name": "Alessandra N Bertolazi", - "author_inst": "Universidade Federal de Santa Maria" - }, - { - "author_name": "Juliana Motta de Oliveira", - "author_inst": "Universidade Federal de Santa Maria" - }, - { - "author_name": "Bianca Lorenzi Negretto", - "author_inst": "Instituto de Psiquiatria de Santa Catarina" - }, - { - "author_name": "Andrea Feijo de Mello", - "author_inst": "Universidade Federal de Sao Paulo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.08.18.21262217", "rel_title": "COVID-19 related messaging, beliefs, information sources, and mitigation behaviors in Virginia: A cross-sectional survey in the summer of 2020", @@ -638768,6 +639482,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.18.21262065", + "rel_title": "Vaccine Effectiveness against Referral to Hospital and Severe Lung Injury Associated with COVID-19: A Population-based Case-control Study in St. Petersburg, Russia", + "rel_date": "2021-08-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.18.21262065", + "rel_abs": "BackgroundResults of a randomised trial showed the safety and efficacy of Gam-COVID-Vac against COVID-19. However, compared to other vaccines used across the globe, the real-world data on the effectiveness of Gam-COVID-Vac, especially against the disease caused by Delta variant of concern, was not available. We aimed to assess the effectiveness of vaccination mainly conducted with Gam-COVID-Vac in St. Petersburg, Russia.\n\nMethodsWe designed a case-control study to assess the vaccine effectiveness (VE) against lung injury and referral to hospital. Self-reported vaccination status was collected for individuals with confirmed SARS-CoV-2 infection who were referred for initial low-dose computed tomography triage in two outpatient centres in July 3 - August 9, 2021 in St. Petersburg, Russia. We used logistic regression models to estimate the adjusted (for age, sex, and triage centre) VE for complete (>14 days after the second dose) vaccination. We estimated the VE against referral for hospital admission, COVID-19-related lung injury assessed with LDCT, and decline in oxygen saturation.\n\nResultsIn the final analysis, 13,893 patients were included, 1,291 (9.3%) of patients met our criteria for complete vaccination status, and 495 (3.6%) were referred to hospital. In the primary analysis, the adjusted VE against referral to hospital was 81% (95% CI: 68-88) for complete vaccination. The VE against referral to hospital was more pronounced in women (84%, 95% CI: 66-92) compared to men (76%, 95% CI: 51-88). Vaccine protective effect increased with increasing lung injury categories, from 54% (95% CI: 48-60) against any sign of lung injury to 76% (95% CI: 59-86) against more than 50% lung involvement. A sharp increase was observed in the probability of hospital admission with age for non-vaccinated patients in relation to an almost flat relationship for the completely vaccinated group.\n\nConclusionsCOVID-19 vaccination was effective against referral to hospital in patients with symptomatic SARS-CoV-2 infection in St. Petersburg, Russia. This protection is probably mediated through VE against lung injury associated with COVID-19.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Anton Barchuk", + "author_inst": "European University at St. Petersburg" + }, + { + "author_name": "Mikhail Cherkashin", + "author_inst": "Medical Institute named after Berezin Sergey" + }, + { + "author_name": "Anna Bulina", + "author_inst": "Institute for Interdisciplinary Health Research, European University at St. Petersburg" + }, + { + "author_name": "Natalia Berezina", + "author_inst": "Medical Institute named after Berezin Sergey" + }, + { + "author_name": "Tatyana Rakova", + "author_inst": "Medical Institute named after Berezin Sergey" + }, + { + "author_name": "Darya Kuplevatskaya", + "author_inst": "Medical Institute named after Berezin Sergey" + }, + { + "author_name": "Oksana Stanevich", + "author_inst": "European University at St. Petersburg" + }, + { + "author_name": "Dmitriy Skougarevskiy", + "author_inst": "European University at St. Petersburg" + }, + { + "author_name": "Artemy Okhotin", + "author_inst": "Tarusa Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.23.21262209", "rel_title": "Population birth outcomes in 2020 and experiences of expectant mothers during the COVID-19 pandemic: a Born in Wales mixed methods study using routine data", @@ -639440,45 +640205,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.08.23.457328", - "rel_title": "Presence and Stability of SARS-CoV-2 on Environmental Currency and Money Cards", - "rel_date": "2021-08-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.23.457328", - "rel_abs": "The highly contagious nature of SARS-CoV-2 has led to several studies on the transmission of the virus. A little studied potential fomite of great concern in the community is currency, which has been shown to harbor microbial pathogens in several studies. Since the onset of the COVID-19 pandemic, many businesses in the United States have limited the use of banknotes in favor of credit cards. However, SARS-CoV-2 has shown greater stability on plastic in several studies. Herein, the stability of SARS-CoV-2 at room temperature on banknotes, money cards and coins was investigated. In vitro studies with live virus suggested SARS-CoV-2 was highly unstable on banknotes, showing an initial rapid reduction in viable virus and no viral detection by 24 hours. In contrast, SARS-CoV-2 was far more stable on money cards with live virus detected after 48 hours. Environmental swabbing of currency and money cards on and near the campus of Brigham Young University supported these results, with no detection of SARS-CoV-2 RNA on banknotes, and a low level on money cards. No viable virus was detected on either. These preliminary results suggest that the use of money cards over banknotes in order to slow the spread of this virus may be ill-advised. These findings should be investigated further through larger environmental studies involving more locations.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Colleen Newey", - "author_inst": "Brigham Young University-Provo: Brigham Young University" - }, - { - "author_name": "Abigail T Olausson", - "author_inst": "Brigham Young University-Provo: Brigham Young University" - }, - { - "author_name": "Alyssa Applegate", - "author_inst": "Brigham Young University-Provo: Brigham Young University" - }, - { - "author_name": "Ann Aubrey Reid", - "author_inst": "Brigham Young University-Provo: Brigham Young University" - }, - { - "author_name": "Richard A Robison", - "author_inst": "Brigham Young University-Provo: Brigham Young University" - }, - { - "author_name": "Julianne H. Grose", - "author_inst": "Brigham Young University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.08.19.21262292", "rel_title": "Seroresponse to SARS-CoV-2 vaccines among maintenance dialysis patients", @@ -640806,6 +641532,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.19.21262267", + "rel_title": "The burden of isolation to the individual: a comparison between isolation for COVID-19 and for other influenza-like illnesses in Japan", + "rel_date": "2021-08-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.19.21262267", + "rel_abs": "At present, there is scarce evidence about how much burden the isolation of COVID-19 patients is. We aimed to assess the differences between COVID-19 and other influenza like illnesses in disease burden brought by isolation. We conducted an online questionnaire survey of 302 people who had COVID-19 or other influenza-like illnesses (ILIs) and compared the burden of isolation due to sickness with one-to-one propensity score matching. The primary outcomes are the duration and productivity losses of isolation, the secondary outcome is quality of life (QOL) valuation on the day of the survey. Acute symptoms of outpatient COVID-19 and other ILIs lasted 17 (interquartile range [IQR] 9-32) and 7 (IQR 4-10) days, respectively. The length of isolation due to COVID-19 was 18 (IQR 10-33) days and that due to other ILIs was 7 (IQR 4-11) days, respectively. The monetary productivity loss of isolation due to COVID-19 was 1424.3 (IQR 825.6-2545.5) USD and that due to other ILIs was 606.1 (IQR 297.0-1090.9) USD, respectively. QOL at the time of the survey was lower in the COVID-19 group than in the \"other ILIs\" group (0.89 and 0.96, p = 0.001). COVID-19 infection imposes a substantial disease burden, even in patients with non-severe disease. This burden is larger for COVID-19 than other ILIs, mainly because the required isolation period is longer.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Shinya Tsuzuki", + "author_inst": "University of Antwerp" + }, + { + "author_name": "Norio Ohmagari", + "author_inst": "National Center for Global Health and Medicine" + }, + { + "author_name": "Philippe Beutels", + "author_inst": "University of Antwerp" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.15.21261243", "rel_title": "Self-testing and vaccination against COVID-19 to minimize school closure", @@ -641234,65 +641987,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.15.21262087", - "rel_title": "The impact of ongoing COVID-19 lockdown on family finances and mental health", - "rel_date": "2021-08-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.15.21262087", - "rel_abs": "ObjectivesIn 2020, Australias successful COVID-19 public health restrictions comprised a national initial lockdown (March-May), and ongoing lockdown (July-November) for metropolitan Victorian residents only. We evaluated the relationships between ongoing lockdown and family finances and mental health.\n\nMethodsIn the June and September 2020 Royal Childrens Hospital National Child Health Polls, caregivers of children in Victoria and New South Wales reported: job/income loss; material deprivation (inability to pay for essential items); income-poverty; mental health (Kessler-6); perceived impact on caregiver/child mental health; and caregiver/child coping. Data from N=1207/902 caregivers in June/September were analysed using Difference-in-Difference modelling (New South Wales provided the comparator).\n\nResultsDuring Victorias ongoing lockdown, job/income loss increased by 11% (95%CI: 3-18%); Kessler-6 poor mental health by 6% (95%CI: -0.3-12%) and perceived negative mental health impacts by 14% for caregivers (95%CI: 6-23%) and 12% for children (95%CI: 4-20%). Female (versus male) caregivers, metropolitan (versus regional/rural) families, and families with elementary school-aged children (versus pre-/high-school) were most affected.\n\nConclusionsOngoing lockdown was associated with negative experiences of mental health, employment, and income, but not deprivation or poverty, likely because of government income supplements introduced early in the pandemic. Future lockdowns require planned responses to outbreaks, and evidence-informed financial and mental health supports.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Anna Price", - "author_inst": "Centre for Community Child Health, Murdoch Children's Research Institute" - }, - { - "author_name": "Diana Contreras-Su\u00e1rez", - "author_inst": "Melbourne Institute: Applied Economic & Social Research" - }, - { - "author_name": "Anna Zhu", - "author_inst": "RMIT University" - }, - { - "author_name": "Natalie Schreurs", - "author_inst": "Centre for Community Child Health, Murdoch Children's Research Institute" - }, - { - "author_name": "Mary-Anne Measey", - "author_inst": "Royal Children's Hospital, Melbourne" - }, - { - "author_name": "Susan Woolfenden", - "author_inst": "University of NSW" - }, - { - "author_name": "Jade Burley", - "author_inst": "University of NSW" - }, - { - "author_name": "Hannah Bryson", - "author_inst": "Centre for Community Child Health, Murdoch Children's Research Institute" - }, - { - "author_name": "Daryl Efron", - "author_inst": "Royal Children's Hospital, Melbourne" - }, - { - "author_name": "Anthea Rhodes", - "author_inst": "Royal Children's Hospital, Melbourne" - }, - { - "author_name": "Sharon Goldfeld", - "author_inst": "Centre for Community Child Health, Murdoch Children's Research Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.08.16.21262115", "rel_title": "Diminishing immune responses against variants of concern in dialysis patients four months after SARS-CoV-2 mRNA vaccination", @@ -642540,6 +643234,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, + { + "rel_doi": "10.1101/2021.08.13.21262037", + "rel_title": "Early Reduction of SARS-CoV-2 Replication in Bronchial Epithelium by Kinin B2 Receptor Antagonism", + "rel_date": "2021-08-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.13.21262037", + "rel_abs": "BackgroundSARS-CoV2 has evolved to enter the host via the ACE2 receptor which is part of the Kinin-kallirein pathway. This complex pathway is only poorly understood in context of immune regulation but critical to control infection. This study examines SARS-CoV2 infection and epithelial mechanisms of the kinin-kallikrein system at the kinin B2 receptor level in SARS-CoV-2 infection that is of direct translational relevance.\n\nMethodsFrom acute SARS-CoV-2-positive patients and -negative controls, transcriptomes of nasal brushings were analyzed. Primary airway epithelial cells (NHBEs) were infected with SARS-CoV-2 and treated with the approved B2R antagonist icatibant. SARS-CoV-2 RNA RT-qPCR, cytotoxicity assays, plaque assays and transcriptome analyses were performed. The treatment effect was further studied in a murine airway inflammation model in vivo.\n\nResultsHere, we report a broad and strong upregulation of kallikreins and the kinin B2 receptor (B2R) in the nasal mucosa of acutely symptomatic SARS-CoV-2-positive patients. A B2R antagonist impeded SARS-CoV-2 replication and spread in NHBEs, as determined in plaque assays on Vero E6 cells. B2R antagonism reduced the expression of SARS-CoV-2 entry receptor ACE2 in vitro and in a murine airway inflammation model in vivo. In addition, it suppressed gene expression broadly, particularly genes involved in G-protein-coupled-receptor signaling and ion transport.\n\nConclusionsIn summary, this study provides evidence that treatment with B2R antagonists protects airway epithelial cells from SARS-CoV-2 by inhibiting its replication and spread, through the reduction of ACE2 levels and the interference with several cellular signaling processes. Future clinical studies need to shed light on the airway protection potential of approved B2R antagonists, like icatibant, in the treatment of early-stage COVID-19.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Constanze A. Jakwerth", + "author_inst": "Center of Allergy & Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, German Research Center for Environmental Health, Member of t" + }, + { + "author_name": "Martin Feuerherd", + "author_inst": "Institute of Virology, Technical University of Munich/Helmholtz Center Munich, Munich, Germany; German Center of Infectiology Research (DZIF)" + }, + { + "author_name": "Ferdinand M. Guerth", + "author_inst": "Center of Allergy & Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, German Research Center for Environmental Health, Member of t" + }, + { + "author_name": "Madlen Oelsner", + "author_inst": "Center of Allergy & Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, German Research Center for Environmental Health, Member of t" + }, + { + "author_name": "Linda Schellhammer", + "author_inst": ") Institute of Laboratory Animal Science, University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Johanna Giglberger", + "author_inst": "Center of Allergy & Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, German Research Center for Environmental Health, Member of t" + }, + { + "author_name": "Lisa Pechtold", + "author_inst": "Department of Otorhinolaryngology and Head and Neck Surgery, Medical School, Technical University of Munich" + }, + { + "author_name": "Claudia Jerin", + "author_inst": "Center of Allergy & Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, German Research Center for Environmental Health, Member of t" + }, + { + "author_name": "Luisa Kugler", + "author_inst": "Department of Otorhinolaryngology and Head and Neck Surgery, Medical School, Technical University of Munich" + }, + { + "author_name": "Carolin Mogler", + "author_inst": "Institute of Pathology, Technical University Munich, Munich, Germany" + }, + { + "author_name": "Bernhard Haller", + "author_inst": "Institute of Medical Informatics, Statistics and Epidemiology, Medical School, Technical University of Munich" + }, + { + "author_name": "Anna Erb", + "author_inst": "Center of Allergy & Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, German Research Center for Environmental Health, Member of t" + }, + { + "author_name": "Barbara Wollenberg", + "author_inst": "Department of Otorhinolaryngology and Head and Neck Surgery, Medical School, Technical University of Munich" + }, + { + "author_name": "Christoph D. Spinner", + "author_inst": "Department of Internal Medicine II, University Hospital rechts der Isar, Medical School, Technical University of Munich" + }, + { + "author_name": "Thorsten Buch", + "author_inst": "Institute of Laboratory Animal Science, University of Zurich, Zurich, Switzerland" + }, + { + "author_name": "Ulrike Protzer", + "author_inst": "Institute of Virology, Technical University of Munich/Helmholtz Center Munich, Munich, Germany; German Center of Infectiology Research (DZIF), Munich partner si" + }, + { + "author_name": "Carsten B. Schmidt-Weber", + "author_inst": "Center of Allergy & Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, German Research Center for Environmental Health, Member of t" + }, + { + "author_name": "Ulrich M. Zissler", + "author_inst": "Center of Allergy & Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, German Research Center for Environmental Health, Member of t" + }, + { + "author_name": "Adam M. Chaker", + "author_inst": "Department of Otorhinolaryngology and Head and Neck Surgery, Medical School, Technical University of Munich" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.11.21261670", "rel_title": "A third COVID-19 vaccine shot markedly boosts neutralizing antibody potency and breadth", @@ -643084,57 +643869,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.14.21261996", - "rel_title": "Association between interruption to medical care and sickness presenteeism during the COVID-19 pandemic: a cross-sectional study in Japan", - "rel_date": "2021-08-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.14.21261996", - "rel_abs": "ObjectivesThis study examined the relationship between interruption to routine medical care during the coronavirus disease 2019 pandemic and sickness presenteeism among workers in Japan.\n\nMethodsA cross-sectional study using data obtained from an internet monitor questionnaire was conducted. Interruption to medical care was defined based on the response \"I have not been able to go to the hospital or receive treatment as scheduled.\" The fraction of sickness presenteeism days in the past 30 days was employed as the primary outcome. A fractional logit model was used for analysis to treat bounded data.\n\nResultsOf the 27,036 participants, 17,526 (65%) were workers who did not require routine medical care, 8,451 (31%) were using medical care as scheduled, and 1,059 (4%) experienced interrupted medical care. The adjusted odds ratio (aOR) of sickness presenteeism was significantly higher among workers who experienced interrupted medical care (3.44; 95% confidence interval [CI]: 3.04-3.89) than those who did not require routine medical care. In terms of symptoms, the highest aOR was observed among workers with mental health symptoms (aOR: 5.59, 95%CI: 5.04-6.20).\n\nConclusionsThis study suggests the importance of continuing necessary treatment during a pandemic to prevent presenteeism.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Makoto Okawara", - "author_inst": "Department of Environmental Epidemiology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Tomohiro Ishimaru", - "author_inst": "Department of Environmental Epidemiology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Seiichiro Tateishi", - "author_inst": "Department of Occupational Medicine, School of Medicine, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Ayako Hino", - "author_inst": "Department of Mental Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Mayumi Tsuji", - "author_inst": "Department of Environmental Health, School of Medicine, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Akira Ogami", - "author_inst": "Department of Work Systems and Health, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Tomohisa Nagata", - "author_inst": "Department of Occupational Health Practice and Management, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Jap" - }, - { - "author_name": "Shinya Matsuda", - "author_inst": "Department of Preventive Medicine and Community Health, School of Medicine, University of Occupational and Environmental Health, Japan" - }, - { - "author_name": "Yoshihisa Fujino", - "author_inst": "Department of Environmental Epidemiology, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.08.16.21262016", "rel_title": "Longitudinal changes in age and race of patients with SARS-CoV-2 in a multi-hospital health system", @@ -644334,6 +645068,37 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.08.18.456769", + "rel_title": "Interaction between spike protein of SARS-CoV-2 and human virus receptor ACE2 using two-color fluorescence cross-correlation spectroscopy", + "rel_date": "2021-08-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.18.456769", + "rel_abs": "Infection with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), is initiated by the interaction between a receptor protein, angiotensin-converting enzyme type 2 (ACE2) on the cell surface, and the viral spike (S) protein. This interaction is similar to the mechanism in SARS-CoV, a close relative of SARS-CoV-2, which was identified in 2003. Drugs and antibodies that inhibit the interaction between ACE2 and S proteins could be key therapeutic methods for preventing viral infection and replication in COVID-19. Here, we demonstrate the interaction between human ACE2 and a fragment of the S protein (S1 subunit) derived from SARS-CoV-2 and SARS-CoV using two-color fluorescence cross-correlation spectroscopy (FCCS), which can detect the interaction of fluorescently labeled proteins. The S1 subunit of SARS-CoV-2 interacted in solution with soluble ACE2, which lacks a transmembrane region, more strongly than that of SARS-CoV. Furthermore, one-to-one stoichiometry of the two proteins during the interaction was indicated. Thus, we propose that this FCCS-based interaction detection system can be used to analyze the interaction strengths of various mutants of the S1 subunit that have evolved during the worldwide pandemic, and also offers the opportunity to screen and evaluate the performance of drugs and antibodies that inhibit the interaction.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Ai Fujimoto", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Yidan Lyu", + "author_inst": "Hokkaido Univeristy" + }, + { + "author_name": "Masataka Kinjo", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Akira Kitamura", + "author_inst": "Hokkaido University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.08.18.456855", "rel_title": "Cap-independent translation and a precisely localized RNA sequence enable SARS-CoV-2 to control host translation and escape anti-viral response", @@ -644706,97 +645471,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.15.21262000", - "rel_title": "Seasonal betacoronavirus antibodies expansion post BNT161b2 vaccination associates with reduced SARS-CoV-2 VoCs neutralization", - "rel_date": "2021-08-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.15.21262000", - "rel_abs": "SARS-CoV-2 vaccination is known to induce antibodies that recognize also variants of concerns (VoCs) of the virus. However, epidemiological and laboratory evidences indicate that these antibodies have a reduce neutralization ability against VoCs. We studied binding and neutralizing antibodies against the Spike RBD and S2 domains of the Wuhan-Hu-1 virus and its alpha and beta VoCs and of seasonal betacoronaviruses (HKU1 and OC43) in a cohort of 31 health care workers vaccinated with BNT162b2-Comirnaty and prospectively followed post-vaccination. The study of sequential samples collected up to 64 days post-vaccination showed that serological assays measuring IgG against Wuhan-Hu-1 antigens were a poor proxy for VoCs neutralization. In addition, in subjects who had asymptomatic or mild COVID-19 prior to vaccination the loss of nAbs following disease can be rapid and protection from re-infection post-vaccination is often no better than in naive subjects. Interestingly, in health care workers naive for SARS-CoV-2 infection, vaccination induced a rapid and transient reactivation of pre-existing seasonal coronaviruses IgG responses that was associated with a subsequent reduced ability to neutralize some VoCs.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Stefania Dispinseri", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Ilaria Marzinotto", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Cristina Brigatti", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Maria Franca Pirillo", - "author_inst": "Istituto Superiore di Sanit\u00e0" - }, - { - "author_name": "Monica Tolazzi", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Elena Bazzigaluppi", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Andrea Canitano", - "author_inst": "Istituto Superiore di Sanit\u00e0" - }, - { - "author_name": "Martina Borghi", - "author_inst": "Istituto Superiore di Sanit\u00e0" - }, - { - "author_name": "Alessandra Gallinaro", - "author_inst": "Istituto Superiore di Sanit\u00e0" - }, - { - "author_name": "Roberta Caccia", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Riccardo Vercesi", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Paul F McKay", - "author_inst": "Imperial College" - }, - { - "author_name": "Fabio Ciceri", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Lorenzo Piemonti", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Donatella Negri", - "author_inst": "Istituto Superiore di Sanit\u00e0" - }, - { - "author_name": "Paola Cinque", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Andrea Cara", - "author_inst": "Istituto Superiore di Sanit\u00e0" - }, - { - "author_name": "Vito Lampasona", - "author_inst": "IRCCS Ospedale San Raffaele" - }, - { - "author_name": "Gabriella Scarlatti", - "author_inst": "IRCCS Ospedale San Raffaele" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.16.456441", "rel_title": "T Cell Predominant Response to AAV-Spike Protects hACE2 Mice from SARS-CoV-2 Pneumonia", @@ -646004,6 +646678,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.08.12.21261952", + "rel_title": "DECREASED BREADTH OF THE ANTIBODY RESPONSE TO THE SPIKE PROTEIN OF SARS-CoV-2 AFTER VACCINATION", + "rel_date": "2021-08-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.12.21261952", + "rel_abs": "The rapid development of vaccines to prevent infection by SARS-CoV-2 virus causing COVID-19 makes necessary to compare the capacity of the different vaccines in terms of development of a protective humoral response. Here, we have used a highly sensitive and reliable flow cytometry method to measure the titers of antibodies of the IgG1 isotype in blood of healthy volunteers after receiving one or two doses of the vaccines being administered in Spain. We took advantage of the multiplexed capacity of the method to measure simultaneously the reactivity of antibodies with the S protein of the original strain Wuhan and the variants B.1.1.7 (Alpha), B.1.617.2 (Delta) and B.1.617.1 (Kappa). We found significant differences in the titer of anti-S antibodies produced after a first dose of the vaccines ChAdOx1 nCov-19/AstraZeneca, mRNA-1273/Moderna, BNT162b2/Pfizer-BioNTech and Ad26.COV.S/Janssen. Most important, we found a relative reduction in the reactivity of the sera with the Alpha, Delta and Kappa variants, versus the Wuhan one, after the second boosting immunization. These data allow to make a comparison of different vaccines in terms of anti-S antibody generation and cast doubts about the convenience of repeatedly immunizing with the same S protein sequence.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Lydia Horndler", + "author_inst": "Centro de Biologia Molecular Severo Ochoa" + }, + { + "author_name": "Pilar Delgado", + "author_inst": "Centro de Biologia Molecular Severo Ochoa" + }, + { + "author_name": "Salvador Romero-Pinedo", + "author_inst": "VITRO SA" + }, + { + "author_name": "Marina Quesada", + "author_inst": "VITRO SA" + }, + { + "author_name": "Ivaylo Balabanov", + "author_inst": "Centro de Biologia Molecular Severo Ochoa" + }, + { + "author_name": "Rocio Laguna-Goya", + "author_inst": "Hospital 12 de Octubre" + }, + { + "author_name": "Patricia Almendro-Vazquez", + "author_inst": "Hospital 12 de Octubre" + }, + { + "author_name": "Miguel A Llamas", + "author_inst": "EMPIREO SL" + }, + { + "author_name": "Manuel Fresno", + "author_inst": "Centro de Biologia Molecular Severo Ochoa" + }, + { + "author_name": "Estela Paz-Artal", + "author_inst": "Hospital 12 de Octubre" + }, + { + "author_name": "Hisse M van Santen", + "author_inst": "Centro de Biologia Molecular Severo Ochoa" + }, + { + "author_name": "Stela Alvarez", + "author_inst": "VITRO SA" + }, + { + "author_name": "Asuncion Olmo", + "author_inst": "VITRO SA" + }, + { + "author_name": "Balbino Alarcon", + "author_inst": "Centro de Biologia Molecular Severo Ochoa" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.11.21261914", "rel_title": "A Third Dose of SARS-CoV-2 Vaccine Increases Neutralizing Antibodies Against Variants of Concern in Solid Organ Transplant Recipients", @@ -646420,61 +647165,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2021.08.11.21261793", - "rel_title": "Development and use analysis of 'gestioemocional.cat', a web app for promoting emotional self-care and access to professional mental health resources during the covid-19 pandemic", - "rel_date": "2021-08-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.11.21261793", - "rel_abs": "BackgroundQuarantines and nationwide lockdowns dictated for containing the spread of the COVID-19 pandemic may lead to distress and increase the frequency of anxiety and depression symptoms among the general population. During the national lockdown of the first wave of the COVID-19 outbreak in Spain, we developed and launched a Web App (Gestioemocional.cat) to promote emotional self-care in the general population and facilitate contact with healthcare professionals.\n\nMethodsGestioemocional.cat targeted all individuals aged 18 years or more and was designed by adapting the contents of a mobile App for adjuvant treatment of post-traumatic stress disorder (i.e., the PTSD Coach App) to the general population and the pandemic/lockdown scenario. We retrospectively assessed the utilization pattern of the Web App using data systematically retrieved from Google Analytics. Data were grouped into three time periods, defined using a join point analysis of COVID-19 incidence in our area: first wave, between-wave period, and second wave.\n\nResultsThe resulting Web App, maintains the navigation structure of the PTSD Coach App, with three main modules: tools for emotional self-care, a self-assessment test, and professional resources for on-demand contact. The self-assessment test combines the Patient Health Questionnaire-2 (PHQ-2) and the 7-item Generalized Anxiety Disorder Scale (GAD-7) and offers professional contact in the advent of a high level of depression and anxiety; contact is prioritized according to a screening questionnaire administered at the time of obtaining individual consent to be contacted. The tools for emotional self-care can be accessed either on-demand or symptom-driven. The utilization analysis showed a high number of weekly accesses during the first wave. In this period, press releases regarding critical events of the pandemic progression and government decisions on containment measures were followed by a utilization peak, irrespective of the sense (i.e., positive or negative) of the information. Positive information pieces (e.g., relaxation of containment measures due to a reduction of COVID-19 cases) resulted in a sharp increase in utilization immediately after information release, followed by a successive decline in utilization. The second wave was characterized by a lower and less responsive utilization of the Web App.\n\nConclusionsmHealth tools may help the general population coping with stressful conditions associated with the pandemic scenario. Future studies shall investigate the effectiveness of these tools among the general population[-]including individuals without diagnosed mental illnesses[-]and strategies to reach as many people as possible.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Sara Guila Fidel-Kinori", - "author_inst": "Vall d'Hebron University Hospital, Barcelona, Spain" - }, - { - "author_name": "Gerard Carot-Sans", - "author_inst": "Catalan Health Service, Barcelona, Spain" - }, - { - "author_name": "Andr\u00e9s Cuartero-Barbanoj", - "author_inst": "Sistema d'Emerg\u00e8ncies M\u00e8diques, L'Hospitalet de Llobregat, Spain" - }, - { - "author_name": "Dami\u00e0 Valero", - "author_inst": "Catalan Health Service, Barcelona, Spain" - }, - { - "author_name": "Jordi Piera-Jim\u00e9nez", - "author_inst": "Catalan Health Service, Barcelona, Spain" - }, - { - "author_name": "Rosa Rom\u00e0-Monf\u00e0", - "author_inst": "Catalan Health Service, Barcelona, Spain" - }, - { - "author_name": "Elisabet Garcia-Ribatallada", - "author_inst": "Catalan Health Service, Barcelona, Spain" - }, - { - "author_name": "Pol P\u00e9rez-Sust", - "author_inst": "Catalan Health Service, Barcelona, Spain" - }, - { - "author_name": "Jordi Blanch-Andreu", - "author_inst": "Catalan Health Service, Barcelona, Spain" - }, - { - "author_name": "Josep Antoni Ramos-Quiroga", - "author_inst": "Vall d'Hebron University Hospital, Barcelona, Spain" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.08.12.21261462", "rel_title": "Field performance of NowCheck Rapid antigen test for SARS-CoV-2 in Kisumu County, western Kenya", @@ -647842,6 +648532,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.08.12.21261976", + "rel_title": "The production of anti-PF4 antibodies in anti-phospholipid antibody-positive patients is not affected by COVID-19 vaccination", + "rel_date": "2021-08-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.12.21261976", + "rel_abs": "Antibodies against cationic platelet chemokine, platelet factor 4 (PF4/CXCL4) have been described in heparin-induced thrombocytopenia (HIT) but also in patients positive for anti-phospholipid antibodies (aPL) even in the absence of heparin treatment and HIT-related clinical manifestations. Anti-PF4 antibodies have been recently described also in subjects who developed thrombosis with thrombocytopenia syndrome (TTS) in association with adenoviral vector-based, but not with mRNA-based COVID-19 vaccines.\n\nWe investigated whether COVID-19 vaccination affects the production of anti-PF4 immunoglobulins detectable by solid phase assay in aPL-positive patients and their ability to induce in vitro platelet activation. Anti-PF4 were found in 9/126 aPL-positive patients, 4/50 COVID-19, 9/49 other infections and 1/50 aPL-negative systemic lupus erythematosus patients. Clinical manifestations of TTS were not observed in any aPL patient positive for anti-PF4, whose sera failed to cause platelet aggregations. The administration of COVID-19 vaccines did not affect the production of anti-PF4 immunoglobulins or their ability to cause platelet aggregation in 44 aPL-positive patients tested before and after vaccination. In conclusion, heparin treatment-independent anti-PF4 antibodies can be found in aPL-positive patients and asymptomatic carriers, but their presence, titer as well as in vitro effect on platelet activation are not affected by COVID-19 vaccination.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Paola Lonati", + "author_inst": "Istituto Auxologico Italiano" + }, + { + "author_name": "Caterina Bodio", + "author_inst": "Istituto Auxologico Italiano" + }, + { + "author_name": "Mariangela Scavone", + "author_inst": "Health Sciences Department, University of Milan, Milan, ITALY" + }, + { + "author_name": "Giuliana Martini", + "author_inst": "Centro Emostasi, Laboratorio Analisi Chimico-Cliniche, ASST-Spedali Civili, Brescia, Italy" + }, + { + "author_name": "Elisa Pesce", + "author_inst": "National Institute of Molecular Genetics" + }, + { + "author_name": "Alessandra Bandera", + "author_inst": "Department of Pathophysiology and Transplantation, University of Milan; Infectious Diseases Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Mil" + }, + { + "author_name": "Andrea Lombardi", + "author_inst": "Department of Pathophysiology and Transplantation, University of Milan; Infectious Diseases Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Mil" + }, + { + "author_name": "Maria Gerosa", + "author_inst": "Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy" + }, + { + "author_name": "Franco Franceschini", + "author_inst": "Department of Clinical and Experimental Sciences, University of Brescia; Unit of Rheumatology and Clinical Immunology, ASST Spedali Civili, Brescia, Italy" + }, + { + "author_name": "Angela Tincani", + "author_inst": "Department of Clinical and Experimental Sciences, University of Brescia; Unit of Rheumatology and Clinical Immunology, ASST Spedali Civili, Brescia, Italy" + }, + { + "author_name": "Gianmarco Podda", + "author_inst": "Health Sciences Department, University of Milan, Milan, Italy" + }, + { + "author_name": "Sergio Abrignani", + "author_inst": "National Institute Molecular Genetics; UniversityMilan, Milan, Italy" + }, + { + "author_name": "Renata Grifantini", + "author_inst": "National Institute Molecular Genetics, Milan, Italy" + }, + { + "author_name": "Marco Cattaneo", + "author_inst": "Health Sciences Department, University of Milan, Milan, Italy" + }, + { + "author_name": "Maria Orietta Borghi", + "author_inst": "Department of Clinical Sciences and Community Health, University of Milan; Istituto Auxologico Italiano, Milan, Italy" + }, + { + "author_name": "Pier Luigi Meroni", + "author_inst": "IRCCS Istituto Auxologico Italiano" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "rheumatology" + }, { "rel_doi": "10.1101/2021.08.12.21261987", "rel_title": "Characterising the persistence of RT-PCR positivity and incidence in a community survey of SARS-CoV-2", @@ -648270,45 +649039,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.08.13.456066", - "rel_title": "SARS-CoV-2 Neutralization in Commercial Lots of Plasma-derived Immunoglobulin", - "rel_date": "2021-08-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.13.456066", - "rel_abs": "IntroductionPatients suffering from primary or secondary immunodeficiency (PID or SID) face times of increased insecurity and discomfort in the light of the raging COVID-19 pandemic, not knowing if and to what extent their comorbidities impact the course of a potential SARS-CoV-2 infection. Furthermore, recently available vaccination options might not be amenable or effective for all patients of this heterogeneous population. Therefore, these patients often rely on passive immunization with plasma-derived, intravenous or subcutaneous immunoglobulin (IVIG/SCIG).\n\nWhether the ongoing COVID-19 pandemic and/or the progress in vaccination programs lead to increased and potentially protective titers in plasma-derived immunoglobulins (Ig) indicated, e.g., for humoral immunodeficiency remains a pressing question for this patient population.\n\nPurposeWe investigated SARS-CoV-2 reactivity of US plasma-derived IVIG/SCIG products from the end of 2020 until 06/2021 as well as in convalescent plasma (CP) from 05/2020 to 08/2020 to determine whether potentially neutralizing antibody titers may be present.\n\nMethodsFinal containers of IVIG/SCIG and CP donations were analyzed by commercial ELISA for anti-SARS-CoV-2 S1-receptor binding domain (RBD) IgG as well as microneutralization assay using a patient-derived SARS-CoV-2 (D614G) isolate. Neutralization capacities of 313 plasma single donations and 119 plasma-derived IVIG/SCIG lots were determined. Results obtained from both analytical methods were normalized against the WHO International Standard. Finally, based on dense pharmacokinetic (PK) profiles of an IVIG preparation from previously published investigations, possible steady-state plasma levels of SARS-CoV-2 neutralization capacities were approximated based on currently measured anti-SARS-CoV-2 potencies in IVIG/SCIG preparations.\n\nResultsCP donations presented with a high variability with regards to anti-SARS-CoV-2 reactivity in ELISA as well as in neutralization testing. While approximately 50% of convalescent donations were none/low neutralizing, approximately 10% were at or above 1000 IU/mL.\n\nIVIG/SCIG lots derived from pre-pandemic plasma donations did not show neutralizing capacities of SARS-CoV-2. Lots produced between 12/2020 and 06/2021, entailing plasma donations after the emergence of SARS-CoV-2 showed a rapid and constant increase in anti-SARS-CoV-2 reactivity and neutralization capacity over time. While lot-to-lot variability was substantial, neutralization capacity increased from a mean of 20 IU/mL in 12/2020 to 505 IU/mL in 06/2021 with a maximum of 864 IU/mL for the most recent lots.\n\nPharmacokinetic extrapolations, based on non-compartmental superposition principles using steady-state reference profiles from previously published PK investigations on IVIG in PID, yielded potential steady-state trough plasma levels of 16 IU/mL of neutralizing SARS-CoV-2 IgG based on the average final container concentration from 05/2021 of 216 IU/mL. Maximum extrapolated trough levels could reach 64 IU/mL based on the latest maximal final container potency tested in 06/2021.\n\nConclusionsSARS-CoV-2 reactivity and neutralization capacity in IVIG/SCIG produced from US plasma rapidly and in part exponentially increased in the first half of 2021. The observed increase of final container potencies is likely trailing the serological status of the US donor population in terms of COVID-19 convalescence and vaccination by at least 5 months due to production lead times and should in principle continue at least until fall 2021. In summary, the data support rapidly increasing levels of anti-SARS-CoV-2 antibodies in IVIG/SCIG products implicating that a certain level of protection could be possible against COVID-19 for regularly substituted PID/SID patients. Nevertheless, more research is still needed to confirm which plasma levels are needed to provide protection against SARS-CoV-2 infection in immune-compromised patients.\n\nPlain Language SummaryPeople with deficiencies in their immune system often have an insufficient antibody response to antigens, e.g., bacteria, viruses, or vaccines. These patients therefore often receive antibodies from healthy people to replace the missing antibodies and build a first line of defense against infections. These antibodies (also called immunoglobulins (Ig)) are prepared from plasma of healthy donors, the liquid fraction of the blood without cells. This plasma is then split up in pharmaceutical production into its protein components. One of these is immunoglobulin G (IgG), which is the protein family that neutralizes/inactivates infectious agents as well as marks these infectious agents so they can be recognized by other parts of the immune system. With the ongoing COVID-19 pandemic and the severe to fatal outcomes for certain patient groups, especially people with impaired immunity, these patients and their physicians are interested in whether their antibody replacement therapy also confers protection against SARS-CoV-2 infection. We analyzed the capability of plasma-derived Ig lots to (i) recognize SARS-CoV-2 protein by ELISA method as well as (ii) neutralize SARS-CoV-2 by neutralization studies using the actual virus under biosafety level 3 (BSL-3) conditions. Here we show increasing anti-SARS-CoV-2 activity over time of manufactured Ig lots produced between 12/2020 and 06/2021. The most recent lots had a neutralizing activity of up to 864 IU/mL. Considering that the USA represents Octapharmas main plasma source, the progress in vaccination levels together with the evolution of the COVID-19 pandemic in this country suggests that the IVIG/SCIG neutralization capacities against SARS-CoV-2 might still increase and could potentially meet a level where antibody plasma concentrations in the patient confer immune protection.\n\nKey PointsO_LIPatients with humoral immunodeficiency rely on plasma-derived immunoglobulin for passive immunization against numerous pathogens.\nC_LIO_LISARS-CoV-2 neutralization capacities of plasma-derived immunoglobulins have increased over time with the ongoing COVID-19 pandemic and vaccination campaigns.\nC_LIO_LIPlasma-derived immunoglobulin in prophylactic use for immunodeficient patients could potentially protect against SARS-CoV-2 infection in the future.\nC_LI", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Andreas Volk", - "author_inst": "Octapharma Biopharmaceuticals GmbH, Virus and Prion Validation, Frankfurt, Germany" - }, - { - "author_name": "Caroline Covini-Souris", - "author_inst": "Octapharma Pharmazeutika Produktionsgesellschaft m.b.H., R&D Plasma, Vienna, Austria" - }, - { - "author_name": "Denis Kuehnel", - "author_inst": "Octapharma Biopharmaceuticals GmbH, Virus and Prion Validation, Frankfurt, Germany" - }, - { - "author_name": "Christian de Mey", - "author_inst": "ACPS-Network GmbH, Wiesbaden, Germany" - }, - { - "author_name": "Juergen Roemisch", - "author_inst": "Octapharma Pharmazeutika Produktionsgesellschaft m.b.H., R&D Plasma, Vienna, Austria" - }, - { - "author_name": "Torben Schmidt", - "author_inst": "Octapharma Biopharmaceuticals GmbH, Virus and Prion Validation, Frankfurt, Germany" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.08.13.456258", "rel_title": "Covid-19 vaccine immunogenicity in people living with HIV-1", @@ -650016,6 +650746,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2021.08.10.21261726", + "rel_title": "COVID-19 Projections for K12 Schools in Fall 2021: Significant Transmission without Interventions", + "rel_date": "2021-08-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.10.21261726", + "rel_abs": "BackgroundMillions of primary school students across the United States are about to return to in-person learning. Amidst circulation of the highly infectious Delta variant, there is danger that without the appropriate safety precautions, substantial amount of school-based spread of COVID-19 may occur.\n\nMethodsWe used an extended Susceptible-Infected-Recovered computational model to estimate the number of new infections during 1 semester among a student population under different assumptions about mask usage, routine testing, and levels of incoming protection. Our analysis considers three levels of incoming protection (30%, 40%, or 50%; denoted as \"low\", \"mid\", or \"high\"). Universal mask usage decreases infectivity by 50%, and weekly testing may occur among 50% of the student population; positive tests prompt quarantine until recovery, with compliance contingent on symptom status.\n\nResultsWithout masking and testing, more than 75% of susceptible students become get infected within three months in all settings. With masking, this values decreases to 50% for \"low\" incoming protection settings (\"mid\"=35%, \"high\"=24%). Testing half the masked population (\"testing\") further drops infections to 22% (16%, 13%).\n\nConclusionWithout interventions in place, the vast majority of susceptible students will become infected through the semester. Universal masking can reduce student infections by 26-78%, and biweekly testing along with masking reduces infections by another 50%. To prevent new infections in the community, limit school absences, and maintain in-person learning, interventions such as masking and testing must be implemented widely, especially among elementary school settings in which children are not yet eligible for the vaccine.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Yiwei Zhang", + "author_inst": "North Carolina State University" + }, + { + "author_name": "Karl Johnson", + "author_inst": "University of North Carolina Gillings School of Global Public Health" + }, + { + "author_name": "Zhuoting Yu", + "author_inst": "Georgia Institute of Technology, Atlanta, GA, United States of America" + }, + { + "author_name": "Akane Fujimoto", + "author_inst": "Georgia Institute of Technology, Atlanta, GA, United States of America" + }, + { + "author_name": "Kristen Hassmiller Lich", + "author_inst": "University of North Carolina" + }, + { + "author_name": "Julie Ivy", + "author_inst": "North Carolina State University" + }, + { + "author_name": "Pinar Keskinocak", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Maria Mayorga", + "author_inst": "North Carolina State University" + }, + { + "author_name": "Julie L Swann", + "author_inst": "North Carolina State University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.10.21261842", "rel_title": "Second round statewide survey for estimation of the burden of active infection and anti-SARS-CoV-2 IgG antibodies in the general population of Karnataka, India", @@ -650624,61 +651405,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.10.21261860", - "rel_title": "Heterogeneity in COVID-19 Pandemic-Induced Lifestyle Stressors Predicts Mental Health in Adults and Children in the US and UK", - "rel_date": "2021-08-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.10.21261860", - "rel_abs": "Identifying predictors of mental health symptoms after the initial phase of the pandemic may inform the development of targeted interventions to reduce its negative long-term mental health consequences. In the current study, we aimed to simultaneously evaluate the prospective influence of life change stress, personal COVID-19 impact, prior mental health, worry about COVID-19, state-level indicators of pandemic threat, and socio-demographic factors on mood and anxiety symptoms in November 2020 among adults and children in the US and UK. We used a longitudinal cohort study using the Coronavirus Health Impact Survey (CRISIS) collected at 3 time points: an initial assessment in April 2020 (\"April\"), a reassessment 3 weeks later (\"May\"), and a 7-month follow-up in November 2020 (\"November\"). Online surveys were collected in the United States and United Kingdom by Prolific Academic, a survey recruitment service, with a final sample of 859 Adults and 780 children (collected via parent report). We found subtypes of pandemic-related life change stress in social and economic domains derived through Louvain Community Detection. We assessed recalled mood and perceived mental health prior to the pandemic; worries about COVID-19; personal and family impacts of COVID-19; and socio-demographic characteristics. Levels of mood symptoms in November 2020 measured with the circumplex model of affect. We found 3 life change stress subtypes among adults and children: Lower Social/Lower Economic (adults and children), Higher Social/Higher Economic (adults and children), Lower Social/Higher Economic (adults), and Intermediate Social/Lower Economic (children). Overall, mood symptoms decreased between April and November 2020, but shifting from lower to higher-stress subtypes between time points was associated with increasing symptoms. For both adults and children, the most informative predictors of mood symptoms in November identified by conditional random forest models were prior mood and perceived mental health, worries about COVID, and sources of life change. The relative importance of these predictors was the most prominent difference in findings between adults and children, with lifestyle changes stress regarding friendships being more predictive of mood outcomes than worries about COVID in children. In the US, objective state-level indicators of COVID-19 threat were less predictive of November mood than these other predictors. We found that in addition to the well-established influences of prior mood and worry, heterogeneous subtypes of pandemic-related stress were differentially associated with mood after the initial phase of the pandemic. Greater research on diverse patterns of pandemic experience may elucidate modifiable targets for treatment and prevention.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Aki Nikolaidis", - "author_inst": "Child Mind Institute" - }, - { - "author_name": "Jacob DeRosa", - "author_inst": "Child Mind Institute" - }, - { - "author_name": "Mirelle Kass", - "author_inst": "Child Mind Institute" - }, - { - "author_name": "Irene Droney", - "author_inst": "Child Mind Institute" - }, - { - "author_name": "Lindsay Alexander", - "author_inst": "Child Mind Institute" - }, - { - "author_name": "Adriana Di Martino", - "author_inst": "Child Mind Institute" - }, - { - "author_name": "Evelyn Bromet", - "author_inst": "Stony Brook University" - }, - { - "author_name": "Kathleen Merikangas", - "author_inst": "National Institute of Mental Health" - }, - { - "author_name": "Michael Milham", - "author_inst": "Child Mind Institute" - }, - { - "author_name": "Diana Paksarian", - "author_inst": "National Institute of Mental Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.08.10.21261816", "rel_title": "Mental health impacts of the COVID-19 pandemic on children and adolescents with chronic health conditions", @@ -651897,6 +652623,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.08.09.21261704", + "rel_title": "Antibody mediated neutralization of authentic SARS-CoV-2 B.1.617 variants harboring L452R and T478K/E484Q", + "rel_date": "2021-08-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.09.21261704", + "rel_abs": "The capacity of convalescent and vaccine-elicited sera and monoclonal antibodies (mAb) to neutralize SARS-CoV-2 variants is currently of high relevance to assess the protection against infections.\n\nWe performed a cell culture-based neutralization assay focusing on authentic SARS-CoV-2 variants B.1.617.1 (Kappa), B.1.617.2 (Delta), B.1.427/B.1.429 (Epsilon), all harboring the spike substitution L452R.\n\nWe found that authentic SARS-CoV-2 variants harboring L452R had reduced susceptibility to convalescent and vaccine-elicited sera and mAbs. Compared to B.1, Kappa and Delta showed a reduced neutralization by convalescent sera by a factor of 8.00 and 5.33, respectively, which constitutes a 2-fold greater reduction when compared to Epsilon. BNT2b2 and mRNA1273 vaccine-elicited sera were less effective against Kappa, Delta, and Epsilon compared to B.1. No difference was observed between Kappa and Delta towards vaccine-elicited sera, whereas convalescent sera were 1.5-fold less effective against Delta, respectively. Both B.1.617 variants Kappa (+E484Q) and Delta (+T478K) were less susceptible to either casirivimab or imdevimab.\n\nIn conclusion, in contrast to the parallel circulating Kappa variant, the neutralization efficiency of convalescent and vaccine-elicited sera against Delta was moderately reduced. Delta was resistant to imdevimab, which however, might be circumvented by a combination therapy with casirivimab together.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Alexander Wilhelm", + "author_inst": "University Hospital Frankfurt, Goethe University Frankfurt" + }, + { + "author_name": "Tuna Toptan", + "author_inst": "University Hospital Frankfurt, Goethe University Frankfurt" + }, + { + "author_name": "Christiane Pallas", + "author_inst": "University Hospital Frankfurt, Goethe University Frankfurt" + }, + { + "author_name": "Timo Wolf", + "author_inst": "University Hospital Frankfurt, Goethe University Frankfurt" + }, + { + "author_name": "Udo Goetsch", + "author_inst": "Public Health Department of the City of Frankfurt am Main" + }, + { + "author_name": "Rene Gottschalk", + "author_inst": "Public Health Department of the City of Frankfurt am Main" + }, + { + "author_name": "Maria JGT Vehreschild", + "author_inst": "University Hospital Frankfurt, Goethe University Frankfurt" + }, + { + "author_name": "Sandra Ciesek", + "author_inst": "University Hospital Frankfurt, Goethe University Frankfurt" + }, + { + "author_name": "Marek Widera", + "author_inst": "University Hospital Frankfurt, Goethe University Frankfurt" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.06.21261491", "rel_title": "Infected surfaces as a source of transmissible material in healthcare settings dealing with COVID 19 patients", @@ -652465,37 +653242,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.08.05.21261562", - "rel_title": "Cryptic Transmission of the Delta Variant AY.3 Sublineage of SARS-CoV-2 among Fully Vaccinated Patients on an Inpatient Ward", - "rel_date": "2021-08-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.05.21261562", - "rel_abs": "BackgroundRecent reports indicate that vaccination is effective in reducing symptomatic infection with the Delta variant of SARS-CoV-2 (DV) but is less protective against asymptomatic transmission of DV in outpatients than for earlier variants.\n\nHere we report cryptic transmission associated with high DV viral load among vaccinated patients on an inpatient medical-surgical ward.\n\nMethodsThis observational study included all persons diagnosed with breakthrough SARS-CoV-2 infections at the VA Boston Healthcare System (VABHS) from March 11, 2021 to July 31, 2021, including those tested for surveillance, admission, symptoms, and as part of an outbreak investigation in July 2021. SARS-CoV-2 infection was diagnosed by reverse-transcription polymerase chain reaction (PCR) (Cepheid). Variants were identified by MassARRAY SARS-CoV-2 Variant Panel (36-plex PCR, Agena BioScience) for most breakthrough cases after June 2021 Viral genomic sequencing was performed by the Jackson Laboratory.\n\nResultsAn inpatient was diagnosed with asymptomatic DV infection on routine pre-discharge testing. Contact tracing detected infection in 6 of 38 patients (15.8%), 1 of 168 staff (0.6%), and 1 of 6 visitors (16.7%). Infection at the time of diagnosis was asymptomatic in 4 proximate, vaccinated patients, 1 vaccinated visitor, and 1 vaccinated employee caring for 1 undiagnosed, infected, vaccinated patient. Patients were unmasked, whereas staff wore surgical masks. PCR cycle threshold (Ct) for breakthrough infections indicated more than 1000-fold higher viral load for DV (Ct:21.7{+/-}4.3; n=15) than for earlier variants (Ct: 31.8{+/-}10.9, n=12; p=.003 (t-test)).\n\nConclusionThese findings demonstrate transmission of DV with high viral load between vaccinated inpatients, the continued efficacy of masking and vaccination for protecting healthcare personnel, and the potential need for post-admission surveillance to prevent cryptic DV transmission.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Katherine Linsenmeyer", - "author_inst": "VA Boston Healthcare System and Boston University School of Medicine" - }, - { - "author_name": "Kalpana Gupta", - "author_inst": "VA Boston HCS and Boston University School of Medicine" - }, - { - "author_name": "Rebecca Madjarov", - "author_inst": "VA Boston Healthcare System" - }, - { - "author_name": "Michael E. Charness", - "author_inst": "VA Boston Healthcare System and Harvard Medical School" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.08.21261768", "rel_title": "Full vaccination suppresses SARS-CoV-2 delta variant mutation frequency", @@ -653803,6 +654549,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.08.08.21261769", + "rel_title": "Anti-CD38 therapy impairs SARS-CoV-2 vaccine response in multiple myeloma patients", + "rel_date": "2021-08-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.08.21261769", + "rel_abs": "Multiple myeloma (MM) patients are at risk of fatal outcome after SARS-CoV-2 infection. Preliminary data suggest that MM patients have an impaired response to vaccination. This prospective study analyzed the humoral and cellular immune responses to two doses of BNT162b2 in 72 MM patients, including 48 receiving anti-CD38 immunotherapy. Results evidenced that MM patients display lower levels of SARS-CoV-2 specific IgG and IgA antibodies and decreased neutralization of alpha and delta variants when compared to healthy controls. They also showed decreased numbers of circulating IFN{gamma}-producing Spike SARS-CoV-2 specific T lymphocytes. This defective immune response was particularly marked in patients receiving anti-CD38 immunotherapy. Furthermore, a retrospective investigation of MM patients among COVID-19-related death in the Paris area suggested a limited efficacy of BNT162b2 in patients treated with anti-CD38. Overall, these results show a decreased immunogenicity of BNT162b2 in MM patients and stress the need for novel strategies to improve SARS-CoV-2 prophylaxis in immunocompromised individuals.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Soledad Henriquez", + "author_inst": "Hopital Cochin" + }, + { + "author_name": "Jeremie Zerbit", + "author_inst": "Hopital Cochin" + }, + { + "author_name": "Timothee Bruel", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Amani Ouedrani", + "author_inst": "Institut Necker" + }, + { + "author_name": "Delphine Planas", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Paul Deschamps", + "author_inst": "Hopital Cochin" + }, + { + "author_name": "Isabelle Staropoli", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Jerome Hadjadj", + "author_inst": "Hopital Cochin" + }, + { + "author_name": "Bruno Varet", + "author_inst": "Hopital Necker-Enfants Malades" + }, + { + "author_name": "Felipe Suarez", + "author_inst": "Hopital Necker-Enfants Malades" + }, + { + "author_name": "Natalia Ermak", + "author_inst": "Hopital Cochin" + }, + { + "author_name": "Didier Bouscary", + "author_inst": "Hopital Cochin" + }, + { + "author_name": "Lise Willems", + "author_inst": "Hopital Cochin" + }, + { + "author_name": "Guillemette Fouquet", + "author_inst": "Hopital Cochin" + }, + { + "author_name": "Justine Decroocq", + "author_inst": "Hopital Cochin" + }, + { + "author_name": "Patricia Franchi", + "author_inst": "Hopital Cochin" + }, + { + "author_name": "Benedicte Deau-Fischer", + "author_inst": "Hopital Cochin" + }, + { + "author_name": "Benjamin Terrier", + "author_inst": "Hopital Cochin" + }, + { + "author_name": "Jerome Tamburini", + "author_inst": "Hopital Cochin" + }, + { + "author_name": "Lucienne Chatenoud", + "author_inst": "Institut Necker" + }, + { + "author_name": "Olivier Schwartz", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Marguerite Vignon", + "author_inst": "Hopital Cochin" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.08.21261745", "rel_title": "Speeding and Traffic-Related Injuries and Fatalities during the 2020 COVID-19 Pandemic: The Cases of Seattle and New York City", @@ -654311,69 +655160,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.08.08.455468", - "rel_title": "A Tethered Ligand Assay to Probe SARS-CoV-2:ACE2 Interactions", - "rel_date": "2021-08-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.08.455468", - "rel_abs": "SARS-CoV-2 infections are initiated by attachment of the receptor-binding domain (RBD) on the viral Spike protein to angiotensin-converting enzyme-2 (ACE2) on human host cells. This critical first step occurs in dynamic environments, where external forces act on the binding partners and multivalent interactions play critical roles, creating an urgent need for assays that can quantitate SARS-CoV-2 interactions with ACE2 under mechanical load and in defined geometries. Here, we introduce a tethered ligand assay that comprises the RBD and the ACE2 ectodomain joined by a flexible peptide linker. Using magnetic tweezers and atomic force spectroscopy as highly complementary single-molecule force spectroscopy techniques, we investigate the RBD:ACE2 interaction over the whole physiologically relevant force range. We combine the experimental results with steered molecular dynamics simulations and observe and assign fully consistent unbinding and unfolding events across the three techniques, enabling us to establish ACE2 unfolding as a molecular fingerprint. Measuring at forces of 2-5 pN, we quantify the force dependence and kinetics of the RBD:ACE2 bond in equilibrium. We show that the SARS-CoV-2 RBD:ACE2 interaction has higher mechanical stability, larger binding free energy, and a lower dissociation rate in comparison to SARS-CoV-1, which helps to rationalize the different infection patterns of the two viruses. By studying how free ACE2 outcompetes tethered ACE2, we show that our assay is sensitive to prevention of bond formation by external binders. We expect our results to provide a novel way to investigate the roles of mutations and blocking agents for targeted pharmaceutical intervention.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Magnus S. Bauer", - "author_inst": "LMU Munich" - }, - { - "author_name": "Sophia Gruber", - "author_inst": "LMU Munich" - }, - { - "author_name": "Adina Hausch", - "author_inst": "LMU Munich" - }, - { - "author_name": "Lukas F. Milles", - "author_inst": "University of Washington" - }, - { - "author_name": "Thomas Nicolaus", - "author_inst": "LMU Munich" - }, - { - "author_name": "Leonard C. Schendel", - "author_inst": "LMU Munich" - }, - { - "author_name": "Pilar Lopez Navajas", - "author_inst": "Biological Research Center Margarita Salas" - }, - { - "author_name": "Erik Procko", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Daniel Lietha", - "author_inst": "Biological Research Center Margarita Salas" - }, - { - "author_name": "Rafael C. Bernardi", - "author_inst": "Auburn University" - }, - { - "author_name": "Hermann E. Gaub", - "author_inst": "LMU Munich" - }, - { - "author_name": "Jan Lipfert", - "author_inst": "LMU Munich" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.08.08.455562", "rel_title": "A broadly neutralizing biparatopic Nanobody protects mice from lethal challenge with SARS-CoV-2 variants of concern", @@ -655785,6 +656571,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.08.03.21261544", + "rel_title": "A booster dose is immunogenic and will be needed for older adults who have completed two doses vaccination with CoronaVac: a randomised, double-blind, placebo-controlled, phase 1/2 clinical trial", + "rel_date": "2021-08-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.03.21261544", + "rel_abs": "ImportanceWhether herd immunity through mass vaccination is sufficient to curb SARS-CoV-2 transmission requires an understanding of the duration of vaccine-induced immunity, and the necessity and timing of booster doses. Objective: To evaluate immune persistence of two priming doses of CoronaVac, and immunogenicity and safety of a third dose in healthy adults [≥]60 years. Design, setting, and participants: We conducted a vaccine booster study built on a single-center, randomized, double-blind phase 1/2 trial of the two-dose schedule of CoronaVac among healthy adults[≥]60 years in Hebei, China. We examined neutralizing antibody titres six months or more after the second dose in all participants. We provided a third dose to 303 participants recruited in phase 2 trial to assess their immune responses.\n\nInterventionsTwo formulations (3 g, and 6 g) were used in phase 1 trial, and an additional formulation of 1.5 g was used in phase 2 trial. All participants were given two doses 28 days apart and followed up 6 months after the second dose. Participants in phase 2 received a third dose 8 months after the second dose.\n\nMain outcomes and measuresGeometric mean titres (GMT) of neutralizing antibodies to live SARS-CoV-2 and adverse events were assessed at multiple time points following vaccination.\n\nResultsNeutralizing antibody titres dropped below the seropositive cutoff of 8 at 6 months after the primary vaccination in all vaccine groups in the phase 1/2 trial. A third dose given 8 months or more after the second dose significantly increased neutralizing antibody levels. In the 3 g group (the licensed formulation), GMT increased to 305 [95%CI 215.3-432.0] on day 7 following the third dose, an approximately 7-fold increase compared with the GMT 28 days after the second dose. All solicited adverse reactions reported within 28 days after a booster dose were of grade 1 or 2 severity.\n\nConclusion and relevanceNeutralizing antibody titres declined substantially six months after two doses of CoronaVac among older adults. A booster dose rapidly induces robust immune responses. This evidence could help policymakers determine the necessity and the timing of a booster dose for older adults.\n\nTrial registrationClinicalTrials.gov (NCT04383574).", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Minjie Li", + "author_inst": "Hebei Center for Disease Control and Prevention, Shijiazhuang, China" + }, + { + "author_name": "Juan Yang", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Lin Wang", + "author_inst": "R&D Department, Sinovac Life Sciences Co., Ltd., Beijing, China" + }, + { + "author_name": "Qianhui Wu", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Zhiwei Wu", + "author_inst": "Hebei Center for Disease Control and Prevention, Shijiazhuang, China" + }, + { + "author_name": "Wen Zheng", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Lei Wang", + "author_inst": "Department of Clinical Research, Sinovac Biotech Co., Ltd., Beijing, China" + }, + { + "author_name": "Wanying Lu", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Xiaowei Deng", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Cheng Peng", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Bihua Han", + "author_inst": "Hebei Center for Disease Control and Prevention, Shijiazhuang, China" + }, + { + "author_name": "Yuliang Zhao", + "author_inst": "Hebei Center for Disease Control and Prevention, Shijiazhuang, China" + }, + { + "author_name": "Hongjie Yu", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Weidong Yin", + "author_inst": "Sinovac Biotech Co., Ltd., Beijing, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.05.21261532", "rel_title": "Safety and Immunogenicity of CpG 1018 and Aluminium Hydroxide-Adjuvanted SARS-CoV-2 S-2P Protein Vaccine MVC-COV1901: A Large-Scale Double-Blinded, Randomised, Placebo-Controlled Phase 2 Trial", @@ -656381,49 +657238,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.08.04.21261576", - "rel_title": "When do elementary students need masks in school? Model-estimated risk of in-school SARS-CoV-2 transmission and related infections among household members before and after student vaccination", - "rel_date": "2021-08-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.04.21261576", - "rel_abs": "BackgroundWhile CDC guidance for K-12 schools recommends indoor masking regardless of vaccination status, final decisions about masking in schools will be made at the local and state level. The impact of the removal of mask restrictions, however, on COVID-19 outcomes for elementary students, educators/staff, and their households is not well known.\n\nMethodsWe used a previously published agent-based dynamic transmission model of SARS-CoV-2 in K-12 schools to simulate an elementary school with 638 students across 12 scenarios: combinations of three viral infectiousness levels (reflecting wild-type virus, alpha variant, and delta variant) and four student vaccination levels (0%, 25%, 50% and 70% coverage). For each scenario, we varied observed community COVID-19 incidence (0 to 50 cases/100,000 people/day) and mitigation effectiveness (0-100% reduction to in-school secondary attack rate), and evaluated two outcomes over a 30 day period: (1) the probability of at least one in-school transmission, and (2) average increase in total infections among students, educators/staff, and their household members associated with moving from more to less intensive mitigation measures.\n\nResultsOver 30 days in the simulated elementary school, the probability of at least one in-school SARS-CoV-2 transmission and the number of estimated additional infections in the immediate school community associated with changes in mitigation measures varied widely. In one scenario with the delta variant and no student vaccination, assuming that baseline mitigation measures of simple ventilation and handwashing reduce the secondary attack rate by 40%, if decision-makers seek to keep the monthly probability of an in-school transmission below 50%, additional mitigation (e.g., masking) would need to be added at a community incidence of approximately 2/100,000/day. Once students are vaccinated, thresholds shift substantially higher.\n\nLimitationsThe interpretation of model results should be limited by the uncertainty in many of the parameters, including the effectiveness of individual mitigation interventions and vaccine efficacy against the delta variant, and the limited scope of the model beyond the school community. Additionally, the assumed case detection rate (33% of cases detected) may be too high in areas with decreased testing capacity.\n\nConclusionDespite the assumption of high adult vaccination, the risks of both in-school SARS-CoV-2 transmission and resulting infections among students, educators/staff, and their household members remain high when the delta variant predominates and students are unvaccinated. Mitigation measures or vaccinations for students can substantially reduce these risks. These findings underscore the potential role for responsive plans, where mitigation is deployed based on local COVID-19 incidence and vaccine uptake.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "John Giardina", - "author_inst": "Center for Health Decision Science, Harvard T.H. Chan School of Public Health, Boston, MA" - }, - { - "author_name": "Alyssa Bilinski", - "author_inst": "Department of Health Services, Policy, and Practice and Department of Biostatistics, Brown School of Public Health, Providence, RI, USA" - }, - { - "author_name": "Meagan C. Fitzpatrick", - "author_inst": "Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD" - }, - { - "author_name": "Emily A. Kendall", - "author_inst": "Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD" - }, - { - "author_name": "Benjamin P. Linas", - "author_inst": "Boston University Schools of Medicine and Public Health, Boston Medical Center, Boston, MA" - }, - { - "author_name": "Joshua Salomon", - "author_inst": "Center for Health Policy and Center for Primary Care and Outcomes Research, Stanford University School of Medicine, Stanford, CA" - }, - { - "author_name": "Andrea L. Ciaranello", - "author_inst": "Division of Infectious Disease and Medical Practice Evaluation Center, Massachusetts General Hospital, Boston, MA, USA" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.08.02.21260667", "rel_title": "Low SARS-CoV-2 infection rate and high vaccine-induced immunity among German healthcare workers at the end of the third wave of the COVID-19 pandemic", @@ -657739,6 +658553,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2021.08.05.21261675", + "rel_title": "Determinants of the COVID-19 Vaccine Hesitancy Spectrum", + "rel_date": "2021-08-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.05.21261675", + "rel_abs": "Polls report nearly one-third of the United States population is skeptical or opposed to getting the COVID-19 vaccine. Most of these polls, as well as the scientific research that has been conducted on vaccine hesitancy, was done prior to vaccine eligibility opening to all adults. Now that COVID-19 vaccines are widely available, further research is needed to understand the factors contributing to vaccine intentions across the vaccine hesitancy spectrum. This study conducted an online survey using the Social Science Research Solution (SSRS) Opinion Panel web panelists, representative of U.S. adults age 18 and older who use the internet, with an oversample of rural-dwelling and minority populations between April 8 and April 22, 2021- as vaccine eligibility opened to the country. We examined the relationship between COVID-19 exposure and socio-demographics with vaccine intentions [eager-to-take, wait-and-see, undecided, refuse] among the unvaccinated using multinomial logistic regressions [ref: fully/partially vaccinated]. Results showed vaccine intentions varied by demographic characteristics and risk exposures during the period that eligibility for the vaccine was extended to all adults.\n\nFunding statementFunding for this research was provided by a grant from the National Science Foundation (Grant #2049886). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Rachael Piltch-Loeb", + "author_inst": "NYU Global Public Health" + }, + { + "author_name": "Diana Silver", + "author_inst": "NYU Global Public Health" + }, + { + "author_name": "Yeerae Kim", + "author_inst": "NYU Global Public Health" + }, + { + "author_name": "Hope Norris", + "author_inst": "NYU Global Public Health" + }, + { + "author_name": "Elizabeth McNeill", + "author_inst": "NYU Global Public Health" + }, + { + "author_name": "David Abramson", + "author_inst": "NYU Global Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.08.05.21261671", "rel_title": "Prevalence and correlates of SARS-CoV-2 seropositivity among people who inject drugs in the San Diego-Tijuana border region", @@ -658303,45 +659156,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.08.06.455384", - "rel_title": "The Inherent Flexibility of Receptor Binding Domains in SARS-CoV-2 Spike Protein", - "rel_date": "2021-08-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.06.455384", - "rel_abs": "Spike (S) protein is the primary antigenic target for neutralization and vaccine development for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It decorates the virus surface and undergoes large conformational changes of its receptor binding domain (RBD) to enter the host cell, as the abundant structural studies suggest. Here, we observe Down, one-Up, one-Open, and two-Up-like structures in enhanced molecular dynamics simulations without pre-defined reaction coordinates. The RBDA transition from Down to one-Up is supported by transient salt-bridges between RBDA and RBDC and by the glycan at N343B. Reduced interactions between RBDA and RBDB induce the RBDB motions toward two-Up. Glycan shielding for neutralizing antibodies is the weakest in one-Open. Cryptic pockets are revealed at the RBD interfaces in intermediate structures between Down and one-Up. The inherent flexibility in S-protein is, thus, essential for the structure transition and shall be considered for antiviral drug rational design or vaccine development.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Hisham M. Dokainish", - "author_inst": "Riken" - }, - { - "author_name": "Suyong Re", - "author_inst": "National Institutes of Biomedical Innovation, Health, and Nutrition" - }, - { - "author_name": "Takaharu Mori", - "author_inst": "Riken" - }, - { - "author_name": "Chigusa Kobayashi", - "author_inst": "Riken" - }, - { - "author_name": "Jaewoon Jung", - "author_inst": "Riken" - }, - { - "author_name": "Yuji Sugita", - "author_inst": "Riken" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.08.06.455405", "rel_title": "RIG-I-induced innate antiviral immunity protects mice from lethal SARS-CoV-2 infection", @@ -659485,6 +660299,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.08.04.21261618", + "rel_title": "Clinical characteristics and outcomes of COVID-19 breakthrough infections among vaccinated patients with systemic autoimmune rheumatic diseases", + "rel_date": "2021-08-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.04.21261618", + "rel_abs": "ObjectiveTo describe the characteristics of COVID-19 vaccine breakthrough infections among systemic autoimmune rheumatic disease (SARD) patients.\n\nMethodsWe identified SARDs patients in a large healthcare system with COVID-19 vaccination [≥]14 days prior to a positive SARS-CoV-2 molecular test. Details of the patients SARD, vaccination status, and COVID-19 infection were extracted.\n\nResultsOf 340 confirmed COVID-19 infections among SARDs patients between December 11th, 2020 (date of first COVID-19 vaccine approval in the US) and July 30th, 2021, we identified 16 breakthrough infections. Seven (44%) received the Pfizer-BioNtech vaccine, five (31%) received the Moderna vaccine, and four (25%) received the Janssen/Johnson & Johnson vaccine. The most common SARDs included rheumatoid arthritis (6, 38%), inflammatory myopathy (3, 19%), and systemic lupus erythematosus (3, 19%). Rituximab (5, 31%), glucocorticoids (4, 25%), and mycophenolate mofetil (4, 25%) were the most frequent treatments. Among the breakthrough infections, 15 (93%) were symptomatic, six (38%) were hospitalized, one (6%) required mechanical ventilation, and two (13%) died.\n\nConclusionsSymptomatic, including severe, breakthrough infections were observed in SARDs patients; many were on treatments associated with attenuated antibody responses to vaccination. Further studies are needed to determine the rate of breakthrough infection associated with SARD treatments and other features.\n\nKey messagesO_ST_ABSWhat is already known about this subject?C_ST_ABSBreakthrough infections following COVID-19 vaccination are expected but some patients with systemic autoimmune rheumatic diseases (SARDs) may be at higher risk because of blunted antibody responses to vaccination associated with rheumatic disease treatments and other factors that remain poorly understood.\n\nWhat does this study add?We identify and describe 16 COVID-19 vaccine breakthrough infections within the Mass General Brigham system between December 11th, 2020 and June 26th, 2021. The vast majority of cases were symptomatic and two were fatal.\n\nHow might this impact on clinical practice or future developments?This study complements observations regarding the attenuated antibody response to COVID-19 vaccination in patients with SARDs by identifying serious clinical outcomes from breakthrough infections in patients receiving DMARDs that have been reported to have blunted vaccine responses. Our study identifies characteristics of COVID-19 breakthrough infections that may guide the prioritization of booster vaccines and other risk-mitigating strategies in patients with SARDs.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Claire Cook", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Naomi Patel", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Kristin D'Silva", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Tiffany T-Y Hsu", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Michael DiIorio", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Lauren Prisco", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Lily Martin", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Kathleen M.M. Vanni", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Alessandra Zaccardelli", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Derrick J. Todd", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Jeffrey A Sparks", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Zachary S Wallace", + "author_inst": "Massachusetts General Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "rheumatology" + }, { "rel_doi": "10.1101/2021.08.04.21261613", "rel_title": "Strategies to Estimate Prevalence of SARS-CoV-2 Antibodies in a Texas Vulnerable Population: Results from Phase I of the Texas Coronavirus Antibody REsponse Survey (TX CARES)", @@ -660513,121 +661390,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.08.05.455290", - "rel_title": "SARS-CoV-2 variants of concern have acquired mutations associated with an increased spike cleavage", - "rel_date": "2021-08-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.08.05.455290", - "rel_abs": "For efficient cell entry and membrane fusion, SARS-CoV-2 spike (S) protein needs to be cleaved at two different sites, S1/S2 and S2 by different cellular proteases such as furin and TMPRSS2. Polymorphisms in the S protein can affect cleavage, viral transmission, and pathogenesis. Here, we investigated the role of arising S polymorphisms in vitro and in vivo to understand the emergence of SARS-CoV-2 variants. First, we showed that the S:655Y is selected after in vivo replication in the mink model. This mutation is present in the Gamma Variant Of Concern (VOC) but it also occurred sporadically in early SARS-CoV-2 human isolates. To better understand the impact of this polymorphism, we analyzed the in vitro properties of a panel of SARS-CoV-2 isolates containing S:655Y in different lineage backgrounds. Results demonstrated that this mutation enhances viral replication and spike protein cleavage. Viral competition experiments using hamsters infected with WA1 and WA1-655Y isolates showed that the variant with 655Y became dominant in both direct infected and direct contact animals. Finally, we investigated the cleavage efficiency and fusogenic properties of the spike protein of selected VOCs containing different mutations in their spike proteins. Results showed that all VOCs have evolved to acquire an increased spike cleavage and fusogenic capacity despite having different sets of mutations in the S protein. Our study demonstrates that the S:655Y is an important adaptative mutation that increases viral cell entry, transmission, and host susceptibility. Moreover, SARS-COV-2 VOCs showed a convergent evolution that promotes the S protein processing.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Alba Escalera", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Ana S. Gonzalez-Reiche", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Sadaf Aslam", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Ignacio Mena", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Rebecca L. Pearl", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Manon Laporte", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Andrea Fossati", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Raveen Rathnasinghe", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Hala Alshammary", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Adriana van de Guchte", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Mehdi Bouhaddou", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Thomas Kehrer", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Lorena Zuliani-Alvarez", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "David A. Meekins", - "author_inst": "Kansas State University" - }, - { - "author_name": "Velmurugan Balaraman", - "author_inst": "Kansas State University" - }, - { - "author_name": "Chester McDowell", - "author_inst": "Kansas State University" - }, - { - "author_name": "Juergen A Richt", - "author_inst": "Kansas State University" - }, - { - "author_name": "Goran Bajic", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Emilia Mia Sordillo", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Nevan Krogan", - "author_inst": "University of California San Francisco" - }, - { - "author_name": "Viviana Simon", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Randy A. Albrecht", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Harm van Bakel", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Adolfo Garcia-Sastre", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Teresa Aydillo", - "author_inst": "Icahn School of Medicine at Mount Sinai Hospital" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.08.05.455262", "rel_title": "Identification of Potent Small Molecule Inhibitors of SARS-CoV-2 Entry", @@ -661719,6 +662481,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2021.08.03.21261441", + "rel_title": "A single intramuscular injection of monoclonal antibody MAD0004J08 induces in healthy adults SARS-CoV-2 neutralising antibody titres exceeding those induced by infection and vaccination", + "rel_date": "2021-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.03.21261441", + "rel_abs": "BackgroundThe emerging threat represented by SARS-CoV-2 variants, demands the development of therapies for better clinical management of COVID-19. MAD0004J08 is an extremely potent Fc-engineered monoclonal antibody (mAb) able to neutralise in vitro all current SARS-CoV-2 variants of concern (VoCs). This ongoing study, evaluates safety, pharmacokinetics and SARS-CoV-2 sera neutralization effect of MAD0004J08 when administered as single dose intramuscularly in healthy adults.\n\nMethodWe conducted a dose escalation study with sequential enrolment of three cohorts, each with an increasing dose level of MAD0004J08 (48mg, 100mg and 400mg). Within each cohort, 10 young healthy adults were randomized with 4:1 ratio to a single intramuscular (i.m.) injection of MAD0004J08 or placebo. The primary endpoint is the proportion of subjects with severe and/or serious treatment emergent adverse events (TEAEs) within 7 days post-treatment. Secondary endpoints reported in this paper are the proportion of subjects with solicited TEAEs up 7 days post dosing, MAD0004J08 serum concentrations and neutralising activity versus the original SARS-COV-2 Wuhan virus at different timepoints post-dosing. As post-hoc analyses, we compared the sera neutralising titres of subjects who received MAD0004J08 with those of people that had received the COVID-19 BNT162b2 mRNA vaccine in the previous sixty days (n=10) and COVID-19 convalescent patients (n=20), and assessed serum neutralisation activity against the B.1.1.7 (alpha), B.1.351 (beta) and B.1.1.248 (gamma) SARS-CoV-2 variants of concern.\n\nFindingsA total of 30 subjects, 10 per cohort, were enrolled and randomized. Data up to 30 days were available and analysed in this report. No severe TEAEs were reported in any of the cohorts in the 7 days post-treatment. MAD0004J08 was detected in the sera of treated subjects within few hours post-administration and reached almost maximal levels on day 8. The geometric mean neutralising titres (GMT) assessed against the original Wuhan virus peaked on day 8 and ranged 226 - 905, 905 - 2,560, and 1,280 - 5,120 for cohort 1, 2 and 3 respectively. The sera neutralising GMT in MAD0004J08 treated subjects in all the three cohorts were found to be 1{middle dot}5-54{middle dot}5-fold higher compared to sera from convalescent patients and 1{middle dot}83- 76{middle dot}4-fold higher compared to sera from COVID-19 vaccinees. Finally, GMT in MAD0004J08 treated subjects showed high neutralising titres versus the B.1.1.7 (alpha), B.1.351 (beta) and B.1.1.248 (gamma) SARS-CoV-2 VoCs.\n\nInterpretationA single dose administration of MAD0004J08 via i.m. route is safe and well tolerated and results in a rapid systemic distribution of the MAD0004J08 and sera neutralising titres higher than COVID-19 convalescent and vaccinated subjects. A single dose administration of MAD0004J08 is also sufficient to effectively neutralise major SARS-CoV-2 variants of concern. Based on these results, a Phase 2-3 trial is ongoing to further assess the safety, dosage, and efficacy of MAD0004J08 in asymptomatic or mild-moderate symptomatic COVID-19 patients.\n\nFundingEU Malaria Fund, Ministero dello Sviluppo Economico, Ministero della Salute, Regione Toscana, Toscana Life Sciences Sviluppo and European Research Council.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PUBMED, MEDLINE and MedRxiv for clinical trials, meta-analyses and randomized controlled trials evaluating the antibody neutralization titres vs. different SARS-CoV-2 variants of concern obtained from subjects who received monoclonal antibodies for the treatment of COVID-19 using the following search terms: (\"COVID-19\" OR \"SARS-CoV-2\") AND (\"monoclonal antibody\" OR \"neutralising antibody\") AND (\"variants\" OR \"variants of concern\"). No relevant studies were identified.\n\nAdded value of this studyThis is the first human study assessing safety, PK and neutralising potential of MAD0004J08, a monoclonal antibody against SARS-CoV-2 wild type Wuhan virus and variants of concern, administered intramuscularly at low dosages (48, 100 and 400 mg). MAD0004J08 showed to be safe and well tolerated in the tested dose range. Anti-spike antibodies were detected in the sera of tested SARS-CoV-2 negative healthy adults few hours post-injection. In addition, the sera obtained from MAD0004J08treated subjects, showed to have high neutralisation titres against the Wuhan virus, the B.1.1.7 (alpha), B.1.351 (beta) and B.1.1.248 (gamma) variants of concern.\n\nImplications of all the available evidenceA potent monoclonal antibody such as MAD0004J08, capable of neutralising multiple variants of concern of SARS-CoV-2 rapidly and long lastingly when given as a single intramuscular injection. The antibody, presently tested in a phase 2-3 efficacy trial, can be a major advancement in the prophylaxis and clinical management of COVID-19, because of its broad spectrum, ease of use in non-hospital settings and economic sustainability.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Simone Lanini", + "author_inst": "Istituto Nazionale per le Malattie Infettive Lazzaro Spallanzani, IRCCS, Rome, Italy" + }, + { + "author_name": "Stefano Milleri", + "author_inst": "Centro Ricerche Cliniche di Verona, University and Hospital Trust of Verona, Verona, Italy" + }, + { + "author_name": "Emanuele Andreano", + "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy" + }, + { + "author_name": "Sarah Nosari", + "author_inst": "AchilleS Vaccine, Siena, Italy" + }, + { + "author_name": "Ida Paciello", + "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy" + }, + { + "author_name": "Giulia Piccini", + "author_inst": "VisMederi S.r.l, Siena, Italy" + }, + { + "author_name": "Alessandra Gentili", + "author_inst": "CROss Research, Mendrisio, Switzerland" + }, + { + "author_name": "Adhuna Phogat", + "author_inst": "Fondazione Toscana Life Sciences, Siena, Italy" + }, + { + "author_name": "Inesa Hyseni", + "author_inst": "VisMederi S.r.l, Siena, Italy; VisMederi Research S.r.l, Siena, Italy" + }, + { + "author_name": "Margherita Leonardi", + "author_inst": "VisMederi S.r.l, Siena, Italy; VisMederi Research S.r.l, Siena, Italy" + }, + { + "author_name": "Alessandro Torelli", + "author_inst": "VisMederi S.r.l, Siena, Italy" + }, + { + "author_name": "Emanuele Montomoli", + "author_inst": "VisMederi S.r.l, Siena, Italy; VisMederi Research S.r.l, Siena, Italy; Department of Molecular and Developmental Medicine, University of Siena, Siena, Italy" + }, + { + "author_name": "Andrea Paolini", + "author_inst": "Fondazione Toscana Life Sciences, Siena, Italy; Toscana Life Sciences Sviluppo, Siena, Italy" + }, + { + "author_name": "Andrea Frosini", + "author_inst": "Fondazione Toscana Life Sciences, Siena, Italy" + }, + { + "author_name": "Andrea Antinori", + "author_inst": "Istituto Nazionale per le Malattie Infettive Lazzaro Spallanzani, IRCCS, Rome, Italy" + }, + { + "author_name": "Emanuele Nicastri", + "author_inst": "Istituto Nazionale per le Malattie Infettive Lazzaro Spallanzani, IRCCS, Rome, Italy" + }, + { + "author_name": "Enrico Girardi", + "author_inst": "Istituto Nazionale per le Malattie Infettive Lazzaro Spallanzani, IRCCS, Rome, Italy" + }, + { + "author_name": "Maria Maddalena Plazzi", + "author_inst": "Istituto Nazionale per le Malattie Infettive Lazzaro Spallanzani, IRCCS, Rome, Italy" + }, + { + "author_name": "Giuseppe Ippolito", + "author_inst": "Istituto Nazionale per le Malattie Infettive Lazzaro Spallanzani, IRCCS, Rome, Italy" + }, + { + "author_name": "Francesco Vaia", + "author_inst": "Istituto Nazionale per le Malattie Infettive Lazzaro Spallanzani, IRCCS, Rome, Italy" + }, + { + "author_name": "Giovanni Della Cioppa", + "author_inst": "Clinical R&D Consultants, Rome, Italy" + }, + { + "author_name": "Rino Rappuoli", + "author_inst": "Monoclonal Antibody Discovery (MAD) Lab, Fondazione Toscana Life Sciences, Siena, Italy; Department of Biotechnology, Chemistry and Pharmacy, University of Sien" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.08.03.21261414", "rel_title": "Azithromycin in patients with Covid-19; a systematic review and metanalysis", @@ -662211,65 +663076,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2021.08.02.21261504", - "rel_title": "SARS-CoV-2 antibody binding and neutralization in dried blood spot eluates and paired plasma", - "rel_date": "2021-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.08.02.21261504", - "rel_abs": "Widescale assessment of SARS-CoV-2-specific antibodies is critical to understanding population seroprevalence, correlates of protection, and the longevity of vaccine-elicited responses. Most SARS-CoV-2 studies characterize antibody responses in plasma/sera. While reliable and broadly used, these samples pose several logistical restrictions such as requiring venipuncture for collection and cold chain for transportation and storage. Dried blood spots (DBS) overcome these barriers as they can be self-collected by fingerstick and mailed and stored at ambient temperature. Here, we evaluate the suitability of DBS for SARS-CoV-2 antibody assays by comparing several antibody responses between paired plasma and DBS from SARS-CoV-2 convalescent and vaccinated individuals. We found that DBS not only reflected plasma antibody binding by ELISA and epitope profiles using phage-display, but also yielded SARS-CoV-2 neutralization titers that highly correlated with paired plasma. Neutralization measurement was further streamlined by adapting assays to a high-throughput 384-well format. This study supports the adoption of DBS for numerous SARS-CoV-2 binding and neutralization assays.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Hannah L. Itell", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Haidyn Weight", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Carolyn S. Fish", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Jennifer K. Logue", - "author_inst": "University of Washington" - }, - { - "author_name": "Nicholas Franko", - "author_inst": "University of Washington" - }, - { - "author_name": "Caitlin R. Wolf", - "author_inst": "University of Washington" - }, - { - "author_name": "Denise J. McCulloch", - "author_inst": "University of Washington" - }, - { - "author_name": "Jared Galloway", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Frederick A. Matsen IV", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Helen Y. Chu", - "author_inst": "University of Washington" - }, - { - "author_name": "Julie Overbaugh", - "author_inst": "Fred Hutchinson Cancer Research Center" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.30.21261372", "rel_title": "Airway recommendations for perioperative patients during the COVID-19 pandemic: a scoping review", @@ -663877,6 +664683,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.30.21261392", + "rel_title": "Existing human mobility data sources poorly predicted the spatial spread of SARS-CoV-2 in Madagascar", + "rel_date": "2021-08-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.30.21261392", + "rel_abs": "For emerging epidemics such as the COVID-19 pandemic, quantifying travel is a key component of developing accurate predictive models of disease spread to inform public health planning. However, in many LMICs, traditional data sets on travel such as commuting surveys as well as non-traditional sources such as mobile phone data are lacking, or, where available, have only rarely been leveraged by the public health community. Evaluating the accuracy of available data to measure transmission-relevant travel may be further hampered by limited reporting of suspected and laboratory confirmed infections. Here, we leverage case data collected as part of a COVID-19 dashboard collated via daily reports from the Malagasy authorities on reported cases of SARS-CoV-2 across the 22 regions of Madagascar. We compare the order of the timing of when cases were reported with predictions from a SARS-CoV-2 metapopulation model of Madagascar informed using various measures of connectivity including a gravity model based on different measures of distance, Internal Migration Flow data, and mobile phone data. Overall, the models based on mobile phone connectivity and the gravity-based on Euclidean distance best predicted the observed spread. The ranks of the regions most remote from the capital were more difficult to predict but interestingly, regions where the mobile phone connectivity model was more accurate differed from those where the gravity model was most accurate. This suggests that there may be additional features of mobility or connectivity that were consistently underestimated using all approaches, but are epidemiologically relevant. This work highlights the importance of data availability and strengthening collaboration among different institutions with access to critical data - models are only as good as the data that they use, so building towards effective data-sharing pipelines is essential.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Tanjona Ramiadantsoa", + "author_inst": "Department of Life Science, University of Fianarantsoa, Madagascar & Department of Mathematics, University of Fianarantsoa, Madagascar & 3. Department of Integ" + }, + { + "author_name": "C. Jessica E. Metcalf", + "author_inst": "Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA & Princeton School of Public and International Affairs, Princeton Unive" + }, + { + "author_name": "Antso Hasina Raherinandrasana", + "author_inst": "Surveillance Unit, Ministry of Health of Madagascar & Faculty of Medicine, University of Antananarivo" + }, + { + "author_name": "Santatra Randrianarisoa", + "author_inst": "Mahaliana Labs SARL, Antananarivo, Madagascar" + }, + { + "author_name": "Benjamin L. Rice", + "author_inst": "Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA & Madagascar Health and Environmental Research (MAHERY), Maroantsetra," + }, + { + "author_name": "Amy Wesolowski", + "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA" + }, + { + "author_name": "Fidiniaina Mamy Randriatsarafara", + "author_inst": "Faculty of Medicine, University of Antananarivo & Direction of preventive Medicine, Ministry of Health" + }, + { + "author_name": "Fidisoa Rasambainarivo", + "author_inst": "Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA & Mahaliana Labs SARL, Antananarivo, Madagascar" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.08.01.454605", "rel_title": "The spike protein of SARS-CoV-2 induces endothelial inflammation through integrin \u03b15\u03b21 and NF-\u03baB", @@ -664261,133 +665114,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.29.21261312", - "rel_title": "COVID-ONE-humoral immune: The One-stop Database for COVID-19-specific Antibody Responses and Clinical Parameters", - "rel_date": "2021-08-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.29.21261312", - "rel_abs": "Coronavirus disease 2019 (COVID-19), which is caused by SARS-CoV-2, varies with regard to symptoms and mortality rates among populations. Humoral immunity plays critical roles in SARS-CoV-2 infection and recovery from COVID-19. However, differences in immune responses and clinical features among COVID-19 patients remain largely unknown. Here, we report a database for COVID-19-specific IgG/IgM immune responses and clinical parameters (COVID-ONE humoral immune). COVID-ONE humoral immunity is based on a dataset that contains the IgG/IgM responses to 21 of 28 known SARS-CoV-2 proteins and 197 spike protein peptides against 2,360 COVID-19 samples collected from 783 patients. In addition, 96 clinical parameters for the 2,360 samples and information for the 783 patients are integrated into the database. Furthermore, COVID-ONE humoral immune provides a dashboard for defining samples and a one-click analysis pipeline for a single group or paired groups. A set of samples of interest is easily defined by adjusting the scale bars of a variety of parameters. After the \"START\" button is clicked, one can readily obtain a comprehensive analysis report for further interpretation. COVID-ONE-humoral immune is freely available at www.COVID-ONE.cn.", - "rel_num_authors": 28, - "rel_authors": [ - { - "author_name": "Zhaowei Xu", - "author_inst": "Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong Universit" - }, - { - "author_name": "Yang Li", - "author_inst": "Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong Universit" - }, - { - "author_name": "Qing Lei", - "author_inst": "Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Likun Huang", - "author_inst": "Fujian Key Laboratory of Crop Breeding by Design, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agricult" - }, - { - "author_name": "Dan-yun Lai", - "author_inst": "Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong Universit" - }, - { - "author_name": "Shu-juan Guo", - "author_inst": "Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong Universit" - }, - { - "author_name": "He-wei Jiang", - "author_inst": "Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong Universit" - }, - { - "author_name": "Hongyan Hou", - "author_inst": "Department of Clinical Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Yun-xiao Zheng", - "author_inst": "Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong Universit" - }, - { - "author_name": "Xue-ning Wang", - "author_inst": "Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong Universit" - }, - { - "author_name": "Jiaoxiang Wu", - "author_inst": "Tongren Hospital, Shanghai Jiao Tong University School of Medicine" - }, - { - "author_name": "Ming-liang Ma", - "author_inst": "Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong Universit" - }, - { - "author_name": "Bo Zhang", - "author_inst": "Department of Clinical Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Hong Chen", - "author_inst": "Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong Universit" - }, - { - "author_name": "Caizheng Yu", - "author_inst": "Department of Public Health, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Jun-biao Xue", - "author_inst": "Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong Universit" - }, - { - "author_name": "Hai-nan Zhang", - "author_inst": "Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong Universit" - }, - { - "author_name": "Huan Qi", - "author_inst": "Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong Universit" - }, - { - "author_name": "Siqi Yu", - "author_inst": "Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University" - }, - { - "author_name": "Mingxi Lin", - "author_inst": "Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, School of Basic Medical Sciences, Fujian Medical University" - }, - { - "author_name": "Yandi Zhang", - "author_inst": "Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Xiaosong Lin", - "author_inst": "Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Zongjie Yao", - "author_inst": "Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Huiming Sheng", - "author_inst": "Tongren Hospital, Shanghai Jiao Tong University School of Medicine" - }, - { - "author_name": "Ziyong Sun", - "author_inst": "Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Feng Wang", - "author_inst": "Department of Clinical Laboratory, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Xionglin Fan", - "author_inst": "Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Sheng-ce Tao", - "author_inst": "Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong Universit" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.29.21261338", "rel_title": "Unrestricted Online Sharing of High-frequency, High-resolution Data on SARS-CoV-2 in Wastewater to Inform the COVID-19 Public Health Response in Greater Tempe, Arizona", @@ -665767,6 +666493,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, + { + "rel_doi": "10.1101/2021.07.23.21260984", + "rel_title": "Staffing and Capacity Planning for SARS-CoV-2 Monoclonal Antibody Infusion Facilities: A Performance Estimation Calculator based on Discrete-Event Simulations", + "rel_date": "2021-07-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.23.21260984", + "rel_abs": "ObjectiveThe COVID-19 pandemic has significantly stressed healthcare systems. The addition of monoclonal antibody (mAb) infusions, which prevent severe disease and reduce hospitalizations, to the repertoire of COVID-19 countermeasures offers the opportunity to reduce system stress but requires strategic planning and use of novel approaches. Our objective was to develop a web-based decision-support tool to help existing and future mAb infusion facilities make better and more informed staffing and capacity decisions.\n\nMaterials and MethodsUsing real-world observations from three medical centers operating with federal field team support, we developed a discrete-event simulation model and performed simulation experiments to assess performance of mAb infusion sites under different conditions.\n\nResults162,000 scenarios were evaluated by simulations. Our analyses revealed that it was more effective to add check-in staff than to add additional nurses for middle-to-large size sites with [≥] 2 infusion nurses; that scheduled appointments performed better than walk-ins when patient load was not high; and that reducing infusion time was particularly impactful when load on resources was only slightly above manageable levels.\n\nDiscussionPhysical capacity, check-in staff, and infusion time were as important as nurses for mAb sites. Health systems can effectively operate an infusion center under different conditions to provide mAb therapeutics even with relatively low investments in physical resources and staff.\n\nConclusionSimulations of mAb infusion sites were used to create a capacity planning tool to optimize resource utility and allocation in constrained pandemic conditions, and more efficiently treat COVID-19 patients at existing and future mAb infusion sites.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Caglar Caglayan", + "author_inst": "Johns Hopkins Applied Physics Laboratory" + }, + { + "author_name": "Jonathan Thornhill", + "author_inst": "Johns Hopkins University Applied Physics Laboratory" + }, + { + "author_name": "Miles A. Stewart", + "author_inst": "Johns Hopkins University Applied Physics Laboratory" + }, + { + "author_name": "Anastasia S. Lambrou", + "author_inst": "Johns Hopkins University Applied Physics Laboratory" + }, + { + "author_name": "Donald Richardson", + "author_inst": "Johns Hopkins University Applied Physics Laboratory" + }, + { + "author_name": "Kaitlin Rainwater-Lovett", + "author_inst": "Johns Hopkins Applied Physics Laboratory" + }, + { + "author_name": "Jeffrey D. Freeman", + "author_inst": "Johns Hopkins University Applied Physics Laboratory" + }, + { + "author_name": "Tiffany Pfundt", + "author_inst": "Assistant Secretary for Preparedness and Response, U.S. Department of Health and Human Services" + }, + { + "author_name": "John T. Redd", + "author_inst": "Assistant Secretary for Preparedness and Response, U.S. Department of Health and Human Services" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2021.07.31.21261387", "rel_title": "Vaccinated and unvaccinated individuals have similar viral loads in communities with a high prevalence of the SARS-CoV-2 delta variant", @@ -666343,57 +667120,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.28.21261286", - "rel_title": "Variations in Non-Pharmaceutical Interventions by State Correlate with COVID-19 Disease Outcomes", - "rel_date": "2021-07-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.28.21261286", - "rel_abs": "The COVID-19 pandemic highlighted the lack of understanding around effective public health interventions to curtail the spread of an emerging respiratory virus. Here, we examined the public health approaches implemented by each state to limit the spread and burden of COVID-19. Our analysis revealed that stronger statewide interventions positively correlated with fewer COVID-19 deaths, but some neighboring states with distinct intervention strategies had similar SARS-CoV-2 case trajectories. Additionally, more than two weeks is needed to observe an impact on SARS-CoV-2 cases after an intervention is implemented. These data provide a critical framework to inform future interventions during emerging pandemics.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Annika J Avery", - "author_inst": "Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Jiayi Wang", - "author_inst": "Statistics and Data Science Department, Carnegie Mellon University" - }, - { - "author_name": "Xinyu Ma", - "author_inst": "Statistics and Data Science Department, Carnegie Mellon University" - }, - { - "author_name": "Qingkai Pan", - "author_inst": "Statistics and Data Science Department, Carnegie Mellon University" - }, - { - "author_name": "Elizabeth E McGrady", - "author_inst": "Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Zongyuan Yuan", - "author_inst": "Statistics and Data Science Department, Carnegie Mellon University" - }, - { - "author_name": "Yuqing Liang", - "author_inst": "Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine" - }, - { - "author_name": "Rebecca Nugent", - "author_inst": "Statistics and Data Science Department, Carnegie Mellon University" - }, - { - "author_name": "Seema S Lakdawala", - "author_inst": "Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.28.21261228", "rel_title": "Effects of SARS-CoV-2 P.1 introduction and the impact of COVID-19 vaccination on the epidemiological landscape of Sao Jose Do Rio Preto, Brazil", @@ -667701,6 +668427,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.24.21261059", + "rel_title": "Data Analysis and Forecasting of COVID-19 Pandemic in Kuwait", + "rel_date": "2021-07-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.24.21261059", + "rel_abs": "The first COVID 19 case of Kuwait was announced on 24th February, 2020 and the daily new cases increases exponentially since then until May, 2020 when the first wave started to decline. The same exponential dynamics has been observed between January and March, 2021. The forecast of new cases and death recorded daily is crucial so that health experts and citizens can be guided in order to avoid escalation of the pandemic. We propose a deterministic method to predict the basic reproduction number Ro of first and second wave of COVID-19 cases in Kuwait and also to forecast the daily new cases and death of the pandemic in the country. Forecasting has been done using ARIMA model, Exponential smoothing model, Holts method, Prophet forecasting model and machine learning models like log-linear, polynomial and support vector regressions. The results presented aligned with other methods used to predict Ro in first and second waves and the forecasting clearly shows the trend of the pandemic in Kuwait. The deterministic prediction of Ro is a good forecasting tool available during the exponential phase of the contagion, which shows an increasing trend during the beginning of the first and second waves of the pandemic in Kuwait.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Kayode Oshinubi", + "author_inst": "University Grenoble Alpes" + }, + { + "author_name": "Fahimah Al-Awadhi", + "author_inst": "Kuwait University" + }, + { + "author_name": "Mustapha Rachdi", + "author_inst": "University Grenoble Alpes" + }, + { + "author_name": "Jacques Demongeot", + "author_inst": "University Grenoble Alpes" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.22.21260973", "rel_title": "A regression discontinuity analysis of the social distancing recommendations for older adults in Sweden during COVID-19", @@ -668237,97 +668994,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.28.21261212", - "rel_title": "An investigation of spatial-temporal patterns and predictions of the COVID-19 pandemic in Colombia, 2020-2021", - "rel_date": "2021-07-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.28.21261212", - "rel_abs": "Colombia announced the first case of severe acute respiratory syndrome coronavirus 2 on March 6, 2020. Since then, the country has reported a total of 4,240,982 cases and 106,544 deaths as of June 30, 2021. This motivates an investigation of the SARS-CoV-2 transmission dynamics at the national and regional level using case incidence data. Mathematical models are employed to estimate the transmission potential and perform short-term forecasts of the COVID-19 epidemic trajectory in Colombia. Furthermore, geographic heterogeneity of COVID-19 in Colombia is examined along with the analysis of mobility and social media trends, showing that the increase in mobility in July 2020 and January 2021 were correlated with surges in case incidence. The estimation of national and regional reproduction numbers shows sustained disease transmission during the early phase of the pandemic, exhibiting sub-exponential growth dynamics. Moreover, most recent estimates of reproduction number are >1.0 at the national and regional levels as of May 30, 2021. Further, the 30-day ahead short-term forecasts obtained from Richards model present a sustained decline in case counts in contrast to the sub-epidemic and GLM model. Nevertheless, our spatial analysis in Colombia shows distinct variations in incidence rate patterns across different departments that can be grouped into four distinct clusters. Lastly, the correlation of social media trends and adherence to social distancing measures is observed by the fact that a spike in the number of tweets indicating the stay-at-home orders was observed in November 2020 when the case incidence had already plateaued.\n\nAuthor summaryAs the COVID-19 pandemic continues to spread across Colombia, studies highlighting the intensity of the pandemic become imperative for appropriate resource allocation and informing public health policies. In this study we utilize mathematical models to infer the transmission dynamics of SARS-CoV-2 at the regional and national level as well as short-term forecast the COVID-19 epidemic trajectory. Moreover, we examine the geographic heterogeneity of the COVID-19 case incidence in Colombia along with the analysis of mobility and social media trends in relation to the observed COVID-19 case incidence in the country. The estimates of reproduction numbers at the national and regional level show sustained disease transmission as of May 30, 2021. Moreover, the 30-day ahead short-term forecasts for the most recent time-period (June 1-June 30, 2021) generated from the mathematical models needs to be interpreted with caution as the Richards model point towards a sustained decline in case incidence contrary to the GLM and sub-epidemic wave model. Nevertheless, the spatial analysis in Colombia shows distinct variations in incidence rate patterns across different departments that can be grouped into four distinct clusters. Lastly, the social media and mobility trends explain the occurrence of case resurgences over the time.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Amna Tariq", - "author_inst": "Georgia State University" - }, - { - "author_name": "Tsira Chakhaia", - "author_inst": "Georgia State University" - }, - { - "author_name": "Sushma Dahal", - "author_inst": "Georgia State University" - }, - { - "author_name": "Alexander Ewing", - "author_inst": "Georgia State University" - }, - { - "author_name": "Xinyi Hua", - "author_inst": "Georgia Southern University" - }, - { - "author_name": "Sylvia K. Ofori", - "author_inst": "Georgia Southern University" - }, - { - "author_name": "Olaseni Prince", - "author_inst": "Georgia State University" - }, - { - "author_name": "Argita Salindri", - "author_inst": "Georgia State University" - }, - { - "author_name": "Ayotomiwa Ezekiel Adeniyi", - "author_inst": "Georgia State University" - }, - { - "author_name": "Juan M. Banda", - "author_inst": "Georgia State University" - }, - { - "author_name": "Pavel Skums", - "author_inst": "Georgia State University" - }, - { - "author_name": "Ruiyan Luo", - "author_inst": "Georgia State University" - }, - { - "author_name": "Leidy Y. Lara-Diaz", - "author_inst": "Universidad de Concepcion, Concepcion, Chile" - }, - { - "author_name": "Raimund Burger", - "author_inst": "Universidad de Concepcion, Concepcion, Chile" - }, - { - "author_name": "Isaac Chun-Hai Fung", - "author_inst": "Georgia Southern University" - }, - { - "author_name": "Eunha Shim", - "author_inst": "Soongsil University" - }, - { - "author_name": "Alexander Kirpich", - "author_inst": "Georgia State University" - }, - { - "author_name": "Anuj Srivastava", - "author_inst": "Florida State University" - }, - { - "author_name": "Gerardo Chowell", - "author_inst": "Georgia State University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.28.21261233", "rel_title": "Genomic epidemiology of SARS-CoV-2 divulge B.1, B.1.36, and B.1.1.7 as the most dominant lineages in first, second, and third wave of SARS-CoV-2 infections in Pakistan", @@ -669511,6 +670177,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.23.21260716", + "rel_title": "Covid-19 Associated Hepatitis in children (CACH) during the second wave of SARS-CoV-2 infections in Central India: Is it a complication or transient phenomenon.", + "rel_date": "2021-07-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.23.21260716", + "rel_abs": "ObjectiveWhile pediatric population has largely remained free of severe COVID-19, in some cases SARS-CoV-2 infection has been associated with complications like Multiple Inflammatory Syndrome in children (MIS-C). We mention another unique presentation subsequent to asymptomatic infection of SARS-CoV-2, a unique form of hepatitis designated by us as COVID-19 Associated Hepatitis in Children (CAH-C). The contrasting clinical presentations, temporal association and viral parameters of CAH-C cases, to the MIS-C cases are presented here.\n\nMethodsAs a retrospective and follow-up observational study we reviewed all children testing positive for SARS-CoV-2 during study period. Children presenting with \"sudden onset of hepatitis, elevated transaminases, non-obstructive jaundice, lacking marked inflammatory responses and without evidence of (a) other known causes of acute hepatitis or previous underlying liver disease (b) multi-system involvement\" were classified as CAH-C, are described here.\n\nResultsAmong 475 children tested positive, 47 patients presented with hepatitis, 37 patients had features of CAH-C, having symptoms of hepatitis only, with un-elevated inflammatory markers and uneventful recovery following supportive treatment. Whereas remaining 10 MIS-C hepatitis had protracted illness, multiple system involvement, required admission to critical care, and had mortality of 30%.\n\nConclusionWith the emergence of newer variants of concern (VOC) including the Delta variant which predominated the second wave of infections in India and has now spread to more than 142 countries with changing presentations, CAH-C might be one of them. Cases of such new entities need to be identified early and differentiated from other emerging syndromes in children during the ongoing pandemic for preventing adversities by timely intervention.\n\nConflicts of interestThe authors declare that they have no conflicts of interest related to the study or its findings. All authors have contributed to the conceptualization and manuscript writing of the study, the final version is approved by all the authors. We declare there are no competing interests involved among the authors.\n\nFunding and ethics approvalCurrent research received no specific grant from any funding agency in the public, commercial or not-for-profit sectors. The follow-up and analysis work was performed after obtaining due approval of human ethics committee of the institution (Ref no. IEC/BMC/80/21).", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Sumit K Rawat", + "author_inst": "Bundelkhand Medical College, India" + }, + { + "author_name": "Ajit anand Asati", + "author_inst": "Bundelkhand Medical College, India" + }, + { + "author_name": "Ashish Jain", + "author_inst": "Bundelkhand Medical College, India" + }, + { + "author_name": "Radha Kant Ratho", + "author_inst": "PGIMER, Chandigarh India" + }, + { + "author_name": "Nitu Mishra", + "author_inst": "Bundelkhand Medical College,India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2021.07.28.21259040", "rel_title": "Outbreak of P.3 (Theta) SARS-CoV-2 emerging variant of concern among food service workers in Louisiana", @@ -670063,69 +670764,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, - { - "rel_doi": "10.1101/2021.07.25.21260967", - "rel_title": "Influence of Novel Coronavirus COVID-19 and HIV: A Scoping Review of Hospital Course and Symptomatology", - "rel_date": "2021-07-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.25.21260967", - "rel_abs": "BackgroundAn outbreak of novel coronavirus (SARS- CoV-2) was observed on December 2019 in Wuhan, China which led to a global pandemic declared in March 2020. As a consequence, it imposed delirious consequences in patients with underlying co - morbid conditions that make them immunocompromised. The purpose of this paper is to provide an in - depth review of influence of COVID - 19 in patients with underlying HIV in terms of mortality and hospitalization.\n\nAuthors also aim to provide a thorough risk analysis of hospitalization, ICU admission and mortality of PLWH and COVID-19. The secondary objective was to analyze the CD4+ count variations and outcome of COVID - 19 and to correlate if ART provided a protective role. Authors also aim to provide an evaluation of typical clinical presentation of COVID-19 in PLWH. ART is found to show activity against SARS-CoV-2 in vitro, and there is some similarity in the structure of HIV-1 gp41 and S2 proteins of SARS-CoV since they both belong to +ssRNA type.\n\nMethodsWe conducted a literature review using search engines namely, Cochrane, PubMed and Google Scholar. The following keywords were targeted: \"COVID-19,\" \"SARS-CoV-2,\" and \"HIV.\" We included case reports, case series, and cohort (retrospective and prospective) studies. We excluded clinical trials and review articles. We came across 23 articles that met the inclusion criteria. PRISMA guidelines were followed for study acquisition (Fig. 9).\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=176 SRC=\"FIGDIR/small/21260967v1_fig9.gif\" ALT=\"Figure 9\">\nView larger version (20K):\norg.highwire.dtl.DTLVardef@1df3963org.highwire.dtl.DTLVardef@30c4c8org.highwire.dtl.DTLVardef@1c729a4org.highwire.dtl.DTLVardef@7f0543_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig.9C_FLOATNO PRISMA guidelines for study acquisition\n\nC_FIG ResultsFrom the 23 studies, we found a total of 651 PLWH with confirmed COVID-19 (549, 91, and 11 in cohorts, case series, and case reports, respectively). The overall risk of hospital admission from pooled data of the 23 reviewed articles was 69.13% (450/651), ICU admission was 12.90% (84/651) in total infected patients, and 18.67% (84/450) among hospitalized patients. The overall case fatality rate from the 23 reviewed articles was 11.21 (73/651).A weak positive correlation was found between CD4+ counts and hospital admissions in case series and case reports, while the weak negative correlation was found in cohorts. For mortality, there was a negative weak association in the cohorts and in case series, while a weak positive was seen in case reports (Fig.7). We assessed the presenting symptoms of PLWH with COVID-19, and our review demonstrated this group does not greatly differ from the rest of the population, as their common presenting symptoms were cough, fever, and SOB.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC=\"FIGDIR/small/21260967v1_fig7.gif\" ALT=\"Figure 7\">\nView larger version (37K):\norg.highwire.dtl.DTLVardef@132a333org.highwire.dtl.DTLVardef@1788387org.highwire.dtl.DTLVardef@10335a5org.highwire.dtl.DTLVardef@1b70c29_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig.7C_FLOATNO Results: As scoping review of HIV and COVID-19\n\nC_FIG ConclusionOur results indicated that there was a high rate of hospitalization, ICU admission, and mortality among patients living with HIV and COVID-19. PLWH needs to be noted as a high-risk group for COVID-19 complications and severity. We recommend that PLWH be closely monitored by their physicians and strictly adhere to antiretroviral therapy and standard universal COVID-19 precautions.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Mona Sheikh", - "author_inst": "Department of Medicine, Larkin Community Hospital South Miami, Florida, US" - }, - { - "author_name": "Shavy Nagpal", - "author_inst": "The Research Institute of St. Joe's Hamilton" - }, - { - "author_name": "Madiha Zaidi", - "author_inst": "Department of Medicine, Larkin Community Hospital South Miami, Florida, US" - }, - { - "author_name": "Rupalakshmi Vijayan", - "author_inst": "Department of Medicine, Larkin Community Hospital South Miami, Florida, US" - }, - { - "author_name": "Wanessa Matos", - "author_inst": "Department of Medicine, Larkin Community Hospital South Miami, Florida, US" - }, - { - "author_name": "Neguemadji Ngardig Ngaba", - "author_inst": "Department of Medicine, Larkin Community Hospital South Miami, Florida, US" - }, - { - "author_name": "Lordstrong Akano", - "author_inst": "Department of Medicine, Larkin Community Hospital South Miami, Florida, US" - }, - { - "author_name": "Shazia Q. Shah", - "author_inst": "Department of Medicine, Larkin Community Hospital South Miami, Florida, US" - }, - { - "author_name": "Samia Jahan", - "author_inst": "Department of Medicine, Larkin Community Hospital South Miami, Florida, US" - }, - { - "author_name": "Camille Go", - "author_inst": "Larkin Hospital" - }, - { - "author_name": "Sindhu Thevuthasan", - "author_inst": "Department of Medicine, Larkin Community Hospital South Miami, Florida, US" - }, - { - "author_name": "George Michel", - "author_inst": "Department of Medicine, Larkin Community Hospital South Miami, Florida, US" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "hiv aids" - }, { "rel_doi": "10.1101/2021.07.26.21261082", "rel_title": "Altered pre-existing SARS-CoV-2-specific T cell responses in elderly individuals", @@ -671761,6 +672399,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, + { + "rel_doi": "10.1101/2021.07.23.21260998", + "rel_title": "Risk of Myocarditis from COVID-19 Infection in People Under Age 20: A Population-Based Analysis", + "rel_date": "2021-07-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.23.21260998", + "rel_abs": "BackgroundThere have been recent reports of myocarditis (including myocarditis, pericarditis or myopericarditis) as a side-effect of mRNA-based COVID-19 vaccines, particularly in young males. Less information is available regarding the risk of myocarditis from COVID-19 infection itself. Such data would be helpful in developing a complete risk-benefit analysis for this population.\n\nMethodsA de-identified, limited data set was created from the TriNetX Research Network, aggregating electronic health records from 48 mostly large U.S. Healthcare Organizations (HCOs). Inclusion criteria were a first COVID-19 diagnosis during the April 1, 2020 - March 31, 2021 time period, with an outpatient visit 1 month to 2 years before, and another 6 months to 2 years before that. Analysis was stratified by sex and age (12-17, 12-15, 16-19). Patients were excluded for any prior cardiovascular condition. Primary outcome was an encounter diagnosis of myocarditis within 90 days following the index date. Rates of COVID-19 cases and myocarditis not identified in the system were estimated and the results adjusted accordingly. Wilson score intervals were used for 95% confidence intervals due to the very low probability outcome.\n\nResultsFor the 12-17-year-old male cohort, 6/6,846 (0.09%) patients developed myocarditis overall, with an adjusted rate per million of 450 cases (Wilson score interval 206 - 982). For the 12-15 and 16-19 male age groups, the adjusted rates per million were 601 (257 - 1,406) and 561 (240 - 1,313).\n\nFor 12-17-year-old females, there were 3 (0.04%) cases of myocarditis of 7,361 patients. The adjusted rate was 213 (73 - 627) per million cases. For the 12-15- and 16-19-year-old female cohorts the adjusted rates per million cases were 235 (64 - 857) and 708 (359 - 1,397).\n\nThe outcomes occurred either within 5 days (40.0%) or from 19-82 days (60.0%).\n\nConclusionsMyocarditis (or pericarditis or myopericarditis) from primary COVID19 infection occurred at a rate as high as 450 per million in young males. Young males infected with the virus are up 6 times more likely to develop myocarditis as those who have received the vaccine.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Mendel E Singer", + "author_inst": "Case Western Reserve University School of Medicine, Cleveland, Ohio, USA" + }, + { + "author_name": "Ira B. Taub", + "author_inst": "Akron Children's Hospital Heart Center, Akron, Ohio, USA" + }, + { + "author_name": "David C. Kaelber", + "author_inst": "Case Western Reserve University at The MetroHealth System, Cleveland, Ohio, USA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.07.26.21261119", "rel_title": "Safety and efficacy of COVID-19 hyperimmune globulin (HIG) solution in the treatment of active COVID-19 infection- Findings from a Prospective, Randomized, Controlled, Multi-Centric Trial", @@ -672229,65 +672894,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2021.07.27.453973", - "rel_title": "Executable Network of SARS-CoV-2-Host Interaction Predicts Drug Combination Treatments", - "rel_date": "2021-07-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.27.453973", - "rel_abs": "The COVID-19 pandemic has pushed healthcare systems globally to a breaking point. The urgent need for effective and affordable COVID-19 treatments calls for repurposing combinations of approved drugs. The challenge is to identify which combinations are likely to be most effective and at what stages of the disease. Here, we present the first disease-stage executable signalling network model of SARS-CoV-2-host interactions used to predict effective repurposed drug combinations for treating early- and late-stage severe disease. Using our executable model, we performed in silico screening of 9870 pairs of 140 potential targets and have identified 12 new drug combinations. Camostat and Apilimod were predicted to be the most promising combination in effectively supressing viral replication in the early stages of severe disease and were validated experimentally in human Caco-2 cells. Our study further demonstrates the power of executable mechanistic modelling to enable rapid pre-clinical evaluation of combination therapies tailored to disease progression. It also presents a novel resource and expandable model system that can respond to further needs in the pandemic.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Rowan Howell", - "author_inst": "University College London" - }, - { - "author_name": "Matthew A Clarke", - "author_inst": "University College London" - }, - { - "author_name": "Ann-Kathrin Reuschl", - "author_inst": "University College London" - }, - { - "author_name": "Tianyi Chen", - "author_inst": "University College London" - }, - { - "author_name": "Sean Abott-Imboden", - "author_inst": "University College London" - }, - { - "author_name": "Mervyn Singer", - "author_inst": "University College London" - }, - { - "author_name": "David M Lowe", - "author_inst": "University College London" - }, - { - "author_name": "Clare L Bennett", - "author_inst": "University College London" - }, - { - "author_name": "Benjamin Chain", - "author_inst": "University College London" - }, - { - "author_name": "Clare Jolly", - "author_inst": "University College London" - }, - { - "author_name": "Jasmin Fisher", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "systems biology" - }, { "rel_doi": "10.1101/2021.07.24.21261074", "rel_title": "A significant increase in Tuberculosis diagnosis is required to mitigate the impact of COVID-19 on its future burden", @@ -673763,6 +674369,73 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.07.23.21260676", + "rel_title": "Can we clinically identify pre-symptomatic and asymptomatic COVID-19?", + "rel_date": "2021-07-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.23.21260676", + "rel_abs": "ObjectivesCOVID-19 has had a severe impact on morbidity and mortality among nursing home (NH) residents. Earlier detection of SARS-CoV-2 may position us to better mitigate risk of spread. Both asymptomatic or pre-symptomatic transmission are common in outbreaks, and threshold temperatures, such as 38C, for screening for infection could miss timely detection in the majority.\n\nDesignRetrospective cohort study using electronic health records\n\nMethodsWe hypothesized that in long-term care residents, temperature trends with SARS-CoV-2 infection could identify infection in pre-symptomatic and asymptomatic individuals earlier. We collected information about age and other demographics, baseline temperature, and specific comorbidities. We created standardized definitions, and an alternative hypothetical model to test measures of temperature variation and compare outcomes to the VA reality.\n\nSettings and participantsOur subjects were 6,176 residents of the VA NHs who underwent SARS-CoV-2 trigger testing.\n\nResultsWe showed that a change from baseline of >0.4C identifies 47% of the SARS-CoV-2 positive NH residents early, and achieves earlier detection by 42.2 hours. Range improves early detection to 55% when paired with a 37.2C cutoff, and achieves earlier detection by 44.4 hours. Temperature elevation >0.4C from baseline, when combined with a 0.7C range, would detect 52% early, leading to earlier detection by more than 3 days in 22% of the residents. This earlier detection comes at the expense of triggering 57,793 tests, as compared to the number of trigger tests ordered in the VA system of 40,691.\n\nConclusion and implicationsOur model suggests that current clinical screening for SARS-CoV-2 in NHs can be substantially improved upon by triggering testing using a patient-derived baseline temperature with a 0.4C degree relative elevation or temperature variability of 0.7C trigger threshold for SARS-CoV2 testing. Such triggers could be automated in facilities that track temperatures in their electronic records.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Salaheldin Elhamamsy", + "author_inst": "Alpert Medical School of Brown University" + }, + { + "author_name": "Frank Devone", + "author_inst": "Providence Veterans Administration Medical Center, Center on Innovation-Long Term Services and Supports" + }, + { + "author_name": "Tom Bayer", + "author_inst": "Alpert Medical School of Brown University" + }, + { + "author_name": "Christopher Halladay", + "author_inst": "Providence Veterans Administration Medical Center, Center on Innovation-Long Term Services and Supports" + }, + { + "author_name": "Marilyne Cadieux", + "author_inst": "Alpert Medical School of Brown University" + }, + { + "author_name": "Kevin McConeghy", + "author_inst": "Providence Veterans Administration Medical Center, Center on Innovation-Long Term Services and Supports" + }, + { + "author_name": "Ashna Rajan", + "author_inst": "Alpert Medical School of Brown University" + }, + { + "author_name": "Moniyka Sachar", + "author_inst": "Alpert Medical School of Brown University" + }, + { + "author_name": "Nadia Mujahid", + "author_inst": "Brown University" + }, + { + "author_name": "Aman Nanda", + "author_inst": "Alpert Medical School of Brown University" + }, + { + "author_name": "Lynn McNicoll", + "author_inst": "Alpert Medical School of Brown University" + }, + { + "author_name": "James Rudolph", + "author_inst": "Providence Veterans Administration Medical Center, Center on Innovation-Long Term Services and Supports" + }, + { + "author_name": "Stefan Gravenstein", + "author_inst": "Alpert Medical School of Brown University, Providence Veterans Administration Medical Center, Center on Innovation-Long Term Services and Supports, Brown School" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "geriatric medicine" + }, { "rel_doi": "10.1101/2021.07.26.453805", "rel_title": "CIGB-300 synthetic peptide, an antagonist of CK2 kinase activity, as a treatment for Covid-19. A computational biology approach", @@ -674199,37 +674872,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.07.22.21260793", - "rel_title": "A spatio-temporal study of state-wide case-fatality risks during the first wave of the COVID-19 pandemic in Mexico", - "rel_date": "2021-07-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.22.21260793", - "rel_abs": "We study case-fatality risks (risks of dying in sick individuals) corresponding to the first wave of the COVID-19 pandemic in Mexico. Spatio-temporal analysis by state were performed, mainly from April to September 2020, including descriptive analyses through mapping and time series representations, and the fit of linear mixed models and time series clustering to analyze trends by state. The association of comorbidities and other variables with the risks were studied by fitting a spatial panel data linear model (splm). As results, we observed that on average the greatest risks were reached by July, and that highest risks were observed in some states, Baja California Norte, Chiapas, and Sonora; interestingly, some densely populated states, as Mexico City, had lower values. Different trends by state were observed, and a four-order polynomial, including fixed and random effects, was necessary to model them. The most general structure is one in which the risks increase and then decrease and was observed in states belonging to two clusters; however, there is a cluster corresponding to states with a retarded increase, and another in which increasing risks through time were observed. A cyclic behavior in terms of states having a second increasing trend was observed. Finally, according to the splm, percentage of men, being in the group of 50 years and over, chronic kidney disease failure, cardiovascular disease, asthma, and hypertension were positively associated with the case-fatality risks. This analysis may provide valuable insight into COVID-19 dynamics in future outbreaks, as well as the determinants of these trends at a state level; and, by combining spatial and temporal information, provide a better understanding of COVID-19 case-fatality.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Ricardo Ram\u00edrez-Aldana", - "author_inst": "Instituto Nacional de Geriatria" - }, - { - "author_name": "Lizbeth Naranjo", - "author_inst": "Departamento de Matem\u00e1ticas, Facultad de Ciencias, Universidad Nacional Aut\u00f3noma de M\u00e9xico" - }, - { - "author_name": "Juan Carlos Gomez-Verjan", - "author_inst": "Instituto Nacional de Geriatr\u00eda" - }, - { - "author_name": "Omar Yaxmehen Bello-Chavolla", - "author_inst": "Instituto Nacional de Geriatria" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.23.21260991", "rel_title": "Knowledge, attitude, and practices towards COVID-19 among the Rohingya refugees in Coxs Bazar, Bangladesh.", @@ -675661,6 +676303,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2021.07.22.21260952", + "rel_title": "Variant-driven multi-wave pattern of COVID-19 via Machine Learning clustering of spike protein mutations", + "rel_date": "2021-07-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.22.21260952", + "rel_abs": "Never before such a vast amount of data, including genome sequencing, has been collected for any viral pandemic than for the current case of COVID-19. This offers the possibility to trace the virus evolution and to assess the role mutations play in its spread within the population, in real time. To this end, we focused on the Spike protein for its central role in mediating viral outbreak and replication in host cells. Employing the Levenshtein distance on the Spike protein sequences, we designed a machine learning algorithm yielding a temporal clustering of the available dataset. From this, we were able to identify and define emerging persistent variants that are in agreement with known evidences. Our novel algorithm allowed us to define persistent variants as chains that remain stable over time and to highlight emerging variants of epidemiological interest as branching events that occur over time. Hence, we determined the relationship and temporal connection between variants of interest and the ensuing passage to dominance of the current variants of concern. Remarkably, the analysis and the relevant tools introduced in our work serve as an early warning for the emergence of new persistent variants once the associated cluster reaches 1% of the time-binned sequence data. We validated our approach and its effectiveness on the onset of the Alpha variant of concern. We further predict that the recently identified lineage AY.4.2 ( Delta plus) is causing a new emerging variant. Comparing our findings with the epidemiological data we demonstrated that each new wave is dominated by a new emerging variant, thus confirming the hypothesis of the existence of a strong correlation between the birth of variants and the pandemic multi-wave temporal pattern. The above allows us to introduce the epidemiology of variants that we described via the Mutation epidemiological Renormalisation Group (MeRG) framework.\n\nHighlightsO_LIObjectives To study the relation among Spike protein mutations, the emergence of relevant variants and the multi-wave pattern of the COVID-19 pandemic.\nC_LIO_LISetting Genomic sequencing of the SARS-CoV-2 Spike proteins in the UK nations (England, Scotland, Wales). Epi-demiological data for the number of infections in the UK nations, South Africa, California and India.\nC_LIO_LIMethodology We design a machine learning algorithm, based on the Levenshtein distance on the Spike protein sequences, that leads to a temporal clustering of the available dataset, from which we define emerging persistent variants. The above allows us to introduce the epidemiology of variants that we described via the Mutation epidemiological Renormalisation Group (MeRG) framework.\nC_LIO_LIResults We show that:\nO_LIOur approach, based only on the Spike protein sequence, allows to efficiently identify the variants of concern (VoCs) and of interest (VoIs), as well as other emerging variants occurring during the diffusion of the virus.\nC_LIO_LIWithin our time-ordered chain analysis, a branching relation emerges, thus permitting to reconstruct the evolutionary diversification of Spike variants and the establishment of the epidemiologically relevant ones.\nC_LIO_LIOur analysis provides an early warning for the emergence of new persistent variants once its associated dominant Spike sequence reaches 1% of the time-binned sequence data. Validation on the onset of the Alpha VoC shows that our early warning is triggered 6 weeks before the WHO classification decision.\nC_LIO_LIComparison with the epidemiological data demonstrates that each new wave is dominated by a new emerging variant, thus confirming the hypothesis that there is a strong correlation between the emergence of variants and the multi-wave temporal pattern depicting the viral spread.\nC_LIO_LIA theory of variant epidemiology is established, which describes the temporal evolution of the number of infected by different emerging variants via the MeRG approach. This is corroborated by empirical data.\nC_LI\nC_LI\n\nO_LIConclusions Applying a ML approach to the temporal variability of the Spike protein sequence enables us to identify, classify and track emerging virus variants. Our analysis is unbiased, in the sense that it does not require any prior knowledge of the variant characteristics, and our results are validated by other informed methods that define variants based on the complete genome. Furthermore, correlating persistent variants of our approach to epidemiological data, we discover that each new wave of the COVID-19 pandemic is driven and dominated by a new emerging variant. Our results are therefore indispensable for further studies on the evolution of SARS-CoV-2 and the prediction of evolutionary patterns that determine current and future mutations of the Spike proteins, as well as their diversification and persistence during the viral spread. Moreover, our ML algorithm works as an efficient early warning system for the emergence of new persistent variants that may pose a threat of triggering a new wave of COVID-19. Capable of a timely identification of potential new epidemiological threats when the variant only represents 1% of the new sequences, our ML strategy is a crucial tool for decision makers to define short and long term strategies to curb future outbreaks. The same methodology can be applied to other viral diseases, influenza included, if sufficient sequencing data is available.\nC_LI", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Adele de Hoffer", + "author_inst": "Politecnico di Torino" + }, + { + "author_name": "Shahram Vatani", + "author_inst": "IP2I de Lyon, CNRS, Lyon University" + }, + { + "author_name": "Corentin Cot", + "author_inst": "IP2I de Lyon, CNRS, Lyon University" + }, + { + "author_name": "Giacomo Cacciapaglia", + "author_inst": "IP2I de Lyon, CNRS, Lyon University" + }, + { + "author_name": "Maria Luisa Chiusano", + "author_inst": "University Federico II of Naples" + }, + { + "author_name": "Andrea Cimarelli", + "author_inst": "ENS Lyon and University of Lyon 1" + }, + { + "author_name": "Francesco Conventi", + "author_inst": "INFN sezione di Napoli, Universita di Napoli Parthenope" + }, + { + "author_name": "Antonio Giannini", + "author_inst": "INFN sezione di Napoli, Universita di Napoli Federico II" + }, + { + "author_name": "Stefan Hohenegger", + "author_inst": "IP2I de Lyon, CNRS, Lyon University" + }, + { + "author_name": "Francesco Sannino", + "author_inst": "Universita di Napoli Federico II, Scuola Superiore Meridionale, INFN sezione di Napoli, CP3-Origins and the Danish Institute for Advanced Study (University of S" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.22.21260852", "rel_title": "Comparison of infected and vaccinated transplant recipients highlights the role of Tfh and neutralizing IgG in COVID-19 protection", @@ -676161,1357 +676858,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.07.21.21260624", - "rel_title": "New susceptibility loci for severe COVID-19 by detailed GWAS analysis in European populations", - "rel_date": "2021-07-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.21.21260624", - "rel_abs": "Given the highly variable clinical phenotype of Coronavirus disease 2019 (COVID-19), a deeper analysis of the host genetic contribution to severe COVID-19 is important to improve our understanding of underlying disease mechanisms. Here, we describe an extended GWAS meta-analysis of a well-characterized cohort of 3,260 COVID-19 patients with respiratory failure and 12,483 population controls from Italy, Spain, Norway and Germany/Austria, including stratified analyses based on age, sex and disease severity, as well as targeted analyses of chromosome Y haplotypes, the human leukocyte antigen (HLA) region and the SARS-CoV-2 peptidome. By inversion imputation, we traced a reported association at 17q21.31 to a highly pleiotropic [~]0.9-Mb inversion polymorphism and characterized the potential effects of the inversion in detail. Our data, together with the 5th release of summary statistics from the COVID-19 Host Genetics Initiative, also identified a new locus at 19q13.33, including NAPSA, a gene which is expressed primarily in alveolar cells responsible for gas exchange in the lung.", - "rel_num_authors": 334, - "rel_authors": [ - { - "author_name": "Frauke Degenhardt", - "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany" - }, - { - "author_name": "David Ellinghaus", - "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany" - }, - { - "author_name": "Simonas Juzenas", - "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany" - }, - { - "author_name": "Jon Lerga-Jaso", - "author_inst": "Institut de Biotecnologia i de Biomedicina, Universitat Autonoma de Barcelona, Bellaterra (Barcelona), Spain" - }, - { - "author_name": "Mareike Wendorff", - "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany" - }, - { - "author_name": "Douglas Maya-Miles", - "author_inst": "Hospital Universitario Virgen del Rocio de Sevilla, Sevilla, Spain" - }, - { - "author_name": "Florian Uellendahl-Werth", - "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany" - }, - { - "author_name": "Hesham ElAbd", - "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany" - }, - { - "author_name": "Malte Christoph Ruehlemann", - "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany" - }, - { - "author_name": "Jatin Arora", - "author_inst": "Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Onur Oezer", - "author_inst": "Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Ploen, Germany" - }, - { - "author_name": "Ole Bernt Lenning", - "author_inst": "Research Department, Stavanger University Hospital" - }, - { - "author_name": "Ronny Myhre", - "author_inst": "Norwegian Institute of Public Health, Division of Health Data and Digitalization, Department of Genetics and Bioinformatics (HDGB) Oslo, Norway" - }, - { - "author_name": "May Sissel Vadla", - "author_inst": "Randaberg Municipality, Norway" - }, - { - "author_name": "Eike Matthias Wacker", - "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany" - }, - { - "author_name": "Lars Wienbrandt", - "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany" - }, - { - "author_name": "Aaron Blandino Ortiz", - "author_inst": "Department of Intensive Care, Hospital Universitario Ramon y Cajal, Instituto Ramon y Cajal de Investigacion Sanitaria (IRYCIS), University of Alcala, Madrid, S" - }, - { - "author_name": "Adolfo de Salazar", - "author_inst": "Ibs.Granada Instituto de Investigacion Biosanitaria, Granada, Spain" - }, - { - "author_name": "Adolfo Garrido Chercoles", - "author_inst": "Osakidetza Basque Health Service, Donostialdea Integrated Health Organisation, Clinical Biochemistry Department, San Sebastian, Spain" - }, - { - "author_name": "Adriana Palom", - "author_inst": "Vall d'Hebron Institut de Recerca (VHIR), Vall B24Hebron Hospital Universitari, Barcelona, Spain" - }, - { - "author_name": "Agustin Ruiz", - "author_inst": "Research Center and Memory Clinic. Ace Alzheimer Center Barcelona, Universitat Internacional de Catalunya, Spain" - }, - { - "author_name": "Alba-Estela Garcia-Fernandez", - "author_inst": "Department of Biochemistry, University Hospital Vall d'Hebron, Barcelona, Spain" - }, - { - "author_name": "Albert Blanco-Grau", - "author_inst": "Department of Biochemistry, University Hospital Vall d'Hebron, Barcelona, Spain" - }, - { - "author_name": "Alberto Mantovani", - "author_inst": "IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy" - }, - { - "author_name": "Alberto Zanella", - "author_inst": "University of Milan, Milan, Italy" - }, - { - "author_name": "Aleksander Rygh Holten", - "author_inst": "Department of Acute Medicine, Oslo University Hospital, Oslo, Norway" - }, - { - "author_name": "Alena Mayer", - "author_inst": "Charite Universitaetsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Alessandra Bandera", - "author_inst": "Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy" - }, - { - "author_name": "Alessandro Cherubini", - "author_inst": "Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy" - }, - { - "author_name": "Alessandro Protti", - "author_inst": "IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy" - }, - { - "author_name": "Alessio Aghemo", - "author_inst": "IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy" - }, - { - "author_name": "Alessio Gerussi", - "author_inst": "European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy" - }, - { - "author_name": "Alfredo Ramirez", - "author_inst": "Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital Cologne, University " - }, - { - "author_name": "Alice Braun", - "author_inst": "Charite Universitaetsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Almut Nebel", - "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany" - }, - { - "author_name": "Ana Barreira", - "author_inst": "Liver Unit, Department of Internal Medicine, Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain" - }, - { - "author_name": "Ana Lleo", - "author_inst": "IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy" - }, - { - "author_name": "Ana Teles", - "author_inst": "Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Ploen, Germany" - }, - { - "author_name": "Anders Kildal", - "author_inst": "Department of Anesthesiology and Intensive Care, University Hospital of North Norway, Tromso, Norway" - }, - { - "author_name": "Andrea Biondi", - "author_inst": "Pediatric Departement and Centro Tettamanti- European Reference Network (ERN) PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM/Osped" - }, - { - "author_name": "Andrea Caballero-Garralda", - "author_inst": "Biochemistry Department, Echevarne Laboratory, Sant Cugat del Valles, Barcelona, Spain" - }, - { - "author_name": "Andrea Ganna", - "author_inst": "Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland" - }, - { - "author_name": "Andrea Gori", - "author_inst": "Centre for Multidisciplinary Research in Health Science (MACH), University of Milan, Milan, Italy" - }, - { - "author_name": "Andreas Glueck", - "author_inst": "Klinik fuer Innere Medizin I, Universitaetsklinikum Schleswig-Holstein, Campus Kiel, Germany" - }, - { - "author_name": "Andreas Lind", - "author_inst": "Department of Microbiology, Oslo University Hospital, Oslo, Norway" - }, - { - "author_name": "Anja Tanck", - "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany" - }, - { - "author_name": "Anke Hinney", - "author_inst": "Department of Child and Adolescent Psychiatry, University Hospital Essen, University of Duisburg-Essen, Essen, Germany" - }, - { - "author_name": "Anna Carreras Carreras Nolla", - "author_inst": "Genomes for Life-GCAT lab. Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain" - }, - { - "author_name": "Anna Ludovica Fracanzani", - "author_inst": "University of Milan, Milan, Italy" - }, - { - "author_name": "Anna Peschuck", - "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany" - }, - { - "author_name": "Annalisa Cavallero", - "author_inst": "Laboratory of Microbiology, San Gerardo Hospital, Monza, Italy" - }, - { - "author_name": "Anne Ma Dyrhol-Riise", - "author_inst": "Department of Infectious diseases, Oslo University Hospital, Oslo, Norway" - }, - { - "author_name": "Antonella Ruello", - "author_inst": "Humanitas Gavazzeni-Castelli, Bergamo, Italy" - }, - { - "author_name": "Antonio Julia", - "author_inst": "Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Barcelona, Spain" - }, - { - "author_name": "Antonio Muscatello", - "author_inst": "Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy" - }, - { - "author_name": "Antonio Pesenti", - "author_inst": "University of Milan, Milan, Italy" - }, - { - "author_name": "Antonio Voza", - "author_inst": "Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy" - }, - { - "author_name": "Ariadna Rando-Segura", - "author_inst": "Microbiology Department, Hospital Universitari Vall d'Hebron, Barcelona, Spain" - }, - { - "author_name": "Aurora Solier", - "author_inst": "Department of Respiratory Diseases, Hospital Universitario Ramon y Cajal, Instituto Ramon y Cajal de Investigacion Sanitaria (IRYCIS), University of Alcala, Cen" - }, - { - "author_name": "Axel Schmidt", - "author_inst": "Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany" - }, - { - "author_name": "Beatriz Cortes", - "author_inst": "Genomes for Life-GCAT lab. Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain" - }, - { - "author_name": "Beatriz Mateos", - "author_inst": "Department of Gastroenterology, Hospital Universitario Ramon y Cajal, University of Alcala, Instituto Ramon y Cajal de Investigacion Sanitaria (IRYCIS), Madrid," - }, - { - "author_name": "Beatriz Nafria-Jimenez", - "author_inst": "Osakidetza Basque Health Service, Donostialdea Integrated Health Organisation, Clinical Biochemistry Department, San Sebastian, Spain" - }, - { - "author_name": "Benedikt Schaefer", - "author_inst": "Medical University of Innsbruck, Department of Medicine I, Gastroenterology, Hepatology and Endocrinology, Innsbruck, Austria" - }, - { - "author_name": "Bjoern Jensen", - "author_inst": "Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Duesseldorf, Medical Faculty Heinrich Heine University, Duesseldorf, Ger" - }, - { - "author_name": "Carla Bellinghausen", - "author_inst": "Department of Respiratory Medicine and Allergology, University Hospital, Goethe University, Frankfurt am Main, Germany" - }, - { - "author_name": "Carlo Maj", - "author_inst": "Institute of Genomic Statistics and Bioinformatics, University Hospital Bonn, Medical Faculty University of Bonn, Venusberg-Campus 1, Bonn, Germany" - }, - { - "author_name": "Carlos Ferrando", - "author_inst": "Centro de Investigacion Biomedica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain" - }, - { - "author_name": "Carmen de la Horra", - "author_inst": "University of Sevilla, Sevilla, Spain" - }, - { - "author_name": "Carmen Quereda", - "author_inst": "Department of Infectious Diseases, Hospital Universitario Ramon y Cajal, Instituto Ramon y Cajal de Investigacion Sanitaria (IRYCIS), University of Alcala, Madr" - }, - { - "author_name": "Carsten Skurk", - "author_inst": "Charite Universitaetsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Charlotte Thibeault", - "author_inst": "Charite Universitaetsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Chiara Scollo", - "author_inst": "Department of Transfusion Medicine and Haematology Laboratory, San Gerardo Hospital, Monza, Italy" - }, - { - "author_name": "Christian Herr", - "author_inst": "Department of Internal Medicine V, Pneumology, Allergology and Intensive Care Medicine, University Hospital Saarland, Homburg/Saar, Germany" - }, - { - "author_name": "Christoph D Spinner", - "author_inst": "Technical University of Munich, School of Medicine, University Hospital rechts der Isar, Department of Internal Medicine II, Munich, Germany" - }, - { - "author_name": "Christoph Gassner", - "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany" - }, - { - "author_name": "Christoph Lange", - "author_inst": "Respiratory Medicine & International Health, University of Luebeck, Luebeck, Germany" - }, - { - "author_name": "Cinzia Hu", - "author_inst": "Internal Medicine Department,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy" - }, - { - "author_name": "Cinzia Paccapelo", - "author_inst": "Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy" - }, - { - "author_name": "Clara Lehmann", - "author_inst": "Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Claudio Angelini", - "author_inst": "Humanitas Clinical and Research Center, IRCCS, Milan, Italy" - }, - { - "author_name": "Claudio Cappadona", - "author_inst": "Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy" - }, - { - "author_name": "Clinton Azuure", - "author_inst": "Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Ploen, Germany" - }, - { - "author_name": "Cristiana Bianco", - "author_inst": "Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy" - }, - { - "author_name": "Cristina Cea", - "author_inst": "Department of Biochemistry, University Hospital Vall d'Hebron, Barcelona, Spain" - }, - { - "author_name": "Cristina Sancho", - "author_inst": "Osakidetza Basque Health Service, Basurto University Hospital, Respiratory Service, Bilbao, Spain" - 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Hospital Universitario Clinico San Cecilio, Granada, Spain" - }, - { - "author_name": "Nicola Montano", - "author_inst": "University of Milan, Milan, Italy" - }, - { - "author_name": "Nicole Braun", - "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany" - }, - { - "author_name": "Nicole Ludwig", - "author_inst": "Center of Human and Molecular Biology, Department of Human Genetics, University Hospital Saarland, Homburg/Saar, Germany" - }, - { - "author_name": "Nikolaus Marx", - "author_inst": "Department of Internal Medicine I, RWTH Aachen University Hospital, Aachen, Germany" - }, - { - "author_name": "Nilda Martinez", - "author_inst": "Department of Anesthesiology, Hospital Universitario Ramon y Cajal, Instituto Ramon y Cajal de Investigacion Sanitaria (IRYCIS), Madrid, Spain" - }, - { - "author_name": "Oliver A Cornely", - "author_inst": "Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Oliver Witzke", - "author_inst": "Department of Infectious Diseases, University Hospital Essen, University Duisburg-Essen, Essen, Germany" - }, - { - "author_name": "Orazio Palmieri", - "author_inst": "Gastroenterology Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy" - }, - { - "author_name": "Paola Faverio", - "author_inst": "Pulmonary Unit, San Gerardo Hospital, Monza, Italy" - }, - { - "author_name": "Paoletta Preatoni", - "author_inst": "Humanitas Clinical and Research Center, IRCCS, Milan, Italy" - }, - { - "author_name": "Paolo Bonfanti", - "author_inst": "School of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy" - }, - { - "author_name": "Paolo Omodei", - "author_inst": "Humanitas Clinical and Research Center, IRCCS, Milan, Italy" - }, - { - "author_name": "Paolo Tentorio", - "author_inst": "IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy" - }, - { - "author_name": "Pedro Castro", - "author_inst": "Hospital Clinic, University of Barcelona, and IDIBAPS, Barcelona, Spain" - }, - { - "author_name": "Pedro M Rodrigues", - "author_inst": "Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, University of the Basque Country (UPV/EH" - }, - { - "author_name": "Pedro Pablo Espana", - "author_inst": "Osakidetza Basque Health Service, Galdakao Hospital, Respiratory Service, Galdakao, Spain" - }, - { - "author_name": "Per Hoffmann", - "author_inst": "Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany" - }, - { - "author_name": "Philip Rosenstiel", - "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany" - }, - { - "author_name": "Philipp Schommers", - "author_inst": "Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Phillip Suwalski", - "author_inst": "Charite Universitaetsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Raul de Pablo", - "author_inst": "Department of Intensive Care, Hospital Universitario Ramon y Cajal, Instituto Ramon y Cajal de Investigacion Sanitaria (IRYCIS), University of Alcala, Madrid, S" - }, - { - "author_name": "Ricard Ferrer", - "author_inst": "Intensive Care Department, Vall d'Hebron University Hospital, SODIR-VHIR research group, Barcelona, Spain" - }, - { - "author_name": "Robert Bals", - "author_inst": "Department of Internal Medicine V, Pneumology, Allergology and Intensive Care Medicine, University Hospital Saarland, Homburg/Saar, Germany" - }, - { - "author_name": "Roberta Gualtierotti", - "author_inst": "University of Milan, Milan, Italy" - }, - { - "author_name": "Rocio Gallego-Duran", - "author_inst": "Instituto de Biomedicina de Sevilla (IBIS), Sevilla, Spain" - }, - { - "author_name": "Rosa Nieto", - "author_inst": "Department of Respiratory Diseases, Hospital Universitario Ramon y Cajal, Instituto Ramon y Cajal de Investigacion Sanitaria (IRYCIS), University of Alcala, Cen" - }, - { - "author_name": "Rossana Carpani", - "author_inst": "Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy" - }, - { - "author_name": "Ruben Morilla", - "author_inst": "Consejo Superior de Investigaciones cientificas, Sevilla, Spain" - }, - { - "author_name": "Salvatore Badalamenti", - "author_inst": "IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy" - }, - { - "author_name": "Sammra Haider", - "author_inst": "Department of Medicine, More & Romsdal Hospital Trust, Molde, Norway" - }, - { - "author_name": "Sandra Ciesek", - "author_inst": "Institute of Medical Virology, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany" - }, - { - "author_name": "Sandra May", - "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany" - }, - { - "author_name": "Sara Bombace", - "author_inst": "Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy" - }, - { - "author_name": "Sara Marsal", - "author_inst": "Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Barcelona, Spain" - }, - { - "author_name": "Sara Pigazzini", - "author_inst": "Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland" - }, - { - "author_name": "Sebastian Klein", - "author_inst": "Division of Intensive Care and Emergency Medicine, Department of Internal Medicine, Medical University Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Serena Pelusi", - "author_inst": "University of Milan, Milan, Italy" - }, - { - "author_name": "Sibylle Wilfling", - "author_inst": "Zentrum fuer Humangenetik Regensburg, Regensburg, Germany" - }, - { - "author_name": "Silvano Bosari", - "author_inst": "University of Milan, Milan, Italy" - }, - { - "author_name": "Sonja Volland", - "author_inst": "Hannover Unified Biobank, Hannover Medical School, Hannover, Germany" - }, - { - "author_name": "Soren Brunak", - "author_inst": "Novo Nordisk Foundation Center for Protein Research, Disease Systems Biology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denm" - }, - { - "author_name": "Soumya Raychaudhuri", - "author_inst": "Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "Stefan Schreiber", - "author_inst": "Klinik fuer Innere Medizin I, Universitaetsklinikum Schleswig-Holstein, Campus Kiel, Germany" - }, - { - "author_name": "Stefanie Heilmann-Heimbach", - "author_inst": "Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany" - }, - { - "author_name": "Stefano Aliberti", - "author_inst": "Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy" - }, - { - "author_name": "Stephan Ripke", - "author_inst": "Charite Universitaetsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Susanne Dudman", - "author_inst": "Institute of Clinical Medicine, University of Oslo, Oslo, Norway" - }, - { - "author_name": "Tanja Wesse", - "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany" - }, - { - "author_name": "Tenghao Zheng", - "author_inst": "School of Biological Sciences, Monash University, Clayton, VIC, Australia" - }, - { - "author_name": "Thomas Bahmer", - "author_inst": "Klinik fuer Innere Medizin I, Universitaetsklinikum Schleswig-Holstein, Campus Kiel, Germany" - }, - { - "author_name": "Thomas Eggermann", - "author_inst": "Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany" - }, - { - "author_name": "Thomas Illig", - "author_inst": "Hannover Unified Biobank, Hannover Medical School, Hannover, Germany" - }, - { - "author_name": "Thorsten Brenner", - "author_inst": "Department of Anesthesiology and Intensive Care Medicine, University Hospital Essen, University Duisburg-Essen, Essen, Germany" - }, - { - "author_name": "Tomas Pumarola", - "author_inst": "Department of Microbiology, University Hospital Vall d'Hebron, Barcelona, Spain" - }, - { - "author_name": "Torsten Feldt", - "author_inst": "Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Duesseldorf, Medical Faculty Heinrich Heine University, Duesseldorf, Ger" - }, - { - "author_name": "Trine Folseraas", - "author_inst": "Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital " - }, - { - "author_name": "Trinidad Gonzalez Cejudo", - "author_inst": "Biochemistry Unit. Hospital Universitario Clinico San Cecilio, Granada, Spain" - }, - { - "author_name": "Ulf Landmesser", - "author_inst": "Charite Universitaetsmedizin Berlin, Berlin Institute of Health, Berlin Germany" - }, - { - "author_name": "Ulrike Protzer", - "author_inst": "Institute of Virology, Technical University Munich/Helmholtz Zentrum Muenchen, Munich, Germany" - }, - { - "author_name": "Ute Hehr", - "author_inst": "Zentrum fuer Humangenetik Regensburg, Regensburg, Germany" - }, - { - "author_name": "Valeria Rimoldi", - "author_inst": "Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy" - }, - { - "author_name": "Valter Monzani", - "author_inst": "Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy" - }, - { - "author_name": "Vegard Skogen", - "author_inst": "Department of Infectious Diseases, University Hospital of North Norway, Tromso, Norway" - }, - { - "author_name": "Verena Keitel", - "author_inst": "Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Duesseldorf, Medical Faculty Heinrich Heine University, Duesseldorf, Ger" - }, - { - "author_name": "Verena Kopfnagel", - "author_inst": "Hannover Unified Biobank, Hannover Medical School, Hannover, Germany" - }, - { - "author_name": "Vicente Friaza", - "author_inst": "Consejo Superior de Investigaciones cientificas, Sevilla, Spain" - }, - { - "author_name": "Victor Andrade", - "author_inst": "Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital Cologne, University " - }, - { - "author_name": "Victor Moreno", - "author_inst": "Catalan Institute of Oncology (ICO), Barcelona, Spain" - }, - { - "author_name": "Wolfgang Albrecht", - "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany" - }, - { - "author_name": "Wolfgang Peter", - "author_inst": "Stefan-Morsch-Stiftung, Birkenfeld, Germany" - }, - { - "author_name": "Wolfgang Poller", - "author_inst": "Charite Universitaetsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Xavier Farre", - "author_inst": "Genomes for Life-GCAT lab. Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain" - }, - { - "author_name": "Xiaoli Yi", - "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany" - }, - { - "author_name": "Xiaomin Wang", - "author_inst": "Charite Universitaetsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Yascha Khodamoradi", - "author_inst": "Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt & Goethe University Frankfurt, Frankfurt am Main, Germany" - }, - { - "author_name": "Zehra Karadeniz", - "author_inst": "Charite Universitaetsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Anna Latiano", - "author_inst": "Gastroenterology Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy" - }, - { - "author_name": "Siegfried Goerg", - "author_inst": "Institute of Transfusionsmedicine, University Hospital Schleswig-Holstein (UKSH), Germany" - }, - { - "author_name": "Petra Bacher", - "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany" - }, - { - "author_name": "Philipp Koehler", - "author_inst": "Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany" - }, - { - "author_name": "Florian Tran", - "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany" - }, - { - "author_name": "Heinz Zoller", - "author_inst": "Medical University of Innsbruck, Department of Medicine I, Gastroenterology, Hepatology and Endocrinology, Innsbruck, Austria" - }, - { - "author_name": "Eva C Schulte", - "author_inst": "Institute of Virology, Technical University Munich/Helmholtz Zentrum Muenchen, Munich, Germany" - }, - { - "author_name": "Bettina Heidecker", - "author_inst": "Charite Universitaetsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Kerstin U Ludwig", - "author_inst": "Institute of Human Genetics, University of Bonn School of Medicine & University Hospital Bonn, Bonn, Germany" - }, - { - "author_name": "Javier Fernandez", - "author_inst": "Hospital Clinic, University of Barcelona, and IDIBAPS, Barcelona, Spain" - }, - { - "author_name": "Manuel Romero-Gomez", - "author_inst": "Centro de Investigacion Biomedica en Red en Enfermedades Hepaticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain" - }, - { - "author_name": "Agustin Albillos", - "author_inst": "Department of Gastroenterology, Hospital Universitario Ramon y Cajal, University of Alcala, Instituto Ramon y Cajal de Investigacion Sanitaria (IRYCIS), Madrid," - }, - { - "author_name": "Pietro Invernizzi", - "author_inst": "European Reference Network on Hepatological Diseases (ERN RARE-LIVER), San Gerardo Hospital, Monza, Italy" - }, - { - "author_name": "Maria Buti", - "author_inst": "Universitat Autonoma de Barcelona, Bellatera, Spain" - }, - { - "author_name": "Stefano Duga", - "author_inst": "Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy" - }, - { - "author_name": "Luis Bujanda", - "author_inst": "Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute, Donostia University Hospital, University of the Basque Country (UPV/EH" - }, - { - "author_name": "Johannes R Hov", - "author_inst": "Section for Gastroenterology, Department of Transplantation Medicine, Division for Cancer Medicine, Surgery and Transplantation, Oslo University Hospital Riksho" - }, - { - "author_name": "Tobias L Lenz", - "author_inst": "Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Ploen, Germany" - }, - { - "author_name": "Rosanna Asselta", - "author_inst": "IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy" - }, - { - "author_name": "Rafael de Cid", - "author_inst": "Genomes for Life-GCAT lab. Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain" - }, - { - "author_name": "Luca Valenti", - "author_inst": "University of Milan, Milan, Italy" - }, - { - "author_name": "Tom Hemming Karlsen", - "author_inst": "Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital " - }, - { - "author_name": "Mario Caceres", - "author_inst": "Institut de Biotecnologia i de Biomedicina, Universitat Autonoma de Barcelona, Bellaterra (Barcelona), Spain" - }, - { - "author_name": "Andre Franke", - "author_inst": "University Hospital Schleswig-Holstein (UKSH), Campus Kiel, Germany" - }, - { - "author_name": "- COVICAT study group", - "author_inst": "" - }, - { - "author_name": "- Covid-19 Aachen Study (COVAS)", - "author_inst": "" - }, - { - "author_name": "- Pa COVID-19 Study Group", - "author_inst": "" - }, - { - "author_name": "- The Humanitas COVID-19 Task Force", - "author_inst": "" - }, - { - "author_name": "- The Humanitas Gavazzeni COVID-19 Task Force", - "author_inst": "" - }, - { - "author_name": "- Norwegian SARS-CoV-2 Study group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2021.07.21.21260961", "rel_title": "Reduced neutralizing activity of post-SARS-CoV-2 vaccination serum against variants B.1.617.2, B.1.351, B.1.1.7+E484K and a sub-variant of C.37", @@ -678651,6 +677997,81 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.07.23.453352", + "rel_title": "Understanding the role of memory re-activation and cross-reactivity in the defense against SARS-CoV-2", + "rel_date": "2021-07-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.23.453352", + "rel_abs": "Recent efforts in understanding the course and severity of SARS-CoV-2 infections have highlighted both potential beneficial as well as detrimental effects of cross-reactive antibodies derived from memory immunity. Specifically, due to a significant degree of sequence similarity between SARS-CoV-2 and other members of the coronavirus family, memory B-cells that emerged from previous infections with endemic human coronaviruses (HCoVs) could be re-activated upon encountering the newly emerged SARS-CoV-2, thus prompting the production of cross-reactive antibodies. Understanding the affinity and concentration of these potentially cross-reactive antibodies to the new SARS-CoV-2 antigens is therefore particularly important when assessing both existing immunity against common HCoVs and adverse effects like antibody-dependent enhancement (ADE) in COVID-19. However, these two fundamental parameters cannot easily be deconvoluted by surface-based assays like enzyme-linked immunosorbent assays (ELISAs) which are routinely used to assess cross-reactivity.\n\nHere, we have used microfluidic antibody-affinity profiling (MAAP) to quantitatively evaluate the humoral immune response in COVID-19 convalescent patients by determining both antibody affinity and concentration against spike antigens of SARS-CoV-2 directly in nine convalescent COVID-19 patient and three pre-pandemic sera that were seropositive for common HCoVs. All 12 sera contained low concentrations of high affinity antibodies against spike antigens of HCoV-NL63 and HCoV-HKU1, indicative of past exposure to these pathogens, while the affinity against the SARS-CoV-2 spike protein was lower. These results suggest that cross-reactivity as a consequence of memory re-activation upon an acute SARS-CoV-2 infection may not be a significant factor in generating immunity against SARS-CoV-2.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Viola Denninger", + "author_inst": "Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, United Kingdom" + }, + { + "author_name": "Catherine K. Xu", + "author_inst": "Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom" + }, + { + "author_name": "Georg Meisl", + "author_inst": "Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom" + }, + { + "author_name": "Alexey S. Morgunov", + "author_inst": "Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, United Kingdom" + }, + { + "author_name": "Sebastian Fiedler", + "author_inst": "Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, United Kingdom" + }, + { + "author_name": "Alison Ilsley", + "author_inst": "Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, United Kingdom" + }, + { + "author_name": "Marc Emmenegger", + "author_inst": "Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland" + }, + { + "author_name": "Anisa Y. Malik", + "author_inst": "Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, United Kingdom" + }, + { + "author_name": "Monika A. Piziorska", + "author_inst": "Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, United Kingdom" + }, + { + "author_name": "Matthias M. Schneider", + "author_inst": "Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom" + }, + { + "author_name": "Sean R. A. Devenish", + "author_inst": "Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, United Kingdom" + }, + { + "author_name": "Vasilis Kosmoliaptsis", + "author_inst": "Department of Surgery, University of Cambridge, Addenbrookes Hospital, Cambridge, CB2 0QQ, United Kingdom" + }, + { + "author_name": "Adriano Aguzzi", + "author_inst": "Institute of Neuropathology, University of Zurich, 8091 Zurich, Switzerland" + }, + { + "author_name": "Heike Fiegler", + "author_inst": "Fluidic Analytics, Unit A, The Paddocks Business Centre, Cherry Hinton Road, Cambridge CB1 8DH, United Kingdom" + }, + { + "author_name": "Tuomas P. J. Knowles", + "author_inst": "Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.07.23.453571", "rel_title": "Effective presence of antibodies against common human coronavirus in IgG immunoglobulin medicinal products.", @@ -679047,205 +678468,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2021.07.19.21260139", - "rel_title": "Plasma cell-free DNA promise disease monitoring and tissue injury assessment of COVID-19", - "rel_date": "2021-07-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.19.21260139", - "rel_abs": "COVID-19 is a huge threat to global health. Due to the lack of definitive etiological therapeutics currently, effective disease monitoring is of high clinical value for better healthcare and management of the large number of COVID-19 patients. In this study, we recruited 37 COVID-19 patients, collected 176 blood samples upon diagnosis and during treatment, and analyzed cell-free DNA (cfDNA) in these samples. We report gross abnormalities in cfDNA of COVID-19 patients, including elevated GC content, altered molecule size and end motif patterns. More importantly, such cfDNA characteristics reflect patient-specific physiological conditions during treatment. Further analysis on tissue origin tracing of cfDNA reveals frequent tissue injuries in COVID-19 patients, which is supported by clinical diagnoses. Hence, we demonstrate the translational merit of cfDNA as valuable analyte for effective disease monitoring, as well as tissue injury assessment in COVID-19 patients.", - "rel_num_authors": 46, - "rel_authors": [ - { - "author_name": "Xin Jin", - "author_inst": "BGI-Shenzhen" - }, - { - "author_name": "Yanqun Wang", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Jinjin Xu", - "author_inst": "BGI-Shenzhen" - }, - { - "author_name": "Yimin Li", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Fanjun Cheng", - "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Yuxue Luo", - "author_inst": "BGI-Shenzhen" - }, - { - "author_name": "Haibo Zhou", - "author_inst": "The Sixth Affiliated Hospital of Guangzhou Medical University" - }, - { - "author_name": "Shanwen Lin", - "author_inst": "Yangjiang People Hospital" - }, - { - "author_name": "Fei Xiao", - "author_inst": "Department of Infectious Diseases, Guangdong Provincial Key Laboratory of Biomedical Imaging, Guangdong Provincial Engineering Research Center of Molecular Imag" - }, - { - "author_name": "Lu Zhang", - "author_inst": "Institute of Infectious disease, Guangzhou Eighth People's Hospital of Guangzhou Medical University" - }, - { - "author_name": "Yu Lin", - "author_inst": "BGI-Shenzhen" - }, - { - "author_name": "Zhaoyong Zhang", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Yan Jin", - "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Fang Zheng", - "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Wei Chen", - "author_inst": "School of Medicine, South China University of Technology" - }, - { - "author_name": "Airu Zhu", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Ye Tao", - "author_inst": "BGI-Shenzhen" - }, - { - "author_name": "Jingxian Zhao", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Tingyou Kuo", - "author_inst": "BGI-Shenzhen" - }, - { - "author_name": "Yuming Li", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Lingguo Li", - "author_inst": "BGI-Shenzhen" - }, - { - "author_name": "Liyan Wen", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Rijing Ou", - "author_inst": "BGI-Shenzhen" - }, - { - "author_name": "Fang Li", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Long Lin", - "author_inst": "BGI-Shenzhen" - }, - { - "author_name": "Yanjun Zhang", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Jing Sun", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Hao Yuan", - "author_inst": "BGI-Shenzhen" - }, - { - "author_name": "Zhen Zhuang", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Haixi Sun", - "author_inst": "BGI-Shenzhen" - }, - { - "author_name": "Zhao Chen", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Jie Li", - "author_inst": "BGI-Shenzhen" - }, - { - "author_name": "Jianfen Zhuo", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Dongsheng Chen", - "author_inst": "BGI-Shenzhen" - }, - { - "author_name": "Shengnan Zhang", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Yuzhe Sun", - "author_inst": "BGI-Shenzhen" - }, - { - "author_name": "Peilan Wei", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Jinwei Yuan", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Tian Xu", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Huanming Yang", - "author_inst": "BGI-Shenzhen" - }, - { - "author_name": "Jian Wang", - "author_inst": "BGI-Shenzhen" - }, - { - "author_name": "Xun Xu", - "author_inst": "BGI-Shenzhen" - }, - { - "author_name": "Nanshan Zhong", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Yonghao Xu", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Kun Sun", - "author_inst": "Shenzhen Bay Laboratory" - }, - { - "author_name": "Jincun Zhao", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2021.07.19.21260758", "rel_title": "The efficacy of vaccines in the context of COVID-19 and its variants: Role of Spatio-temporal boundary", @@ -680677,6 +679899,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.19.21260714", + "rel_title": "Anaphylactic events in mRNA vaccines: a reporting case-control study", + "rel_date": "2021-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.19.21260714", + "rel_abs": "BackgroundmRNA vaccines are a novel method of eliciting immunity, and play a significant role in the global fight against COVID-19. Anaphylactic reactions are a widespread concern driving vaccine hesitancy due to the serious and potentially fatal nature of anaphylaxis. A quantitative estimation of the risk of anaphylactic and ana-phylactoid reactions deriving from mRNA vaccines is of a significant public health importance.\n\nObjectiveTo estimate the relative Reporting Odds Ratio of anaphylactic and ana-phylactoid reactions following mRNA vaccination vis-a-vis other vaccinations.\n\nDesignReporting case-control study.\n\nSettingPersons reporting adverse events following vaccination to VAERS whose reports were received between 01 January 2000 and 02 July 2021, inclusive.\n\nPatientsEach case of anaphylaxis or anaphylactoid reaction was matched with 2.7 unique controls on average, by gender and age rounded to the nearest integer.\n\nMeasurementsOverall and stratified Reporting Odds Ratios (ROR) were calculated. Stratified contingency tables were tested for homogeneity using the Breslow-Day procedure, and Cochran-Mantel-Haenszel statistics were calculated to test the hypothesis of a ROR of unity.\n\nResults2,665 cases of anaphylaxis or anaphylactoid reactions and 7,125 controls of non-anaphylactic/anaphylactoid reports were compared. The ROR of an anaphylactic or anaphylactoid reaction was 1.325 (95% CI: 1.212 - 1.448, p < 0.001). The matched set of cases and controls revealed an expected inhomogeneity by sex (with women slightly more likely to report anaphylactic presentations) and age band strata (with a bimodal distribution that reflects the common incidence of anaphylactic and allergic pathologies). No significant increase in the risk of anaphylactic adverse events was witnessed among persons who self-reported previous allergic reactions to vaccines. A slightly elevated ROR was observed with patients who reported a history of allergic reactions to NSAIDs and/or fluoroquinolone antibiotics. The precise meaning and relevance of this finding remains to be elucidated.\n\nLimitationsAs a reporting study using data from VAERS, our analysis is subject tunder- and overreporting, the extent of each of which is not known with any degree of precision. Since the Emergency Use Authorizations for both mRNA vaccines mandate reporting of all serious adverse events, reporting bias is likely in favour of non-mRNA vaccines, where such reporting is not mandatory in adults. Consequently, this analysis may exaggerate the ROR of anaphylactic and anaphylactoid events associated with mRNA vaccines, which may in reality be significantly lower.\n\nConclusionsmRNA vaccination is not associated with a statistically significant higher risk of reporting an anaphylactic adverse event to VAERS. Anaphylaxis is a serious but very rare complication of all immunisations. No significant increase in reporting odds was found in any age group or gender, nor in most cases of previously known allergic adverse events in relation to vaccines. This study contributes to the growing body of evidence proving the safety and tolerability of mRNA vaccines.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Chris von Csefalvay", + "author_inst": "Starschema" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.19.21260744", "rel_title": "Association between reactogenicity and SARS-CoV-2 antibodies after the second dose of the BNT162b2 COVID-19 vaccine", @@ -681473,109 +680714,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.19.21260759", - "rel_title": "Development and validation of a prognostic model for COVID-19: a population-based cohort study in Iceland", - "rel_date": "2021-07-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.19.21260759", - "rel_abs": "BackgroundThe severity of SARS-CoV-2 infection varies from asymptomatic state to severe respiratory failure and the clinical course is difficult to predict. The aim of the study was to develop a prognostic model to predict the severity of COVID-19 at the time of diagnosis and determine risk factors for severe disease.\n\nMethodsAll SARS-CoV-2-positive adults in Iceland were prospectively enrolled into a telehealth service at diagnosis. A multivariable proportional-odds logistic regression model was derived from information obtained during the enrollment interview with those diagnosed before May 1, 2020 and validated in those diagnosed between May 1 and December 31, 2020. Outcomes were defined on an ordinal scale; no need for escalation of care during follow-up, need for outpatient visit, hospitalization, and admission to intensive care unit (ICU) or death. Risk factors were summarized as odds ratios (OR) adjusted for confounders identified by a directed acyclic graph.\n\nResultsThe prognostic model was derived from and validated in 1,625 and 3,131 individuals, respectively. In total, 375 (7.9%) only required outpatient visits, 188 (4.0%) were hospitalized and 50 (1.1%) were either admitted to ICU or died due to complications of COVID-19. The model included age, sex, body mass index (BMI), current smoking, underlying conditions, and symptoms and clinical severity score at enrollment. Discrimination and calibration were excellent for outpatient visit or worse (C-statistic 0.75, calibration intercept 0.04 and slope 0.93) and hospitalization or worse (C-statistic 0.81, calibration intercept 0.16 and slope 1.03). Age was the strongest risk factor for adverse outcomes with OR of 75-compared to 45-year-olds, ranging from 5.29-17.3. Higher BMI consistently increased the risk and chronic obstructive pulmonary disease and chronic kidney disease correlated with worse outcomes.\n\nConclusionOur prognostic model can accurately predict the outcome of SARS-CoV-2 infection using information that is available at the time of diagnosis.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Elias Eythorsson", - "author_inst": "Landspitali - The National University Hospital of Iceland" - }, - { - "author_name": "Valgerdur Bjarnadottir", - "author_inst": "Landspitali - The National University Hospital of Iceland" - }, - { - "author_name": "Hrafnhildur Linnet Runolfsdottir", - "author_inst": "Landspitali - The National University Hospital of Iceland" - }, - { - "author_name": "Dadi Helgason", - "author_inst": "Landspitali - The National University Hospital of Iceland" - }, - { - "author_name": "Ragnar Freyr Ingvarsson", - "author_inst": "Landspitali - The National University Hospital of Iceland" - }, - { - "author_name": "Helgi K Bjornsson", - "author_inst": "Landspitali - The National University Hospital of Iceland" - }, - { - "author_name": "Lovisa Bjork Olafsdottir", - "author_inst": "Landspitali - The National University Hospital of Iceland" - }, - { - "author_name": "Solveig Bjarnadottir", - "author_inst": "Landspitali - The National University Hospital of Iceland" - }, - { - "author_name": "Arnar Snaer Agustsson", - "author_inst": "Landspitali - The National University Hospital of Iceland" - }, - { - "author_name": "Kristin Oskarsdottir", - "author_inst": "Landspitali - The National University Hospital of Iceland" - }, - { - "author_name": "Hrafn Hliddal Thorvaldsson", - "author_inst": "Landspitali - The National University Hospital of Iceland" - }, - { - "author_name": "Gudrun Kristjansdottir", - "author_inst": "Landspitali - The National University Hospital of Iceland" - }, - { - "author_name": "Aron Hjalti Bjornsson", - "author_inst": "Landspitali - The National University Hospital of Iceland" - }, - { - "author_name": "Arna R Emilsdottir", - "author_inst": "Landspitali - The National University Hospital of Iceland" - }, - { - "author_name": "Brynja Armannsdottir", - "author_inst": "Landspitali - The National University Hospital of Iceland" - }, - { - "author_name": "Olafur Gudlaugsson", - "author_inst": "Landspitali - The National University Hospital of Iceland" - }, - { - "author_name": "Sif Hansdottir", - "author_inst": "Landspitali - The National University Hospital of Iceland" - }, - { - "author_name": "Magnus Gottfredsson", - "author_inst": "Landspitali - The National University Hospital of Iceland" - }, - { - "author_name": "Agnar Bjarnason", - "author_inst": "Landspitali - The National University Hospital of Iceland" - }, - { - "author_name": "Martin I Sigurdsson", - "author_inst": "Landspitali - The National University Hospital of Iceland" - }, - { - "author_name": "Olafur S Indridason", - "author_inst": "Landspitali - The National University Hospital of Iceland" - }, - { - "author_name": "Runolfur Palsson", - "author_inst": "Landspitali - The National University Hospital of Iceland" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.19.21260694", "rel_title": "SARS-CoV-2-specific Humoral Immune Responses after A Single Dose of Inactivated Whole-virus SARS-CoV-2 Vaccine in Kidney Transplant Recipients: An Initial Report", @@ -682771,6 +681909,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.07.21.21260906", + "rel_title": "Disentangling post-vaccination symptoms from early COVID-19", + "rel_date": "2021-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.21.21260906", + "rel_abs": "BackgroundIdentifying and testing individuals likely to have SARS-CoV-2 is critical for infection control, including post-vaccination. Vaccination is a major public health strategy to reduce SARS-CoV-2 infection globally. Some individuals experience systemic symptoms post-vaccination, which overlap with COVID-19 symptoms. This study compared early post-vaccination symptoms in individuals who subsequently tested positive or negative for SARS-CoV-2, using data from the COVID Symptom Study (CSS) app.\n\nDesignWe conducted a prospective observational study in UK CSS participants who were asymptomatic when vaccinated with Pfizer-BioNTech mRNA vaccine (BNT162b2) or Oxford-AstraZeneca adenovirus-vectored vaccine (ChAdOx1 nCoV-19) between 8 December 2020 and 17 May 2021, who subsequently reported symptoms within seven days (other than local symptoms at injection site) and were tested for SARS-CoV-2, aiming to differentiate vaccination side-effects per se from superimposed SARS-CoV-2 infection. The post-vaccination symptoms and SARS-CoV-2 test results were contemporaneously logged by participants. Demographic and clinical information (including comorbidities) were also recorded. Symptom profiles in individuals testing positive were compared with a 1:1 matched population testing negative, including using machine learning and multiple models including UK testing criteria.\n\nFindingsDifferentiating post-vaccination side-effects alone from early COVID-19 was challenging, with a sensitivity in identification of individuals testing positive of 0.6 at best. A majority of these individuals did not have fever, persistent cough, or anosmia/dysosmia, requisite symptoms for accessing UK testing; and many only had systemic symptoms commonly seen post-vaccination in individuals negative for SARS-CoV-2 (headache, myalgia, and fatigue).\n\nInterpretationPost-vaccination side-effects per se cannot be differentiated from COVID-19 with clinical robustness, either using symptom profiles or machine-derived models. Individuals presenting with systemic symptoms post-vaccination should be tested for SARS-CoV-2, to prevent community spread.\n\nFundingZoe Limited, UK Government Department of Health and Social Care, Wellcome Trust, UK Engineering and Physical Sciences Research Council, UK National Institute for Health Research, UK Medical Research Council and British Heart Foundation, Alzheimers Society, Chronic Disease Research Foundation, Massachusetts Consortium on Pathogen Readiness (MassCPR).\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThere are now multiple surveillance platforms internationally interrogating COVID-19 and/or post-vaccination side-effects. We designed a study to examine for differences between vaccination side-effects and early symptoms of COVID-19. We searched PubMed for peer-reviewed articles published between 1 January 2020 and 21 June 2021, using keywords: \"COVID-19\" AND \"Vaccination\" AND (\"mobile application\" OR \"web tool\" OR \"digital survey\" OR \"early detection\" OR \"Self-reported symptoms\" OR \"side-effects\"). Of 185 results, 25 studies attempted to differentiate symptoms of COVID-19 vs. post-vaccination side-effects; however, none used artificial intelligence (AI) technologies (\"machine learning\") coupled with real-time data collection that also included comprehensive and systematic symptom assessment. Additionally, none of these studies attempt to discriminate the early signs of infection from side-effects of vaccination (specifically here: Pfizer-BioNTech mRNA vaccine (BNT162b2) and Oxford-AstraZeneca adenovirus-vectored vaccine (ChAdOx1 nCoV-19)). Further, none of these studies sought to provide comparisons with current testing criteria used by healthcare services.\n\nAdded value of this studyThis study, in a uniquely large community-based cohort, uses prospective data capture in a novel effort to identify individuals with COVID-19 in the immediate post-vaccination period. Our results show that early symptoms of SARS-CoV-2 cannot be differentiated from vaccination side-effects robustly. Thus, post-vaccination systemic symptoms should not be ignored, and testing should be considered to prevent COVID-19 dissemination by vaccinated individuals.\n\nImplications of all the available evidenceOur study demonstrates the critical importance of testing symptomatic individuals - even if vaccinated - to ensure early detection of SARS-CoV-2 infection, helping to prevent future pandemic waves in the UK and elsewhere.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Liane S Canas", + "author_inst": "School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK" + }, + { + "author_name": "Marc F. Osterdahl", + "author_inst": "Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK" + }, + { + "author_name": "Jie Deng", + "author_inst": "School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK" + }, + { + "author_name": "Christina Hu", + "author_inst": "ZOE Limited, London, UK" + }, + { + "author_name": "Somesh Selvachandran", + "author_inst": "ZOE Limited, London, UK" + }, + { + "author_name": "Lorenzo Polidori", + "author_inst": "ZOE Limited, London, UK" + }, + { + "author_name": "Anna May", + "author_inst": "ZOE Limited, London, UK" + }, + { + "author_name": "Erika Molteni", + "author_inst": "School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK" + }, + { + "author_name": "Benjamin Murray", + "author_inst": "School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK" + }, + { + "author_name": "Liyuan Chen", + "author_inst": "School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK" + }, + { + "author_name": "Eric Kerfoot", + "author_inst": "School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK" + }, + { + "author_name": "Kerstin Klaser", + "author_inst": "School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK" + }, + { + "author_name": "Michela Antonelli", + "author_inst": "School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK" + }, + { + "author_name": "Alexander Hammers", + "author_inst": "School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; King's College London & Guy's and St Thomas' PET Centre, London, UK" + }, + { + "author_name": "Tim Spector", + "author_inst": "Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK." + }, + { + "author_name": "Sebastien Ourselin", + "author_inst": "School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK" + }, + { + "author_name": "Claire J. Steves", + "author_inst": "Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK." + }, + { + "author_name": "Carole H. Sudre", + "author_inst": "School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK; Medical Research Council Unit for Lifelong Health and Ageing, Departme" + }, + { + "author_name": "Marc Modat", + "author_inst": "School of Biomedical Engineering and Imaging Sciences, King's College London, London, UK" + }, + { + "author_name": "Emma L. Duncan", + "author_inst": "Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2021.07.21.21260756", "rel_title": "Workplace risk management for SARS-CoV-2: a three-step early in-tervention strategy for effective containment of infection chains with special regards to virus variants with increased infectivity", @@ -683259,45 +682492,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.07.20.21260892", - "rel_title": "Variation in SARS-CoV-2 bioaerosol production in exhaled breath", - "rel_date": "2021-07-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.20.21260892", - "rel_abs": "Using face mask bioaerosol sampling, we found substantial variation between individuals in SARS-CoV-2 copies exhaled over a 15-minute period, which moderately correlated with nasal swab viral load. Talking was associated with a median of 2 log10 greater exhaled viral copies. Exposure varies substantially between individuals but may be risk stratified by nasal swab viral load and whether the exposure involved conversation.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Renu Verma", - "author_inst": "Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Eugene Kim", - "author_inst": "Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Nicholas Degner", - "author_inst": "Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Katharine S. Walter", - "author_inst": "Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Upinder Singh", - "author_inst": "Division of Infectious Diseases and Geographic Medicine, Dept of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA" - }, - { - "author_name": "Jason R Andrews", - "author_inst": "Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.20.21260871", "rel_title": "Asthma and the Risk of SARS-CoV-2 Infection Among Children and Adolescents", @@ -684369,6 +683563,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.19.21260803", + "rel_title": "B cell numbers predict humoral and cellular response upon SARS-CoV-2 vaccination among patients treated with rituximab", + "rel_date": "2021-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.19.21260803", + "rel_abs": "ObjectivesPatients with autoimmune inflammatory rheumatic diseases receiving rituximab (RTX) therapy show substantially impaired anti-SARS-CoV-2 vaccine humoral but partly inducible cellular immune responses. However, the complex relationship between antigen-specific B and T cells and the level of B cell repopulation necessary to achieve anti-vaccine responses remain largely unknown.\n\nMethodsAntibody responses to SARS-CoV-2 vaccines and induction of antigen-specific B and CD4/CD8 T cell subsets were studied in 19 rheumatoid arthritis (RA) and ANCA-associated vasculitis (AAV) patients receiving RTX, 12 RA patients on other therapies and 30 healthy controls after SARS-CoV-2 vaccination with either mRNA or vector based vaccines.\n\nResultsA minimum of 10 B cells/{micro}L in the peripheral circulation was necessary in RTX patients to mount seroconversion to anti-S1 IgG upon SARS-CoV-2 vaccination. RTX patients lacking IgG seroconversion showed reduced antigen-specific B cells, lower frequency of TfH-like cells as well as less activated CD4 and CD8 T cells compared to IgG seroconverted RTX patients. Functionally relevant B cell depletion resulted in impaired IFN{gamma} secretion by spike-specific CD4 T cells. In contrast, antigen-specific CD8 T cells were reduced in patients independently of IgG formation.\n\nConclusionsPatients receiving rituximab with B cell numbers above 10 B cells/{micro}l were able to mount humoral and more robust cellular responses after SARS-CoV-2 vaccination that may permit optimization of vaccination in these patients. Mechanistically, the data emphasize the crucial role of co-stimulatory B cell functions for the proper induction of CD4 responses propagating vaccine-specific B and plasma cell differentiation.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Ana-Luisa Stefanski", + "author_inst": "Department of Rheumatology and Clinical Immunology, Charite Universitatsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Hector Rincon-Arevalo", + "author_inst": "Department of Rheumatology and Clinical Immunology, Charite Universitatsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Eva Schrezenmeier", + "author_inst": "Department of Nephrology and Medical Intensive Care, Charite Universitatsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Kirsten Karberg", + "author_inst": "Rheumatology outpatient office Berlin, Germany" + }, + { + "author_name": "Franziska Szelinski", + "author_inst": "Department of Rheumatology and Clinical Immunology, Charite Universitatsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Jacob Ritter", + "author_inst": "Department of Rheumatology and Clinical Immunology, Charite Universitatsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Bernd Jahrsdoerfer", + "author_inst": "Institute of Transfusion Medicine, Ulm University, Ulm, Germany and Institute for Clinical Transfusion Medicine and Immunogenetics, German Red Cross Blood Trans" + }, + { + "author_name": "Hubert Schrezenmeier", + "author_inst": "Institute of Transfusion Medicine, Ulm University, Ulm, Germany and Institute for Clinical Transfusion Medicine and Immunogenetics, German Red Cross Blood Trans" + }, + { + "author_name": "Carolin Ludwig", + "author_inst": "Institute of Transfusion Medicine, Ulm University, Ulm, Germany and Institute for Clinical Transfusion Medicine and Immunogenetics, German Red Cross Blood Trans" + }, + { + "author_name": "Arne Sattler", + "author_inst": "Department for General, Visceral and Vascular Surgery, Charite Universitatsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Katja Kotsch", + "author_inst": "Department for General, Visceral and Vascular Surgery, Charite Universitatsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Yidan Chen", + "author_inst": "Department of Rheumatology and Clinical Immunology, Charite Universitatsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Anne Claussnitzer", + "author_inst": "AGZ Rheumatology Charite Berlin, Germany" + }, + { + "author_name": "Hildrun Haibel", + "author_inst": "Department of Gastroenterology, Infectiology and Rheumatology (including Nutrition Medicine), Charite Universitatsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Fabian Proft", + "author_inst": "Department of Gastroenterology, Infectiology and Rheumatology (including Nutrition Medicine), Charite Universitatsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Gabriella Maria Guerra", + "author_inst": "Deutsches Rheumaforschungszentrum (DRFZ), Berlin, Germany" + }, + { + "author_name": "Pawel Durek", + "author_inst": "Deutsches Rheumaforschungszentrum (DRFZ), Berlin, Germany" + }, + { + "author_name": "Frederik Heinrich", + "author_inst": "Deutsches Rheumaforschungszentrum (DRFZ), Berlin, Germany" + }, + { + "author_name": "Marta Ferreira Gomes", + "author_inst": "Deutsches Rheumaforschungszentrum (DRFZ), Berlin, Germany" + }, + { + "author_name": "Gerd R. Burmester", + "author_inst": "Department of Rheumatology and Clinical Immunology, Charite Universitatsmedizin Berlin, Berlin, Germany" + }, + { + "author_name": "Andreas Radbruch", + "author_inst": "Deutsches Rheumaforschungszentrum (DRFZ), Berlin, Germany" + }, + { + "author_name": "Mir-Farzin Mashreghi", + "author_inst": "Deutsches Rheumaforschungszentrum (DRFZ), Berlin, Germany" + }, + { + "author_name": "Andreia C. Lino", + "author_inst": "Deutsches Rheumaforschungszentrum (DRFZ), Berlin, Germany" + }, + { + "author_name": "Thomas Doerner", + "author_inst": "Department of Rheumatology and Clinical Immunology, Charite Universitatsmedizin Berlin, Berlin, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "rheumatology" + }, { "rel_doi": "10.1101/2021.07.22.453029", "rel_title": "CD8+ T cell signature in acute SARS-CoV-2 infection identifies memory precursors", @@ -684877,73 +684182,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2021.07.20.453054", - "rel_title": "Discovery of nanobodies against SARS-CoV-2 and an uncommon neutralizing mechanism", - "rel_date": "2021-07-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.20.453054", - "rel_abs": "SARS-CoV-2 and its variants continue to threaten public health. The virus recognizes the host cell by attaching its Spike receptor-binding domain (RBD) to the host receptor ACE2. Therefore, RBD is a primary target for neutralizing antibodies and vaccines. Here we report the isolation, and biological and structural characterization of two single-chain antibodies (nanobodies, DL4 and DL28) from RBD-immunized alpaca. Both nanobodies bind Spike with affinities that exceeded the detection limit (picomolar) of the biolayer interferometry assay and neutralize the original SARS-CoV- 2 strain with IC50 of 0.086 g mL-1 (DL4) and 0.385 g mL-1 (DL28). DL4 and a more potent, rationally designed mutant, neutralizes the Alpha variant as potently as the original strain but only displays marginal activity against the Beta variant. By contrast, the neutralizing activity of DL28, when in the Fc-fused divalent form, was less affected by the mutations in the Beta variant (IC50 of 0.414 g mL-1 for Alpha, 1.060 g mL-1 for Beta). Crystal structure studies reveal that DL4 blocks ACE2-binding by direct competition, while DL28 neutralizes SARS-CoV-2 by an uncommon mechanism through which DL28 distorts the receptor-binding motif in RBD and hence prevents ACE2-binding. Our work provides two neutralizing nanobodies for potential therapeutic development and reveals an uncommon mechanism to design and screen novel neutralizing antibodies against SARS-CoV-2.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Dianfan Li", - "author_inst": "Chinese Academy of Sciences" - }, - { - "author_name": "Tingting Li", - "author_inst": "CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS)" - }, - { - "author_name": "Bingjie Zhou", - "author_inst": "CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS" - }, - { - "author_name": "Zhipu Luo", - "author_inst": "Soochow University" - }, - { - "author_name": "Yanling Lai", - "author_inst": "CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences (CAS)" - }, - { - "author_name": "Suqiong Huang", - "author_inst": "CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS" - }, - { - "author_name": "Yuanze Zhou", - "author_inst": "Nanjing Crycision Biotech Co., Ltd." - }, - { - "author_name": "Anupriya Gautam", - "author_inst": "CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS" - }, - { - "author_name": "Salome Bourgeau", - "author_inst": "CAS Key Laboratory of Molecular Virology & Immunology, Institut Pasteur of Shanghai CAS" - }, - { - "author_name": "Shurui Wang", - "author_inst": "Nanjing Crycision Biotech Co., Ltd" - }, - { - "author_name": "Juan Bao", - "author_inst": "State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology" - }, - { - "author_name": "Jingquan Tan", - "author_inst": "Nanjing Crycision Biotech Co., Ltd" - }, - { - "author_name": "Dimitri Lavillette", - "author_inst": "Institut Pasteur Shanghai Chine Academy of Sciences" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.07.21.453140", "rel_title": "Distinct shifts in site-specific glycosylation pattern of SARS-CoV-2 spike proteins associated with arising mutations in the D614G and Alpha variants", @@ -686267,6 +685505,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, + { + "rel_doi": "10.1101/2021.07.17.452778", + "rel_title": "HLA-dependent variation in SARS-CoV-2 CD8+ T cell cross-reactivity with human coronaviruses", + "rel_date": "2021-07-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.17.452778", + "rel_abs": "Pre-existing T cell immunity to SARS-CoV-2 in individuals without prior exposure to SARS-CoV-2 has been reported in several studies. While emerging evidence hints toward prior exposure to common-cold human coronaviruses (HCoV), the extent of- and conditions for-cross-protective immunity between SARS-CoV-2 and HCoVs remain open. Here, by leveraging a comprehensive pool of publicly available functionally evaluated SARS-CoV-2 peptides, we report 126 immunogenic SARS-CoV-2 peptides with high sequence similarity to 285 MHC-presented target peptides from at least one of four HCoV, thus providing a map describing the landscape of SARS-CoV-2 shared and private immunogenic peptides with functionally validated T cell responses. Using this map, we show that while SARS-CoV-2 immunogenic peptides in general exhibit higher level of dissimilarity to both self-proteome and -microbiomes, there exist several SARS-CoV-2 immunogenic peptides with high similarity to various human protein coding genes, some of which have been reported to have elevated expression in severe COVID-19 patients. We then combine our map with a SARS-CoV-2-specific TCR repertoire data from COVID-19 patients and healthy controls and show that whereas the public repertoire for the majority of convalescent patients are dominated by TCRs cognate to private SARS-CoV-2 peptides, for a subset of patients, more than 50% of their public repertoires that show reactivity to SARS-CoV-2, consist of TCRs cognate to shared SARS-CoV-2-HCoV peptides. Further analyses suggest that the skewed distribution of TCRs cognate to shared and private peptides in COVID-19 patients is likely to be HLA-dependent. Finally, by utilising the global prevalence of HLA alleles, we provide 10 peptides with known cognate TCRs that are conserved across SARS-CoV-2 and multiple human coronaviruses and are predicted to be recognised by a high proportion of the global population. Overall, our work indicates the potential for HCoV-SARS-CoV-2 reactive CD8+ T cells, which is likely dependent on differences in HLA-coding genes among individuals. These findings may have important implications for COVID-19 heterogeneity and vaccine-induced immune responses as well as robustness of immunity to SARS-CoV-2 and its variants.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Paul Buckley", + "author_inst": "Oxford University" + }, + { + "author_name": "Chloe Hyun-jung Lee", + "author_inst": "Oxford University" + }, + { + "author_name": "Mariana Pereira Pinho", + "author_inst": "Oxford University" + }, + { + "author_name": "Rosana Ottakandathil Babu", + "author_inst": "Oxford University" + }, + { + "author_name": "Jeongmin Woo", + "author_inst": "Oxford University" + }, + { + "author_name": "Agne Antanaviciute", + "author_inst": "Oxford University" + }, + { + "author_name": "Alison Simmons", + "author_inst": "The University of Oxford" + }, + { + "author_name": "Graham Ogg", + "author_inst": "The University of Oxford" + }, + { + "author_name": "Hashem Koohy", + "author_inst": "The University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.07.20.453011", "rel_title": "Previously unrecognized non-reproducible antibody-antigen interactions and their implications for diagnosis of viral infections including COVID-19", @@ -686711,53 +686000,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.07.15.21260346", - "rel_title": "Elderly acceptance of telemedicine use in Hong Kong during and after the COVID-19 pandemic: a cross-sectional cohort survey", - "rel_date": "2021-07-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.15.21260346", - "rel_abs": "BackgroundTelemedicine services worldwide have experienced an unprecedented boom since the beginning of the COVID-19 pandemic. Multiple studies have noted telemedicine as an effective alternative to traditional face-to-face management of patients. This study provides insight into public perception and impression of telemedicine in Hong Kong, specifically among the elderly who are the most vulnerable to COVID-19.\n\nMethodsFace-to-face surveys were conducted on elderly relatives of current medical students at the Chinese University of Hong Kong who were aged [≥] 60 years. The survey included socio-demographic details; past medical history; and concerns towards telemedicine use. Univariate and multivariable regression analyses were conducted to examine statistically significant associations. The primary outcomes are consideration of telemedicine use during: (1) a severe outbreak; and (2) after the COVID-19 pandemic.\n\nResults109 surveys were conducted. Multivariable regression analyses revealed that expectation of government subsidies for telemedicine services was the strongest common driver, and also the only positive independent predictors of telemedicine use for both during a severe outbreak, as well as after the COVID-19 pandemic. No negative independent predictors of telemedicine use during severe outbreak were found. Negative independent predictors of telemedicine use after the COVID-19 pandemic included old age, and living in the New Territories.\n\nConclusionsGovernment support such as telemedicine-specific subsidies will be crucial in promoting telemedicine use in Hong Kong both during a severe outbreak and after the current COVID-19 pandemic. Robust dissemination of information regarding the pros and cons of telemedicine towards the public, especially towards the elderly population, is warranted.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Maxwell Chun Yin Choi", - "author_inst": "Faculty of Medicine, The Chinese University of Hong Kong" - }, - { - "author_name": "Shing Him Chu", - "author_inst": "Faculty of Medicine, The Chinese University of Hong Kong" - }, - { - "author_name": "Lok Lam Siu", - "author_inst": "Faculty of Medicine, The Chinese University of Hong Kong" - }, - { - "author_name": "Anakin Gajy Tse", - "author_inst": "Faculty of Medicine, The Chinese University of Hong Kong" - }, - { - "author_name": "Justin Che Yuen Wu", - "author_inst": "Division of Gastroenterology and Hepatology, Department of Medicine and Therapeutics, The Chinese University of Hong Kong" - }, - { - "author_name": "Hong Fung", - "author_inst": "CUHK Medical Centre" - }, - { - "author_name": "Billy Chi Fai Chiu", - "author_inst": "CUHK Medical Centre" - }, - { - "author_name": "Vincent Chung Tong Mok", - "author_inst": "Division of Neurology, Department of Medicine and Therapeutics, The Chinese University of Hong Kong" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.07.19.21260302", "rel_title": "Natural immunity against COVID-19 significantly reduces the risk of reinfection: findings from a cohort of sero-survey participants", @@ -688165,6 +687407,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.16.21260630", + "rel_title": "ABO and Rh blood groups, demographics, and comorbidities in COVID-19 related deaths: a retrospective study in Split-Dalmatia County, Croatia", + "rel_date": "2021-07-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.16.21260630", + "rel_abs": "AimTo examine ABO and Rh blood group distribution in COVID-19 related deaths considering demographics and pathological conditions.\n\nMaterials and MethodsWe conducted a retrospective study at the University Hospital Centre Split, Croatia, that included 245 COVID-positive individuals that died from April 8, 2020, to January 25, 2021. From the hospital database, we extracted data on their blood groups, demographics, and pre-existing comorbidities. To compare findings with the general population, we used information from collected blood group donations (n = 101357) and statistical reports of non-COVID deaths from 2019 (n = 4968).\n\nResultsThe proportion of males was significantly higher in analyzed subjects than in non- COVID deaths from 2019 (63.7% vs. 48.9%, P < 0.001), while the proportion of older individuals did not differ (P = 0.8). The most common pre-existing diseases were hypertension (59.6%), diabetes (37.1%), heart failure (28.8%), digestive disorder (26.5%), and solid tumor (21.6%). The ABO distribution in the deceased and donors group showed statistically significant differences, with the higher prevalence of A/AB group and lower prevalence of 0, but with individual differences significant only for AB and non-AB groups. There was a significantly reduced proportion of females within the deceased with group 0 (P = 0.014) and a higher proportion of AB individuals with coronary heart disease (P = 0.024), while other differences were not significant.\n\nConclusionThe study confirmed a higher risk of death in male individuals. The lower proportion of type 0 in deceased individuals was more pronounced in females, implying that group 0 is not necessarily an independent protective factor. Among analyzed comorbidities, coronary heart disease was identified as a potential risk factor for AB individuals.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ivan Brdar", + "author_inst": "Department of Internal Emergency Medicine, Split University Hospital Centre, Split, Croatia" + }, + { + "author_name": "Ivan Jerkovi\u0107", + "author_inst": "University Department of Forensic Sciences, University of Split, Split, Croatia" + }, + { + "author_name": "\u017deljana Ba\u0161i\u0107", + "author_inst": "University Department of Forensic Sciences, University of Split, Split, Croatia" + }, + { + "author_name": "Nenad Kunac", + "author_inst": "Department of Pathology, Forensic Medicine and Cytology, Split University Hospital Centre, Split, Croatia" + }, + { + "author_name": "Deny An\u0111elinovi\u0107", + "author_inst": "Department of Dermatovenerology, University Hospital Center Split, Split, Croatia" + }, + { + "author_name": "Jo\u0161ko Bezi\u0107", + "author_inst": "Department of Pathology, Forensic Medicine and Cytology, Split University Hospital Centre, Split, Croatia" + }, + { + "author_name": "Ivana Kru\u017ei\u0107", + "author_inst": "University Department of Forensic Sciences, University of Split, Split, Croatia" + }, + { + "author_name": "Arijana Vuko", + "author_inst": "Department of Pathology, Forensic Medicine and Cytology, Split University Hospital Centre, Split, Croatia" + }, + { + "author_name": "\u0160imun An\u0111elinovi\u0107", + "author_inst": "Department of Pathology, Forensic Medicine and Cytology, Split University Hospital Centre, Split, Croatia; School of Medicine, University of Split, Split, Croat" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.16.21260642", "rel_title": "Vaccination is Australia's most important COVID-19 public health action, even though herd immunity is unlikely", @@ -688709,105 +688002,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.07.16.452733", - "rel_title": "One mucosal administration of a live attenuated recombinant COVID-19 vaccine protects non-human primates from SARS-CoV-2", - "rel_date": "2021-07-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.16.452733", - "rel_abs": "Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 global pandemic. SARS-CoV-2 is an enveloped RNA virus that relies on its trimeric surface glycoprotein, spike, for entry into host cells. Here we describe the COVID-19 vaccine candidate MV-014-212, a live attenuated, recombinant human respiratory syncytial virus (RSV) expressing a chimeric SARS-CoV-2 spike as the only viral envelope protein. MV-014-212 was attenuated and immunogenic in African green monkeys (AGMs). One mucosal administration of MV-014-212 in AGMs protected against SARS-CoV-2 challenge, reducing by more than 200- fold the peak shedding of SARS-CoV-2 in the nose. MV-014-212 elicited mucosal immunity in the nose and neutralizing antibodies in serum that exhibited cross-neutralization against two virus variants of concern. Intranasally delivered, live attenuated vaccines such as MV-014-212 entail low-cost manufacturing suitable for global deployment. MV-014-212 is currently in phase 1 clinical trials as a single-dose intranasal COVID-19 vaccine.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Mariana F. Tioni", - "author_inst": "Meissa Vaccines" - }, - { - "author_name": "Robert Jordan", - "author_inst": "Bill & Melinda Gates Foundation, Seattle WA 98102" - }, - { - "author_name": "Angie Silva Pena", - "author_inst": "Meissa Vaccines Inc, Redwood City, CA 94065" - }, - { - "author_name": "Aditya Garg", - "author_inst": "Meissa Vaccines Inc, Redwood City, CA 94065" - }, - { - "author_name": "Danlu Wu", - "author_inst": "Meissa Vaccines Inc, Redwood City, CA 94065" - }, - { - "author_name": "Shannon I. Phan", - "author_inst": "Meissa Vaccines Inc, Redwood City, CA 94065" - }, - { - "author_name": "Xing Cheng", - "author_inst": "Meissa Vaccines Inc, Redwood City, CA 94065" - }, - { - "author_name": "Jack Greenhouse", - "author_inst": "BIOQUAL Inc., Rockville, MD 20850" - }, - { - "author_name": "Tatyana Orekov", - "author_inst": "BIOQUAL Inc., Rockville, MD 20850" - }, - { - "author_name": "Daniel Valentin", - "author_inst": "BIOQUAL Inc., Rockville, MD 20850" - }, - { - "author_name": "Swagata Kar", - "author_inst": "BIOQUAL Inc., Rockville, MD 20850" - }, - { - "author_name": "Laurent Pessaint", - "author_inst": "BIOQUAL Inc., Rockville, MD 20850" - }, - { - "author_name": "Hanne Andersen", - "author_inst": "BIOQUAL Inc., Rockville, MD 20850" - }, - { - "author_name": "Christopher C. Stobart", - "author_inst": "Department of Biological Sciences, Butler University, Indianapolis, IN 46208" - }, - { - "author_name": "Melissa H. Bloodworth", - "author_inst": "Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232" - }, - { - "author_name": "R. Stokes Peebles Jr.", - "author_inst": "Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232. Department of " - }, - { - "author_name": "Yang Liu", - "author_inst": "Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX 77550" - }, - { - "author_name": "Xuping Xie", - "author_inst": "Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX 77550" - }, - { - "author_name": "Pei-Yong Shi", - "author_inst": "Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston TX 77550" - }, - { - "author_name": "Martin L. Moore", - "author_inst": "Meissa Vaccines Inc, Redwood City, CA 94065" - }, - { - "author_name": "Roderick S. Tang", - "author_inst": "Meissa Vaccines Inc, Redwood City, CA 94065" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.07.16.452709", "rel_title": "SARS-CoV-2 Spike Pseudoviruses: A Useful tool to study virus entry and address emerging neutralization escape phenotypes", @@ -690067,6 +689261,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hiv aids" }, + { + "rel_doi": "10.1101/2021.07.12.21260377", + "rel_title": "Impact of BNT162b2 vaccination and isolation on SARS-CoV-2 transmission in Israeli households: an observational study", + "rel_date": "2021-07-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.12.21260377", + "rel_abs": "BackgroundMassive vaccination rollouts against SARS-CoV-2 infections have facilitated the easing of control measures in countries like Israel. While several studies have characterized the effectiveness of vaccines against severe forms of COVID-19 or SARS-CoV-2 infection, estimates of their impact on transmissibility remain limited. Here, we evaluated the role of vaccination and isolation on SARS-CoV-2 transmission within Israeli households.\n\nMethodsFrom December 2020 to April 2021, confirmed cases were identified among healthcare workers of the Sheba Medical Centre and their family members. Households were recruited and followed up with repeated PCR for a minimum of ten days after case confirmation. Symptoms and vaccination information were collected at the end of follow-up. We developed a data augmentation Bayesian framework to ascertain how age, isolation and BNT162b2 vaccination with more than 7 days after the 2nd dose impacted household transmission of SARS-CoV-2.\n\nFindings210 households with 215 index cases were enrolled. 269 out of 687 (39%) household contacts developed a SARS-CoV-2 infection. Of those, 170 (63%) developed symptoms. Children below 12 years old were less susceptible than adults/teenagers (Relative Risk RR=0{middle dot}50, 95% Credible Interval CI 0{middle dot}32-0{middle dot}79). Vaccination reduced the risk of infection among adults/teenagers (RR=0{middle dot}19, 95% CI 0{middle dot}07-0{middle dot}40). Isolation reduced the risk of infection of unvaccinated adult/teenager (RR=0{middle dot}11, 95% CI 0{middle dot}05-0{middle dot}19) and child contacts (RR=0{middle dot}16, 95% CI 0{middle dot}07-0{middle dot}31) compared to unvaccinated adults/teenagers that did not isolate. Infectivity was significantly reduced in vaccinated cases (RR=0{middle dot}22, 95% CI 0{middle dot}06-0{middle dot}70).\n\nInterpretationWithin households, vaccination reduces both the risk of infection and of transmission if infected. When contacts were not vaccinated, isolation also led to important reductions in the risk of transmission. Vaccinated contacts might reduce their risk of infection if they isolate, although this requires confirmation with additional data.\n\nFundingSheba Medical Center.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThe efficacy of vaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmissions in households remains understudied. On June 28, 2021, we searched PubMed and medRxiv for articles published between December 1, 2020, and June 28, 2021, using the following combination of search terms: (\"COVID-19\" OR \"SARS-CoV-2\") AND (\"household*\" OR \"famil*\") AND \"transmission\" AND \"vaccination\". Our search yielded two articles that investigated the effect of vaccination on SARS-CoV-2 transmission in households. They showed a lower risk of infection in households with vaccinees. Vaccine efficacy on the risk of infection was estimated to 80% after the 2nd dose, and vaccine efficacy on the risk of transmission if infected was estimated to 49% 21 days after the 1st dose. However, these estimates are derived from surveillance data with no active follow-up of the households. In addition, the impact of isolation precautions has not been assessed.\n\nAdded value of this studyBased on the active follow-up of households of health care workers from the Sheba Medical Center in Israel, we estimated the effect of vaccination on household transmission. To our knowledge, our study is the first to conjointly investigate the effect of vaccination, age, and isolation precautions on the risk of infection and the risk of transmission in households while accounting for tertiary infections in the household, infections within the community, the reduced infectivity of asymptomatic cases, misidentification of index cases, and household size. Our study confirmed the high efficacy of BNT-162b2 vaccination to reduce infection risk and transmission risk. It also suggests that isolation might remain beneficial to vaccinated contacts.\n\nImplications of all the available evidenceVaccination reduces susceptibility to infection and case infectivity in households. Isolation precautions also mitigate the risk of infection and should be implemented whenever a household member is infected. They might remain beneficial to vaccinated contacts.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Maylis Layan", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Mayan Gilboa", + "author_inst": "Sheba Medical Center" + }, + { + "author_name": "Tal Gonen", + "author_inst": "Sheba Medical Center" + }, + { + "author_name": "Miki Goldenfeld", + "author_inst": "Sheba Medical Center" + }, + { + "author_name": "Lilac Meltzer", + "author_inst": "Sheba Medical Center" + }, + { + "author_name": "Alessio Andronico", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Nathanael Hoze", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Simon Cauchemez", + "author_inst": "Institut Pasteur" + }, + { + "author_name": "Gili Regev-Yochay", + "author_inst": "Sheba Medical Center, Israel" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.12.21260385", "rel_title": "Estimating the effectiveness of first dose of COVID-19 vaccine against mortality in England: a quasi-experimental study", @@ -690707,45 +689952,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.07.12.21258827", - "rel_title": "Olfactory detection of human odorant signatures in Covid patients by trained dogs", - "rel_date": "2021-07-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.12.21258827", - "rel_abs": "The objective of the study was to verify the ability of specially trained dogs to detect the odour of people ill with COVID-19 and, at the same time, to use the outcome of this research in the future, whether in combatting a similar pandemic or in the field of medicine in the shape of a biological detector in uncovering different diseases. Our key assumption was that the disease will change the active odour signature of the individuals just like other diseases (TBC, malaria, tumours, etc.). The pilot study was conducted in two places, based on the same protocolar methods, and it included four specially trained detection dogs in total. For the first phase of the project, we obtained 156 positive and 72 negative odour samples primarily from a hospital. Each detection dog involved in the study was imprinted with the smell samples of Covid-positive people. The first experiment only involved two dogs. With the other two dogs, the phase of imprinting a specific smell was longer, possibly because these dogs were burdened with previous training. During a presentation of 100 randomised positive samples, the experimental dogs showed a 95% reliability rate. Data from this pilot study show that specially trained dogs are able to detect and identify the odour samples of people infected with the SARS-CoV-2 coronavirus.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Lenka Vlachova", - "author_inst": "Search and Rescue Czech Republic" - }, - { - "author_name": "Gustav Hotovy", - "author_inst": "Search and Rescue Czech Republic" - }, - { - "author_name": "Jiri Slechta", - "author_inst": "Search and Rescue Czech Republic" - }, - { - "author_name": "Roman Vana", - "author_inst": "Search and Rescue Czech Republic" - }, - { - "author_name": "Milena Vokralova", - "author_inst": "Search and Rescue Czech Republic" - }, - { - "author_name": "Jiri Zeman", - "author_inst": "Search and Rescue Czech Republic" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.07.12.21260387", "rel_title": "Lessons learned and lessons missed: Impact of the Covid-19 pandemic on all-cause mortality in 40 industrialised countries prior to mass vaccination", @@ -691861,6 +691067,57 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.07.16.452680", + "rel_title": "Intestinal organoids expose heterogeneity in SARS-CoV-2 susceptibility", + "rel_date": "2021-07-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.16.452680", + "rel_abs": "Gastrointestinal effects associated with COVID-19 are highly variable for reasons that are not understood. In this study, we used intestinal organoid-derived cultures differentiated from primary human specimens as a model to examine inter-individual variability. Infection of intestinal organoids derived from different donors with SARS-CoV-2 resulted in orders of magnitude differences in virus replication in small intestinal and colonic organoid-derived monolayers. Susceptibility to infection correlated with ACE2 expression level and was independent of donor demographic or clinical features. ACE2 transcript levels in cell culture matched the amount of ACE2 in primary tissue indicating this feature of the intestinal epithelium is retained in the organoids. Longitudinal transcriptomics of organoid-derived monolayers identified a delayed yet robust interferon signature, the magnitude of which corresponded to the degree of SARS-CoV-2 infection. Interestingly, virus with the Omicron variant spike protein infected the organoids with the highest infectivity, suggesting increased tropism of the virus for intestinal tissue. These results suggest that heterogeneity in SARS-CoV-2 replication in intestinal tissues results from differences in ACE2 levels, which may underlie variable patient outcomes.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Kyung Ku Jang", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "Maria E Kaczmarek", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "Simone Dallari", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "Ying-Han Chen", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "Takuya Tada", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "Jordan Axelrad", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "Nathaniel R Landau", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "Kenneth A Stapleford", + "author_inst": "New York University Grossman School of Medicine" + }, + { + "author_name": "Ken Cadwell", + "author_inst": "New York University Grossman School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "cell biology" + }, { "rel_doi": "10.1101/2021.07.14.21260488", "rel_title": "SARS-CoV-2 Antibody Lateral Flow Assay for antibody prevalence studies following vaccine roll out: a Diagnostic Accuracy Study", @@ -692277,61 +691534,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.12.21260358", - "rel_title": "Increase in SARS-CoV-2 seroprevalence in healthy blood donors after the second wave of COVID-19 pandemic in South-Eastern Italy: evidence for asymptomatic young individuals as potential virus spreaders", - "rel_date": "2021-07-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.12.21260358", - "rel_abs": "BackgroundItaly has been the first among western countries to experience SARS-CoV-2 spread during which the southern regions were also heavily affected by the pandemic. To understand and monitor properly the evolution of COVID-19 pandemic, population based seroprevalence studies are a valid tool for the infection rates and effective prevalence of the SARS-CoV-2.\n\nAimIn this prospective study, we assessed the changes in SARS-CoV-2 seroprevalence rates among non-vaccinated blood donors in South-Eastern Italy over May 2020 to March 2021.\n\nMethods8,183 healthy blood donors referring to the Transfusion Center at the University Hospital \"Riuniti\" of Foggia (Italy) for blood donation in the period May 2020-March 2021 were tested for anti-SARS-CoV-2 antibodies by Ortho Clinical Diagnostics VITROS(R) 3600. None of the considered subjects had a diagnosed symptomatic COVID-19 infection.\n\nResultsOverall, 516 resulted positive for anti-SARS-CoV-2 IgG antibodies (6.3%, 95% CI, 0.03-0.15%), 387 (4.7%) were male and 129 (1.7%) female. A statistically significant increase in the seropositive population was found from May 2020 to March 2021 (Fishers p<0.001). The difference of the seroprevalence was significant in terms of age but not sex (2-sided p<0.05 for age; 2-sided p>0.05 for sex) in both groups.\n\nConclusionOur study shows a significant increase in the SARS-CoV-2 seroprevalence among blood donors and suggests a potential role of asymptomatic individuals in continuing the spread of the pandemic. These results may contribute to establishing containment measures and priorities in vaccine campaigns.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Francescopaolo Antonucci", - "author_inst": "Ospedali Riuniti University Hospital, Foggia, Italy" - }, - { - "author_name": "jose Ramon fiore", - "author_inst": "University of Foggia, Foggi, iTALY" - }, - { - "author_name": "lucia de feo", - "author_inst": "Ospedali Riuniti Foggia, Foggia, Italy" - }, - { - "author_name": "tommaso granato", - "author_inst": "ospedaliriunitifoggia, foggia, italy" - }, - { - "author_name": "Mariantonietta Di Stefano", - "author_inst": "University of Foggia, Foggia, Italy" - }, - { - "author_name": "giuseppina faleo", - "author_inst": "University of Foggia, Foggia, Italy" - }, - { - "author_name": "ahmad mohamed farhan", - "author_inst": "University of Dammam, Dammam,, Saudi Arabia" - }, - { - "author_name": "maurizio margaglione", - "author_inst": "University of Foggia, Foggia, Italy" - }, - { - "author_name": "michele centra", - "author_inst": "Ospedali riuniti foggia, foggia, Italy" - }, - { - "author_name": "teresa antonia santantonio", - "author_inst": "university of foggia, foggia, italy" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.12.21260359", "rel_title": "DNR order in SARS-CoV-2 patients: preliminary guidelines validation and quality of palliative care in a single Swiss COVID-19 Center.", @@ -693630,6 +692832,217 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.13.21260273", + "rel_title": "Clinical characterization and Genomic analysis of COVID-19 breakthrough infections during second wave in different states of India", + "rel_date": "2021-07-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.13.21260273", + "rel_abs": "During March to June 2021 India has experienced a deadly second wave of COVID-19 with an increased number of post-vaccination breakthrough infections reported across the country. To understand the possible reason of these breakthroughs we collected 677 clinical samples (throat swab/ nasal swabs) of individuals who had received two doses (n=592) and one dose (n=85) of vaccines (Covishield and Covaxin,) and tested positive for COVID-19, from 17 states/Union Territories of country. These cases were telephonically interviewed and clinical data was analyzed. A total of 511 SARS-CoV-2 genomes were recovered with genome coverage of higher than 98% from both the cases. Analysis of both the cases determined that 86.69% (n=443) of them belonged to the Delta variant along with Alpha, Kappa, Delta AY.1 and Delta AY.2. The Delta variant clustered into 4 distinct sub-lineages. Sub-lineage-I had mutations: ORF1ab-A1306S, P2046L, P2287S, V2930L, T3255I, T3446A, G5063S, P5401L, A6319V and N-G215C; Sub-lineage -II : ORF1ab- P309L, A3209V, V3718A, G5063S, P5401L and ORF7a-L116F; Sub-lineage -III : ORF1ab- A3209V, V3718A, T3750I, G5063S, P5401L and Spike-A222V; Sub-lineage -IV ORF1ab- P309L, D2980N, F3138S and spike - K77T. This study indicated that majority of the clinical cases in the breakthrough were infected with the Delta variant and only 9.8% cases required hospitalization while fatality was observed in only 0.4% cases. This clearly suggests that the vaccination does provide reduction in hospital admission and mortality.", + "rel_num_authors": 49, + "rel_authors": [ + { + "author_name": "Nivedita Gupta", + "author_inst": "Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi, India Pin-110029" + }, + { + "author_name": "Harmanmeet Kaur", + "author_inst": "Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi, India Pin-110029" + }, + { + "author_name": "Pragya Yadav", + "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" + }, + { + "author_name": "Labanya Mukhopadhyay", + "author_inst": "Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi, India Pin-110029" + }, + { + "author_name": "Rima R Sahay", + "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" + }, + { + "author_name": "Abhinendra Kumar", + "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" + }, + { + "author_name": "Dimpal A Nyayanit", + "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" + }, + { + "author_name": "Anita M Shete", + "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" + }, + { + "author_name": "Savita Patil", + "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" + }, + { + "author_name": "Triparna Dutta Majumdar", + "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" + }, + { + "author_name": "Salaj Rana", + "author_inst": "Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi, India Pin-110029" + }, + { + "author_name": "Swati Gupta", + "author_inst": "Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi, India Pin-110029" + }, + { + "author_name": "Jitendra Narayan", + "author_inst": "Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi, India Pin-110029" + }, + { + "author_name": "Neetu Vijay", + "author_inst": "Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi, India Pin-110029" + }, + { + "author_name": "Pradip Barde", + "author_inst": "VRDL National Institute of Research in Tribal Health (NIRTH) Jabalpur - 482003" + }, + { + "author_name": "Gita Natrajan", + "author_inst": "VRDL, Department of Microbiology, KEM Medical College, Mumbai - 400012" + }, + { + "author_name": "Amurtha Kumari B", + "author_inst": "VRDL, Department of Microbiology, Mysore Medical College, Mysore - 570015" + }, + { + "author_name": "Manasa P Kumari", + "author_inst": "VRDL, Department of Microbiology, Mysore Medical College, Mysore - 570015" + }, + { + "author_name": "Debasis Biswas", + "author_inst": "VRDL, Department of Microbiology, All India Institute of Medical Sciences, Bhopal -462020" + }, + { + "author_name": "Jyoti Iravane", + "author_inst": "VRDL, Government Medical College, Aurangabad - 431001" + }, + { + "author_name": "Sharmila Raut", + "author_inst": "VRDL, Indira Gandhi Government Medical College Nagpur - 440012" + }, + { + "author_name": "Shanta Dutta", + "author_inst": "VRDL, National Institute of Cholera and Enteric Diseases, Kolkata - 700010" + }, + { + "author_name": "Sulochana Devi", + "author_inst": "VRDL, Regional Institute of Medical Sciences, Imphal - 795004" + }, + { + "author_name": "Purnima Barua", + "author_inst": "VRDL, Jorhat Medical College, Jorhat - 785001" + }, + { + "author_name": "Piyali Gupta", + "author_inst": "VRDL, Mahatma Gandhi Memorial Medical College, Jamshedpur - 831020" + }, + { + "author_name": "Biswa Borkakoty", + "author_inst": "VRDL, ICMR-Regional Medical Research Centre, Dibrugarh - 786001" + }, + { + "author_name": "Deepjyoti Kalita", + "author_inst": "VRDL, All India Institutes of Medical Sciences, Rishikesh - 249203" + }, + { + "author_name": "Kanwardeep Dhingra", + "author_inst": "VRDL, Government Medical College, Amritsar - 143001" + }, + { + "author_name": "Bashir Fomda", + "author_inst": "VRDL, Sher-i-Kashmir Institute of Medical Sciences, Srinagar - 190011" + }, + { + "author_name": "Yash Joshi", + "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" + }, + { + "author_name": "Kapil Goyal", + "author_inst": "Department of Virology, Postgraduate Institute of Medical Education and Research, Chandigarh - 160012" + }, + { + "author_name": "Reena John", + "author_inst": "VRDL, Government Medical College, Thrissur - 680596" + }, + { + "author_name": "Ashok Munivenkatappa", + "author_inst": "ICMR-National Institute of Virology Field Unit, Bangalore - 560011" + }, + { + "author_name": "Rahul Dhodapkar", + "author_inst": "VRDL, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry - 605006" + }, + { + "author_name": "Priyanka Pandit", + "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" + }, + { + "author_name": "Sarada Devi", + "author_inst": "VRDL, Government Medical College, Thiruvanthapuram -695011" + }, + { + "author_name": "Manisha Dudhmal", + "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" + }, + { + "author_name": "Deepa Kinariwala", + "author_inst": "VRDL, B. J. Medical College, Ahmedabad - 380016" + }, + { + "author_name": "Neeta Khandelwal", + "author_inst": "VRDL, Government Medical College, Surat - 395001" + }, + { + "author_name": "Yogendra Kumar Tiwari", + "author_inst": "VRDL, Jhalawar Medical College, Jhalawar - 326001" + }, + { + "author_name": "P K Khatri", + "author_inst": "VRDL, Dr. Sampurnanand Medical College, Jodhpur - 342003" + }, + { + "author_name": "Anjali Gupta", + "author_inst": "VRDL, Sarder Patel Medical College, Bikaner - 334001" + }, + { + "author_name": "Himanshu Khatri", + "author_inst": "VRDL, Department of Microbiology, GMERS Medical College, Himmatnagar - 383001" + }, + { + "author_name": "Bharati Malhotra", + "author_inst": "VRDL, Sawai Man Singh Medical College, Jaipur - 302004" + }, + { + "author_name": "Mythily Nagasundaram", + "author_inst": "VRDL, Coimbatore Medical College, Coimbatore - 641018" + }, + { + "author_name": "Lali Dar", + "author_inst": "VRDL, All India Institute of Medical Sciences, Delhi - 110029" + }, + { + "author_name": "Nazira Sheikh", + "author_inst": "VRDL, Dr. V.M Government Medical College, Solapur - 413003" + }, + { + "author_name": "Neeraj Aggarwal", + "author_inst": "Indian Council of Medical Research, V. Ramalingaswami Bhawan, Ansari Nagar, New Delhi, India Pin-110029" + }, + { + "author_name": "Priya Abraham", + "author_inst": "Indian Council of Medical Research-National Institute of Virology, Pune, India Pin-411021" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.13.21258757", "rel_title": "Prospective, Randomized, Parallel-Group, Open-Label Study to Evaluate the Efficacy and Safety of IMU-838, in Combination with Oseltamivir, in Adults with Coronavirus Disease 19 The IONIC Trial", @@ -694190,33 +693603,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2021.07.11.21260148", - "rel_title": "ONLINE QUERIES AS A CRITERION FOR EVALUATION OF THE EPIDEMIOLOGICAL STATUS AND EFFECTIVENESS OF COVID-19 EPIDEMIC CONTROL MEASURES", - "rel_date": "2021-07-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.11.21260148", - "rel_abs": "Monitoring online queries can provide early and accurate information about the spread of COVID-19 in the population and about the effectiveness of COVID-19 epidemic control measures.\n\nThe purpose of the studyAssessment of significance of online queries regarding smell impairment to evaluate the epidemiological status and effectiveness of COVID-19 epidemic control measures.\n\nMaterials and methodsWeekly online queries from Yandex Russian users regarding smell impairment were analysed in regions and large cities of Russia from 16/3/2020 to 21/2/2021. A total of 81 regions of Russia and several large cities, such as Moscow, St. Petersburg, and Nizhny Novgorod, were included in the study.\n\nResultsA strong positive direct correlation (r>0.7) was found between the number of smell-related queries in Yandex new cases of COVID-19 in 59 out of 85 Russian regions and large cities (70%). During the \"first\" peak of COVID-19 incidence in Russia (April-May 2020), the increase in the number of smell-related queries outpaced the increase in the number of new cases by 1-2 weeks in 23 out of 59 regions of Russia. During the \"second\" peak of COVID-19 incidence in Russia (October-December 2020), the increase in the number of smell-related queries outpaced the increase in the number of new cases by 1-2 weeks in 36 regions of Russia, including Moscow. We also estimated the increase in the query/new case ratio during the \"second\" peak of incidence for 45 regions. It was found that the query/new case ratio increased by more than 100% in 24 regions. The regions where the increase in queries was more than 160% compared to new infection cases during the \"second\" peak of incidence demonstrated significantly higher search activity related to levofloxacin than the regions where the increase in queries was lower than 160% compared to the increase in new infection cases.\n\nConclusionThe sudden interest in smell impairment and growing frequency of online queries among the population can be used as an indicator of the spread of coronavirus infection among the population as well as for evaluation of the effectiveness of COVID-19 epidemic control measures.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Kuvat Momynaliev", - "author_inst": "Central Research Institute of Epidemiology of the Federal Service for Customers Rights Protection and Human Well-Being Surveillance, Moscow, Russia" - }, - { - "author_name": "Dimash Khoroshun", - "author_inst": "Central Research Institute of Epidemiology of the Federal Service for Customers Rights Protection and Human Well-Being Surveillance, Moscow, Russia" - }, - { - "author_name": "Vasiliy Akimkin", - "author_inst": "Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being, Moscow, Russia" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.07.11.21260325", "rel_title": "Mapping First to Second wave transition of covid19 Indian data via Sigmoid function and prediction of Third wave", @@ -695496,6 +694882,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2021.07.10.21260297", + "rel_title": "Does trust in government improve Covid-19's crisis management?", + "rel_date": "2021-07-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.10.21260297", + "rel_abs": "Countries have adopted several measures to control the spread of Covid-19. However, substantial differences remain in terms of performance in controlling the virus, potentially due to heterogeneity in citizen engagement with government measures. Drawing on this observation, this paper seeks to analyze the effect of pre-crisis ties, particularly trust in government, on crisis management, proxied by the number of Covid-19 cases and deaths per million population. We examine this question based on a sample of 41 countries for which data are available. Results reveal that a high level of trust in government predicts better crisis management in terms of relatively low levels of cases and deaths. These results, which successfully pass a series of robustness tests, may vary according to level of contamination and increase with time.\n\nJEL ClassificationE71, H12, I12, I18, I38, Z18", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Ablam Estel Apeti", + "author_inst": "UCA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2021.07.12.21260298", "rel_title": "Machine Learning Model for Predicting Number of COVID19 Cases in Countries with Low Number of Tests", @@ -696016,77 +695421,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.12.21259864", - "rel_title": "Evidence of SARS-Cov-2-specific memory B cells six months after vaccination with BNT162b2 mRNA vaccine", - "rel_date": "2021-07-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.12.21259864", - "rel_abs": "SARS-CoV-2 mRNA vaccines have demonstrated high efficacy and immunogenicity, but limited information is currently available on memory B cells generation and long-term persistence. Here, we investigated Spike-specific memory B cells and humoral responses in 145 subjects, up to six months after the BNT162b2 vaccine (Comirnaty) administration. Spike-specific antibody titers peaked 7 days after the second dose and significant titers and neutralizing activity were still observed after six months, despite a progressive decline over time. Concomitant to antibody reduction, Spike-specific memory B cells, mostly IgG class-switched, increased in blood of vaccinees and persisted six months after vaccination. Following in vitro restimulation, circulating memory B cells reactivated and produced Spike-specific antibodies. A high frequency of Spike-specific IgG+ plasmablasts, identified by computational analysis 7 days after boost, positively correlated with the generation of IgG+ memory B cells at six months.\n\nThese data demonstrate that mRNA BNT162b2 vaccine elicits strong B cell immunity with Spike-specific memory B cells that still persist six months after vaccination, playing a crucial role for rapid response to SARS-CoV-2 virus encounter.\n\nOne Sentence SummarymRNA BNT162b2 vaccine elicits persistent spike-specific memory B cells crucial for rapid response to SARS-CoV-2 virus encounter", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Annalisa Ciabattini", - "author_inst": "Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena; Siena, Italy" - }, - { - "author_name": "Gabiria Pastore", - "author_inst": "Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena; Siena, Italy" - }, - { - "author_name": "Fabio Fiorino", - "author_inst": "Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena; Siena, Italy" - }, - { - "author_name": "Jacopo Polvere", - "author_inst": "Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena; Siena, Italy" - }, - { - "author_name": "Simone Lucchesi", - "author_inst": "Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena; Siena, Italy" - }, - { - "author_name": "Elena Pettini", - "author_inst": "Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena; Siena, Italy" - }, - { - "author_name": "Stefano Auddino", - "author_inst": "Department of Medical Biotechnologies, University of Siena; Siena, Italy" - }, - { - "author_name": "Ilaria Rancan", - "author_inst": "Department of Medical Biotechnologies, University of Siena, Siena, Italy; Department of Medical Sciences, Infectious and Tropical Diseases Unit, University Hosp" - }, - { - "author_name": "Miriam Durante", - "author_inst": "Department of Medical Biotechnologies, University of Siena; Siena, Italy" - }, - { - "author_name": "Michele Miscia", - "author_inst": "Department of Medical Biotechnologies, University of Siena; Siena, Italy; Department of Medical Sciences, Infectious and Tropical Diseases Unit, University Hosp" - }, - { - "author_name": "Barbara Rossetti", - "author_inst": "Department of Medical Sciences, Infectious and Tropical Diseases Unit, University Hospital of Siena; Siena, Italy" - }, - { - "author_name": "Massimiliano Fabbiani", - "author_inst": "Department of Medical Sciences, Infectious and Tropical Diseases Unit, University Hospital of Siena; Siena, Italy" - }, - { - "author_name": "Francesca Montagnani", - "author_inst": "Department of Medical Biotechnologies, University of Siena; Siena, Italy; Department of Medical Sciences, Infectious and Tropical Diseases Unit, University Hosp" - }, - { - "author_name": "Donata Medaglini", - "author_inst": "Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena; Siena, Italy" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.08.21260194", "rel_title": "Humoral immune response in inactivated SARS-CoV-2 vaccine: When should a booster dose be administered?", @@ -697190,6 +696524,197 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.07.07.21260122", + "rel_title": "Viral infection and Transmission in a large well-traced outbreak caused by the Delta SARS-CoV-2 variant", + "rel_date": "2021-07-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.07.21260122", + "rel_abs": "We report the first local transmission of the SARS-CoV-2 Delta variant in mainland China. All 167 infections could be traced back to the first index case. Daily sequential PCR testing of the quarantined subjects indicated that the viral loads of Delta infections, when they first become PCR+, were on average [~]1000 times greater compared to A/B lineage infections during initial epidemic wave in China in early 2020, suggesting potentially faster viral replication and greater infectiousness of Delta during early infection. We performed high-quality sequencing on samples from 126 individuals. Reliable epidemiological data meant that, for 111 transmission events, the donor and recipient cases were known. The estimated transmission bottleneck size was 1-3 virions with most minor intra-host single nucleotide variants (iSNVs) failing to transmit to the recipients. However, transmission heterogeneity of SARS-CoV-2 was also observed. The transmission of minor iSNVs resulted in at least 4 of the 30 substitutions identified in the outbreak, highlighting the contribution of intra-host variants to population level viral diversity during rapid spread. Disease control activities, such as the frequency of population testing, quarantine during pre-symptomatic infection, and level of virus genomic surveillance should be adjusted in order to account for the increasing prevalence of the Delta variant worldwide.", + "rel_num_authors": 44, + "rel_authors": [ + { + "author_name": "Baisheng Li", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Aiping Deng", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Kuibiao Li", + "author_inst": "Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, China" + }, + { + "author_name": "Yao Hu", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Zhencui Li", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Qianling Xiong", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Zhe Liu", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Qianfang Guo", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Lirong Zou", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Huan Zhang", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Meng Zhang", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Fangzhu Ouyang", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Juan Su", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Wenzhe Su", + "author_inst": "Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, China" + }, + { + "author_name": "Jing Xu", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Huifang Lin", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Jing Sun", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Jinju Peng", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Huimin Jiang", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Pingping Zhou", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Ting Hu", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Min Luo", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Yingtao Zhang", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Huanying Zheng", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Jianpeng Xiao", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Tao Liu", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Rongfei Che", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Hanri Zeng", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Zhonghua Zheng", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Yushi Huang", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Jianxiang Yu", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Lina Yi", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Jie Wu", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Jingdiao Chen", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Haojie Zhong", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Xiaoling Deng", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "min Kang", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Oliver G. Pybus", + "author_inst": "Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK" + }, + { + "author_name": "Matthew Hall", + "author_inst": "Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK" + }, + { + "author_name": "Katrina A. Lythgoe", + "author_inst": "Big Data Institute, Nuffield Department of Medicine, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK" + }, + { + "author_name": "Yan Li", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Jun Yuan", + "author_inst": "Guangzhou Center for Disease Control and Prevention, Guangzhou, Guangdong, China" + }, + { + "author_name": "Jianfeng He", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + }, + { + "author_name": "Jing Lu", + "author_inst": "Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong, China;Guangdong Workstation for Emerging Infectious Disease Control and Pr" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.11.451951", "rel_title": "Niclosamide reverses SARS-CoV-2 control of lipophagy", @@ -697750,49 +697275,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.07.08.21259912", - "rel_title": "Efficacy and safety of Andrographis paniculata extract in patients with mild COVID-19: A randomized controlled trial", - "rel_date": "2021-07-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.08.21259912", - "rel_abs": "ObjectivesTo assess the efficacy and safety of Andrographis paniculata extract (APE) in adults with mild COVID-19.\n\nMethodsSixty-three adults aged 18-60 years, without co-morbidity, with laboratory-confirmed mild COVID-19, were randomized 1:1 to receive APE (60 mg andrographolide, t.i.d, for 5 days) or placebo within 24 hours after admission, plus standard supportive care. The outcomes were clinical recovery rates by Day 5 using self-assessment scores, pneumonia by chest X-rays, nasopharyngeal SARS-CoV-2 detection by rRT-PCR on Day 5, changes of serum CRP levels, and adverse drug reactions. Chest X-rays and blood tests for CRP, liver and renal function, were performed on Days 1, 3, and 5.\n\nResultsBaseline characteristics of patients in the APE-treatment (n=29) and placebo-control (n=28) groups were comparable. None had self-assessment scores showing complete clinical recovery by Day 5. Pneumonia occurred in 0/29 (0%) versus 3/28 (10.7%), (p=0.112). On Day 5, patients with SARS-CoV-2 detection were 10/29 (34.5%) versus 16/28 (57.1%), (p=0.086); patients with CRP >10 mg/L were 0/29 (0%) versus 5/28 (17.9%), (p=0.023), for APE-treatment and placebo-control groups, respectively. All three patients with pneumonia had substantially rising serum CRP; and high CRP levels on Day 5. None had evidence of hematologic, hepatic or renal impairment.\n\nConclusionEven though the study was limited by small sample size, our findings suggested promising efficacy and safety of the APE-treatment regimen in adults with mild COVID-19. Further studies, with adequate power to assure these findings, are required.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Kulthanit Wanaratna", - "author_inst": "Thai Traditional Medicines Research Institute" - }, - { - "author_name": "Pornvimol Leethong", - "author_inst": "Samutprakarn Hospital, Ministry of Public Heath, Thailand" - }, - { - "author_name": "Nitapha Inchai", - "author_inst": "Department of Thai Traditional and Alternative Medicine, Ministry of Public Heath, Thailand" - }, - { - "author_name": "Wararath Chueawiang", - "author_inst": "Department of Thai Traditional and Alternative Medicine, Ministry of Public Heath, Thailand" - }, - { - "author_name": "Pantitra Sriraksa", - "author_inst": "Department of Thai Traditional and Alternative Medicine, Ministry of Public Heath, Thailand" - }, - { - "author_name": "Anutida Tabmee", - "author_inst": "Department of Thai Traditional and Alternative Medicine, Ministry of Public Heath, Thailand" - }, - { - "author_name": "Sayomporn Sirinavin", - "author_inst": "Division of Infectious Diseases, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Thailand" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.06.21260086", "rel_title": "Proxalutamide (GT0918) Reduces the Rate of Hospitalization in mild-to-moderate COVID-19 Female Patients: A Randomized Double-Blinded Placebo-Controlled Two-Arm Parallel Trial.", @@ -698984,6 +698466,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.07.09.451770", + "rel_title": "A photoactivable natural product with broad antiviral activity against enveloped viruses including highly pathogenic coronaviruses", + "rel_date": "2021-07-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.09.451770", + "rel_abs": "The SARS-CoV-2 outbreak has highlighted the need for broad-spectrum antivirals against coronaviruses (CoVs). Here, pheophorbide a (Pba) was identified as a highly active antiviral molecule against HCoV-229E after bioguided fractionation of plant extracts. The antiviral activity of Pba was subsequently shown for SARS-CoV-2 and MERS-CoV, and its mechanism of action was further assessed, showing that Pba is an inhibitor of coronavirus entry by directly targeting the viral particle. Interestingly, the antiviral activity of Pba depends on light exposure, and Pba was shown to inhibit virus-cell fusion by stiffening the viral membrane as demonstrated by cryo-electron microscopy. Moreover, Pba was shown to be broadly active against several other enveloped viruses, and reduced SARS-CoV-2 and MERS-CoV replication in primary human bronchial epithelial cells. Pba is the first described natural antiviral against SARS-CoV-2 with direct photosensitive virucidal activity that holds potential for COVID-19 therapy or disinfection of SARS-CoV-2 contaminated surfaces.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Simon Bordage", + "author_inst": "Univ Lille" + }, + { + "author_name": "Moussa Bamba", + "author_inst": "Univ Lille" + }, + { + "author_name": "Marion Decossas", + "author_inst": "CNRS" + }, + { + "author_name": "Fezan H. Tra Bi", + "author_inst": "Univ Nangui Abrogoua" + }, + { + "author_name": "Olivier Lambert", + "author_inst": "CNRS" + }, + { + "author_name": "Sevser Sahpaz", + "author_inst": "Unive Lille" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.07.08.21260212", "rel_title": "RISK OF ON JOB NON COMPLIANCE TOWARDS VARIOUS COVID-19 STANDARD & TRANSMISSION BASED INFECTION PREVENTION & CONTROL MEASURES/PRECAUTIONS AMONG THE HEALTHCARE WORKS WORKING IN OPD SETTINGs OF PUBLIC SECTOR TERTIORY CARE HOSPITALS OF QUETTA BALOCHISTAN. (Prospective cohort study).", @@ -699424,85 +698945,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.30.21259763", - "rel_title": "Which children and young people are at higher risk of severe disease and death after SARS-CoV-2 infection: a systematic review and individual patient meta-analysis", - "rel_date": "2021-07-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.30.21259763", - "rel_abs": "BackgroundWe aimed to use individual patient data to describe pre-existing factors associated with severe disease, primarily admission to critical care, and death secondary to SARS-CoV-2 infection in children and young people (CYP) in hospital.\n\nMethodsWe searched Pubmed, European PMC, Medline and Embase for case series and cohort studies that included all CYP admitted to hospital with [≥]30 CYP with SARS-CoV-2 or [≥]5 CYP with PIMS-TS or MIS-C. Eligible studies contained 1) details of age, sex, ethnicity or co-morbidities, and 2) an outcome which included admission to critical care, mechanical invasive ventilation, cardiovascular support, or death. Studies reporting outcomes in more restricted grouping of co-morbidities were eligible for narrative review. Authors of eligible studies were approached for individual patient data (IPD). We used random effects meta-analyses for aggregate study-level data and multilevel mixed effect models for IPD data to examine risk factors (age, sex, comorbidities) associated with admission to critical care and death. Data shown are odds ratios and 95% confidence intervals (CI).\n\nFindings81 studies were included, 57 in the meta-analysis (of which 22 provided IPD) and 26 in the narrative synthesis. Most studies had an element of bias in their design or reporting. Sex was not associated with critical care or death. Compared with CYP aged 1-4 years, infants had increased odds of admission to critical care (OR 1.63 (95% CI 1.40-1.90)) and death (OR 2.08 (1.57-2.86)). Odds of death were increased amongst CYP over 10 years (10-14 years OR 2.15 (1.54-2.98); >14 years OR 2.15 (1.61-2.88)).\n\nNumber of comorbid conditions was associated with increased odds of admission to critical care and death for COVID-19 in a dose-related fashion. For critical care admission odds ratios were: 1 comorbidity 1.49 (1.45-1.53); 2 comorbidities 2.58 (2.41-2.75); [≥]3 comorbidities 2.97 (2.04-4.32), and for death: 1 comorbidity 2.15 (1.98-2.34); 2 comorbidities 4.63 (4.54-4.74); [≥]3 co-morbidities 4.98 (3.78-6.65). Odds of admission to critical care were increased for all co-morbidities apart from asthma (0.92 (0.91-0.94)) and malignancy (0.85 (0.17-4.21)) with an increased odds of death in all co-morbidities considered apart from asthma. Neurological and cardiac comorbidities were associated with the greatest increase in odds of severe disease or death. Obesity increased the odds of severe disease and death independently of other comorbidities.\n\nInterpretationHospitalised CYP at greatest vulnerability of severe disease or death from SARS-CoV-2 infection are infants, teenagers, those with cardiac or neurological conditions, or 2 or more comorbid conditions, and those who are obese. These groups should be considered higher priority for vaccination and for protective shielding when appropriate. Whilst odds ratios were high, the absolute increase in risk for most comorbidities was small compared to children without underlying conditions.\n\nFundingRH is in receipt of a funded fellowship from Kidney Research UK. JW is in receipt of a Medical Research Council Fellowship.\n\nPutting Research Into ContextO_ST_ABSEvidence before this studyC_ST_ABSThe risk factors for severe disease following SARS-CoV-2 infection in adults has been extensively studied and reported, with good evidence that increasing age, non-white ethnicity, male gender and co-morbidities increase the risk. SARS-CoV-2 infection in children and young people (CYP) infrequently results in hospital admission and very rarely causes severe disease and death, making it difficult to discern the impact of a range of potential risk factors for severe disease in the many small to moderate sized published studies. More recent larger publications have aimed to address this question in specific populations but the global experience has not been described. We searched Pubmed, European PMC, Medline and Embase from the 1st January 2020 to 21st May 2021 for case series and cohort studies that included all CYP admitted to hospital with 30 children with reverse transcriptase-PCR confirmed SARS-CoV-2 or 5 CYP defined as having PIMS-TS or MIS-C. 57 studies met the eligibility criteria for meta-analysis.\n\nAdded value of this studyTo our knowledge, this is the first meta-analysis to use individual patient data to compare the odds and risk of critical care admission and death in CYP with COVID-19 and PIMS-TS. We find that the odds of severe disease in hospitalised children is increased in those with multiple co-morbidities, cardiac and neurological co-morbidities and those who are obese. However, the additional risk compared to children without co-morbidity is small.\n\nImplications of all the available evidenceSevere COVID-19 and PIMS-TS, whilst rare, can occur in CYP. We have identified pre-existing risk factors for severe disease after SARS-CoV-2 and recommend that those with co-orbidities which place them in the highest risk groups are prioritised for vaccination.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Rachel Harwood", - "author_inst": "Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool" - }, - { - "author_name": "Helen Yan", - "author_inst": "Medical School, UCL, London" - }, - { - "author_name": "Nish Talawila Da Camara", - "author_inst": "Royal College of Paediatrics and Child Health, London" - }, - { - "author_name": "Clare Smith", - "author_inst": "NHS England and NHS Improvement, London" - }, - { - "author_name": "Joseph Ward", - "author_inst": "UCL Great Ormond St. Institute of Child Health, London" - }, - { - "author_name": "Catrin Tudur-Smith", - "author_inst": "Department of Statistics, University of Liverpool, Liverpool" - }, - { - "author_name": "Michael Linney", - "author_inst": "University Hospitals Sussex NHS Foundation Trust" - }, - { - "author_name": "Matthew Clark", - "author_inst": "NHS England and NHS Improvement, London" - }, - { - "author_name": "Elizabeth Whittaker", - "author_inst": "Imperial College London, London" - }, - { - "author_name": "Defne Saatci", - "author_inst": "Imperial College London, London" - }, - { - "author_name": "Peter J Davis", - "author_inst": "Paediatric Intensive Care Unit, Bristol Royal Hospital for Children, Bristol" - }, - { - "author_name": "Karen Luyt", - "author_inst": "Bristol Medical School, University of Bristol, Bristol" - }, - { - "author_name": "Elizabeth S Draper", - "author_inst": "PICANet, Department of Health Sciences, University of Leicester, Leicester" - }, - { - "author_name": "Simon Kenny", - "author_inst": "NHS England and NHS Improvement, London" - }, - { - "author_name": "Lorna K Fraser", - "author_inst": "Martin House Research Centre, Dept of Health Sciences, University of York" - }, - { - "author_name": "Russell M Viner", - "author_inst": "UCL Great Ormond St. Institute of Child Health, London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2021.07.07.21260156", "rel_title": "COVID-19 deaths and hospitalizations averted by rapid vaccination rollout in the United States", @@ -700950,6 +700392,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.07.07.21259916", + "rel_title": "Modeling the emergence of vaccine-resistant variants with Gaussian convolution.COVID-19: Could the wrong strategy ruin vaccine efficiency?", + "rel_date": "2021-07-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.07.21259916", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWThe SARS-CoV-2 virus, which is responsible for the COVID-19 pandemic, has been shown to mutate. In the absence of a vaccine, natural selection will favor variants with higher transmissibility rates. However, when a substantial portion of the population is vaccinated, natural selection will shift towards favoring variants that can resist the vaccine. These variants can therefore become dominant and even cancel out the benefit of the vaccine. This paper develops a compartmental model which simulates this phenomenon and shows how various vaccination strategies can lead to the emergence of vaccine-resistant variants.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Christian Bongiorno", + "author_inst": "University Paris-Saclay, CentraleSupelec" + }, + { + "author_name": "John Cagnol", + "author_inst": "University Paris-Saclay, CentraleSupelec" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.07.21259779", "rel_title": "Deaths in Children and Young People in England following SARS-CoV-2 infection during the first pandemic year: a national study using linked mandatory child death reporting data", @@ -701378,253 +700843,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.08.21259776", - "rel_title": "Effectiveness of SARS-CoV-2 mRNA Vaccines for Preventing Covid-19 Hospitalizations in the United States", - "rel_date": "2021-07-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.08.21259776", - "rel_abs": "BackgroundAs SARS-CoV-2 vaccination coverage increases in the United States (US), there is a need to understand the real-world effectiveness against severe Covid-19 and among people at increased risk for poor outcomes.\n\nMethodsIn a multicenter case-control analysis of US adults hospitalized March 11 - May 5, 2021, we evaluated vaccine effectiveness to prevent Covid-19 hospitalizations by comparing odds of prior vaccination with an mRNA vaccine (Pfizer-BioNTech or Moderna) between cases hospitalized with Covid-19 and hospital-based controls who tested negative for SARS-CoV-2.\n\nResultsAmong 1210 participants, median age was 58 years, 22.8% were Black, 13.8% were Hispanic, and 20.6% had immunosuppression. SARS-CoV-2 lineage B.1.1.7 was most common variant (59.7% of sequenced viruses). Full vaccination (receipt of two vaccine doses [≥]14 days before illness onset) had been received by 45/590 (7.6%) cases and 215/620 (34.7%) controls. Overall vaccine effectiveness was 86.9% (95% CI: 80.4 to 91.2%). Vaccine effectiveness was similar for Pfizer-BioNTech and Moderna vaccines, and highest in adults aged 18-49 years (97.3%; 95% CI: 78.9 to 99.7%). Among 45 patients with vaccine-breakthrough Covid hospitalizations, 44 (97.8%) were [≥]50 years old and 20 (44.4%) had immunosuppression. Vaccine effectiveness was lower among patients with immunosuppression (59.2%; 95% CI: 11.9 to 81.1%) than without immunosuppression (91.3%; 95% CI: 85.5 to 94.7%).\n\nConclusionDuring March-May 2021, SARS-CoV-2 mRNA vaccines were highly effective for preventing Covid-19 hospitalizations among US adults. SARS-CoV-2 vaccination was beneficial for patients with immunosuppression, but effectiveness was lower in the immunosuppressed population.", - "rel_num_authors": 58, - "rel_authors": [ - { - "author_name": "Mark W. Tenforde", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Manish M. Patel", - "author_inst": "US Centers for Disease Control and Prevention" - }, - { - "author_name": "Adit A. Ginde", - "author_inst": "University of Colorado School of Medicine" - }, - { - "author_name": "David J. Douin", - "author_inst": "University of Colorado School of Medicine" - }, - { - "author_name": "H. Keipp Talbot", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Jonathan D. Casey", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Nicholas M. Mohr", - "author_inst": "University of Iowa" - }, - { - "author_name": "Anne Zepeski", - "author_inst": "University of Iowa" - }, - { - "author_name": "Manjusha Gaglani", - "author_inst": "Baylor Scott and White Health, Texas A&M University College of Medicine" - }, - { - "author_name": "Tresa McNeal", - "author_inst": "Baylor Scott and White Health, Texas A&M University College of Medicine" - }, - { - "author_name": "Shekhar Ghamande", - "author_inst": "Baylor Scott and White Health, Texas A&M University College of Medicine" - }, - { - "author_name": "Nathan I. Shapiro", - "author_inst": "Beth Israel Deaconess Medical Center" - }, - { - "author_name": "Kevin W. Gibbs", - "author_inst": "Wake Forest School of Medicine" - }, - { - "author_name": "D. Clark Files", - "author_inst": "Wake Forest School of Medicine" - }, - { - "author_name": "David N. Hager", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Arber Shehu", - "author_inst": "Johns Hopkins University School of Medicine" - }, - { - "author_name": "Matthew E. Prekker", - "author_inst": "Hennepin County Medical Center" - }, - { - "author_name": "Heidi L. Erickson", - "author_inst": "Hennepin County Medical Center" - }, - { - "author_name": "Matthew C. Exline", - "author_inst": "The Ohio State University" - }, - { - "author_name": "Michelle N. Gong", - "author_inst": "Montefiore Health System, Albert Einstein College of Medicine" - }, - { - "author_name": "Amira Mohamed", - "author_inst": "Montefiore Health System, Albert Einstein College of Medicine" - }, - { - "author_name": "Daniel J. Henning", - "author_inst": "University of Washington" - }, - { - "author_name": "Jay S. Steingrub", - "author_inst": "Baystate Medical Center" - }, - { - "author_name": "Ithan D. Peltan", - "author_inst": "Intermountain Medical Center" - }, - { - "author_name": "Samuel M. Brown", - "author_inst": "Intermountain Medical Center" - }, - { - "author_name": "Emily T. Martin", - "author_inst": "University of Michigan" - }, - { - "author_name": "Arnold S. Monto", - "author_inst": "University of Michigan" - }, - { - "author_name": "Akram Khan", - "author_inst": "Oregon Health and Sciences University" - }, - { - "author_name": "C. Terri Hough", - "author_inst": "Oregon Health and Sciences University" - }, - { - "author_name": "Laurence Busse", - "author_inst": "Emory University" - }, - { - "author_name": "Caitlin C. ten Lohuis", - "author_inst": "Emory University" - }, - { - "author_name": "Abhijit Duggal", - "author_inst": "Cleveland Clinic" - }, - { - "author_name": "Jennifer G. Wilson", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Alexandra June Gordon", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Nida Qadir", - "author_inst": "University of California-Los Angeles" - }, - { - "author_name": "Steven Y. Chang", - "author_inst": "University of California-Los Angeles" - }, - { - "author_name": "Christopher Mallow", - "author_inst": "University of Miami" - }, - { - "author_name": "Hayley B. Gershengorn", - "author_inst": "University of Miami" - }, - { - "author_name": "Hilary M. Babcock", - "author_inst": "Washington University" - }, - { - "author_name": "Jennie H. Kwon", - "author_inst": "Washington University" - }, - { - "author_name": "Natasha Halasa", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "James D. Chappell", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Adam S. Lauring", - "author_inst": "University of Michigan" - }, - { - "author_name": "Carlos G. Grijalva", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Todd W. Rice", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Ian D. Jones", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "William B. Stubblefield", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Adrienne Baughman", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Kelsey N. Womack", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Christopher J. Lindsell", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Kimerly W. Hart", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Yuwei Zhu", - "author_inst": "Vanderbilt University Medical Center" - }, - { - "author_name": "Samantha M. Olson", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Meagan Stephenson", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Stephanie J. Schrag", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Miwako Kobayashi", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Jennifer R. Verani", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Wesley H. Self", - "author_inst": "Vanderbilt University Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.06.21259982", "rel_title": "Early initiation of corticosteroids in patients hospitalized with COVID-19 not requiring intensive respiratory support: cohort study", @@ -702852,6 +702070,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2021.07.03.21259943", + "rel_title": "Masks in a Post COVID-19 World: A Better Alternative to Curtailing Influenza?", + "rel_date": "2021-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.03.21259943", + "rel_abs": "Over the course of the coronavirus pandemic, it has become apparent that non-pharmaceutical interventions such as masks and social distancing are of great help in mitigating the transmission of airborne infectious diseases. Additionally, data from respiratory specimen analysis from the past year show that current mask mandates established for COVID-19 have inadvertently reduced the rates of other respiratory diseases, including influenza. Thus, the question arises as to whether comparatively mild measures should be kept in place after the pandemic to reduce the impact of influenza. In this study, we employed a series of differential equations to simulate past influenza seasons, assuming people wore face masks. This was achieved by introducing a variable to account for the efficacy and prevalence of masks and then analyzing its impact on influenza transmission rate in an SEIR model fit to the actual past seasons. We then compared influenza rates in this hypothetical scenario with the actual rates over the seasons. Our results show that several combinations of mask efficacy and prevalence can significantly reduce the burden of seasonal influenza. Particularly, our simulations suggest that a minority of individuals wearing masks greatly reduce the number of influenza infections. Considering the efficacy rates of masks and the relatively insignificant monetary cost, we highlight that it may be a viable alternative or complement to influenza vaccinations. We conclude with a brief discussion of our results and other practical aspects", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Henri Froese", + "author_inst": "Goethe-University Frankfurt am Main" + }, + { + "author_name": "Angel G. A. Prempeh", + "author_inst": "Saginaw Valley State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.03.21259961", "rel_title": "Predictors of black fungus fear during the COVID-19 pandemic among the Bangladeshi health workers: a cross-sectional study", @@ -703432,41 +702673,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.03.21254541", - "rel_title": "Anticoagulants and Antiplatelets in COVID-19: Impact on Survival and Thromboembolism Development", - "rel_date": "2021-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.03.21254541", - "rel_abs": "BackgroundHigher rates of venous and arterial thromboembolism have been noted in coronavirus disease-2019 (COVID-19). There has been limited research on the impact of anticoagulant and antiplatelet choice in COVID-19.\n\nMethodsThis was a single-centre retrospective cohort study of 933 patients with COVID-19 infection presenting between 01/02/2020 and 31/05/2020. Survival time at 90 days post-diagnosis and thromboembolism development were the measured outcomes.\n\nResultsOf 933 total patients, mean age was 68 years and 54.4% were male. 297 (31.8%) did not survive at 90 days. A Cox proportional hazards model analysis found no statistically significant relationship between anticoagulant or antiplatelet choice and survival (p<0.05).\n\n57 (6.3%) developed thromboembolism. Antiplatelet choice was not shown to have a statistically significant relationship with thromboembolism development. Warfarin and direct oral anticoagulant (DOAC) use did not have a statistically significant impact on thromboembolism development (p<0.05). Therapeutic low-molecular-weight heparin (LMWH) use was associated with increased thromboembolism risk (Odds ratio = 14.327, 95% CI 1.904 - 107.811, p = 0.010).\n\nConclusionsAntiplatelet choice was shown to have no impact on survival or thromboembolism development in COVID-19. Anticoagulant choice did not impact survival or thromboembolism development, aside from LMWH. Therapeutic LMWH use was associated with increased risk of thromboembolism. However, it should be noted that the sample size for patients using therapeutic LMWH was small (n=4), and there may be confounding variables affecting both LMWH use and thromboembolism development. These findings should be repeated with a larger sample of patients using therapeutic LMWH with additional adjustment for cofounding variables.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Thomas Salmon", - "author_inst": "Liverpool University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Mitchell Titley", - "author_inst": "Liverpool University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Zaid Noori", - "author_inst": "Liverpool University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Mark Crosby", - "author_inst": "Liverpool University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Rajiv Sankaranarayanan", - "author_inst": "Liverpool University Hospitals NHS Foundation Trust" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2021.07.07.21260121", "rel_title": "SARS-CoV-2 IgG detection in human oral fluids", @@ -704666,6 +703872,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.05.21260012", + "rel_title": "A decision-tree approach to treat platelet hyperactivity and anomalous blood clotting in acute COVID-19 patients", + "rel_date": "2021-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.05.21260012", + "rel_abs": "An important component of severe COVID-19 disease is virus-induced endothelilitis. This leads to disruption of normal endothelial function, initiating a state of failing normal clotting physiology. Massively increased levels of von Willebrand Factor (VWF) lead to overwhelming platelet activation, as well as activation of the enzymatic (intrinsic) clotting pathway. In addition, there is an impaired fibrinolysis, caused by, amongst others, increased levels of alpha-(2) antiplasmin. The end result is hypercoagulation [proven by thromboelastography(R) (TEG(R))] and reduced fibrinolysis, inevitably leading to a difficult-to-overcome hypercoagulated physiological state. Platelets in circulation also plays a significant role in clot formation, but themselves may also drive hypercoagulation when they are overactivated due to the interactions of their receptors with the endothelium, immune cells or circulating inflammatory molecules. From the literature it is clear that the role of platelets in severely ill COVID-19 patients has been markedly underestimated or even ignored. We here highlight the value of early management of severe COVID-19 coagulopathy as guided by TEG(R), microclot and platelet mapping. We also argue that the failure of clinical trials, where the efficacy of prophylactic versus therapeutic clexane (low molecular weight heparin (LMWH)) were not always successful, might be because the significant role of platelet activation was not taken into account during the planning of the trial. We conclude that, because of the overwhelming alteration of clotting, the outcome of any trial evaluating an any single anticoagulant, including thrombolytic, would be negative. Here we suggest the use of the degree of platelet dysfunction and presence of microclots in circulation, together with TEG(R), should be used as a guideline for disease severity. A multi-pronged approach, guided by TEG(R) and platelet mapping, would be required to maintain normal clotting physiology in severe COVID-19 disease.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Gert J Laubscher", + "author_inst": "Mediclinic Stellenbosch" + }, + { + "author_name": "Petrus J Lourens", + "author_inst": "Mediclinic Stellenbosch" + }, + { + "author_name": "Chantelle Venter", + "author_inst": "Stellenbosch University" + }, + { + "author_name": "Douglas B Kell", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Etheresia Pretorius", + "author_inst": "Stellenbosch University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2021.07.05.21259933", "rel_title": "Sex-specific epidemiological and clinical characteristics of Covid-19 patients in the southeast region of Bangladesh", @@ -705110,57 +704351,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.06.21260055", - "rel_title": "Critical timing for triggering public health interventions to prevent COVID-19 resurgence: a mathematical modelling study", - "rel_date": "2021-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.06.21260055", - "rel_abs": "To prevent the catastrophic health and economic consequences from COVID-19 epidemics, some nations have aimed for no community transmission outside of quarantine. To achieve this, governments have had to respond rapidly to outbreaks with public health interventions. But the exact characteristics of an outbreak that trigger these measures differ and are poorly defined. We used existing data from epidemics in Australia to establish a practical model to assist stakeholders in making decisions about the optimal timing and extent of interventions. We found that the number of reported cases on the day that interventions commenced strongly predicted the size of the outbreaks. We quantified how effective interventions were at containing outbreaks in relation to the number of cases at the time the interventions commenced. We also found that containing epidemics from novel variants that had higher transmissibility would require more stringent interventions that commenced earlier. In contrast, increasing vaccination coverage would enable more relaxed interventions. Our model highlights the importance of early and decisive action in the early phase of an outbreak if governments aimed for zero community transmission, although new variants and vaccination coverage may change this.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Zhuoru Zou", - "author_inst": "Xi'an Jiaotong University Health Science Centre" - }, - { - "author_name": "Christopher K Fairley", - "author_inst": "Monash University" - }, - { - "author_name": "Mingwang Shen", - "author_inst": "Xi'an Jiaotong University" - }, - { - "author_name": "Nick Scott", - "author_inst": "Burnet Institute" - }, - { - "author_name": "Xianglong Xu", - "author_inst": "Monash University" - }, - { - "author_name": "Zengbin Li", - "author_inst": "Xi'an Jiaotong University Health Science Centre" - }, - { - "author_name": "Rui Li", - "author_inst": "Xi'an Jiaotong University Health Science Centre" - }, - { - "author_name": "Guihua Zhuang", - "author_inst": "Xi'an Jiaotong University Health Science Centre" - }, - { - "author_name": "Lei Zhang", - "author_inst": "Melboune Sexual Health Centre" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.05.21259105", "rel_title": "SARS-CoV-2 Infections in mRNA Vaccinated Individuals are Biased for Viruses Encoding Spike E484K and Associated with Reduced Infectious Virus Loads that Correlate with Respiratory Antiviral IgG levels.", @@ -706812,6 +706002,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.04.21259954", + "rel_title": "Predictors of hospitalisation and death due to SARS-CoV-2 infection in Finland: a population-based register study with implications to vaccinations", + "rel_date": "2021-07-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.04.21259954", + "rel_abs": "IntroductionThe aim of this study was to investigate how age and underlying medical conditions affect the risk of severe outcomes following SARS-CoV-2 infection and how they should be weighed while prioritising vaccinations against COVID-19.\n\nMethodsThis population-based register study includes all SARS-CoV-2 PCR-test-positive cases until 24 Feb 2021, based on the Finnish National Infectious Diseases Register. The cases were linked to other registers to identify presence of comorbidities and severe outcomes (hospitalisation, intensive care treatment, death). The odds of severe outcomes were compared in those with and without the pre-specified comorbidities using logistic regression. Furthermore, population-based rates were compared between those with a given comorbidity and those without any of the specified comorbidities using negative binomial regression.\n\nResultsAge and various comorbidities were found to be predictors of severe COVID-19. Compared to 60-69-year-olds, the odds ratio (OR) of death was 7.1 for 70-79-year-olds, 26.7 for 80-89-year-olds, and 55.8 for [≥]90-year-olds. Among the 20-69-year-olds, chronic renal disease (OR 9.4), malignant neoplasms (5.8), hematologic malignancy (5.6), chronic pulmonary disease (5.4), and cerebral palsy or other paralytic syndromes (4.6) were strongly associated with COVID-19 mortality; severe disorders of the immune system (8.0), organ or stem cell transplant (7.2), chronic renal disease (6.7), and diseases of myoneural junction and muscle (5.5) were strongly associated with COVID-19 hospitalisation. Type 2 diabetes and asthma, two very common comorbidities, were associated with all three outcomes, with ORs from 2.1 to 4.3. The population-based rate of SARS-CoV-2 infection decreased with age. Taking the 60-69-year-olds as reference, the rate ratio was highest (3.0) for 20-29-year-olds but <1 for 70-79-year-olds and 80-89-year-olds.\n\nConclusionComorbidities predispose for severe COVID-19 among younger ages. In vaccine prioritisation both the risk of infection and the risk of severe outcomes, if infected, should be combined.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Heini Salo", + "author_inst": "Finnish Institute for Health and Welfare (THL)" + }, + { + "author_name": "Toni Lehtonen", + "author_inst": "Finnish Institute for Health and Welfare" + }, + { + "author_name": "Kari Auranen", + "author_inst": "University of Turku and Finnish Institute for Health and Welfare" + }, + { + "author_name": "Ulrike Baum", + "author_inst": "Finnish Institute for Health and Welfare" + }, + { + "author_name": "Tuija Leino", + "author_inst": "Finnish Institute for Health and Welfare" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.07.04.21259991", "rel_title": "Transmission dynamics of COVID-19 in Ghana and the impact of public health interventions", @@ -707224,45 +706449,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, - { - "rel_doi": "10.1101/2021.07.04.21259985", - "rel_title": "Covid-19 Vaccination in Pregnancy: A Systematic Review", - "rel_date": "2021-07-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.04.21259985", - "rel_abs": "ObjectivePregnancy is a risk factor for severe Covid-19. Looking for safe vaccines that evoke protective maternal and fetal antibody response is important.\n\nMethodsWe searched from registries (ClinicalTrials.gov, the WHO Clinical Trial Registry, and the EU Clinical Trial Registry) and databases (MEDLINE, ScienceDirect, Cochrane Library, Proquest, and Springer) up until June 20, 2021. Articles were selected based on inclusion and exclusion criteria after duplicates were removed. Infection rate, maternal antibody response, placental antibody transfer, and adverse events were described. This systematic review was performed with quality assessment and semi-quantitative synthesis according to PRISMA guidelines.\n\nResultsTwelve observational studies with a total of 40.509 pregnant women included. The mRNA based vaccines (Pfizer-BioNTech and Moderna) can prevent future SARS-CoV-2 infections (p=0.0004). Both vaccines did not affect pregnancy, delivery, and neonatal outcomes. The most commonly encountered adverse reactions are injection-site pain, fatigue, and headache but only transient. Antibody responses were rapid after the prime dose of vaccines. After booster, antibody responses were higher and associated with better placental antibody transfer. Longer intervals between first vaccination dose and delivery were also associated with higher antibody fetal IgG and better antibody transfer ratio.\n\nConclusionsThe Pfizer-BioNTech and Moderna vaccines are efficacious for preventing future SARS-CoV-2 infections. These vaccines can be considered as a safe option for pregnancy and their fetus. Two doses of vaccines were recommended for more robust maternal and fetal antibody responses. Longer latency was associated with higher fetal antibody responses.\n\nSystematic Review RegistrationPROSPERO (CRD42021261684)", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Nando Reza Pratama", - "author_inst": "Faculty of Medicine, Airlangga University" - }, - { - "author_name": "Ifan Ali Wafa", - "author_inst": "Faculty of Medicine, Airlangga University" - }, - { - "author_name": "David Setyo Budi", - "author_inst": "Faculty of Medicine, Airlangga University" - }, - { - "author_name": "Manesha Putra", - "author_inst": "University of Colorado Anschutz School of Medicine" - }, - { - "author_name": "Manggala Pasca Wardhana", - "author_inst": "Faculty of Medicine, Airlangga University" - }, - { - "author_name": "Citrawati Dyah Kencono Wungu", - "author_inst": "Faculty of Medicine, Airlangga University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2021.07.05.21260022", "rel_title": "Giving birth in a Pandemic: Women's Birth Experiences in England during COVID-19", @@ -708366,6 +707552,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.07.01.21259879", + "rel_title": "Multi-site clinical validation of Isothermal Amplification based SARS-COV-2 detection assays using different sampling strategies", + "rel_date": "2021-07-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.01.21259879", + "rel_abs": "BackgroundIsothermal amplification-based tests were developed as rapid, low-cost, and simple alternatives to real-time reverse transcriptase-polymerase chain reaction (RT-PCR) tests for SARS-COV-2 detection.\n\nMethodsClinical performance of two isothermal amplification-based tests (Atila Biosystems iAMP COVID-19 detection test and OptiGene COVID-19 Direct Plus RT-LAMP test) was compared to clinical RT-PCR assays using different sampling strategies. A total of 1378 participants were tested across four study sites.\n\nResultsCompared to standard of care RT-PCR testing, the overall sensitivity and specificity of the Atila iAMP test for detection of SARS-CoV-2 were 76.2% and 94.9%, respectively, and increased to 88.8% and 89.5%, respectively, after exclusion of an outlier study site. Sensitivity varied based on the anatomic collected site. Sensitivity for nasopharyngeal was 65.4% (range across study sites:52.8%-79.8%), mid-turbinate 88.2%, saliva 55.1% (range across study sites:42.9%-77.8%) and anterior nares 66.7% (range across study sites:63.6%-76.5%). The specificity for these anatomic collection sites ranged from 96.7% to 100%. Sensitivity improved in symptomatic patients (overall 82.7%) and those with a higher viral load (overall 92.4% for ct[≤]25). Sensitivity and specificity of the OptiGene Direct Plus RT-LAMP test, conducted at a single study-site, were 25.5% and 100%, respectively.\n\nConclusionsThe Atila iAMP COVID test with mid-turbinate sampling is a rapid, low-cost assay for detecting SARS-COV-2, especially in symptomatic patients and those with a high viral load, and could be used to reduce the risk of SARS-COV-2 transmission in clinical settings. Variation of performance between study sites highlights the need for site-specific clinical validation of these assays before clinical adoption.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Kanan T Desai", + "author_inst": "Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, USA" + }, + { + "author_name": "Karla Alfaro", + "author_inst": "Basic Health International, Pittsburgh, USA" + }, + { + "author_name": "Laura Mendoza", + "author_inst": "Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asuncion, San Lorenzo, Paraguay" + }, + { + "author_name": "Matthew Faron", + "author_inst": "Medical College of Wisconsin, Milwaukee, USA" + }, + { + "author_name": "Brian Mesich", + "author_inst": "Medical College of Wisconsin, Milwaukee, USA" + }, + { + "author_name": "Mauricio Maza", + "author_inst": "Basic Health International, Pittsburgh, USA" + }, + { + "author_name": "Rhina Dominguez", + "author_inst": "Research Unit, El Salvador National Institute of Health (INS), El Salvador" + }, + { + "author_name": "Adriana Valenzuela", + "author_inst": "Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asuncion, San Lorenzo, Paraguay" + }, + { + "author_name": "Chyntia Diaz", + "author_inst": "Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asuncion, San Lorenzo, Paraguay" + }, + { + "author_name": "Magaly Martinez", + "author_inst": "Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asuncion, San Lorenzo, Paraguay" + }, + { + "author_name": "Juan C Felix", + "author_inst": "Medical College of Wisconsin, Milwaukee, USA" + }, + { + "author_name": "Rachel Masch", + "author_inst": "Basic Health International, Pittsburgh, USA; The Mount Sinai Hospital, New York, USA" + }, + { + "author_name": "Sofia Gabrilovich", + "author_inst": "Rutgers New Jersey Medical School, Newark, USA" + }, + { + "author_name": "Michael Plump", + "author_inst": "Rutgers New Jersey Medical School, Newark, USA" + }, + { + "author_name": "Akiva P Novetsky", + "author_inst": "Rutgers New Jersey Medical School, Newark, USA; Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA" + }, + { + "author_name": "Mark H Einstein", + "author_inst": "Rutgers New Jersey Medical School, Newark, USA; Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA" + }, + { + "author_name": "Nataki C Douglas", + "author_inst": "Rutgers New Jersey Medical School, Newark, USA" + }, + { + "author_name": "Miriam Cremer", + "author_inst": "Basic Health International, Pittsburgh, USA; Cleveland Clinic Lerner College of Medicine, Clevland, USA" + }, + { + "author_name": "Nicolas Wentzensen", + "author_inst": "Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, USA" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.07.02.21259857", "rel_title": "The toll of COVID-19 on African children: A descriptive analysis on the COVID-19-related morbidity and mortality among the pediatric population in Sub-Saharan Africa", @@ -708822,157 +708099,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.05.451222", - "rel_title": "Broadly neutralizing antibodies to SARS-related viruses can be readily induced in rhesus macaques", - "rel_date": "2021-07-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.07.05.451222", - "rel_abs": "To prepare for future coronavirus (CoV) pandemics, it is desirable to generate vaccines capable of eliciting neutralizing antibody responses against multiple CoVs. Because of the phylogenetic similarity to humans, rhesus macaques are an animal model of choice for many virus-challenge and vaccine-evaluation studies, including SARS-CoV-2. Here, we show that immunization of macaques with SARS-CoV-2 spike (S) protein generates potent receptor binding domain cross- neutralizing antibody (nAb) responses to both SARS-CoV-2 and SARS-CoV-1, in contrast to human infection or vaccination where responses are typically SARS-CoV-2-specific. Furthermore, the macaque nAbs are equally effective against SARS-CoV-2 variants of concern. Structural studies show that different immunodominant sites are targeted by the two primate species. Human antibodies generally target epitopes strongly overlapping the ACE2 receptor binding site (RBS), whereas the macaque antibodies recognize a relatively conserved region proximal to the RBS that represents another potential pan-SARS-related virus site rarely targeted by human antibodies. B cell repertoire differences between the two primates appear to significantly influence the vaccine response and suggest care in the use of rhesus macaques in evaluation of vaccines to SARS-related viruses intended for human use.\n\nONE SENTENCE SUMMARYBroadly neutralizing antibodies to an unappreciated site of conservation in the RBD in SARS- related viruses can be readily induced in rhesus macaques because of distinct properties of the naive macaque B cell repertoire that suggest prudence in the use of the macaque model in SARS vaccine evaluation and design.", - "rel_num_authors": 34, - "rel_authors": [ - { - "author_name": "Wan-ting He", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Meng Yuan", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Sean Callaghan", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Rami Musharrafieh", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Ge Song", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Murillo Silva", - "author_inst": "Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA" - }, - { - "author_name": "Nathan Beutler", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Wen-Hsin Lee", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Peter Yong", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Jonathan L. Torres", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Mariane Melo", - "author_inst": "Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA" - }, - { - "author_name": "Panpan Zhou", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Fangzhu Zhao", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Xueyong Zhu", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Linghang Peng", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Deli Huang", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Fabio Anzanello", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "James Ricketts", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Mara Parren", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Elijah Garcia", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Melissa Ferguson", - "author_inst": "Alpha Genesis, Yemassee, SC 29945, USA" - }, - { - "author_name": "William Rinaldi", - "author_inst": "Alpha Genesis, Yemassee, SC 29945, USA" - }, - { - "author_name": "Stephen A. Rawlings", - "author_inst": "Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA." - }, - { - "author_name": "David Nemazee", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Davey M. Smith", - "author_inst": "Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA." - }, - { - "author_name": "Bryan Briney", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Yana Safonova", - "author_inst": "Computer Science and Engineering Department, University of California, San Diego (UCSD), La Jolla, CA 92037, USA" - }, - { - "author_name": "Thomas Rogers", - "author_inst": "Division of Infectious Diseases, Department of Medicine, University of California, San Diego, La Jolla, CA 92037, USA." - }, - { - "author_name": "Shane Crotty", - "author_inst": "Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA" - }, - { - "author_name": "Darrell J. Irvine", - "author_inst": "Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA" - }, - { - "author_name": "Andrew B. Ward", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Ian A. Wilson", - "author_inst": "Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Dennis R. Burton", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - }, - { - "author_name": "Raiees Andrabi", - "author_inst": "Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA 92037, USA." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.07.01.21259785", "rel_title": "Risk factors for intensive care admission and death amongst children and young people admitted to hospital with COVID-19 and PIMS-TS in England during the first pandemic year", @@ -710096,6 +709222,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.06.28.21259629", + "rel_title": "Implications of COVID-19 vaccination and public health countermeasures on SARS-CoV-2 variants of concern in Canada: evidence from a spatial hierarchical cluster analysis", + "rel_date": "2021-07-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.28.21259629", + "rel_abs": "BackgroundThe influence of coronavirus disease-2019 (COVID-19) containment measures on variants of concern (VOC) has been understudied in Canada. Our objective was to identify provinces with disproportionate prevalence of VOC relative to COVID-19 mitigation efforts in provinces and territories in Canada.\n\nMethodsWe analyzed publicly available provincial- and territorial-level data on the prevalence of VOCs in relation to mitigating factors (summarized in three measures: 1. strength of public health countermeasures: stringency index, 2. how much people moved about outside their homes: mobility index, and 3. vaccine intervention: proportion of Canadian population fully vaccinated). Using spatial agglomerative hierarchical cluster analysis (unsupervised machine learning), the provinces and territories were grouped into clusters by stringency index, mobility index and full vaccine coverage. Kruskal-Wallis test was used to determine the differences in the prevalence of VOC (Alpha, or B.1.1.7, Beta, or B.1.351, Gamma, or P.1, and Delta, or B.1.617.2 variants) between the clusters.\n\nResultsThree clusters of vaccine uptake and countermeasures were identified. Cluster 1 consisted of the three Canadian territories, and characterized by higher degree of vaccine deployment and lesser degree of countermeasures. Cluster 2 (located in Central Canada and Atlantic region) was typified by lesser implementation of vaccine deployment and moderate countermeasures. The third cluster was formed by provinces in the Pacific region, Central Canada, and Prairie region, with moderate vaccine deployment but stronger countermeasures. The overall and variant-specific prevalence were significantly different across the clusters.\n\nInterpretationThis study found that implementation of COVID-19 public health measures varied across the provinces and territories. Considering the high prevalence of VOCs in Canada, completing the second dose of COVID-19 vaccine in a timely manner is crucial.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Daniel A Adeyinka", + "author_inst": "Department of Community Health and Epidemiology, College of Medicine, University of Saskatchewan, Saskatoon, Canada" + }, + { + "author_name": "Cheryl Camillo", + "author_inst": "Johnson-Shoyama Graduate School of Public Policy, University of Regina, Regina, Saskatchewan and Coronavirus Variants Rapid Response Network" + }, + { + "author_name": "Wendie Marks", + "author_inst": "Department of Community Health and Epidemiology, College of Medicine, University of Saskatchewan, Saskatoon, Canada and Coronavirus Variants Rapid Response Netw" + }, + { + "author_name": "Nazeem Muhajarine", + "author_inst": "U of Saskatchewan and Saskatchewan Population Health and Evaluation Research Unit (SPHERU) and Coronavirus Variants Rapid Response Network" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.30.21259752", "rel_title": "Importance of epidemic severity and vaccine mode of action and availability for delaying the second vaccine dose", @@ -710464,93 +709621,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.07.02.21259665", - "rel_title": "Assessment and Modeling of COVID-19 Outcomes in a Longitudinal Cohort of Hospitalized Adults", - "rel_date": "2021-07-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.07.02.21259665", - "rel_abs": "BackgroundWhile several demographic and clinical correlates of Coronavirus Disease 2019 (COVID-19) outcome have been identified, they remain imprecise tools for clinical management of disease. Furthermore, there are limited data on how these factors are associated with virological and immunological parameters over time.\n\nMethods and FindingsNasopharyngeal swabs and blood samples were longitudinally collected from a cohort of 58 hospitalized adults with COVID-19 in Chicago, Illinois between March 27 and June 9, 2020. Samples were assessed for SARS-CoV-2 viral load, viral genotype, viral diversity, and antibody titer. Demographic and clinical information, including patient blood tests and several composite measures of disease severity, were extracted from electronic health records. All parameters were assessed for association with three patient outcome groups: discharge without intensive care unit (ICU) admission (n = 23), discharge with ICU admission (n = 29), and COVID-19 related death (n = 6). Higher age, male sex, and higher body mass index (BMI) were significantly associated with ICU admission. At hospital admission, higher 4C Mortality scores and lactate dehydrogenase (LDH) levels were likewise associated with ICU admission. Longitudinal trends in Deterioration Index (DI) score, Modified Early Warning Score (MEWS), and serum neutrophil count were also associated with ICU admission, though only the retrospectively calculated median DI score was predictive of death. While viral load and genotype were not significantly associated with outcome in this study, viral load did correlate positively with C-reactive protein levels and negatively with D-dimer, lymphocyte count, and antibody titer. Intra-host viral genetic diversity resulted in changes in viral genotype in some participants over time, though intra-host evolution was not associated with outcome. A stepwise-generated multivariable model including BMI, lymphocyte count at admission, and neutrophil count at admission was sufficient to predict outcome with a 0.82 accuracy rate in this cohort.\n\nConclusionsThese studies suggest that COVID-19 disease severity and poor outcomes among hospitalized patients are likely driven by dysfunctional host responses to infection and underlying co-morbid conditions rather than SARS-CoV-2 viral loads. Several parameters, including 4C mortality score, LDH levels, and DI score, were ultimately predictive of participant outcome and warrant further exploration in larger cohort studies for use in clinical management and risk assessment. Finally, the prevalence of intra-host diversity and viral evolution in hospitalized patients suggests a mechanism for population-level change, further emphasizing the need for effective antivirals to suppress viral replication and to avoid the emergence of new variants.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Lacy M Simons", - "author_inst": "Northwestern University" - }, - { - "author_name": "Ramon Lorenzo-Redondo", - "author_inst": "Northwestern University" - }, - { - "author_name": "Meg Gibson", - "author_inst": "Northwestern University" - }, - { - "author_name": "Sarah L Kinch", - "author_inst": "Northwestern University" - }, - { - "author_name": "Jacob P Vandervaart", - "author_inst": "Northwestern University" - }, - { - "author_name": "Nina L Reiser", - "author_inst": "Northwestern University" - }, - { - "author_name": "Mesut Eren", - "author_inst": "Northwestern University" - }, - { - "author_name": "Elizabeth Lux", - "author_inst": "Northwestern University" - }, - { - "author_name": "Elizabeth McNally", - "author_inst": "Northwestern University Feinberg School of Medicine" - }, - { - "author_name": "Anat R Tambur", - "author_inst": "Northwestern University" - }, - { - "author_name": "Douglas E Vaughan", - "author_inst": "Northwestern University" - }, - { - "author_name": "Kelly R Bachta", - "author_inst": "Northwestern University" - }, - { - "author_name": "Alexis R. Demonbreun", - "author_inst": "Northwestern University" - }, - { - "author_name": "Karla J.F. Satchell", - "author_inst": "Northwestern University" - }, - { - "author_name": "Chad J Achenbach", - "author_inst": "Northwestern University" - }, - { - "author_name": "Egon A Ozer", - "author_inst": "Northwestern University" - }, - { - "author_name": "Michael G Ison", - "author_inst": "Northwestern University" - }, - { - "author_name": "Judd F. Hultquist", - "author_inst": "Northwestern University Feinberg School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.07.01.21259833", "rel_title": "COVID-19 vaccines dampen genomic diversity of SARS-CoV-2: Unvaccinated patients exhibit more antigenic mutational variance", @@ -711806,6 +710876,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.29.21259707", + "rel_title": "A new model of unreported COVID-19 cases outperforms three known epidemic-growth models in describing data from Cuba and Spain", + "rel_date": "2021-07-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.29.21259707", + "rel_abs": "Estimating the unreported cases of Covid-19 in a region/country is a complicated problem. We propose a new mathematical model that, combined with a deterministic model of the total growth of cases, describes the time evolution of the unreported cases for each reported Covid-19 case. The new model considers the growth of unreported cases in plateau periods and the decrease towards the end of an epidemic wave. We combined the new model with a Gompertz-growth model, a generalized logistic model, and a susceptible-infectious-removed (SIR) model; and fitted them via Bayesian methods to data from Cuba and Spain. The combined-model fits yielded better Bayesian-Information-Criterion values than the Gompertz, logistic, and SIR models alone. This suggests the new model can achieve improved descriptions of the evolution of a Covid-19 epidemic wave. The new model is also able to provide reliable predictions of the epidemic evolution in a short period of time. We include in the paper the steps that researchers should take to use the new model for predictions with other data.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Erick E. Ramirez-Torres", + "author_inst": "Universidad de Oriente" + }, + { + "author_name": "Antonio R. Selva Castaneda", + "author_inst": "Universidad de Oriente" + }, + { + "author_name": "Luis Randez", + "author_inst": "Universidad de Zaragoza" + }, + { + "author_name": "Luis E. V. Garcia", + "author_inst": "Centro Provincial de Higiene, Epidemiologia y Microbiologia" + }, + { + "author_name": "Luis E. B. Cabrales", + "author_inst": "Universidad de Oriente" + }, + { + "author_name": "Scott A. Sisson", + "author_inst": "University of New South Wales" + }, + { + "author_name": "Juan I. Montijano", + "author_inst": "Universidad de Zaragoza" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.28.21259409", "rel_title": "Predictors of Depression and Anxiety Symptoms in Brazil during COVID-19", @@ -712258,53 +711371,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.28.21259452", - "rel_title": "Persistent symptoms following SARS-CoV-2 infection in a random community sample of 508,707 people", - "rel_date": "2021-07-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.28.21259452", - "rel_abs": "BackgroundLong COVID, describing the long-term sequelae after SARS-CoV-2 infection, remains a poorly defined syndrome. There is uncertainty about its predisposing factors and the extent of the resultant public health burden, with estimates of prevalence and duration varying widely.\n\nMethodsWithin rounds 3-5 of the REACT-2 study, 508,707 people in the community in England were asked about a prior history of COVID-19 and the presence and duration of 29 different symptoms. We used uni-and multivariable models to identify predictors of persistence of symptoms (12 weeks or more). We estimated the prevalence of symptom persistence at 12 weeks, and used unsupervised learning to cluster individuals by symptoms experienced.\n\nFindingsAmong the 508,707 participants, the weighted prevalence of self-reported COVID-19 was 19.2% (95% CI: 19.1,19.3). 37.7% of 76,155 symptomatic people post COVID-19 experienced at least one symptom, while 14.8% experienced three or more symptoms, lasting 12 weeks or more. This gives a weighted population prevalence of persistent symptoms of 5.75% (5.68, 5.81) for one and 2.22% (2.1, 2.26) for three or more symptoms. Almost a third of people (8,771/28,713 [30.5%]) with at least one symptom lasting 12 weeks or more reported having had severe COVID-19 symptoms (\"significant effect on my daily life\") at the time of their illness, giving a weighted prevalence overall for this group of 1.72% (1.69,1.76). The prevalence of persistent symptoms was higher in women than men (OR: 1.51 [1.46,1.55]) and, conditional on reporting symptoms, risk of persistent symptoms increased linearly with age by 3.5 percentage points per decade of life. Obesity, smoking or vaping, hospitalisation, and deprivation were also associated with a higher probability of persistent symptoms, while Asian ethnicity was associated with a lower probability. Two stable clusters were identified based on symptoms that persisted for 12 weeks or more: in the largest cluster, tiredness predominated, while in the second there was a high prevalence of respiratory and related symptoms.\n\nInterpretationA substantial proportion of people with symptomatic COVID-19 go on to have persistent symptoms for 12 weeks or more, which is age-dependent. Clinicians need to be aware of the differing manifestations of Long COVID which may require tailored therapeutic approaches. Managing the long-term sequelae of SARS-CoV-2 infection in the population will remain a major challenge for health services in the next stage of the pandemic.\n\nFundingThe study was funded by the Department of Health and Social Care in England.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSRecent systematic reviews have documented the wide range of symptoms and reported prevalence of persistent symptoms following COVID-19. A dynamic review of Long COVID studies (NIHR Evidence) in March 2021 summarised the literature on the prevalence of persistent symptoms after acute COVID19, and reported that most studies (14) were of hospitalised patients, with higher prevalence of persistent symptoms compared with two community-based studies. There was limited evidence from community studies beyond 12 weeks. Another systematic review reported a median of over 70% of people with symptoms lasting at least 60 days. A review of risk factors for Long COVID found consistent evidence for an increased risk amongst women and those with high body mass index (BMI) but inconsistent findings on the role of age and little evidence concerning risks among different socioeconomic or ethnic groups which are often not well captured in routine healthcare records. Long COVID is increasingly recognised as heterogenous, likely underpinned by differing biological mechanisms, but there is not yet consensus on defining subtypes of the condition.\n\nAdded value of this studyThis community-based study of over half a million people was designed to be representative of the adult population of England. A random sample of adults ages 18 years and above registered with a GP were invited irrespective of previous access to services for COVID-19, providing an estimate of population prevalence that was representative of the whole population. The findings show substantial declines in symptom prevalence over the first 12 weeks following Covid-19, reported by nearly one fifth of respondents, of whom over a third remained symptomatic at 12 weeks and beyond, with little evidence for decline thereafter.\n\nRisk factors identified for persistent symptoms (12 weeks or more) suggestive of Long COVID confirm some previous findings - an increased risk in women, obese and overweight individuals and those hospitalised for COVID-19, with strong evidence for an increasing risk with age. Additional evidence was found for an increased risk in those with lower income, smoking or vaping and healthcare or care home workers. A lower risk was found in those of Asian ethnicity.\n\nClustering identified two distinct groups of individuals with different symptom profiles at 12 weeks, highlighting the heterogeneity of clinical presentation. The smaller cluster had higher prevalence of respiratory and related symptoms, while for those in the larger cluster tiredness was the dominant symptom, with lower prevalence of organ-specific symptoms.\n\nImplications of available evidenceThere is a high prevalence of persistent symptoms beyond 12 weeks after acute COVID-19, with little evidence of decline thereafter. This highlights the needs for greater support for patients, both through specialised services and, for those from low-income settings, financial support. The understanding that there are distinct clusters of persistent symptoms, the most common of which is dominated by fatigue, is important for the recognition and clinical management of the condition outside of specialised services.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Matthew Whitaker", - "author_inst": "Imperial College London" - }, - { - "author_name": "Joshua Elliott", - "author_inst": "Imperial College London" - }, - { - "author_name": "Marc Chadeau-Hyam", - "author_inst": "Imperial College London" - }, - { - "author_name": "Steven Riley", - "author_inst": "Dept Inf Dis Epi, Imperial College" - }, - { - "author_name": "Ara Darzi", - "author_inst": "Imperial College London" - }, - { - "author_name": "Graham Cooke", - "author_inst": "Imperial College London" - }, - { - "author_name": "Helen Ward", - "author_inst": "Imperial College London" - }, - { - "author_name": "Paul Elliott", - "author_inst": "Imperial College London School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.28.21259546", "rel_title": "Clinicogenomic analysis of breakthrough infections by SARS CoV2 variants after ChAdOx1 nCoV- 19 vaccination in healthcare workers", @@ -713688,6 +712754,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.25.21259525", + "rel_title": "COVID-19 in Children with Down Syndrome: Data from the Trisomy 21 Research Society Survey", + "rel_date": "2021-07-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.25.21259525", + "rel_abs": "ImportanceAdults with Down syndrome (DS) are at higher risk for severe outcomes of coronavirus disease 2019 (COVID-19), but further evidence is required to determine the exact risks for children with DS. The clinical features and epidemiological characteristics of COVID-19 in children with DS, and risk factors for severe outcomes, must be established to inform COVID-19 shielding advice and vaccination priority.\n\nObjectiveTo determine risk factors for a severe course of COVID-19 in pediatric DS patients and to compare the prevalence of severe COVID-19 between pediatric patients with and without DS.\n\nDesignThis retrospective cohort study included pediatric cases (aged <18 years) with DS from the Trisomy 21 Research Society international survey and pediatric cases from the general population published by the US Centers for Disease Control and Prevention (COVID-NET) collected during the first wave of the COVID-19 pandemic (controls).\n\nSettingCohorts included 328 children with DS (127 hospitalized, 39%) and 224 children without DS (all hospitalized) with COVID-19. Of the pediatric DS patients, 64.1% were from low-to-middle-income countries (LMICs), and 35.9% from high-income countries (HICs).\n\nParticipantsClinicians, family members, or caregivers completed the survey on behalf of children with DS affected by COVID-19.\n\nResultsAmong the 328 COVID-19 patients with DS; older age, obesity, and epilepsy were significant risk factors for hospitalization; and age and thyroid disorder were significant risk factors for acute respiratory distress syndrome. The 127 hospitalized COVID-19 patients with DS had a higher incidence of cough, fever, nasal signs and shortness of breath than controls. Compared with controls, hospitalized children with DS (especially those from LMICs) had a higher prevalence of COVID-19-related medical complications (pneumonia, ARDS, acute renal failure).\n\nConclusions and relevanceChildren with DS are at higher risk for severe COVID-19 than the general pediatric population. Efforts should be made to monitor the health of children and young people with DS during the ongoing pandemic and to report any COVID-19 signs and symptoms in a timely manner, especially for those who have comorbidities which are risk factors for severe COVID-19. When vaccination rollout for pediatric populations begins, children with DS should be prioritised.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhat are the epidemiological and clinical characteristics of coronavirus disease 2019 (COVID-19) in paediatric patients with Down syndrome (DS)?\n\nFindingsHospitalised COVID-19 patients <18 years of age with DS from a range of countries had a higher incidence of respiratory symptoms, fever, and several medical complications from COVID-19 than patients without DS <18 years from the United States (US). Older age, obesity, and epilepsy were significant risk factors for hospitalisation among paediatric COVID-19 patients with DS; and age and thyroid disorder were significant risk factors for acute respiratory distress syndrome. Mortality rates were low in all paediatric COVID-19 patients (with and without DS), in contrast to previous findings in adults with DS (who exhibit higher mortality than those without DS).\n\nSignificanceChildren with DS are at increased risk for more severe presentations of COVID-19. Efforts should be made to ensure comprehensive and early detection of COVID-19 in this population, and to identify children with DS who present comorbidities that pose a risk for a severe course of COVID-19. Children with DS should be prioritised for COVID-19 vaccination as part of childrens vaccination programmes.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "David Tresco Emes", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Anke H\u00fcls", + "author_inst": "Department of Epidemiology and Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA" + }, + { + "author_name": "Nicole Baumer", + "author_inst": "Boston Childrens Hospital and Harvard Medical School, Boston, MA, USA" + }, + { + "author_name": "Mara Dierssen", + "author_inst": "Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Doctor Aiguader 88,Barcelona, Spain. Universitat Pompeu Fabra (UPF), Bar" + }, + { + "author_name": "Shiela Puri", + "author_inst": "Down Syndrome Medical Interest Group UK. Leeds Community Healthcare NHS Trust." + }, + { + "author_name": "Lauren Russel", + "author_inst": "Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia, USA" + }, + { + "author_name": "Stephanie L Sherman", + "author_inst": "Department of Human Genetics, School of Medicine, Emory University, Atlanta, Georgia, USA" + }, + { + "author_name": "Andre Strydom", + "author_inst": "Institute of Psychiatry, Psychology, and Neuroscience, Department of Forensic and Neurodevelopmental Sciences, Kings College London, London, United Kingdom; The" + }, + { + "author_name": "Stefania Bargagna", + "author_inst": "Fondazione Stella Maris IRCCS, Pisa, Italy" + }, + { + "author_name": "Ana Cl\u00e1udia Brand\u00e3o", + "author_inst": "Hospital Israelita Albert Einstein, Sao Paulo, SP, Brazil" + }, + { + "author_name": "Alberto C.S. Costa", + "author_inst": "Departments of Pediatrics and of Psychiatry, School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA" + }, + { + "author_name": "Brian Allen Chicoine", + "author_inst": "Advocate Medical Group Adult Down Syndrome Center, Park Ridge, IL, USA" + }, + { + "author_name": "Sujay Ghosh", + "author_inst": "Cytogenetics and Genomics Research Unit. Department of Zoology, University of Calcutta.Kolkata. West Bengal, India" + }, + { + "author_name": "Anne-Sophie Rebillat", + "author_inst": "Institut J\u00e9r\u00f4me Lejeune, Paris, France" + }, + { + "author_name": "Giuseppina Sgandurra", + "author_inst": "Department of Developmental Neuroscience, IRCCS Fondazione Stella Maris, Pisa, Italy; Department of Clinical and Experimental Medicine, University of Pisa, Pi" + }, + { + "author_name": "Diletta Valentini", + "author_inst": "Pediatric Unit, Bambino Ges\u00f9 Children's Hospital, IRCCS, Rome, Italy" + }, + { + "author_name": "Tilman R Rohrer", + "author_inst": "Division of Pediatric Endocrinology, Saarland University Medical Center, Homburg/Saar, Germany" + }, + { + "author_name": "Johannes Levin", + "author_inst": "Department of Neurology, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, Munich, Germany. German Center for Neurodegenerative Diseases, site Munich. Munich Cluster for " + }, + { + "author_name": "Monica Lakhanpaul", + "author_inst": "UCL- Great Ormond Street Institute of Child Health, London, United Kingdom; Whittington NHS Trust, London, United Kingdom; Down Syndrome Medical Interest Group," + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.23.21259395", "rel_title": "COVID-19 Flow-Maps: An open geographic information system on COVID-19 and human mobility for Spain", @@ -714328,49 +713485,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.06.27.21259131", - "rel_title": "Face mask use and associated factors among students in rural Eastern Uganda amidst the COVID-19 pandemic", - "rel_date": "2021-07-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.27.21259131", - "rel_abs": "BackgroundThe Corona Virus Disease of 2019 (COVID-19) has gravely affected several aspects of national and global society, including education. Given the risk it poses, the Government of Uganda (GOU) adopted and recommended face mask use as one of the preventive measures to limit its transmission in communities. However, there is limited data on the levels of face mask usage and associated factors among students in schools in Uganda. This study aimed at assessing the face mask usage and associated factors among students in schools in rural Eastern Uganda amidst the COVID-19 pandemic.\n\nMethodsA cross sectional quantitative descriptive study was conducted among 423 students in schools in rural Eastern Uganda. Multi-stage sampling method was employed in the selection of study participants. The data was collected by trained data collectors using structured questionnaires pre-installed on ODK enabled smart phones. The data entered was cleaned using Excel 2016 and exported to Stata14.0 statistical software (Statacorp, College station, Texas, USA) for analysis. Bivariate and multivariable logistic regression analyses were employed using 95% CI (confidence interval). Variables with p-value < 0.20 and those with literature backup evidence were included in the multivariable model. Variables with p-value < 0.05 were considered to be statistically significant. This study revealed that less than three quarters (62.3%) wore face masks correctly.\n\nResultsAlmost all, 98.9% of the participants mentioned that they wore face masks due to fear of missing classes and 49.0% disagreed that they were vulnerable to COVID-19. Students in boarding schools (AOR = 1.61, 95%CI: 1.05-2.47), those who believed that they were vulnerable to COVID-19 (AOR = 1.70, 95%CI: 1.11-2.10), and those who disagreed that masks are uncomfortable (AOR = 1.62, 95%CI: 1.06-2.46) were more likely to wear facemasks correctly.\n\nConclusionThis study revealed that more than a third of the students did not wear face masks correctly. Correct wearing of face masks was associated with being in a boarding school, belief that they were susceptible to COVID-19, and disagreeing that masks were uncomfortable. This therefore highlights the need for sensitization programmes in academic institutions in order to improve students perceptions toward COVID-19 and face masks, and consequently increase correct face mask usage in schools.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Denis Mwesige", - "author_inst": "Faculty of Science and Technology, Cavendish University Uganda" - }, - { - "author_name": "Aisha Nalugya", - "author_inst": "Department of Disease control and Environmental Health, School of Public Health, College of Health Sciences, Makerere University" - }, - { - "author_name": "Douglas Bulafu", - "author_inst": "Elevate Research and Health Services Limited" - }, - { - "author_name": "Arnold Tigaiza", - "author_inst": "Elevate Research and Health Services Limited" - }, - { - "author_name": "Bridget Tamale Nagawa", - "author_inst": "Elevate Research and Health Services Limited" - }, - { - "author_name": "Emmanuel Balinda", - "author_inst": "Elevate Research and Health Services Limited" - }, - { - "author_name": "Abel Wilson Walekhwa", - "author_inst": "Department of Disease control and Environmental Health, School of Public Health, College of Health Sciences, Makerere University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.06.28.21259028", "rel_title": "Enhancing epidemiological investigation of nosocomial SARS-CoV-2 infection with whole genome sequencing: A retrospective cohort study across four hospitals in the UK.", @@ -715858,6 +714972,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "otolaryngology" }, + { + "rel_doi": "10.1101/2021.06.28.21259671", + "rel_title": "Dimeric IgA is a specific biomarker of recent SARS-CoV-2 infection", + "rel_date": "2021-07-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.28.21259671", + "rel_abs": "Current tests for SARS-CoV-2 antibodies (IgG, IgM, IgA) cannot differentiate recent and past infections. We describe a point of care, lateral flow assay for SARS-CoV-2 dIgA based on the highly selective binding of dIgA to a chimeric form of secretory component (CSC), that distinguishes dIgA from monomeric IgA. Detection of specific dIgA uses a complex of biotinylated SARS-CoV-2 receptor binding domain and streptavidin-colloidal gold. SARS-CoV-2-specific dIgA was measured both in 112 cross-sectional samples and a longitudinal panel of 362 plasma samples from 45 patients with PCR-confirmed SARS-CoV-2 infection, and 193 discrete pre-COVID-19 or PCR-negative patient samples. The assay demonstrated 100% sensitivity from 11 days post-symptom onset, and a specificity of 98.2%. With an estimated half-life of 6.3 days, dIgA provides a unique biomarker for the detection of recent SARS-CoV-2 infections with potential to enhance diagnosis and management of COVID-19 at point-of-care.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Heidi E Drummer", + "author_inst": "Burnet Institute" + }, + { + "author_name": "Huy Van", + "author_inst": "Burnet Institute" + }, + { + "author_name": "Ethan Klock", + "author_inst": "JHU" + }, + { + "author_name": "Shuning Zheng", + "author_inst": "Burnet Institute" + }, + { + "author_name": "Zihui Wei", + "author_inst": "Burnet Institute" + }, + { + "author_name": "Irene Boo", + "author_inst": "Burnet Institute" + }, + { + "author_name": "Rob J Center", + "author_inst": "Burnet Institute" + }, + { + "author_name": "Fan Li", + "author_inst": "Burnet Institute" + }, + { + "author_name": "Purnima Bhat", + "author_inst": "Australian National University" + }, + { + "author_name": "Rosemary Ffrench", + "author_inst": "National Serology Reference Laboratory" + }, + { + "author_name": "Jillian S.Y. Lau", + "author_inst": "Monash University" + }, + { + "author_name": "James McMahon", + "author_inst": "Monash University" + }, + { + "author_name": "Oliver Laeyendecker", + "author_inst": "NIAID & JHMI" + }, + { + "author_name": "Reinaldo E Fernandez", + "author_inst": "JHU" + }, + { + "author_name": "Yukari C Manabe", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Sabra L Klein", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Thomas C Quinn", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "David A Anderson", + "author_inst": "Burnet Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.29.21259693", "rel_title": "Recovery of serum testosterone levels is an accurate predictor of survival from COVID-19 in male patients", @@ -716498,41 +715699,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.28.21259620", - "rel_title": "The Evolution of Young People's Mental Health during COVID-19: Evidence from four Low-and-Middle-Income-Countries", - "rel_date": "2021-07-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.28.21259620", - "rel_abs": "BackgroundThough COVID-19 presents less risk to young people of serious morbidity or mortality, the resulting economic crisis has impacted their livelihoods. There is relatively little evidence on young peoples mental health in Low-and-Middle-Income-Countries (LMICs) as the pandemic has progressed.\n\nMethodsTwo consecutive phone-surveys (August/October and November/December 2020) in Ethiopia, India, Peru and Vietnam interviewed around 9,000 participants of a 20-year cohort study who grew up in poverty (now aged 19 and 26). We investigate how young peoples mental health has evolved in the four countries during the pandemic. Rates of (at least mild) anxiety (depression) measured by GAD-7 (PHQ-8) were compared across countries; between males/females, and food secure/food insecure households.\n\nResultsOverall, rates of at least mild anxiety (depression) significantly decreased in all countries but Ethiopia as infection rates fell. However, young people in food insecure households report high rates of anxiety and depression and have not shown consistent improvements. Food insecure households are poorer, and have significantly more children (p<0.05) except in Ethiopia.\n\nConclusionsFood insecurity has increased during the COVID-19 pandemic and is negatively associated with young peoples mental health. Urgent support is needed for the most vulnerable.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Catherine Porter", - "author_inst": "Lancaster University" - }, - { - "author_name": "Annina Hittmeyer", - "author_inst": "Oxford Department of International Development, University of Oxford" - }, - { - "author_name": "Marta Favara", - "author_inst": "Oxford Department of International Development, University of Oxford" - }, - { - "author_name": "Douglas Scott", - "author_inst": "Oxford Department of International Development, University of Oxford" - }, - { - "author_name": "Alan S\u00e1nchez", - "author_inst": "Grupo de An\u00e1lisis para el Desarrollo (GRADE)" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.06.28.21259558", "rel_title": "A cross-sectional study of the association between frequency of telecommuting and unhealthy dietary habits among Japanese workers during the COVID-19 pandemic", @@ -717852,6 +717018,37 @@ "type": "confirmatory results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.06.30.450531", + "rel_title": "Early detection of SARS-CoV-2 in circulating immune cells in a mouse model", + "rel_date": "2021-06-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.30.450531", + "rel_abs": "SARS-CoV-2 infects the respiratory tract, lung and then other organs. However, its pathogenesis remains largely unknown. We used RareScope Fluorescence Light Sheet Microscopy (FLSM) and fluorescent in situ hybridization of RNA (RNA-FISH) to detect SARS-CoV-2 RNA and dissemination kinetics in mouse blood circulation. By RNA-FISH, we found that SARS-CoV-2 RNA-positive leukocytes, including CD11c cells, appeared as early as one day after infection and continued through day 10 post infection. Our data suggest that SARS-CoV-2-permissive leukocytes contribute to systemic viral dissemination, and RNA-FISH combined with FLSM can be utilized as a sensitive tool for SARS-CoV-2 detection in blood specimens.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Tingting Geng", + "author_inst": "School of Medicine, UConn Health" + }, + { + "author_name": "Spencer Keilich", + "author_inst": "QCDx LLC" + }, + { + "author_name": "Fyl Tafas", + "author_inst": "QCDx LLC" + }, + { + "author_name": "PENGHUA WANG", + "author_inst": "University of Connecticut Health Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.06.29.450372", "rel_title": "Epitope order Matters in multi-epitope-based peptide (MEBP) vaccine design: An in silico study", @@ -718252,57 +717449,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2021.06.30.450547", - "rel_title": "Computational saturation mutagenesis of SARS-CoV-1 spike glycoprotein: stability, binding affinity, and comparison with SARS-CoV-2", - "rel_date": "2021-06-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.30.450547", - "rel_abs": "Severe Acute respiratory syndrome coronavirus (SARS-CoV-1) attaches to the host cell surface to initiate the interaction between the receptor-binding domain (RBD) of its spike glycoprotein (S) and the human Angiotensin-converting enzyme (hACE2) receptor. SARS-CoV-1 mutates frequently because of its RNA genome, which challenges the antiviral development. Here, we performed computational saturation mutagenesis of the S protein of SARS-CoV-1 to identify the residues crucial for its functions. We used the structure-based energy calculations to analyze the effects of the missense mutations on the SARS-CoV-1 S stability and the binding affinity with hACE2. The sequence and structure alignment showed similarities between the S proteins of SARS-CoV-1 and SARS-CoV-2. Interestingly, we found that target mutations of S protein amino acids generate similar effects on their stabilities between SARS-CoV-1 and SARS-CoV-2. For example, G839W of SARS-CoV-1 corresponds to G857W of SARS-CoV-2, which decrease the stability of their S glycoproteins. The viral mutation analysis of the two different SARS-CoV-1 isolates showed that mutations, T487S and L472P, weakened the S-hACE2 binding of the 2003-2004 SARS-CoV-1 isolate. In addition, the mutations of L472P and F360S destabilized the 2003-2004 viral isolate. We further predicted that many mutations on N-linked glycosylation sites would increase the stability of the S glycoprotein. Our results can be of therapeutic importance in the design of antivirals or vaccines against SARS-CoV-1 and SARS-CoV-2.\n\nAuthor SummarySevere acute respiratory syndrome coronavirus (SARS-CoV-1) is an RNA virus that undergoes frequent mutations, which may result in more virulent SARS-CoV-1 variants. To prevent another pandemic in the future, scientists must understand the mechanisms of viral mutations and predict if any variants could become a dominant. The infection of SARS-CoV-1 in cells is largely depending on the interactions of the viral Spike (S) and human angiotensin-converting enzyme 2 (hACE2). We applied a computational method to predict S missense mutations that will make SARS-CoV-1 more virulent. We are interested in the variants that can change SARS-CoV-1 spike protein stability and/or change the virus-receptor interactions. We mutated each residue of SARS-CoV-1 spike to all possible amino acids; we calculated the differences between the folding energy and binding energy of each variant and the wildtype and identified the target S mutations with significant effects on protein stability and protein-protein interaction. We found some viral mutations could destabilize S and weaken S-hACE2 binding of SARS-CoV-1 isolate. Our results show that the computational saturation mutagenesis is a reliable approach in the analysis and prediction of missense mutations.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Adebiyi Sobitan", - "author_inst": "Howard University College of Arts and Sciences" - }, - { - "author_name": "Vidhyanand Mahase", - "author_inst": "Howard University College of Arts and Sciences" - }, - { - "author_name": "Raina Rhoades", - "author_inst": "Howard University College of Arts and Sciences" - }, - { - "author_name": "Dejaun Williams", - "author_inst": "Howard University College of Arts and Sciences" - }, - { - "author_name": "Dongxiao Liu", - "author_inst": "Howard University College of Medicine" - }, - { - "author_name": "Yixin Xie", - "author_inst": "The University of Texas at El Paso" - }, - { - "author_name": "Lin Li", - "author_inst": "The University of Texas at El Paso" - }, - { - "author_name": "Qiyi Tang", - "author_inst": "Howard University College of Medicine" - }, - { - "author_name": "Shaolei Teng", - "author_inst": "Howard University College of Arts and Sciences" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.06.29.450452", "rel_title": "Host cellular RNA helicases regulate SARS-CoV-2 infection", @@ -720014,6 +719160,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.06.22.21257103", + "rel_title": "Is Second dose of vaccination useful in previously SARS-CoV-2 infected Health Care Workers?", + "rel_date": "2021-06-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.22.21257103", + "rel_abs": "SummaryVaccines are the most important public health measure to protect people from COVID-19 worldwide. In addition, healthcare workers account for a large number of infected people. Then, protecting this population from COVID-19 seems crucial in the preservation of healthcare systems. In a context of few doses available, serological assays could be useful to decide whether one or two doses are needed. Our results show that a first dose of BNT162b2 mRNA vaccine seems to act as a boost after SARS-CoV-2 infection in healthcare workers with a previous SARS-CoV-2 infection and a second dose might not be required.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Gauthier Pean de Ponfilly", + "author_inst": "Groupe Hospitalier Paris Saint-Joseph" + }, + { + "author_name": "Benoit Pilmis", + "author_inst": "Groupe Hospitalier Paris Saint-Joseph" + }, + { + "author_name": "Iheb El Kaibi", + "author_inst": "Groupe Hospitalier Paris Saint Joseph" + }, + { + "author_name": "Nathalie Castreau", + "author_inst": "Groupe Hospitalier Paris Saint Joseph" + }, + { + "author_name": "Sophie Laplanche", + "author_inst": "Groupe Hospitalier Paris Saint Joseph" + }, + { + "author_name": "Alban Le Monnier", + "author_inst": "Groupe Hospitalier Paris Saint-Joseph" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.21.21258543", "rel_title": "Long Term Health Consequences of COVID-19 in Hospitalized Patients from North India: A follow up study of upto 12 months", @@ -720538,25 +719723,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.23.21259394", - "rel_title": "Macro-Level Drivers of SARS-CoV-2 Transmission: A Data-Driven Analysis of Factors Contributing to Epidemic Growth During the First Wave of outbreaks in the United States", - "rel_date": "2021-06-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.23.21259394", - "rel_abs": "BackgroundMany questions remain unanswered about how SARS-CoV-2 transmission is influenced by aspects of the economy, environment, and health. A better understanding of how these factors interact can help us to design early health prevention and control strategies, and develop better predictive models for public health risk management of SARS-CoV-2. This study examines the associations between COVID-19 epidemic growth and macro-level determinants of transmission such as climate, socio-economic factors, demographic factors, and population health, during the first wave of outbreaks in the United States.\n\nMethodsA spatial-temporal data-set was created by collating information from a variety of data sources including the Johns Hopkins Universitys Centre for Systems Science and Engineering, the United States Census Bureau, the USDA Economic Research Service, the United States EPA, the National Climatic Data Center, the CDC and the Oxford COVID-19 Government Response Tracker (OxCGRT). A unique data-driven study design was implemented that allows us to assess the relationship between COVID-19 case and death epidemic doubling times and explanatory variables using a Generalized Additive Model (GAM).\n\nResultsThe main factors associated with case doubling times are higher population density, home overcrowding, manufacturing, and recreation industries. Poverty was also an important predictor of faster epidemic growth perhaps because of factors associated with in-work poverty-related conditions, although poverty is also a predictor of poor population health which is likely driving case and death reporting. Air pollution and diabetes were other important drivers of case reporting. Warmer temperatures are associated with slower epidemic growth, which is most likely explained by human behaviors associated with warmer locations i.e ventilating homes and workplaces. and socializing outdoors. The main factors associated with death doubling times were population density, poverty older age, diabetes, and air pollution. Temperature was also slightly significant slowing death doubling times.\n\nConclusionsSuch findings help underpin current understanding of the disease epidemiology and also supports current policy and advice recommending ventilation of homes, work-spaces, and schools, along with social distancing and mask-wearing. The results also suggest that states which adopted more stringent containment measures early on did have some success suppressing the virus. We can presume that if this was replicated at a federal level, much better outcomes would have been observed across the United States.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Matthew Watts", - "author_inst": "ICTA-UAB" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.24.21259107", "rel_title": "SARS-CoV-2 lineage B.1.1.7 is associated with greater disease severity among hospitalised women but not men", @@ -722600,6 +721766,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.20.21259178", + "rel_title": "Taiwan on track to end third COVID-19 community outbreak", + "rel_date": "2021-06-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.20.21259178", + "rel_abs": "Since the start of the COVID-19 pandemic on December 31st, 2019, with the World Health Organization being notified of pneumonia of unknown cause in Wuhan (China), Taiwan has successfully ended two COVID-19 community outbreaks. For 19 days, the third community outbreak has now been successfully suppressed, putting Taiwan on path to end it too around Aug. 16th based on our forecast using an exponential model. Since May 28th the 7-day average of reported confirmed infected, which peaked at 593, has been falling to 204 on June 16th and the 7-day average of reported suspected and excluded cases increased to above 25 000. Resulting in a decrease in the ratio of the 7-day average of local & unknown confirmed to suspected cases-the identified control variable-to less than one third of its peak value. The later is a hallmark of working contact tracing, which together with testing and isolation of infected are the keys to ending the community outbreak.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Torbj\u00f6rn E. M. Nordling", + "author_inst": "National Cheng Kung University" + }, + { + "author_name": "Yu-Heng Rain", + "author_inst": "National Cheng Kung University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.20.21259188", "rel_title": "Association between preference and e-learning readiness among the Bangladeshi female nursing students in the Covid-19 pandemic: a cross-sectional study", @@ -723304,41 +722493,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.24.21259469", - "rel_title": "Monitoring SARS-CoV-2 Populations in Wastewater by Amplicon Sequencing and Using the Novel Program SAM Refiner", - "rel_date": "2021-06-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.24.21259469", - "rel_abs": "Sequencing SARS-CoV-2 from wastewater has become a useful tool in monitoring the spread of variants. We use a novel computation workflow with SARS-CoV-2 amplicon sequencing in order to track wastewater populations of the virus. As part of this workflow, we developed a program for both variant reporting and removal of PCR generated chimeric sequences. With these methods, we are able to track viral population dynamics over time. We observe the emergence of the variants of concern B.1.1.7 and P.1, and their displacement of the D614G B.1 variant.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Devon A Gregory", - "author_inst": "University of Missouri" - }, - { - "author_name": "Chris G Wieberg", - "author_inst": "MO Department of Natural Resources" - }, - { - "author_name": "Jeff Wenzel", - "author_inst": "MO Department of Health and Senior Services" - }, - { - "author_name": "Chung-Ho Lin", - "author_inst": "University of Missouri" - }, - { - "author_name": "Marc C Johnson", - "author_inst": "University of Missouri" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.22.21258711", "rel_title": "Hidden fraction of Polish population immune to SARS-CoV-2 in May 2021", @@ -724618,6 +723772,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nutrition" }, + { + "rel_doi": "10.1101/2021.06.20.21259219", + "rel_title": "Clinical Manifestations and Pregnancy Outcomes of Covid-19 in Indonesian Referral Hospital in Central Pandemic Area", + "rel_date": "2021-06-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.20.21259219", + "rel_abs": "ObjectivesThe data on clinical manifestations and pregnancy outcomes of pregnant women with COVID-19 are limited, particularly in developing countries. The aim of this study is to analyze the clinical manifestations and pregnancy outcomes in COVID-19 maternal cases in a large referral hospital in Indonesia\n\nMethodsThe study used a prospective cohort design of all pregnant women with suspected COVID-19. Subjects were divided into COVID-19 and non COVID-19 group based on real-time polymerase chain reaction (RT-PCR) of SARS-CoV-2. The clinical characteristics, laboratory results, and pregnancy outcomes were then compared between both groups.\n\nResultsFrom 141 suspected maternal cases, 62 COVID-19 cases were confirmed (43.9%), while 79 suspected cases were found to be negative (56.1%). The clinical manifestations and laboratory findings between the two groups were not significantly different (p>0.05). However, the maternal mortality directly caused by COVID-19 was significantly higher compared to the non-COVID-19 group (8.3 vs 1.3%; p=0.044; OR 6.91, 95% CI: 0.79-60.81).\n\nConclusionsThe clinical manifestation and laboratory of suspected pregnant women with positive and negative RT-PCR COVID-19 result are similiar. However, within the Indonesian setting, COVID-19 strongly increases the risk of maternal death through both direct and indirect factors.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Muhammad Ilham Aldika Akbar", + "author_inst": "Faculty of Medicine Universitas Airlangga" + }, + { + "author_name": "Khanizyah Erza Gumilar", + "author_inst": "Universitas Airlangga Academic Hospital" + }, + { + "author_name": "Rino Andriya", + "author_inst": "Universitas Airlangga Academic Hospital" + }, + { + "author_name": "Manggala Pasca Wardhana", + "author_inst": "Faculty of Medicine Universitas Airlangga" + }, + { + "author_name": "Pungky Mulawardhana", + "author_inst": "Faculty of Medicine Universitas Airlangga" + }, + { + "author_name": "Jimmy Yanuar Annas", + "author_inst": "Faculty of Medicine Universitas Airlangga" + }, + { + "author_name": "Ernawati Ernawati", + "author_inst": "Faculty of Medicine Universitas Airlangga" + }, + { + "author_name": "Muhammad Ardian Cahya Laksana", + "author_inst": "Faculty of Medicine Universitas Airlangga" + }, + { + "author_name": "Gus Dekker", + "author_inst": "Lyell McEwin Hospital, The University of Adelaide, Adelaide, South Australia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.21.21259230", "rel_title": "Switched forced SEIRDV compartmental models to monitor COVID-19 spread and immunization in Italy", @@ -724962,97 +724167,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.22.21259316", - "rel_title": "Investigating phenotypes of pulmonary COVID-19 recovery: a longitudinal observational prospective multicenter trial", - "rel_date": "2021-06-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.22.21259316", - "rel_abs": "BackgroundCOVID-19 is associated with long-term pulmonary symptoms and may result in chronic pulmonary impairment. The optimal procedures to prevent, identify, monitor, and treat these pulmonary sequelae are elusive.\n\nResearch questionTo characterize the kinetics of pulmonary recovery, risk factors and constellations of clinical features linked to persisting radiological lung findings after COVID-19.\n\nStudy design and methodsA longitudinal, prospective, multicenter, observational cohort study including COVID-19 patients (n = 108). Longitudinal pulmonary imaging and functional readouts, symptom prevalence, clinical and laboratory parameters were collected during acute COVID-19 and at 60-, 100- and 180-days follow-up visits. Recovery kinetics and risk factors were investigated by logistic regression. Classification of clinical features and study participants was accomplished by k-means clustering, the k-nearest neighbors (kNN), and naive Bayes algorithms.\n\nResultsAt the six-month follow-up, 51.9% of participants reported persistent symptoms with physical performance impairment (27.8%) and dyspnea (24.1%) being the most frequent. Structural lung abnormalities were still present in 45.4% of the collective, ranging from 12% in the outpatients to 78% in the subjects treated at the ICU during acute infection. The strongest risk factors of persisting lung findings were elevated interleukin-6 (IL6) and C-reactive protein (CRP) during recovery and hospitalization during acute COVID-19. Clustering analysis revealed association of the lung lesions with increased anti-S1/S2 antibody, IL6, CRP, and D-dimer levels at the early follow-up suggesting non-resolving inflammation as a mechanism of the perturbed recovery.\n\nFinally, we demonstrate the robustness of risk class assignment and prediction of individual risk of delayed lung recovery employing clustering and machine learning algorithms.\n\nInterpretationSeverity of acute infection, and systemic inflammation is strongly linked to persistent post-COVID-19 lung abnormality. Automated screening of multi-parameter health record data may assist the identification of patients at risk of delayed pulmonary recovery and optimize COVID-19 follow-up management.\n\nClinical Trial RegistrationClinicalTrials.gov: NCT04416100", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Thomas Sonnweber", - "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Piotr Tymoszuk", - "author_inst": "Data Analytics As a Service Tirol" - }, - { - "author_name": "Sabina Sachanic", - "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Anna Boehm", - "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Alex Pizzini", - "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Anna Luger", - "author_inst": "Department of Radiology, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Christoph Schwabl", - "author_inst": "Department of Radiology, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Manfred Nairz", - "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Kurz Katharina", - "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Sabine Koppelstaetter", - "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Magdalena Aichner", - "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Puchner Bernhard", - "author_inst": "The Karl Landsteiner Institute, Reha Zentrum Muenster, Muenster, Austria" - }, - { - "author_name": "Alexander Egger", - "author_inst": "Central Institute of Medical and Chemical Laboratory Diagnostics, University Hospital Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Gregor Hoermann", - "author_inst": "Central Institute of Medical and Chemical Laboratory Diagnostics, University Hospital Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Ewald Ewald Woell", - "author_inst": "Department of Internal Medicine, St. Vinzenz Hospital, Zams, Austria" - }, - { - "author_name": "Guenter Weiss", - "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Gerlig Widmann", - "author_inst": "Department of Radiology, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Ivan Tancevski", - "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria" - }, - { - "author_name": "Judith Loeffler-Ragg", - "author_inst": "Department of Internal Medicine II, Medical University of Innsbruck, Innsbruck, Austria" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.21.21259213", "rel_title": "Integrating epidemiological and clinical predictors of SARS-CoV2 infection in students and school staff in the state of Sao Paulo", @@ -726332,6 +725446,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, + { + "rel_doi": "10.1101/2021.06.22.21259308", + "rel_title": "Expert Opinion on COVID-19 Vaccination and the Use of Cladribine Tablets in Clinical Practice", + "rel_date": "2021-06-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.22.21259308", + "rel_abs": "BackgroundGaps in current evidence and guidance leave clinicians with unanswered questions on the use of cladribine tablets for the treatment of multiple sclerosis (MS) in the era of the COVID-19 pandemic, in particular relating to COVID-19 vaccination.\n\nObjectiveWe describe a consensus-based program led by international MS experts with the aim of supplementing current guidelines and treatment labels by providing timely recommendations relating to COVID-19 vaccination and the use of cladribine tablets in clinical practice.\n\nMethodsA steering committee (SC) of 10 international MS experts identified seven clinical questions to answer concerning the use of cladribine tablets and COVID-19 vaccination, which addressed issues relating to patient selection, timing and efficacy, and safety. Clinical recommendations to address each question were drafted using available evidence combined with expert opinion from the SC. An extended faculty of 28 MS experts, representing 19 countries, in addition to the 10 SC members, voted on the recommendations. Consensus on recommendations was achieved when [≥]75% of respondents expressed an agreement score of 7-9, on a 9-point scale.\n\nResultsConsensus was achieved on all 13 recommendations. Clinical recommendations are provided on whether all patients with MS receiving cladribine tablets should be vaccinated against COVID-19, and whether they should be prioritized; the timing of vaccination around dosing of cladribine tablets (i.e., before and after a treatment course); and the safety of COVID-19 vaccination for these patients.\n\nConclusionsThese expert recommendations provide timely guidance on COVID-19 vaccination in patients receiving cladribine tablets, which is relevant to everyday clinical practice.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Peter Rieckmann", + "author_inst": "Center for Clinical Neuroplasticity, Medical Park Loipl, Bischofswiesen, Department of Neurology, University of Erlangen, Germany" + }, + { + "author_name": "Diego Centonze", + "author_inst": "Unit of Neurology and Neurorehabilitation, IRCCS Neuromed, Pozzilli (IS), Italy" + }, + { + "author_name": "Gavin Giovannoni", + "author_inst": "Queen Mary University of London, Blizard Institute, Barts and The London School of Medicine and Dentistry, London, UK" + }, + { + "author_name": "Le H Hua", + "author_inst": "Cleveland Clinic Lou Ruvo Center for Brain Health, Las Vegas, NV, USA" + }, + { + "author_name": "Celia Oreja-Guevara", + "author_inst": "Neurology, Hospital Clinico San Carlos, Idissc, Madrid, Spain and Departamento de Medicina, Facultad de Medicina, Universidad Complutense de Madrid, Spain" + }, + { + "author_name": "Daniel Selchen", + "author_inst": "University of Toronto, Division of Neurology, St. Michael's Hospital, Toronto, ON, Canada" + }, + { + "author_name": "Per Soelberg Sorensen", + "author_inst": "Danish Multiple Sclerosis Center, Department of Neurology, University of Copenhagen and Rigshospitalet, Copenhagen, Denmark" + }, + { + "author_name": "Patrick Vermersch", + "author_inst": "Univ. Lille, INSERM-U1172, CHU Lille, FHU Precise, Lille, France" + }, + { + "author_name": "Heinz Wiendl", + "author_inst": "Department of Neurology, Institute of Translational Neurology, University of Munster, Munster, Germany" + }, + { + "author_name": "Hashem Salloukh", + "author_inst": "Merck KGaA, Darmstadt, Germany" + }, + { + "author_name": "Bassem I Yammout", + "author_inst": "Nehme and Therese Tohme Multiple Sclerosis Center, American University of Beirut, Beirut, Lebanon and Neurology Institute, Harley Street Medical Center, Abu Dha" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2021.06.20.21259194", "rel_title": "Optimal Selection of COVID-19 Vaccination Sites at the Municipal Level", @@ -726716,49 +725889,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.06.23.449535", - "rel_title": "Integrative COVID-19 Biological Network Inference with Probabilistic Core Decomposition", - "rel_date": "2021-06-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.23.449535", - "rel_abs": "The SARS-CoV-2 coronavirus is responsible for millions of deaths around the world. To help contribute to the understanding of crucial knowledge and to further generate new hypotheses relevant to SARS-CoV-2 and human protein interactions, we make use of the information abundant Biomine probabilistic database and extend the experimentally identified SARS-CoV-2-human protein-protein interaction (PPI) network in silico. We generate an extended network by integrating information from the Biomine database, the PPI network, and other experimentally validated results. To generate novel hypotheses, we focus on the high-connectivity sub-communities that overlap most with the integrated experimentally validated results in the extended network. Therefore, we propose a new data analysis pipeline that can efficiently compute core decomposition on the extended network and identify dense subgraphs. We then evaluate the identified dense subgraph and the generated hypotheses in three contexts: literature validation for uncovered virus targeting genes and proteins, gene function enrichment analysis on subgraphs, and literature support on drug repurposing for identified tissues and diseases related to COVID-19. The majority types of the generated hypotheses are proteins with their encoding genes and we rank them by sorting their connections to the integrated experimentally validated nodes. In addition, we compile a comprehensive list of novel genes, and proteins potentially related to COVID-19, as well as novel diseases which might be comorbidities. Together with the generated hypotheses, our results provide novel knowledge relevant to COVID-19 for further validation.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Yang Guo", - "author_inst": "University of Victoria" - }, - { - "author_name": "Fatemeh Esfahani", - "author_inst": "University of Victoria" - }, - { - "author_name": "Xiaojian Shao", - "author_inst": "National Research Council Canada" - }, - { - "author_name": "Venkatesh Srinivasan", - "author_inst": "University of Victoria" - }, - { - "author_name": "Alex Thomo", - "author_inst": "University of Victoria" - }, - { - "author_name": "Li Xing", - "author_inst": "University of Saskatchewan" - }, - { - "author_name": "Xuekui Zhang", - "author_inst": "University of Victoria" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.06.24.449811", "rel_title": "Pyrimidine biosynthesis inhibitors synergize with nucleoside analogs to block SARS-CoV-2 infection", @@ -728082,6 +727212,57 @@ "type": "confirmatory results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.06.22.449540", + "rel_title": "Escherichia coli recombinant expression of SARS-CoV-2 protein fragments.", + "rel_date": "2021-06-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.22.449540", + "rel_abs": "We have developed a method for the inexpensive, high-level expression of antigenic protein fragments of SARS-CoV-2 proteins in Escherichia coli. Our approach used the thermophilic family 9 carbohydrate-binding module (CBM9) as an N-terminal carrier protein and affinity tag. The CBM9 module was joined to SARS-CoV-2 protein fragments via a flexible proline-threonine linker, which proved to be resistant to E. coli proteases. Two CBM9-spike protein fragment fusion proteins and one CBM9-nucleocapsid fragment fusion protein largely resisted protease degradation, while most of the CBM9 fusion proteins were degraded at some site in the SARS-CoV-2 protein fragment. All fusion proteins were expressed in E. coli at about 0.1 g/L, and could be purified with a single affinity binding step using inexpensive cellulose powder. Three purified CBM9-SARS-CoV-2 fusion proteins were tested and found to bind antibody directed to the appropriate SARS-CoV-2 antigenic region. The largest intact CBM9 fusion protein incorporates spike protein amino acids 540-588, which is a conserved region immediately C-terminal to the receptor binding domain that is widely recognized by human convalescent sera and contains a putative protective epitope.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Bailey E McGuire", + "author_inst": "University of Victoria" + }, + { + "author_name": "Julia E Mela", + "author_inst": "University of Victoria" + }, + { + "author_name": "Vanessa C Thompson", + "author_inst": "University of Victoria" + }, + { + "author_name": "Logan R Cucsksey", + "author_inst": "University of Victoria" + }, + { + "author_name": "Claire E Stevens", + "author_inst": "University of Victoria" + }, + { + "author_name": "Ralph L McWhinnie", + "author_inst": "University of Victoria" + }, + { + "author_name": "Dirk FH Winkler", + "author_inst": "Kinexus Bioinformatics Corporation" + }, + { + "author_name": "Steven Pelech", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Francis E Nano", + "author_inst": "University of Victoria" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.06.23.449568", "rel_title": "Increased lung cell entry of B.1.617.2 and evasion of antibodies induced by infection and BNT162b2 vaccination", @@ -728406,245 +727587,6 @@ "type": "new results", "category": "scientific communication and education" }, - { - "rel_doi": "10.1101/2021.06.18.21258477", - "rel_title": "The polarity and specificity of SARS-CoV2 -specific T lymphocyte responses determine disease susceptibility", - "rel_date": "2021-06-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.18.21258477", - "rel_abs": "Optimal vaccination and immunotherapy against coronavirus disease COVID-19 relies on the in-depth comprehension of immune responses determining the individual susceptibility to be infected by SARS-CoV-2 and to develop severe disease. We characterized the polarity and specificity of circulating SARS-CoV-2-specific T cell responses against whole virus lysates or 186 unique peptides derived from the SARS-CoV-2 or SARS-CoV-1 ORFeome on 296 cancer-bearing and 86 cancer-free individuals who were either from the pre-COVID-19 era (67 individuals) or contemporary COVID-19-free (237 individuals) or who developed COVID-19 (78 individuals) in 2020/21. The ratio between the prototypic T helper 1 (TH1) cytokine, interleukin-2, and the prototypic T helper 2 (TH2) cytokine, interleukin-5 (IL-5), released from SARS-CoV-2-specific memory T cells measured in early 2020, among SARS-CoV-2-negative persons, was associated with the susceptibility of these individuals to develop PCR-detectable SARS-CoV-2 infection in late 2020 or 2021. Of note, T cells from individuals who recovered after SARS-CoV-2 re-infection spontaneously produced elevated levels of IL-5 and secreted the immunosuppressive TH2 cytokine interleukin-10 in response to SARS-CoV-2 lysate, suggesting that TH2 responses to SARS-CoV-2 are inadequate. Moreover, individuals susceptible to SARS-CoV-2 infection exhibited a deficit in the TH1 peptide repertoire affecting the highly mutated receptor binding domain (RBD) amino acids (331-525) of the spike protein. Finally, current vaccines successfully triggered anti-RBD specific TH1 responses in 88% healthy subjects that were negative prior to immunization. These findings indicate that COVID-19 protection relies on TH1 cell immunity against SARS-CoV-2 S1-RBD which in turn likely drives the phylogenetic escape of the virus. The next generation of COVID-19 vaccines should elicit high-avidity TH1 (rather than TH2)-like T cell responses against the RBD domain of current and emerging viral variants.", - "rel_num_authors": 56, - "rel_authors": [ - { - "author_name": "Jean-Eudes FAHRNER", - "author_inst": "Universit\u00e9 Paris-Saclay, Le Kremlin-Bic\u00eatre, France. Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale, UMR1015, Gustave Roussy, Villejuif, France. Tran" - }, - { - "author_name": "Agathe CARRIER", - "author_inst": "Gustave Roussy, Villejuif, France Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale, UMR1015, Gustave Roussy, Villejuif, France." - }, - { - "author_name": "- Lyon COVID study group", - "author_inst": "-" - }, - { - "author_name": "Eric DE SOUSA", - "author_inst": "ImmunoTherapy/ImmunoSurgery, Champalimaud Foundation, Lisboa, Portugal." - }, - { - "author_name": "Damien DRUBAY", - "author_inst": "Gustave Roussy, Villejuif, France D\u00e9partement de Biostatistique et d'Epid\u00e9miologie, Gustave Roussy, Universit\u00e9 Paris-Saclay, Villejuif, France." - }, - { - "author_name": "Agathe DUBUISSON", - "author_inst": "Gustave Roussy, Villejuif, France Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale, UMR1015, Gustave Roussy, Villejuif, France." - }, - { - "author_name": "Arthur GERAUD", - "author_inst": "Gustave Roussy, Villejuif, France D\u00e9partement d'Oncologie M\u00e9dicale, Gustave Roussy, Villejuif, France. D\u00e9partement d'Innovation Th\u00e9rapeutique et d'Essais Pr\u00e9coc" - }, - { - "author_name": "Anne-Ga\u00eblle GOUBET", - "author_inst": "Universit\u00e9 Paris-Saclay, Facult\u00e9 de M\u00e9decine, Le Kremlin-Bic\u00eatre, France. Gustave Roussy, Villejuif, France Institut National de la Sant\u00e9 et de la Recherche M\u00e9d" - }, - { - "author_name": "Gladys FERRERE", - "author_inst": "Gustave Roussy, Villejuif, France Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale, UMR1015, Gustave Roussy, Villejuif, France." - }, - { - "author_name": "Yacine HADDAD", - "author_inst": "Gustave Roussy, Villejuif, France Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale, UMR1015, Gustave Roussy, Villejuif, France." - }, - { - "author_name": "Imran LAHMAR", - "author_inst": "Universit\u00e9 Paris-Saclay, Facult\u00e9 de M\u00e9decine, Le Kremlin-Bic\u00eatre, France. Gustave Roussy, Villejuif, France Institut National de la Sant\u00e9 et de la Recherche M\u00e9d" - }, - { - "author_name": "Marine MAZZENGA", - "author_inst": "Gustave Roussy, Villejuif, France 3Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale, UMR1015, Gustave Roussy, Villejuif, France." - }, - { - "author_name": "Clea MELENOTTE", - "author_inst": "Gustave Roussy, Villejuif, France Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale, UMR1015, Gustave Roussy, Villejuif, France." - }, - { - "author_name": "Marion PICARD", - "author_inst": "Gustave Roussy, Villejuif, France Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale, UMR1015, Gustave Roussy, Villejuif, France." - }, - { - "author_name": "Cassandra THELEMAQUE", - "author_inst": "Gustave Roussy, Villejuif, France 3Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale, UMR1015, Gustave Roussy, Villejuif, France." - }, - { - "author_name": "Luigi CERBONE", - "author_inst": "Gustave Roussy, Villejuif, France 9D\u00e9partement d'Oncologie M\u00e9dicale, Gustave Roussy, Villejuif, France." - }, - { - "author_name": "Joana R. L\u00c9RIAS", - "author_inst": "ImmunoTherapy/ImmunoSurgery, Champalimaud Foundation, Lisboa, Portugal." - }, - { - "author_name": "Ariane LAPARRA", - "author_inst": "Gustave Roussy, Villejuif, France 9D\u00e9partement d'Oncologie M\u00e9dicale, Gustave Roussy, Villejuif, France. D\u00e9partement d'Innovation Th\u00e9rapeutique et d'Essais Pr\u00e9co" - }, - { - "author_name": "Alice BERNARD", - "author_inst": "Gustave Roussy, Villejuif, France D\u00e9partement d'Oncologie M\u00e9dicale, Gustave Roussy, Villejuif, France. D\u00e9partement d'Innovation Th\u00e9rapeutique et d'Essais Pr\u00e9coc" - }, - { - "author_name": "Beno\u00eet KLOECKNER", - "author_inst": "Gustave Roussy, Villejuif, France Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale, UMR1015, Gustave Roussy, Villejuif, France." - }, - { - "author_name": "Marianne GAZZANO", - "author_inst": "Gustave Roussy, Villejuif, France Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale, UMR1015, Gustave Roussy, Villejuif, France." - }, - { - "author_name": "Fran\u00e7ois-Xavier DANLOS", - "author_inst": "Universit\u00e9 Paris-Saclay, Facult\u00e9 de M\u00e9decine, Le Kremlin-Bic\u00eatre, France. Gustave Roussy, Villejuif, France3Institut National de la Sant\u00e9 et de la Recherche M\u00e9" - }, - { - "author_name": "Safae TERRISSE", - "author_inst": "Gustave Roussy, Villejuif, France Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale, UMR1015, Gustave Roussy, Villejuif, France." - }, - { - "author_name": "Carolina ALVES COSTA SILVA", - "author_inst": "Universit\u00e9 Paris-Saclay, Facult\u00e9 de M\u00e9decine, Le Kremlin-Bic\u00eatre, France. Gustave Roussy, Villejuif, France Institut National de la Sant\u00e9 et de la Recherche M\u00e9d" - }, - { - "author_name": "Eugenie PIZZATO", - "author_inst": "Gustave Roussy, Villejuif, France Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale, UMR1015, Gustave Roussy, Villejuif, France." - }, - { - "author_name": "Caroline FLAMENT", - "author_inst": "Gustave Roussy, Villejuif, France Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale, UMR1015, Gustave Roussy, Villejuif, France." - }, - { - "author_name": "Pierre LY", - "author_inst": "Gustave Roussy, Villejuif, France 3Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale, UMR1015, Gustave Roussy, Villejuif, France." - }, - { - "author_name": "Eric TARTOUR", - "author_inst": "Department of Immunology, H\u00f4pital Europ\u00e9en Georges Pompidou, AP-HP, Paris, France. 15PARCC, INSERM U970" - }, - { - "author_name": "Lydia MEZIANI", - "author_inst": "Gustave Roussy, Villejuif, France" - }, - { - "author_name": "Abdelhakim AHMED-BELKACEM", - "author_inst": "Univ Paris Est Creteil, INSERM U955, IMRB, Creteil, France" - }, - { - "author_name": "Makoto MIYARA", - "author_inst": "Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale, U1135, Centre d'Immunologie et des Maladies Infectieuses, H\u00f4pital Piti\u00e9-Salp\u00eatri\u00e8re, Assistance Publi" - }, - { - "author_name": "Guy Gorochov", - "author_inst": "Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale, U1135, Centre d'Immunologie et des Maladies Infectieuses, H\u00f4pital Piti\u00e9-Salp\u00eatri\u00e8re, Assistance Publi" - }, - { - "author_name": "Fabrice BARLESI", - "author_inst": "Gustave Roussy, Villejuif, France D\u00e9partement d'Oncologie M\u00e9dicale, Gustave Roussy, Villejuif, France. Aix Marseille University, CNRS, INSERM, CRCM, Marseille, " - }, - { - "author_name": "Caroline PRADON", - "author_inst": "Gustave Roussy, Villejuif, France Centre de ressources biologiques, ET-EXTRA, Gustave Roussy, Villejuif, France. 20D\u00e9partement de Biologie M\u00e9dicale et Pathologi" - }, - { - "author_name": "Emmanuelle GALLOIS", - "author_inst": "Gustave Roussy, Villejuif, France D\u00e9partement de Biologie M\u00e9dicale et Pathologie M\u00e9dicales, service de microbiologie, Gustave Roussy, Villejuif, France." - }, - { - "author_name": "Fanny POMMERET", - "author_inst": "Gustave Roussy, Villejuif, France D\u00e9partement Interdisciplinaire d'Organisation des Parcours Patients, Gustave Roussy, Villejuif, France." - }, - { - "author_name": "Emeline COLOMBA", - "author_inst": "Gustave Roussy, Villejuif, France D\u00e9partement d'Oncologie M\u00e9dicale, Gustave Roussy, Villejuif, France." - }, - { - "author_name": "Pernelle LAVAUD", - "author_inst": "Gustave Roussy, Villejuif, France D\u00e9partement d'Oncologie M\u00e9dicale, Gustave Roussy, Villejuif, France." - }, - { - "author_name": "Eric DEUTSCH", - "author_inst": "Gustave Roussy, Villejuif, France Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale, U1030, Gustave Roussy, Villejuif, France. D\u00e9partement de Radioth\u00e9ra" - }, - { - "author_name": "Bertrand GACHOT", - "author_inst": "Gustave Roussy, Villejuif, France Service de Pathologie Infectieuse, Gustave Roussy, Villejuif, France." - }, - { - "author_name": "Jean-Philippe SPANO", - "author_inst": "Department of Medical Oncology, Piti\u00e9-Salp\u00eatri\u00e8re Hospital, APHP, Sorbonne Universit\u00e9, Paris, France" - }, - { - "author_name": "Mansouria Merad", - "author_inst": "Service de m\u00e9decine aigu\u00eb d'urgence en canc\u00e9rologie, Gustave Roussy, Villejuif, France." - }, - { - "author_name": "Florian SCOTTE", - "author_inst": "Gustave Roussy, Villejuif, France D\u00e9partement Interdisciplinaire d'Organisation des Parcours Patients, Gustave Roussy, Villejuif, France." - }, - { - "author_name": "Aur\u00e9lien MARABELLE", - "author_inst": "D\u00e9partement d'Oncologie M\u00e9dicale, Gustave Roussy, Villejuif, France. D\u00e9partement d'Innovation Th\u00e9rapeutique et d'Essais Pr\u00e9coces (DITEP), Gustave Roussy, Villej" - }, - { - "author_name": "Frank GRISCELLI", - "author_inst": "Gustave Roussy, Villejuif, France D\u00e9partement de Biologie M\u00e9dicale et Pathologie M\u00e9dicales, service de microbiologie, Gustave Roussy, Villejuif, France." - }, - { - "author_name": "Jean-Yves BLAY", - "author_inst": "Centre L\u00e9on B\u00e9rard, Lyon, France. Universit\u00e9 Claude Bernard, Lyon, France.34Unicancer, Paris, France" - }, - { - "author_name": "Jean-Charles SORIA", - "author_inst": "Universit\u00e9 Paris-Saclay, Facult\u00e9 de M\u00e9decine, Le Kremlin-Bic\u00eatre, France. 2Gustave Roussy, Villejuif, France" - }, - { - "author_name": "Fabrice ANDRE", - "author_inst": "Universit\u00e9 Paris-Saclay, Facult\u00e9 de M\u00e9decine, Le Kremlin-Bic\u00eatre, France. 2Gustave Roussy, Villejuif, France Institut National de la Sant\u00e9 et de la Recherche M\u00e9" - }, - { - "author_name": "Mathieu Chevalier", - "author_inst": "INSERM UMR 976, Institut de recherche Saint-Louis, Universit\u00e9 de Paris, Paris, France" - }, - { - "author_name": "Sophie CAILLAT-ZUCMAN", - "author_inst": "Laboratory of Immunology, AP-HP, H\u00f4pital Saint Louis, INSERM UMR1149, Universit\u00e9 de Paris, Paris, France" - }, - { - "author_name": "Florence FENOLLAR", - "author_inst": "Institut Hospitalo-Universitaire M\u00e9diterran\u00e9e Infection, Marseille, France" - }, - { - "author_name": "Bernard LA SCOLA", - "author_inst": "Institut Hospitalo-Universitaire M\u00e9diterran\u00e9e Infection, Marseille, France." - }, - { - "author_name": "Guido KROEMER", - "author_inst": "Centre de Recherche des Cordeliers, Equipe labelisee par la Ligue contre le cancer, Universite de Paris, Sorbonne Universite, Inserm U1138, Institut Universitai" - }, - { - "author_name": "Markus MAEURER", - "author_inst": "13ImmunoTherapy/ImmunoSurgery, Champalimaud Foundation, Lisboa, Portugal. 45Medizinische Klinik, Johannes Gutenberg University Mainz, Germany. 46Division of Inf" - }, - { - "author_name": "Lisa DEROSA", - "author_inst": "Universit\u00e9 Paris-Saclay, Facult\u00e9 de M\u00e9decine, Le Kremlin-Bic\u00eatre, France. 2Gustave Roussy, Villejuif, France Institut National de la Sant\u00e9 et de la Recherche M\u00e9" - }, - { - "author_name": "Laurence ZITVOGEL", - "author_inst": "Universit\u00e9 Paris-Saclay, Facult\u00e9 de M\u00e9decine, Le Kremlin-Bic\u00eatre, France. Gustave Roussy, Villejuif, France Institut National de la Sant\u00e9 et de la Recherche M\u00e9d" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.21.449165", "rel_title": "Integrative analysis of multi-omics reveals gene regulatory networks across brain regions from risk variants to phenotypes of Alzheimer's disease and Covid-19", @@ -729500,6 +728442,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.18.21258796", + "rel_title": "COVID in Post Vaccinated individuals- Beacon of Light", + "rel_date": "2021-06-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.18.21258796", + "rel_abs": "IntroductionCOVISHIELD and COVAXIN have been introduced post rapid approval as COVID vaccines in India, which has the second most COVID cases across countries. These vaccines are being administered in a two-dose schedule from 16 Jan 2021. This study deals with the clinical profile of individuals who developed COVID infection post-COVID vaccination.\n\nThis is the first study of similar nature in India.\n\nMethodologyThe study population comprised of individuals who were detected to be COVID positive 04 weeks post-vaccination and were compared with individuals detected positive within the first 04 weeks of vaccination. Data was collected in a digital questionnaire format and analyzed with SPSS v-23 software. Clinical features were profiled in detail. Chi-square analysis was done to find out the association of various demographic features with the severity of the disease.\n\nResultsIn the study population, fever was the commonest symptom (75.1%) followed by anosmia (72.1%), and shortness of breath (16.3%). There was a lower incidence of fever, cough, dyspnea, and requirement of hospitalization in the study population as compared to the control group and previous epidemiological data. The time required for complete recovery and disease severity was favorable in our study population. There was a significant correlation in the rate of hospitalization among the study group and the comparative group (p=0.0001) and between the number of dosage of COVID vaccine with the lowest SpO2 recorded (p=0.001).\n\nConclusionThis study will boost the ongoing initiative of having a maximal vaccinated population countrywide and emphasize the need for two doses of vaccination.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "V K Sashindran", + "author_inst": "Dept of Internal Medicine, 7 Air Force Hospital, Kanpur" + }, + { + "author_name": "K Rajesh", + "author_inst": "Dept of Internal Medicine, 7 Air Force Hospital, Kanpur" + }, + { + "author_name": "Ankur Nigam", + "author_inst": "Public Health Specialist, Gangtok" + }, + { + "author_name": "Sourya Sourabh Mohakuda", + "author_inst": "Dept of Internal Medicine, 7 Air Force Hospital,Kanpur" + }, + { + "author_name": "Navin Bhati", + "author_inst": "Dept of Internal Medicine, 7 Air Force Hospital, Kanpur" + }, + { + "author_name": "Mohapatra D", + "author_inst": "Dept of Internal Medicine, 7 Air Force Hospital, Kanpur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.15.21258991", "rel_title": "Data-Driven Patterns in Protective Effects of Ibuprofen and Ketorolac on Hospitalized Covid-19 Patients", @@ -729740,57 +728721,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2021.06.21.449352", - "rel_title": "Cytoplasmic tail truncation of SARS-CoV-2 Spike protein enhances titer of pseudotyped vectors but masks the effect of the D614G mutation", - "rel_date": "2021-06-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.21.449352", - "rel_abs": "The high pathogenicity of SARS-CoV-2 requires it to be handled under biosafety level 3 conditions. Consequently, Spike protein pseudotyped vectors are a useful tool to study viral entry and its inhibition, with retroviral, lentiviral (LV) and vesicular stomatitis virus (VSV) vectors the most commonly used systems. Methods to increase the titer of such vectors commonly include concentration by ultracentrifugation and truncation of the Spike protein cytoplasmic tail. However, limited studies have examined whether such a modification also impacts the proteins function. Here, we optimized concentration methods for SARS-CoV-2 Spike pseudotyped VSV vectors, finding that tangential flow filtration produced vectors with more consistent titers than ultracentrifugation. We also examined the impact of Spike tail truncation on transduction of various cell types and sensitivity to convalescent serum neutralization. We found that tail truncation increased Spike incorporation into both LV and VSV vectors and resulted in enhanced titers, but had no impact on sensitivity to convalescent serum inhibition. In addition, we analyzed the effect of the D614G mutation, which became a dominant SARS-CoV-2 variant early in the pandemic. Our studies revealed that, similar to the tail truncation, D614G independently increases Spike incorporation and vector titers, but that this effect is masked by also including the cytoplasmic tail truncation. Therefore, the use of full-length Spike protein, combined with tangential flow filtration, is recommended as a method to generate high titer pseudotyped vectors that retain native Spike protein functions.\n\nIMPORTANCEPseudotyped viral vectors are useful tools to study the properties of viral fusion proteins, especially those from highly pathogenic viruses. The Spike protein of SARS-CoV-2 has been investigated using pseudotyped lentiviral and VSV vector systems, where truncation of its cytoplasmic tail is commonly used to enhance Spike incorporation into vectors and to increase the titers of the resulting vectors. However, our studies have shown that such effects can also mask the phenotype of the D614G mutation in the ectodomain of the protein, which was a dominant variant early in the COVID-19 pandemic. To better ensure the authenticity of Spike protein phenotypes when using pseudotyped vectors, we therefore recommend using full-length Spike proteins, combined with tangential flow filtration methods of concentration, if higher titer vectors are required.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Hsu-Yu Chen", - "author_inst": "University of Southern California" - }, - { - "author_name": "Chun Huang", - "author_inst": "University of Southern California" - }, - { - "author_name": "Lu Tian", - "author_inst": "University of Southern California" - }, - { - "author_name": "Xiaoli Huang", - "author_inst": "University of Southern California" - }, - { - "author_name": "Chennan Zhang", - "author_inst": "University of Southern California" - }, - { - "author_name": "George Nicholas Llewellyn", - "author_inst": "University of Southern California" - }, - { - "author_name": "Geoffrey L. Rogers", - "author_inst": "University of Southern California" - }, - { - "author_name": "Ya-Wen Chen", - "author_inst": "University of Southern California" - }, - { - "author_name": "Paula M. Cannon", - "author_inst": "University of Southern California" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.06.22.449355", "rel_title": "Detection of antibodies neutralizing historical and emerging SARS-CoV-2 strains using a thermodynamically coupled de novo biosensor system", @@ -730874,6 +729804,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.06.17.21258956", + "rel_title": "School teachers' self-reported fear and risk perception during the COVID-19 pandemic - a nationwide survey in Germany", + "rel_date": "2021-06-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.17.21258956", + "rel_abs": "BackgroundWith COVID-19 cases peaking, COVID-19 vaccination programs starting and health systems reaching their limits in winter 2020/21, schools remained closed in many countries despite ever-recurring debates. To better understand teachers fear of infection and risk perception we conducted a survey in Germany.\n\nMethodsParticipants were recruited through various associations and invited to take part in a cross-sectional COVID-19 specific online survey. Anonymous demographic and self-reported data were collected from those who gave their informed consent. Descriptive statistical analysis was performed. To evaluate with fear associated factors of contracting SARS-CoV-2, an adjusted multivariable regression analysis was performed.\n\nResults6.753 teachers gave their informed consent to answer the online survey. The median age of the teachers was 43 years with 77% being female. Most teachers worked in high schools (29%) and elementary schools (26%). Most participants (73%) feared to contract SARS-CoV-2 at school while 77% intended to be vaccinated against COVID-19. 98% considered students to pose the greatest risk. Multivariable regression analysis revealed that female and younger teachers were significantly more anxious to get infected with SARS-CoV-2 and that the odds teachers were more anxious was 9 times higher for those who favored re-opening of schools the least (p < 0.001).\n\nConclusionsTo the authors knowledge, this is the first study to describe teachers fear and risk perception of COVID-19 and their attitude towards vaccinations in a nationwide survey. The anxiety correlates to the COVID-19 protection measures demanded. Teachers fear is the driving factor and not a rational logic.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Stefanie Weinert", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Anja Thronicke", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Maximilian Hinse", + "author_inst": "Charite - Universitaetsmedizin Berlin" + }, + { + "author_name": "Friedemann Schad", + "author_inst": "Research Institute Havelhoehe" + }, + { + "author_name": "Harald Matthes", + "author_inst": "Charite - Universitaetsmedizin Berlin" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.06.17.21259121", "rel_title": "Development of an index to assess Covid-19 hospital care installed capacity in the 450 Brazilian Health Regions", @@ -731482,61 +730447,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.18.21258649", - "rel_title": "Large-scale screening of asymptomatic for SARS-CoV-2 variants of concern and rapid P.1 takeover, Curitiba, Brazil", - "rel_date": "2021-06-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.18.21258649", - "rel_abs": "To provide a safer environment for individuals working on-site at the Federal University of Parana, Curitiba, Brazil, we performed a large-scale mass testing SARS-CoV-2 program coupled with variant genotyping using two PCR-based approaches. We observed a fast dominance of the Gamma variant, displacing other variants in less than three months.\n\nArticle Summary LineCoronavirus variants of concern may use asymptomatic population as silent spreaders to perform a fast displacement of previous established strains.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Douglas Adamoski", - "author_inst": "Universidade Federal do Parana" - }, - { - "author_name": "Jaqueline Carvalho de Oliveira", - "author_inst": "Universidade Federal do Parana" - }, - { - "author_name": "Ana Claudia Bonatto", - "author_inst": "Universidade Federal do Parana" - }, - { - "author_name": "Roseli Wassem", - "author_inst": "Universidade Federal do Parana" - }, - { - "author_name": "Meri Bordignon Nogueira", - "author_inst": "Universidade Federal do Parana" - }, - { - "author_name": "Sonia Mara Raboni", - "author_inst": "Universidade Federal do Parana" - }, - { - "author_name": "Edvaldo da Silva Trindade", - "author_inst": "Universidade Federal do Parana" - }, - { - "author_name": "Emanuel Maltempi de Souza", - "author_inst": "Universidade Federal do Parana" - }, - { - "author_name": "- SCB-UFPR COVID-19 team", - "author_inst": "Universidade Federal do Parana" - }, - { - "author_name": "Daniela Fiori Gradia", - "author_inst": "Universidade Federal do Parana" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.15.21258940", "rel_title": "Next generation plasma proteome profiling of COVID-19 patients with mild to moderate symptoms", @@ -733223,6 +732133,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.16.21259029", + "rel_title": "A Short Plus Long-Amplicon Based Sequencing Approach Improves Genomic Coverage and Variant Detection In the SARS-CoV-2 Genome", + "rel_date": "2021-06-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.16.21259029", + "rel_abs": "High viral transmission in the COVID-19 pandemic has enabled SARS-CoV-2 to acquire new mutations that impact genome sequencing methods. The ARTIC.v3 primer pool that amplifies short amplicons in a multiplex-PCR reaction is one of the most widely used methods for sequencing the SARS-CoV-2 genome. We observed that some genomic intervals are poorly captured with ARTIC primers. To improve the genomic coverage and variant detection across these intervals, we designed long amplicon primers and evaluated the performance of a short (ARTIC) plus long amplicon (MRL) sequencing approach. Sequencing assays were optimized on VR-1986D-ATCC RNA followed by sequencing of nasopharyngeal swab specimens from five COVID-19 positive patients. ARTIC data covered >90% of the virus genome fraction in the positive control and four of the five patient samples. Variant analysis in the ARTIC data detected 67 mutations, including 66 single nucleotide variants (SNVs) and one deletion in ORF10. Of 66 SNVs, five were present in the spike gene, including nt22093 (M177I), nt23042 (S494P), nt23403 (D614G), nt23604 (P681H), and nt23709 (T716I). The D614G mutation is a common variant that has been shown to alter the fitness of SARS-CoV-2. Two spike protein mutations, P681H and T716I, which are represented in the B.1.1.7 lineage of SARS-CoV-2, were also detected in one patient. Long-amplicon data detected 58 variants, of which 70% were concordant with ARTIC data. Combined analysis of ARTIC +MRL data revealed 22 mutations that were either ambiguous (17) or not called at all (5) in ARTIC data due to poor sequencing coverage. For example, a common mutation in the ORF3a gene at nt25907 (G172V) was missed by the ARTIC assay. Hybrid data analysis improved sequencing coverage overall and identified 59 high confidence mutations for phylogenetic analysis. Thus, we show that while the short amplicon (ARTIC) assay provides good genomic coverage with high throughput, complementation of poorly captured intervals with long amplicon data can significantly improve SARS-CoV-2 genomic coverage and variant detection.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Carlos Arana", + "author_inst": "UT Southwestern Medical Center" + }, + { + "author_name": "Chaoying Liang", + "author_inst": "UT Southwestern Medical Center" + }, + { + "author_name": "Matthew Brock", + "author_inst": "UT Southwestern Medical Center" + }, + { + "author_name": "Bo Zhang", + "author_inst": "University of Texas Southwestern Medical Center" + }, + { + "author_name": "Jinchun Zhou", + "author_inst": "University of Texas Southwestern Medical Center" + }, + { + "author_name": "Li Chen", + "author_inst": "University of Texas Southwestern Medical Center" + }, + { + "author_name": "Brandi Cantarel", + "author_inst": "University of Texas Southwestern Medical Center" + }, + { + "author_name": "Jeffrey SoRelle", + "author_inst": "University of Texas Southwestern Medical Center, Dallas" + }, + { + "author_name": "Lora V. Hooper", + "author_inst": "University of Texas Southwestern Medical Center" + }, + { + "author_name": "Prithvi Raj", + "author_inst": "University of Texas Southwestern Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2021.06.17.21259066", "rel_title": "Seroprevalence of COVID-19 in HIV Population", @@ -733755,61 +732720,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.06.18.449086", - "rel_title": "Differences in IgG antibody responses following BNT162b2 and mRNA-1273 Vaccines", - "rel_date": "2021-06-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.18.449086", - "rel_abs": "Studies examining antibody responses by vaccine brand are lacking and may be informative for optimizing vaccine selection, dosage, and regimens. The purpose of this study is to assess IgG antibody responses following immunization with BNT162b2 (30 g S protein) and mRNA-1273 (100 g S protein) vaccines. A cohort of clinicians at a non-for-profit organization is being assessed clinically and serologically following immunization with BNT162b2 or mRNA-1273. IgG responses were measured at the Remington Laboratory by an IgG against the SARS-CoV-2 spike protein-receptor binding domain. Mixed-effect linear (MEL) regression modeling was used to examine whether the SARS-CoV-2 IgG level differed by vaccine brand, dosage, or days since vaccination. Among 532 SARS-CoV-2 seronegative participants, 530 (99.6%) seroconverted with either vaccine. After adjustments for age and gender MEL regression modeling revealed that the average IgG increased after the second dose compared to the first dose (p<0.001). Overall, titers peaked at week six for both vaccines. Titers were significantly higher for mRNA-1273 vaccine on days 14-20 (p < 0.05), 42-48 (p < 0.01), 70-76 (p < 0.05), 77-83 (p < 0.05), and higher for BNT162b2 vaccine on days 28-34 (p < 0.001). In two participants taking immunosuppressive drugs SARS-CoV-2 IgG remained negative. mRNA-1273 elicited both earlier and higher IgG antibody responses than BNT162b2, possibly due to the higher S-protein delivery. Prospective clinical and serological follow-up of defined cohorts such as this may prove useful in determining antibody protection and whether differences in antibody kinetics between the vaccines have manufacturing relevance and clinical significance.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Jose Gilberto Montoya", - "author_inst": "Palo Alto Medical Foundation" - }, - { - "author_name": "Amy E Adams", - "author_inst": "Palo Alto Foundation Medical Group" - }, - { - "author_name": "Valerie Bonetti", - "author_inst": "Palo Alto Medical Foundation" - }, - { - "author_name": "Sien Deng", - "author_inst": "Center for Health Systems Research, Sutter Health, Palo Alto Medical Foundation Research Institute" - }, - { - "author_name": "Nan A Link", - "author_inst": "Palo Alto Foundation Medical Group" - }, - { - "author_name": "Suzanne Pertsch", - "author_inst": "Palo Alto Foundation Medical Group" - }, - { - "author_name": "Kjerstie Olson", - "author_inst": "Dr Jack S. Remington Laboratory for Specialty Diagnostics" - }, - { - "author_name": "Martina Li", - "author_inst": "Center for Health Systems Research, Sutter Health, Palo Alto Medical Foundation Research Institute" - }, - { - "author_name": "Ellis C Dillon", - "author_inst": "Center for Health Systems Research, Sutter Health, Palo Alto Medical Foundation Research Institute" - }, - { - "author_name": "Dominick L. Frosch", - "author_inst": "Center for Health Systems Research, Sutter Health, Palo Alto Medical Foundation Research Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.06.18.449054", "rel_title": "The percentage of Monocytes CD39+ is higher in Pregnant COVID-19 than in Non-Pregnant COVID-19 patients", @@ -735117,6 +734027,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, + { + "rel_doi": "10.1101/2021.06.15.21258978", + "rel_title": "Inequities among vulnerable communities during the COVID-19 vaccine rollout", + "rel_date": "2021-06-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.15.21258978", + "rel_abs": "ImportanceFederal and state governments sought to prioritize vulnerable communities in the vaccine rollout through various methods of prioritization, and it is necessary to understand whether inequities exist.\n\nObjectiveTo assess whether vulnerable counties have achieved similar rates of coverage to non-vulnerable areas, and how vaccine acceptance varies by vulnerability.\n\nDesign, Setting, and ParticipantsWe use population-weighted univariate linear regressions to associate the COVID-19 Community Vulnerability Index (CCVI) and its 7 constituent themes with a county-level time series of vaccine coverage and vaccine acceptance. We fit a multilevel model to understand how vulnerability within and across states associates with coverage as of May 8, 2021.\n\nMain Outcome(s) and Measure(s)The COVID-19 Community Vulnerability Index was used as a metric for county-level vulnerability. County-level daily COVID-19 vaccination data on both first doses administered and people fully vaccinated from April 3, 2021 through May 8, 2021 were extracted from the Covid Act Now API. County-level daily COVID-19 vaccine acceptance survey data from January 6, 2021 through May 4, 2021 were obtained via the Carnegie Mellon University Delphi Groups COVIDcast API.\n\nResultsVulnerable counties have consistently lagged less vulnerable counties. As of May 8, the top third of vulnerable counties in the US had fully vaccinated 11.3% fewer people than the bottom third (30.7% vs 34.6% of adult population; linear regression, p= 2.2e-16), and 12.1% fewer initiated vaccinations (40.1% vs 45.6%; linear regression, p= 2.2e-16)). Six out of seven dimensions of vulnerability, including Healthcare System Factors and Socioeconomic Status, predicted lower coverage whereas the Population Density theme associated with higher coverage. Vulnerable counties have also consistently had a slightly lower level of vaccine acceptance, though as of May 4, 2021 this difference was observed to be only 0.7% between low- and high-vulnerability counties (high: 86.1%, low: 85.5%, p=0.027).\n\nConclusions and RelevanceThe vaccination gap between vulnerable and non-vulnerable counties is substantial and not readily explained by a difference in acceptance. Vulnerable populations continue to need additional support, and targeted interventions are necessary to achieve similar coverage in vulnerable counties compared to those less vulnerable to COVID-19.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSAre the US counties most vulnerable to COVID-19 also facing the lowest vaccination coverage?\n\nFindingsUS populations with increased health, social, and economic vulnerabilities have experienced consistently lower vaccination coverage. As of May 8, on average, the top third of vulnerable counties across the US had fully vaccinated 11.3% fewer people than the least vulnerable third. There is only a 0.7% difference in vaccine acceptance between the 2 cohorts..\n\nMeaningThe gap in vaccination coverage among vulnerable US communities cannot be explained by lower acceptance. Structural barriers need to be addressed to decrease these inequities.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Nicholas Stewart", + "author_inst": "Surgo Ventures" + }, + { + "author_name": "Peter Smittenaar", + "author_inst": "Surgo Ventures" + }, + { + "author_name": "Staci Sutermaster", + "author_inst": "Surgo Ventures" + }, + { + "author_name": "Lindsay Coome", + "author_inst": "Surgo Ventures" + }, + { + "author_name": "Sema K. Sgaier", + "author_inst": "Surgo Ventures" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.06.15.21259004", "rel_title": "Long COVID symptoms from Reddit: Characterizing post-COVID syndrome from patient reports", @@ -735549,29 +734494,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.16.21258981", - "rel_title": "Remdesivir to treat COVID-19: can dosing be optimized?", - "rel_date": "2021-06-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.16.21258981", - "rel_abs": "The antiviral remdesivir has been approved by regulatory bodies such as EMA and FDA for the treatment of COVID-19. However, its efficacy is debated and toxicity concerns might limit the therapeutic range of this drug. Computational models that aid in balancing efficacy and toxicity would be of great help. Parametrizing models is difficult because the prodrug remdesivir is metabolized to its active form (RDV-TP) upon cell entry, which complicates dose-activity relationships.\n\nHere, we employ a computational model that allows predicting drug efficacy based on the binding affinity of RDV-TP for its target polymerase in SARS-CoV-2. We identify an optimal infusion rate to maximize remdesivir efficacy. We also assess drug efficacy in suppressing both wild-type and resistant strains, and thereby selection of resistance.\n\nOur results differ from predictions using prodrug dose-response curves (pseudo-EC50s). We expect that reaching 90% inhibition (EC90) is insufficient to suppress SARS-CoV-2 in lungs. While standard dosing mildly inhibits viral polymerase and therefore likely reduces morbidity, we also expect selection for resistant mutants for most realistic parameter ranges. To increase efficacy and safeguard against resistance, we recommend continuing remdesivir use with companion antivirals and/or with dosing regimens that substantially increase the levels of RDV-TP.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Jessica M Conway", - "author_inst": "Penn State" - }, - { - "author_name": "Pia Abel zur Wiesch", - "author_inst": "Penn State" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "pharmacology and therapeutics" - }, { "rel_doi": "10.1101/2021.06.16.21259019", "rel_title": "What can we learn from COVID-19 data by using epidemic models with unidentified infectious cases?", @@ -737163,6 +736085,145 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.06.12.448080", + "rel_title": "High efficacy of therapeutic equine hyperimmune antibodies against SARS CoV-2 variants of concern", + "rel_date": "2021-06-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.12.448080", + "rel_abs": "SARS-CoV-2 variants of concern (VoC) show reduced neutralization by vaccine-induced and therapeutic monoclonal antibodies. We tested therapeutic equine polyclonal antibodies (pAbs) against four VoC (alpha, beta, epsilon and gamma). We show that equine pAbs efficiently neutralize VoC, suggesting they are an effective, broad coverage, low-cost and a scalable COVID-19 treatment.", + "rel_num_authors": 31, + "rel_authors": [ + { + "author_name": "Andres Moreira-Soto", + "author_inst": "Charit\u00e9-Universit\u00e4tsmedizin Berlin" + }, + { + "author_name": "Mauricio Arguedas", + "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" + }, + { + "author_name": "Hebleen Brenes", + "author_inst": "INCIENSA, Ministry of Health, Costa Rica" + }, + { + "author_name": "Willem Buj\u00e1n", + "author_inst": "School of Medicine, Universidad de Costa Rica" + }, + { + "author_name": "Eugenia Corrales-Aguilar", + "author_inst": "CIET, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" + }, + { + "author_name": "Cecilia D\u00edaz", + "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" + }, + { + "author_name": "Ann Echeverri", + "author_inst": "Caja Costarricense del Seguro Social, Costa Rica" + }, + { + "author_name": "Marietta Flores-D\u00edaz", + "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" + }, + { + "author_name": "Aar\u00f3n G\u00f3mez", + "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" + }, + { + "author_name": "Andr\u00e9s Hern\u00e1ndez", + "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" + }, + { + "author_name": "Mar\u00eda Herrera", + "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" + }, + { + "author_name": "Guillermo Le\u00f3n", + "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" + }, + { + "author_name": "Rom\u00e1n Macaya", + "author_inst": "Caja Costarricense del Seguro Social, Costa Rica" + }, + { + "author_name": "Arne Kh\u00fcne", + "author_inst": "Charit\u00e9-Universit\u00e4tsmedizin Berlin" + }, + { + "author_name": "Jose Arturo Molina-Mora", + "author_inst": "Research Center in Tropical Diseases, University of Costa Rica" + }, + { + "author_name": "Javier Mora", + "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" + }, + { + "author_name": "Alfredo Sanabria", + "author_inst": "Caja Costarricense del Seguro Social, Costa Rica" + }, + { + "author_name": "Andr\u00e9s S\u00e1nchez", + "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" + }, + { + "author_name": "Laura S\u00e1nchez", + "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" + }, + { + "author_name": "\u00c1lvaro Segura", + "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" + }, + { + "author_name": "Eduardo Segura", + "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" + }, + { + "author_name": "Daniela Solano", + "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" + }, + { + "author_name": "Claudio Soto", + "author_inst": "INCIENSA, Ministry of Health, Costa Rica" + }, + { + "author_name": "Jennifer L. Stynoski", + "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" + }, + { + "author_name": "Mariangela Vargas", + "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" + }, + { + "author_name": "Mauren Villalta", + "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" + }, + { + "author_name": "Chantal Reusken", + "author_inst": "Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" + }, + { + "author_name": "Chistian Drosten", + "author_inst": "Charit\u00e9-Universit\u00e4tsmedizin Berlin" + }, + { + "author_name": "Jos\u00e9 Mar\u00eda Guti\u00e9rrez", + "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" + }, + { + "author_name": "Alberto Alape-Gir\u00f3n", + "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" + }, + { + "author_name": "Jan Felix Drexler", + "author_inst": "Charit\u00e9-Universit\u00e4tsmedizin Berlin" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.06.15.21258542", "rel_title": "Casirivimab and imdevimab in patients admitted to hospital with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial", @@ -737843,57 +736904,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2021.06.12.21258829", - "rel_title": "The Spectre of SARS-CoV-2 in the Ambient Urban Natural Water in Ahmedabad and Guwahati: A Tale of Two Cities", - "rel_date": "2021-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.12.21258829", - "rel_abs": "COVID-19 positive patients can egest live SARS-CoV-2 virus and viral genome fragments through faecal matter and urine, raising concerns about viral transmission through faecal-oral route and/or contaminated aerosolized water. These worries are heightened in many low and middle income nations, where raw sewage is often dumped into surface waterways and open defecation betide. In this manuscript, we attempt to discern the presence of SARS-CoV-2 genetic material (ORF-1ab, N and S genes) in two urban cities of India viz., Ahmedabad, in western India with several WWTPs; and Guwahati in the north-eastern part of the country with no such treatment plants. The study was carried out to establish applicability of WBE for COVID-19 surveillance as a potential tool for public health monitoring at the community level. 25.8% and 20% of the surface water samples had detectable SARS-CoV-2 RNA load in Ahmedabad and Guwahati, respectively. The high concentration of gene (ORF-1ab - 800 copies/L for Sabarmati river, Ahmedabad and S-gene - 565 copies/L for Bharalu urban river, Guwahati) found in natural waters indicates WWTPs do not always completely remove the genetic material of the virus. The study shows the applicability of WBE surveillance of COVID-19 in cities with low sanitation as well as in rural areas. The method used in this study cannot detect the live viruses, hence further research is required to evaluate the transmission implication of COVID-19 via ambient water, if any.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC=\"FIGDIR/small/21258829v3_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (45K):\norg.highwire.dtl.DTLVardef@19a51dborg.highwire.dtl.DTLVardef@743707org.highwire.dtl.DTLVardef@1c8b608org.highwire.dtl.DTLVardef@26cd43_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LINatural urban waters show the presence of SARS-CoV-2 RNA.\nC_LIO_LILake water receiving runoff containing SARS-CoV-2 genes reflected positive sign early\nC_LIO_LIViral RNA in surface water reflects incomplete removal of gene fragments in WWTPs.\nC_LIO_LIResidence time and fate owing to viral RNA in natural waters needs further research.\nC_LI", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Manish Kumar", - "author_inst": "IIT Gandhinagar" - }, - { - "author_name": "Payal Mazumder", - "author_inst": "IIT Guwahati, India" - }, - { - "author_name": "Jyoti Prakash Deka", - "author_inst": "Guwahati University, Assam, India" - }, - { - "author_name": "Vaibhav Srivastava", - "author_inst": "IIT Gandhinagar, India" - }, - { - "author_name": "Chandan Mahanta", - "author_inst": "IIT Guwahati, India" - }, - { - "author_name": "Ritusmita Goswami", - "author_inst": "TISS, Guwahati" - }, - { - "author_name": "Shilangi Gupta", - "author_inst": "IIT Gandhinagar" - }, - { - "author_name": "Madhvi Joshi", - "author_inst": "GBRC, Gandhinagar, India" - }, - { - "author_name": "Algappan Ramanathan", - "author_inst": "JNU, New Delhi, India" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.16.448640", "rel_title": "SARS-CoV-2 envelope-protein corruption of homeostatic signaling mechanisms in mammalian cells", @@ -739324,6 +738334,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2021.06.11.21258765", + "rel_title": "Factors associated with COVID-19 susceptibility and severity in patients with multiple sclerosis: A systematic review", + "rel_date": "2021-06-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.11.21258765", + "rel_abs": "BackgroundWe conducted this systematic review to identify factors associated with coronavirus disease (COVID-19) susceptibility and outcomes among people with multiple sclerosis (MS).\n\nMethodsAvailable studies from PubMed, Scopus, EMBASE, Web of Science, and gray literature including reference list and conference abstracts were searched from December 1, 2019, through April 12, 2021. We included cross-sectional, case-control, and cohort studies that reported risk factors of contracting COVID-19 or its outcome in patients with MS on univariate or multivariate regression analyses.\n\nResultsOut of the initial 2719 records and 1553 conference abstracts, a total of 20 studies were included. Factors associated with COVID-19 susceptibility were reported in 11 studies and risk factors for infection outcomes were discussed in 10. History of contact with an infected is strongly suggested as a risk factor for COVID-19 susceptibility. Other factors that could be associated with contracting infection are younger age, relapsing course, and anti-CD20 agents. The evidence suggests that increasing age, greater MS severity, treatment with anti-CD20 agents, previous use of corticosteroids, and specific comorbidities (obesity and coronary artery disease) could be independently associated with worse infection outcomes. Male sex is likely to be a risk factor for more severe disease. The black or African American race was reported as a possible risk factor.\n\nConclusionDue to a paucity of research and methodological issues, no risk factors for COVID-19 susceptibility and outcomes neither be confirmed nor excluded. Further large studies are needed to address factors associated with COVID-19 susceptibility and severity.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Mahdi Barzegar", + "author_inst": "Isfahan Neuroscience Resaerch Center" + }, + { + "author_name": "Sara Bagherieh", + "author_inst": "Isfahan Neurosciences Research Center" + }, + { + "author_name": "Shakiba Houshi", + "author_inst": "Isfahan Neurosciences Research Center" + }, + { + "author_name": "Mozhgan Sadat Hashemi", + "author_inst": "Students' Scientific Research Center" + }, + { + "author_name": "Ghasem Pishgahi", + "author_inst": "Students' Scientific Research Center" + }, + { + "author_name": "Alireza Afshari-Safavi", + "author_inst": "Department of Biostatistics and Epidemiology, Faculty of Health, North Khorasan University of Medical Sciences, Bojnurd, Iran" + }, + { + "author_name": "Omid Mirmosayyeb", + "author_inst": "Isfahan Neuroscience Research Center" + }, + { + "author_name": "Vahid Shaygannejad", + "author_inst": "Isfahan Neurosciences Research Center" + }, + { + "author_name": "Aram Zabeti", + "author_inst": "Department of Neurology and Rehabilitation Medicine , University of Cincinnati , Cincinnati , OH , USA" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2021.06.11.21258690", "rel_title": "Brain imaging before and after COVID-19 in UK Biobank", @@ -739684,57 +738745,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.14.21258871", - "rel_title": "SARS-CoV-2 Spike protein binding of glycated serum albumin - its potential role in the pathogenesis of the COVID-19 clinical syndromes and bias towards individuals with pre-diabetes/type 2 diabetes & metabolic diseases.", - "rel_date": "2021-06-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.14.21258871", - "rel_abs": "Since the immune response to SARS-CoV2 infection requires antibody recognition of the Spike protein, we used MagMix, a semi-automated magnetic rack to reproducibly isolate patient plasma proteins bound to a pre-fusion stabilised Spike and nucleocapsid proteins conjugated to magnetic beads. Once eluted, MALDI-ToF mass spectrometry identified a range of immunoglobulins, but also in Spike protein magnetic beads we found a high affinity for human serum albumin. Careful mass comparison revealed a preferential capture of advanced glycation end product (AGE) glycated human serum albumin by the pre-fusion Spike protein.\n\nThe ability of bacteria and viruses to surround themselves with serum proteins is a recognised process of immune evasion. A lower serum albumin concentration is a reported feature of COVID-19 patients with severe symptoms and high probability of death. This binding preference of the Spike protein for AGE glycated serum albumin may contribute to immune evasion and influence the severity & pathology of SARS-COV2 towards acute respiratory distress. Thus, it can be hypothesised, contributing to the symptom severity bias and mortality risk for the elderly and those with (pre)diabetic and atherosclerotic/metabolic diseases who contract SARS-CoV2 infections.\n\nGraphic abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC=\"FIGDIR/small/21258871v3_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (43K):\norg.highwire.dtl.DTLVardef@2d9e7org.highwire.dtl.DTLVardef@1300c4corg.highwire.dtl.DTLVardef@1776193org.highwire.dtl.DTLVardef@a6ffc6_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jason K Iles", - "author_inst": "MAP Sciences" - }, - { - "author_name": "Raminta Zmuidinaite", - "author_inst": "MAP Sciences" - }, - { - "author_name": "Christoph Saddee", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Anna Gardiner", - "author_inst": "MAP Sciences" - }, - { - "author_name": "Jonathan Lacy", - "author_inst": "MAP Sciences" - }, - { - "author_name": "Stephen Harding", - "author_inst": "The Binding Site Group" - }, - { - "author_name": "Jernej Ule", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Debra Roblett", - "author_inst": "The Francis Crick Insitute" - }, - { - "author_name": "Raymond Kruse Iles", - "author_inst": "MAP Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.13.21258859", "rel_title": "Immunogenicity and reactogenicity of a heterologous COVID-19 prime-boost vaccination compared with homologous vaccine regimens", @@ -740411,6 +739421,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, + { + "rel_doi": "10.1101/2021.06.10.21258714", + "rel_title": "Phase 1 Trial of Cyclosporine for Hospitalized Patients with COVID-19", + "rel_date": "2021-06-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.10.21258714", + "rel_abs": "Coronavirus Disease 2019 (COVID-19) remains a global health emergency with limited treatment options, lagging vaccine rates and inadequate healthcare resources in the face of an ongoing calamity. The disease is characterized by immune dysregulation and cytokine storm. Cyclosporine A (CSA) is a calcineurin inhibitor that modulates cytokine production and may have direct antiviral properties against coronaviruses. To test whether a short course of treatment was safe in COVID-19 patients, we treated 10 hospitalized, oxygen requiring, non-critically ill patients with CSA at a starting dose of 9mg/kg/day. Five patients experienced adverse events, none were serious, and transaminitis was most common. No subject enrolled in this trial required intensive care unit (ICU)-level care and all patients were discharged alive from the hospital. Further, CSA treatment was associated with significant reductions in serum cytokines and chemokines important in COVID-19 hyper-inflammation, including CXCL10. In conclusion, short courses of CSA appear safe and feasible in COVID-19 patients requiring oxygen and therefore, may be a useful adjunct in resource-poor or resource-limited health care settings.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Emily A Blumberg", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Pablo Tebas", + "author_inst": "Perelman School of Medicine at the University of Pennsylvania" + }, + { + "author_name": "Ian Frank", + "author_inst": "Perelman School of Medicine at the University of Pennsylvania" + }, + { + "author_name": "Amy Marshall", + "author_inst": "Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania" + }, + { + "author_name": "Anne Chew", + "author_inst": "Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania" + }, + { + "author_name": "Elizabeth A Veloso", + "author_inst": "Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania" + }, + { + "author_name": "Alison Carulli", + "author_inst": "Hospital of the University of Pennsylvania" + }, + { + "author_name": "Walter Rogal", + "author_inst": "Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania" + }, + { + "author_name": "Avery L Gaymon", + "author_inst": "Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania" + }, + { + "author_name": "Aliza H Schmidt", + "author_inst": "Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania" + }, + { + "author_name": "Tiffany Barnette", + "author_inst": "Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania" + }, + { + "author_name": "Renee Jurek", + "author_inst": "Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania" + }, + { + "author_name": "Hooman Noorchashm", + "author_inst": "unaffiliated" + }, + { + "author_name": "Wei-Ting Hwang", + "author_inst": "Perelman School of Medicine at the University of Pennsylvania" + }, + { + "author_name": "Julia Han Noll", + "author_inst": "Center for Cellular Immunotherapies, Department of Microbiology, Parker Institute for Cancer Immunotherapy, Perelman School of Medicine, University of Pennsylv" + }, + { + "author_name": "Joseph A Fraietta", + "author_inst": "Center for Cellular Immunotherapies, Perelman School of Medicine, University of Pennsylvania" + }, + { + "author_name": "Carl H June", + "author_inst": "Department of Medicine, Division of Hematology, Parker Institute for Cancer Immunotherapy, Perelman School of Medicine at the University of Pennsylvania" + }, + { + "author_name": "Elizabeth O Hexner", + "author_inst": "Department of Medicine, Division of Hematology, Perelman School of Medicine at the University of Pennsylvania" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.09.21258644", "rel_title": "Targeted vaccination and the speed of SARS-CoV-2 adaptation", @@ -740891,61 +739988,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.11.21258445", - "rel_title": "Estimating the Burden of SARS-CoV-2 among the Rohingya Refugees", - "rel_date": "2021-06-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.11.21258445", - "rel_abs": "BackgroundSince the emergence of the COVID-19 pandemic, substantial concern has surrounded its impact among the Rohingya refugees living in the Kutupalong-Balukhali refugee camps in Bangladesh. Early modeling work projected a massive outbreak was likely after an introduction of the SARS-CoV-2 virus into the camps. Despite this, only 317 laboratory-confirmed cases and 10 deaths were reported through October 2020. While these official numbers portray a situation where the virus has been largely controlled, other sources contradict this, suggesting the low reported numbers to be a result of limited care seeking and testing, highlighting a population not willing to seek care or be tested. SARS-CoV-2 seroprevalence estimates from similar a timeframe in India (57%) and Bangladesh (74%) further sow doubt that transmission had been controlled. Here we explore multiple data sources to understand the plausibility of a much larger SARS-CoV-2 outbreak among the Rohingya refugees.\n\nMethodsWe used a mixed approach to analyze SARS-CoV-2 transmission using multiple available datasets. Using data from reported testing, cases, and deaths from the World Health Organization (WHO) and from WHOs Emergency Warning, Alert, and Response System, we characterized the probabilities of care seeking, testing, and being positive if tested. Unofficial death data, including reported pre-death symptoms, come from a community-based mortality survey conducted by the International Organization for Migration (IOM),) in addition to community health worker reported deaths. We developed a probabilistic inference framework, drawing on these data sources, to explore three scenarios of what might have happened among the Rohingya refugees.\n\nResultsAmong the 144 survey-identified deaths, 48 were consistent with suspected COVID-19. These deaths were consistent with viral exposures during Ramadan, a period of increased social contacts, and coincided with a spike in reported cases and testing positivity in June 2020. The age profile of suspected COVID-19 deaths mirrored that expected. Through the probability framework, we find that under each scenario, a substantial outbreak likely occurred, though the cumulative size and timing vary considerably. In conjunction with the reported and suspected deaths, the data suggest a large outbreak could have occurred early during spring 2020. Furthermore, while many mild and asymptomatic infections likely occurred, death data analyzed suggest there may have been significant unreported mortality.\n\nConclusionsWith the high population density, inability to home isolate adequately, and limited personal protective equipment, infection prevention and control in the Rohingya population is extremely challenging. Despite the low reported numbers of cases and deaths, our results suggest an early large-scale outbreak is consistent with multiple sources of data, particularly when accounting for limited care seeking behavior and low infection severity among this young population. While the currently available data do not allow us to estimate the precise incidence, these results indicate substantial unrecognized SARS-CoV-2 transmission may have occurred in these camps. However, until serological testing provides more conclusive evidence, we are only able to speculate about the extent of transmission among the Rohingya.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Shaun A Truelove", - "author_inst": "Departments of International Health and Epidemiology, Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Sonia A Hegde", - "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Lori Niehaus", - "author_inst": "Department of International Health, Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Natalya Kostandova", - "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Chiara Altare", - "author_inst": "Department of International Health, Johns Hopkins Bloomberg School of Public Health, Center for Humanitarian Health" - }, - { - "author_name": "V. Bhargavi Rao", - "author_inst": "Medecins Sans Frontieres (MSF), London, UK" - }, - { - "author_name": "Julianna Smith", - "author_inst": "MSF, Cox's Bazar, Bangladesh" - }, - { - "author_name": "Philipp du Cros", - "author_inst": "Burnett Institute, Melbourne, Australia" - }, - { - "author_name": "Andrew S. Azman", - "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health; MSF, Geneva, Switzerland" - }, - { - "author_name": "Paul Spiegel", - "author_inst": "Department of International Health, Johns Hopkins Bloomberg School of Public Health, Center for Humanitarian Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.06.10.21255008", "rel_title": "Patient Outcomes and Lessons-Learned from Treating Patients with Severe COVID-19 at a Long-Term Acute Care Hospital", @@ -742257,6 +741299,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.10.21258682", + "rel_title": "Cross-neutralizing activity against SARS-CoV-2 variants in COVID-19 patients: Comparison of four waves of the pandemic in Japan", + "rel_date": "2021-06-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.10.21258682", + "rel_abs": "In March 2021, Japan is facing a 4th wave of SARS-CoV-2 infection. To prevent further spread of infection, sera cross-neutralizing activity of patients previously infected with conventional SARS-CoV-2 against novel variants is important but is not firmly established. We investigated the neutralizing potency of 81 COVID-19 patients sera from 4 waves of pandemic against SARS-CoV-2 variants using their authentic viruses. Most sera had neutralizing activity against all variants, showing similar activity against B.1.1.7 and D614G, but lower activity especially against B.1.351. In the 4th wave, sera-neutralizing activity against B.1.1.7 was significantly higher than that against any other variants, including D614G. The cross-neutralizing activity of convalescent sera was effective against all variants but was potentially weaker for B.1.351.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Koichi Furukawa", + "author_inst": "Kobe University" + }, + { + "author_name": "Lidya Handayani Tjan", + "author_inst": "Kobe University" + }, + { + "author_name": "Silvia Sutandhio", + "author_inst": "Kobe University" + }, + { + "author_name": "Yukiya Kurahashi", + "author_inst": "Kobe University" + }, + { + "author_name": "Sachiyo Iwata", + "author_inst": "Hyogo Prefectural Kakogawa Medical Center" + }, + { + "author_name": "Yoshiki Tohma", + "author_inst": "Hyogo Prefectural Kakogawa Medical Center" + }, + { + "author_name": "Shigeru Sano", + "author_inst": "Hyogo Prefectural Kakogawa Medical Center" + }, + { + "author_name": "Sachiko Nakamura", + "author_inst": "Hyogo Prefectural Kakogawa Medical Center" + }, + { + "author_name": "Mitsuhiro Nishimura", + "author_inst": "Kobe University" + }, + { + "author_name": "Jun Arii", + "author_inst": "Kobe University" + }, + { + "author_name": "Tatsunori Kiriu", + "author_inst": "Kobe University" + }, + { + "author_name": "Masatsugu Yamamoto", + "author_inst": "Kobe University" + }, + { + "author_name": "Tatsuya Nagano", + "author_inst": "Kobe University" + }, + { + "author_name": "Yoshihiro Nishimura", + "author_inst": "Kobe University" + }, + { + "author_name": "Yasuko Mori", + "author_inst": "Kobe University Graduate School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.11.21258760", "rel_title": "Convalescent Plasma in Critically ill Patients with COVID-19", @@ -742673,53 +741790,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.10.21254528", - "rel_title": "NEWS-2 score assessment of inpatient referral during the COVID 19 epidemic", - "rel_date": "2021-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.10.21254528", - "rel_abs": "AimTo manage patients with suspected coronavirus disease (COVID-19) when they arrive at the hospital emergency department (ED), a clinical severity score is required to quickly identify patients requiring immediate hospital admission and close monitoring. The aim of this study was to evaluate, within the context of the pandemic, the performance of National Early Warning Score 2 (NEWS-2) to anticipate the admission of patients with suspected COVID-19 to a specialised emergency care unit.\n\nMethodsThis retrospective study was conducted on patients presenting at the COVID-19 entrance of the ED of the Vert-Galant private hospital (Paris, France) during the first national pandemic peak from March 20 to April 20, 2020. All patients completed a questionnaire and clinical data and vital signs were recorded. Statistical analysis and modelling were used to estimate the ability of different scores (NEWS-2, qSOFA, CRB-65) to predict hospital emergency admission and/or early COVID-19 diagnosis.\n\nResultsNEWS-2, with a cut off value of 5, predicted hospital admission with 82% sensitivity, 98% specificity and an area under the curve (AUC) of 96%. NEWS-2 was superior to qSOFA and CRB-65 scores for predicting hospital admission of COVID-19 patients. Multilinear or logistic regression analysis of clinical data did not improve this result.\n\nConclusionNEWS-2 is an excellent score to predict hospital admission of COVID-19 patients.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Valerie FAURE", - "author_inst": "Emergency Department, Hopital prive du Vert Galant Groupe Ramsey, Tremblay en France, France. tel. +33 1 86869300" - }, - { - "author_name": "Marc SOURIS", - "author_inst": "Unit\u00e9 Mixte de Recherche Unit\u00e9 des virus \u00e9mergents (UVE Aix-Marseille Univ-IRD 190-INSERM 1207), Marseille 13005 France" - }, - { - "author_name": "Arnaud WILMET", - "author_inst": "Health for Development (H4D), 92 avenue Kl\u00e9ber, 75116 Paris, France" - }, - { - "author_name": "Franck BAUDINO", - "author_inst": "Health for Development (H4D), 92 avenue Kl\u00e9ber, 75116 Paris, France" - }, - { - "author_name": "Albert BRIZIO", - "author_inst": "SMUR, Hopital Delafontaine, Centre Hospitalier de Saint Denis, Saint Denis, France" - }, - { - "author_name": "Christopher MALHAIRE", - "author_inst": "Emergency Department, Hopital priv\u00e9 du Vert Galant Groupe Ramsey, Tremblay en France, France. tel. +33 1 86869300" - }, - { - "author_name": "Francois-Xavier PECCAUD", - "author_inst": "Emergency Department, H\u00f4pital priv\u00e9 du Vert Galant Groupe Ramsey, Tremblay en France, France. tel. +33 1 86869300" - }, - { - "author_name": "Jean-Paul GONZALEZ", - "author_inst": "School of Medicine, Georgetown University, Department of Microbiology & Immunology, Washington, DC 20057 USA." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2021.06.08.21258523", "rel_title": "A novel strategy for the detection of SARS-CoV-2 variants based on multiplex PCR-MALDI-TOF MS", @@ -743911,6 +742981,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.06.07.21258497", + "rel_title": "Data-driven methodology for discovery and response to pulmonary symptomology in hypertension through AI and machine learning: Application to COVID-19 related pharmacovigilance", + "rel_date": "2021-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.07.21258497", + "rel_abs": "BackgroundPotential therapy and confounding factors including typical co-administered medications, patients disease states, disease prevalence, patient demographics, medical histories, and reasons for prescribing a drug often are incomplete, conflicting, missing, or uncharacterized in spontaneous adverse drug event (ADE) reporting systems. These missing or incomplete features can affect and limit the application of quantitative methods in pharmacovigilance for meta-analyses of data during randomized clinical trials.\n\nMethodsIn this study, we implemented adaptive signal detection approaches to correct spurious association, hidden factors, and confounder misclassification when the covariates are unknown or unmeasured on medications affecting the renin-angiotensin system (RAS), potentially creating an increased risk of life-threatening outcomes in high-risk patients.\n\nResultsFollowing multiple filtering stages to exclude insignificant and noise-driven reports, we found that drugs from antihypertensives agents, urologicals, and antithrombotic agents (macitentan, bosentan, epoprostenol, selexipag, sildenafil, tadalafil, and beraprost) form a similar class with a significantly higher incidence of pADEs. Macitentan and bosentan were associates with 64% and 56% of pADEs, respectively. Because these two medications are prescribed in diseases affecting pulmonary function and may be likely to emerge among the highest reported pADEs, in fact, they serve to validate the methods utilized here. Conversely, doxazosin and rilmenidine were found to have the least pADEs in selected drugs from hypertension patients. Nifedipine and candesartan were also found by our signal detection methods to form a drug cluster, shown by several studies an effective combination of these drugs on lowering blood pressure and appeared an improved side effect profile in comparison with single-agent monotherapy.\n\nConclusionsWe consider pulmonary ADE (pADE) profiles in a long-standing group of therapeutics, RAS-acting agents, in patients with hypertension associated with high-risk for COVID-19. Using these techniques, we confirmed our hypothesis that drugs from the same drug class could have very different pADE profiles affecting outcomes in acute respiratory illness. We found that several indidvual drugs have significant differences between their drug classes and compared to other drug classes.\n\nFundingGJW and MJD accepted funding from BioNexus KC for funding on this project but BioNexus KC had no direct role in this article.\n\nClinical trial numberN/A\n\nAuthor SummaryUnderlying comorbidities continue to negatively affect COVID-19 patients. A recent focus has been on medications affecting RAS. Therefore, with the advent of COVID-19 acute respiratory distress syndrome (ARDS) in high-risk patients with hypertension, identifying specific RAS medications with the lowest incidence of pADEs would be beneficial. For this purpose, we curated the FDA ADE database to search for information related to human pADEs. As part of post-marketing drug safety surveillance, state/federal regulatory agencies and other institutions provide massive collections of ADE reports, these large data-sets present an opportunity to investigate ADEs to provide patient management based on comparative population data analysis. The abundance and prevalence of ADEs are not always detectable during randomized clinical trials and before a drug receives FDA approval for use in the clinic, which may appear with more widespread use. This is especially true for specific agents or diseases since there are simply too few events to be assessed, even in a large clinical trial for side effect profiles of specific disease states. For this purpose, we employed a novel method identifying extraneous causes of differential reporting including sampling variance and selection biases by reducing the effect of covariates.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Xuan Xu", + "author_inst": "1DATA Consortium, Kansas State University Olathe, Department of Mathematics, Kansas State University" + }, + { + "author_name": "Jessica Kawakami", + "author_inst": "1DATA Consortium, School of Pharmacy, Division of Pharmacology and Pharmaceutical Sciences, University of Missouri-Kansas City, Molecular Biology and Biochemis" + }, + { + "author_name": "Nuwan Indika Millagaha Gedara", + "author_inst": "1DATA Consortium, Department of Business Economics, University of Colombo" + }, + { + "author_name": "Jim Riviere", + "author_inst": "1DATA Consortium, Kansas State University and North Carolina State University" + }, + { + "author_name": "Emma Meyer", + "author_inst": "1DATA Consortium, University of Missouri-Kansas City School of Pharmacy" + }, + { + "author_name": "Gerald J Wyckoff", + "author_inst": "1DATA Consortium, Molecular Biology and Biochemistry, SBC University of Missouri-Kansas City School of Pharmacy, Division of Pharmacology and Pharmaceutical Sci" + }, + { + "author_name": "Majid Jaberi-Douraki", + "author_inst": "1DATA Consortium, Kansas State University Olathe, Department of Mathematics, Kansas State University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2021.06.09.21258617", "rel_title": "Vaccination reduces need for emergency care in breakthrough COVID-19 infections: A multicenter cohort study", @@ -744491,133 +743604,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.06.10.447999", - "rel_title": "A combination of RBD and NTD neutralizing antibodies limits the generation of SARS-CoV-2 spike neutralization-escape mutants", - "rel_date": "2021-06-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.10.447999", - "rel_abs": "Most known SARS-CoV-2 neutralizing antibodies (nAbs), including those approved by the FDA for emergency use, inhibit viral infection by targeting the receptor-binding domain (RBD) of the spike (S) protein. Variants of concern (VOC) carrying mutations in the RBD or other regions of S reduce the effectiveness of many nAbs and vaccines by evading neutralization. Therefore, therapies that are less susceptible to resistance are urgently needed. Here, we characterized the memory B-cell repertoire of COVID-19 convalescent donors and analyzed their RBD and non-RBD nAbs. We found that many of the non-RBD-targeting nAbs were specific to the N-terminal domain (NTD). Using neutralization assays with authentic SARS-CoV-2 and a recombinant vesicular stomatitis virus carrying SARS-CoV-2 S protein (rVSV-SARS2), we defined a panel of potent RBD and NTD nAbs. Next, we used a combination of neutralization-escape rVSV-SARS2 mutants and a yeast display library of RBD mutants to map their epitopes. The most potent RBD nAb competed with hACE2 binding and targeted an epitope that includes residue F490. The most potent NTD nAb epitope included Y145, K150 and W152. As seen with some of the natural VOC, the neutralization potencies of COVID-19 convalescent sera were reduced by 4-16-fold against rVSV-SARS2 bearing Y145D, K150E or W152R spike mutations. Moreover, we found that combining RBD and NTD nAbs modestly enhanced their neutralization potential. Notably, the same combination of RBD and NTD nAbs limited the development of neutralization-escape mutants in vitro, suggesting such a strategy may have higher efficacy and utility for mitigating the emergence of VOC.\n\nImportanceThe US FDA has issued emergency use authorizations (EUAs) for multiple investigational monoclonal antibody (mAb) therapies for the treatment of mild to moderate COVID-19. These mAb therapeutics are solely targeting the receptor binding domain of the SARS-CoV-2 spike protein. However, the N-terminal domain of the spike protein also carries crucial neutralizing epitopes. Here, we show that key mutations in the N-terminal domain can reduce the neutralizing capacity of convalescent COVID-19 sera. We report that a combination of two neutralizing antibodies targeting the receptor binding and N-terminal domains may have higher efficacy and is beneficial to combat the emergence of virus variants.", - "rel_num_authors": 28, - "rel_authors": [ - { - "author_name": "Denise Haslwanter", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "M. Eugenia Dieterle", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Anna Z. Wec", - "author_inst": "Adimab LLC" - }, - { - "author_name": "Mrunal Sakharkar", - "author_inst": "Adimab LLC" - }, - { - "author_name": "Catalina Florez", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Karen Tong", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "C. Garrett Rappazzo", - "author_inst": "Adimab LLC" - }, - { - "author_name": "Gorka Lasso", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Olivia Vergnolle", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Ariel S. Wirchnianski", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Robert H. Bortz III", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Ethan Laudermilch", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "J. Maximilian Fels", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Amanda Mengotto", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Ryan J Malonis", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "George I Georgiev", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Jose Quiroz", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Daniel Wrapp", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "Nianshuang Wang", - "author_inst": "University of Texas" - }, - { - "author_name": "Jason Barnhill", - "author_inst": "United States Military Academy at West Point" - }, - { - "author_name": "John M Dye", - "author_inst": "US Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Jason S. McLellan", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Johanna P. Daily", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Jonathan R. Lai", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Andrew S Herbert", - "author_inst": "USAMRIID" - }, - { - "author_name": "Laura Walker", - "author_inst": "Adimab LLC" - }, - { - "author_name": "Kartik Chandran", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Rohit K. Jangra", - "author_inst": "Albert Einstein College of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.06.11.448032", "rel_title": "Control of SARS-CoV-2 infection after Spike DNA or Spike DNA+Proteinco-immunization in rhesus macaques", @@ -745785,6 +744771,145 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.08.21258069", + "rel_title": "Bovine Colostrum Derived Antibodies Against SARS-CoV-2 Show Great Potential to Serve as a Prophylactic Agent", + "rel_date": "2021-06-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.08.21258069", + "rel_abs": "Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) until now imposes a serious burden to health systems globally. Despite worldwide vaccination, social distancing and wearing masks, the spread of the virus is still ongoing. One of the mechanisms how neutralizing antibodies (NAbs) block virus entry into cells encompasses interaction inhibition between the cell surface receptor angiotensin-converting enzyme 2 (ACE2) and the spike (S) protein of SARS-CoV-2. SARS-CoV-2 specific NAb development can be induced in the blood of cattle. Pregnant cows produce NAbs upon immunization, and antibodies move into the colostrum just before calving. Here we immunized cows with SARS-CoV-2 S1 receptor binding domain (RBD) protein in proper adjuvant solutions, followed by one boost with SARS-CoV-2 trimeric S protein, and purified immunoglobulins from colostrum. We demonstrate that this preparation indeed blocks interaction between the trimeric S protein and ACE2 in different in vitro assays. Moreover, we describe the formulation of purified immunoglobulin preparation into a nasal spray. When administered to human subjects, the formulation persists on the nasal mucosa for at least 4 hours as determined by a clinical study. Therefore, we are presenting a solution that shows great potential to serve as a prophylactic agent against SARS-CoV-2 infection as an additional measure to vaccination and wearing masks. Moreover, our technology allows for a rapid and versatile adaption for preparing prophylactic treatments against other diseases by using the defined characteristics of antibody movement into the colostrum.\n\nSignificanceSARS-CoV-2 infections continue to be a high-risk factor for mankind. Antibodies with the potential to neutralize the virus and thus its entry into the host cell have been shown to impose a potent measure against the infection. Human derived neutralizing antibodies are therapeutics and thus fall under the legislation of drugs. However, an alternative could be the purification of efficient neutralizing antibodies from other species. Here, we present immunization of pregnant cows with spike protein of SARS-CoV-2 which results in high quantities of colostrum immunoglobulins that can be easily harvested and safely purified within a remarkably short time. The colostrum immunoglobulin preparation has a great potential to serve in formulations that can be used as prophylactic agent against SARS-CoV-2 infection.", + "rel_num_authors": 31, + "rel_authors": [ + { + "author_name": "Kadri Kangro", + "author_inst": "Icosagen Cell Factory" + }, + { + "author_name": "Mihhail Kurashin", + "author_inst": "Icosagen Cell Factory" + }, + { + "author_name": "Kiira Gildemann", + "author_inst": "Icosagen Cell Factory" + }, + { + "author_name": "Eve Sankovski", + "author_inst": "Icosagen Cell Factory" + }, + { + "author_name": "Eva Zusinaite", + "author_inst": "University of Tartu" + }, + { + "author_name": "Laura Sandra Lello", + "author_inst": "University of Tartu" + }, + { + "author_name": "Raini Pert", + "author_inst": "Icosagen Cell Factory" + }, + { + "author_name": "Ants Kavak", + "author_inst": "Estonian University of Life Sciences" + }, + { + "author_name": "Vaino Poikalainen", + "author_inst": "Teadus ja Tegu" + }, + { + "author_name": "Lembit Lepasalu", + "author_inst": "Teadus ja Tegu" + }, + { + "author_name": "Marilin Kuusk", + "author_inst": "Icosagen Cell Factory" + }, + { + "author_name": "Robin Pau", + "author_inst": "Icosagen Cell Factory" + }, + { + "author_name": "Sander Piiskop", + "author_inst": "Chemi-Pharm" + }, + { + "author_name": "Siimu Rom", + "author_inst": "Chemi-Pharm" + }, + { + "author_name": "Ruth Oltjer", + "author_inst": "Chemi-Pharm" + }, + { + "author_name": "Kairi Tiirik", + "author_inst": "University of Tartu" + }, + { + "author_name": "Karin Kogermann", + "author_inst": "University of Tartu" + }, + { + "author_name": "Mario Plaas", + "author_inst": "University of Tartu" + }, + { + "author_name": "Toomas Tiirats", + "author_inst": "Estonian University of Life Sciences" + }, + { + "author_name": "Birgit Aasmae", + "author_inst": "Estonian University of Life Sciences" + }, + { + "author_name": "Mihkel Plaas", + "author_inst": "Tartu University Hospital" + }, + { + "author_name": "Dagni Krinka", + "author_inst": "Icosagen AS" + }, + { + "author_name": "Ene Talpsep", + "author_inst": "Icosagen AS" + }, + { + "author_name": "Meelis Kadaja", + "author_inst": "Icosagen Cell Factory" + }, + { + "author_name": "Joachim Matthias Gerhold", + "author_inst": "Icosagen Cell Factory" + }, + { + "author_name": "Anu Planken", + "author_inst": "Icosagen Cell Factory, North-Estonian Medical Centre" + }, + { + "author_name": "Andres Tover", + "author_inst": "Icosagen Cell Factory" + }, + { + "author_name": "Andres Merits", + "author_inst": "University of Tartu" + }, + { + "author_name": "Andres Mannik", + "author_inst": "Icosagen Cell Factory" + }, + { + "author_name": "Mart Ustav Jr.", + "author_inst": "Icosagen Cell Factory" + }, + { + "author_name": "Mart Ustav", + "author_inst": "Icosagen Cell Factory" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.07.21258332", "rel_title": "Single-dose mRNA vaccine effectiveness against SARS-CoV-2, including P.1 and B.1.1.7 variants: a test-negative design in adults 70 years and older in British Columbia, Canada", @@ -746305,65 +745430,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.06.09.21258609", - "rel_title": "Depressive and anxiety symptoms and COVID-19-related factors among men and women in Nigeria", - "rel_date": "2021-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.09.21258609", - "rel_abs": "Despite the greater adverse economic impacts in low and middle-income (LAMI) compared to high-income countries, fewer studies have investigated the associations between COVID-19-related stressor and mental health in LAMI countries. The objectives of this study were to determine the associations between COVID-19-related stressors and anxiety and depressive symptoms while controlling for known risk and protective factors and to investigate any sex differences. An online survey was carried out to assess sociodemographic, psychosocial (previous mental health conditions, sexual orientation, intimate partner violence and perceived social support) and COVID-19-related variables. Hierarchical linear regression was carried out with anxiety and depressive symptoms as separate outcomes. Of the COVID-19-related factors, testing positive for COVID-19 infection, having COVID-19 symptoms, having other medical conditions, self-isolating due to COVID-19 symptoms, worry about infection, perception of the pandemic as a threat to income and isolation during the lockdown were significantly associated with higher anxiety and depressive symptoms. Of these, worry about infection, isolation during lockdown and disruption due to the pandemic retained independent associations with both outcomes. The variance in anxiety and depressive symptoms explained by COVID-19-related factors was larger in women (6.1% and respectively) compared to men (6.1% and respectively). COVID-19-related stressors are associated with higher anxiety and depressive symptoms, with these effects being larger in men compared to women. Enhancing social support can be an affordable strategy to mitigate this risk but this needs to be investigated using appropriate designs.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Olakunle Ayokunmi Oginni", - "author_inst": "Department of Mental Health, Obafemi Awolowo University, Ile-Ife, Nigeria" - }, - { - "author_name": "Ibidunni O Oloniniyi", - "author_inst": "Department of Mental Health, Obafemi Awolowo University, Ile-Ife, Nigeria" - }, - { - "author_name": "Olanrewaju Ibigbami", - "author_inst": "Department of Mental Health, Obafemi Awolowo University, Ile-Ife, Nigeria" - }, - { - "author_name": "Victor Ugo", - "author_inst": "Mentally Aware Nigeria Initiative and United for Global Mental Health. London, United Kingdom" - }, - { - "author_name": "Ayomipo Amiola", - "author_inst": "Mental Health Unit, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria" - }, - { - "author_name": "Adedotun Ogunbajo", - "author_inst": "Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, United State of America" - }, - { - "author_name": "Oladoyin Esan", - "author_inst": "Mental Health Unit, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria" - }, - { - "author_name": "Aderopo Adelola", - "author_inst": "Mental Health Unit, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria" - }, - { - "author_name": "Oluwatosin Daropale", - "author_inst": "Health Centre, Joseph Ayo Babalola University, Ikeji, Osun, Nigeria" - }, - { - "author_name": "Matthew Ebuka", - "author_inst": "Mental Health Unit, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria" - }, - { - "author_name": "Boladale Mapayi", - "author_inst": "Department of Mental Health, Obafemi Awolowo University, Ile-Ife, Nigeria" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.06.08.21258593", "rel_title": "Assessing the Impact of Mask Usage on COVID-19 Transmission Using a Computer Simulation", @@ -747839,6 +746905,81 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2021.06.08.447613", + "rel_title": "Cellular Activities of SARS-CoV-2 Main Protease Inhibitors Reveal Their Unique Characteristics", + "rel_date": "2021-06-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.08.447613", + "rel_abs": "As an essential enzyme of SARS-CoV-2, the pathogen of COVID-19, main protease (MPro) triggers acute toxicity to its human cell host, an effect that can be alleviated by an MPro inhibitor with cellular potency. By coupling this toxicity alleviation with the expression of an MPro-eGFP fusion protein in a human cell host for straightforward characterization with fluorescent flow cytometry, we developed an effective method that allows bulk analysis of cellular potency of MPro inhibitors. In comparison to an antiviral assay in which MPro inhibitors may target host proteases or other processes in the SARS-CoV-2 life cycle to convene strong antiviral effects, this novel assay is more advantageous in providing precise cellular MPro inhibition information for assessment and optimization of MPro inhibitors. We used this assay to analyze 30 literature reported MPro inhibitors including MPI1-9 that were newly developed aldehyde-based reversible covalent inhibitors of MPro, GC376 and 11a that are two investigational drugs undergoing clinical trials for the treatment of COVID-19 patients in United States, boceprevir, calpain inhibitor II, calpain inhibitor XII, ebselen, bepridil that is an antianginal drug with potent anti-SARS-CoV-2 activity, and chloroquine and hydroxychloroquine that were previously shown to inhibit MPro. Our results showed that most inhibitors displayed cellular potency much weaker than their potency in direct inhibition of the enzyme. Many inhibitors exhibited weak or undetectable cellular potency up to 10 M. On contrary to their strong antiviral effects, 11a, calpain inhibitor II, calpain XII, ebselen, and bepridil showed relatively weak to undetectable cellular MPro inhibition potency implicating their roles in interfering with key steps other than just the MPro catalysis in the SARS-CoV-2 life cycle to convene potent antiviral effects. characterization of these molecules on their antiviral mechanisms will likely reveal novel drug targets for COVID-19. Chloroquine and hydroxychloroquine showed close to undetectable cellular potency to inhibit MPro. Kinetic recharacterization of these two compounds rules out their possibility as MPro inhibitors. Our results also revealed that MPI5, 6, 7, and 8 have high cellular and antiviral potency with both IC50 and EC50 values respectively below 1 M. As the one with the highest cellular and antiviral potency among all tested compounds, MPI8 has a remarkable cellular MPro inhibition IC50 value of 31 nM that matches closely to its strong antiviral effect with an EC50 value of 30 nM. Given its strong cellular and antiviral potency, we cautiously suggest that MPI8 is ready for preclinical and clinical investigations for the treatment of COVID-19.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Wenyue Cao", + "author_inst": "Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University" + }, + { + "author_name": "Chia-Chuan D Cho", + "author_inst": "Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University" + }, + { + "author_name": "Zhi Z Geng", + "author_inst": "Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University" + }, + { + "author_name": "Xinyu R Ma", + "author_inst": "Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University" + }, + { + "author_name": "Robert Allen", + "author_inst": "Sorrento Therapeutics, Inc" + }, + { + "author_name": "Namir Shaabani", + "author_inst": "Sorrento Therapeutics, Inc." + }, + { + "author_name": "Erol C Vatansever", + "author_inst": "Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University" + }, + { + "author_name": "Yugendar R Alugubelli", + "author_inst": "Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University" + }, + { + "author_name": "Yuying Ma", + "author_inst": "Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University" + }, + { + "author_name": "William H Ellenburg", + "author_inst": "Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University" + }, + { + "author_name": "Kai S Yang", + "author_inst": "Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University" + }, + { + "author_name": "Yuchen Qiao", + "author_inst": "Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University" + }, + { + "author_name": "Henry Ji", + "author_inst": "Sorrento Therapeutics, Inc." + }, + { + "author_name": "Shiqing Xu", + "author_inst": "Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University" + }, + { + "author_name": "Wenshe Ray Liu", + "author_inst": "Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.06.07.447341", "rel_title": "The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour", @@ -748431,41 +747572,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.06.09.21258553", - "rel_title": "Analysis of cell-mediated immunity in people with long Covid.", - "rel_date": "2021-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.09.21258553", - "rel_abs": "IntroductionThe objective of this study is to analyse the specific immune response against SARS-CoV-2 in those affected by Long Covid (LC), attributable to T cells (cell-mediated immunity) and to carry out a parallel analysis of the humoral response and lymphocyte typing.\n\nMethodologyDescriptive cross-sectional study of 74 patients with LC for at least 4 months since diagnosis. The collected data were: information on the COVID-19 episode and the persistent symptoms, medical history and a specific cell-mediated immunity to SARS-CoV-2 through flow cytometry, assessing the release of interferon-gamma (IFN-{gamma}) by T4 lymphocytes, T8 lymphocytes and NK cells. Descriptive and comparative analyses were carried out.\n\nResultsPatients with LC had negative serology for Covid-19 in 89% of cases but 96% showed specific cellular immunity to SARS-CoV-2 an average of 9.5 months after infection: 89% of this response corresponded to T8 lymphocytes, 58% to NK cells, and 51% to T4 lymphocyte (20% negligibly positive). Most of them had altered immune cell typing and we found that T4 lymphocyte counts were low in 34% of cases and NK cell high in 64%. Macrophage populations were detected in the peripheral blood of 7% of them. Patients displayed a higher percentage of illnesses related to &[Prime]abnormal&[Prime] immune responses, either preceding SARS-CoV-2 infection (43%) or following it in 23% of cases.\n\nConclusionThe immune system appears to have an important involvement in the development of LC and viral persistence could be the cause or consequence of it. Further analysis with a control group should be performed.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Nerea Montes", - "author_inst": "Long Covid Autonomous Communities Together Spain (Investigation group) & Aragon Health Service" - }, - { - "author_name": "\u00c8lia Dom\u00e8nech", - "author_inst": "Long Covid Autonomous Communities Together Spain (Investigation group)" - }, - { - "author_name": "Silvia Guerrero", - "author_inst": "Long Covid Autonomous Communities Together Spain (Investigation group)" - }, - { - "author_name": "Barbara Olivan-Blazquez", - "author_inst": "Institute for Health Research Arag\u00f3n (IIS Arag\u00f3n) & University of Zaragoza, Zaragoza, Spain" - }, - { - "author_name": "Rosa Magall\u00f3n-Botaya", - "author_inst": "Institute for Health Research Aragon (IIS Aragon) & University of Zaragoza, Zaragoza, Spain" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2021.06.02.21258223", "rel_title": "Drug Repurposing of potential drug targets for treatment of COVID-19", @@ -749817,6 +748923,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.03.21258299", + "rel_title": "SARS-CoV-2 Seroprevalence Among Firefighters in Los Angeles, California", + "rel_date": "2021-06-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.03.21258299", + "rel_abs": "ObjectiveWe estimate the seroprevalence of SARS-CoV-2 antibodies among firefighters in the Los Angeles, California fire department in October 2020 and compare demographic and contextual factors for seropositivity.\n\nMethodsWe conducted a serologic survey of firefighters in Los Angeles, California, USA, in October 2020. Individuals were classified as seropositive for SARS-CoV-2 if they tested positive for immunoglobulin G, immunoglobulin M, or both. We compared demographic and contextual factors for seropositivity.\n\nResultsOf 713 participants, 8.9% tested positive for SARS-CoV-2 antibodies. Seropositivity was not associated with gender, age, or race/ethnicity. Furthermore, firefighters who worked in zip codes with lower income or higher share of minority population did not have higher rates of SARS-CoV-2 infection. Seropositivity was highest among firefighters who reported working in the vicinity of Los Angeles International Airport, which had a known outbreak in July 2020.\n\nConclusionsSeroprevalence among firefighters was no higher than seroprevalence in the general population, suggesting that workplace safety protocols, such as access to PPE and testing, can mitigate increased risk of infection at work. Workplace safety protocols for firefighters also eliminated differences in disease burden by geography and race/ethnicity observed in the general population.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Karen Mulligan", + "author_inst": "University of Southern California" + }, + { + "author_name": "Anders H Berg", + "author_inst": "Department of Pathology, Cedars-Sinai Medical Center" + }, + { + "author_name": "Marc Eckstein", + "author_inst": "Los Angeles Fire Department" + }, + { + "author_name": "Acacia Hori", + "author_inst": "University of Southern California" + }, + { + "author_name": "Anna Rodriguez", + "author_inst": "Sol Price School of Public Policy and Leonard D. Schaffer Center for Health Policy & Economics, University of Southern California" + }, + { + "author_name": "Omar Toubat", + "author_inst": "University of Southern California" + }, + { + "author_name": "Neeraj Sood", + "author_inst": "Sol Price School of Public Policy and Leonard D. Schaffer Center for Health Policy & Economics, University of Southern California" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.05.21258394", "rel_title": "The Effect of Pandemic Prevalence on the Reported Efficacy of SARS-CoV-2 Vaccine Candidates: A Systematic Review and Meta-analysis", @@ -750361,45 +749510,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.06.04.21257951", - "rel_title": "Early Epidemiological Evidence of Public Health Value of WA Notify, a Smartphone-based Exposure Notification Tool: Modeling COVID-19 Cases Averted in Washington State", - "rel_date": "2021-06-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.04.21257951", - "rel_abs": "BackgroundSecure and anonymous smartphone-based exposure notification tools are recently developed public health interventions that aim to reduce COVID-19 transmission and supplement traditional public health suriveillance. We assessed the impact of Washington States exposure notification tool, WA Notify, in mitigating the spread of COVID-19 during its first four months of implementation.\n\nMethodsDue to the constraints of privacy-preservation, aggregate metrics and disparate data sources were utilized to estimate the number of COVID-19 cases averted based on a modelling approach adapted from Wymant et al (2021) using the following parameters: number of notifications generated; the probability that a notified individual goes on to become a case; expected fraction of transmissions preventable by strict quarantine after notification; actual adherence to quarantine; and expected size of the full transmission chain if a contact had not been notified.\n\nResultsThe model was run on a range of secondary attack rates (5.1%-13.706%) and quarantine effectiveness (53% and 64%). Assuming a 12.085% secondary attack rate and 53% quarantine effectiveness, the model shows that 5,500 cases (central 95% range of sensitivity analyses 2,800-8,200) were averted statewide during the first four months of its implementation. Based on an estimated COVID-19 case fatality of 1.4%, WA Notify saved 40-115 lives during the study period.\n\nConclusionsThese findings demonstrate the value of exposure notification tools as a novel public health intervention to mitigate the spread of COVID-19 in the U.S. As new variants emerge and non-essential travel bans are lifted, exposure notification tools may continue to play a valuable role in limiting the spread of COVID-19.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Courtney Segal", - "author_inst": "University of Washington" - }, - { - "author_name": "Zhehao Zhang", - "author_inst": "University of Washington" - }, - { - "author_name": "Bryant T Karras", - "author_inst": "Washington State Department of Health" - }, - { - "author_name": "Debra Revere", - "author_inst": "University of Washington" - }, - { - "author_name": "Gregory Zane", - "author_inst": "Washington State Department of Health" - }, - { - "author_name": "Janet G Baseman", - "author_inst": "University of Washington" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.06.06.21258417", "rel_title": "Immunogenicity of the ChAdOx1 nCoV-19 and the BBV152 Vaccines in Patients with Autoimmune Rheumatic Diseases", @@ -751595,6 +750705,45 @@ "type": "new results", "category": "genetics" }, + { + "rel_doi": "10.1101/2021.06.03.21258238", + "rel_title": "Inferring SARS-CoV-2 RNA shedding into wastewater relative to time of infection", + "rel_date": "2021-06-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.03.21258238", + "rel_abs": "Since the start of the COVID-19 pandemic, there has been interest in using wastewater monitoring as an approach for disease surveillance. A significant uncertainty that would improve interpretation of wastewater monitoring data is the intensity and timing with which individuals shed RNA from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into wastewater. By combining wastewater and case surveillance data sets from a university campus during a period of heightened surveillance, we inferred that individual shedding of RNA into wastewater peaks on average six days (50% uncertainty interval (UI): 6 - 7; 95% UI: 4 - 8) following infection, and that wastewater measurements are highly overdispersed (negative binomial dispersion parameter, k = 0.39 (95% credible interval: 0.32 - 0.48)). This limits the utility of wastewater surveillance as a leading indicator of secular trends in SARS-CoV-2 transmission during an epidemic, and implies that it could be most useful as an early warning of rising transmission in areas where transmission is low or clinical testing is delayed or of limited capacity.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Sean M. Cavany", + "author_inst": "University of Notre Dame" + }, + { + "author_name": "Aaron Bivins", + "author_inst": "University of Notre Dame" + }, + { + "author_name": "Zhenyu Wu", + "author_inst": "University of NotreDame" + }, + { + "author_name": "Devin North", + "author_inst": "University of Notre Dame" + }, + { + "author_name": "Kyle Bibby", + "author_inst": "University of Notre Dame" + }, + { + "author_name": "Alex Perkins", + "author_inst": "University of Notre Dame" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.06.03.21258290", "rel_title": "ASSESSMENT OF PERFORMANCE AND IMPLEMENTATION CHARACTERISTICS OF RAPID POINT OF CARE SARS-CoV-2 ANTIGEN TESTING IN KENYA", @@ -752051,53 +751200,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.04.447160", - "rel_title": "Drug Repurposing for the SARS-CoV-2 Papain-Like Protease", - "rel_date": "2021-06-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.04.447160", - "rel_abs": "As the pathogen of COVID-19, SARS-CoV-2 encodes two essential cysteine proteases that process the pathogens two large polypeptide translates ORF1a and ORF1ab in human host cells to form 15 functionally important, mature nonstructural proteins. One of the two enzymes, papain-like protease or PLpro, also possesses deubiquitination and deISGylation activities that suppresses host innate immune responses toward SARS-CoV-2 infection. Therefore, PLpro is a potential COVID-19 drug target. To repurpose drugs for PLpro, we experimentally screened 33 deubiquitinase and 37 cysteine protease inhibitors on their inhibition of PLpro. Our results showed that 15 deubiquitinase and 1 cysteine protease inhibitors exhibit potent inhibition of PLpro at 200 M. More comprehensive characterizations revealed 7 inhibitors GRL0617, SJB2-043, TCID, DUB-IN-1, DUB-IN-3, PR-619, and S130 with an IC50 value below 60 M and four inhibitors GRL0617, SJB2-043, TCID, and PR-619 with an IC50 value below 10 M. Among four inhibitors with an IC50 value below 10 M, SJB2-043 is the most unique in that it doesnt fully inhibit PLpro but has an outstanding IC50 value of 0.56 M. SJB2-043 likely binds to an allosteric site of PLpro to convene its inhibition effect, which needs to be further investigated. As a pilot study, the current work indicates that COVID-19 drug repurposing by targeting PLpro holds promises but in-depth analysis of repurposed drugs is necessary to avoid omitting allosteric inhibitors.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Chia-Chuan D Cho", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Shuhua G Li", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Kai S Yang", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Tyler J Lalonde", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Ge Yu", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Yuchen Qiao", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Shiqing Xu", - "author_inst": "Texas A&M University" - }, - { - "author_name": "Wenshe Ray Liu", - "author_inst": "Texas A&M University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.06.03.21258248", "rel_title": "Comparison of antigen- and RT-PCR-based testing strategies for detection of Sars-Cov-2 in two high-exposure settings", @@ -753193,6 +752295,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.31.21257591", + "rel_title": "Chronic SARS-CoV-2 infection and viral evolution in a hypogammaglobulinaemic individual.", + "rel_date": "2021-06-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.31.21257591", + "rel_abs": "There is widespread interest in the capacity for SARS-CoV-2 evolution in the face of selective pressures from host immunity, either naturally acquired post-exposure or from vaccine acquired immunity. Allied to this is the potential for long perm persistent infections within immune compromised individuals to allow a broader range of viral evolution in the face of sub-optimal immune driven selective pressure. Here we report on an immunocompromised individual who is hypogammaglobulinaemic and was persistently infected with SARS-CoV-2 for over 290 days, the longest persistent infection recorded in the literature to date. During this time, nine samples of viral nucleic acid were obtained and analysed by next-generation sequencing. Initially only a single mutation (L179I) was detected in the spike protein relative to the prototypic SARS-CoV-2 Wuhan-Hu-1 isolate, with no further changes identified at day 58. However, by day 155 the spike protein had acquired a further four amino acid changes, namely S255F, S477N, H655Y and D1620A and a two amino acid deletion ({Delta}H69/{Delta}V70). Infectious virus was cultured from a nasopharyngeal sample taken on day 155 and next-generation sequencing confirmed that the mutations in the virus mirrored those identified by sequencing of the corresponding swab sample. The isolated virus was susceptible to remdesivir in vitro, however a 17-day course of remdesivir started on day 213 had no effect on the viral RT-PCR cycle threshold (Ct) value. On day 265 the patient was treated with the combination of casirivimab and imdevimab. The patient experienced progressive resolution of all symptoms over the next 8 weeks and by day 311 the virus was no longer detectable by RT-PCR. The {Delta}H69/{Delta}V70 deletion in the N-terminus of the spike protein which arose in our patient is also present in the B.1.1.7 variant of concern and has been associated with viral escape mutagenesis after treatment of another immunocompromised patient with convalescent plasma. Our data confirms the significance of this deletion in immunocompromised patients but illustrates it can arise independently of passive antibody transfer, suggesting the deletion may be an enabling mutation that compensates for distant changes in the spike protein that arise under selective pressure.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Maia Kavanagh Williamson", + "author_inst": "School of Cellular and Molecular Medicine, University of Bristol" + }, + { + "author_name": "Fergus Hamilton", + "author_inst": "Infection Sciences, North Bristol NHS Trust, BS10 5NB and MRC Integrative Epidemiology Unit, University of Bristol" + }, + { + "author_name": "Stephanie Hutchings", + "author_inst": "Public Health England South West Virology Laboratory, Southmead Hospital, BS10 5NB" + }, + { + "author_name": "Hannah M Pymont", + "author_inst": "Public Health England South West Virology Laboratory, Southmead Hospital, BS10 5NB and 2.\tInfection Sciences, North Bristol NHS Trust, BS10 5NB" + }, + { + "author_name": "Mark Hackett", + "author_inst": "Infection Sciences, North Bristol NHS Trust, BS10 5NB" + }, + { + "author_name": "David Arnold", + "author_inst": "Academic Respiratory Unit, North Bristol NHS Trust, BS10 5NB" + }, + { + "author_name": "Nick Maskell", + "author_inst": "Academic Respiratory Unit, North Bristol NHS Trust, BS10 5NB / University of Bristol" + }, + { + "author_name": "Alasdair P MacGowan", + "author_inst": "North Bristol NHS Trust" + }, + { + "author_name": "mahableshwar Albur", + "author_inst": "Infection Sciences, North Bristol NHS Trust, BS10 5NB" + }, + { + "author_name": "Megan Jenkins", + "author_inst": "Infection Sciences, North Bristol NHS Trust, BS10 5NB" + }, + { + "author_name": "Izak Heys", + "author_inst": "Infection Sciences, North Bristol NHS Trust, BS10 5NB" + }, + { + "author_name": "Francesca Knapper", + "author_inst": "Infection Sciences, North Bristol NHS Trust, BS10 5NB" + }, + { + "author_name": "Mustafa Elsayed", + "author_inst": "Infection Sciences, North Bristol NHS Trust, BS10 5NB" + }, + { + "author_name": "Rachel Milligan", + "author_inst": "School of Cellular and Molecular Medicine, University of Bristol" + }, + { + "author_name": "- The COVID-19 Genomics UK (COG-UK) Consortium", + "author_inst": "" + }, + { + "author_name": "Peter Muir", + "author_inst": "Public Health England South West Virology Laboratory, Southmead Hospital, BS10 5NB" + }, + { + "author_name": "Barry Vipond", + "author_inst": "Public Health England South West Virology Laboratory, Southmead Hospital, BS10 5NB" + }, + { + "author_name": "David A Matthews", + "author_inst": "School of Cellular and Molecular Medicine, University of Bristol" + }, + { + "author_name": "Ed Moran", + "author_inst": "Infection Sciences, North Bristol NHS Trust, BS10 5NB" + }, + { + "author_name": "Andrew D. D. Davidson", + "author_inst": "School of Cellular and Molecular Medicine, University of Bristol" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.03.21258106", "rel_title": "Human genetic factors associated with pneumonia susceptibility, a cue for COVID-19 mortality", @@ -753669,37 +752866,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.06.04.447114", - "rel_title": "Sub-Picomolar Detection of SARS-CoV-2 RBD via Computationally-Optimized Peptide Beacons", - "rel_date": "2021-06-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.04.447114", - "rel_abs": "The novel coronavirus SARS-CoV-2 continues to pose a significant global health threat. Along with vaccines and targeted therapeutics, there is a critical need for rapid diagnostic solutions. In this work, we employ deep learning-based protein design to engineer molecular beacons that function as conformational switches for high sensitivity detection of the SARS-CoV-2 spike protein receptor binding domain (S-RBD). The beacons contain two peptides, together forming a heterodimer, and a binding ligand between them to detect the presence of S-RBD. In the absence of S-RBD (OFF), the peptide beacons adopt a closed conformation that opens when bound to the S-RBD and produces a fluorescence signal (ON), utilizing a fluorophore-quencher pair at the two ends of the heterodimer stems. Two candidate beacons, C17LC21 and C21LC21, can detect the S-RBD with limits of detection (LoD) in the sub-picomolar range. We envision that these beacons can be easily integrated with on-chip optical sensors to construct a point-of-care diagnostic platform for SARS-CoV-2.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Soumya P. Tripathy", - "author_inst": "MIT Media Lab" - }, - { - "author_name": "Manvitha Ponnapati", - "author_inst": "MIT Media Lab" - }, - { - "author_name": "Joseph M Jacobson", - "author_inst": "MIT Media Lab" - }, - { - "author_name": "Pranam Chatterjee", - "author_inst": "MIT Media Lab" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2021.06.04.447090", "rel_title": "Genome-scale CRISPR Screens Identify Host Factors that Promote Human Coronavirus Infection", @@ -754863,6 +754029,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, + { + "rel_doi": "10.1101/2021.06.03.21258293", + "rel_title": "Interim estimates of increased transmissibility, growth rate, and reproduction number of the Covid-19 B.1.617.2 variant of concern in the United Kingdom", + "rel_date": "2021-06-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.03.21258293", + "rel_abs": "This paper relates to data from the Wellcome Sanger Institute, UK, regarding Covid-19 genomic surveillance. We use a simple model to give point estimates of the effective reproduction numbers of the B.1.617.2 and B.1.1.7 lineages in England, from sequenced data as at 15 May 2021. Comparison with the estimated reproduction number of B.1.1.7 enables an estimate of the increased transmissibility of B.1.617.2. We conclude that it is almost certain that there is increased transmissibility that will rapidly lead to B.1.617.2 becoming the prevailing variant in the UK. The derived estimates of increased transmissibility have uncertainty relating to the actual distribution of the generation interval, but they do point, under present conditions of vaccination coverage and NPIs, to exponential growth of positive cases.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "John S Dagpunar", + "author_inst": "University of Southampton" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.06.01.21257759", "rel_title": "Immunological dysfunction persists for 8 months following initial mild-moderate SARS-CoV-2 infection", @@ -755699,29 +754884,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.06.01.21258150", - "rel_title": "Ten months of temporal variation in the clinical journey of hospitalised patients with COVID-19: an observational cohort", - "rel_date": "2021-06-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.06.01.21258150", - "rel_abs": "BackgroundThere is potentially considerable variation in the nature and duration of the care provided to hospitalised patients during an ongoing infectious disease epidemic or pandemic. Improvements in care and clinician confidence may shorten the time spent as an inpatient, or the need for admission to an intensive care unit (ICU) or high density unit (HDU), while novel treatment modalities may reduce the time course of illness. On the other hand, limited resources at times of high demand may lead to rationing of resources, with less beneficial consequences. Despite little evidence on how the values of such variables change over the course of a crisis (such as the current COVID-19 pandemic), they may nevertheless be used as proxies for disease severity, outcome measures for clinical trials, and to inform planning and logistics. We hypothesise that variation of this kind has been present over the first year of the pandemic.\n\nMethods and FindingsWe investigate such time trends in an extremely large international cohort of 142,540 patients with symptom onset of, or hospital admission for, COVID-19 during 2020. The variables investigated are time from symptom onset to hospital admission, probability of ICU/HDU admission, time from hospital admission to ICU/HDU admission, case fatality ratio (CFR) and total length of hospital stay. Time from hospital symptom onset to hospital admission showed a rapid decline during the first months of the pandemic followed by peaks during August/September and December. ICU/HDU admission was more frequent from June to August, while there were only modest time trends in time from hospital admission to ICU/HDU. The CFR was lowest from June to August, a trend mostly driven by patients with no ICU/HDU admission. Raw numbers for overall hospital stay showed little overall variation over the time period, but further examination reveals a clear decline in time to discharge for ICU/HDU survivors. The main limitations are that these are predominantly severe COVID-19 cases, and that there are temporal, spatial and demographic biases present in an observational study of this kind.\n\nConclusionsOur results establish that variables of these kinds have limitations when used as outcome measures in a rapidly-evolving situation.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Matthew Hall", - "author_inst": "University of Oxford" - }, - { - "author_name": "- ISARIC Clinical Characterisation Group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.06.02.21258218", "rel_title": "Whole blood-based measurement of SARS-CoV-2-specific T cell responses reveals asymptomatic infection and vaccine efficacy in healthy subjects and patients with solid organ cancers", @@ -757017,6 +756179,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.06.02.446343", + "rel_title": "Common cardiac medications potently inhibit ACE2 binding to the SARS-CoV-2 Spike, and block virus penetration into human lung cells", + "rel_date": "2021-06-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.02.446343", + "rel_abs": "To initiate SARS-CoV-2 infection, the Receptor Binding Domain (RBD) on the viral spike protein must first bind to the host receptor ACE2 protein on pulmonary and other ACE2-expressing cells. We hypothesized that cardiac glycoside drugs might block the binding reaction between ACE2 and the Spike (S) protein, and thus block viral penetration into target cells. To test this hypothesis we developed a biochemical assay for ACE2:Spike binding, and tested cardiac glycosides as inhibitors of binding. Here we report that ouabain, digitoxin, and digoxin are high-affinity competitive inhibitors of ACE2 binding to the Wuhan S1 and the European [E614G] S1 proteins. These drugs also inhibit ACE2 binding to the Wuhan RBD, as well as to RBD proteins containing the S. Africa [E484K], Mink [Y453F] and UK [N501Y] mutations. As hypothesized, we also found that ouabain and digitoxin blocked penetration by SARS-CoV-2 Spike-pseudotyped virus into human lung cells. These data indicate that cardiac glycosides may block viral penetration into the target cell by first inhibiting ACE2:Spike binding. Clinical concentrations of ouabain and digitoxin are relatively safe for short term use for subjects with normal hearts. It has therefore not escaped our attention that these common cardiac medications could be deployed worldwide as inexpensive repurposed drugs for anti-COVID-19 therapy.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Hung Caohuy", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Ofer Eidelman", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Tinghua Chen", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Qingfeng Yang", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Alakesh Bera", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Nathan Walton", + "author_inst": "Uniformed Services University of the Health Sciences" + }, + { + "author_name": "Harvey B Pollard", + "author_inst": "Uniformed Services University of the Health Sciences" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2021.06.02.446813", "rel_title": "Efficient discovery of potently neutralizing SARS-CoV-2 antibodies using LIBRA-seq with ligand blocking", @@ -757629,77 +756834,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.25.21257820", - "rel_title": "The Female Predominant Persistent Immune Dysregulation of the Post COVID Syndrome: A Cohort Study", - "rel_date": "2021-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.25.21257820", - "rel_abs": "ObjectiveTo describe the clinical data from the first 107 patients seen in the Mayo Clinic Post COVID-19 Care Clinic (PCOCC).\n\nPatients and MethodsAfter IRB approval, we reviewed the charts of 107 patients seen between January 19, 2021 and April 29, 2021 in the Mayo Clinic Post COVID Care Clinic (PCOCC) in order to describe the first 107 patients treated through the Mayo Clinic PCOCC. Data was abstracted from the electronic medical record into a standardized database to facilitate analysis. Phenotypes of patients seen in the PCOCC clinic were identified by expert review of predominant symptom clusters.\n\nResultsThe majority of patients seen in our clinic were female (75%, 80/107), and the median age at presentation was 47 years (interquartile range [IQR] 37, 55). All had Post Acute Sequelae of SARS-CoV-2 infection (PASC) with six clinical phenotypes being identified - fatigue predominant (n=68), dyspnea predominant (n=23), myalgia predominant (n=6), orthostasis predominant (n=6), chest pain predominant (n=3), and headache predominant (n=1). The fatigue-predominant phenotype was more common in women (84%, p=0.006) and the dyspnea-predominant phenotype was more common in men (52%, p=0.002). IL-6 was elevated in 61% of patients (69% of women, p=0.0046) which was statistically discordant with elevation in CRP and ESR which was identified in 17% and 20% of cases respectively (p<0.001). Four PASC phenotypes (fatigue-predominant, myalgia-predominant, orthostasis predominant, and headache-predominant) were associated with central sensitization (CS), and higher IL-6 levels than those phenotypes not associated with CS (p=0.013). Patients with CS phenotypes after COVID-19 infection (post COVID syndrome) were predominantly female (80%, p=0.0085).\n\nConclusionIn our post COVID clinic, we observed several distinct clinical phenotypes. Fatigue-predominance was the most common presentation and was associated with elevated IL-6 levels and female gender. Dyspnea-predominance was more common in men and was not associated with elevated IL-6 levels. IL-6 levels were significantly elevated in patients with PASC and discordant with ESR and CRP, particularly in those with central sensitization phenotypes.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Ravindra Ganesh", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Stephanie L Grach", - "author_inst": "Mayo Clinic School of Graduate Medical Education" - }, - { - "author_name": "Dennis M Bierle", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Bradley R Salonen", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Nerissa M Collins", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Avni Y Joshi", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Neal D Boeder Jr.", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Christopher V Anstine", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Michael R Mueller", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Elizabeth C Wight", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Ivana T Croghan", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Andrew D Badley", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Rickey E Carter", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Ryan T Hurt", - "author_inst": "Mayo Clinic" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.26.21257488", "rel_title": "Clinical validation of colorimetric RT-LAMP, a fast, highly sensitive and specific COVID-19 molecular diagnostic tool that is robust to detect SARS-CoV-2 variants of concern", @@ -758723,6 +757857,137 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.26.21257441", + "rel_title": "Emerging SARS-CoV-2 variants of concern evade humoral immune responses from infection and vaccination", + "rel_date": "2021-06-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.26.21257441", + "rel_abs": "Emerging SARS-CoV-2 variants pose a threat to human immunity induced by natural infection and vaccination. We assessed the recognition of three variants of concern (B.1.1.7, B.1.351 and P.1) in cohorts of COVID-19 patients ranging in disease severity (n = 69) and recipients of the Pfizer/BioNTech vaccine (n = 50). Spike binding and neutralization against all three VOC was substantially reduced in the majority of samples, with the largest 4-7-fold reduction in neutralization being observed against B.1.351. While hospitalized COVID-19 patients and vaccinees maintained sufficient neutralizing titers against all three VOC, 39% of non-hospitalized patients did not neutralize B.1.351. Moreover, monoclonal neutralizing antibodies (NAbs) show sharp reductions in their binding kinetics and neutralizing potential to B.1.351 and P.1, but not to B.1.1.7. These data have implications for the degree to which pre-existing immunity can protect against subsequent infection with VOC and informs policy makers of susceptibility to globally circulating SARS-CoV-2 VOC.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Tom G. Caniels", + "author_inst": "1 Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." + }, + { + "author_name": "Ilja Bontjer", + "author_inst": "1 Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." + }, + { + "author_name": "Karlijn van der Straten", + "author_inst": "1 Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." + }, + { + "author_name": "Meliawati Poniman", + "author_inst": "1 Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." + }, + { + "author_name": "Judith A. Burger", + "author_inst": "1 Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." + }, + { + "author_name": "Brent Appelman", + "author_inst": "2 Center for Experimental and Molecular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherl" + }, + { + "author_name": "Ayesha H.A. Lavell", + "author_inst": "3 Department of Internal Medicine, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." + }, + { + "author_name": "Melissa Oomen", + "author_inst": "1 Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." + }, + { + "author_name": "Gert-Jan Godeke", + "author_inst": "4 Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands." + }, + { + "author_name": "Coralie Valle", + "author_inst": "4 Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands." + }, + { + "author_name": "Ramona Moegling", + "author_inst": "4 Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands." + }, + { + "author_name": "Hugo D.G. van Willigen", + "author_inst": "1 Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." + }, + { + "author_name": "Elke Wynberg", + "author_inst": "5 Department of Infectious Diseases, Public Health Service of Amsterdam, GGD, Amsterdam, the Netherlands." + }, + { + "author_name": "Michiel Schinkel", + "author_inst": "2 Center for Experimental and Molecular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherl" + }, + { + "author_name": "Lonneke A. van Vught", + "author_inst": "2 Center for Experimental and Molecular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherl" + }, + { + "author_name": "Denise Guerra", + "author_inst": "1 Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." + }, + { + "author_name": "Jonne L. Snitselaar", + "author_inst": "1 Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." + }, + { + "author_name": "Devidas N. Chaturbhuj", + "author_inst": "6 Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, USA." + }, + { + "author_name": "Isabel Cuella Martin", + "author_inst": "1 Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." + }, + { + "author_name": "- Amsterdam UMC COVID-19 S3/HCW study group", + "author_inst": "" + }, + { + "author_name": "John P. Moore", + "author_inst": "6 Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, USA." + }, + { + "author_name": "Menno D. de Jong", + "author_inst": "1 Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." + }, + { + "author_name": "Chantal Reusken", + "author_inst": "4 Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands." + }, + { + "author_name": "Jonne J. Sikkens", + "author_inst": "3 Department of Internal Medicine, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." + }, + { + "author_name": "Marije K. Bomers", + "author_inst": "3 Department of Internal Medicine, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." + }, + { + "author_name": "Godelieve J. de Bree", + "author_inst": "7 Department of Internal Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." + }, + { + "author_name": "Marit J. van Gils", + "author_inst": "1 Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." + }, + { + "author_name": "Dirk Eggink", + "author_inst": "4 Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands." + }, + { + "author_name": "Rogier W. Sanders", + "author_inst": "1 Department of Medical Microbiology, Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, the Netherlands." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.26.21257700", "rel_title": "Safety and immunogenicity of a recombinant DNA COVID-19 vaccine containing the coding regions of the spike and nucleocapsid proteins: Preliminary results from an open-label, phase 1 trial in healthy adults aged 19-55 years", @@ -759311,81 +758576,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.05.31.21257656", - "rel_title": "Acute kidney injury in hospitalized patients due to COVID-19", - "rel_date": "2021-06-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.31.21257656", - "rel_abs": "The incidence of acute kidney injury (AKI) in hospitalized patients with coronavirus disease 2019 (COVID-19) is variable, being associated with worse outcomes. The objectives of the study were to evaluate the incidence, risk factors and impact of AKI in subjects hospitalized for COVID-19 in two third- level hospitals in Cordoba, Argentina.\n\nA retrospective cohort study was conducted. 448 adults who were consecutively hospitalized for COVID-19 between March and the end of October 2020 at Hospital Privado Universitario de Cordoba and Hospital Raul Angel Ferreyra were included. The incidence of AKI was 19% (n = 85). 50.6% presented AKI stage 1 (n=43), 20% stage 2 (n=17) and 29.4% stage 3 (n=25, of which 18 required renal replacement therapy). In the multivariate analysis, the variables that were independently associated with AKI were: age (adjusted Odd ratio -aOR- =1.30, 95%CI=1.04-1.63, p=0.022), history of chronic kidney disease (aOR=9.92, 95%CI=4.52-21.77, p<0.001), blood neutrophil count at admission (aOR=1.09, 95%CI=1.01-1.18, p=0.037) and requirement for mechanical ventilation (MV) (aOR=6.69, 95%CI=2.24-19.9, p=0.001). AKI was associated with longer hospitalization, greater admission and length of stay in the intensive care unit, a positive association with bacterial superinfection, sepsis, respiratory distress syndrome, MV requirement and mortality (mortality with AKI=47.1% vs without AKI=12.4%, p<0.001). AKI was independently associated with higher mortality (aOR=3.32, 95%CI=1.6-6.9, p=0.001).\n\nIn conclusion, the incidence of AKI in adults hospitalized for COVID-19 was 19% and had a clear impact on morbidity and mortality. Local predisposing factors for AKI were identified.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Pehu\u00e9n Fern\u00e1ndez", - "author_inst": "Department of Nephrology, Hospital Privado Universitario de C\u00f3rdoba, C\u00f3rdoba, Argentina" - }, - { - "author_name": "Emanuel Jos\u00e9 Saad", - "author_inst": "Department of Internal Medicine, Hospital Privado Universitario de C\u00f3rdoba, C\u00f3rdoba, Argentina" - }, - { - "author_name": "Augusto Douthat", - "author_inst": "Department of Internal Medicine, Hospital Privado Universitario de C\u00f3rdoba, C\u00f3rdoba, Argentina" - }, - { - "author_name": "Federico Ariel Marucco", - "author_inst": "Department of Internal Medicine, Hospital Privado Universitario de C\u00f3rdoba, C\u00f3rdoba, Argentina" - }, - { - "author_name": "Mar\u00eda Celeste Heredia", - "author_inst": "Department of Internal Medicine, Hospital Privado Universitario de C\u00f3rdoba, C\u00f3rdoba, Argentina" - }, - { - "author_name": "Ayel\u00e9n Tarditi Barra", - "author_inst": "Department of Internal Medicine, Hospital Privado Universitario de C\u00f3rdoba, C\u00f3rdoba, Argentina" - }, - { - "author_name": "Silvina Trinidad Rodriguez Bonazzi", - "author_inst": "Department of Internal Medicine, Hospital Privado Universitario de C\u00f3rdoba, C\u00f3rdoba, Argentina" - }, - { - "author_name": "Melani Zlotogora", - "author_inst": "Department of Internal Medicine, Hospital Privado Universitario de C\u00f3rdoba, C\u00f3rdoba, Argentina" - }, - { - "author_name": "Mar\u00eda Antonella Correa Barovero", - "author_inst": "Department of Internal Medicine, Hospital Privado Universitario de C\u00f3rdoba, C\u00f3rdoba, Argentina" - }, - { - "author_name": "Sof\u00eda Villada", - "author_inst": "Department of Infectious Diseases, Hospital Privado Universitario de C\u00f3rdoba, C\u00f3rdoba, Argentina" - }, - { - "author_name": "Juan Pablo Maldonado", - "author_inst": "Department of Nephrology, Hospital Privado Universitario de C\u00f3rdoba, C\u00f3rdoba, Argentina" - }, - { - "author_name": "Juan Pablo Caeiro", - "author_inst": "Department of Infectious Diseases, Hospital Privado Universitario de C\u00f3rdoba, C\u00f3rdoba, Argentina" - }, - { - "author_name": "Ricardo Arturo Albertini", - "author_inst": "Department of Internal Medicine, Hospital Privado Universitario de C\u00f3rdoba, C\u00f3rdoba, Argentina" - }, - { - "author_name": "Jorge Luis De La Fuente", - "author_inst": "Department of Nephrology, Hospital Privado Universitario de C\u00f3rdoba, C\u00f3rdoba, Argentina" - }, - { - "author_name": "Walter Guillermo Douthat", - "author_inst": "Department of Nephrology, Hospital Privado Universitario de C\u00f3rdoba, C\u00f3rdoba, Argentina" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "nephrology" - }, { "rel_doi": "10.1101/2021.05.30.21256718", "rel_title": "Clarity Plus\u2122 digital PCR: A novel platform for absolute quantification of SARS-CoV-2", @@ -760429,6 +759619,53 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.06.01.446579", + "rel_title": "SARS-CoV-2 Spreads through Cell-to-Cell Transmission", + "rel_date": "2021-06-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.06.01.446579", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a highly transmissible coronavirus responsible for the global COVID-19 pandemic. Herein we provide evidence that SARS-CoV-2 spreads through cell-cell contact in cultures, mediated by the spike glycoprotein. SARS-CoV-2 spike is more efficient in facilitating cell-to-cell transmission than SARS-CoV spike, which reflects, in part, their differential cell-cell fusion activity. Interestingly, treatment of cocultured cells with endosomal entry inhibitors impairs cell-to-cell transmission, implicating endosomal membrane fusion as an underlying mechanism. Compared with cell-free infection, cell-to-cell transmission of SARS-CoV-2 is refractory to inhibition by neutralizing antibody or convalescent sera of COVID-19 patients. While ACE2 enhances cell-to-cell transmission, we find that it is not absolutely required. Notably, despite differences in cell-free infectivity, the variants of concern (VOC) B.1.1.7 and B.1.351 have similar cell-to-cell transmission capability. Moreover, B.1.351 is more resistant to neutralization by vaccinee sera in cell-free infection, whereas B.1.1.7 is more resistant to inhibition by vaccine sera in cell-to-cell transmission. Overall, our study reveals critical features of SARS-CoV-2 spike-mediated cell-to-cell transmission, with important implications for a better understanding of SARS-CoV-2 spread and pathogenesis.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Cong Zeng", + "author_inst": "The Ohio State University" + }, + { + "author_name": "John P. Evans", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Tiffany King", + "author_inst": "Nationwdie Childrens Hospital" + }, + { + "author_name": "Yi-Min Zheng", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Eugene M. Oltz", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Sean P. J. Whelan", + "author_inst": "Washington University in Saint Louis" + }, + { + "author_name": "Linda Saif", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Shan-Lu Liu", + "author_inst": "The Ohio State University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.05.28.446136", "rel_title": "First evidence of SARS-CoV-2 genome detection in zebra mussel (Dreissena polymorpha).", @@ -760753,37 +759990,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2021.05.28.21258007", - "rel_title": "Temporal stability and detection sensitivity of the dry swab-based diagnosis of SARS-CoV-2", - "rel_date": "2021-05-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.28.21258007", - "rel_abs": "The rapid spread and evolution of various strains of SARS-CoV-2, the virus responsible for COVID-19, continues to challenge the disease controlling measures globally. Alarming concern is, the number of second wave infections surpassed the first wave and the onset of severe symptoms manifesting rapidly. In this scenario, testing of maximum population in less time and minimum cost with existing diagnostic amenities is the only possible way to control the spread of the virus. The previously described RNA extraction-free methods using dry swab have been shown to be advantageous in these critical times by different studies. In this work, we show the temporal stability and performance of the dry swab viral detection method at two different temperatures. Contrived dry swabs holding serially diluted SARS-CoV-2 strains A2a and A3i at 25{degrees}C (room temperature; RT) and 4{degrees}C were subjected to direct RT-PCR and compared with standard VTM-RNA based method. The results clearly indicate that dry swab method of RNA detection is as efficient as VTM-RNA-based method in both strains, when checked for up to 72 hours. The lesser CT values of dry swab samples in comparison to that of the VTM-RNA samples suggest better sensitivity of the method within 48 hours of time. The results collectively suggest that dry swab samples are stable at RT for 24 hours and the detection of SARS-CoV-2 RNA by RT-PCR do not show variance from VTM-RNA. This extraction free, direct RT-PCR method holds phenomenal standing in the present life-threatening circumstances due to SARS-CoV-2.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Gokulan CG", - "author_inst": "CSIR-Centre for Cellular and Molecular Biology" - }, - { - "author_name": "Uday Kiran", - "author_inst": "CSIR-Centre for Cellular and Molecular Biology" - }, - { - "author_name": "Santosh Kumar Kuncha", - "author_inst": "CSIR-Centre for Cellular and Molecular Biology" - }, - { - "author_name": "Rakesh K Mishra", - "author_inst": "CSIR-Centre for Cellular and Molecular Biology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.31.21257910", "rel_title": "Mendelian randomization analyses show that higher acetyl-carnitine and carnitine levels in blood protect against severe Covid19", @@ -761894,6 +761100,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.28.21257967", + "rel_title": "Effectiveness of the Covid-19 vaccine in preventing infection in dental practitioners: results of a cross-sectional questionnaire based survey", + "rel_date": "2021-05-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.28.21257967", + "rel_abs": "India started its vaccination program at the beginning of 2021, the main beneficiaries being health workers and frontline workers including police, paramilitary forces, sanitation workers, and disaster management volunteers in the first phase. By the time, the second wave of Covid-19 impacted India, approximately 14 million healthcare and frontline workers, including dentists had been vaccinated.\n\nAimTo study the effectiveness of vaccination on a subset of high-risk healthcare workers i.e. dentists in preventing Covid-19 during the second wave of the pandemic.\n\nStudy designA questionnaire based pan-India online survey was carried out to record the Covid-related experiences of dentists prior to and after vaccination.\n\nResultThe sample size for this survey was 4493 respondents from across India. During the second wave, 9.18% (n=364) respondents became positive in spite of the vaccine, while 14.69%(n=78) became positive in the unvaccinated group. A chi-square test of independence was performed to examine the relation between vaccination and the Covid positivity rate in all age groups. The relation between these variables was highly significant, [X2 (1, N = 4493) = 15.9809, p=.000064].\n\nConclusionOur pan-India online survey inferred that vaccination has a definitive role to play in reducing the positivity rate amongst dentists during the second wave of the pandemic across all age groups.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Sanjeev Kumar", + "author_inst": "Faculty of Dental Sciences, SGT University, Gurugram" + }, + { + "author_name": "Susmita Saxena", + "author_inst": "ESIC Dental College & Hospital, Rohini, New Delhi" + }, + { + "author_name": "Mansi Atri", + "author_inst": "ESIC Dental College & Hospital, Rohini, New Delhi" + }, + { + "author_name": "Sunil Kumar Chamola", + "author_inst": "Faculty of Medicine & Health Sciences, SGT University, Gurugram" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "dentistry and oral medicine" + }, { "rel_doi": "10.1101/2021.05.27.21257918", "rel_title": "Monitoring emergence of SARS-CoV-2 B.1.1.7 Variant through the Spanish National SARS-CoV-2 Wastewater Surveillance System (VATar COVID-19) from December 2020 to March 2021", @@ -762414,105 +761651,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.29.443900", - "rel_title": "Broadening a SARS-CoV-1 neutralizing antibody for potent SARS-CoV-2 neutralization through directed evolution", - "rel_date": "2021-05-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.29.443900", - "rel_abs": "The emergence of SARS-CoV-2 underscores the need for strategies to rapidly develop neutralizing monoclonal antibodies that can function as prophylactic and therapeutic agents and to help guide vaccine design. Here, we demonstrate that engineering approaches can be used to refocus an existing neutralizing antibody to a related but resistant virus. Using a rapid affinity maturation strategy, we engineered CR3022, a SARS-CoV-1 neutralizing antibody, to bind SARS-CoV-2 receptor binding domain with >1000-fold improved affinity. The engineered CR3022 neutralized SARS-CoV-2 and provided prophylactic protection from viral challenge in a small animal model of SARS-CoV-2 infection. Deep sequencing throughout the engineering process paired with crystallographic analysis of an enhanced antibody elucidated the molecular mechanisms by which engineered CR3022 can accommodate sequence differences in the epitope between SARS-CoV-1 and SARS-CoV-2. The workflow described provides a blueprint for rapid broadening of neutralization of an antibody from one virus to closely related but resistant viruses.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Fangzhu Zhao", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Meng Yuan", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Celina Keating", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Namir Shabaani", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Oliver Limbo", - "author_inst": "IAVI" - }, - { - "author_name": "Collin Joyce", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Jordan Woehl", - "author_inst": "IAVI" - }, - { - "author_name": "Shawn Barman", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Alison Burns", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Xueyong Zhu", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Michael Ricciardi", - "author_inst": "George Washington University" - }, - { - "author_name": "Linghang Peng", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Jessica Smith", - "author_inst": "IAVI" - }, - { - "author_name": "Deli Huang", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Bryan Briney", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Devin Sok", - "author_inst": "IAVI" - }, - { - "author_name": "David Nemazee", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "John Teiijaro", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Ian A. Wilson", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Dennis Burton", - "author_inst": "Scripps Institute" - }, - { - "author_name": "Joseph G Jardine", - "author_inst": "IAVI" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2021.05.29.446267", "rel_title": "Amyloidogenic proteins in the SARS-CoV and SARS-CoV-2 proteomes", @@ -763564,6 +762702,153 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.05.28.446200", + "rel_title": "A suitable murine model for studying respiratory coronavirus infection and therapeutic countermeasures in BSL-2 laboratories", + "rel_date": "2021-05-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.28.446200", + "rel_abs": "Several animal models are being used to explore important features of COVID-19, nevertheless none of them recapitulates all aspects of the disease in humans. The continuous refinement and development of other options of in vivo models are opportune, especially ones that are carried out at BSL-2 (Biosafety Level 2) laboratories. In this study, we investigated the suitability of the intranasal infection with the murine betacoronavirus MHV-3 to recapitulate multiple aspects of the pathogenesis of COVID-19 in C57BL/6J mice. We demonstrate that MHV-3 replicated in lungs 1 day after inoculation and triggered respiratory inflammation and dysfunction. This MHV-model of infection was further applied to highlight the critical role of TNF in cytokine-mediated coronavirus pathogenesis. Blocking TNF signaling by pharmacological and genetic strategies greatly increased the survival time and reduces lung injury of MHV-3-infected mice. In vitro studies showed that TNF blockage decreased SARS-CoV-2 replication in human epithelial lung cells and resulted in the lower release of IL-6 and IL-8 cytokines beyond TNF itself. Taken together, our results demonstrate that this model of MHV infection in mice is a useful BSL-2 screening platform for evaluating pathogenesis for human coronaviruses infections, such as COVID-19.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Ana Claudia dos Santos Pereira Andrade", + "author_inst": "Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" + }, + { + "author_name": "Gabriel Henrique Campolina-Silva", + "author_inst": "Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" + }, + { + "author_name": "Celso Martins Queiroz-Junior", + "author_inst": "Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" + }, + { + "author_name": "Leonardo Camilo de Oliveira", + "author_inst": "Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" + }, + { + "author_name": "Larisse de Souza Barbosa Lacerda", + "author_inst": "Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" + }, + { + "author_name": "Jordane Clarisse Pimenta", + "author_inst": "Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" + }, + { + "author_name": "Filipe Resende Oliveira de Souza", + "author_inst": "Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" + }, + { + "author_name": "Ian de Meira Chaves", + "author_inst": "Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" + }, + { + "author_name": "Ingredy Beatriz Passos", + "author_inst": "Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" + }, + { + "author_name": "Danielle Cunha Teixeira", + "author_inst": "Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" + }, + { + "author_name": "Paloma Graziele Bittencourt-Silva", + "author_inst": "Department of Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil." + }, + { + "author_name": "Priscila Aparecida Costa Valadao", + "author_inst": "Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" + }, + { + "author_name": "Leonardo Rossi-Oliveira", + "author_inst": "Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" + }, + { + "author_name": "Maisa Mota Antunes", + "author_inst": "Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" + }, + { + "author_name": "Andre Felipe Almeida Figueiredo", + "author_inst": "Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" + }, + { + "author_name": "Natalia Teixeira Wnuk", + "author_inst": "Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" + }, + { + "author_name": "Jairo R Temerozo", + "author_inst": "Laboratory on Thymus Research, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, RJ, Brazil, National Institute for Science and Technology on Neuroimmunomodulati" + }, + { + "author_name": "Andre Costa Ferreira", + "author_inst": "Laboratorio de Pesquisas Pre clinicas, Universidade Iguacu, Rio de Janeiro, RJ, Brazil; Oswaldo Cruz Foundation Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil" + }, + { + "author_name": "Allysson Cramer", + "author_inst": "Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" + }, + { + "author_name": "Cleida Aparecida Oliveira", + "author_inst": "Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" + }, + { + "author_name": "Ricardo Duraes-Carvalho", + "author_inst": "Laboratory of Virology, Universidade Estadual de Campinas UNICAMP, Campinas, Sao Paulo, Brazil" + }, + { + "author_name": "Clarice Weis Arns", + "author_inst": "Laboratory of Virology, Universidade Estadual de Campinas UNICAMP, Campinas, Sao Paulo, Brazil" + }, + { + "author_name": "Pedro Pires Goulart Guimaraes", + "author_inst": "Department of Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" + }, + { + "author_name": "Guilherme Mattos Jardim Costa", + "author_inst": "Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" + }, + { + "author_name": "Gustavo Batista de Menezes", + "author_inst": "Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" + }, + { + "author_name": "Cristina Guatimosim", + "author_inst": "Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" + }, + { + "author_name": "Glauber Santos Ferreira da Silva", + "author_inst": "Department of Physiology and Biophysics, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil." + }, + { + "author_name": "Thiago Moreno L. Souza", + "author_inst": "National Institute for Science and Technology on Innovation on Diseases of Neglected Populations (INCT/IDNP), Center for Technological Development in Health (CD" + }, + { + "author_name": "Breno Rocha Barrioni", + "author_inst": "Department of Metallurgical Engineering and Materials, Federal University of Minas Gerais, School of Engineering, Belo Horizonte, Brazil" + }, + { + "author_name": "Marivalda de Magalhaes Pereira", + "author_inst": "Department of Metallurgical Engineering and Materials, Federal University of Minas Gerais, School of Engineering, Belo Horizonte, Brazil" + }, + { + "author_name": "Lirlandia Pires de Sousa", + "author_inst": "Department of Clinical and Toxicological Analysis, Faculty of Pharmacy, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil." + }, + { + "author_name": "Mauro Martins Teixeira", + "author_inst": "2)\tDepartment of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" + }, + { + "author_name": "Vivian Vasconcelos Costa", + "author_inst": "Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.05.21.21257574", "rel_title": "Mortality audit of cancer patients with SARS-CoV-2 positivity or COVID-19", @@ -764096,41 +763381,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.05.28.446020", - "rel_title": "Evaluating the risk of SARS-CoV-2 transmission to bats using a decision analytical framework", - "rel_date": "2021-05-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.28.446020", - "rel_abs": "Preventing wildlife disease outbreaks is a priority issue for natural resource agencies, and management decisions can be urgent, especially in epidemic circumstances. With the emergence of SARS-CoV-2, wildlife agencies were concerned whether the activities they authorize might increase the risk of viral transmission from humans to North American bats but had a limited amount of time in which to make decisions. We provide a description of how decision analysis provides a powerful framework to analyze and re-analyze complex natural resource management problems as knowledge evolves. Coupled with expert judgment and avenues for the rapid release of information, risk assessment can provide timely scientific information for evolving decisions. In April 2020, the first rapid risk assessment was conducted to evaluate the risk of transmission of SARS-CoV-2 from humans to North American bats.\n\nBased on the best available information, and relying heavily on formal expert judgment, the risk assessment found a small possibility of transmission during summer work activities. Following that assessment, additional knowledge and data emerged, such as bat viral challenge studies, that further elucidated the risks of human-to-bat transmission and culminated in a second risk assessment in the fall of 2020. We update the first SARS-CoV-2 risk assessment with new estimates of little brown bat (Myotis lucifugus) susceptibility and new management alternatives, using findings from the prior two risk assessments and other empirical studies. We highlight the strengths of decision analysis and expert judgment not only to frame decisions and produce useful science in a timely manner, but also to serve as a framework to reassess risk as understanding improves. For SARS-CoV-2 risk, new knowledge led to an 88% decrease in the median number of bats estimated to be infected per 1000 encountered when compared to earlier results. The use of facemasks during, or a negative COVID-19 test prior to, bat encounters further reduced those risks. Using a combination of decision analysis, expert judgment, rapid risk assessment, and efficient modes of information distribution, we provide timely science support to decision makers for summer bat work in North America.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Jonathan D Cook", - "author_inst": "U.S. Geological Survey" - }, - { - "author_name": "Evan H. Cambell Grant", - "author_inst": "U.S. Geological Survey" - }, - { - "author_name": "Jeremy T. H. Coleman", - "author_inst": "U.S. Fish and Wildlife Service" - }, - { - "author_name": "Jonathan M. Sleeman", - "author_inst": "U.S. Geological Survey" - }, - { - "author_name": "Michael C. Runge", - "author_inst": "U.S. Geological Survey" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "ecology" - }, { "rel_doi": "10.1101/2021.05.28.446179", "rel_title": "Biophysical characterization of the SARS-CoV-2 E protein", @@ -765077,6 +764327,49 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.05.27.445985", + "rel_title": "SARS-CoV-2 inactivation by human defensin HNP1 and retrocyclin RC-101", + "rel_date": "2021-05-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.27.445985", + "rel_abs": "Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 is an enveloped virus responsible for the COVID-19 respiratory disease pandemic. While induction of adaptive antiviral immunity via vaccination holds promise for combatting the pandemic, the emergence of new potentially more transmissible and vaccine-resistant variants of SARS-CoV-2 is an ever-present threat. Thus, it remains essential to better understand innate immune mechanisms that are active against the virus. One component of the innate immune system with broad anti-pathogen, including antiviral, activity is a group of cationic immune peptides termed defensins. The defensins ability to neutralize enveloped and non-enveloped viruses and to inactivate numerous bacterial toxins correlate with their ability to promote the unfolding of thermodynamically pliable proteins. Accordingly, we found that human neutrophil a-defensin HNP1 and retrocyclin RC-101 destabilize SARS-CoV-2 Spike protein and interfere with Spike-mediated membrane fusion and SARS-CoV-2 infection in cell culture. We show that HNP1 binds to Spike with submicromolar affinity. Although binding of HNP1 to serum albumin is more than 20-fold weaker, serum reduces the anti-SARS-CoV-2 activity of HNP1. At high concentrations of HNP1, its ability to inactivate the virus was preserved even in the presence of serum. These results suggest that specific a- and 8-defensins may be valuable tools in developing SARS-CoV-2 infection prevention strategies.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Elena Kudryashova", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Ashley Zani", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Geraldine Vilmen", + "author_inst": "National Cancer Institute, NIH" + }, + { + "author_name": "Amit Sharma", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Wuyuan Lu", + "author_inst": "Fudan University, Shanghai, China" + }, + { + "author_name": "Jacob S. Yount", + "author_inst": "The Ohio State University" + }, + { + "author_name": "Dmitri S. Kudryashov", + "author_inst": "The Ohio State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.05.26.445838", "rel_title": "Reduced sensitivity of infectious SARS-CoV-2 variant B.1.617.2 to monoclonal antibodies and sera from convalescent and vaccinated individuals", @@ -765625,109 +764918,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.25.21257828", - "rel_title": "Correlation of the commercial anti-SARS-CoV-2 receptor binding domain antibody test with the chemiluminescent reduction neutralizing test and possible detection of antibodies to emerging variants", - "rel_date": "2021-05-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.25.21257828", - "rel_abs": "BackgroundSerological tests are beneficial for recognizing the immune response against SARS-CoV-2. To identify protective immunity, optimization of the chemiluminescent reduction neutralizing test (CRNT), using pseudotyped SARS-CoV-2, is critical. Whether commercial antibody tests are comparably accurate is unknown.\n\nMethodsSerum samples collected before variants were locally found were obtained from confirmed COVID-19 patients (n = 74), confirmed non-COVID-19 individuals (n = 179), and unscreened individuals (suspected healthy individuals, n = 229). The convalescent phase was defined as the period after day 10 from disease onset. The CRNT against pseudotyped viruses displaying the wild-type spike protein and a commercially available anti-receptor binding domain (RBD) antibody test were assayed. The CRNT was also assayed, using South African (SA) and United Kingdom (UK)-derived variants.\n\nResultsThe CRNT (cut off value, 50% inhibition) and the anti-RBD antibody test (cut off value, 0.8 U/mL) concurred regarding symptomatic COVID-19 patients in the convalescent phase and clearly differentiated between patients and suspected healthy individuals (sensitivity; 95.8% and 100%, specificity; 99.1% and 100%, respectively). Anti-RBD antibody test results correlated with neutralizing titer (r = 0.47, 95% CI 0.20-0.68). Compared with the wild-type, CRNT reduction was observed for the SA and UK-derived variants. Of the samples with [≥]100 U/mL by the anti-RBD antibody test, 77.8% and 88.9% showed [≥]50% neutralization against the UK and the SA variants, respectively.\n\nConclusionThe CRNT and commercial anti-RBD antibody test effectively classified convalescent COVID-19 patients. The strong positive results using the commercial antibody test can reflect neutralizing activity against emerging variants.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Yoshitomo Morinaga", - "author_inst": "University of Toyama" - }, - { - "author_name": "Hideki Tani", - "author_inst": "Toyama Institute of Health" - }, - { - "author_name": "Yasushi Terasaki", - "author_inst": "Toyama City Hospital" - }, - { - "author_name": "Satoshi Nomura", - "author_inst": "Toyama City Hospital" - }, - { - "author_name": "Hitoshi Kawasuji", - "author_inst": "Toyama University Graduate School of Medicine and Pharmaceutical Sciences" - }, - { - "author_name": "Takahisa Shimada", - "author_inst": "Toyama Institute of Health" - }, - { - "author_name": "Emiko Igarashi", - "author_inst": "Toyama Institute of Health" - }, - { - "author_name": "Yumiko Saga", - "author_inst": "Toyama Institute of Health" - }, - { - "author_name": "Yoshihiro Yoshida", - "author_inst": "University of Toyama" - }, - { - "author_name": "Rei Yasukochi", - "author_inst": "University of Toyama" - }, - { - "author_name": "Makito Kaneda", - "author_inst": "University of Toyama" - }, - { - "author_name": "Yushi Murai", - "author_inst": "University of Toyama" - }, - { - "author_name": "Akitoshi Ueno", - "author_inst": "University of Toyama" - }, - { - "author_name": "Yuki Miyajima", - "author_inst": "University of Toyama" - }, - { - "author_name": "Yasutaka Fukui", - "author_inst": "University of Toyama" - }, - { - "author_name": "Kentaro Nagaoka", - "author_inst": "University of Toyama" - }, - { - "author_name": "Chikako Ono", - "author_inst": "Osaka University" - }, - { - "author_name": "Yoshiharu Matsuura", - "author_inst": "Osaka University" - }, - { - "author_name": "Takashi Fujimura", - "author_inst": "Toyama City Hospital" - }, - { - "author_name": "Yoichi Ishida", - "author_inst": "Toyama City Hospital" - }, - { - "author_name": "Kazunori Oishi", - "author_inst": "Toyama Institute of Health" - }, - { - "author_name": "Yoshihiro Yamamoto", - "author_inst": "Toyama University Graduate School of Medicine and Pharmaceutical Sciences" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.25.21257823", "rel_title": "Estimating the wave 1 and wave 2 infection fatality rates from SARS-CoV-2 in India", @@ -767363,6 +766553,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.05.26.445843", + "rel_title": "Variable Induction of Pro-inflammatory Cytokines by Commercial SARS CoV-2 Spike Protein Reagents: Potential Impacts of LPS on In Vitro Modeling and Pathogenic Mechanisms In Vivo", + "rel_date": "2021-05-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.26.445843", + "rel_abs": "Proinflammatory cytokine production following infection with severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) is associated with poor clinical outcomes. Like SARS CoV-1, SARS CoV-2 enters host cells via its spike protein, which attaches to angiotensin-converting enzyme 2 (ACE2). As SARS CoV-1 spike protein is reported to induce cytokine production, we hypothesized that this pathway could be a shared mechanism underlying pathogenic immune responses. We herein compared the capabilities of Middle East Respiratory Syndrome (MERS), SARS CoV-1 and SARS CoV-2 spike proteins to induce cytokine expression in human peripheral blood mononuclear cells (PBMC). We observed that only specific commercial lots of SARS CoV-2 induce cytokine production. Surprisingly, recombinant SARS CoV-2 spike proteins from different vendors and batches exhibited different patterns of cytokine induction, and these activities were not inhibited by blockade of spike protein-ACE2 binding using either soluble ACE2 or neutralizing anti-S1 antibody. Moreover, commercial spike protein reagents contained varying levels of endotoxin, which correlated directly with their abilities to induce cytokine production. The lipopolysaccharide (LPS) inhibitor, polymyxin B, blocked this cytokine induction activity. In addition, SARS CoV-2 spike protein avidly bound soluble LPS in vitro, rendering it a cytokine inducer. These results not only suggest caution in monitoring the purity of SARS CoV-2 spike protein reagents, but they indicate the possibility that interactions of SARS CoV-2 spike protein with LPS from commensal bacteria in virally infected mucosal tissues could promote pathogenic inflammatory cytokine production.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Weiming Ouyang", + "author_inst": "FDA" + }, + { + "author_name": "Tao Xie", + "author_inst": "FDA" + }, + { + "author_name": "Hui Fang", + "author_inst": "FDA" + }, + { + "author_name": "Chunling Gao", + "author_inst": "FDA" + }, + { + "author_name": "Tzanko Stantchev", + "author_inst": "FDA" + }, + { + "author_name": "Kathleen A. Clouse", + "author_inst": "FDA" + }, + { + "author_name": "Kun Yuan", + "author_inst": "FDA" + }, + { + "author_name": "Tongzhong Ju", + "author_inst": "FDA" + }, + { + "author_name": "David M. Frucht", + "author_inst": "FDA" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.05.26.445422", "rel_title": "A modular molecular framework for quickly estimating the binding affinity of the spike protein of SARS-CoV-2 variants for ACE2, in presence of mutations at the spike receptor binding domain.", @@ -767799,37 +767040,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.21.21257612", - "rel_title": "COVID-19 vaccination hesitancy model: The impact of vaccine education on controlling the outbreak in the United States", - "rel_date": "2021-05-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.21.21257612", - "rel_abs": "The coronavirus outbreak continues to pose a significant challenge to human lives globally. Many efforts have been made to develop vaccines to combat this virus. However, with the arrival of the COVID-19 vaccine, there is hesitancy and a mixed reaction toward getting the vaccine. We develop a mathematical model to analyze and investigate the impacts of education on individuals hesitant to get vaccinated. The findings indicate that vaccine education can substantially minimize the daily cumulative cases and deaths of COVID-19 in the United States. The results also show that vaccine education significantly increases the number of willing susceptible individuals, and with a high vaccination rate and vaccine effectiveness, the outbreak can be controlled in the US.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Bismark Oduro", - "author_inst": "California University of Pennsylvania" - }, - { - "author_name": "Attou Miloua", - "author_inst": "California University of PA" - }, - { - "author_name": "Ofosuhene O. Apenteng", - "author_inst": "National Food Institute, Technical University of Denmark" - }, - { - "author_name": "Prince P. Osei", - "author_inst": "University of Haifa, Mount Carmel" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.18.21257385", "rel_title": "Mask mandate and use efficacy in state-level COVID-19 containment", @@ -768761,6 +767971,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.05.24.21257710", + "rel_title": "Nursing students' attitudes, knowledge, and willingness to receive the COVID-19 vaccine: A cross-sectional study", + "rel_date": "2021-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.24.21257710", + "rel_abs": "AimTo investigate nursing students konwledge, attitudes and willingness to receive the COVID-19 vaccine, and the influencing factors.\n\nBackgroundVaccination is one of the effective measures to prevent COVID-19, but the vaccination acceptance varies across countries and populations. As reserve nurses, nursing students have both the professionalism of medical personnel and the special characteristics of school students, their attitudes, knowledge, and willingness to receive the COVID-19 vaccine may greatly affect the vaccine acceptance of the population now and in the future. But little research has been done on vaccine acceptance among nursing students.\n\nDesignA cross-sectional survey of nursing students was conducted via online questionnaires in March 2021.\n\nMethodsDescriptive statistics, independent sample t tests/one-way ANOVA (normal distribution), Mann-Whitney U tests/Kruskal-Wallis H tests (skewness distribution) and multivariate linear regression were performed.\n\nResultsThe score rate of attitude, knowledge and vaccination willingness were 70.07%, 80.70% and 84.38% respectively. Attitude was significantly influenced by family economic conditions and whether a family member had been vaccinated. The main factors influencing knowledge were gender, grade and academic background. In terms of willingness, gender, academic background, visits to risk areas, whether family members were vaccinated, and whether they had side effects were significant influencing factors.\n\nConclusionsThe vaccine acceptance of nursing students was fair. Greater focus needed to be placed on the males, those of younger age, with a science background, and having low grades, as well as on students whose family members had not received the COVID-19 vaccine or had side effects from the vaccine. Targeted intervention strategies were recommended to improve vaccination rates.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Ning Jiang", + "author_inst": "Shandong First Medical University" + }, + { + "author_name": "Baojian Wei", + "author_inst": "School of Nursing, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian 271000, Shandong, China." + }, + { + "author_name": "Hua Lin", + "author_inst": "School of Nursing, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian 271000, Shandong, China." + }, + { + "author_name": "Youjuan Wang", + "author_inst": "Shandong First Medical University & Shandong Academy of Medical Sciences, Taian 271000, Shandong, China." + }, + { + "author_name": "Shouxia Chai", + "author_inst": "School of Nursing, Hubei University of Medicine, Shiyan 442000, Hubei, China." + }, + { + "author_name": "Wei Liu", + "author_inst": "School of Nursing, Shandong First Medical University & Shandong Academy of Medical Sciences, Taian 271000, Shandong, China." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "nursing" + }, { "rel_doi": "10.1101/2021.05.23.21257686", "rel_title": "Addressing anti-syncytin antibody levels, and fertility and breastfeeding concerns, following BNT162B2 COVID-19 mRNA vaccination", @@ -769545,33 +768794,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.05.24.445517", - "rel_title": "Evolutionary Inference Predicts Novel ACE2 Protein Interactions Relevant to COVID-19 Pathologies", - "rel_date": "2021-05-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.24.445517", - "rel_abs": "Angiotensin-converting enzyme 2 (ACE2) is the cell receptor that the coronavirus SARS-CoV-2 binds to and uses to enter and infect human cells. COVID-19, the pandemic disease caused by the coronavirus, involves diverse pathologies beyond those of a respiratory disease, including micro-thrombosis (micro-clotting), cytokine storms, and inflammatory responses affecting many organ systems. Longer-term chronic illness can persist for many months, often well after the pathogen is no longer detected. A better understanding of the proteins that ACE2 interacts with can reveal information relevant to these disease manifestations and possible avenues for treatment. We have undertaken an approach to predict candidate ACE2 interacting proteins which uses evolutionary inference to identify a set of mammalian proteins that \"coevolve\" with ACE2. The approach, called evolutionary rate correlation (ERC), detects proteins that show highly correlated evolutionary rates during mammalian evolution. Such proteins are candidates for biological interactions with the ACE2 receptor. The approach has uncovered a number of key ACE2 protein interactions of potential relevance to COVID-19 pathologies. Some proteins have previously been reported to be associated with severe COVID-19, but are not currently known to interact directly with ACE2, while additional predicted novel ACE2 interactors are of potential relevance to the disease. Using reciprocal rankings of protein ERCs, we have identified strongly interconnected ACE2 associated protein networks relevant to COVID-19 pathologies. ACE2 has clear connections to coagulation pathway proteins, such as Coagulation Factor V and fibrinogen components FGG, FGB, and FGA, the latter possibly mediated through ACE2 connections to Clusterin (which clears misfolded extracellular proteins) and GPR141 (whose functions are relatively unknown). ACE2 also connects to proteins involved in cytokine signaling and immune response (e.g. IFNAR2, XCR1, and TLR8), and to Androgen Receptor (AR). The ERC prescreening approach has also elucidated possible functions for previously uncharacterized proteins and possible new functions for well-characterized ones. Suggestions are made for the validation of ERC predicted ACE2 protein interactions. We propose that ACE2 has novel protein interactions that are disrupted during SARS-CoV-2 infection, contributing to the spectrum of COVID-19 pathologies.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Austin Alves Varela", - "author_inst": "University of Rochester" - }, - { - "author_name": "Sammy Cheng", - "author_inst": "University of Rochester" - }, - { - "author_name": "John Haynes Werren", - "author_inst": "University of Rochester" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.05.24.445532", "rel_title": "Infection of brain pericytes underlying neuropathology of COVID-19 patients", @@ -770875,6 +770097,57 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.05.20.21257545", + "rel_title": "Are we allowed to visit now? Concerns and issues surrounding vaccination and infection risks in UK care homes during COVID-19", + "rel_date": "2021-05-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.20.21257545", + "rel_abs": "BackgroundVaccination uptake in the UK and increased care home testing are likely affecting care home visitation. With scant scientific evidence to date, the aim of this longitudinal qualitative study was to explore the impact of both (vaccination and testing) on the conduct and experiences of care home visits.\n\nMethodsFamily carers of care home residents with dementia and care home staff from across the UK took part in baseline (October/November 2020) and follow-up interviews (March 2021). Public advisers were involved in all elements of the research. Data were analysed using thematic analysis.\n\nResultsAcross 62 baseline and follow-up interviews with family carers (n=26; 11) and care home staff (n=16; 9), five core themes were developed: Delayed and inconsistent offers of face-to-face visits; Procedures and facilitation of visits; Frustration and anger among family carers; Variable uptake of the COVID-19 vaccine; Misinformation, education, and free choice. The variable uptake in staff, compared to family carers, was a key factor seemingly influencing visitation, with a lack of clear guidance leading care homes to implement infection control measures and visitation rights differently.\n\nConclusionsWe make five recommendations in this paper to enable improved care home visitation in the ongoing, and in future, pandemics. Visits need to be enabled and any changes to visiting rights must be used as a last resort, reviewed regularly in consultation with residents and carers and restored as soon as possible as a top priority, whilst more education needs to be provided surrounding vaccination for care home staff.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Clarissa Marie Giebel", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Kerry Hanna", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Jacqueline Cannon", + "author_inst": "Lewy Body Society" + }, + { + "author_name": "Paul Marlow", + "author_inst": "NIHR ARC NWC" + }, + { + "author_name": "Hilary Tetlow", + "author_inst": "NIHR ARC NWC" + }, + { + "author_name": "Stephen Mason", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Justine Shenton", + "author_inst": "Sefton Advocacy" + }, + { + "author_name": "Manoj Rajagopal", + "author_inst": "Lancashire & South Cumbria NHS Trust" + }, + { + "author_name": "Mark Gabbay", + "author_inst": "University of Liverpool" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "geriatric medicine" + }, { "rel_doi": "10.1101/2021.05.20.21257536", "rel_title": "RT-qPCR detection of SARS-CoV-2 mutations S 69-70 del, S N501Y and N D3L associated with variants of concern in Canadian wastewater samples", @@ -771367,57 +770640,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2021.05.20.21256954", - "rel_title": "Efficacy and safety of novel probiotic formulation in adult Covid19 outpatients: a randomized, placebo-controlled clinical trial", - "rel_date": "2021-05-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.20.21256954", - "rel_abs": "BackgroundProbiotics have been proposed as adjuvants for Coronavirus Disease 2019 (Covid19) but randomized controlled trials (RCT) are lacking.\n\nMethodsSingle-center, quadruple-blinded RCT. Symptomatic Covid 19 outpatients (aged 18 to 60 years) with positive SARS-CoV2 nucleic acids test were randomized to active (n=150; [≥]2x109 colony-forming units (CFU) of probiotic strains Lactiplantibacillus plantarum KABP022, KABP023 and KAPB033, plus strain Pediococcus acidilactici KABP021) or placebo (n=150), take orally once daily for 30 days. Oral acetaminophen was allowed and controlled as co-intervention. Primary endpoint included: i) proportion of patients in complete remission (both symptoms and nucleic acids test) or progressing to moderate or severe disease with hospitalization; ii) death rate and duration on Intensive Care Unit (ICU). Safety was assessed in all patients. This study is registered at ClinicalTrials.gov (NCT04517422).\n\nFindings300 subjects were randomized (median age 37.0 years [range 18 to 60], 161 [53.7%] women, 126 [42.0%] having known metabolic risk factors), and 293 completed the study (97.7%). Remission was achieved by 78 of 147 (53.1%) in the active group compared to 41 of 146 (28.1%) in placebo (P<0.0001; ARR=25.0% [95%CI 14.1-35.9%]), still significant after multiplicity correction for the primary endpoint. No hospitalizations or deaths occurred during the study, precluding the assessment of efficacy on these endpoints. No serious adverse events occurred during the study. Replication studies with this probiotic formula are warranted.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Pedro Gutierrez-Castrellon", - "author_inst": "Centro de Investigacion Translacional en Ciencias de la Salud, Hospital General Dr. Manuel Gea Gonzalez (Mexico City, MEXICO)" - }, - { - "author_name": "Tania Gandara-Marti", - "author_inst": "Centro de Investigacion Translacional en Ciencias de la Salud, Hospital General Dr. Manuel Gea Gonzalez (Mexico City, MEXICO)" - }, - { - "author_name": "Ana Teresa Abreu y Abreu", - "author_inst": "Hospital Angeles Pedregal (Mexico City, MEXICO)" - }, - { - "author_name": "Cesar D Nieto-Rufino", - "author_inst": "Centro de Investigacion Translacional en Ciencias de la Salud, Hospital General Dr. Manuel Gea Gonzalez (Mexico City, MEXICO)" - }, - { - "author_name": "Eduardo Lopez-Orduna", - "author_inst": "DiagnoMol SA (Mexico City, MEXICO)" - }, - { - "author_name": "Irma Jimenez-Escobar", - "author_inst": "Centro de Investigacion Translacional en Ciencias de la Salud, Hospital General Dr. Manuel Gea Gonzalez (Mexico City, MEXICO)" - }, - { - "author_name": "Carlos Jimenez-Gutierrez", - "author_inst": "Centro de Investigacion Translacional en Ciencias de la Salud, Hospital General Dr. Manuel Gea Gonzalez (Mexico City, MEXICO)" - }, - { - "author_name": "Gabriel Lopez-Vazquez", - "author_inst": "International Scientific Council for Probiotics (Mexico City, MEXICO)" - }, - { - "author_name": "Jordi Espadaler-Mazo", - "author_inst": "AB-BIOTICS SA (Barcelona, SPAIN)" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.20.21257520", "rel_title": "ACTIVATE-2: A DOUBLE-BLIND RANDOMIZED TRIAL OF BCG VACCINATION AGAINST COVID19 IN INDIVIDUALS AT RISK", @@ -772857,6 +772079,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.21.21257589", + "rel_title": "The risk of SARS-CoV-2 outbreaks in low prevalence settings following the removal of travel restrictions", + "rel_date": "2021-05-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.21.21257589", + "rel_abs": "Countries around the world have introduced travel restrictions to reduce SARS-CoV-2 transmission. As vaccines are gradually rolled out, attention has turned to when travel restrictions and other non-pharmaceutical interventions (NPIs) can be relaxed. Here, using SARS-CoV-2 as a case study, we develop a mathematical branching process model to assess the risk that, following the removal of NPIs, cases introduced into new locations initiate a local outbreak. Our model accounts for changes in background population immunity due to vaccination. We consider two locations in which the vaccine rollout has progressed quickly - specifically, the Isle of Man (a British crown dependency in the Irish Sea) and the country of Israel. Rather than aiming to make exact quantitative predictions about the outbreak risk in different locations, we instead use data from these locations to demonstrate the general principle that the outbreak risk is unlikely to be eliminated completely when travel restrictions and other NPIs are removed in low prevalence settings. This conclusion holds even once vaccine programmes are completed. Key factors underlying these results are the potential for transmission even following vaccination, incomplete vaccine uptake, and the recent emergence of SARS-CoV-2 variants with increased transmissibility. Combined, these factors suggest that when travel restrictions are relaxed, it will still be necessary to implement surveillance of incoming passengers to identify infected individuals quickly. This measure, as well as tracing and testing (and/or isolating) contacts of detected infected passengers, should remain in place to suppress potential outbreaks until case numbers globally are reduced.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Rahil Sachak-Patwa", + "author_inst": "University of Oxford" + }, + { + "author_name": "Helen M Byrne", + "author_inst": "University of Oxford" + }, + { + "author_name": "Louise Dyson", + "author_inst": "University of Warwick" + }, + { + "author_name": "Robin N Thompson", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.20.21257517", "rel_title": "Public Health and Health Systems Impacts of SARS-CoV-2 Variants of Concern: A Rapid Scoping Review", @@ -773565,85 +772818,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.19.21257439", - "rel_title": "Rapid And high throughput RT-qPCR assay for identification and differentiation between SARS-CoV-2 variants B.1.1.7 and B.1.351", - "rel_date": "2021-05-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.19.21257439", - "rel_abs": "Emerging SARS-CoV-2 (SC-2) variants with increased infectivity and vaccine resistance are of major concern. Rapid identification of such variants is important for the public health activities and provide valuable data for epidemiological and policy decision making. We developed a multiplex quantitative RT-qPCR (qPCR) assay that can specifically identify and differentiate between the emerging B.1.1.7 and B.1.351 SC-2 variants. In a single assay, we combined four reactions: one that detects SC-2 RNA independently of the strain, one that detects the D3L mutation, which is specific to variant B.1.1.7, and one that detects the 242-244 deletion, which is specific to variant B.1.351. The fourth reaction identifies human RNAseP gene, serving as an endogenous control for RNA extraction integrity. We show that the strain-specific reactions target mutations that are strongly associated with the target variants, and not with other major known variants. The assays specificity was tested against a panel of respiratory pathogens (n=16), showing high specificity towards SC-2 RNA. The assays sensitivity was assessed using both In-vitro transcribed RNA and clinical samples, and was determined to be between 20 and 40 viral RNA copies per reaction. The assay performance was corroborated with Sanger and whole genome sequencing, showing complete agreement with the sequencing results. The new assay is currently implemented in the routine diagnostic work at the Central Virology Laboratory, and may be used in other laboratories to facilitate the diagnosis of these major worldwide circulating SC-2 variants.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Oran Erster", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - }, - { - "author_name": "Ella Mendelson", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - }, - { - "author_name": "Virginia Levy", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - }, - { - "author_name": "Areej Kabat", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - }, - { - "author_name": "Batya Mannasse", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - }, - { - "author_name": "Hadar Asraf", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - }, - { - "author_name": "Roberto Azar", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - }, - { - "author_name": "Yaniv Ali", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - }, - { - "author_name": "Rachel Shirazi", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - }, - { - "author_name": "Efrat Bucris", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - }, - { - "author_name": "Dana Bar-Ilan", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - }, - { - "author_name": "Orna Mor", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - }, - { - "author_name": "Michal Mandelboim", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - }, - { - "author_name": "Danit Sofer", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - }, - { - "author_name": "Shai Fleishon", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - }, - { - "author_name": "Neta S Zukerman", - "author_inst": "Central Virology Laboratory, Public Health Services, Ministry of Health, Chaim Sheba Medical Center, Ramat Gan, Israel" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.19.21257473", "rel_title": "Characterization of the Second Wave of the COVID-19 Pandemic in India: A Google Trends Analysis", @@ -774851,6 +774025,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "endocrinology" }, + { + "rel_doi": "10.1101/2021.05.20.21257556", + "rel_title": "A 2SIR-VD Model for Optimizing Geographical COVID-19 Vaccine Distribution in the Philippines", + "rel_date": "2021-05-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.20.21257556", + "rel_abs": "COVID-19 is a novel respiratory disease first identified in Wuhan, China, that is caused by the novel coronavirus, SARS-CoV-2. It has triggered a global pandemic of historic proportions. The government of the Philippines began its national vaccine drive on March 1, 2021, with the goal of vaccinating seventy million of its citizens by the end of the calendar year. To determine the optimum geographical distribution strategy in the Philippines for the limited supply of vaccines that is currently available, we developed and adapted a basic SIR model that allows us to understand the evolution of a pandemic when public health authorities are vaccinating two susceptible populations within a country with different vaccine rates. Our analysis with our 2SIR-VD model revealed that prioritizing vaccine deployment to the National Capital Region (NCR) of the Philippines minimized the number of COVID-19 cases in the country. We therefore recommend deploying 90% of the available vaccine supply to the NCR to mitigate viral transmission there. The remaining 10% would allow the rest of the archipelago to vaccinate all of their senior citizens, thus shielding this vulnerable population against severe disease and death from COVID-19.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Allan Paolo Almajose", + "author_inst": "University of the Philippines - Diliman" + }, + { + "author_name": "Angus White", + "author_inst": "Providence College" + }, + { + "author_name": "Chelsea Diego", + "author_inst": "University of Santo Tomas" + }, + { + "author_name": "Red Lazaro", + "author_inst": "University of Santo Tomas" + }, + { + "author_name": "Nicanor Austriaco", + "author_inst": "University of Santo Tomas" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.19.21257474", "rel_title": "Short Telomeres and a T-Cell Shortfall in COVID-19: The Aging Effect", @@ -775319,37 +774528,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.05.21.445090", - "rel_title": "Water-triggered, irreversible conformational change of SARS-CoV-2 main protease on passing from the solid state to aqueous solution", - "rel_date": "2021-05-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.21.445090", - "rel_abs": "The main protease from SARS-CoV-2 is a homodimer. Yet, a recent 0.1 ms long molecular dynamics simulation shows that it readily undergoes a symmetry breaking event on passing from the solid state to the aqueous solution. As a result, the subunits present distinct conformations of the binding pocket. By analysing this long time simulation, here we uncover a previously unrecognised role of water molecules in triggering the transition. Interestingly, each subunit presents a different collection of long-lived water molecules. Enhanced sampling methods performed here, along with machine learning approaches, further establish that the transition to the asymmetric state is essentially irreversible.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Narjes Ansari", - "author_inst": "Italian Institute of Technology" - }, - { - "author_name": "Valerio Rizzi", - "author_inst": "Italian Institute of Technology" - }, - { - "author_name": "Paolo Carloni", - "author_inst": "Forschungszentrum Julich" - }, - { - "author_name": "Michele Parrinello", - "author_inst": "Italian Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2021.05.20.444918", "rel_title": "Structure and dynamics of RNA guanine quadruplexes in SARS-CoV-2 genome. Original strategies against emerging viruses", @@ -776697,6 +775875,105 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.05.20.444848", + "rel_title": "Alum:CpG adjuvant enables SARS-CoV-2 RBD-induced protection in aged mice and synergistic activation of human elder type 1 immunity", + "rel_date": "2021-05-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.20.444848", + "rel_abs": "Global deployment of vaccines that can provide protection across several age groups is still urgently needed to end the COVID-19 pandemic especially for low- and middle-income countries. While vaccines against SARS-CoV-2 based on mRNA and adenoviral-vector technologies have been rapidly developed, additional practical and scalable SARS-CoV-2 vaccines are needed to meet global demand. In this context, protein subunit vaccines formulated with appropriate adjuvants represent a promising approach to address this urgent need. Receptor-binding domain (RBD) is a key target of neutralizing antibodies (Abs) but is poorly immunogenic. We therefore compared pattern recognition receptor (PRR) agonists, including those activating STING, TLR3, TLR4 and TLR9, alone or formulated with aluminum hydroxide (AH), and benchmarked them to AS01B and AS03-like emulsion-based adjuvants for their potential to enhance RBD immunogenicity in young and aged mice. We found that the AH and CpG adjuvant formulation (AH:CpG) demonstrated the highest enhancement of anti-RBD neutralizing Ab titers in both age groups ([~]80-fold over AH), and protected aged mice from the SARS-CoV-2 challenge. Notably, AH:CpG-adjuvanted RBD vaccine elicited neutralizing Abs against both wild-type SARS-CoV-2 and B.1.351 variant at serum concentrations comparable to those induced by the authorized mRNA BNT162b2 vaccine. AH:CpG induced similar cytokine and chemokine gene enrichment patterns in the draining lymph nodes of both young adult and aged mice and synergistically enhanced cytokine and chemokine production in human young adult and elderly mononuclear cells. These data support further development of AH:CpG-adjuvanted RBD as an affordable vaccine that may be effective across multiple age groups.\n\nOne Sentence SummaryAlum and CpG enhance SARS-CoV-2 RBD protective immunity, variant neutralization in aged mice and Th1-polarizing cytokine production by human elder leukocytes.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Marisa E. McGrath", + "author_inst": "Department of Microbiology and Immunology, University of Maryland School of Medicine" + }, + { + "author_name": "Robert E. Haupt", + "author_inst": "Department of Microbiology and Immunology, University of Maryland School of Medicine" + }, + { + "author_name": "Hyuk-Soo Seo", + "author_inst": "Department of Cancer Biology, Dana-Farber Cancer Institute" + }, + { + "author_name": "Kijun Song", + "author_inst": "Department of Cancer Biology, Dana-Farber Cancer Institute" + }, + { + "author_name": "Andrew Z. Xu", + "author_inst": "Department of Cancer Biology, Dana-Farber Cancer Institute" + }, + { + "author_name": "Timothy M. Caradonna", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Jared Feldman", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Blake M. Hauser", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Aaron G. Schmidt", + "author_inst": "Ragon Institute of MGH, MIT, and Harvard" + }, + { + "author_name": "Robert K. Ernst", + "author_inst": "Department of Microbial Pathogenesis, University of Maryland School of Dentistry" + }, + { + "author_name": "Carly Dillen", + "author_inst": "Department of Microbiology and Immunology, University of Maryland School of Medicine" + }, + { + "author_name": "Stuart M. Weston", + "author_inst": "Department of Microbiology and Immunology, University of Maryland School of Medicine" + }, + { + "author_name": "Robert M. Johnson", + "author_inst": "Department of Microbiology and Immunology, University of Maryland School of Medicine" + }, + { + "author_name": "Holly L. Hammond", + "author_inst": "Department of Microbiology and Immunology, University of Maryland School of Medicine" + }, + { + "author_name": "Romana Mayer", + "author_inst": "Department of Pathology, University of Maryland Medical Center" + }, + { + "author_name": "Allen Burke", + "author_inst": "Department of Pathology, University of Maryland Medical Center" + }, + { + "author_name": "Aiquan Chang", + "author_inst": "Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Jingyou Yu", + "author_inst": "Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Dan H. Barouch", + "author_inst": "Center for Virology and Vaccine Research, Beth Israel Deaconess Medical Center" + }, + { + "author_name": "Sirano Dhe-Paganon", + "author_inst": "Department of Cancer Biology, Dana-Farber Cancer Institute" + }, + { + "author_name": "Matthew Frieman", + "author_inst": "Department of Microbiology and Immunology, University of Maryland School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.05.19.444889", "rel_title": "An AAV-ie based Vaccine effectively protects against SARS-CoV-2 and Circulating Variants", @@ -777333,61 +776610,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2021.05.13.21257067", - "rel_title": "Contact tracing indicators for COVID-19: rapid scoping review and conceptual framework", - "rel_date": "2021-05-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.13.21257067", - "rel_abs": "BackgroundContact tracing is one of the key interventions in response to the COVID-19 pandemic but its implementation varies widely across countries. There is little guidance on how to monitor contact tracing performance, and no systematic overview of indicators to assess contact tracing systems or conceptual framework for such indicators exists to date.\n\nMethodsWe conducted a rapid scoping review using a systematic literature search strategy in the peer-reviewed and grey literature as well as open source online documents. We developed a conceptual framework to map indicators by type (input, process, output, outcome, impact) and thematic area (human resources, financial resources, case investigation, contact identification, contact testing, contact follow up, case isolation, contact quarantine, transmission chain interruption, incidence reduction).\n\nResultsWe identified a total of 153 contact tracing indicators from 1,555 peer-reviewed studies, 894 studies from grey literature sources, and 15 sources from internet searches. Two-thirds of indicators were process indicators (102; 67%), while 48 (31%) indicators were output indicators. Only three (2%) indicators were input indicators. Indicators covered seven out of ten conceptualized thematic areas, with more than half being related to either case investigation (37; 24%) or contact identification (44; 29%). There were no indicators for the input area \"financial resources\", the outcome area \"transmission chain interruption\", and the impact area \"incidence reduction\".\n\nConclusionsAlmost all identified indicators were either process or output indicators focusing on case investigation, contact identification, case isolation or contact quarantine. We identified important gaps in input, outcome and impact indicators, which constrains evidence-based assessment of contact tracing systems. A universally agreed set of indicators is needed to allow for cross-system comparisons and to improve the performance of contact tracing systems.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Florian Vogt", - "author_inst": "University of New South Wales" - }, - { - "author_name": "Karishma Kurup", - "author_inst": "Independent public health consultant, New Delhi, India" - }, - { - "author_name": "Paul Mussleman", - "author_inst": "University of Alabama at Birmingham, Birmingham, USA" - }, - { - "author_name": "Caroline Habrun", - "author_inst": "University of New Mexico, New Mexico Emerging Infections Program, NM, USA" - }, - { - "author_name": "Madeleine Crowe", - "author_inst": "World Health Organization, Health Emergencies Programme, Geneva, Switzerland" - }, - { - "author_name": "Alexandra Woodward", - "author_inst": "Global Emerging Infections Surveillance, Armed Forces Health Surveillance Division, U.S. Department of Defense, Silver Spring, Maryland, United States of Americ" - }, - { - "author_name": "Giovanna Jaramillo-Gutierrez", - "author_inst": "World Health Organization, Global Outbreak Alert & Response Network, Geneva, Switzerland" - }, - { - "author_name": "John Kaldor", - "author_inst": "The Kirby Institute, University of New South Wales, Sydney, NSW, Australia" - }, - { - "author_name": "Sirenda Vong", - "author_inst": "World Health Organization, World Health Emergencies, South East Asia Regional Office, New Delhi, India" - }, - { - "author_name": "Victor Del Rio Vilas", - "author_inst": "World Health Organization, World Health Emergencies, South East Asia Regional Office, New Delhi, India" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.05.18.21257110", "rel_title": "Assessment of the infectious threshold of SARS-CoV-2 in primary airway epithelial cells", @@ -778483,6 +777705,33 @@ "type": "new results", "category": "pharmacology and toxicology" }, + { + "rel_doi": "10.1101/2021.05.17.20249000", + "rel_title": "Virtually in Synch: A Pilot Study on Affective Dimensions of Dancing with Parkinson's during COVID- 19", + "rel_date": "2021-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.17.20249000", + "rel_abs": "Loss of social supports and community programs due to lockdowns and other measures associated with COVID-19 has been linked with concerns over mental health and feelings of isolation. These challenges can be particularly acute for the elderly and people living with chronic or pervasive health conditions. Dance for PD, a program specifically developed for people living with Parkinsons Disease, formerly offered in hundreds of locations around the globe, either halted or shifted to a virtual format. Our study investigates the transition of these dance-based programs to an online environment, with the aim of determining the extent to which a virtual format provides affective support or other benefits. Given the increased incidence of mental health problems and social isolation associated with COVID-19, this investigation aims to contribute to the development of better supports for vulnerable populations while helping us understand the specific contributions of dance-based programs in a virtual environment.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Katayoun Ghanai", + "author_inst": "York University" + }, + { + "author_name": "Rebecca E Barnstaple", + "author_inst": "York University" + }, + { + "author_name": "Joseph FX DeSouza", + "author_inst": "York University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "rehabilitation medicine and physical therapy" + }, { "rel_doi": "10.1101/2021.05.14.21257209", "rel_title": "Prediction of the effective reproduction number of COVID-19 in Greece. A machine learning approach using Google mobility data.", @@ -778875,45 +778124,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.05.13.21257164", - "rel_title": "KL-MOB Automated Covid-19 Recognition Using a Novel Approach Based on Image Enhancement and a Modified MobileNet CNN", - "rel_date": "2021-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.13.21257164", - "rel_abs": "The emergence of the novel coronavirus pneumonia (Covid-19) pandemic at the end of 2019 led to chaos worldwide. The world breathed a sigh of relief when some countries announced that they had obtained the appropriate vaccine and gradually began to distribute it. Nevertheless, the emergence of another wave of this disease has returned us to the starting point. At present, early detection of infected cases has been the paramount concern of both specialists and health researchers. This paper aims to detect infected patients through chest x-ray images. The large dataset available online for Covid-19 (COVIDx) was used in this research. The dataset consists of 2,128 x-ray images of Covid-19 cases, 8,066 normal cases, and 5,575 cases of pneumonia. A hybrid algorithm was applied to improve image quality before conducting the neural network training process. This algorithm consisted of combining two different noise reduction filters in the images, followed by a contrast enhancement algorithm. In this paper, for Covid-19 detection, a novel convolution neural network (CNN) architecture, KL-MOB (Covid-19 detection network based on MobileNet structure), was proposed. KL-MOB performance was boosted by adding the Kullback-Leibler (KL) divergence loss function at the end when trained from scratch. The Kullback-Leibler (KL) divergence loss function was adopted as content-based image retrieval and fine-grained classification to improve the quality of image representation. This paper yielded impressive results, overall benchmark accuracy, sensitivity, specificity, and precision of 98.7%, 98.32%, 98.82%, and 98.37%, respectively. The promising results in this research may enable other researchers to develop modern and innovative methods to aid specialists. The tremendous potential of the method proposed in this research can also be utilized to detect Covid-19 quickly and safely in patients throughout the world.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Mundher Mohammed Taresh", - "author_inst": "Computer Science, College of Information Science and Engineering, Hunan university, Chang Sha, Hunan, China" - }, - { - "author_name": "Ning bo Zhu", - "author_inst": "Computer Science, College of Information Science and Engineering, Hunan university, Chang Sha, Hunan, China" - }, - { - "author_name": "Asaad Shakir Hameed", - "author_inst": "Department of Mathematics, General Directorate of Thi-Qar Education, Ministry of education, Iraq" - }, - { - "author_name": "Modhi Lafta Mutar", - "author_inst": "Department of Mathematics, General Directorate of Thi-Qar Education, Ministry of education, Thi-Qar, Iraq" - }, - { - "author_name": "Talal Ahmed Ali Ali Ahmed Ali Ali", - "author_inst": "Computer Science, College of Information Science and Engineering, Hunan university, Chang Sha, Hunan, China" - }, - { - "author_name": "Mohammed Alghaili", - "author_inst": "Computer Science, College of Information Science and Engineering, Hunan university, Chang Sha, Hunan, China" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.05.15.21257271", "rel_title": "SARS-CoV-2 transmission in K-12 schools in the Vancouver Coastal Health Region: a descriptive epidemiologic study", @@ -781785,6 +780995,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.12.21257120", + "rel_title": "Performance evaluation of the BD SARS-CoV-2 reagents for the BD MAX\u2122 system", + "rel_date": "2021-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.12.21257120", + "rel_abs": "BackgroundThe RT-qPCR assay for detecting SARS-CoV-2 virus is the favorable approach to test suspected COVID-19 cases. However, discordant results can occur when two or more assays are compared. Variability in analytical sensitivities between assays, among other factors, may account for these differences in reporting.\n\nMethodsThe limits of detection (LOD) for the BD SARS-CoV-2 Reagents for BD MAX System (\"MAX SARS-CoV-2 assay\"), the Biomerieux BioFire(R) Respiratory Panel 2.1 (\"BioFire SARS-CoV-2 assay\"), the Roche cobas SARS-CoV-2 assay (\"cobas SARS-CoV-2 assay\"), and the Hologic Aptima(R) SARS-CoV-2 assay Panther(R) (\"Aptima SARS-CoV-2 assay\") RT-qPCR systems were determined using a total of 84 contrived nasopharyngeal specimens with seven target levels for each comparator. The positive and negative percent agreement (PPA and NPA, respectively) for the MAX SARS-CoV-2 assay were compared to the Aptima SARS-CoV-2 assay in a post-market clinical study utilizing 708 paired nasopharyngeal specimens collected from suspected COVID-19 cases. Discordant results were further tested by the cobas and BioFire SARS-CoV-2 assays.\n\nResultsThe measured LOD for the MAX SARS-CoV-2 assay (251 copies/mL) was comparable to the cobas SARS-CoV-2 assay (298 copies/mL) and the BioFire SARS-CoV-2 assay (302 copies/mL); the Aptima SARS-CoV-2 assay had a LOD of 612 copies/mL. The MAX SARS-CoV-2 assay had a PPA of 100% (95%CI: [97.3%-100.0%]) and a NPA of 96.7% (95%CI: [94.9%-97.9%]) when compared to the Aptima SARS-CoV-2 assay.\n\nConclusionsThe MAX SARS-CoV-2 assay exhibited a high analytical sensitivity and specificity for SARS-CoV-2 detection. The clinical performance of the MAX SARS-CoV-2 assay agreed with another sensitive EUA cleared assay.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Karen Yanson", + "author_inst": "Becton, Dickinson and Company" + }, + { + "author_name": "William LaViers", + "author_inst": "Becton, Dickinson and Company" + }, + { + "author_name": "Lori Neely", + "author_inst": "Becton, Dickinson and Company" + }, + { + "author_name": "Elizabeth Lockamy", + "author_inst": "Becton, Dickinson and Company" + }, + { + "author_name": "Luis Carlos Castillo-Hernandez", + "author_inst": "CTMD Research" + }, + { + "author_name": "Christopher Oldfied", + "author_inst": "Fellows Research Alliance, Inc" + }, + { + "author_name": "Ron Ackerman", + "author_inst": "Comprehensive Clinical Trials" + }, + { + "author_name": "Jamie Ackerman", + "author_inst": "Comprehensive Clinical Research, LLC" + }, + { + "author_name": "Daniel Ortiz", + "author_inst": "Beaumont Health" + }, + { + "author_name": "Sixto Pacheco", + "author_inst": "BioCollections Worldwide Inc" + }, + { + "author_name": "Patricia Simner", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Stephen Young", + "author_inst": "TriCore Reference Laboratories" + }, + { + "author_name": "Erin McElvania", + "author_inst": "NorthShore University HealthSystem" + }, + { + "author_name": "Yu-Chih Lin", + "author_inst": "Becton, Dickinson and Company" + }, + { + "author_name": "Charles Cooper", + "author_inst": "Becton, Dickinson and Company" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.08.21256896", "rel_title": "Epidemiological characteristics and incubation period of SARS-CoV-2 during the 2020-2021 winter pandemic wave in north China: an observational study", @@ -782189,241 +781474,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.16.21257283", - "rel_title": "Early Anakinra Treatment for COVID-19 Guided by Urokinase Plasminogen Receptor", - "rel_date": "2021-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.16.21257283", - "rel_abs": "BackgroundIn a previous open-label trial, early anakinra treatment guided by elevated soluble urokinase plasminogen activator receptor (suPAR) prevented progression of COVID-19 pneumonia into respiratory failure.\n\nMethodsIn the SAVE-MORE multicenter trial, 594 hospitalized patients with moderate and severe COVID-19 pneumonia and plasma suPAR 6 ng/ml or more and receiving standard-of-care were 1:2 randomized to subcutaneous treatment with placebo or 100 mg anakinra once daily for 10 days. The primary endpoint was the overall clinical status of the 11-point World Health Organization ordinal Clinical Progression Scale (WHO-CPS) at day 28. The changes of the WHO-CPS and of the sequential organ failure assessment (SOFA) score were the main secondary endpoints.\n\nResultsAnakinra-treated patients were distributed to lower strata of WHO-CPS by day 28 (adjusted odds ratio-OR 0.36; 95%CI 0.26-0.50; P<0.001); anakinra protected from severe disease or death (6 or more points of WHO-CPS) (OR: 0.46; P: 0.010). The median absolute decrease of WHO-CPS in the placebo and anakinra groups from baseline was 3 and 4 points respectively at day 28 (OR 0.40; P<0.0001); and 2 and 3 points at day 14 (OR 0.63; P: 0.003); the absolute decrease of SOFA score was 0 and 1 points (OR 0.63; P: 0.004). 28-day mortality decreased (hazard ratio: 0.45; P: 0.045). Hospital stay was shorter.\n\nConclusionsEarly start of anakinra treatment guided by suPAR provides 2.78 times better improvement of overall clinical status in moderate and severe COVID-19 pneumonia.\n\n(Sponsored by the Hellenic Institute for the Study of Sepsis ClinicalTrials.gov identifier, NCT04680949)", - "rel_num_authors": 55, - "rel_authors": [ - { - "author_name": "Evdoxia Kyriazopoulou", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Garyfallia Poulakou", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Haralampos Milionis", - "author_inst": "University of Ioannina, Medical School" - }, - { - "author_name": "Simeon Metallidis", - "author_inst": "Aristotle University of Thessaloniki, Medical School" - }, - { - "author_name": "Georgios Adamis", - "author_inst": "G. Gennimatas General Hospital of Athens" - }, - { - "author_name": "Konstantinos Tsiakos", - "author_inst": "Sotiria General Hospital of Chest Diseases" - }, - { - "author_name": "Archontoula Fragkou", - "author_inst": "Elpis General Hospital of Athens" - }, - { - "author_name": "Aggeliki Rapti", - "author_inst": "Sotiria General Hospital of Chest Diseases" - }, - { - "author_name": "Christina Danoulari", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Massimo Fantoni", - "author_inst": "Fondazione Policlinico Gemelli IRCCS" - }, - { - "author_name": "Ioannis Kalomenidis", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Georgios Chrysos", - "author_inst": "Tzaneio General Hospital of Piraeus" - }, - { - "author_name": "Andrea Angheben", - "author_inst": "IRCSS Sacro Cuore Hospital" - }, - { - "author_name": "Ilias Kainis", - "author_inst": "Sotiria General Hospital of Chest Diseases of Athens" - }, - { - "author_name": "Zoi Alexiou", - "author_inst": "Thriasio General Hospital of Eleusis" - }, - { - "author_name": "Francesco Castelli", - "author_inst": "Brescia ASST Spedali Civili Hospital, University of Brescia" - }, - { - "author_name": "Francesco Saverio Serino", - "author_inst": "Hospital of Jesolo" - }, - { - "author_name": "Petros Bakakos", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Emanuele Nicastri", - "author_inst": "Spallanzani Institute of Rome" - }, - { - "author_name": "Vassiliki Tzavara", - "author_inst": "Korgialeneion-Benakeion General Hospital of Athens" - }, - { - "author_name": "Evangelos Kostis", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Lorenzo Dagna", - "author_inst": "IRCCS Ospedale San Raffaele & Vita-Salute San Raffaele University" - }, - { - "author_name": "Panagiotis Koufargyris", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Katerina Dimakou", - "author_inst": "Sotiria General Hospital of Chest Diseases" - }, - { - "author_name": "Glykeria Tzatzagou", - "author_inst": "Papageorgiou General Hospital of Thessaloniki" - }, - { - "author_name": "Maria Chini", - "author_inst": "Korgialeneion-Benakeion General Hospital of Athens" - }, - { - "author_name": "Matteo Bassetti", - "author_inst": "Ospedale Policlinico San Martino IRCCS and Department of Health Sciences, University of Genova" - }, - { - "author_name": "Konstantina Katrini", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Vasileios Kotsis", - "author_inst": "Aristotle University of Thessaloniki, Medical School" - }, - { - "author_name": "George Tsoukalas", - "author_inst": "Sotiria General Hospital of Chest Diseases of Athens" - }, - { - "author_name": "Carlo Selmi", - "author_inst": "Humanitas Research Hospital of Milan" - }, - { - "author_name": "Ioannis Bliziotis", - "author_inst": "Asklipieio General Hospital of Voula" - }, - { - "author_name": "Michael Samarkos", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Michael Doumas", - "author_inst": "Aristotle University of Thessaloniki, Medical School" - }, - { - "author_name": "Sofia Ktena", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Aikaterini Masgala", - "author_inst": "Konstantopouleio General Hospital of Athens" - }, - { - "author_name": "Ilias Papanikolaou", - "author_inst": "General Hospital of Kerkyra" - }, - { - "author_name": "Aikaterini Argyraki", - "author_inst": "Sotiria General Hospital of Chest Diseases of Athens" - }, - { - "author_name": "Chiara Simona Cardellino", - "author_inst": "IRCSS Sacro Cuore Hospital" - }, - { - "author_name": "Eleni-Ioanna Katsigianni", - "author_inst": "Hellenic Institute for the Study of Sepsis" - }, - { - "author_name": "Efthymia Giannitsioti", - "author_inst": "Tzaneio General Hospital of Piraeus" - }, - { - "author_name": "Antonella Cingolani", - "author_inst": "Fondazione Policlinico Gemelli IRCCS" - }, - { - "author_name": "Karolina Akinosoglou", - "author_inst": "University of Patras Medical School" - }, - { - "author_name": "Orestis Liatsis-Douvitsas", - "author_inst": "Hellenic Institute for the Study of Sepsis" - }, - { - "author_name": "Styliani Symbardi", - "author_inst": "Thriasio General Hospital of Eleusis" - }, - { - "author_name": "Maria Mouktaroudi", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Giuseppe Ippolito", - "author_inst": "INMI Lazzaro Spallanzani IRCCS" - }, - { - "author_name": "Eleni Florou", - "author_inst": "Hellenic Institute for the Study of Sepsis" - }, - { - "author_name": "Antigone Kotsaki", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Mihai Netea", - "author_inst": "Radboud University" - }, - { - "author_name": "jesper eugen-olsen", - "author_inst": "Copenhagen University Hospital Hvidovre" - }, - { - "author_name": "Miltiades Kyprianou", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Periklis Panagopoulos", - "author_inst": "Democritus University of Thrace, Medical School" - }, - { - "author_name": "George N Dalekos", - "author_inst": "National Expertise Center of Greece in Autoimmune Liver Diseases, General University Hospital of Larissa" - }, - { - "author_name": "Evangelos Giamarellos-Bourboulis", - "author_inst": "National and Kapodistrian University of Athens" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.18.21256717", "rel_title": "Effect of COVID-19 on inequalities in premature mortality in England: an analysis of excess mortality by deprivation and ethnicity", @@ -783675,6 +782725,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.05.11.21257004", + "rel_title": "SARS-CoV-2 R.1 lineage variants prevailed in Tokyo in March 2021", + "rel_date": "2021-05-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.11.21257004", + "rel_abs": "BackgroundThe spread of SARS-CoV-2 variants, such as B.1.1.7 and B.1.351, has become a crucial issue worldwide. Therefore, we began testing all patients with COVID-19 for the N501Y and E484K mutations associated with SARS-CoV-2.\n\nStudy designNasopharyngeal swab samples from 108 patients who visited our hospital between February and April 2021 were analyzed. The samples were analyzed using reverse transcription-polymerase chain reaction with melting curve analysis to detect the N501Y and E484K mutations. A part of the samples were also subjected to whole genome sequencing. Clinical parameters such as mortality and admission to the intensive care unit were analyzed to examine the association between increased disease severity and the E484K mutation.\n\nResultsThe ratio of cases showing the 501N+484K mutation rapidly increased from 8% in February to 46% in March. Whole genome sequencing revealed that the viruses with 501N+484K mutation are R.1 lineage variants. Evidence of increased disease severity related to the R.1 variants were not found.\n\nConclusionsWe found that the R.1 lineage variants rapidly prevailed in Tokyo in March 2021.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Katsutoshi Nagano", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Chihiro Tani-Sassa", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Yumi Iwasaki", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Yuna Takatsuki", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Sonoka Yuasa", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Yuta Takahashi", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Jun Nakajima", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Kazunari Sonobe", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Naoya Ichimura", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Yoko Nukui", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Hiroaki Takeuchi", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Kousuke Tanimoto", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Yukie Tanaka", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Akinori Kimura", + "author_inst": "Tokyo Medical and Dental University" + }, + { + "author_name": "Shuji Tohda", + "author_inst": "Tokyo Medical and Dental University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.11.21256972", "rel_title": "SARS-CoV-2 mRNA vaccines induce a greater array of spike-specific antibody isotypes with more potent complement binding capacity than natural infection", @@ -784139,65 +783264,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.05.12.21257123", - "rel_title": "Occupation and COVID-19 mortality in England: a national linked data study of 14.3 million adults", - "rel_date": "2021-05-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.12.21257123", - "rel_abs": "ObjectiveTo estimate occupational differences in COVID-19 mortality, and test whether these are confounded by factors, such as regional differences, ethnicity and education or due to non-workplace factors, such as deprivation or pre-pandemic health.\n\nDesignRetrospective cohort study\n\nSettingPeople living in private households England\n\nParticipants14,295,900 people aged 40-64 years (mean age 52 years, 51% female) who were alive on 24 January 2020, living in private households in England in 2019, were employed in 2011, and completed the 2011 census.\n\nMain outcome measuresCOVID-19 related death, assessed between 24 January 2020 and 28 December 2020. We estimated age-standardised mortality rates per 100,000 person-years at risk (ASMR) stratified by sex and occupations. To estimate the effect of occupation due to work-related exposures, we used Cox proportional hazard models to adjust for confounding (region, ethnicity, education), as well as non-workplace factors that are related to occupation.\n\nResultsThere is wide variation between occupations in COVID-19 mortality. Several occupations, particularly those involving contact with patients or the public, show three-fold or four-fold risks. These elevated risks were greatly attenuated after adjustment for confounding and mediating non-workplace factors. For example, the hazard ratio (HR) for men working as taxi and cab drivers or chauffeurs changed from 4.60 [95%CI 3.62-5.84] to 1.47 [1.14-1.89] after adjustment. More generally, the overall HR for men working in essential occupations compared with men in non-essential occupations changed from 1.45 [1.34 - 1.56] to 1.22 [1.13 - 1.32] after adjustment. For most occupations, confounding and other mediating factors explained about 70% to 80% of the age-adjusted hazard ratios.\n\nConclusionsWorking conditions are likely to play a role in COVID-19 mortality, particularly in occupations involving contact with COVID-19 patients or the public. However, there is also a substantial contribution from non-workplace factors, including regional factors, socio-demographic factors, and pre-pandemic health.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Vahe Nafilyan", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Piotr Pawelek", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Daniel Ayoubkhani", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Sarah Rhodes", - "author_inst": "School of Health Sciences, University of Manchester" - }, - { - "author_name": "Lucy Pembrey", - "author_inst": "Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Melissa Matz", - "author_inst": "Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Michel P Coleman", - "author_inst": "Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Claudia Allemani", - "author_inst": "Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Ben Windsor-Shellard", - "author_inst": "Office for National Statistics" - }, - { - "author_name": "Martie van Tongeren", - "author_inst": "School of Health Sciences, University of Manchester" - }, - { - "author_name": "Neil Pearce", - "author_inst": "London School of Hygiene and Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.13.21257144", "rel_title": "REACT-1 round 11 report: low prevalence of SARS-CoV-2 infection in the community prior to the third step of the English roadmap out of lockdown", @@ -785717,6 +784783,41 @@ "type": "new results", "category": "scientific communication and education" }, + { + "rel_doi": "10.1101/2021.05.16.444344", + "rel_title": "Key informant perceptions on wildlife hunting in India during the COVID-19 lockdown", + "rel_date": "2021-05-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.16.444344", + "rel_abs": "Lockdowns intended to control the COVID-19 pandemic resulted in major socioeconomic upheavals across the world. While there were numerous reports of these lockdowns benefiting wildlife by reducing human movement and habitat disturbance, increased hunting during these lockdowns emerged as a conservation concern, particular in tropical Asia and Africa. We used online interviews with key informants including wildlife researchers, enforcement staff and NGO employees (N=99), and media reports (N=98), to examine the impacts of Indias COVID-19 lockdown (March-May 2020) on wildlife hunting across the country. We asked whether and how hunting patterns changed during the lockdown, and explored socioeconomic and institutional factors underlying these changes. Over half the interviewees spread over 43 administrative districts perceived hunting (mammals, in particular) to have increased during the lockdown relative to a pre-lockdown reference period. Interviewees identified household consumption (53% of respondents) and sport and recreation (34%) as main motivations for hunting during the lockdown, and logistical challenges for enforcement (36%), disruption of food supply (32%), and need for recreational opportunities (32%) as key factors associated with hunting during this period. These insights were corroborated by statements by experts extracted from media articles. Collectively, our findings suggest that the COVID-19 lockdown potentially increased hunting across much of India, and emphasize the role of livelihood and food security in mitigating threats to wildlife during such periods of acute socioeconomic perturbation.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Uttara Mendiratta", + "author_inst": "WCS-India" + }, + { + "author_name": "Munib Khanyari", + "author_inst": "Nature Conservation Foundation" + }, + { + "author_name": "Nandini Velho", + "author_inst": "Srishti Manipal Institute of Art, Design, Law and Technology" + }, + { + "author_name": "Kulbhushansingh Suryawanshi", + "author_inst": "Nature Conservation Foundation" + }, + { + "author_name": "Nirmal U. Kulkarni", + "author_inst": "WCS-India" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "ecology" + }, { "rel_doi": "10.1101/2021.05.13.21256857", "rel_title": "A Predictive Modelling Framework for COVID-19 Transmission to Inform the Management of Mass Events", @@ -786160,45 +785261,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.05.14.444076", - "rel_title": "The Spike Proteins of SARS-CoV-2 B.1.617 and B.1.618 Variants Identified in India Provide Partial Resistance to Vaccine-elicited and Therapeutic Monoclonal Antibodies.", - "rel_date": "2021-05-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.14.444076", - "rel_abs": "Highly transmissible SARS-CoV-2 variants recently identified in India designated B.1.617 and B.1.618 have mutations within the spike protein that may contribute to their increased transmissibility and that could potentially result in re-infection or resistance to vaccine-elicited antibody. B.1.617 encodes a spike protein with mutations L452R, E484Q, D614G and P681R while the B.1.618 spike has mutations {Delta}145-146, E484K and D614G. We generated lentiviruses pseudotyped by the variant proteins and determined their resistance to neutralization by convalescent sera, vaccine-elicited antibodies and therapeutic monoclonal antibodies. Viruses with B.1.617 and B.1.618 spike were neutralized with a 2-5-fold decrease in titer by convalescent sera and vaccine-elicited antibodies. The E484Q and E484K versions were neutralized with a 2-4-fold decrease in titer. Virus with the B.1.617 spike protein was neutralized with a 4.7-fold decrease in titer by the Regeneron monoclonal antibody cocktail as a result of the L452R mutation. The modest neutralization resistance of the variant spike proteins to vaccine elicited antibody suggests that current vaccines will remain protective against the B.1.617 and B.1.618 variants.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Takuya Tada", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Hao Zhou", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Belinda M Dcosta", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Marie I Samanovic", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Mark J Mulligan", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Nathaniel R Landau", - "author_inst": "NYU Grossman School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.05.15.444275", "rel_title": "Allicin inhibits SARS-CoV-2 replication and abrogates the antiviral host response in the Calu-3 proteome", @@ -787794,6 +786856,141 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.05.11.443572", + "rel_title": "Siglec-1 on dendritic cells mediates SARS-CoV-2 trans-infection of target cells while on macrophages triggers proinflammatory responses", + "rel_date": "2021-05-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.11.443572", + "rel_abs": "COVID-19 pandemic is not yet under control by vaccination, and effective antivirals are critical for preparedness. Here we report that macrophages and dendritic cells, key antigen presenting myeloid cells (APCs), are largely resistant to SARS-CoV-2 infection. APCs effectively captured viruses within cellular compartments that lead to antigen degradation. Macrophages sense SARS-CoV-2 and released higher levels of cytokines, including those related to cytokine storm in severe COVID-19. The sialic acid-binding Ig-like lectin 1 (Siglec-1/CD169) present on APCs, which interacts with sialylated gangliosides on membranes of retroviruses or filoviruses, also binds SARS-CoV-2 via GM1. Blockage of Siglec-1 receptors by monoclonal antibodies reduces SARS-CoV-2 uptake and transfer to susceptible target cells. APCs expressing Siglec-1 and carrying SARS-CoV-2 are found in pulmonary tissues of non-human primates. Single cell analysis reveals the in vivo induction of cytokines in those macrophages. Targeting Siglec-1 could offer cross-protection against SARS-CoV-2 and other enveloped viruses that exploit APCs for viral dissemination, including those yet to come in future outbreaks.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Daniel Perez-Zsolt", + "author_inst": "Irsicaixa" + }, + { + "author_name": "Jordana Munoz Basagoiti", + "author_inst": "IrsiCaixa" + }, + { + "author_name": "Jordi Rodo", + "author_inst": "IRTA-CRESA" + }, + { + "author_name": "Marc Elousa", + "author_inst": "CNAG CRG, Centre for Genomic Regulation (CRG)" + }, + { + "author_name": "Dalia Raich Regue", + "author_inst": "IrsiCaixa" + }, + { + "author_name": "Critina Risco", + "author_inst": "Centro Nacional de Biotecnologia, CSIC" + }, + { + "author_name": "Martin Sachse", + "author_inst": "Centro Nacional de Biotecnologia, CSIC" + }, + { + "author_name": "Maria Pino", + "author_inst": "Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University" + }, + { + "author_name": "Sanjeev Gumber", + "author_inst": "Division of Microbiology and Immunology, Yerkes National Primate Research Center, Emory University" + }, + { + "author_name": "Mirko Paiardini", + "author_inst": "Emory University" + }, + { + "author_name": "Jakub Chojnacki", + "author_inst": "IrsiCaixa AIDS Research Institute" + }, + { + "author_name": "Itziar Erkizia", + "author_inst": "AIDS research Institute, Irsicaixa" + }, + { + "author_name": "Xabier Muniz", + "author_inst": "IrsiCaixa AIDS Research Institute" + }, + { + "author_name": "Ester Ballana", + "author_inst": "IrsiCaixa AIDS Research Institute" + }, + { + "author_name": "Eva Riveira Munoz", + "author_inst": "IrsiCaixa AIDS Research Institute" + }, + { + "author_name": "Marc Noguera-Julian", + "author_inst": "irsiCaixa Institute for AIDS research" + }, + { + "author_name": "Roger Paredes", + "author_inst": "IrsiCaixa AIDS Research Institute" + }, + { + "author_name": "Benjamin Trinite", + "author_inst": "IrsiCaixa AIDS Research Institute" + }, + { + "author_name": "Ferran Tarres Freixas", + "author_inst": "IrsiCaixa AIDS Research Institute" + }, + { + "author_name": "Ignacio Blanco", + "author_inst": "Hospital Germans Trias i Pujol" + }, + { + "author_name": "Victor Guallar", + "author_inst": "Barcelona Supercomputing Center" + }, + { + "author_name": "Jorge Carrillo", + "author_inst": "Institut de Recerca de la SIDA irsiCaixa" + }, + { + "author_name": "Julia Blanco", + "author_inst": "Institut de Recerca de la SIDA irsiCaixa" + }, + { + "author_name": "Amalio Telenti", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Holger Heyn", + "author_inst": "CNAG-CRG" + }, + { + "author_name": "Joaquim Segales", + "author_inst": "IRTA-CReSA" + }, + { + "author_name": "Bonaventura Clotet", + "author_inst": "AIDS Research Institute IrsiCaixa" + }, + { + "author_name": "Javier Martinez-Picado", + "author_inst": "IrsiCaixa AIDS Research Institute" + }, + { + "author_name": "Julia Vergara-Alert", + "author_inst": "IRTA-CRESA" + }, + { + "author_name": "Nuria Izquierdo-Useros", + "author_inst": "AIDS Research Institute IrsiCaixa" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.05.14.444205", "rel_title": "Common Mechanism of SARS-CoV and SARS-CoV-2 Pathogenesis across Species", @@ -788374,41 +787571,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.06.21256757", - "rel_title": "COVID-19 outbreak rates and infection attack rates associated with the workplace: a descriptive epidemiological study", - "rel_date": "2021-05-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.06.21256757", - "rel_abs": "BackgroundA large number of COVID-19 outbreaks/clusters have been reported in a variety of workplace settings since the start of the pandemic. However, information on the rate of outbreak occurrences which helps to identify the type of workplaces that are more likely to experience an outbreak, or infection attack rates which estimates the potential extent of the virus transmission in an outbreak, has not yet been available to inform intervention strategies to limit transmission.\n\nObjectivesTo link datasets on workplace settings and COVID-19 workplace outbreaks in England in order to: identify the geographical areas and workplace sectors with a high rate of outbreaks; and compare infection attack rates by workplace size and sector.\n\nMethodsWe analysed Public Health England (PHE) HPZone data on COVID-19 outbreaks in workplaces, covering the time period of 18 May - 12 October 2020. The workplaces analysed excluded care homes, hospitals and educational settings. We calculated the workplace outbreak rates by nine English regions, 151 Upper Tier Local Authorities (UTLAs) and twelve industrial sectors, using National Population Database (NPD) data extracted in May 2019 on the total number of the relevant workplaces as the denominator. We also calculated the infection attack rates by enterprise size (small, medium, large) and industrial sector, using PHE Situations of Interest (SOI) data on the number of test-confirmed COVID-19 cases in a workplace outbreak as the numerator, and using NPD data on the number employed in that workplace as the denominator.\n\nResultsIn total, 1,317 confirmed workplace outbreaks were identified from HPZone data, of which 1,305 were available for estimation of outbreak rates. The average outbreak rate was 66 per 100,000 workplaces. Of the nine geographical regions in England, the North West had the highest workplace outbreak rate (155/100,000 workplaces), based on 351 outbreaks. Of the UTLAs, the highest workplace outbreak rate was Blackburn with Darwen (387/100,000 workplaces). The industrial sector with the highest workplace outbreak rate was manufacturers and packers of food (1,672/100,000), based on 117 outbreaks: this was consistent across seven of the regions. In addition, high outbreak rates in warehouses were observed in the East Midlands and the North West.\n\nIn total, 390 outbreaks were identified from SOI data and 264 of them allowed for estimation of attack rates. The overall median attack rate was 3.4% of the employed persons with confirmed COVID-19 at a workplace with an outbreak. Most of these outbreaks (162) had an attack rate less than 6%. However, in a small number of outbreaks (57) the attack rate was over 15%. The attack rates increased as the size of the enterprise decreased. The highest attack rate was for outbreaks in close contact services (median 16.5%), which was followed by outbreaks in restaurants and catering (median 10.2%), and in manufacturers and packers of non-food products (median 6.7%).\n\nConclusionsOur linked dataset analysis approach allows early identification of geographical regions and industrial sectors with higher rates of COVID-19 workplace outbreaks as well as estimation of attack rates by enterprise size and sector. This can be used to inform interventions to limit transmission of the virus. Our approach to analysing the workplace outbreak data can also be applied to calculation of outbreak rates and attack rates in other types of settings such as care homes, hospitals and educational settings.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Yiqun Chen", - "author_inst": "Health and Safety Executive, UK" - }, - { - "author_name": "Timothy Aldridge", - "author_inst": "Health and Safety Executive, UK" - }, - { - "author_name": "- UK COVID-19 National Core Studies Consortium", - "author_inst": "" - }, - { - "author_name": "Claire F Ferraro", - "author_inst": "National Infection Service, Public Health England, UK" - }, - { - "author_name": "Fu-Meng Khaw", - "author_inst": "Public Health England, UK" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.07.21256821", "rel_title": "SARS-CoV-2 nai\u0308ve and recovered individuals show qualitatively different antibody responses following mRNA vaccination", @@ -789636,6 +788798,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.08.21256867", + "rel_title": "SARS-CoV-2 lineage dynamics in England from January to March 2021 inferred from representative community samples", + "rel_date": "2021-05-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.08.21256867", + "rel_abs": "Genomic surveillance for SARS-CoV-2 lineages informs our understanding of possible future changes in transmissibility and vaccine efficacy. However, small changes in the frequency of one lineage over another are often difficult to interpret because surveillance samples are obtained from a variety of sources. Here, we describe lineage dynamics and phylogenetic relationships using sequences obtained from a random community sample who provided a throat and nose swab for rt-PCR during the first three months of 2021 as part of the REal-time Assessment of Community Transmission-1 (REACT-1) study. Overall, diversity decreased during the first quarter of 2021, with the B.1.1.7 lineage (first identified in Kent) predominant, driven by a 0.3 unit higher reproduction number over the prior wild type. During January, positive samples were more likely B.1.1.7 in younger and middle-aged adults (aged 18 to 54) than in other age groups. Although individuals infected with the B.1.1.7 lineage were no more likely to report one or more classic COVID-19 symptoms compared to those infected with wild type, they were more likely to be antibody positive 6 weeks after infection. Viral load was higher in B.1.1.7 infection as measured by cycle threshold (Ct) values, but did not account for the increased rate of testing positive for antibodies. The presence of infections with non-imported B.1.351 lineage (first identified in South Africa) during January, but not during February or March, suggests initial establishment in the community followed by fade-out. However, this occurred during a period of stringent social distancing and targeted public health interventions and does not immediately imply similar lineages could not become established in the future. Sequence data from representative community surveys such as REACT-1 can augment routine genomic surveillance.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Oliver Eales", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "Andrew Page", + "author_inst": "Quadram Institute, Norwich, UK" + }, + { + "author_name": "Sonja N. Tang", + "author_inst": "School of Public Health, Imperial College London, UK" + }, + { + "author_name": "Caroline E. Walters", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "Haowei Wang", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "David Haw", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "Alexander J. Trotter", + "author_inst": "Quadram Institute, Norwich, UK" + }, + { + "author_name": "Thanh Le Viet", + "author_inst": "Quadram Institute, Norwich, UK" + }, + { + "author_name": "Ebenezer Foster-Nyarko", + "author_inst": "Quadram Institute, Norwich, UK" + }, + { + "author_name": "Sophie Prosolek", + "author_inst": "Quadram Institute, Norwich, UK" + }, + { + "author_name": "Christina Atchinson", + "author_inst": "School of Public Health, Imperial College London, UK" + }, + { + "author_name": "Deborah Ashby", + "author_inst": "School of Public Health, Imperial College London, UK" + }, + { + "author_name": "Graham Cooke", + "author_inst": "Department of Infectious Disease, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedic" + }, + { + "author_name": "Wendy Barclay", + "author_inst": "Department of Infectious Disease, Imperial College London, UK" + }, + { + "author_name": "Christl A Donnelly", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "Justin O'Grady", + "author_inst": "Quadram Institute, Norwich, UK" + }, + { + "author_name": "Erik Volz", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + }, + { + "author_name": "- The COVID-19 Genomics UK (COG-UK) Consortium", + "author_inst": "" + }, + { + "author_name": "Ara Darzi", + "author_inst": "Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Research Centre, UK Institute of Global Health Innovation a" + }, + { + "author_name": "Helen Ward", + "author_inst": "School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear" + }, + { + "author_name": "Paul Elliott", + "author_inst": "School of Public Health, Imperial College London, UK Imperial College Healthcare NHS Trust, UK National Institute for Health Research Imperial Biomedical Resear" + }, + { + "author_name": "Steven Riley", + "author_inst": "School of Public Health, Imperial College London, UK MRC Centre for Global infectious Disease Analysis and Abdul Latif Jameel Institute for Disease and Emergenc" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.11.21257040", "rel_title": "Trajectories of child emotional and behavioural difficulties before and during the COVID-19 pandemic in a longitudinal UK cohort", @@ -790840,61 +790105,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.12.21256693", - "rel_title": "Nanopore Sequencing of SARS-CoV-2: Comparison of Short and Long PCR-tiling Amplicon Protocols", - "rel_date": "2021-05-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.12.21256693", - "rel_abs": "Surveillance of the SARS-CoV-2 variants including the quickly spreading mutants by rapid and near real-time sequencing of the viral genome provides an important tool for effective health policy decision making in the ongoing COVID-19 pandemic. Here we evaluated PCR-tiling of short ([~]400-bp) and long ([~]2 and [~]2.5-kb) amplicons combined with nanopore sequencing on a MinION device for analysis of the SARS-CoV-2 genome sequences. Analysis of several sequencing runs demonstrated that using the long amplicon schemes outperforms the original protocol based on the 400-bp amplicons. It also illustrated common artefacts and problems associated with this approach, such as uneven genome coverage, variable fraction of discarded sequencing reads, as well as the reads derived from the viral sub-genomic RNAs and/or human and bacterial contamination.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Brona Brejova", - "author_inst": "Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava" - }, - { - "author_name": "Kristina Borsova", - "author_inst": "Institute of Virology, Biomedical Research Center of the Slovak Academy of Sciences" - }, - { - "author_name": "Viktoria Hodorova", - "author_inst": "Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava" - }, - { - "author_name": "Viktoria Cabanova", - "author_inst": "Institute of Virology, Biomedical Research Center of the Slovak Academy of Sciences" - }, - { - "author_name": "Askar Gafurov", - "author_inst": "Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava" - }, - { - "author_name": "Dominika Fricova", - "author_inst": "Institute of Neuroimmunology, Slovak Academy of Sciences" - }, - { - "author_name": "Martina Nebohacova", - "author_inst": "Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava" - }, - { - "author_name": "Tomas Vinar", - "author_inst": "Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava" - }, - { - "author_name": "Boris Klempa", - "author_inst": "Institute of Virology, Biomedical Research Center of the Slovak Academy of Sciences" - }, - { - "author_name": "Jozef Nosek", - "author_inst": "Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.12.21256874", "rel_title": "Plans to vaccinate children for COVID-19: a survey of US parents", @@ -792038,6 +791248,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.07.21256856", + "rel_title": "A model to analyze rideshare data to surveil novel strains of SARS-CoV-2", + "rel_date": "2021-05-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.07.21256856", + "rel_abs": "BackgroundThe emergence of novel, potentially vaccine-resistant strains of SARS-CoV-2 poses a serious risk to public health. The interactions between passengers and drivers facilitated by rideshare platforms such as Uber are, essentially, a series of partially standardized, random experiments of SARS-CoV-2 transmission. Rideshare companies share data with government health agencies, but no statistical method is available to aggregate these data for the systematic study of the transmission dynamics of COVID-19.\n\nMethodsWe develop a proof-of-concept model for the analysis of data from rideshare interactions merged with COVID-19 diagnosis records. Using simulated data with rideshare volumes, disease prevalence, and diagnosis rates based on a large US city, we use the model to test hypotheses about the emergence of viral strains and their transmission characteristics in the presence of non-pharmaceutical interventions and superspreaders.\n\nFindingsData from 10 simulated trials of SARS-CoV-2 propagation within the Los Angeles rideshare network resulted in an average of 190,387.1 potentially infectious rideshare interactions. Assuming access to data on 25% of the total estimated infections (Partial Reporting), these interactions resulted in an average of 409.0 diagnosed rideshare infections given our transmission model assumptions. For each of the 10 simulated trials, analysis given Partial Reporting could consistently differentiate between a baseline strain and an emergent, more infectious viral strain, enabling hypothesis testing about transmission characteristics.\n\nInterpretationSimulated evaluation of a novel statistical model suggests that rideshare data combined with COVID-19 diagnosis data have the potential to automate continued surveillance of emergent novel strains of SARS-CoV-2 and their transmission characteristics.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Conrad W Safranek", + "author_inst": "Stanford University" + }, + { + "author_name": "David Scheinker", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.10.21256933", "rel_title": "Fixed dosing of tocilizumab in ICU admitted COVID-19 patients is a superior choice compared to bodyweight based dosing; an observational population pharmacokinetic and pharmacodynamic study", @@ -792614,49 +791847,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.10.21256996", - "rel_title": "Quantifying the potential for dominant spread of SARS-CoV-2 variant B.1.351 in the United States", - "rel_date": "2021-05-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.10.21256996", - "rel_abs": "Recent evidence suggests that some new SARS-CoV-2 variants with spike mutations, such as P.1 (Gamma) and B.1.617.2 (Delta), exhibit partial immune evasion to antibodies generated by natural infection or vaccination. By considering the Gamma and Delta variants in a multi-variant transmission dynamic model, we evaluated the dominance of these variants in the United States (US) despite mounting vaccination coverage and other circulating variants. Our results suggest that while the dominance of the Gamma variant is improbable, the Delta variant would become the most prevalent variant in the US, driving a surge in infections and hospitalizations. Our study highlights the urgency for accelerated vaccination and continued adherence to non-pharmaceutical measures until viral circulation is driven low.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Pratha Sah", - "author_inst": "Yale University" - }, - { - "author_name": "Thomas N Vilches", - "author_inst": "York University" - }, - { - "author_name": "Affan Shoukat", - "author_inst": "Yale University" - }, - { - "author_name": "Meagan C Fitzpatrick", - "author_inst": "University of Maryland" - }, - { - "author_name": "Abhishek Pandey", - "author_inst": "Yale University" - }, - { - "author_name": "Seyed M Moghadas", - "author_inst": "York University" - }, - { - "author_name": "Alison P. Galvani", - "author_inst": "Yale University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.10.21256966", "rel_title": "Cohort-based surveillance of SARS-CoV2 transmission mirrors infection rates at the population level: a one-year longitudinal study", @@ -794364,6 +793554,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.10.21256529", + "rel_title": "Severity assessment of single dose Oxford-AstraZeneca vaccinated individuals infected with SARS CoV-2 in the Southeast Bangladesh", + "rel_date": "2021-05-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.10.21256529", + "rel_abs": "The present global endeavor to uncover the most effective vaccines against severe acute respiratory syndrome coronavirus (SARS-CoV-2) that can tremendously prevent transmission, infection and significantly reduce public health risk. COVID-19 vaccination program is underway in different parts of the world including Bangladesh but till to date there is no available health data revealed among the vaccinated peoples. We conducted a cross-sectional study from February 15 to April 15, 2021 to assess the health status of 1st dose Oxford-AstraZeneca vaccinated individuals infected with SARS CoV-2. Standard virological method, real-time reverse transcriptase-polymerase chain reaction (RT-qPCR) was performed to detect SARS-CoV-2 and the different health parameters from vaccinated individuals were collected through direct mobile phone contact using pre-structured questionnaires. A total of 6146 suspected samples were tested and 1752 were found positive for SARS-CoV-2, of them 200 individuals were identified who received 1st dose of COVID-19 vaccine. Within the test period, majority of male (65.6%) and female (34.4%) carried moderate numbers of viruses which comprise between 30.01-35 cyclic threshold (ct) values. Among the vaccinated individuals, 165 (82.5%; 95% CI: 76.51 - 87.5) persons were not hospitalized and 177 (88.5%; 95% CI: 83.24 - 92.57) did not show any respiratory difficulties. Only a few (16) (8%; 95% CI: 4.64 - 12.67) of COVID-19 positive patients needed extra oxygen support and 199 (99.5%; 95% CI: 97.25 - 99.99) individuals didnt require any intensive care unit (ICU) interference. Overall, oxygen saturation was recorded around 96.8% and respiratory difficulties did not extend more than 5 days, irrespective of age and sex during the infection period. Within the vaccinated COVID-19 positive individuals 113 (56.5%; 95% CI: 49.33 - 63.48) and 111(55.5%; 95% CI: 48.32 - 62.51) persons have normal physiological taste and smell. However, we have found a larger proportion of vaccinated persons (129) (64.5%; 95% CI: 57.44 - 71.12) carrying different comorbidity, among them high blood pressure 36 (27.9%; 95% CI, 20.37 - 36.48) and diabetes 32 (24.8%; 95% CI: 17.63 - 33.18) were found more prevalent. Moreover, the significant finding of the present study was 199 (99.5%; 95% CI: 97.25 - 99.99) vaccinated individuals survived with good health conditions and became negative in RT-qPCR. The authors suggest that health risk assessment among the COVID-19 vaccinated persons when infected with SARS-CoV-2 is crucial and time demanding task for the whole world. However, the present study illustrates that the administration of the 1st dose Oxford-AstraZeneca vaccine significantly reduces health risk during the COVID-19 infection period.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Eaftekhar Ahmed Rana", + "author_inst": "Chattogram Veterinary and Animal Sciences University" + }, + { + "author_name": "Pronesh Dutta", + "author_inst": "Chattogram Veterinary and Animal Sciences University" + }, + { + "author_name": "Md. Sirazul Islam", + "author_inst": "Chattogram Veterinary and Animal Sciences University" + }, + { + "author_name": "Tanvir Ahmad Nizami", + "author_inst": "Chattogram Veterinary and Animal Sciences University" + }, + { + "author_name": "Tridip Das", + "author_inst": "Chattogram Veterinary and Animal Sciences University" + }, + { + "author_name": "Sharmin Chowdhury", + "author_inst": "Chattogram Veterinary and Animal Sciences University" + }, + { + "author_name": "Goutam Buddha Das", + "author_inst": "Chattogram Veterinary and Animal Sciences University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.05.06.21256773", "rel_title": "Risk of COVID-19 infection and work place exposure of front-line mass media professionals", @@ -794812,837 +794045,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2021.05.11.21256877", - "rel_title": "A blood atlas of COVID-19 defines hallmarks of disease severity and specificity", - "rel_date": "2021-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.11.21256877", - "rel_abs": "Treatment of severe COVID-19 is currently limited by clinical heterogeneity and incomplete understanding of potentially druggable immune mediators of disease. To advance this, we present a comprehensive multi-omic blood atlas in patients with varying COVID-19 severity and compare with influenza, sepsis and healthy volunteers. We identify immune signatures and correlates of host response. Hallmarks of disease severity revealed cells, their inflammatory mediators and networks as potential therapeutic targets, including progenitor cells and specific myeloid and lymphocyte subsets, features of the immune repertoire, acute phase response, metabolism and coagulation. Persisting immune activation involving AP-1/p38MAPK was a specific feature of COVID-19. The plasma proteome enabled sub-phenotyping into patient clusters, predictive of severity and outcome. Tensor and matrix decomposition of the overall dataset revealed feature groupings linked with disease severity and specificity. Our systems-based integrative approach and blood atlas will inform future drug development, clinical trial design and personalised medicine approaches for COVID-19.", - "rel_num_authors": 204, - "rel_authors": [ - { - "author_name": "- The COvid-19 Multi-omics Blood ATlas (COMBAT) Consortium", - "author_inst": "" - }, - { - "author_name": "David J Ahern", - "author_inst": "University of Oxford" - }, - { - "author_name": "Zhichao Ai", - "author_inst": "University of Oxford" - }, - { - "author_name": "Mark Ainsworth", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Chris Allan", - "author_inst": "University of Oxford" - }, - { - "author_name": "Alice Allcock", - "author_inst": "University of Oxford" - }, - { - "author_name": "Azim Ansari", - "author_inst": "University of Oxford" - }, - { - "author_name": "Carolina V Arancibia-Carcamo", - "author_inst": "University of Oxford" - }, - { - "author_name": "Dominik Aschenbrenner", - "author_inst": "University of Oxford" - }, - { - "author_name": "Moustafa Attar", - "author_inst": "University of Oxford" - }, - { - "author_name": "J. Kenneth Baillie", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Eleanor Barnes", - "author_inst": "University of Oxford" - }, - { - "author_name": "Rachael Bashford-Rogers", - "author_inst": "University of Oxford" - }, - { - "author_name": "Archana Bashyal", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Sally Beer", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Georgina Berridge", - "author_inst": "University of Oxford" - }, - { - "author_name": "Amy Beveridge", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sagida Bibi", - "author_inst": "University of Oxford" - }, - { - "author_name": "Tihana Bicanic", - "author_inst": "St George's University of London" - }, - { - "author_name": "Luke Blackwell", - "author_inst": "University of Oxford" - }, - { - "author_name": "Paul Bowness", - "author_inst": "University of Oxford" - }, - { - "author_name": "Andrew Brent", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Andrew Brown", - "author_inst": "University of Oxford" - }, - { - "author_name": "John Broxholme", - "author_inst": "University of Oxford" - }, - { - "author_name": "David Buck", - "author_inst": "University of Oxford" - }, - { - "author_name": "Katie L Burnham", - "author_inst": "Wellcome Sanger Institute" - }, - { - "author_name": "Helen Byrne", - "author_inst": "University of Oxford" - }, - { - "author_name": "Susana Camara", - "author_inst": "University of Oxford" - }, - { - "author_name": "Ivan Candido Ferreira", - "author_inst": "University of Oxford" - }, - { - "author_name": "Philip Charles", - "author_inst": "University of Oxford" - }, - { - "author_name": "Wentao Chen", - "author_inst": "University of Oxford" - }, - { - "author_name": "Yi-Ling Chen", - "author_inst": "University of Oxford" - }, - { - "author_name": "Amanda Chong", - "author_inst": "University of Oxford" - }, - { - "author_name": "Elizabeth Clutterbuck", - "author_inst": "University of Oxford" - }, - { - "author_name": "Mark Coles", - "author_inst": "University of Oxford" - }, - { - "author_name": "Christopher P Conlon", - "author_inst": "University of Oxford" - }, - { - "author_name": "Richard Cornall", - "author_inst": "University of Oxford" - }, - { - "author_name": "Adam P Cribbs", - "author_inst": "University of Oxford" - }, - { - "author_name": "Fabiola Curion", - "author_inst": "University of Oxford" - }, - { - "author_name": "Emma E Davenport", - "author_inst": "Wellcome Sanger Institute" - }, - { - "author_name": "Neil Davidson", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Simon Davis", - "author_inst": "University of Oxford" - }, - { - "author_name": "Calliope Dendrou", - "author_inst": "University of Oxford" - }, - { - "author_name": "Julie Dequaire", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Lea Dib", - "author_inst": "University of Oxford" - }, - { - "author_name": "James Docker", - "author_inst": "University of Oxford" - }, - { - "author_name": "Christina Dold", - "author_inst": "University of Oxford" - }, - { - "author_name": "Tao Dong", - "author_inst": "University of Oxford" - }, - { - "author_name": "Damien Downes", - "author_inst": "University of Oxford" - }, - { - "author_name": "Alexander Drakesmith", - "author_inst": "University of Oxford" - }, - { - "author_name": "Susanna J Dunachie", - "author_inst": "University of Oxford" - }, - { - "author_name": "David A Duncan", - "author_inst": "University of Oxford" - }, - { - "author_name": "Chris Eijsbouts", - "author_inst": "University of Oxford" - }, - { - "author_name": "Robert Esnouf", - "author_inst": "University of Oxford" - }, - { - "author_name": "Alexis Espinosa", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Rachel Etherington", - "author_inst": "University of Oxford" - }, - { - "author_name": "Benjamin Fairfax", - "author_inst": "University of Oxford" - }, - { - "author_name": "Rory Fairhead", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Hai Fang", - "author_inst": "University of Oxford" - }, - { - "author_name": "Shayan Fassih", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Sally Felle", - "author_inst": "University of Oxford" - }, - { - "author_name": "Maria Fernandez Mendoza", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Ricardo Ferreira", - "author_inst": "University of Oxford" - }, - { - "author_name": "Roman Fischer", - "author_inst": "University of Oxford" - }, - { - "author_name": "Thomas Foord", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Aden Forrow", - "author_inst": "University of Oxford" - }, - { - "author_name": "John Frater", - "author_inst": "University of Oxford" - }, - { - "author_name": "Anastasia Fries", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Veronica Gallardo Sanchez", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Lucy Garner", - "author_inst": "University of Oxford" - }, - { - "author_name": "Clementine Geeves", - "author_inst": "University of Oxford" - }, - { - "author_name": "Dominique Georgiou", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Leila Godfrey", - "author_inst": "University of Oxford" - }, - { - "author_name": "Tanya Golubchik", - "author_inst": "University of Oxford" - }, - { - "author_name": "Maria Gomez Vazquez", - "author_inst": "University of Oxford" - }, - { - "author_name": "Angie Green", - "author_inst": "University of Oxford" - }, - { - "author_name": "Hong Harper", - "author_inst": "University of Oxford" - }, - { - "author_name": "Heather A Harrington", - "author_inst": "University of Oxford" - }, - { - "author_name": "Raphael Heilig", - "author_inst": "University of Oxford" - }, - { - "author_name": "Svenja Hester", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jennifer Hill", - "author_inst": "University of Oxford" - }, - { - "author_name": "Charles Hinds", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Clare Hird", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Ling-Pei Ho", - "author_inst": "University of Oxford" - }, - { - "author_name": "Renee Hoekzema", - "author_inst": "University of Oxford" - }, - { - "author_name": "Benjamin Hollis", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jim Hughes", - "author_inst": "University of Oxford" - }, - { - "author_name": "Paula Hutton", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Matthew Jackson", - "author_inst": "University of Oxford" - }, - { - "author_name": "Ashwin Jainarayanan", - "author_inst": "University of Oxford" - }, - { - "author_name": "Anna James-Bott", - "author_inst": "University of Oxford" - }, - { - "author_name": "Kathrin Jansen", - "author_inst": "University of Oxford" - }, - { - "author_name": "Katie Jeffery", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Elizabeth Jones", - "author_inst": "University of Oxford" - }, - { - "author_name": "Luke Jostins", - "author_inst": "University of Oxford" - }, - { - "author_name": "Georgina Kerr", - "author_inst": "University of Oxford" - }, - { - "author_name": "David Kim", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Paul Klenerman", - "author_inst": "University of Oxford" - }, - { - "author_name": "Julian C Knight", - "author_inst": "University of Oxford" - }, - { - "author_name": "Vinod Kumar", - "author_inst": "University of Oxford" - }, - { - "author_name": "Piyush Kumar Sharma", - "author_inst": "University of Oxford" - }, - { - "author_name": "Prathiba Kurupati", - "author_inst": "University of Oxford" - }, - { - "author_name": "Andrew Kwok", - "author_inst": "University of Oxford" - }, - { - "author_name": "Angela Lee", - "author_inst": "University of Oxford" - }, - { - "author_name": "Aline Linder", - "author_inst": "University of Oxford" - }, - { - "author_name": "Teresa Lockett", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Lorne Lonie", - "author_inst": "University of Oxford" - }, - { - "author_name": "Maria Lopopolo", - "author_inst": "University of Oxford" - }, - { - "author_name": "Martyna Lukoseviciute", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jian Luo", - "author_inst": "University of Oxford" - }, - { - "author_name": "Spyridoula Marinou", - "author_inst": "University of Oxford" - }, - { - "author_name": "Brian Marsden", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jose Martinez", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Philippa Matthews", - "author_inst": "University of Oxford" - }, - { - "author_name": "Michalina Mazurczyk", - "author_inst": "University of Oxford" - }, - { - "author_name": "Simon McGowan", - "author_inst": "University of Oxford" - }, - { - "author_name": "Stuart McKechnie", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Adam Mead", - "author_inst": "University of Oxford" - }, - { - "author_name": "Alexander J Mentzer", - "author_inst": "University of Oxford" - }, - { - "author_name": "Yuxin Mi", - "author_inst": "University of Oxford" - }, - { - "author_name": "Claudia Monaco", - "author_inst": "University of Oxford" - }, - { - "author_name": "Ruddy Montadon", - "author_inst": "University of Oxford" - }, - { - "author_name": "Giorgio Napolitani", - "author_inst": "University of Oxford" - }, - { - "author_name": "Isar Nassiri", - "author_inst": "University of Oxford" - }, - { - "author_name": "Alex Novak", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Darragh O'Brien", - "author_inst": "University of Oxford" - }, - { - "author_name": "Daniel O'Connor", - "author_inst": "University of Oxford" - }, - { - "author_name": "Denise O'Donnell", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Graham Ogg", - "author_inst": "University of Oxford" - }, - { - "author_name": "Lauren Overend", - "author_inst": "University of Oxford" - }, - { - "author_name": "Inhye Park", - "author_inst": "University of Oxford" - }, - { - "author_name": "Ian Pavord", - "author_inst": "University of Oxford" - }, - { - "author_name": "Yanchun Peng", - "author_inst": "University of Oxford" - }, - { - "author_name": "Frank Penkava", - "author_inst": "University of Oxford" - }, - { - "author_name": "Mariana Pereira Pinho", - "author_inst": "University of Oxford" - }, - { - "author_name": "Elena Perez", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Andrew J Pollard", - "author_inst": "University of Oxford" - }, - { - "author_name": "Fiona Powrie", - "author_inst": "University of Oxford" - }, - { - "author_name": "Bethan Psaila", - "author_inst": "University of Oxford" - }, - { - "author_name": "T. Phuong Quan", - "author_inst": "University of Oxford" - }, - { - "author_name": "Emmanouela Repapi", - "author_inst": "University of Oxford" - }, - { - "author_name": "Santiago Revale", - "author_inst": "University of Oxford" - }, - { - "author_name": "Laura Silva-Reyes", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jean-Baptiste Richard", - "author_inst": "University of Oxford" - }, - { - "author_name": "Charlotte Rich-Griffin", - "author_inst": "University of Oxford" - }, - { - "author_name": "Thomas Ritter", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Christine S Rollier", - "author_inst": "University of Oxford" - }, - { - "author_name": "Matthew Rowland", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Fabian Ruehle", - "author_inst": "University of Oxford" - }, - { - "author_name": "Mariolina Salio", - "author_inst": "University of Oxford" - }, - { - "author_name": "Stephen N Sansom", - "author_inst": "University of Oxford" - }, - { - "author_name": "Alberto Santos Delgado", - "author_inst": "University of Oxford" - }, - { - "author_name": "Tatjana Sauka-Spengler", - "author_inst": "University of Oxford" - }, - { - "author_name": "Ron Schwessinger", - "author_inst": "University of Oxford" - }, - { - "author_name": "Giuseppe Scozzafava", - "author_inst": "University of Oxford" - }, - { - "author_name": "Gavin Screaton", - "author_inst": "University of Oxford" - }, - { - "author_name": "Anna Seigal", - "author_inst": "University of Oxford" - }, - { - "author_name": "Malcolm G Semple", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Martin Sergeant", - "author_inst": "University of Oxford" - }, - { - "author_name": "Christina Simoglou Karali", - "author_inst": "University of Oxford" - }, - { - "author_name": "David Sims", - "author_inst": "University of Oxford" - }, - { - "author_name": "Donal Skelly", - "author_inst": "University of Oxford" - }, - { - "author_name": "Hubert Slawinski", - "author_inst": "University of Oxford" - }, - { - "author_name": "Alberto Sobrinodiaz", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Nikolaos Sousos", - "author_inst": "University of Oxford" - }, - { - "author_name": "Lizzie Stafford", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Lisa Stockdale", - "author_inst": "University of Oxford" - }, - { - "author_name": "Marie Strickland", - "author_inst": "University of Oxford" - }, - { - "author_name": "Otto Sumray", - "author_inst": "University of Oxford" - }, - { - "author_name": "Bo Sun", - "author_inst": "University of Oxford" - }, - { - "author_name": "Chelsea Taylor", - "author_inst": "University of Oxford" - }, - { - "author_name": "Stephen Taylor", - "author_inst": "University of Oxford" - }, - { - "author_name": "Adan Taylor", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Supat Thongjuea", - "author_inst": "University of Oxford" - }, - { - "author_name": "Hannah Thraves", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "John A Todd", - "author_inst": "University of Oxford" - }, - { - "author_name": "Adriana Tomic", - "author_inst": "University of Oxford" - }, - { - "author_name": "Orion Tong", - "author_inst": "University of Oxford" - }, - { - "author_name": "Amy Trebes", - "author_inst": "University of Oxford" - }, - { - "author_name": "Dominik Trzupek", - "author_inst": "University of Oxford" - }, - { - "author_name": "Felicia A Tucci", - "author_inst": "University of Oxford" - }, - { - "author_name": "Lance Turtle", - "author_inst": "Liverpool University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Irina Udalova", - "author_inst": "University of Oxford" - }, - { - "author_name": "Holm Uhlig", - "author_inst": "University of Oxford" - }, - { - "author_name": "Erinke van Grinsven", - "author_inst": "University of Oxford" - }, - { - "author_name": "Iolanda Vendrell", - "author_inst": "University of Oxford" - }, - { - "author_name": "Marije Verheul", - "author_inst": "University of Oxford" - }, - { - "author_name": "Alexandru Voda", - "author_inst": "University of Oxford" - }, - { - "author_name": "Guanlin Wang", - "author_inst": "University of Oxford" - }, - { - "author_name": "Lihui Wang", - "author_inst": "University of Oxford" - }, - { - "author_name": "Dapeng Wang", - "author_inst": "University of Oxford" - }, - { - "author_name": "Peter Watkinson", - "author_inst": "University of Oxford" - }, - { - "author_name": "Robert Watson", - "author_inst": "University of Oxford" - }, - { - "author_name": "Michael Weinberger", - "author_inst": "University of Oxford" - }, - { - "author_name": "Justin Whalley", - "author_inst": "University of Oxford" - }, - { - "author_name": "Lorna Witty", - "author_inst": "University of Oxford" - }, - { - "author_name": "Katherine Wray", - "author_inst": "University of Oxford" - }, - { - "author_name": "Luzheng Xue", - "author_inst": "University of Oxford" - }, - { - "author_name": "Hing Yuen Yeung", - "author_inst": "University of Oxford" - }, - { - "author_name": "Zixi Yin", - "author_inst": "University of Oxford" - }, - { - "author_name": "Rebecca K Young", - "author_inst": "Oxford University Hospitals NHS Foundation Trust" - }, - { - "author_name": "Jonathan Youngs", - "author_inst": "St George's University of London" - }, - { - "author_name": "Ping Zhang", - "author_inst": "University of Oxford" - }, - { - "author_name": "Yasemin-Xiomara Zurke", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.08.21256866", "rel_title": "Antibody Responses After a Single Dose of ChAdOx1 nCoV-19 Vaccine in Healthcare Workers Previously Infected with SARS-CoV-2", @@ -796850,6 +795252,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2021.05.07.21256839", + "rel_title": "Cross-sectional study of the association between perceived organizational support and COVID-19 vaccine intention", + "rel_date": "2021-05-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.07.21256839", + "rel_abs": "ObjectivesThis study examined the association between perceived organizational support (POS) and COVID-19 vaccine intention and the influence of the implementation of workplace infection prevention measures.\n\nMethodsWe analyzed 23,846 workers using data from an Internet survey of workers aged 20-65 years conducted in December 2020, during a period of widespread COVID-19 infection in Japan.\n\nResultsA higher POS was associated with a higher intention to vaccinate. The relationship between POS and vaccine intention was attenuated when adjusted for infection prevention measures in the workplace.\n\nConclusionsIn workplaces where POS is present, a sense of responsibility to the group and altruistic behavior may arise. This means employees act to acquire herd immunity to protect others, which may result in increased vaccine intention. The association between POS and vaccination intention was attenuated by adjusting for workplace infection prevention measures, which suggested that infection prevention measures may be a confounding factor or that POS created a health climate that promoted infection prevention measures. The results suggest that working to improve employee well-being and implementing appropriate workplace infection prevention measures during infectious disease outbreaks may promote vaccination behavior and contribute to the acquisition of herd immunity in the community.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Yuichi Kobayashi", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Tomohisa Nagata", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Yoshihisa Fujino", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Ayako Hino", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Seiichiro Tateishi", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Akira Ogami", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Mayumi Tsuji", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Shinya Matsuda", + "author_inst": "University of Occupational and Environmental Health, Japan" + }, + { + "author_name": "Koji Mori", + "author_inst": "University of Occupational and Environmental Health, Japan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2021.05.05.21256384", "rel_title": "Genomic and epidemiological analysis of SARS-CoV-2 viruses in Sri Lanka", @@ -797458,45 +795911,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, - { - "rel_doi": "10.1101/2021.05.08.21256792", - "rel_title": "Yet another lockdown? A large-scale study on people's unwillingness to be confined during the first 5 months of the COVID-19 pandemic in Spain", - "rel_date": "2021-05-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.08.21256792", - "rel_abs": "Population confinements have been one of the most widely adopted non-pharmaceutical interventions (NPIs) implemented by governments across the globe to help contain the spread of the SARS-CoV-2 virus. While confinement measures have been proven to be effective to reduce the number of infections, they entail significant economic and social costs. Thus, different policy makers and social groups have exhibited varying levels of acceptance of this type of measures. In this context, understanding the factors that determine the willingness of individuals to be confined during a pandemic is of paramount importance, particularly, to policy and decision-makers. In this paper, we study the factors that influence the unwillingness to be confined during the COVID-19 pandemic by means of a large-scale, online population survey deployed in Spain. We apply both quantitative (logistic regression) and qualitative (automatic pattern discovery) methods and consider socio-demographic, economic and psychological factors, together with the 14-day cumulative incidence per 100,000 inhabitants. Our analysis of 109,515 answers to the survey covers data spanning over a 5-month time period to shed light on the impact of the passage of time. We find evidence of pandemic fatigue as the percentage of those who report an unwillingness to be in confinement increases over time; we identify significant gender differences, with women being generally less likely than men to be able to sustain long-term confinement of at least 6 months; we uncover that the psychological impact was the most important factor to determine the willingness to be in confinement at the beginning of the pandemic, to be replaced by the economic impact as the most important variable towards the end of our period of study. Our results highlight the need to design gender and age specific public policies, to implement psychological and economic support programs and to address the evident pandemic fatigue as the success of potential future confinements will depend on the populations willingness to comply with them.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Marina Martinez-Garcia", - "author_inst": "Jaume I University" - }, - { - "author_name": "Alejandro Rabasa", - "author_inst": "Miguel Hernandez University" - }, - { - "author_name": "Xavier Barber", - "author_inst": "Miguel Hernandez University" - }, - { - "author_name": "Kristina Polotskaya", - "author_inst": "Miguel Hernandez University" - }, - { - "author_name": "Kristof Roomp", - "author_inst": "Microsoft" - }, - { - "author_name": "Nuria Oliver", - "author_inst": "ELLIS Unit Alicante Foundation and Data-Pop Alliance" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.05.04.21255000", "rel_title": "COVID-19 Compromises In The Medical Practice And The Consequential Effect On Endometriosis Patients", @@ -799016,6 +797430,57 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.05.07.443114", + "rel_title": "Following the Trail of One Million Genomes: Footprints of SARS-CoV-2 Adaptation to Humans", + "rel_date": "2021-05-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.07.443114", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has accumulated genomic mutations at an approximately linear rate since it first infected human populations in late 2019. Controversies remain regarding the identity, proportion, and effects of adaptive mutations as SARS-CoV-2 evolves from a bat-to a human-adapted virus. The potential for vaccine-escape mutations poses additional challenges in pandemic control. Despite being of great interest to therapeutic and vaccine development, human-adaptive mutations in SARS-CoV-2 are masked by a genome-wide linkage disequilibrium under which neutral and even deleterious mutations can reach fixation by chance or through hitchhiking. Furthermore, genome-wide linkage equilibrium imposes clonal interference by which multiple adaptive mutations compete against one another. Informed by insights from microbial experimental evolution, we analyzed close to one million SARS-CoV-2 genomes sequenced during the first year of the COVID-19 pandemic and identified putative human-adaptive mutations according to the rates of synonymous and missense mutations, temporal linkage, and mutation recurrence. Furthermore, we developed a forward-evolution simulator with the realistic SARS-CoV-2 genome structure and base substitution probabilities able to predict viral genome diversity under neutral, background selection, and adaptive evolutionary models. We conclude that adaptive mutations have emerged early, rapidly, and constantly to dominate SARS-CoV-2 populations despite clonal interference and purifying selection. Our analysis underscores a need for genomic surveillance of mutation trajectories at the local level for early detection of adaptive and immune-escape variants. Putative human-adaptive mutations are over-represented in viral proteins interfering host immunity and binding host-cell receptors and thus may serve as priority targets for designing therapeutics and vaccines against human-adapted forms of SARS-CoV-2.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Saymon Akther", + "author_inst": "Graduate Center, City University of New York" + }, + { + "author_name": "Edgaras Bezrucenkovas", + "author_inst": "Hunter College City University of New York" + }, + { + "author_name": "Li Li", + "author_inst": "Graduate Center, City University of New York" + }, + { + "author_name": "Brian Sulkow", + "author_inst": "Hunter College City University of New York" + }, + { + "author_name": "Lia Di", + "author_inst": "Hunter College City University of New York" + }, + { + "author_name": "Desiree Pante", + "author_inst": "Hunter College City University of New York" + }, + { + "author_name": "Che L. Martin", + "author_inst": "New York Presbyterian Hospital" + }, + { + "author_name": "Benjamin J. Luft", + "author_inst": "Stony Brook University" + }, + { + "author_name": "Weigang Qiu", + "author_inst": "Hunter College of The City University of New York" + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2021.05.09.443238", "rel_title": "Design of the SARS-CoV-2 RBD vaccine antigen improves neutralizing antibody response", @@ -799688,73 +798153,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2021.05.05.21256677", - "rel_title": "SARS-CoV-2 RNA in urban wastewater samples to monitor the COVID-19 epidemic in Lombardy, Italy (March - June 2020)", - "rel_date": "2021-05-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.05.21256677", - "rel_abs": "Wastewater-based viral surveillance is a promising approach to monitor the circulation of SARS-CoV-2 in the general population. The aim of this study was to develop an analytical method to detect SARS-CoV-2 RNA in urban wastewater, to be implemented in the framework of a surveillance network in the Lombardy region (Northern Italy). This area was the first hotspot of COVID-19 in Europe. Composite 24h samples were collected weekly in eight cities from end-March to mid-June 2020 (first peak of the epidemic). The method developed and optimized, involved virus concentration, using PEG centrifugation, and one-step real-time RT-PCR for analysis. SARS-CoV-2 RNA was identified in 65 (61%) out of 107 samples, and the viral concentrations (up to 2.1 E +05 copies/L) were highest in March-April. By mid-June, wastewater samples tested negative in all the cities. Viral loads were used for inter-city comparison and Brembate, Ranica and Lodi had the highest. The pattern of decrease of SARS-CoV-2 in wastewater was closely comparable to the decline of active COVID-19 cases in the population, reflecting the effect of lock-down. Wastewater surveillance of SARS-CoV-2 can integrate ongoing virological surveillance of COVID-19, providing information from both symptomatic and asymptomatic individuals, and monitoring the effect of health interventions.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Sara Castiglioni", - "author_inst": "Istituto di Ricerche Farmacologiche Mario Negri IRCCS" - }, - { - "author_name": "Silvia Schiarea", - "author_inst": "Istituto di Ricerche Farmacologiche Mario Negri IRCCS" - }, - { - "author_name": "Laura Pellegrinelli", - "author_inst": "University of Milan" - }, - { - "author_name": "Valeria Primache", - "author_inst": "University of Milan" - }, - { - "author_name": "Cristina Galli", - "author_inst": "University of Milan" - }, - { - "author_name": "Laura Bubba", - "author_inst": "University of Milan" - }, - { - "author_name": "Federica Mancinelli", - "author_inst": "Istituto di Ricerche Farmacologiche Mario Negri IRCCS" - }, - { - "author_name": "Marilisa Marinelli", - "author_inst": "Bio-Rad Laboratories" - }, - { - "author_name": "Danilo Cereda", - "author_inst": "Regione Lombardia" - }, - { - "author_name": "Emanuela Ammoni", - "author_inst": "Regione Lombardia" - }, - { - "author_name": "Elena Pariani", - "author_inst": "University of Milan" - }, - { - "author_name": "Ettore Zuccato", - "author_inst": "Istituto di Ricerche Farmacologiche Mario Negri IRCCS" - }, - { - "author_name": "Sandro Binda", - "author_inst": "University of Milan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.05.05.21256667", "rel_title": "The impact of COVID-19 on the provision of respectful maternity care: findings from a global survey of health workers", @@ -801530,6 +799928,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.06.21256523", + "rel_title": "The COVID-19 pandemic storm in India", + "rel_date": "2021-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.06.21256523", + "rel_abs": "The sharp increase in the number of new COVID-19 patients in India in the second half of April 2021 has caused alarm around the world. A detailed analysis of this pandemic storm is still ahead. We present the results of anterior analysis using a generalized SIR-model (susceptible-infected-removed). The final size of this pandemic wave and its duration are predicted. Obtained results show that the COVID-19 pandemic will be a problem for mankind for a very long time.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Igor Nesteruk", + "author_inst": "Institute of Hydromechanics National Academy of sciences of Ukraine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.06.21256651", "rel_title": "Higher case fatality rate among obstetric patients with COVID-19 in the second year of pandemic in Brazil: do new genetic variants play a role?", @@ -801910,33 +800327,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.04.21256635", - "rel_title": "Visual Exploratory Analysis of COVID-19 Pandemic: One Year After the Outbreak", - "rel_date": "2021-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.04.21256635", - "rel_abs": "BackgroundGovernments across the globe have taken different measures to handle the Covid-19 outbreak since it began in early 2020. Countries implemented various policies and restrictive measures to prevent transmission of the virus, reduce the impacts of the outbreak (i.e., individual, social, and economic), and provide effective control measures. Although it has been over one year since the outbreak started, few studies have examined the long-term effects of the pandemic. Furthermore, researchers need to examine which government intervention variables are the most, and least, effective. Such analysis is critical to determine the best practices in support of policy decisions.\n\nMethodsVisual exploratory data analysis (V-EDA) offers a user-friendly data visualization model to evaluate the impact of the pandemic. It allows one to observe visual patterns of trends. The V-EDA was conducted on one year data for the COVID-19 Pandemic, one year after the outbreak between 1 January and 31 December, 2020. The data were analyzed using the students t-test to verify if there was a statistical difference between two independent groups, and the Spearman test was also used to analyze the correlation coefficient between two quantitative datasets and their positive or negative inclination.\n\nFindingsWe found that high-testing countries had more cases per million than low-testing countries. For low-testing countries, however, there was a positive correlation between the testing level and the number of cases per million. This suggests that high-testing countries tested in a preventive manner while low-testing countries may have a higher number of cases than those confirmed. The poorest developing countries have reduced testing which can coincide with the reduction in new cases, which we did not observe in the high-testing countries. Among the restrictive measures analyzed, a higher population aged 70 or older and lower GDP per capita was related to a higher case fatality ratio. Restrictive measures reduce the number of new cases after four weeks, indicating the minimum time required for the measures to have a positive effect. Finally, public event cancellation, international travel control, school closing, contact tracing, and facial coverings were the most important measures to reduce virus spread. We observed that countries with the lowest number of cases had a higher stringency index.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Amril Nazir", - "author_inst": "Zayed University" - }, - { - "author_name": "Suleyman Ulusoy", - "author_inst": "American University of Ras Al Khaimah" - }, - { - "author_name": "Lujaini Lotfi", - "author_inst": "AnalytiCray Solutions" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.05.04.21256662", "rel_title": "Teletherapy for children with developmental disorders during the COVID-19 pandemic in the Philippines: a mixed-methods evaluation from the perspectives of parents and therapists", @@ -803452,6 +801842,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.05.06.21256476", + "rel_title": "Japan's Covid mitigation strategy and its epidemic prediction", + "rel_date": "2021-05-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.06.21256476", + "rel_abs": "The COVID-19 epidemic curve in Japan was constructed based on daily reported data from January 14, 2020 until April 20, 2021. A SEIR compartmental model was used for the curve fitting by updating the estimation per wave. In the current vaccination pace of 1/1000, restrictions (state of emergency in Japan) would be repeated 4 times until the end of next March. In the case of 1/500, another round of restriction would be required in the summer 2021, after which the infection would be mitigated. In the case of 1/250, there would be no need for restriction after the current spring restriction. The scenario of completing the vaccination of 110 million people by the end of March 2020 corresponds to the case of 1/250 in this curve. When considering the likely spread of variant with greater infectiousness (here we assume 1.3 times greater than the original virus), 1/500 pace of vaccination would not be enough to contain it and need several series of restrictions. There are currently several variants of concern that are already spreading in urban areas in this country. In the new stage of the replacement of variants, if the vaccination pace could not be quadrupled from the current pace, Japan could not become a zero covid (zero corona) country at least one year.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Yasuharu Tokuda", + "author_inst": "Muribushi Okinawa Center for Teaching Hospitals" + }, + { + "author_name": "Toshikazu Kuniya", + "author_inst": "Kobe University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.05.07.21256652", "rel_title": "Safety and immunogenicity of INO-4800 DNA vaccine against SARS-CoV-2: a preliminary report of a randomized, blinded, placebo-controlled, Phase 2 clinical trial in adults at high risk of viral exposure", @@ -803992,125 +802405,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.05.03.21256520", - "rel_title": "The BNT162b2 mRNA vaccine against SARS-CoV-2 reprograms both adaptive and innate immune responses", - "rel_date": "2021-05-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.03.21256520", - "rel_abs": "The mRNA-based BNT162b2 protects against severe disease and mortality caused by SARS-CoV-2 through induction of specific antibody and T-cell responses. Much less is known about its broad effects on immune responses against other pathogens. In the present study, we investigated the specific adaptive immune responses induced by BNT162b2 vaccination against various SARS-CoV-2 variants, as well as its effects on the responsiveness of human immune cells upon stimulation with heterologous viral, bacterial, and fungal pathogens. BNT162b2 vaccination induced effective humoral and cellular immunity against SARS-CoV-2 that started to wane after six months. We also observed long-term transcriptional changes in immune cells after vaccination, as assessed by RNA sequencing. Additionally, vaccination with BNT162b2 modulated innate immune responses as measured by the production of inflammatory cytokines when stimulated with various microbial stimuli other than SARS-CoV-2, including higher IL-1/IL-6 release and decreased production of IFN-. Altogether, these data expand our knowledge regarding the overall immunological effects of this new class of vaccines and underline the need of additional studies to elucidate their effects on both innate and adaptive immune responses.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Konstantin Fohse", - "author_inst": "Radboud university medical center Nijmegen, The Netherlands" - }, - { - "author_name": "Busra Geckin", - "author_inst": "Radboud university medical center Nijmegen, The Netherlands" - }, - { - "author_name": "Martijn Zoodsma", - "author_inst": "Helmholtz Centre for Infection Research" - }, - { - "author_name": "Gizem Kilic", - "author_inst": "Radboud university medical center Nijmegen, The Netherlands" - }, - { - "author_name": "Zhaoli Liu", - "author_inst": "Helmholtz-Zentrum fur Infektionsforschung GmbH" - }, - { - "author_name": "Rutger J. Roring", - "author_inst": "Radboud university medical center Nijmegen, The Netherlands" - }, - { - "author_name": "Gijs J. Overheul", - "author_inst": "Radboud university medical center Nijmegen, The Netherlands" - }, - { - "author_name": "Josephine S. van de Maat", - "author_inst": "Radboud university medical center Nijmegen, The Netherlands" - }, - { - "author_name": "Ozlem Bulut", - "author_inst": "Radboud university medical center Nijmegen, The Netherlands" - }, - { - "author_name": "Jacobien J. Hoogerwerf", - "author_inst": "Radboud university medical center Nijmegen, The Netherlands" - }, - { - "author_name": "Jaap ten Oever", - "author_inst": "Radboud university medical center Nijmegen, The Netherlands" - }, - { - "author_name": "Elles Simonetti", - "author_inst": "Radboud university medical center Nijmegen, The Netherlands" - }, - { - "author_name": "Heiner Schaal", - "author_inst": "Institut of Virology, University Hospital Dusseldorf" - }, - { - "author_name": "Ortwin Adams", - "author_inst": "Institut of Virology, University Hospital Dusseldorf" - }, - { - "author_name": "Lisa Muller", - "author_inst": "Institut of Virology, University Hospital Dusseldorf" - }, - { - "author_name": "Philipp N. Ostermann", - "author_inst": "Institut of Virology, University Hospital Dusseldorf" - }, - { - "author_name": "Frank L. van de Veerdonk", - "author_inst": "Radboud university medical center Nijmegen, The Netherlands" - }, - { - "author_name": "Leo A. B. Joosten", - "author_inst": "Radboud university medical center Nijmegen, The Netherlands" - }, - { - "author_name": "Bart L. Haagmans", - "author_inst": "Erasmus medical center Rotterdam, The Netherlands" - }, - { - "author_name": "Reinout van Crevel", - "author_inst": "Radboud university medical center Nijmegen, The Netherlands" - }, - { - "author_name": "Ronald P. van Rij", - "author_inst": "Radboud university medical center Nijmegen, The Netherlands" - }, - { - "author_name": "Corine GeurtsvanKessel", - "author_inst": "Erasmus medical center Rotterdam, The Netherlands" - }, - { - "author_name": "Marien I. de Jonge", - "author_inst": "Radboud university medical center Nijmegen, The Netherlands" - }, - { - "author_name": "Yang Li", - "author_inst": "Centre for Individualised Infection Medicine (CiiM) & TWINCORE, joint ventures between the Helmholtz-Centre for Infection Research (HZI) and the Hannover Medica" - }, - { - "author_name": "Jorge Dominguez-Andres", - "author_inst": "Radboud university medical center Nijmegen, The Netherlands" - }, - { - "author_name": "Mihai G. Netea", - "author_inst": "Radboud university medical center Nijmegen, The Netherlands" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.05.03.21256556", "rel_title": "Estimating vaccine efficacy against transmission via effect on viral load", @@ -805662,6 +803956,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.05.02.21256474", + "rel_title": "Infants are more susceptible to COVID-19 than children", + "rel_date": "2021-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.02.21256474", + "rel_abs": "Angiotensin-converting enzyme 2 (ACE2) has been found to mediate the host cell entry of SARS-CoV-2 that causes COVID-19. However, the link between ACE2 and the observed susceptibility of SARS-CoV-2 infection remains elusive. In contrast, observational studies can help identify the susceptibility biomarker of SARS-CoV-2 infection, those associated with age for example. Data of all PCR tests performed in the state of Sao Paulo of Brazil were gathered from the government database and were analyzed using multivariate logistic regression. Adjusted odds ratios for positive test results were calculated with the adjustment of age, gender, and comorbidities. Over 1.7 million test results were included in the study of which 38% were positive. Elderly was most vulnerable to SARS-CoV-2 infection. While underages were less susceptible than adults aged below 60 years, susceptibility was not equal among different pediatric groups. It is found that age and susceptibility to SARS-CoV-2 infection are not inversely related, but U-shaped, with infants more susceptible than children. Biomarkers that are linearly associated with age cannot explain the reduced susceptibility in children. These include lymphocyte count and cross-reactive antibodies against other coronaviruses that offers cross-protection. The expression level of ACE2 may still be able to explain but further investigations are needed.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Char Leung", + "author_inst": "Deakin University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.05.442536", "rel_title": "Uncovering cryptic pockets in the SARS-CoV-2 spike glycoprotein", @@ -806093,37 +804406,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.05.04.442701", - "rel_title": "SARS-CoV-2 cell-to-cell infection is resistant to neutralizing antibodies", - "rel_date": "2021-05-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.04.442701", - "rel_abs": "The COVID-19 pandemic caused by SARS-CoV-2 has posed a global threat to human lives and economics. One of the best ways to determine protection against the infection is to quantify the neutralizing activity of serum antibodies. Multiple assays have been developed to validate SARS-CoV-2 neutralization; most of them utilized lentiviral or vesicular stomatitis virus-based particles pseudotyped with the spike (S) protein, making them safe and acceptable to work with in many labs. However, these systems are only capable of measuring infection with purified particles. This study has developed a pseudoviral assay with replication-dependent reporter vectors that can accurately quantify the level of infection directly from the virus producing cell to the permissive target cell. Comparative analysis of cell-free and cell-to-cell infection revealed that the neutralizing activity of convalescent sera was more than tenfold lower in cell cocultures than in the cell-free mode of infection. As the pseudoviral system could not properly model the mechanisms of SARS-CoV-2 transmission, similar experiments were performed with replication-competent coronavirus, which detected nearly complete SARS-CoV-2 cell-to-cell infection resistance to neutralization by convalescent sera. Based on available studies, this is the first attempt to quantitatively measure SARS-CoV-2 cell-to-cell infection, for which the mechanisms are largely unknown. The findings suggest that this route of SARS-CoV-2 transmission could be of great importance for treatment and prevention of COVID-19.\n\nImportanceImmune surveillance of viral or bacterial infections is largely mediated by neutralizing antibodies. Antibodies against the SARS-CoV-2 spike protein are produced after vaccination or infection, but their titers only partly reflect the degree of protection against infection. To identify protective antibodies, a neutralization test with replicating viruses or pseudoviruses (PVs) is required. This study developed lentiviral-based PV neutralization assays that, unlike similar systems reported earlier, enable quantitative measurement of SARS-CoV-2 neutralization in cell cocultures. Using both PVs and replication-competent virus, it was demonstrated that SARS-CoV-2 cell-to-cell infection is considerably more resistant to serum neutralization than infection with purified viral particles. The tests are easy to set up in many labs, and are believed to be more informative for monitoring SARS-CoV-2 collective immunity or entry inhibitor screening.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Natalia Kruglova", - "author_inst": "Institute of Gene Biology RAS" - }, - { - "author_name": "Andrei E. Siniavin", - "author_inst": "Ivanovsky Institute of Virology, Gamaleya National Center for Epidemiology and Microbiology" - }, - { - "author_name": "Vladimir A. Gushchin", - "author_inst": "Federal Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya" - }, - { - "author_name": "Dmitriy Mazurov", - "author_inst": "Institute of Gene Biology RAS" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.05.04.442686", "rel_title": "Emerging genetic diversity of SARS-CoV-2 RNA dependent RNA polymerase (RdRp) alters its B-cell epitopes", @@ -807655,6 +805937,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, + { + "rel_doi": "10.1101/2021.05.03.21256506", + "rel_title": "Comprehensive mapping of neutralizing antibodies against SARS-CoV-2 variants induced by natural infection or vaccination", + "rel_date": "2021-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.03.21256506", + "rel_abs": "BackgroundImmunity after SARS-CoV-2 infection or vaccination has been threatened by recently emerged SARS-CoV-2 variants. A systematic summary of the landscape of neutralizing antibodies against emerging variants is needed.\n\nMethodsWe systematically searched PubMed, Embase, Web of Science, and 3 pre-print servers for studies that evaluated neutralizing antibodies titers induced by previous infection or vaccination against SARS-CoV-2 variants and comprehensively collected individual data. We calculated lineage-specific GMTs across different study participants and types of neutralization assays.\n\nFindingsWe identified 56 studies, including 2,483 individuals and 8,590 neutralization tests, meeting the eligibility criteria. Compared with lineage B, we estimate a 1.5-fold (95% CI: 1.0-2.2) reduction in neutralization against the B.1.1.7, 8.7-fold (95% CI: 6.5-11.7) reduction against B.1.351 and 5.0-fold (95% CI: 4.0-6.2) reduction against P.1. The estimated neutralization reductions for B.1.351 compared to lineage B were 240.2-fold (95% CI: 124.0-465.6) reduction for non-replicating vector platform, 4.6-fold (95% CI: 4.0-5.2) reduction for RNA platform, and 1.6-fold (95% CI: 1.2-2.1) reduction for protein subunit platform. The neutralizing antibodies induced by administration of inactivated vaccines and mRNA vaccines against lineage P.1 were also remarkably reduced by an average of 5.9-fold (95% CI: 3.7-9.3) and 1.5-fold (95% CI: 1.2-1.9).\n\nInterpretationOur findings indicate that the antibody response established by natural infection or vaccination might be able to effectively neutralize B.1.1.7, but neutralizing titers against B.1.351 and P.1 suffered large reductions. Standardized protocols for neutralization assays, as well as updating immune-based prevention and treatment, are needed.\n\nFundingChinese National Science Fund for Distinguished Young Scholars\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSSeveral newly emerged SARS-CoV-2 variants have raised significant concerns globally, and there is concern that SARS-CoV-2 variants can evade immune responses that are based on the prototype strain. It is not known to what extent do emerging SARS-CoV-2 variants escape the immune response induced by previous infection or vaccination. However, existing studies of neutralizing potency against SARS-CoV-2 variants are based on limited numbers of samples and lack comparability between different laboratory methods. Furthermore, there are no studies providing whole picture of neutralizing antibodies induced by prior infections or vaccination against emerging variants. Therefore, we systematically reviewed and quantitively synthesized evidence on the degree to which antibodies from previous SARS-CoV-2 infection or vaccination effectively neutralize variants.\n\nAdded value of this studyIn this study, 56 studies, including 2,483 individuals and 8,590 neutralization tests, were identified. Antibodies from natural infection or vaccination are likely to effectively neutralize B.1.1.7, but neutralizing titers against B.1.351 and P.1 suffered large reductions. Lineage B.1.351 escaped natural-infection-mediated neutralization the most, with GMT of 79.2 (95% CI: 68.5-91.6), while neutralizing antibody titers against the B.1.1.7 variant were largely preserved (254.6, 95% CI: 214.1-302.8). Compared with lineage B, we estimate a 1.5-fold (95% CI: 1.0-2.2) reduction in neutralization against the B.1.1.7, 8.7-fold (95% CI: 6.5-11.7) reduction against B.1.351 and 5.0-fold (95% CI: 4.0-6.2) reduction against P.1. The neutralizing antibody response after vaccinating with non-replicating vector vaccines against lineage B.1.351 was worse than responses elicited by vaccines on other platforms, with levels lower than that of individuals who were previously infected. The neutralizing antibodies induced by administration of inactivated vaccines and mRNA vaccines against lineage P.1 were also remarkably reduced by an average of 5.9-fold (95% CI: 3.7-9.3) and 1.5-fold (95% CI: 1.2-1.9).\n\nImplications of all the available evidenceOur findings indicate that antibodies from natural infection of the parent lineage of SARS-CoV-2 or vaccination may be less able to neutralize some emerging variants, and antibody-based therapies may need to be updated. Furthermore, standardized protocols for neutralizing antibody testing against SARS-CoV-2 are needed to reduce lab-to-lab variations, thus facilitating comparability and interpretability across studies.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Xinhua Chen", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Zhiyuan Chen", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Andrew S Azman", + "author_inst": "Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA" + }, + { + "author_name": "Ruijia Sun", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Wanying Lu", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Nan Zheng", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Jiaxin Zhou", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Qianhui Wu", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Xiaowei Deng", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Zeyao Zhao", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Xinghui Chen", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Shijia Ge", + "author_inst": "Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China" + }, + { + "author_name": "Juan Yang", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + }, + { + "author_name": "Daniel T Leung", + "author_inst": "Division of Infectious Diseases, University of Utah School of Medicine, Salt Lake City, UT, USA" + }, + { + "author_name": "Hongjie Yu", + "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.05.02.21256495", "rel_title": "Male-Female Disparities in Years of Potential Life Lost Attributable to COVID-19 in the United States: A State-by-State Analysis", @@ -808003,53 +806360,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.05.04.442648", - "rel_title": "Immunolocalization studies of vimentin and ACE2 on the surface of cells exposed to SARS-CoV-2 Spike proteins", - "rel_date": "2021-05-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.04.442648", - "rel_abs": "The Spike protein from SARS-CoV-2 mediates docking of the virus onto cells and contributes to viral invasion. Several cellular receptors are involved in SARS-CoV-2 Spike docking at the cell surface, including ACE2 and neuropilin. The intermediate filament protein vimentin has been reported to be present at the surface of certain cells and act as a co-receptor for several viruses; furthermore, its potential involvement in interactions with Spike proteins has been proposed. Here we have explored the binding of Spike protein constructs to several cell types using low-temperature immunofluorescence approaches in live cells, to minimize internalization. Incubation of cells with tagged Spike S or Spike S1 subunit led to discrete dotted patterns at the cell surface, which showed scarce colocalization with a lipid raft marker, but consistent coincidence with ACE2. Under our conditions, vimentin immunoreactivity appeared as spots or patches unevenly distributed at the surface of diverse cell types. Remarkably, several observations including potential antibody internalization and adherence to cells of vimentin-positive structures present in the extracellular medium exposed the complexity of vimentin cell surface immunoreactivity, which requires careful assessment. Notably, overall colocalization of Spike and vimentin signals markedly varied with the cell type and the immunodetection sequence. In turn, vimentin-positive spots moderately colocalized with ACE2; however, a particular enrichment was detected at elongated structures positive for acetylated tubulin, consistent with primary cilia, which also showed Spike binding. Thus, these results suggest that vimentin-ACE2 interaction could occur at selective locations near the cell surface, including ciliated structures, which can act as platforms for SARS-CoV-2 docking.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Vasiliki Lalioti", - "author_inst": "Centro de Investigaciones Biol\u00f3gicas Margarita Salas, CSIC" - }, - { - "author_name": "Silvia Gonz\u00e1lez-Sanz", - "author_inst": "Centro de Investigaciones Biol\u00f3gicas Margarita Salas, CSIC" - }, - { - "author_name": "Irene Lois-Bermejo", - "author_inst": "Centro de Investigaciones Biol\u00f3gicas Margarita Salas, CSIC" - }, - { - "author_name": "Patricia Gonz\u00e1lez-Jim\u00e9nez", - "author_inst": "Centro de Investigaciones Biol\u00f3gicas Margarita Salas, CSIC" - }, - { - "author_name": "\u00c1lvaro Viedma-Poyatos", - "author_inst": "Centro de Investigaciones Biol\u00f3gicas Margarita Salas, CSIC" - }, - { - "author_name": "Andrea Merino", - "author_inst": "Centro de Investigaciones Biol\u00f3gicas Margarita Salas, CSIC" - }, - { - "author_name": "Mar\u00eda A Pajares", - "author_inst": "Centro de Investigaciones Biol\u00f3gicas Margarita Salas, CSIC" - }, - { - "author_name": "Dolores P\u00e9rez-Sala", - "author_inst": "Centro de Investigaciones Biol\u00f3gicas Margarita Salas, CSIC" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2021.04.30.442229", "rel_title": "The Immunological Factors Predisposing To Severe COVID-19 Are Already Present In Healthy Elderly And Men", @@ -809165,6 +807475,141 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.05.03.442371", + "rel_title": "Impaired T-cell and antibody immunity after COVID-19 infection in chronically immunosuppressed transplant recipients", + "rel_date": "2021-05-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.03.442371", + "rel_abs": "Assessment of T-cell immunity to the COVID-19 coronavirus requires reliable assays and is of great interest, given the uncertain longevity of the antibody response. Some recent reports have used immunodominant spike (S) antigenic peptides and anti-CD28 co-stimulation in varying combinations to assess T-cell immunity to SARS-CoV-2. These assays may cause T-cell hyperstimulation and could overestimate antiviral immunity in chronically immunosuppressed transplant recipients, who are predisposed to infections and vaccination failures. Here, we evaluate CD154-expressing T-cells induced by unselected S antigenic peptides in 204 subjects-103 COVID-19 patients and 101 healthy unexposed subjects. Subjects included 72 transplanted and 130 non-transplanted subjects. S-reactive CD154+T-cells co-express and can thus substitute for IFN{gamma} (n=3). Assay reproducibility in a variety of conditions was acceptable with coefficient of variation of 2-10.6%. S-reactive CD154+T-cell frequencies were a) higher in 42 healthy unexposed transplant recipients who were sampled pre-pandemic, compared with 59 healthy non-transplanted subjects (p=0.02), b) lower in Tr COVID-19 patients compared with healthy transplant patients (p<0.0001), c) lower in Tr patients with severe COVID-19 (p<0.0001), or COVID-19 requiring hospitalization (p<0.05), compared with healthy Tr recipients. S-reactive T-cells were not significantly different between the various COVID-19 disease categories in NT recipients. Among transplant recipients with COVID-19, cytomegalovirus co-infection occurred in 34%; further, CMV-specific T-cells (p<0.001) and incidence of anti-receptor-binding-domain IgG (p=0.011) were lower compared with non-transplanted COVID-19 patients. Healthy unexposed transplant recipients exhibit pre-existing T-cell immunity to SARS-CoV-2. COVID-19 infection leads to impaired T-cell and antibody responses to SARS-CoV-2 and increased risk of CMV co-infection in transplant recipients.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Chethan Ashokkumar", + "author_inst": "Plexision Inc., Pittsburgh, PA" + }, + { + "author_name": "Vinayak Rohan", + "author_inst": "Medical University of South Carolina, Charleston, SC" + }, + { + "author_name": "Alexander H Kroemer", + "author_inst": "Medstar Georgetown Transplant Institute, Washington, DC" + }, + { + "author_name": "Sohail Rao", + "author_inst": "DHR Health and DHR Health Institute for Research and Development, Edinburg, Tx, University of Houston, Houston, TX" + }, + { + "author_name": "George Mazariegos", + "author_inst": "Hillman Center for Pediatric Transplantation, University of Pittsburgh, PA" + }, + { + "author_name": "Brandon W Higgs", + "author_inst": "Hillman Center for Pediatric Transplantation, University of Pittsburgh, PA" + }, + { + "author_name": "Satish Nadig", + "author_inst": "Medical University of South Carolina, Charleston, SC" + }, + { + "author_name": "Jose Almeda", + "author_inst": "DHR Health and DHR Health Institute for Research and Development, Edinburg, Tx, University of Houston, Houston, TX" + }, + { + "author_name": "Harmeet Dhani", + "author_inst": "Medstar Georgetown Transplant Institute, Washington, DC" + }, + { + "author_name": "Khalid Khan", + "author_inst": "Medstar Georgetown Transplant Institute, Washington, DC" + }, + { + "author_name": "Nada Yazigi", + "author_inst": "Medstar Georgetown Transplant Institute, Washington, DC" + }, + { + "author_name": "Udeme Ekong", + "author_inst": "Medstar Georgetown Transplant Institute, Washington, DC" + }, + { + "author_name": "Stuart Kaufman", + "author_inst": "Medstar Georgetown Transplant Institute, Washington, DC" + }, + { + "author_name": "Monica M Betancourt-Garcia", + "author_inst": "DHR Health and DHR Health Institute for Research and Development, Edinburg, Tx, University of Houston, Houston, TX" + }, + { + "author_name": "Kavitha Mukund", + "author_inst": "University of California, San Diego, CA" + }, + { + "author_name": "Pradeep Sethi", + "author_inst": "Plexision Inc., Pittsburgh, PA" + }, + { + "author_name": "Shikhar Mehrotra", + "author_inst": "Medical University of South Carolina, Charleston, SC" + }, + { + "author_name": "Kyle Soltys", + "author_inst": "Hillman Center for Pediatric Transplantation, University of Pittsburgh, PA" + }, + { + "author_name": "Manasi S Singh", + "author_inst": "Medical University of South Carolina, Charleston, SC" + }, + { + "author_name": "Geoffrey Bond", + "author_inst": "Hillman Center for Pediatric Transplantation, University of Pittsburgh, PA" + }, + { + "author_name": "Ajai Khanna", + "author_inst": "Hillman Center for Pediatric Transplantation, University of Pittsburgh, PA" + }, + { + "author_name": "Mylarappa Ningappa", + "author_inst": "Hillman Center for Pediatric Transplantation, University of Pittsburgh, PA" + }, + { + "author_name": "Brianna Spishock", + "author_inst": "Plexision Inc., Pittsburgh, PA" + }, + { + "author_name": "Elizabeth Sindhi", + "author_inst": "Plexision Inc., Pittsburgh, PA" + }, + { + "author_name": "Neha Atale", + "author_inst": "Plexision Inc., Pittsburgh, PA" + }, + { + "author_name": "Maggie Saunders", + "author_inst": "Plexision Inc., Pittsburgh, PA" + }, + { + "author_name": "Prabhakar Baliga", + "author_inst": "Medical University of South Carolina, Charleston, SC" + }, + { + "author_name": "Thomas Fishbein", + "author_inst": "Medstar Georgetown Transplant Institute, Washington, DC" + }, + { + "author_name": "Shankar Subramaniam", + "author_inst": "University of California, San Diego, CA" + }, + { + "author_name": "Rakesh Sindhi", + "author_inst": "Hillman Center for Pediatric Transplantation, University of Pittsburgh, PA and Plexision Inc., Pittsburgh, PA" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.05.03.442538", "rel_title": "CCR2-dependent monocyte-derived cells restrict SARS-CoV-2 infection", @@ -809452,20 +807897,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.05.04.21256489", - "rel_title": "COVID-19 VACCINE PERCEPTIONS AND DIFFERENCES BY SEX, AGE, AND EDUCATION: FINDINGS FROM A CROSS-SECTIONAL ASSESSMENT OF 1367 COMMUNITY ADULTS IN ONTARIO", - "rel_date": "2021-05-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.05.04.21256489", - "rel_abs": "BackgroundCOVID-19 is a global pandemic and vaccination efforts may be impeded by vaccine hesitancy. The present study examined willingness to receive COVID-19 vaccine, the associated reasons for willingness/unwillingness, and vaccine safety perceptions in a cross-sectional assessment of community adults in Ontario.\n\nMethods1367 individuals (60.3% female, M age = 38.6) completed an online assessment between January 15, 2021 and February 15, 2021. Perceptions were investigated in general and by age, sex and education.\n\nResultsOverall, 82.8% sample reported they were willing to receive a COVID-19 vaccine and 17.2% reported they were unwilling. The three most common reasons for unwillingness were long-term side effects (65.5%), immediate side effects (60.5%), and lack of trust in the vaccine (55.2%). Vaccine willingness significantly differed by sex and education level, with female participants and those with less than a bachelors degree being more likely to report unwillingness. Perception of COVID-19 vaccine safety was significantly lower (-10.7%) than vaccines in general and differed by age, sex and education, with females, older adults, and individuals with less than a bachelors degree reporting lower perceived COVID-19 vaccine safety.\n\nConclusionIn this sample of community adults, under one in five individuals was unwilling to receive a COVID-19 vaccine, but with higher rates in population subgroups. Targeting public health messaging to females and individuals with less than Bachelors degree, and addressing concerns about long-term and immediate side effects may increase vaccine uptake.", - "rel_num_authors": 0, - "rel_authors": null, - "version": "1", - "license": "", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.05.04.21256497", "rel_title": "Distinct patterns of blood cytokines beyond a cytokine storm predict mortality in COVID-19", @@ -810541,6 +808972,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2021.04.30.21256219", + "rel_title": "Data driven phenotyping and COVID-19 case definitions: a pattern recognition approach.", + "rel_date": "2021-05-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.30.21256219", + "rel_abs": "IntroductionCOVID-19 has pathological pulmonary as well as several extrapulmonary manifestations and thus many different symptoms may arise in patients. The aim of our study was to determine COVID-19 syndromic phenotypes in a data driven manner using survey results extracted from Carnegie Mellon Universitys Delphi Group.\n\nMethodsMonthly survey results (>1 million responders per month; 320.326 responders with positive COVID-19 test and disease duration <30 days were included in this study) were used sequentially in identifying and validating COVID-19 syndromic phenotypes. Logistic Regression Weighted Multiple Correspondence Analysis (LRW-MCA) was used as a preprocessing procedure, in order to weight and transform symptoms recorded by the survey to eigenspace coordinates (i.e. object scores per case / dimension), with a goal of capturing a total variance of > 75%. These scores along with symptom duration were subsequently used by the Two Step Clustering algorithm to produce symptom clusters. Post-hoc logistic regression models adjusting for age, gender and comorbidities and confirmatory linear principal components analyses were used to further explore the data. The model created from 66.165 included responders in August, was subsequently validated in data from March - December 2020.\n\nResultsFive validated COVID-19 syndromes were identified in August: 1. Afebrile (0%), Non-Coughing (0%), Oligosymptomatic (ANCOS) 2. Febrile (100%) Multisymptomatic (FMS) 3. Afebrile (0%) Coughing (100%) Oligosymptomatic (ACOS), 4. Oligosymptomatic with additional self-described symptoms (100%; OSDS) and 5. Olfaction / Gustatory Impairment Predominant (100%; OGIP).\n\nDiscussionWe present 5 distinct symptom phenotypes within the COVID-19 spectrum that remain stable within 9 - 12 days of first symptom onset. The typical febrile respiratory phenotype is presented as a minority among identified syndromes, a finding that may impact both epidemiological surveillance norms and transmission dynamics.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Georgios D. Vavougios", + "author_inst": "University of Thessaly" + }, + { + "author_name": "Christoforos Konstantatos", + "author_inst": "Department of Business Administration, University of Patras, University of Patras, Greece" + }, + { + "author_name": "Pavlos Christoforos Sinigalias", + "author_inst": "Department of Mechanical Engineering and Aeronautics, University of Patras, Greece" + }, + { + "author_name": "Sotirios G Zarogiannis", + "author_inst": "Department of Physiology, Faculty of Medicine, School of Health Sciences, University of Thessaly, BIOPOLIS, Larissa 41500, Greece." + }, + { + "author_name": "Kostas Kolomvatos", + "author_inst": "Department of Computer Science and Telecommunications, University of Thessaly, Papasiopoulou 2 - 4, Galaneika, Lamia 35131, Greece." + }, + { + "author_name": "George Stamoulis", + "author_inst": "Department of Electrical and Computer Engineering, University of Thessaly, 37 Glavani to 28th October Str, Deligiorgi Building, 4th floor, Volos 38221, Greece" + }, + { + "author_name": "Konstantinos I. Gourgoulianis", + "author_inst": "Department of Respiratory Medicine, Faculty of Medicine, School of Health Sciences, University of Thessaly, Biopolis, Larissa 41500, Greece" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.29.21256178", "rel_title": "American older adults in COVID-19 Times: Vulnerability types, aging attitudes and emotional responses", @@ -811133,97 +809607,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.05.03.441080", - "rel_title": "Human organoid systems reveal in vitro correlates of fitness for SARS-CoV-2 B.1.1.7", - "rel_date": "2021-05-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.05.03.441080", - "rel_abs": "A new phase of the COVID-19 pandemic has started as several SARS-CoV-2 variants are rapidly emerging globally, raising concerns for increased transmissibility. As animal models and traditional in vitro systems may fail to model key aspects of the SARS-CoV-2 replication cycle, representative in vitro systems to assess variants phenotypically are urgently needed. We found that the British variant (clade B.1.1.7), compared to an ancestral SARS-CoV-2 clade B virus, produced higher levels of infectious virus late in infection and had a higher replicative fitness in human airway, alveolar and intestinal organoid models. Our findings unveil human organoids as powerful tools to phenotype viral variants and suggest extended shedding as a correlate of fitness for SARS-CoV-2.\n\nOne-Sentence SummaryBritish SARS-CoV-2 variant (clade B.1.1.7) infects organoids for extended time and has a higher fitness in vitro.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Mart M Lamers", - "author_inst": "Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands." - }, - { - "author_name": "Tim I Breugem", - "author_inst": "Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands." - }, - { - "author_name": "Anna Z Mykytyn", - "author_inst": "Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands." - }, - { - "author_name": "Yiquan Wang", - "author_inst": "Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA" - }, - { - "author_name": "Nathalie Groen", - "author_inst": "Single Cell Discoveries, Utrecht, The Netherlands." - }, - { - "author_name": "Kevin Knoops", - "author_inst": "The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands." - }, - { - "author_name": "Debby Schipper", - "author_inst": "Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands." - }, - { - "author_name": "Jelte van der Vaart", - "author_inst": "Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, The Netherlands." - }, - { - "author_name": "Charlotte D Koopman", - "author_inst": "Single Cell Discoveries, Utrecht, The Netherlands." - }, - { - "author_name": "Jingshu Zhang", - "author_inst": "Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands." - }, - { - "author_name": "Douglas C Wu", - "author_inst": "Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA" - }, - { - "author_name": "Petra B van den Doel", - "author_inst": "Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands." - }, - { - "author_name": "Theo Bestebroer", - "author_inst": "Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands." - }, - { - "author_name": "Corine C GeurtsvanKessel", - "author_inst": "Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands." - }, - { - "author_name": "Peter J Peters", - "author_inst": "The Maastricht Multimodal Molecular Imaging Institute, Maastricht University, Maastricht, Netherlands." - }, - { - "author_name": "Mauro J Muraro", - "author_inst": "Single Cell Discoveries, Utrecht, The Netherlands." - }, - { - "author_name": "Hans Clevers", - "author_inst": "Oncode Institute, Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center, Utrecht, The Netherlands." - }, - { - "author_name": "Nicholas C Wu", - "author_inst": "Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA" - }, - { - "author_name": "Bart L Haagmans", - "author_inst": "Viroscience Department, Erasmus Medical Center, Rotterdam, Netherlands." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.05.01.442304", "rel_title": "SARS-CoV-2 Genome Sequencing Methods Differ In Their Ability To Detect Variants From Low Viral Load Samples", @@ -812475,6 +810858,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.04.30.442029", + "rel_title": "Evolutionary insights into a non-coding deletion of SARS-CoV-2 B.1.1.7", + "rel_date": "2021-05-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.30.442029", + "rel_abs": "Three prevalent SARS-CoV-2 Variants of Concern (VOCs) were emerged and caused epidemic waves. It is essential to uncover the key genetic changes that cause the high transmissibility of VOCs. However, different viral mutations are generally tightly linked so traditional population genetic methods may not reliably detect beneficial mutation. In this study, we proposed a new pandemic-scale phylogenomic approach to detect mutations crucial to transmissibility. We analyzed 3,646,973 high-quality SARS-CoV-2 genomic sequences and the epidemiology metadata. Based on the sequential occurrence order of mutations and the instantaneously accelerated furcation rate, the analysis revealed that two non-coding mutations at the position of 28271 (g.a28271-/t) might be crucial for the high transmissibility of Alpha, Delta and Omicron VOCs. Both two mutations cause an A-to-T change at the core Kozak site of the N gene. The analysis also revealed that the non-coding mutations (g.a28271-/t) alone are unlikely to cause high viral transmissibility, indicating epistasis or multilocus interaction in viral transmissibility. A convergent evolutionary analysis revealed that g.a28271-/t, S:P681H/R and N:R203K/M occur independently in the three-VOC lineages, suggesting a potential interaction among these mutations. Therefore, this study unveils that non-synonymous and non-coding mutations could affect the transmissibility synergistically.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Jianing Yang", + "author_inst": "Shanghai Institute of Nutrition and Health" + }, + { + "author_name": "Guoqing Zhang", + "author_inst": "Shanghai Institute of Nutrition and Health" + }, + { + "author_name": "Dalang Yu", + "author_inst": "Shanghai Institute of Nutrition and Health" + }, + { + "author_name": "Ruifang Cao", + "author_inst": "Shanghai Institute of Nutrition and Health" + }, + { + "author_name": "Xiaoxian Wu", + "author_inst": "Institute of Plant Physiology and Ecology" + }, + { + "author_name": "Yunchao Ling", + "author_inst": "Shanghai Institute of Nutrition and Health" + }, + { + "author_name": "Yi-Hsuan Pan", + "author_inst": "East China Normal University" + }, + { + "author_name": "Chunyan Yi", + "author_inst": "Shanghai Institute of Biochemistry and Cell Biology" + }, + { + "author_name": "Xiaoyu Sun", + "author_inst": "Shanghai Institute of Biochemistry and Cell Biology" + }, + { + "author_name": "Bing Sun", + "author_inst": "Shanghai Institute of Biochemistry and Cell Biology" + }, + { + "author_name": "Yu Zhang", + "author_inst": "Institute of Plant Physiology and Ecology" + }, + { + "author_name": "Guo-Ping Zhao", + "author_inst": "Institute of Plant Physiology and Ecology" + }, + { + "author_name": "Yixue Li", + "author_inst": "Shanghai Institute of Nutrition and Health" + }, + { + "author_name": "Haipeng Li", + "author_inst": "Shanghai Institute of Nutrition and Health" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2021.04.29.21256294", "rel_title": "Elevated blood glucose levels as a primary risk factor for the severity of COVID-19", @@ -812871,37 +811325,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.27.21256210", - "rel_title": "U.S. Regional Differences in Physical Distancing: Evaluating Racial and Socioeconomic Divides During the COVID-19 Pandemic", - "rel_date": "2021-04-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.27.21256210", - "rel_abs": "Health varies by U.S. region of residence. Despite regional heterogeneity in the outbreak of COVID-19, regional differences in physical distancing behaviors over time are relatively unknown. This study examines regional variation in physical distancing trends during the COVID-19 pandemic and investigates variation by race and socioeconomic status (SES) within regions.\n\nData from the 2015-2019 five-year American Community Survey were matched with anonymized location pings data from over 20 million mobile devices (SafeGraph, Inc.) at the Census block group level. We visually present trends in the stay-at-home proportion by Census region, race, and SES throughout 2020 and conduct regression analyses to statistically examine these patterns.\n\nFrom March to December, the stay-at-home proportion was highest in the Northeast (0.25 in March to 0.35 in December) and lowest in the South (0.24 to 0.30). Across all regions, the stay-at-home proportion was higher in block groups with a higher percentage of Blacks, as Blacks disproportionately live in urban areas where stay-at-home rates were higher (0.009 [CI: 0.008, 0.009]). In the South, West, and Midwest, higher-SES block groups stayed home at the lowest rates pre-pandemic; however, this trend reversed throughout March before converging in the months following. In the Northeast, lower-SES block groups stayed home at comparable rates to higher-SES block groups during the height of the pandemic but diverged in the months following.\n\nDifferences in physical distancing behaviors exist across U.S. regions, with a pronounced Southern and rural disadvantage. Results can be used to guide reopening and COVID-19 mitigation plans.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Emma Zang", - "author_inst": "Yale University" - }, - { - "author_name": "Jessica West", - "author_inst": "Duke University" - }, - { - "author_name": "Nathan Kim", - "author_inst": "Yale University" - }, - { - "author_name": "Christina Pao", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.29.21256267", "rel_title": "A snapshot of a pandemic : the interplay between social isolation and COVID-19 dynamics in Brazil", @@ -813883,6 +812306,41 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.04.29.442038", + "rel_title": "ACE2 glycans preferentially interact with the RBD of SARS-CoV-2 over SARS-CoV", + "rel_date": "2021-04-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.29.442038", + "rel_abs": "We report a distinct difference in the interactions of the glycans of the host-cell receptor, ACE2, with SARS-CoV-2 and SARS-CoV S-protein receptor-binding domains (RBDs). Our analysis demonstrates that the ACE2 glycan at N90 may offer protection against infections of both coronaviruses, while the ACE2 glycan at N322 enhances interactions with the SARS-CoV-2 RBD. The interactions of the ACE2 glycan at N322 with SARS-CoV RBD are blocked by the presence of the RBD glycan at N357 of the SARS-CoV RBD. The absence of this glycosylation site on SARS-CoV-2 RBD may enhance its binding with ACE2.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Atanu Acharya", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Diane Lynch", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Anna Pavlova", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Yui Tik Pang", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "James Gumbart", + "author_inst": "Georgia Institute of Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.04.30.442139", "rel_title": "Cell-free glycoengineering of the recombinant SARS-CoV-2 spike glycoprotein", @@ -814467,45 +812925,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.27.21255023", - "rel_title": "Large university with high COVID-19 incidence did not increase risk to non-student population", - "rel_date": "2021-04-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.27.21255023", - "rel_abs": "Large US colleges and universities that re-opened campuses in the fall of 2020 and the spring of 2021 experienced high per capita rates of COVID-19. Returns to campus were controversial because they posed a risk to the surrounding communities. A large university in Pennsylvania that returned to in-person instruction in the fall of 2020 and spring of 2021 reported high incidence of COVID-19 among students. However, the co-located non-student resident population in the county experienced fewer COVID-19 cases per capita than reported in neighboring counties. Activity patterns from mobile devices indicate that the non-student resident population near the university restricted their movements during the pandemic more than residents of neighboring counties. Preventing cases in student and non-student populations requires different, specifically targeted strategies.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Nita Bharti", - "author_inst": "The Pennsylvania State University" - }, - { - "author_name": "Brian Lambert", - "author_inst": "The Pennsylvania State University" - }, - { - "author_name": "Cara Exten", - "author_inst": "The Pennsylvania State University" - }, - { - "author_name": "Christina Faust", - "author_inst": "The Pennsylvania State University" - }, - { - "author_name": "Matthew Ferrari", - "author_inst": "The Pennsylvania State University" - }, - { - "author_name": "Anthony Robinson", - "author_inst": "The Pennsylvania State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.27.21255706", "rel_title": "Surging COVID-19 in Bangladesh driven by B.1.351 variant", @@ -815893,6 +814312,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.26.21256093", + "rel_title": "Impairment of T cells' antiviral and anti-inflammation immunities dominates the death from COVID-19", + "rel_date": "2021-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.26.21256093", + "rel_abs": "Clarifying dominant factors determining the immune heterogeneity from non-survivors to survivors is crucial for developing therapeutics and vaccines against COVID-19. The main difficulty is quantitatively analyzing the multi-level clinical data, including viral dynamics, immune response, and tissue damages. Here, we adopt a top-down modelling approach to quantify key functional aspects and their dynamical interplay in the battle between the virus and the immune system, yielding an accurate description of real-time clinical data involving hundreds of patients for the first time. The quantification of antiviral responses demonstrates that, compared to antibodies, T cells play a more dominant role in virus clearance, especially for mild patients (96.5%). Moreover, the anti-inflammatory responses, namely the cytokine inhibition and tissue repair rates, also positively correlate with T cell number and are significantly suppressed in non-survivors. Simulations show that the lack of T cells leads to more significant inflammation, proposing an explanation for the monotonous increase of COVID-19 mortality with age and higher mortality for males. We conclude that T cells play a crucial role in the immunity against COVID-19, which reveals a new direction----improvement of T cell number for advancing current prevention and treatment.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Zhen-su She", + "author_inst": "Peking University" + }, + { + "author_name": "Gregory Scholes", + "author_inst": "Princeton University" + }, + { + "author_name": "Luhao Zhang", + "author_inst": "Princeton University" + }, + { + "author_name": "Rong Li", + "author_inst": "Peking University" + }, + { + "author_name": "Gang Song", + "author_inst": "Beijing Hospital" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.27.21254849", "rel_title": "Local emergence and decline of a SARS-CoV-2 variant with mutations L452R and N501Y in the spike protein", @@ -816501,121 +814955,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.25.21256067", - "rel_title": "Trends of SARS-CoV-2 antibody prevalence in selected regions across Ghana", - "rel_date": "2021-04-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.25.21256067", - "rel_abs": "To estimate the level of community exposure to SARS-CoV-2 in Ghana, we conducted phased seroprevalence studies of 2729 participants in selected locations across Ghana. Phase I screening (August 2020) covered a total of 1305 individuals screened at major markets/lorry stations, major shopping malls, hospitals and research institutions involved in COVID-19 work. The screening was performed using a strip-in-cassette lateral flow type Rapid Diagnostic Test (RDT) kit that simultaneously and separately detected IgM and IgG antibodies against SARS-CoV-2 nucleocapsid protein. In Phase I, 252/1305 (19%) tested positive for IgM or IgG or both. Exposure rate was significantly higher among individuals tested at markets/lorry stations (26.9%) compared to those at Shopping Malls (9.4%). The 41-60-years age group had the highest exposure rate (27.2%). People with only a basic level or no formal education had a higher exposure rate (26.2%) than those with tertiary level education (13.1%); and higher in informally employed workers (24.0%) than those in the formal sector (15.0%). Phases II and III screening activities in October and December 2020, respectively, showed no evidence of increased seroprevalence, indicating either a reduced transmission rate or loss of antibody expression in a subset of the participants. The Upper East region has the lowest exposure rate, with only 4 of 200 participants (2%) seropositivity. Phase IV screening in February 2021 showed that exposure rates in the upper income earners (26.2%) had almost doubled since August 2020, reflective of Ghanas second wave of symptomatic COVID-19 cases, which began in December 2020. The Phase IV results suggest that seroprevalence levels have become so high that the initial socioeconomic stratification of exposure has been lost. Overall, the data indicates a much higher COVID-19 seroprevalence in the Greater Accra Region than was officially acknowledged, likely implying a considerably lower case fatality rate than the current national figure of 0.84%. Additionally, the high exposure levels seen in the communities suggest that COVID-19 in Ghana still predominantly presents with none-to-mild symptoms. Our results lay the foundation for more extensive SARS-CoV-2 surveillance in Ghana and the West African sub-region, including deploying rapid antigen test kits in concert to determine the actual infection burden since antibody development lags infection.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Peter Kojo Quashie", - "author_inst": "West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana" - }, - { - "author_name": "Joe Kimanthi Mutungi", - "author_inst": "West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana" - }, - { - "author_name": "Francis Dzabeng", - "author_inst": "West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana" - }, - { - "author_name": "Daniel Oduro-Mensah", - "author_inst": "University of Ghana" - }, - { - "author_name": "Precious C Opurum", - "author_inst": "West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana" - }, - { - "author_name": "Kesego Tapela", - "author_inst": "University of Ghana" - }, - { - "author_name": "Aniefiouk John Udoakang", - "author_inst": "West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana" - }, - { - "author_name": "- WACCBIP COVID-19 Team", - "author_inst": "-" - }, - { - "author_name": "Ivy Asante", - "author_inst": "Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana" - }, - { - "author_name": "Lily Paemka", - "author_inst": "Department of Biochemistry, Cell and Molecular Biology, University of Ghana" - }, - { - "author_name": "Frederick Kumi-Ansah", - "author_inst": "Cape Coast Teaching Hospital" - }, - { - "author_name": "Osbourne Quaye", - "author_inst": "Department of Biochemistry, Cell and Molecular Biology, University of Ghana" - }, - { - "author_name": "Emmanuella Amoako", - "author_inst": "Cape Coast Teaching Hospital" - }, - { - "author_name": "Ralph Armah", - "author_inst": "Department of Internal Medicine, Surgery, Pediatrics and Emergency Medicine, Greater Accra Regional Hospital" - }, - { - "author_name": "Charlyne Kilba", - "author_inst": "Department of Internal Medicine, Surgery, Pediatrics and Emergency Medicine, Greater Accra Regional Hospital" - }, - { - "author_name": "Nana Afia Boateng", - "author_inst": "Department of Internal Medicine, Surgery, Pediatrics and Emergency Medicine, Greater Accra Regional Hospital" - }, - { - "author_name": "Michael F Ofori", - "author_inst": "Immunology Department, Noguchi Memorial Institute for Medical Research, University of Ghana" - }, - { - "author_name": "George Boateng Kyei", - "author_inst": "University of Ghana Medical Centre" - }, - { - "author_name": "Yaw Bediako", - "author_inst": "West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana" - }, - { - "author_name": "Nicaise T Ndam", - "author_inst": "UMR 216 MERIT-IRD, Universit\u00e9 de Paris" - }, - { - "author_name": "James Abugri", - "author_inst": "C.K. Tedam University of Technology and Applied Sciences" - }, - { - "author_name": "Patrick Ansah", - "author_inst": "Navrongo Health Research Centre, Navrongo, Upper East Region, Ghana" - }, - { - "author_name": "William Kwabena Ampofo", - "author_inst": "Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana" - }, - { - "author_name": "Francisca Mutapi", - "author_inst": "13.\tNIHR Global Health Research Unit Tackling Infections to Benefit Africa (TIBA), and Institute of Immunology and Infection Research, School of Biological Scie" - }, - { - "author_name": "Gordon A Awandare", - "author_inst": "West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.26.21256102", "rel_title": "Physician Perceptions of Surveillance: Wearables, Apps, and Bots for COVID-19", @@ -817831,6 +816170,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.04.27.21256221", + "rel_title": "The herbal combination of Sugarcane, Black Myrobalan, and mastic as a supplementary treatment for COVID-19: a randomized clinical trial", + "rel_date": "2021-04-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.27.21256221", + "rel_abs": "BackgroundGiven the COVID-19 pandemics, researchers are beseeched for effective treatments. Herbal medicine is also queried for potential supplementary treatments for COVID-19. We aimed to evaluate the effects of Sugarcane, Black Myrobalan, and Mastic herbal medications for COVID-19 patients.\n\nMethodsThis was a double-blinded randomized clinical trial study conducted over three months from May to July 2020 in patients admitted with a diagnosis of COVID-19 in Peymaniyeh Hospital in Jahrom, Iran. The intervention group received the treatment protocol approved by the Ministry of Health of Iran during the period of hospitalization and the herbal supplement obtained from the combination of black myrobalan and mastic and sugarcane, twice a day (3g of herbal supplements). All patients were compared in terms of demographic variables, vital signs, clinical and laboratory variables.\n\nResults72 patients with COVID-19, divided into intervention (n=37) and control (n=35) groups. intervention and control groups had not any significant difference in terms of baseline characteristics. The time-to-event analysis revealed a significant difference in 4 symptoms of cough, fever, dyspnea, and myalgia (P<0.05). The Control group had a significantly lower decrease in C-reactive protein during 7 days (P<0.05). Patients in the herbal supplement group were hospitalized for 4.12 days and in the control group were hospitalized for 8.37 days (P=0.001). ICU admission and death only happened in 3 (8.6%) patients of the control group.\n\nConclusionWhile advanced studies with more sample size are needed; the proposed combination seems to be effective in the symptom treatment and reducing the length of hospitalization.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Alireza Hashemi Shiri", + "author_inst": "Complementary Medicine Researcher, Jahrom University of Medical Sciences, Jahrom, Iran." + }, + { + "author_name": "Esmayil Rayatdoost", + "author_inst": "Department of Emergency Medicine, Jahrom University of Medical Sciences, Jahrom, Iran." + }, + { + "author_name": "Hamid Afkhami", + "author_inst": "Bachelor of Science in Medical Laboratory Science, Jahrom University of Medical Sciences, Jahrom, Iran." + }, + { + "author_name": "Ruhollah Ravanshad", + "author_inst": "Bachelor of Science in Nursing, Jahrom University of Medical Sciences, Jahrom, Iran." + }, + { + "author_name": "Seyed Ehsan Hosseini", + "author_inst": "Bachelor of Science in Nursing, Jahrom University of Medical Sciences, Jahrom, Iran." + }, + { + "author_name": "Navid Kalani", + "author_inst": "Research center for social Determinants of Health, Jahrom University of Medical Sciences, Jahrom, Iran." + }, + { + "author_name": "Rahim Raoufi", + "author_inst": "Department of Infectious Diseases, Faculty of Medicine, University of Medical Sciences, Jahrom, Iran." + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2021.04.24.21255968", "rel_title": "MORTALITY OF CARE HOME RESIDENTS AND COMMUNITY-DWELLING CONTROLS DURING THE COVID-19 PANDEMIC IN 2020: MATCHED COHORT STUDY", @@ -818419,81 +816801,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.19.21255714", - "rel_title": "Antibody response after COVID-19 mRNA vaccination in relation to age, sex, and side effects", - "rel_date": "2021-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.19.21255714", - "rel_abs": "BackgroundThe mRNA vaccines for SARS-CoV2 have proven highly effective and are currently used to vaccinate all age groups against COVID-19. Despite their high efficacy in clinical trials, there is limited data on the impact of age, sex, and side effects on vaccine-induced immune responses.\n\nMethodsWe here studied the development of SARS-CoV-2 Spike protein RBD domain antibodies after two doses of the Pfizer-BioNTech Comirnaty mRNA vaccine in 118 healthy volunteers and correlated their immune response with age, sex, and side effects reported after the vaccinations.\n\nFindingsOur findings show a robust immune response to the Spike proteins RBD region after the first and the second vaccination dose. However, we also saw a decline of antibody levels at 6 weeks versus 1 week after the second dose, suggesting a waning of the immune response over time. Regardless of this, the antibody levels at 6 weeks after the second dose remained significantly higher than before the vaccination, after the first dose, or in COVID-19 convalescent individuals. We found a decreased vaccination efficacy but fewer adverse events in older individuals, and that mRNA vaccination is less efficient in older males whereas the detrimental impact of age on vaccination outcome is abolished in females at 6 weeks after the second dose.\n\nInterpretationThe Pfizer-BioNTech Comirnaty mRNA vaccine induces a strong immune response after two doses of vaccination but older individuals develop fewer side effects and decreased antibody levels at 6 weeks. The waning of anti-viral antibodies in particular in older male individuals suggests that both age and male sex act as risk factors in the immune response to the SARS-CoV-2 mRNA vaccine.\n\nFundingThe study was supported by the Centre of Excellence in Translational Genomics (EXCEGEN), and the Estonian Research Council grant PRG377 and SYNLAB Estonia.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThe first studies addressing the immune responses in older individuals after the single-dose administration of the SARS-CoV-2 mRNA vaccines have been published. We searched PubMed and medRxiv for publications on the immune response of SARS-CoV-2-mRNA vaccines, published in English, using the search terms \"SARS-CoV-2\", \"COVID-19\", \"vaccine response\", \"mRNA vaccine\", up to April 15th, 2021. To date, most mRNA vaccine response studies have not been peer-reviewed, and data on the role of age, sex and side effects on SARS-CoV-2-mRNA vaccines in real vaccination situations is limited. Some studies have found a weaker immune response in older individuals after the first dose and these have been measured at a relatively short period (within 1-2 weeks) after the first dose but little longer-term evidence exists on the postvaccination antibody persistence. Even less information is available on sex differences or correlations with mRNA vaccine side effects.\n\nAdded value of this studyIn this study, we assessed the antibody response up to 6 weeks after the second dose of Pfizer-BioNTech Comirnaty mRNA vaccine in 118 individuals. Our findings show a strong initial immune response after the first dose and an even higher Spike RBD antibody levels at 1 week after the second dose, but these significantly declined at 6 weeks after the second dose. We also found a weaker immune response and faster waning of antibodies in older vaccinated individuals, which correlated with fewer side effects at the time of vaccinations. Furthermore, although overall female and male vaccinees responded similarly, we found that age-related waning of the vaccine-related antibodies was stronger amongst older males whereas in females the impact of age was lost at 6 weeks after the second dose.\n\nImplications of all the available evidenceNew mRNA vaccines are now applied worldwide as they have shown high efficacy in clinical trials. Our results show that two doses of Pfizer-BioNTech Comirnaty mRNA vaccine induce a strong antibody response to Spike RBD region but these high levels decline 1.5 months after the second dose in most of the vaccinated individuals. Nevertheless, even at 6 weeks after the second dose, they stay significantly higher than at prevaccination, after the first dose of vaccine, or in Covid-19 postinfection. These findings also implicate that fewer adverse effects may indicate lower antibody response after the vaccination and point to the need for more individualized vaccination protocols, in particular among older people.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Paul Naaber", - "author_inst": "SYNLAB Eesti; University of Tartu" - }, - { - "author_name": "Liina Tserel", - "author_inst": "University of Tartu" - }, - { - "author_name": "Kadri Kangro", - "author_inst": "Icosagen Cell Factory" - }, - { - "author_name": "Epp Sepp", - "author_inst": "University of Tartu" - }, - { - "author_name": "Virge Jurjenson", - "author_inst": "SYNLAB Eesti" - }, - { - "author_name": "Ainika Adamson", - "author_inst": "SYNLAB Eesti" - }, - { - "author_name": "Liis Haljasmagi", - "author_inst": "University of Tartu" - }, - { - "author_name": "Pauliina Rumm", - "author_inst": "University of Tartu" - }, - { - "author_name": "Regina Maruste", - "author_inst": "University ofTartu" - }, - { - "author_name": "Jaanika Karner", - "author_inst": "University of Tartu" - }, - { - "author_name": "Joachim M Gerhold", - "author_inst": "Icosagen Cell Factory" - }, - { - "author_name": "Anu Planken", - "author_inst": "Icosagen Cell Factory" - }, - { - "author_name": "Mart Ustav", - "author_inst": "Icosagen Cell Factory" - }, - { - "author_name": "Kai Kisand", - "author_inst": "University of Tartu" - }, - { - "author_name": "Part Peterson", - "author_inst": "University of Tartu" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.19.21255738", "rel_title": "Association of ABO blood group with COVID-19 severity, acute phase reactants and mortality", @@ -819540,6 +817847,65 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.04.27.441589", + "rel_title": "Long-lasting humoral immunity in Covid-19 infected patients at a University Hospital Clinic in Ostergotland County Council during 2020-2021.", + "rel_date": "2021-04-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.27.441589", + "rel_abs": "Longitudinal serum samples and nasopharyngeal/nasal swab samples were collected from forty-eight individuals (median age 66yrs) with Covid-19 PCR-positive test results at Linkoping University Hospital. Samples were collected from initial visit and for 6 months follow up. Presence of serum IgG and IgA against SARS-CoV-2 antigens (S1-spike, nucleocapsid and NSP3) were analyzed. Nasal swabs were tested for presence of IgA against the outer envelope S1 spike protein. Ninety-two percent of participants were seropositive against SARS-CoV-2 recombinant proteins at day 28 from study entry and all (100%) were seropositive from samples collected at 2 months or later. The most common antibody responses (both serum IgG, mainly IgG1 and IgA) were detected against the S1-spike protein and the nucleoprotein. In samples collected from nasal tissues considerably lower frequencies of IgA-positive reactivities were detected. Sixteen to 18 percent of study participants showed detectable IgA levels in nasal samples, except at day 60 when 36% of tested individuals showed presence of IgA against the S1-spike protein. The study suggests that the absolute majority of studied naturally infected Covid-19 patient in the Linkoping, Ostergotland health region develop over 6 months lasting detectable levels of serum IgG and IgA responses towards the SARS-CoV-2 S1-spike protein as well as against the nucleoprotein, but not against the non-structural protein 3.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Jorma Hinkula", + "author_inst": "Linkoping University" + }, + { + "author_name": "Mohammad Azharuddin", + "author_inst": "Linkoping University" + }, + { + "author_name": "Daniel Aili", + "author_inst": "Linkopings Universitet" + }, + { + "author_name": "Sajjad Naeimipour", + "author_inst": "Linkoping University" + }, + { + "author_name": "Robert Selegard", + "author_inst": "Linkopings Universitet" + }, + { + "author_name": "Maria Sunnerhagen", + "author_inst": "Linkopings Universitet" + }, + { + "author_name": "Hirak K Patra", + "author_inst": "Univercity College London" + }, + { + "author_name": "Sofia K Sjoberg", + "author_inst": "Linkoping University hospital" + }, + { + "author_name": "Katarina Niward", + "author_inst": "Linkoping University" + }, + { + "author_name": "Hakan Hanberger", + "author_inst": "Linkoping University" + }, + { + "author_name": "Asa Ostholm-Balked", + "author_inst": "Linkoping University hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.04.26.441518", "rel_title": "Nucleocapsid vaccine elicits spike-independent SARS-CoV-2 protective immunity", @@ -820048,77 +818414,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.26.21256131", - "rel_title": "SARS-CoV-2 subgenomic RNA kinetics in longitudinal clinical samples", - "rel_date": "2021-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.26.21256131", - "rel_abs": "BackgroundGiven the persistence of viral RNA in clinically recovered COVID-19 patients, subgenomic RNAs (sgRNA) have been reported as potential molecular viability markers for SARS-CoV-2. However, few data are available on their longitudinal kinetics, compared with genomic RNA (gRNA), in clinical samples.\n\nMethodsWe analyzed 536 samples from 205 patients with COVID-19 from placebo-controlled, outpatient trials of Peginterferon Lambda-1a (Lambda; n=177) and favipiravir (n=359). Nasal swabs were collected at three time points in the Lambda (Day 1, 4 and 6) and favipiravir (Day 1, 5, and 10) trials. N-gene gRNA and sgRNA were quantified by RT-qPCR. To investigate the decay kinetics in vitro, we measured gRNA and sgRNA in A549ACE2+ cells infected with SARS-CoV-2, following treatment with remdesivir or DMSO control.\n\nResultsAt six days in the Lambda trial and ten days in the favipiravir trial, sgRNA remained detectable in 51.6% (32/62) and 49.5% (51/106) of the samples, respectively. Cycle threshold (Ct) values for gRNA and sgRNA were highly linearly correlated (Pearsons r=0.87) and the rate of increase did not differ significantly in Lambda (1.36 cycles/day vs 1.36 cycles/day; p = 0.97) or favipiravir (1.03 cycles/day vs 0.94 cycles/day; p=0.26) trials. From samples collected 15-21 days after symptom onset, sgRNA was detectable in 48.1% (40/83) of participants. In SARS-CoV-2 infected A549ACE2+ cells treated with remdesivir, the rate of Ct increase did not differ between gRNA and sgRNA.\n\nConclusionsIn clinical samples and in vitro, sgRNA was highly correlated with gRNA and did not demonstrate different decay patterns to support its application as a viability marker.\n\nSummaryWe observed prolonged detection of subgenomic RNA in nasal swabs and equivalent decay rates to genomic RNA in both longitudinal nasal swabs and in remdesivir-treated A549ACE2+ cells infected with SARS-CoV-2. Taken together, these findings suggest that subgenomic RNA from SARS-CoV-2 is comparably stable to genomic RNA and that its detection is therefore not a more reliable indicator of replicating virus.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Renu Verma", - "author_inst": "Stanford School of Medicine" - }, - { - "author_name": "Eugene Kim", - "author_inst": "Stanford School of Medicine" - }, - { - "author_name": "Giovanny Joel Martinez-Colon", - "author_inst": "Stanford School of Medicine" - }, - { - "author_name": "Prasanna Jagannathan", - "author_inst": "STANFORD SCHOOL OF MEDICINE" - }, - { - "author_name": "Arjun Rustagi", - "author_inst": "Stanford University" - }, - { - "author_name": "Julie Parsonnet", - "author_inst": "Stanford School of Medicine" - }, - { - "author_name": "Hector Bonilla", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Chaitan Khosla", - "author_inst": "Stanford University" - }, - { - "author_name": "Marisa Holubar", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Aruna Subramanian", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Upinder Singh", - "author_inst": "Stanford University" - }, - { - "author_name": "Yvonne Maldonado", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Catherine A Blish", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Jason R Andrews", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.24.21255827", "rel_title": "It's complicated: characterizing the time-varying relationship between cell phone mobility and COVID-19 spread in the US", @@ -821338,6 +819633,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.04.23.441187", + "rel_title": "Predicted structural mimicry of spike receptor-binding motifs from highly pathogenic human coronaviruses", + "rel_date": "2021-04-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.23.441187", + "rel_abs": "Viruses often encode proteins that mimic host proteins in order to facilitate infection. Little work has been done to understand the potential mimicry of the SARS-CoV-2, SARS-CoV, and MERS-CoV spike proteins, particularly the receptor-binding motifs, which could be important in determining tropism of the virus. Here, we use structural bioinformatics software to characterize potential mimicry of the three coronavirus spike protein receptor-binding motifs. We utilize sequence-independent alignment tools to compare structurally known or predicted three-dimensional protein models with the receptor-binding motifs and verify potential mimicry with protein docking simulations. Both human and non-human proteins were found to be similar to all three receptor-binding motifs. Similarity to human proteins may reveal which pathways the spike protein is co-opting, while analogous non-human proteins may indicate shared host interaction partners and overlapping antibody cross-reactivity. These findings can help guide experimental efforts to further understand potential interactions between human and coronavirus proteins.\n\nHighlightsO_LIPotential coronavirus spike protein mimicry revealed by structural comparison\nC_LIO_LIHuman and non-human protein potential interactions with virus identified\nC_LIO_LIPredicted structural mimicry corroborated by protein-protein docking\nC_LIO_LIEpitope-based alignments may help guide vaccine efforts\nC_LI\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC=\"FIGDIR/small/441187v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (22K):\norg.highwire.dtl.DTLVardef@1f09454org.highwire.dtl.DTLVardef@19a5557org.highwire.dtl.DTLVardef@158d3fdorg.highwire.dtl.DTLVardef@c59511_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Christopher A Beaudoin", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Arian Rokkum Jamasb", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Ali Alsulami", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Liviu Copoiu", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Andries J van Tonder", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Sharif Hala", + "author_inst": "King Saud bin Abdulaziz University for Health Sciences" + }, + { + "author_name": "Bridget P Bannerman", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Sherine E Thomas", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Sundeep Chaitanya Vedithi", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Pedro H M Torres", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Tom L Blundell", + "author_inst": "University of Cambridge" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.04.22.21255922", "rel_title": "Role of non-aerosols activities in the transmission of SARS-Cov-2 infection among health care workers.", @@ -821862,25 +820216,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.22.21255941", - "rel_title": "Predicting the end of Covid-19 infection for various countries using a stochastic agent-based model taking into account vaccination rates and the new mutant", - "rel_date": "2021-04-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.22.21255941", - "rel_abs": "Using a stochastic, agent-based model, the course of infection since the first occurrence of a Covid-19 infection is simulated for various countries, taking into account the new, more infectious mutant and the vaccinations. The simulation shows that the course of infection for the United Kingdom (UK) and Israel is surprisingly good. For the other countries, an end date for the infection can be predicted based on the course of the simulation. For Germany, the course is calculated in a second scenario, assuming a higher vaccination rate.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Manfred Karl Robert Eissler", - "author_inst": "Praxis Dres Eissler" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.04.23.21255994", "rel_title": "Depression and Anxiety Symptoms in Young Adults Before and During the Covid-19 Pandemic: Evidence from a Canadian Population-Based Cohort", @@ -823032,6 +821367,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2021.04.17.21255642", + "rel_title": "Monitoring global trends in Covid-19 vaccination intention and confidence: a social media-based deep learning study", + "rel_date": "2021-04-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.17.21255642", + "rel_abs": "BackgroundThis study developed deep learning models to monitor global intention and confidence of Covid-19 vaccination in real time.\n\nMethodsWe collected 6.73 million English tweets regarding Covid-19 vaccination globally from January 2020 to February 2021. Fine-tuned Transformer-based deep learning models were used to classify tweets in real time as they relate to Covid-19 vaccination intention and confidence. Temporal and spatial trends were performed to map the global prevalence of Covid-19 vaccination intention and confidence, and public engagement on social media was analyzed.\n\nFindingsGlobally, the proportion of tweets indicating intent to accept Covid-19 vaccination declined from 64.49% on March to 39.54% on September 2020, and then began to recover, reaching 52.56% in early 2021. This recovery in vaccine acceptance was largely driven by the US and European region, whereas other regions experienced the declining trends in 2020. Intent to accept and confidence of Covid-19 vaccination were relatively high in South-East Asia, Eastern Mediterranean, and Western Pacific regions, but low in American, European, and African regions. 12.71% tweets expressed misinformation or rumors in South Korea, 14.04% expressed distrust in government in the US, and 16.16% expressed Covid-19 vaccine being unsafe in Greece, ranking first globally. Negative tweets, especially misinformation or rumors, were more engaged by twitters with fewer followers than positive tweets.\n\nInterpretationThis global real-time surveillance study highlights the importance of deep learning based social media monitoring to detect emerging trends of Covid-19 vaccination intention and confidence to inform timely interventions.\n\nFundingNational Natural Science Foundation of China.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWith COVID-19 vaccine rollout, each country should investigate its vaccination intention in local contexts to ensure massive vaccination. We searched PubMed for all articles/preprints until April 9, 2021 with the keywords \"(\"Covid-19 vaccines\"[Mesh] OR Covid-19 vaccin*[TI]) AND (confidence[TI] OR hesitancy[TI] OR acceptance[TI] OR intention[TI])\". We identified more than 100 studies, most of which are country-level cross-sectional surveys, and the largest global survey of Covid-19 vaccine acceptance only covered 32 countries to date. However, how Covid-19 vaccination intention changes over time remain unknown, and many countries are not covered in previous surveys yet. A few studies assessed public sentiments towards Covid-19 vaccination using social media data, but only targeting limited geographical areas. There is a lack of real-time surveillance, and no study to date has globally monitored Covid-19 vaccination intention in real time.\n\nAdded value of this studyTo our knowledge, this is the largest global monitoring study of Covid-19 vaccination intention and confidence with social media data in over 100 countries from the beginning of the pandemic to February 2021. This study developed deep learning models by fine-tuning a Bidirectional Encoder Representation from Transformer (BERT)-based model with 8000 manually-classified tweets, which can be used to monitor Covid-19 vaccination beliefs using social media data in real time. It achieves temporal and spatial analyses of the evolving beliefs to Covid-19 vaccines across the world, and also an insight for many countries not yet covered in previous surveys. This study highlights that the intention to accept Covid-19 vaccination have experienced a declining trend since the beginning of the pandemic in all world regions, with some regions recovering recently, though not to their original levels. This recovery was largely driven by the US and European region (EUR), whereas other regions experienced the declining trends in 2020. Intention to accept and confidence of Covid-19 vaccination were relatively high in South-East Asia region (SEAR), Eastern Mediterranean region (EMR), and Western Pacific region (WPR), but low in American region (AMR), EUR, and African region (AFR). Many AFR countries worried more about vaccine effectiveness, while EUR, AMR, and WPR concerned more about vaccine safety (the most concerns with 16.16% in Greece). Online misinformation or rumors were widespread in AMR, EUR, and South Korea (12.71%, ranks first globally), and distrust in government was more prevalent in AMR (14.04% in the US, ranks first globally). Our findings can be used as a reference point for survey data on a single country in the future, and inform timely and specific interventions for each country to address Covid-19 vaccine hesitancy.\n\nImplications of all the available evidenceThis global real-time surveillance study highlights the importance of deep learning based social media monitoring as a quick and effective method for detecting emerging trends of Covid-19 vaccination intention and confidence to inform timely interventions, especially in settings with limited sources and urgent timelines. Future research should build multilingual deep learning models and monitor Covid-19 vaccination intention and confidence in real time with data from multiple social media platforms.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Xinyu Zhou", + "author_inst": "Fudan University" + }, + { + "author_name": "Alex de Figueiredo", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Qin Xu", + "author_inst": "Fudan University" + }, + { + "author_name": "Leesa Lin", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Per E Kummervold", + "author_inst": "FISABIO-Public Health" + }, + { + "author_name": "Heidi Larson", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Mark Jit", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Zhiyuan Hou", + "author_inst": "Fudan University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.04.23.21255564", "rel_title": "County-Level Estimates of Excess Mortality associated with COVID-19 in the United States", @@ -823436,73 +821818,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.22.21255631", - "rel_title": "Risk Profile of Thanksgiving Gatherers and Subsequent SARS-CoV2 Testing and Diagnosis", - "rel_date": "2021-04-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.22.21255631", - "rel_abs": "BackgroundDuring Fall 2020 in the United States (U.S.), despite high COVID-19 case numbers and recommendations from public health officials not to travel and gather with individuals outside ones household, millions of people gathered for Thanksgiving. The objective of this study was to understand if individuals behaviors and risk perceptions influenced their decision to gather, and if they did gather, their subsequent test seeking and diagnoses.\n\nMethodsParticipants were part of the CHASING COVID Cohort study - a U.S. national prospective cohort. The study sample consisted of participants who completed routine questionnaires before and after Thanksgiving. Non-pharmaceutical interventions (NPIs) use informed behavioral risk scores and a score of perceived risk of COVID-19 were assigned to each participant. Multinomial logistic regression models were used to assess the association between higher risk behaviors and gathering with other households, and the association of gathering with subsequent testing and test positivity.\n\nResultsA total of 1,932 (40.5%) cohort participants spent Thanksgiving with individuals from at least one other household. Participants with higher behavioral risk scores had greater odds of gathering with one other household (aOR: 2.35, 95% CI: 2.0, 2.7), two other households (aOR: 4.54, 95% CI: 3.7, 5.6), and three or more other households (aOR: 5.44, 95% CI: 4.1, 7.2). Participants perceiving COVID-19 as a low-risk to themselves and others had greater odds of gathering with one other household (aOR: 1.12, 95% CI: 0.97, 1.3), two other households (aOR: 1.39, 95% CI: 1.1, 1.7), and three or more other households (aOR: 1.86, 95% CI: 1.4, 2.4). Those who spent Thanksgiving with one or more other households had 1.23 times greater odds (95% CI: 1.1, 1.4) of having a COVID-19 test afterward. There was no association between gathering for Thanksgiving and subsequent COVID-19 test positivity or developing COVID-19 symptoms.\n\nConclusionsThose who gathered with other households for Thanksgiving tended to engage in higher-risk activities. Thanksgiving gathering with other households was not associated with subsequently testing positive for COVID-19, but only a small proportion obtained post-travel testing. Public health messaging should emphasize behavior change strategies that promote safer gathering.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "William You", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York (CUNY)" - }, - { - "author_name": "Madhura S. Rane", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York (CUNY)" - }, - { - "author_name": "Rebecca Zimba", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York (CUNY); New York City, New York USA" - }, - { - "author_name": "Amanda Berry", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York (CUNY)" - }, - { - "author_name": "Sarah G Kulkarni", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York (CUNY)" - }, - { - "author_name": "Drew A Westmoreland", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York (CUNY)" - }, - { - "author_name": "Angela Parcesepe", - "author_inst": "Department of Maternal and Child Health, Gillings School of Public Health, University of North Carolina" - }, - { - "author_name": "Mindy Chang", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York (CUNY)" - }, - { - "author_name": "Andrew R Maroko", - "author_inst": "CUNY Graduate School of Public Health and Health Policy" - }, - { - "author_name": "Shivani Kochhar", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York (CUNY)" - }, - { - "author_name": "Chloe Mirzayi", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York (CUNY)" - }, - { - "author_name": "Christian Grov", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York (CUNY)" - }, - { - "author_name": "Denis Nash", - "author_inst": "Institute for Implementation Science in Population Health (ISPH), City University of New York (CUNY);" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.23.21255974", "rel_title": "Exploring the Behavioral Determinants of COVID-19 Vaccine Acceptance among an Urban Population in Bangladesh: Implications for Behavior Change Interventions", @@ -824506,6 +822821,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.22.21255913", + "rel_title": "Impact of vaccination on SARS-CoV-2 cases in the community: a population-based study using the UK COVID-19 Infection Survey", + "rel_date": "2021-04-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.22.21255913", + "rel_abs": "ObjectivesTo assess the effectiveness of COVID-19 vaccination in preventing SARS-CoV-2 infection in the community.\n\nDesignProspective cohort study.\n\nSettingThe UK population-representative longitudinal COVID-19 Infection Survey.\n\nParticipants373,402 participants aged [≥]16 years contributing 1,610,562 RT-PCR results from nose and throat swabs between 1 December 2020 and 3 April 2021.\n\nMain outcome measuresNew RT-PCR-positive episodes for SARS-CoV-2 overall, by self-reported symptoms, by cycle threshold (Ct) value (<30 versus [≥]30), and by gene positivity (compatible with the B.1.1.7 variant versus not).\n\nResultsOdds of new SARS-CoV-2 infection were reduced 65% (95% CI 60 to 70%; P<0.001) in those [≥]21 days since first vaccination with no second dose versus unvaccinated individuals without evidence of prior infection (RT-PCR or antibody). In those vaccinated, the largest reduction in odds was seen post second dose (70%, 95% CI 62 to 77%; P<0.001).There was no evidence that these benefits varied between Oxford-AstraZeneca and Pfizer-BioNTech vaccines (P>0.9).There was no evidence of a difference in odds of new SARS-CoV-2 infection for individuals having received two vaccine doses and with evidence of prior infection but not vaccinated (P=0.89). Vaccination had a greater impact on reducing SARS-CoV-2 infections with evidence of high viral shedding Ct<30 (88% reduction after two doses; 95% CI 80 to 93%; P<0.001) and with self-reported symptoms (90% reduction after two doses; 95% CI 82 to 94%; P<0.001); effects were similar for different gene positivity patterns.\n\nConclusionVaccination with a single dose of Oxford-AstraZeneca or Pfizer-BioNTech vaccines, or two doses of Pfizer-BioNTech, significantly reduced new SARS-CoV-2 infections in this large community surveillance study. Greater reductions in symptomatic infections and/or infections with a higher viral burden are reflected in reduced rates of hospitalisations/deaths, but highlight the potential for limited ongoing transmission from asymptomatic infections in vaccinated individuals.\n\nRegistrationThe study is registered with the ISRCTN Registry, ISRCTN21086382.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Emma Pritchard", + "author_inst": "University of Oxford" + }, + { + "author_name": "Philippa Matthews", + "author_inst": "University of Oxford" + }, + { + "author_name": "Nicole Stoesser", + "author_inst": "University of Oxford" + }, + { + "author_name": "David Eyre", + "author_inst": "University of Oxford" + }, + { + "author_name": "Owen Gethings", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Karina-Doris Vitha", + "author_inst": "University of Oxford" + }, + { + "author_name": "Joel Jones", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Thomas House", + "author_inst": "University of Manchester" + }, + { + "author_name": "Harper VanSteenhouse", + "author_inst": "Glasgow Lighthouse Laboratory" + }, + { + "author_name": "Iain Bell", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "John Bell", + "author_inst": "University of Oxford" + }, + { + "author_name": "John Newton", + "author_inst": "Public Health England" + }, + { + "author_name": "Jeremy Farrar", + "author_inst": "Wellcome Trust" + }, + { + "author_name": "Ian Diamond", + "author_inst": "Office for National Statistics," + }, + { + "author_name": "Emma Rourke", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Ruth Studley", + "author_inst": "Office for National Statistics" + }, + { + "author_name": "Derrick W Crook", + "author_inst": "NIHR Oxford Biomedical Research Centre" + }, + { + "author_name": "tim E peto", + "author_inst": "oxford university" + }, + { + "author_name": "Ann Sarah Walker", + "author_inst": "University of Oxford" + }, + { + "author_name": "Koen B Pouwels", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.21.21255873", "rel_title": "Real World Effectiveness of COVID-19 mRNA Vaccines against Hospitalizations and Deaths in the United States", @@ -824894,33 +823304,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.22.21255953", - "rel_title": "COVID-19 pandemic: Analyzing of spreading behavior, the impact of restrictions and prevention measures in Germany and Japan.", - "rel_date": "2021-04-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.22.21255953", - "rel_abs": "In December 2019, the world was confronted with the outbreak of the respiratory disease COVID-19. The COVID-19 epidemic evolved at the beginning of 2020 into a pandemic, which continues to this day. The incredible speed of the spread and the consequences of the infection had a worldwide impact on societies and health systems. Governments enforced many measures to control the COVID-19 pandemic: Restrictions (e.g. lockdown), medical care (e.g. intensive care) and medical prevention (e.g. hygiene concept). This leads to a different spreading behavior of the COVID-19 pandemic, depending on measures. Furthermore, the spreading behavior is influenced by culture and geographical impacts. The spreading behavior of COVID-19 related to short time intervals can be described by Weibull distribution models, common in reliability engineering, in a sound way. The interpretation of the model parameters allows the assessment of the COVID-19 spreading characteristics. This paper shows results of a research study of the COVID-19 spreading behavior depending on different pandemic time phases within Germany and Japan. Both countries are industrial nations, but have many differences with respect to historical development, culture and geographical conditions. Consequently, the chosen government measures have different impacts on the control of the COVID-19 pandemic. The research study contains the analyses of different pandemic time intervals in Germany and Japan: The breakout phase in spring 2020 and subsequently following waves until winter season 2020/2021.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Stefan Bracke", - "author_inst": "University of Wuppertal, Germany" - }, - { - "author_name": "Alicia Puls", - "author_inst": "University of Wuppertal" - }, - { - "author_name": "Masato Inoue", - "author_inst": "Meiji University, Japan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.21.21255473", "rel_title": "Clinical Trends Among U.S. Adults Hospitalized with COVID-19, March-December 2020", @@ -826504,6 +824887,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.20.21255796", + "rel_title": "Analysis of the Number of Tests, the Positivity Rate, and Their Dependency Structure during COVID-19 Pandemic", + "rel_date": "2021-04-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.20.21255796", + "rel_abs": "BackgroundApplying recent advances in medical instruments, information technology, and unprecedented data sharing into COVID-19 research revolutionized medical sciences, and causes some unprecedented analyses, discussions, and models.\n\nMethodsModeling of this dependency is done using four classes of copulas: Clayton, Frank, Gumbel, and FGM. The estimation of the parameters of the copulas is obtained using the maximum likelihood method. To evaluate the goodness of fit of the copulas, we calculate AIC. All computations are conducted on Matlab R2015b, R 4.0.3, Maple 2018a, and EasyFit 5.6, and the plots are created on software Matlab R2015b and R 4.0.3.\n\nResultsAs time passes, the number of tests increases, and the positivity rate becomes lower. The epidemic peaks are occasions that violate the stated general rule -due to the early growth of the number of tests. If we divide data of each country into peaks and otherwise, about both of them, the rising number of tests is accompanied by decreasing the positivity rate.\n\nConclusionThe positivity rate can be considered a representative of the level of the spreading. Approaching zero positivity rate is a good criterion to scale the success of a health care system in fighting against an epidemic. We expect that if the number of tests is great enough, the positivity rate does not depend on the number of tests. Accordingly, the number and accuracy of tests can play a vital role in the quality level of epidemic data.\n\nKey messages- In a country, increasing the positivity rate is more representative than increasing the number of tests to warn about an epidemic peak.\n- Approaching zero positivity rate is a good criterion to scale the success of a health care system in fighting against an epidemic.\n- Except for the first half of the epidemic peaks, in a country, the higher number of tests is associated with a lower positivity rate.\n- In countries with high test per million, there is no significant dependency between the number of tests and positivity rate.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Babak Jamshidi", + "author_inst": "Kermanshah University of Medical Sciences" + }, + { + "author_name": "Hakim Bekrizadeh", + "author_inst": "Payame Noor University" + }, + { + "author_name": "Shahriar Jamshidi Zargaran", + "author_inst": "Isfahan University of Medical Sciences" + }, + { + "author_name": "Mansour Rezaei", + "author_inst": "Kermanshah University of Medical Sciences" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.20.21255829", "rel_title": "Manufacturer Signal-to-Cutoff Threshold Underestimates Cumulative Incidence of SARS-CoV-2 Infection: Evidence from the Los Angeles Firefighters Study", @@ -826928,69 +825342,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.19.21255723", - "rel_title": "B and T cell immune responses elicited by the BNT162b2 (Pfizer BioNTech) COVID-19 vaccine in nursing home residents", - "rel_date": "2021-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.19.21255723", - "rel_abs": "ObjectivesThe immunogenicity of the BNT162b2 COVID-19 vaccine is understudied in elderly people with comorbidities. We assessed SARS-CoV-2-S-targeted antibody and T cell responses following full vaccination in nursing home residents (NHR).\n\nMethodsWe recruited 60 NHR (44 female; median age, 87.5 years), of whom 10 had previously had COVID-19, and 18 healthy controls (15 female; median age, 48.5 years). Pre- and post-vaccination blood specimens were available for quantitation of total antibodies binding RBD and enumeration of SARS-CoV-2-S-reactive IFN-{gamma} CD4+ and CD8+ T cells by flow cytometry.\n\nResultsThe seroconversion rate in presumably SARS-CoV-2 naive NHR (95.3%), either with or without comorbidities, was similar to controls (94.4%). A robust booster effect was documented in NHR with prior COVID-19. Plasma antibody levels were higher in convalescent NHR than in individuals across the other two groups. A large percentage of NHR had SARS-CoV-2 S-reactive IFN-{gamma} CD8+ and/or CD4+ T cells at baseline, in contrast to healthy controls. Either CD8+ and/or CD4+ T-cell responses were documented in all control subjects after vaccination. Contrariwise, the percentage of NHR exhibiting detectable SARS-CoV-2 IFN-{gamma} CD8+ or CD4+ T-cell responses (or both), irrespective of their baseline SARS-CoV-2 infection status, dropped consistently after vaccination. Overall, SARS-CoV-2 IFN-{gamma} CD8+ and CD4+ T-cell responses in NHR decreased in post-vaccination specimens.\n\nConclusionThe BNT162b2 COVID-19 vaccine elicits robust SARS-CoV-2-S antibody responses in NHR. Nevertheless, the frequency and magnitude of detectable SARS-CoV-2 IFN-{gamma} T-cell responses after vaccination was lower in NHR compared to controls.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Ignacio Torres", - "author_inst": "Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain." - }, - { - "author_name": "Eliseo Albert", - "author_inst": "Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain." - }, - { - "author_name": "Estela Gimenez", - "author_inst": "Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain." - }, - { - "author_name": "Maria Jesus Alcaraz", - "author_inst": "Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain." - }, - { - "author_name": "Pilar Botija", - "author_inst": "Direccion de Atencion Primaria, Departamento de Salud Clinico-Malvarrosa, Hospital Clinico Universitario de Valencia, Valencia, Spain." - }, - { - "author_name": "Paula Amat", - "author_inst": "Hematology Service Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain." - }, - { - "author_name": "Maria Jose Remigia", - "author_inst": "Hematology Service Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain." - }, - { - "author_name": "Maria Jose Beltran", - "author_inst": "Direccion de Enfermeria, Departamento de Salud Clinico-Malvarrosa, Hospital Clinico Universitario de Valencia, Valencia, Spain." - }, - { - "author_name": "Celia Rodado", - "author_inst": "Comision Departamental de control de Residencias. Departamento de Salud Valencia Clinico Malvarrosa." - }, - { - "author_name": "Dixie Huntley", - "author_inst": "Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain." - }, - { - "author_name": "Beatriz Olea", - "author_inst": "Microbiology Service, Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain." - }, - { - "author_name": "David Navarro", - "author_inst": "Clinic University Hospital, INCLIVA Health Research Institute, Valencia, Spain." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.19.21255750", "rel_title": "ReCOVer study: A Cross-sectional Observational Study to Identify the Rehabilitation Need in Post-discharge COVID-19 Survivors", @@ -828246,6 +826597,20 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.21.440861", + "rel_title": "InterARTIC: an interactive web application for whole-genome nanopore sequencing analysis of SARS-CoV-2 and other viruses", + "rel_date": "2021-04-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.21.440861", + "rel_abs": "MotivationInterARTIC is an interactive web application for the analysis of viral whole-genome sequencing (WGS) data generated on Oxford Nanopore Technologies (ONT) devices. A graphical interface enables users with no bioinformatics expertise to analyse WGS experiments and reconstruct consensus genome sequences from individual isolates of viruses, such as SARS-CoV-2. InterARTIC is intended to facilitate widespread adoption and standardisation of ONT sequencing for viral surveillance and molecular epidemiology.\n\nWorked exampleWe demonstrate the use of InterARTIC for the analysis of ONT viral WGS data from SARS-CoV-2 and Ebola virus, using a laptop computer or the internal computer on an ONT GridION sequencing device. We showcase the intuitive graphical interface, workflow customisation capabilities and job-scheduling system that facilitate execution of small- and large-scale WGS projects on any common virus.\n\nImplementationInterARTIC is a free, open-source web application implemented in Python. The application can be downloaded as a set of pre-compiled binaries that are compatible with all common Ubuntu distributions, or built from source. For further details please visit: https://github.com/Psy-Fer/interARTIC/.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.04.22.21255574", "rel_title": "Mutation-specific SARS-CoV-2 PCR Screen: Rapid and Accurate Detection of Variants of Concern and the Identification of a Newly Emerging Variant with Spike L452R Mutation", @@ -828878,61 +827243,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.21.440801", - "rel_title": "Comparative Analysis of Emerging B.1.1.7+E484K SARS-CoV-2 isolates from Pennsylvania", - "rel_date": "2021-04-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.21.440801", - "rel_abs": "Rapid whole genome sequencing of SARS-CoV-2 has presented the ability to detect new emerging variants of concern in near real time. Here we report the genome of a virus isolated in Pennsylvania in March 2021 that was identified as lineage B.1.1.7 (VOC-202012/01) that also harbors the E484K spike mutation, which has been shown to promote \"escape\" from neutralizing antibodies in vitro. We compare this sequence to the only 5 other B.1.1.7+E484K genomes from Pennsylvania, all of which were isolated in mid March. Beginning in February 2021, only a small number (n=60) of isolates with this profile have been detected in the US, and only a total of 253 have been reported globally (first in the UK in December 2020). Comparative genomics of all currently available high coverage B.1.1.7+E484K genomes (n=235) available on GISAID suggested the existence of 7 distinct groups or clonal complexes (CC; as defined by GNUVID) bearing the E484K mutation raising the possibility of 7 independent acquisitions of the E484K spike mutation in each background. Phylogenetic analysis suggested the presence of at least 3 distinct clades of B.1.1.7+E484K circulating in the US, with the Pennsylvanian isolates belonging to two distinct clades. Increased genomic surveillance will be crucial for detection of emerging variants of concern that can escape natural and vaccine induced immunity.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Azad Ahmed", - "author_inst": "Drexel University College of Medicine" - }, - { - "author_name": "John Everett", - "author_inst": "Perelman School of Medicine, University of Pennsylvania, Philadelphia" - }, - { - "author_name": "Shantan Reddy", - "author_inst": "Perelman School of Medicine, University of Pennsylvania, Philadelphia" - }, - { - "author_name": "Emilie Rabut", - "author_inst": "Hospital of the University of Pennsylvania" - }, - { - "author_name": "Jasmine Deseignora", - "author_inst": "Hospital of the University of Pennsylvania" - }, - { - "author_name": "Michael D. Feldman", - "author_inst": "Perelman School of Medicine, University of Pennsylvania" - }, - { - "author_name": "Kyle G. Rodino", - "author_inst": "Perelman School of Medicine, University of Pennsylvania" - }, - { - "author_name": "Frederic Bushman", - "author_inst": "Perelman School of Medicine, University of Pennsylvania, Philadelphia" - }, - { - "author_name": "Rebecca M. Harris", - "author_inst": "Perelman School of Medicine, University of Pennsylvania" - }, - { - "author_name": "Josh Chang Mell", - "author_inst": "Drexel University College of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2021.04.21.21255676", "rel_title": "Prediction of COVID-19 cases during Tokyo's Olympic and Paralympic Games", @@ -830156,6 +828466,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.13.21255445", + "rel_title": "Point-of-Care Ultrasound (POCUS) Predicts Clinical Outcomes in Patients with COVID-19.", + "rel_date": "2021-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.13.21255445", + "rel_abs": "IntroductionPoint-of-care ultrasound (POCUS) may detect the cardiopulmonary manifestations of COVID-19 and expediently predict patient outcomes.\n\nMethodsWe conducted a prospective cohort study at four medical centers from 3/2020-1/2021 to evaluate POCUS findings and clinical outcomes with COVID-19. Our inclusion criteria included adult patients hospitalized for COVID-19 who received cardiac or lung POCUS with a 12-zone protocol. Images were interpreted by two reviewers blinded to clinical outcomes. Our primary outcome was ICU admission incidence. Secondary outcomes included intubation and supplemental oxygen usage.\n\nResultsN=160 patients (N=201 scans) were included. Scans were collected a median 23 hours (IQR:7-80) from emergency department triage. Triage POCUS findings associated with ICU admission included B-lines (OR 4.41 [95% CI:1.71-14.30]; p<0.01) or consolidation (OR 2.49 [95% CI:1.35-4.86]; p<0.01). B-lines were associated with intubation (OR 3.10 [95% CI:1.15-10.27]; p=0.02) and supplemental oxygen usage (OR 3.74 [95% CI:1.63-8.63; p<0.01).\n\nConsolidations present on triage were associated with the need for oxygen at discharge (OR 2.16 [95% CI: 1.01-4.70]; p=0.047). A normal lung triage scan was protective for ICU admission (OR 0.28 [95% CI:0.09-0.75; p<0.01) or need for supplemental oxygen during the hospitalization (OR 0.26 [95% CI:0.11-0.61]; p<0.01). Triage cardiac POCUS scans were not associated with any outcomes.\n\nDiscussionLung POCUS findings detected early in the hospitalization may provide expedient risk stratification for important COVID-19 clinical outcomes, including ICU admission, intubation, or need for oxygen on discharge. A normal admission scan appears protective against adverse outcomes, which may aid in triage decisions of patients.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Andre Kumar", + "author_inst": "Stanford Unviersity" + }, + { + "author_name": "Yingjie Weng", + "author_inst": "Stanford University" + }, + { + "author_name": "Sally Graglia", + "author_inst": "UCSF" + }, + { + "author_name": "Thomas Lew", + "author_inst": "Stanford University" + }, + { + "author_name": "Kavita Gandhi", + "author_inst": "UCSF" + }, + { + "author_name": "Farhan Lalani", + "author_inst": "UCSF" + }, + { + "author_name": "David Chia", + "author_inst": "UCSF" + }, + { + "author_name": "Youyou Duanmu", + "author_inst": "Stanford" + }, + { + "author_name": "Trevor Jensen", + "author_inst": "UCSF" + }, + { + "author_name": "Viveta Lobo", + "author_inst": "Stanford" + }, + { + "author_name": "Jeffrey Nahn", + "author_inst": "UCSF" + }, + { + "author_name": "Nicholas Iverson", + "author_inst": "UCSF" + }, + { + "author_name": "Molly Rosenthal", + "author_inst": "UCSF" + }, + { + "author_name": "Andrea Gordon", + "author_inst": "Stanford" + }, + { + "author_name": "John Kugler", + "author_inst": "Stanford" + }, + { + "author_name": "Minh Chi Tran", + "author_inst": "Stanford" + }, + { + "author_name": "Xiaolin Jia", + "author_inst": "Stanford" + }, + { + "author_name": "Charles Liao", + "author_inst": "Stanford" + }, + { + "author_name": "Alice Cha", + "author_inst": "Stanford" + }, + { + "author_name": "Evan Baum", + "author_inst": "Stanford" + }, + { + "author_name": "Douglas Halket", + "author_inst": "Stanford" + }, + { + "author_name": "Jai Madhok", + "author_inst": "Stanford" + }, + { + "author_name": "Muhammad Fazal", + "author_inst": "Stanford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.13.21255438", "rel_title": "Cyclooxygenase inhibitor use is associated with increased COVID-19 severity", @@ -830552,49 +828969,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.14.21255490", - "rel_title": "Expectant parents' perceptions of healthcare and support during COVID-19 in the UK: A thematic analysis.", - "rel_date": "2021-04-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.14.21255490", - "rel_abs": "BackgroundIn response to the COVID-19 pandemic, expectant parents experienced changes in the availability and uptake of both NHS community and hospital-based healthcare.\n\nObjectiveTo examine how COVID-19 and its societal related restrictions have impacted the provision of healthcare support for pregnant women during the COVID-19 pandemic.\n\nMethodA thematic analysis using an inductive approach was undertaken of data from open-ended responses using data from the national COVID in Context of Pregnancy, Infancy and Parenting (CoCoPIP) Study online survey (N = 507 families).\n\nResultsThe overarching theme identified was the way in which the changes to healthcare provision increased parents anxiety levels, and feelings of not being supported. Five sub-themes, associated with the first wave of the pandemic, were identified: (1) rushed and/or fewer antenatal appointments, (2) lack of sympathy from healthcare workers, (3) lack of face-to-face appointments, (4) requirement to attend appointments without a partner, and (5) requirement to use PPE. A sentiment analysis, that used quantitative techniques, revealed participant responses to be predominantly negative (50.1%), with a smaller proportion of positive (21.8%) and neutral (28.1%) responses found.\n\nConclusionThis study provides evidence indicating that the changes to healthcare services for pregnant women during the pandemic increased feelings of anxiety and have left women feeling inadequately supported. Our findings highlight the need for compensatory social and emotional support for new and expectant parents while COVID-19 related restrictions continue to impact on family life and society.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ezra Aydin", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Kevin A Glasgow", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Staci Weiss", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Topun Austin", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Mark Johnson", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Jane Barlow", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sarah Lloyd-Fox", - "author_inst": "University of Cambridge" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.14.21255519", "rel_title": "The COvid-19 Pandemic and Exercise (COPE) Trial: A multi-group randomized controlled trial comparing effects of an app-based, at-home exercise program to waitlist control on depressive symptoms", @@ -831826,6 +830200,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.17.21255656", + "rel_title": "Rapid detection of SARS CoV-2 N501Y mutation in clinical samples", + "rel_date": "2021-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.17.21255656", + "rel_abs": "Severe acute respiratory syndrome coronavirus-2 (SARS CoV-2) variants poses major threats in increasing infectivity, transmission, mortality of Coronavirus Disease 2019 (Covid-19). Additionally, SARS CoV-2 variants resist antibody neutralizations or may abolish vaccine efficacies. Researches to develop economical and fast methods will support the developing or poor countries to challenge the Covid-19 pandemic via tracking common mutations that may help to deploy the vaccination programs and control the virus. Current study has developed a novel low-cost rapid technique, exploiting real time PCR probes and conventional PCR specific primers, to identify N501Y mutation, which was independently emerged in the UK, South African and Brazilian variants. Currently, these variants tend to spread to all over the world and seem to be more infectious, transmissible and fatal. This study helps tracking the N501Y mutation for understanding its clinical and epidemiological characteristics, in those countries where sequencing facilities are lacking or expensive. Further study should focus on other common mutations in the variants of concerns of SARS CoV-2.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Sirwan M.A. Al-Jaf", + "author_inst": "University of Garmian" + }, + { + "author_name": "Sherko Subhan Niranji", + "author_inst": "University of Garmian" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.19.21255759", "rel_title": "Analyzing the effect of relaxing restriction on the COVID-19 outbreak for some US states", @@ -832306,65 +830703,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.04.14.21255476", - "rel_title": "Geographic and demographic heterogeneity of SARS-CoV-2 diagnostic testing in Illinois, USA, March to December 2020", - "rel_date": "2021-04-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.14.21255476", - "rel_abs": "BackgroundAvailability of SARS-CoV-2 testing in the United States (U.S.) has fluctuated through the course of the COVID-19 pandemic, including in the U.S. state of Illinois. Despite substantial ramp-up in test volume, access to SARS-CoV-2 testing remains limited, heterogeneous, and insufficient to control spread.\n\nMethodsWe compared SARS-CoV-2 testing rates across geographic regions, over time, and by demographic characteristics (i.e., age and racial/ethnic groups) in Illinois during March through December 2020. We compared age-matched case fatality ratios and infection fatality ratios through time to estimate the fraction of SARS-CoV-2 infections that have been detected through diagnostic testing.\n\nResultsBy the end of 2020, initial geographic differences in testing rates had closed substantially. Case fatality ratios were higher in non-Hispanic Black and Hispanic/Latino populations in Illinois relative to non-Hispanic White populations, suggesting that tests were insufficient to accurately capture the true burden of COVID-19 disease in the minority populations during the initial epidemic wave. While testing disparities decreased during 2020, Hispanic/Latino populations consistently remained the least tested at 1.87 tests per 1000 population per day compared with 2.58 and 2.87 for non-Hispanic Black and non-Hispanic White populations, respectively, at the end of 2020. Despite a large expansion in testing since the beginning of the first wave of the epidemic, we estimated that over half (50-80%) of all SARS-CoV-2 infections were not detected by diagnostic testing and continued to evade surveillance.\n\nConclusionsSystematic methods for identifying relatively under-tested geographic regions and demographic groups may enable policymakers to regularly monitor and evaluate the shifting landscape of diagnostic testing, allowing officials to prioritize allocation of testing resources to reduce disparities in COVID-19 burden and eventually reduce SARS-CoV-2 transmission.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Tobias M Holden", - "author_inst": "Northwestern University" - }, - { - "author_name": "Reese AK Richardson", - "author_inst": "Northwestern University" - }, - { - "author_name": "Philip Arevalo", - "author_inst": "University of Chicago" - }, - { - "author_name": "Wayne A Duffus", - "author_inst": "CDC/IDPH" - }, - { - "author_name": "Manuela Runge", - "author_inst": "Northwestern University" - }, - { - "author_name": "Elena Whitney", - "author_inst": "University of Chicago" - }, - { - "author_name": "Leslie Wise", - "author_inst": "Illinois Dept of Public Health" - }, - { - "author_name": "Ngozi O Ezike", - "author_inst": "Illinois Dept of Public Health" - }, - { - "author_name": "Sarah Patrick", - "author_inst": "Illinois Dept of Public Health" - }, - { - "author_name": "Sarah Cobey", - "author_inst": "University of Chicago" - }, - { - "author_name": "Jaline Gerardin", - "author_inst": "Northwestern University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.19.21254974", "rel_title": "A Simplified Point-of-Care Lung Ultrasound Protocol to Detect Coronavirus Disease 2019 in Inpatients: A Prospective Observational Study", @@ -833980,6 +832318,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.04.13.21255281", + "rel_title": "The increase in the risk of severity and fatality rate of covid-19 in southern Brazil after the emergence of the Variant of Concern (VOC) SARS-CoV-2 P.1 was greater among young adults without pre-existing risk conditions", + "rel_date": "2021-04-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.13.21255281", + "rel_abs": "BackgroundThe SARS-CoV-2 P.1 variant has been considered as \"variant of concern (VOC)\" since the end of 2020 when it was firstly identified in the Brazilian state of Amazonas and from there spread to other regions of Brazil. This variant was associated with an increase in transmissibility and worsening of the epidemiological situation in the places where it was detected. The aim of this study was to analyze the severity profile of covid-19 cases in the Rio Grande do Sul state, southern region of Brazil, before and after the emergence of the P.1 variant, considering also the context of the hospitals overload and the collapse of health services.\n\nMethodsWe analyzed data from the Influenza Epidemiological Surveillance Information System, SIVEP-Gripe (Sistema de Informacao de Vigilancia Epidemiologica da Gripe) and compare two epidemiological periods: the \"first wave\" comprised by cases occurred during November and December 2020 (EW 45 to 53) and the \"second wave\" with cases occurred in February 2021 (EW 5 to 8), considering that in this month there was a predominance of the new variant P.1. We calculated the proportion of severe forms among the total cases of covid-19, the case fatality rates (CFR) and hospital case fatality rate (hCFR) over both waves time set using the date of onset of symptoms as a reference. We analyzed separately the patients without pre-existing conditions of risk, by age and sex. For comparison between periods, we calculated the Risk Ratio (RR) with their respective 95% confidence intervals and the p-values.\n\nFindingsWe observed that in the second wave there were an increase in the proportion of severe cases and covid-19 deaths among younger age groups and patients without pre-existing conditions of risk. The proportion of people under the age of 60 among the cases that evolved to death raised from 18% (670 deaths) in November and December (1st wave) to 28% (1370 deaths) in February (2nd wave). A higher proportion of patients without pre-existing risk conditions was also observed among those who evolved to death due to covid-19 in the second wave (22%, 1,077 deaths) than in the first one (13%, 489 deaths). The CFR for covid-19 increased overall and in different age groups, in both sexes. The increase occurred in a greatest intensity in the population between 20 and 59 years old and among patients without pre-existing risk conditions. Female 20 to 39 years old, with no pre-existing risk conditions, were at risk of death 5.65 times higher in February (95%CI = 2.9 - 11.03; p <0.0001) and in the age group of 40 and 59 years old, this risk was 7.7 times higher (95%CI = 5.01-11.83; p <0.0001) comparing with November-December.\n\nInterpretationOur findings showed an increase in the proportion of young people and people without previous illnesses among severe cases and deaths in the state of RS after the identification of the local transmission of variant P.1 in the state. There was also an increase in the proportion of severe cases and in the CFR, in almost all subgroups analyzed, this increase was heterogeneous in different age groups and sex. As far as we know, these are the first evidences that the P.1 variant can disproportionately increase the risk of severity and deaths among population without pre-existing diseases, suggesting related changes in pathogenicity and virulence profiles. New studies still need to be done to confirm and deepen these findings.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Andre R R Freitas", + "author_inst": "Faculdade de Medicina Sao Leopoldo Mandic de Campinas" + }, + { + "author_name": "Daniele R Q Lemos", + "author_inst": "Faculdade de Medicina do Centro Universitario Christus" + }, + { + "author_name": "Otto A Beckedorff", + "author_inst": "Faculdade de Medicina Sao Leopoldo Mandic de Campinas" + }, + { + "author_name": "Luciano P G Cavalcante", + "author_inst": "Programa de Pos-graduacao em Saude Coletiva da Universidade Federal do Ceara, Fortaleza-CE -" + }, + { + "author_name": "Andre M Siqueira", + "author_inst": "Instituto Nacional de Infectologia Evandro Chagas - FIOCRUZ" + }, + { + "author_name": "Regiane C S Mello", + "author_inst": "Programa de Pos-graduacao em Saude Coletiva - Faculdade de Medicina Sao Leopoldo Mandic de Campinas" + }, + { + "author_name": "Eliana N C Barros", + "author_inst": "Centro de Farmacovigilancia, Seguranca Clinica e Gestao de Risco do Instituto Butantan." + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.12.21255368", "rel_title": "A point-of-care lateral flow assay for neutralising antibodies against SARS-CoV-2", @@ -834664,77 +833045,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.12.21255330", - "rel_title": "Identification of natural SARS-CoV-2 infection in seroprevalence studies among vaccinated populations", - "rel_date": "2021-04-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.12.21255330", - "rel_abs": "ImportanceIdentification of SARS-CoV-2 infection via antibody assays is important for monitoring natural infection rates. Most antibody assays cannot distinguish natural infection from vaccination.\n\nObjectiveTo assess the accuracy of a nucleocapsid-containing assay in identifying natural infection among vaccinated individuals.\n\nDesignA longitudinal cohort comprised of healthcare workers (HCW) in the Minneapolis/St. Paul metropolitan area was enrolled. Two rounds of seroprevalence studies separated by one month were conducted from 11/2020-1/2021. Capillary blood from round 1 and 2 was tested for IgG antibodies against SARS-CoV-2 spike proteins with a qualitative chemiluminescent ELISA (spike-only assay). In a subsample of participants (n=82) at round 2, a second assay was performed that measured IgGs reactive to SARS-CoV-2 nucleocapsid protein (nucleocapsid-containing assay). Round 1 biospecimen collections occurred prior to vaccination in all participants. Vaccination status at round 2 was determined via self-report.\n\nSettingThe Minneapolis/St. Paul, Minnesota metropolitan area.\n\nParticipantsHCW age 18-80 years.\n\nExposuresRound 1 recent SARS-CoV-2 infection assessed via a spike-only assay and participant self-report.\n\nOutcomesRound 2 SARS-CoV-2 infection assessed via the nucleocapsid-containing assay. Area under the curve (AUC) was computed to determine the discriminatory ability of round 2 IgG reactivity to nucleocapsid for identification of recent infection determined during round 1\n\nResultsParticipants had a mean age of 40 (range=23-66) years, 83% were female, 46% reported vaccination prior to the round 2 testing. Round 1 seroprevalence was 9.5%. Among those not recently infected, when comparing vaccinated vs. unvaccinated individuals, elevated levels of spike 1 (p<0.001) and spike 2 (p=0.01) were observed while nucleocapsid levels were not statistically significantly different (p=0.90). Among all participants, nucleocapsid response predicted recent infection with an AUC(95%CI) of 0.93(0.88,0.99). Among individuals vaccinated >10 days prior to antibody testing, the specificity of the nucleocapsid-containing assay was 92% and while the specificity of the spike-only assay was 0%.\n\nConclusions and RelevanceAn IgG assay identifying reactivity to nucleocapsid protein is an accurate predictor of natural infection among vaccinated individuals while a spike-only assay performed poorly. In the era of SARS-CoV-2 vaccination, seroprevalence studies monitoring natural infection will require assays that do not rely on spike-protein response alone.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Ryan T Demmer", - "author_inst": "Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN; Department of Epidemiology, Mailman School of " - }, - { - "author_name": "Brett Baumgartner", - "author_inst": "Quansys Biosciences, Logan, UT" - }, - { - "author_name": "Talia D Wiggen", - "author_inst": "Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN" - }, - { - "author_name": "Angela K Ulrich", - "author_inst": "Center for Infectious Disease Research and Policy, University of Minnesota, Minneapolis, MN" - }, - { - "author_name": "Ali J Strickland", - "author_inst": "Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN" - }, - { - "author_name": "Brianna M Naumchik", - "author_inst": "Medical School, University of Minnesota, Minneapolis, MN" - }, - { - "author_name": "Bruno Bohn", - "author_inst": "Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN" - }, - { - "author_name": "Sara Walsh", - "author_inst": "NORC at the University of Chicago, Health Sciences, Chicago, IL" - }, - { - "author_name": "Stephen Smith", - "author_inst": "NORC at the University of Chicago, Health Sciences, Chicago, IL" - }, - { - "author_name": "Susan Kline", - "author_inst": "Division of Infectious Diseases and International Medicine, Medical School, University of Minnesota, Minneapolis, MN" - }, - { - "author_name": "Steve D Stovitz", - "author_inst": "Department of Family Medicine and Community Health, Medical School, University of Minnesota, Minneapolis, MN" - }, - { - "author_name": "Stephanie Yendell", - "author_inst": "Minnesota Department of Health, St. Paul, MN" - }, - { - "author_name": "Tim Beebe", - "author_inst": "Division of Health Policy and Management, School of Public Health, University of Minnesota, Minneapolis, MN" - }, - { - "author_name": "Craig Hedberg", - "author_inst": "Division of Environmental Health Sciences, School of Public Health, University of Minnesota, Minneapolis, MN" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.13.21255347", "rel_title": "Primary care and point-of-care testing during a pandemic: Clinician's perspectives on integrating rapid testing for COVID-19 into the primary care pathway", @@ -835966,6 +834276,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "palliative medicine" }, + { + "rel_doi": "10.1101/2021.04.19.440452", + "rel_title": "Rapid decay of host basal mRNAs during SARS-CoV-2 infection perturbs host antiviral mRNA biogenesis and export", + "rel_date": "2021-04-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.19.440452", + "rel_abs": "A key feature of the mammalian innate immune response to viral infection is the transcriptional induction of interferon (IFN) genes, which encode for secreted proteins that prime the antiviral response and limit viral replication and dissemination. A hallmark of severe COVID-19 disease caused by SARS-CoV-2 is the low presence of IFN proteins in patient serum despite elevated levels of IFN-encoding mRNAs, indicative of post-transcriptional inhibition of IFN protein production. Herein, we show SARS-CoV-2 infection limits type I and type III IFN biogenesis by preventing the release of mRNA from their sites of transcription and/or triggering their nuclear degradation. In addition, SARS-CoV-2 infection inhibits nuclear-cytoplasmic transport of IFN mRNAs as a consequence of widespread cytosolic mRNA degradation mediated by both activation of the host antiviral endoribonuclease, RNase L, and by the SARS-CoV-2 protein, Nsp1. These findings argue that inhibition of host and/or viral Nsp1-mediated mRNA decay, as well as IFN treatments, may reduce viral-associated pathogenesis by promoting the innate immune response.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "James M Burke", + "author_inst": "University of Colorado Boulder" + }, + { + "author_name": "Laura A St Clair", + "author_inst": "Colorado State University" + }, + { + "author_name": "Rushika Perera", + "author_inst": "Colorado State University" + }, + { + "author_name": "Roy Parker", + "author_inst": "University of Colorado Boulder; Howard Hughes Medical Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.04.16.21255459", "rel_title": "Increased Transmissibility of SARS-CoV-2 Lineage B.1.1.7 by Age and Viral Load: Evidence from Danish Households", @@ -836498,57 +834839,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.04.13.21255413", - "rel_title": "The impact of population mobility on COVID-19 incidence and socioeconomic disparities at the sub-city level in 314 Latin American cities", - "rel_date": "2021-04-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.13.21255413", - "rel_abs": "BackgroundLittle is known about the impact of changes in mobility at the sub-city level on subsequent COVID-19 incidence or the contribution of mobility to socioeconomic disparities in COVID-19 incidence.\n\nMethodsWe compiled aggregated mobile phone location data, COVID-19 confirmed cases, and features of the urban and social environments to analyze linkages between population mobility, COVID-19 incidence, and educational attainment at the sub-city level among cities with >100,000 inhabitants in Argentina, Brazil, Colombia, Guatemala, and Mexico from March to August 2020. We used mixed effects negative binomial regression to examine longitudinal associations between changes in weekly mobility (lags 1-6 weeks) and subsequent COVID-19 incidence at the sub-city level, adjusting for urban environmental factors.\n\nFindingsAmong 1,031 sub-cities representing 314 cities in five Latin American countries, 10% higher weekly mobility was associated with 8.5% (95% CI 7.4% to 9.5%) higher weekly COVID-19 incidence the following week. This association gradually declined as the lag between mobility and COVID-19 incidence increased and was not different from the null at a six-week lag. We found evidence that suggests differences in mobility reductions are a driver of socioeconomic disparities in COVID-19 incidence.\n\nInterpretationLower population movement within a sub-city is associated with lower risk of subsequent COVID-19 incidence among residents of that sub-city. Implementing policies that reduce population mobility at the sub-city level may be an impactful COVID-19 mitigation strategy that takes equity into consideration and reduces economic and social disruption at the city or regional level.\n\nFundingWellcome Trust", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Josiah L Kephart", - "author_inst": "Dornsife School of Public Health, Drexel University, USA" - }, - { - "author_name": "Xavier Delclos-Alio", - "author_inst": "Institute of Urban and Regional Development, University of California, Berkeley, USA" - }, - { - "author_name": "Usama Bilal", - "author_inst": "Dornsife School of Public Health, Drexel University, USA" - }, - { - "author_name": "Olga L Sarmiento", - "author_inst": "School of Medicine, Universidad de Los Andes, Colombia" - }, - { - "author_name": "Tonatiuh Barrientos-Gutierrez", - "author_inst": "Center for Population Health Research, National Institute of Public Health, Mexico" - }, - { - "author_name": "Manuel Ramirez-Zea", - "author_inst": "INCAP Research Center for the Prevention of Chronic Diseases, Institute of Nutrition of Central America and Panama, Guatemala" - }, - { - "author_name": "D. Alex Quistberg", - "author_inst": "Dornsife School of Public Health, Drexel University, USA" - }, - { - "author_name": "Daniel A Rodriguez", - "author_inst": "Department of City and Regional Planning and Institute for Transportation Studies, University of California, Berkeley, USA" - }, - { - "author_name": "Ana V Diez Roux", - "author_inst": "Dornsife School of Public Health, Drexel University, USA" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.04.12.21255329", "rel_title": "Comparison of preprints and final journal publications from COVID-19 Studies: Discrepancies in results reporting and spin in interpretation", @@ -837800,6 +836090,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.04.11.21255289", + "rel_title": "An explicit formula for minimizing the infected peak in an SIR epidemic model when using a fixed number of complete lockdowns", + "rel_date": "2021-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.11.21255289", + "rel_abs": "Careful timing of NPIs (non-pharmaceutical interventions) such as social distancing may avoid high \"second waves\" of infections of COVID-19. This paper asks what should be the timing of a set of k complete-lockdowns of prespecified lengths (such as two weeks) so as to minimize the peak of the infective compartment. Perhaps surprisingly, it is possible to give an explicit and easily computable rule for when each lockdown should commence. Simulations are used to show that the rule remains fairly accurate even if lockdowns are not perfect.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Eduardo Sontag", + "author_inst": "Northeastern University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.10.21255251", "rel_title": "Controlling long-term SARS-CoV-2 infections is important for slowing viral evolution", @@ -838364,33 +836673,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.04.10.21254878", - "rel_title": "Preparations of Dutch emergency departments for the COVID-19 pandemic: a questionnaire-based study", - "rel_date": "2021-04-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.10.21254878", - "rel_abs": "BackgroundThe onset of the COVID-19 pandemic was characterized by rapidly increasing patient volumes, which necessitated a swift emergency department (ED) overhaul. Challenges mainly concerned surge capacity, frontline staff protection and the segregation of patients with suspected COVID-19. To date, only few studies have assessed nation-wide ED preparedness for the COVID-19 pandemic. This study aimed to form an overview of preparations that were taken in Dutch EDs during the initial phase of this public health crisis.\n\nMethodsThis study was designed as a nation-wide, cross-sectional, questionnaire-based study among Dutch hospital organizations with [≥]1 ED. The questionnaire was conducted between the first and the second wave of the COVID-19 pandemic in the Netherlands and contained close-ended and open-ended questions on changes in ED infrastructure, ED workforce adaptions and the role of emergency physicians (EPs) in the hospitals crisis organization.\n\nResultsOverall response rate was 79.5%. All EDs had made preparations in anticipation of a possible COVID-19 surge. Treatment capacity was expanded in 69.7% of EDs, with a median increase of 49% (IQR 32.5-72.7%). COVID-19 suspected patients were segregated from non-COVID-19 patients in 86.4% of EDs. Non-COVID-19 patients were more often assessed at alternative locations than patients with suspected COVID-19 infection. In 81.8% of EDs the workforce was expanded, which mainly concerned expansion of nursing staff. A formal role of EPs in the hospitals crisis organization was reported by 93.9% of EP staffed hospital organizations.\n\nConclusionAll Dutch EDs made preparations for COVID-19 in a short time span and with many uncertainties. Preparations predominantly concerned expansion of treatment capacity and segregation of COVID-19 ED care. EPs had a prominent role, both in direct patient COVID-19 ED care and in the hospitals crisis organizations. Although it is vital for EDs to be able to dynamically adapt to community needs, variability of pandemic ED preparedness was high.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Rory D O' Connor", - "author_inst": "Department of Emergency Medicine, Jeroen Bosch Hospital, Henri Dunantstraat 1, 5223 GZ 's-Hertogenbosch, The Netherlands" - }, - { - "author_name": "Dennis G Barten", - "author_inst": "Department of Emergency Medicine, VieCuri Medical Center, Tegelseweg 210, 5912 BL Venlo, The Netherlands" - }, - { - "author_name": "Gideon HP Latten", - "author_inst": "Department of Emergency Medicine, Zuyderland Medical Center, Henri Dunantstraat 5, 6419 PC Heerlen, The Netherlands" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2021.04.13.21254841", "rel_title": "A very simple model to account for the rapid rise of the British variant of SARS-CoV-2 in several countries and the world", @@ -839642,6 +837924,77 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.04.16.440104", + "rel_title": "Homo-harringtonine (HHT) - A highly effective drug against coronaviruses and the potential for large-scale clinical applications", + "rel_date": "2021-04-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.16.440104", + "rel_abs": "In the search for treatment schemes of COVID-19, we start by examining the general weakness of coronaviruses and then identify approved drugs attacking that weakness. The approach, if successful, should identify drugs with a specific mechanism that is at least as effective as the best drugs proposed and are ready for clinical trials. All coronaviruses translate their non-structural proteins ([~]16) in concatenation, resulting in a very large super-protein. Homo-harringtonine (HHT), which has been approved for the treatment of leukemia, blocks protein elongation very effectively. Hence, HHT can repress the replication of many coronaviruses at the nano-molar concentration. In two mouse models, HHT clears SARS-CoV-2 in 3 days, especially by nasal dripping of 40 ug per day. We also use dogs to confirm the safety of HHT delivered by nebulization. The nebulization scheme could be ready for large-scale applications at the onset of the next epidemics. For the current COVID-19, a clinical trial has been approved by the Ditan hospital of Beijing but could not be implemented for want of patients. The protocol is available to qualified medical facilities.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Hai-Jun Wen", + "author_inst": "State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China" + }, + { + "author_name": "Pei Lin", + "author_inst": "State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China" + }, + { + "author_name": "Zhi-Chao Xu", + "author_inst": "State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China" + }, + { + "author_name": "Wen-Bin He", + "author_inst": "State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Science, Kunming 650223, China" + }, + { + "author_name": "Jing Feng", + "author_inst": "State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Science, Kunming 650223, China" + }, + { + "author_name": "Si-Jin Wu", + "author_inst": "Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Scien" + }, + { + "author_name": "Guo-Dong Wang", + "author_inst": "State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology / Center for Excellence in Animal Evolution and Genetics, Chinese Academy " + }, + { + "author_name": "Xue-Mei Lyu", + "author_inst": "State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology / Center for Excellence in Animal Evolution and Genetics, Chinese Academy " + }, + { + "author_name": "Feng-Liang Liu", + "author_inst": "Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences / Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming I" + }, + { + "author_name": "Yong-Tang Zheng", + "author_inst": "Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences / Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming I" + }, + { + "author_name": "Hui Zeng", + "author_inst": "Beijing Ditan Hospital, Capital Medical University, Beijing 100102, China" + }, + { + "author_name": "Xiong-Lei He", + "author_inst": "State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China" + }, + { + "author_name": "Fu-Jie Zhang", + "author_inst": "Beijing Ditan Hospital, Capital Medical University, Beijing 100102, China" + }, + { + "author_name": "Chung-I Wu", + "author_inst": "State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China / Southern Marine Science and Engineering Guangdong" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.04.12.21255201", "rel_title": "Predicting severe COVID-19 outcomes for triage and resource allocation", @@ -840034,37 +838387,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2021.04.09.21255215", - "rel_title": "Impacts of COVID-19 on sick leave", - "rel_date": "2021-04-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.09.21255215", - "rel_abs": "AimTo explore sick leave after COVID-19, by comparing doctor-certified sick leave for up to 6 months after testing for SARS-CoV-2 across employees who tested positive and negative.\n\nMethodsIn all persons (20-70 year of age) with an employment contract, who were tested for the SARS-CoV-2 in Norway from March 1st to November 1st 2020 (N=740 182 with mean [SD] age 39 [13] years, 44% men), we used a difference-in-difference design to contrast doctor-certified sick leave before and after testing, across employees with negative test and positive test by age and sex groups.\n\nResultsSick leave for those testing positive (N=11 414) remained elevated for up to 2 months after testing when compared to those testing negative (N= 728 768), for men and women aged 20-44 and for men aged 45-70 years (relative increase in sick-leave [~]344-415%, (Ball strata=0.079, 95% CI=0.076, 0.082). The increase in sick leave was prolonged for women aged 45-70 years only, persisting for up to 4 months after testing positive (relative increase = 35%, B=0.010, 95% CI=0.004-0.035).\n\nConclusionSick leave following COVID-19 is elevated for up to two to four months after initial infection, thereafter not elevated compared with employees who tested negative for COVID-19. Women aged 45-70 years tend to have a larger impact of COVID-19 on their work ability than men and younger women.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Katrine Damgaard Skyrud", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Kjetil Elias Telle", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Kjersti Helene Hernaes", - "author_inst": "Norwegian Institute of Public Health" - }, - { - "author_name": "Karin Magnusson", - "author_inst": "Norwegian Institute of Public Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.04.09.21255047", "rel_title": "Multicenter evaluation of a fully automated high-throughput SARS-CoV-2 antigen immunoassay", @@ -841292,6 +839614,37 @@ "type": "new results", "category": "bioengineering" }, + { + "rel_doi": "10.1101/2021.04.15.439956", + "rel_title": "Time-series trend of pandemic SARS-CoV-2 variants visualized using batch-learning self-organizing map for oligonucleotide compositions", + "rel_date": "2021-04-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.15.439956", + "rel_abs": "To confront the global threat of coronavirus disease 2019, a massive number of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome sequences have been decoded, with the results promptly released through the GISAID database. Based on variant types, eight clades have already been defined in GISAID, but the diversity can be far greater. Owing to the explosive increase in available sequences, it is important to develop new technologies that can easily grasp the whole picture of the big-sequence data and support efficient knowledge discovery. An ability to efficiently clarify the detailed time-series changes in genome-wide mutation patterns will enable us to promptly identify and characterize dangerous variants that rapidly increase their population frequency. Here, we collectively analyzed over 150,000 SARS-CoV-2 genomes to understand their overall features and time-dependent changes using a batch-learning self-organizing map (BLSOM) for oligonucleotide composition, which is an unsupervised machine learning method. BLSOM can separate clades defined by GISAID with high precision, and each clade is subdivided into clusters, which shows a differential increase/decrease pattern based on geographic region and time. This allowed us to identify prevalent strains in each region and to show the commonality and diversity of the prevalent strains. Comprehensive characterization of the oligonucleotide composition of SARS-CoV-2 and elucidation of time-series trends of the population frequency of variants can clarify the viral adaptation processes after invasion into the human population and the time-dependent trend of prevalent epidemic strains across various regions, such as continents.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Takashi Abe", + "author_inst": "Smart Information Systems, Faculty of Engineering, Niigata University" + }, + { + "author_name": "Ryuki Furukawa", + "author_inst": "Smart Information Systems, Faculty of Engineering, Niigata University" + }, + { + "author_name": "Yuki Iwasaki", + "author_inst": "Nagahama Institute of Bio-Science and Technology" + }, + { + "author_name": "Toshimichi Ikemura", + "author_inst": "Nagahama Institute of Bio-Science and Technology" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.04.15.440004", "rel_title": "Computationally prioritized drugs inhibit SARS-CoV-2 infection and syncytia formation", @@ -841912,77 +840265,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.04.14.439793", - "rel_title": "Neuropilin-1 Mediates SARS-CoV-2 Infection in Bone Marrow-derived Macrophages", - "rel_date": "2021-04-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.14.439793", - "rel_abs": "SARS-CoV-2 infection in human can cause medical complications across various tissues and organs. Despite of the advances to understanding the pathogenesis of SARS-CoV-2, its tissue tropism and interactions with host cells have not been fully understood. Existing clinical data have suggested possible SARS-CoV-2 infection in human skeleton system. In the present study, we found that authentic SARS-CoV-2 could efficiently infect human and mouse bone marrow-derived macrophages (BMMs) and alter the expression of macrophage chemotaxis and osteoclast-related genes. Importantly, in a mouse SARS-CoV-2 infection model that was enabled by the intranasal adenoviral (AdV) delivery of human angiotensin converting enzyme 2 (hACE2), SARS-CoV-2 was found to be present in femoral BMMs as determined by in situ immunofluorescence analysis. Using single-cell RNA sequencing (scRNA-Seq), we characterized SARS-CoV-2 infection in BMMs. Importantly, SARS-CoV-2 entry on BMMs appeared to be dependent on the expression of neuropilin-1 (NRP1) rather than the widely recognized receptor ACE2. It was also noted that unlike brain macrophages which displayed aging-dependent NRP1 expression, BMMs from neonatal and aged mice had constant NRP1 expression, making BMMs constantly vulnerable target cells for SARS-CoV-2. Furthermore, it was found that the abolished SARS-CoV-2 entry in BMM-derived osteoclasts was associated with the loss of NRP1 expression during BMM-to-osteoclast differentiation. Collectively, our study has suggested that NRP1 can mediate SARS-CoV-2 infection in BMMs, which precautions the potential impact of SARS-CoV-2 infection on human skeleton system.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Gao Junjie", - "author_inst": "Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Shanghai Sixth People Hospital, Shanghai, 200233, China" - }, - { - "author_name": "Mei Hong", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China" - }, - { - "author_name": "Sun Jing", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Li Hao", - "author_inst": "Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Shanghai Sixth People Hospital, Shanghai, 200233, China" - }, - { - "author_name": "Huang Yuege", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China" - }, - { - "author_name": "Tang Yanhong", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Duan Linwei", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Liu Delin", - "author_inst": "Centre for Orthopaedic Research, School of Surgery, The University of Western Australia, Nedlands, Western Australia, 6009, Australia" - }, - { - "author_name": "Wang Qiyang", - "author_inst": "Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Shanghai Sixth People Hospital, Shanghai, 200233, China" - }, - { - "author_name": "Gao Youshui", - "author_inst": "Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Shanghai Sixth People Hospital, Shanghai, 200233, China" - }, - { - "author_name": "Song Ke", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China" - }, - { - "author_name": "Zhao Jincun", - "author_inst": "State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Aff" - }, - { - "author_name": "Zhang Changqing", - "author_inst": "Department of Orthopaedics, Shanghai Jiao Tong University Affiliated Shanghai Sixth People Hospital, Shanghai, 200233, China" - }, - { - "author_name": "Liu Jia", - "author_inst": "Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.04.13.439709", "rel_title": "Structural basis for enhanced infectivity and immune evasion of SARS-CoV-2 variants", @@ -843146,6 +841428,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2021.04.08.21255167", + "rel_title": "Refining long-COVID by a prospective multimodal evaluation of patients with long-term symptoms related to SARS-CoV-2 infection", + "rel_date": "2021-04-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.08.21255167", + "rel_abs": "BackgroundCOVID-19 long-haulers or \"long-COVID\" represent 10% of COVID-19 patients and remain understudied.\n\nMethodsIn this prospective study, we recruited 30 consecutive patients seeking medical help for persistent symptoms (> 30 days) attributed to COVID-19. All reported a viral illness compatible with COVID-19. The patients underwent a multi-modal evaluation including clinical, psychological, virological, specific immunological assays and were followed longitudinally.\n\nResultsThe median age was 40 [interquartile range: 35-54] and 18 (60%) were female. After a median time of 152 [102-164] days after symptom onset, fever, cough and dyspnea were less frequently reported as compared with the initial presentation, but paresthesia and burning pain emerged in 18 (60%) and 13 (43%) patients, respectively. The clinical examination was unremarkable in all patients although the median fatigue and pain visual analogic scales were 7 [5-8] and 5 [2-6], respectively.\n\nExtensive biological studies were unremarkable, as were multiplex cytokine and ultra-sensitive interferon-a2 measurements. At this time, nasopharyngeal swab and stool RT-PCR were negative for all tested patients. Using SARS-CoV-2 serology and IFN-{gamma} ELISPOT, we found evidence of a previous SARS-CoV-2 infection in 50% (15/30) of patients, with objective evidence of lack or waning of immune response in two. Finally, psychiatric evaluation showed that 11 (36.7%), 13 (43.3%) and 9 (30%) patients had a positive screening for anxiety, depression and post-traumatic stress disorder, respectively.\n\nConclusionsHalf of patients seeking medical help for long-COVID lack SARS-CoV-2 immunity. The presence of SARS-CoV-2 immunity did not cluster clinically or biologically long haulers, who reported severe fatigue, altered quality of life, and exhibited psychological distress.\n\nKey pointsO_LIAmong 30 consecutive patients reporting persistent symptoms (median 6 months) self-attributed to COVID-19, pain, fatigue and disability were reported in virtually all patients.\nC_LIO_LIMore than one third of patients suffer from psychological disorders such as anxiety, depression and/or post-traumatic stress disorder, regardless of SARS-CoV-2 immunity.\nC_LIO_LIAt the time of evaluation, only 50% of patients had cellular and/or humoral sign of a past SARS-CoV-2, and serology positivity varied depending of the kit used.\nC_LIO_LIExhaustive clinical, biological and immunological evaluations failed to find an alternative diagnosis, or to identify specific cytokine signature including type I interferon.\nC_LI", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Marc SCHERLINGER", + "author_inst": "CHU de Strasbourg" + }, + { + "author_name": "Renaud Felten", + "author_inst": "Rheumatology department, Strasbourg University Hospital" + }, + { + "author_name": "Floriane Gallais", + "author_inst": "Virology department, Strasbourg University Hospital" + }, + { + "author_name": "Charlotte Nazon", + "author_inst": "Virology department, Strasbourg University Hospital" + }, + { + "author_name": "Emmanuel Chatelus", + "author_inst": "Rheumatology department, Strasbourg University Hospital" + }, + { + "author_name": "Luc Pijnenburg", + "author_inst": "Rheumatology department, Strasbourg University Hospital" + }, + { + "author_name": "Amaury Mengin", + "author_inst": "Psychiatry department, Strasbourg University Hospital" + }, + { + "author_name": "Adrien Gras", + "author_inst": "Psychiatry department, Strasbourg University Hospital" + }, + { + "author_name": "Pierre Vidailhet", + "author_inst": "Psychiatry department, Strasbourg University Hospital" + }, + { + "author_name": "Rachel Arnould-Michel", + "author_inst": "Rheumatology department, Strasbourg University Hospital" + }, + { + "author_name": "Sabrina Bibi-triki", + "author_inst": "Laboratoire d immunoRhumatologie Moleculaire, Institut national de la sante et de la recherche medicale (INSERM) UMR_S 1109" + }, + { + "author_name": "Raphael Carapito", + "author_inst": "Laboratoire d immunoRhumatologie Moleculaire, Institut national de la sante et de la recherche medicale (INSERM) UMR_S 1109" + }, + { + "author_name": "Seiamak Bahram", + "author_inst": "Laboratoire d immunoRhumatologie Moleculaire, Institut national de la sante et de la recherche medicale (INSERM) UMR_S 1109" + }, + { + "author_name": "sophie trouillet-assant", + "author_inst": "Hospices Civils de Lyon" + }, + { + "author_name": "Magali Perret", + "author_inst": "Hospices civils de Lyon" + }, + { + "author_name": "Alexandre Belot", + "author_inst": "Hospices Civils de Lyon" + }, + { + "author_name": "Laurent Arnaud", + "author_inst": "Rheumatology department, Strasbourg University Hospital" + }, + { + "author_name": "Jacques-Eric Gottenberg", + "author_inst": "Rheumatology department, Strasbourg University Hospital" + }, + { + "author_name": "Samira Fafi-Kremer", + "author_inst": "Virology department, Strasbourg University Hospital" + }, + { + "author_name": "Jean Sibilia", + "author_inst": "Rheumatology department, Strasbourg University Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.08.21255169", "rel_title": "The allometric propagation of COVID-19 is explained by human travel", @@ -843450,45 +841827,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.09.21255179", - "rel_title": "SARS-CoV-2 UK, South African and Brazilian Variants in Karachi- Pakistan", - "rel_date": "2021-04-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.09.21255179", - "rel_abs": "COVID-19 pandemic has been evolving in Pakistan since the UK, South African and Brazilian variants have started surfacing which are known for increase transmissibility and can also be responsible for escape from immune responses. The gold standard to detect these variants of concern is sequencing, however routine genomic surveillance in resource limited countries like Pakistan is not always readily available. With the emergence of variants of concern and a dearth of facilities for genomic scrutiny leaves policy makers and health authorities an inconsistent and twisted image to make decisions. The inadvertent detection of B.1.1.7 by target failure because of a key deletion in spike {Delta}69-70 in the UK by commercially available COVID-19 PCR assay helps to understand target failures as an alternative approach to detect variants. It was ascertained further that a deletion in the ORF1a gene (ORF1a {Delta}3675-3677) found common in B.1.1.7, B.135 and P.1 variants of concern. The Real Time Quantitative PCR (RT-qPCR) assay for detection of emergence and spread of SARS-CoV-2 variants, by these target failures is used here. The positive samples archived in respective labs were divided in two groups used in the present study. Group I constitutes 261 positive samples out of 16964 (1.53%) collected from August till September 2020. Group II include 3501 positive samples out of 46041 (7.60%) from November 2020 till January 2021. In positive samples of group I, no variant of concern was found. A staggering difference in results was noted in group II where positivity ratio increased exponentially and the variants of concern started appearing in significant numbers (53.64% overall). This is indicative that the third wave in Pakistan is due to the importation of SARS-CoV-2 variants. This calls for measures to increase surveillance by RT-qPCR which would help authorities in decision making.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Adnan Khan", - "author_inst": "Karachi Institute of Radiotherapy and Nuclear Medicine (KIRAN)" - }, - { - "author_name": "Muhammad Hanif", - "author_inst": "1) Karachi Institute of Radiotherapy and Nuclear Medicine (KIRAN), Karachi and 2) Advanced Laboratories, Karachi" - }, - { - "author_name": "Sarosh Syed", - "author_inst": "Advanced Laboratories, Karachi" - }, - { - "author_name": "Akhtar Ahmed", - "author_inst": "Karachi Institute of Radiotherapy and Nuclear Medicine (KIRAN), Karachi" - }, - { - "author_name": "Saqib Ghazali", - "author_inst": "Karachi Institute of Radiotherapy and Nuclear Medicine (KIRAN), Karachi" - }, - { - "author_name": "Rafiq Khanani", - "author_inst": "1) Advanced Laboratories, Karachi 2) Citilab Diagnostic Center, Karachi and 3) Global Research and Reference Labs, Karachi" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.09.21255232", "rel_title": "Inpatient outcomes for hospitalized older adults with rhinovirus.", @@ -844952,6 +843290,65 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2021.04.13.439668", + "rel_title": "From partial to whole genome imputation of SARS-CoV-2 for epidemiological surveillance", + "rel_date": "2021-04-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.13.439668", + "rel_abs": "Backgroundthe current SARS-CoV-2 pandemic has emphasized the utility of viral whole genome sequencing in the surveillance and control of the pathogen. An unprecedented ongoing global initiative is increasingly producing hundreds of thousands of sequences worldwide. However, the complex circumstances in which viruses are sequenced, along with the demand of urgent results, causes a high rate of incomplete and therefore useless, sequences. However, viral sequences evolve in the context of a complex phylogeny and therefore different positions along the genome are in linkage disequilibrium. Therefore, an imputation method would be able to predict missing positions from the available sequencing data.\n\nResultsWe developed impuSARS, an application that includes Minimac, the most widely used strategy for genomic data imputation and, taking advantage of the enormous amount of SARS-CoV-2 whole genome sequences available, a reference panel containing 239,301 sequences was built. The impuSARS application was tested in a wide range of conditions (continuous fragments, amplicons or sparse individual positions missing) showing great fidelity when reconstructing the original sequences. The impuSARS application is also able to impute whole genomes from commercial kits covering less than 20% of the genome or only from the Spike protein with a precision of 0.96. It also recovers the lineage with a 100% precision for almost all the lineages, even in very poorly covered genomes (< 20%)\n\nConclusionsimputation can improve the pace of SARS-CoV-2 sequencing production by recovering many incomplete or low-quality sequences that would be otherwise discarded. impuSARS can be incorporated in any primary data processing pipeline for SARS-CoV-2 whole genome sequencing.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Francisco M Ortuno", + "author_inst": "Clinical Bioinformatics Area. Fundacion Progreso y Salud, Sevilla, Spain" + }, + { + "author_name": "Carlos Loucera", + "author_inst": "Clinical Bioinformatics Area. Fundacion Progreso y Salud, Sevilla, Spain" + }, + { + "author_name": "Carlos S Casimiro-Soriguer", + "author_inst": "Clinical Bioinformatics Area. Fundacion Progreso y Salud, Sevilla, Spain" + }, + { + "author_name": "Jose A Lepe", + "author_inst": "Hospital Universitario Virgen del Rocio. Sevilla, Spain" + }, + { + "author_name": "Pedro Camacho Martinez", + "author_inst": "Hospital Universitario Virgen del Rocio. Sevilla, Spain" + }, + { + "author_name": "Laura Merino Diaz", + "author_inst": "Hospital Universitario Virgen del Rocio. Sevilla,Spain" + }, + { + "author_name": "Natalia Chueca", + "author_inst": "Hospital Universitario San Cecilio, Granada, Spain" + }, + { + "author_name": "Adolfo de Salazar", + "author_inst": "Hospital Universitario San Cecilio, Granada, Spain" + }, + { + "author_name": "Federico Garcia", + "author_inst": "Hospital Universitario San Cecilio, Granada, Spain" + }, + { + "author_name": "Javier Perez-Florido", + "author_inst": "Clinical Bioinformatics Area. Fundacion Progreso y Salud, Sevilla, Spain" + }, + { + "author_name": "Joaquin Dopazo", + "author_inst": "Clinical Bioinformatics Area, Fundacion Progreso y Salud, Sevilla, Spain" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2021.04.07.21255010", "rel_title": "The effects of quality of evidence communication on perception of public health information about COVID-19: two randomised controlled trials", @@ -845432,29 +843829,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, - { - "rel_doi": "10.1101/2021.04.08.21255046", - "rel_title": "COVID-19 and mortality risk in patients with psychiatric disorders", - "rel_date": "2021-04-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.08.21255046", - "rel_abs": "COVID-19 has already caused the deaths of over 2.5 million people worldwide. Patients with certain medical conditions and severe psychiatric disorders are at increased risk of dying from it. However, such people have a reduced life expectancy anyway, raising the question whether COVID-19 incurs a specific risk for such patients for dying, over and above the risk of dying from other causes.\n\nWe analysed the UK Biobank data of half a million middle-aged participants from the UK. From the start of 2020 up to 24th January 2021, 894 participants had died from COVID-19 and another 4,562 had died from other causes. We demonstrate that the risk of dying from COVID-19 among patients with mental health problems, especially those with dementia, schizophrenia, or bipolar disorder, is increased compared to the risk of dying from other causes. This increase among patients with severe psychiatric disorders cannot be explained solely by the higher rate of diabetes or cardiovascular disorders.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "George Kirov", - "author_inst": "Cardiff University" - }, - { - "author_name": "Emily Baker", - "author_inst": "Cardiff University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2021.04.07.21255079", "rel_title": "Participating in vaccine research for COVID-19 in Senegal: trust and information", @@ -846586,6 +844960,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.08.21255144", + "rel_title": "Accuracy of antigen and nucleic acid amplification testing on saliva and naopharyngeal samples for detection of SARS-CoV-2 in ambulatory care", + "rel_date": "2021-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.08.21255144", + "rel_abs": "BackgroundNasopharyngeal sampling for nucleic acid amplification testing (NAAT) is the current standard diagnostic test for of coronavirus disease 2019 (COVID-19). However, the NAAT technique is lengthy and nasopharyngeal sampling requires trained personnel. Saliva NAAT represents an interesting alternative but diagnostic performances vary widely between studies.\n\nObjectiveTo assess the diagnostic accuracy of a nasopharyngeal point-of-care antigen (Ag) test and of saliva NAAT for detection of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), as compared to nasopharyngeal NAAT.\n\nDesignProspective participant enrollment from 19 October through 18 December 2020.\n\nSettingTwo community COVID-19 screening centers in Paris, France.\n\nParticipants1452 ambulatory children and adults referred for SARS-CoV-2 testing.\n\nInterventionsNAAT on a saliva sample (performed with three different protocols for pre-processing, amplification and detection of SARS-CoV-2) and Ag testing on a nasopharyngeal sample.\n\nMeasurementsPerformance of saliva NAAT and nasopharyngeal Ag testing.\n\nResultsOverall, 129/1443 (9%) participants tested positive on nasopharyngeal NAAT (102/564 [18%] in symptomatic and 27/879 [3%] in asymptomatic participants). Sensitivity was of 94% (95% CI, 86% to 98%), 23% (CI, 14% to 35%), 94% (CI, 88% to 97%) and 96% (CI, 91% to 99%) for the nasopharyngeal Ag test and the three different protocols of saliva NAAT, respectively. Estimates of specificity were above 95% for all methods. Diagnostic accuracy was similar in symptomatic and asymptomatic individuals.\n\nLimitationsFew children (n=122, 8%) were included.\n\nConclusionIn the ambulatory setting, diagnostic accuracy of nasopharyngeal Ag testing and of saliva NAAT seems similar to that of nasopharyngeal NAAT, subject to strict compliance with specific pre-processing and amplification protocols.\n\nRegistration numberNCT04578509\n\nFunding SourcesFrench Ministry of Health and the Assistance Publique-Hopitaux de Paris Foundation.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Solen Kerneis", + "author_inst": "Universite de Paris, Assistance Publique-Hopitaux de Paris, hopital Bichat" + }, + { + "author_name": "Caroline Elie", + "author_inst": "APHP" + }, + { + "author_name": "Jacques Fourgeaud", + "author_inst": "APHP" + }, + { + "author_name": "Laure Choupeaux", + "author_inst": "APHP" + }, + { + "author_name": "Severine Mercier Delarue", + "author_inst": "APHP" + }, + { + "author_name": "Marie Laure Alby", + "author_inst": "COVISAN" + }, + { + "author_name": "Pierre Quentin", + "author_inst": "COVISAN" + }, + { + "author_name": "Juliette Pavie", + "author_inst": "APHP" + }, + { + "author_name": "Patricia Brazille", + "author_inst": "APHP" + }, + { + "author_name": "Marie Laure Nere", + "author_inst": "APHP" + }, + { + "author_name": "Marine Minier", + "author_inst": "APHP" + }, + { + "author_name": "Audrey Gabassi", + "author_inst": "APHP" + }, + { + "author_name": "Aurelien Gibaud", + "author_inst": "APHP" + }, + { + "author_name": "Sebastien Gauthier", + "author_inst": "APHP" + }, + { + "author_name": "Chrystel Leroy", + "author_inst": "APHP" + }, + { + "author_name": "Etienne Voirin Mathieu", + "author_inst": "APHP" + }, + { + "author_name": "Claire Poyart", + "author_inst": "APHP" + }, + { + "author_name": "Michel Vidaud", + "author_inst": "APHP" + }, + { + "author_name": "Beatrice Parfait", + "author_inst": "APHP" + }, + { + "author_name": "Constance Delaugerre", + "author_inst": "APHP" + }, + { + "author_name": "Jean Marc Treluyer", + "author_inst": "APHP" + }, + { + "author_name": "Jerome Le Goff", + "author_inst": "APHP" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.08.21255109", "rel_title": "Incidence of Long-term Post-acute Sequelae of SARS-CoV-2 Infection Related to Pain and Other Symptoms: A Living Systematic Review and Meta-analysis", @@ -847154,129 +845631,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.04.10.439275", - "rel_title": "CoVac501, a self-adjuvanting peptide vaccine conjugated with TLR7 agonists, against SARS-CoV-2 induces protective immunity", - "rel_date": "2021-04-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.10.439275", - "rel_abs": "Safe, economical and effective vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are needed to achieve adequate herd immunity and halt the pandemic. We have constructed a novel SARS-CoV-2 vaccine, CoVac501, which is a self-adjuvanting peptide vaccine conjugated with Toll-like receptor 7 (TLR7) agonists. The vaccine contains two immunodominant peptides screened from receptor-binding domain (RBD) and is fully chemically synthesized. And the vaccine has optimized nanoemulsion formulation, outstanding stability and safety. In non-human primates (NHPs), CoVac501 elicited high and persistent titers of RBD-specific and protective neutralizing antibodies (NAbs), which were also effective to RBD mutations. CoVac501 was found to elicit the increase of memory T cells, antigen-specific CD8+ T cell responses and Th1-biased CD4+ T cell immune responses in NHPs. More importantly, the sera from the immunized NHPs can prevent infection of live SARS-CoV-2 in vitro.\n\nOne-Sentence SummaryA novel SARS-CoV-2 vaccine we developed, CoVac501, which is a fully chemically synthesized and self-adjuvanting peptides conjugated with TLR7 agonists, can induce high-efficient humoral and cellular immune responses against SARS-CoV-2.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "Yiru Long", - "author_inst": "State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy" - }, - { - "author_name": "Jianhua Sun", - "author_inst": "State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy" - }, - { - "author_name": "Tingting Liu", - "author_inst": "State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China." - }, - { - "author_name": "Feng Tang", - "author_inst": "State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy" - }, - { - "author_name": "Xinxin Zhang", - "author_inst": "State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy" - }, - { - "author_name": "Qiuping Qin", - "author_inst": "State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China." - }, - { - "author_name": "Yunqiu Miao", - "author_inst": "State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy" - }, - { - "author_name": "Xiaoyan Pan", - "author_inst": "Wuhan institute of virology, Chinese academy of sciences" - }, - { - "author_name": "Qi An", - "author_inst": "Shanghai King-Cell Biotechnology Co., Ltd., No. 1136 Langong Road, Jinshan District, Shanghai" - }, - { - "author_name": "Mian Qin", - "author_inst": "Zhongshan Institute for Drug Discovery, Institutes of Drug Discovery and Development, Chinese Academy of Sciences, Zhongshan, 528400, China." - }, - { - "author_name": "Xiankun Tong", - "author_inst": "State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China." - }, - { - "author_name": "Xionghua Peng", - "author_inst": "State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China." - }, - { - "author_name": "Pan Yu", - "author_inst": "State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China." - }, - { - "author_name": "Peng Zhu", - "author_inst": "State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China." - }, - { - "author_name": "Weiliang Zhu", - "author_inst": "State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy" - }, - { - "author_name": "Yachun Zhang", - "author_inst": "Shanghai King-Cell Biotechnology Co., Ltd., No. 1136 Langong Road, Jinshan District, Shanghai" - }, - { - "author_name": "Leike Zhang", - "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences" - }, - { - "author_name": "Gengfu Xiao", - "author_inst": "Chinese Academy of Sciences" - }, - { - "author_name": "Jianping Zuo", - "author_inst": "State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy" - }, - { - "author_name": "Wei Tang", - "author_inst": "State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy" - }, - { - "author_name": "Ji Zhou", - "author_inst": "School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen University, Shenzhen, 518060, China; International Cancer Center, Nation" - }, - { - "author_name": "Zhijian Xu", - "author_inst": "Shanghai Institute of Materia Medica, Chinese Academy of Sciences" - }, - { - "author_name": "Yong Gan", - "author_inst": "State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy" - }, - { - "author_name": "Jin Ren", - "author_inst": "State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy" - }, - { - "author_name": "Wei Huang", - "author_inst": "State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy" - }, - { - "author_name": "Guangyi Jin", - "author_inst": "School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen University, Shenzhen, 518060, China; International Cancer Center, Nation-" - }, - { - "author_name": "Likun Gong", - "author_inst": "State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China; University of Chinese Academy" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.04.10.439161", "rel_title": "Quantatitive Analysis of Conserved Sites on the SARS-CoV-2 Receptor-Binding Domain to Promote Development of Universal SARS-Like Coronavirus Vaccines", @@ -848532,6 +846886,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.08.21254705", + "rel_title": "Real-world Effect of Monoclonal Antibody Treatment in COVID-19 Patients in a Diverse Population in the United States", + "rel_date": "2021-04-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.08.21254705", + "rel_abs": "BackgroundMonoclonal antibodies (mAbs) against SARS-CoV-2 are a promising treatment for limiting the progression of COVID-19 and decreasing strain on hospitals. Their use, however, remains limited, particularly in disadvantaged populations.\n\nMethodsElectronic health records were reviewed from SARS-CoV-2 patients at a single medical center in the United States that initiated mAb infusions in January 2021 with the support of the U.S. Department of Health and Human Services National Disaster Medical System. Patients who received mAbs were compared to untreated patients from the time period before mAb availability who met eligibility criteria for mAb treatment. We used logistic regression to measure the effect of mAb treatment on the risk of hospitalization or emergency department (E.D.) visit within 30 days of laboratory-confirmed COVID-19.\n\nResultsOf 598 COVID-19 patients, 270 (45%) received bamlanivimab and 328 (55%) were untreated. Two hundred and thirty-one patients (39%) were Hispanic. Among treated patients, 5/270 (1.9%) presented to the E.D. or required hospitalization within 30 days of a positive SARS-CoV-2 test, compared to 39/328 (12%) untreated patients (p<0.001). After adjusting for age, gender, and comorbidities, the risk of E.D. visit or hospitalization was 82% lower in mAb-treated patients compared to untreated patients (95% confidence interval [CI]: 66%-94%).\n\nConclusionsIn this diverse, real-world COVID-19 patient population, mAb treatment significantly decreased the risk of subsequent E.D. visit or hospitalization. Broader treatment with mAbs, including in disadvantaged patient populations, can decrease the burden on hospitals and should be facilitated in all populations in the United States to ensure health equity.\n\nSummaryIn a diverse, real-world COVID-19 patient population, treatment with monoclonal antibodies significantly decreased the risk of subsequent emergency department visit or hospitalization within 30 days of a positive SARS-CoV-2 viral test.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Kaitlin Rainwater-Lovett", + "author_inst": "Johns Hopkins Applied Physics Laboratory" + }, + { + "author_name": "John T. Redd", + "author_inst": "Office of the Assistant Secretary of Preparedness and Response, U.S. Department of Health and Human Services, Washington, DC" + }, + { + "author_name": "Miles A. Stewart", + "author_inst": "Johns Hopkins Applied Physics Laboratory" + }, + { + "author_name": "Natalia Elias Calles", + "author_inst": "TMC HealthCare" + }, + { + "author_name": "Tyler Cluff", + "author_inst": "TMC HealthCare" + }, + { + "author_name": "Mike Fang", + "author_inst": "Johns Hopkins Applied Physics Laboratory" + }, + { + "author_name": "Mark J. Panaggio", + "author_inst": "Johns Hopkins Applied Physics Laboratory" + }, + { + "author_name": "Anastasia S. Lambrou", + "author_inst": "Johns Hopkins Applied Physics Laboratory" + }, + { + "author_name": "Jonathan K. Thornhill", + "author_inst": "Johns Hopkins Applied Physics Laboratory" + }, + { + "author_name": "Christopher Bradburne", + "author_inst": "Johns Hopkins Applied Physics Laboratory" + }, + { + "author_name": "Samuel Imbriale", + "author_inst": "Johns Hopkins Applied Physics Laboratory" + }, + { + "author_name": "Jeffrey D. Freeman", + "author_inst": "Johns Hopkins Applied Physics Laboratory" + }, + { + "author_name": "Michael Anderson", + "author_inst": "Office of the Assistant Secretary of Preparedness and Response, US Department of Health and Human Services" + }, + { + "author_name": "Robert P. Kadlec", + "author_inst": "Office of the Assistant Secretary of Preparedness and Response, US Department of Health and Human Services" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.04.08.21255135", "rel_title": "Early evidence of COVID-19 vaccine effectiveness within the general population of California", @@ -849004,85 +847429,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.04.21254881", - "rel_title": "Neutralization of SARS-CoV-2 variants by convalescent and vaccinated serum", - "rel_date": "2021-04-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.04.21254881", - "rel_abs": "We tested human sera from large, demographically balanced cohorts of BNT162b2 vaccine recipients (n=51) and COVID-19 patients (n=44) for neutralizing antibodies against SARS-CoV-2 variants B.1.1.7 and B.1.351. Although the effect is more pronounced in the vaccine cohort, both B.1.1.7 and B.1.351 show significantly reduced levels of neutralization by vaccinated and convalescent sera. Age is negatively correlated with neutralization in vaccinee, and levels of variant-specific RBD antibodies are proportional to neutralizing activities.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Timothy A. Bates", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Hans C Leier", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Zoe L Lyski", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Savannah K McBride", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Felicity J Coulter", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Jules B Weinstein", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "James R Goodman", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Zhengchun Lu", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Sarah A. R. Siegel", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Peter Sullivan", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Matt Strnad", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Amanda E Brunton", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "David X Lee", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Marcel E Curlin", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "William B Messer", - "author_inst": "Oregon Health & Science University" - }, - { - "author_name": "Fikadu G Tafesse", - "author_inst": "Oregon Health & Science University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.06.21254882", "rel_title": "Evidence for increased breakthrough rates of SARS-CoV-2 variants of concern in BNT162b2 mRNA vaccinated individuals", @@ -850062,6 +848408,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.04.05.21254919", + "rel_title": "Identifiability and Predictability of Integer- and Fractional-Order Epidemiological Models Using Physics-Informed Neural Networks", + "rel_date": "2021-04-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.05.21254919", + "rel_abs": "We analyze a plurality of epidemiological models through the lens of physics-informed neural networks (PINNs) that enable us to identify multiple time-dependent parameters and to discover new data-driven fractional differential operators. In particular, we consider several variations of the classical susceptible-infectious-removed (SIR) model by introducing more compartments and delay in the dynamics described by integer-order, fractional-order, and time-delay models. We report the results for the spread of COVID-19 in New York City, Rhode Island and Michigan states, and Italy, by simultaneously inferring the unknown parameters and the unobserved dynamics. For integer-order and time-delay models, we fit the available data by identifying time-dependent parameters, which are represented by neural networks (NNs). In contrast, for fractional differential models, we fit the data by determining different time-dependent derivative orders for each compartment, which we represent by NNs. We investigate the identifiability of these unknown functions for different datasets, and quantify the uncertainty associated with NNs and with control measures in forecasting the pandemic.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ehsan Kharazmi", + "author_inst": "Brown University" + }, + { + "author_name": "Min Cai", + "author_inst": "Brown University and Shanghai University" + }, + { + "author_name": "Xiaoning Zheng", + "author_inst": "Brown University and Jinan University" + }, + { + "author_name": "Guang Lin", + "author_inst": "Purdue University" + }, + { + "author_name": "George Em Karniadakis", + "author_inst": "Brown University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.08.21254762", "rel_title": "Companionship for women using English maternity services during COVID-19: National and organisational perspectives", @@ -850734,105 +849115,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.04.07.438806", - "rel_title": "Identifying SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of nsp5 Main Protease", - "rel_date": "2021-04-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.07.438806", - "rel_abs": "The coronavirus 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), spread around the world with unprecedented health and socio-economic effects for the global population. While different vaccines are now being made available, very few antiviral drugs have been approved. The main viral protease (nsp5) of SARS-CoV-2 provides an excellent target for antivirals, due to its essential and conserved function in the viral replication cycle. We have expressed, purified and developed assays for nsp5 protease activity. We screened the nsp5 protease against a custom chemical library of over 5,000 characterised pharmaceuticals. We identified calpain inhibitor I and three different peptidyl fluoromethylketones (FMK) as inhibitors of nsp5 activity in vitro, with IC50 values in the low micromolar range. By altering the sequence of our peptidomimetic FMK inhibitors to better mimic the substrate sequence of nsp5, we generated an inhibitor with a subnanomolar IC50. Calpain inhibitor I inhibited viral infection in monkey-derived Vero E6 cells, with an EC50 in the low micromolar range. The most potent and commercially available peptidyl-FMK compound inhibited viral growth in Vero E6 cells to some extent, while our custom peptidyl FMK inhibitor offered a marked antiviral improvement.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Clovis Basier", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Rupert Beale", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Ganka Bineva-Todd", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Berta Canal", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Joseph F Curran", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Tom D Deegan", - "author_inst": "The University of Dundee" - }, - { - "author_name": "John FX Diffley", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Ryo Fujisawa", - "author_inst": "The University of Dundee" - }, - { - "author_name": "Michael Howell", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Dhira Joshi", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Karim Labib", - "author_inst": "The University of Dundee" - }, - { - "author_name": "Chew Theng Lim", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Jennifer Milligan", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Hema Nagaraj", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "George Papageorgiou", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Christelle Soudy", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Kang Wei Tan", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Rachel Ulferts", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Florian Weissmann", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Mary Wu", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Theresa U Zeisner", - "author_inst": "The Francis Crick Institute" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.04.07.438807", "rel_title": "Identifying SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of Nsp12/7/8 RNA-dependent RNA Polymerase", @@ -852672,6 +850954,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.01.21254765", + "rel_title": "Mental health inequalities in healthcare, economic, and housing disruption during COVID -19: an investigation in 12 longitudinal studies", + "rel_date": "2021-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.01.21254765", + "rel_abs": "BackgroundThe COVID-19 pandemic and associated virus suppression measures have disrupted lives and livelihoods and people already experiencing mental ill-health may have been especially vulnerable.\n\nAimTo quantify mental health inequalities in disruptions to healthcare, economic activity and housing.\n\nMethod59,482 participants in 12 UK longitudinal adult population studies with data collected prior to and during the COVID-19 pandemic. Within each study we estimated the association between psychological distress assessed pre-pandemic and disruptions since the start of the pandemic to three domains: healthcare (medication access, procedures, or appointments); economic activity (employment, income, or working hours); and housing (change of address or household composition). Meta-analyses were used to pool estimates across studies.\n\nResultsAcross the analysed datasets, one to two-thirds of participants experienced at least one disruption, with 2.3-33.2% experiencing disruptions in two or more domains. One standard deviation higher pre-pandemic psychological distress was associated with: (i) increased odds of any healthcare disruptions (OR=1.30; [95% CI:1.20-1.40]) with fully adjusted ORs ranging from 1.24 [1.09-1.41] for disruption to procedures and 1.33 [1.20- 1.49] for disruptions to prescriptions or medication access; (ii) loss of employment (OR=1.13 [1.06-1.21]) and income (OR=1.12 [1.06 -1.19]) and reductions in working hours/furlough (OR=1.05 [1.00-1.09]); (iii) no associations with housing disruptions (OR=1.00 [0.97-1.03]); and (iv) increased likelihood of experiencing a disruption in at least two domains (OR=1.25 [1.18-1.32]) or in one domain (OR=1.11 [1.07-1.16]) relative to no disruption.\n\nConclusionPeople experiencing psychological distress pre-pandemic have been more likely to experience healthcare and economic disruptions, and clusters of disruptions across multiple domains during the pandemic. Failing to address these disruptions risks further widening the existing inequalities in mental health.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Giorgio Di Gessa", + "author_inst": "Institute of Epidemiology and Health Care, University College London" + }, + { + "author_name": "Jane Maddock", + "author_inst": "MRC Unit for Lifelong Health and Ageing, University College London" + }, + { + "author_name": "Michael J Green", + "author_inst": "MRC/CSO Social & Public Health Sciences Unit, University of Glasgow" + }, + { + "author_name": "Ellen J Thompson", + "author_inst": "Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, Kings College London" + }, + { + "author_name": "Eoin McElroy", + "author_inst": "Department of Neuroscience, Psychology and Behaviour, University of Leicester" + }, + { + "author_name": "Helena L Davies", + "author_inst": "Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, Kings College London" + }, + { + "author_name": "Jessica Mundy", + "author_inst": "Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, Kings College London" + }, + { + "author_name": "Anna J Stevenson", + "author_inst": "Centre for Genomic and Experimental Medicine, University of Edinburgh" + }, + { + "author_name": "Alex S.F Kwong", + "author_inst": "Division of Psychiatry, University of Edinburgh and MRC Integrative Epidemiology Unit, University of Bristol" + }, + { + "author_name": "Gareth J Griffith", + "author_inst": "MRC Integrative Epidemiology Unit, University of Bristol" + }, + { + "author_name": "Srinivasa Vittal Katikireddi", + "author_inst": "MRC/CSO Social & Public Health Sciences Unit, University of Glasgow" + }, + { + "author_name": "Claire L Niedzwiedz", + "author_inst": "Institute of Health & Wellbeing, University of Glasgow" + }, + { + "author_name": "George B Ploubidis", + "author_inst": "Centre for Longitudinal Studies, UCL Social Research Institute, University College London" + }, + { + "author_name": "Emla Fitzsimons", + "author_inst": "Centre for Longitudinal Studies, UCL Social Research Institute, University College London" + }, + { + "author_name": "Morag Henderson", + "author_inst": "Centre for Longitudinal Studies, UCL Social Research Institute, University College London" + }, + { + "author_name": "Richard J. Silverwood", + "author_inst": "Centre for Longitudinal Studies, UCL Social Research Institute, University College London" + }, + { + "author_name": "Nishi Chaturvedi", + "author_inst": "MRC Unit for Lifelong Health and Ageing, University College London" + }, + { + "author_name": "Gerome Breen", + "author_inst": "Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, Kings College London and Maudsley Biomedical Research Cen" + }, + { + "author_name": "Claire J Steves", + "author_inst": "Department of Twin Research and Genetic Epidemiology, School of Life Course Sciences, Kings College London" + }, + { + "author_name": "Andrew Steptoe", + "author_inst": "Institute of Epidemiology and Health Care, University College London" + }, + { + "author_name": "David J Porteous", + "author_inst": "Centre for Genomic and Experimental Medicine, University of Edinburgh" + }, + { + "author_name": "Praveetha Patalay", + "author_inst": "Centre for Longitudinal Studies and MRC Unit for Lifelong Health and Ageing, University College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.04.01.21254770", "rel_title": "Relative expression of pro-inflammatory molecules in COVID-19 patients manifested disease severities.", @@ -853080,53 +851465,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.04.05.21254897", - "rel_title": "No Evidence of Infectious SARS-CoV-2 in Human Milk: Analysis of a Cohort of 110 Lactating Women", - "rel_date": "2021-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.05.21254897", - "rel_abs": "BackgroundSARS-CoV-2 infections of infants and toddlers are usually mild but can result in life-threatening disease. SARS-CoV-2 RNA been detected in the breast milk of lactating women, but the potential role of breastfeeding in transmission to infants has remained uncertain.\n\nMethodsBreast milk specimens were examined for the presence of the virus by RT-PCR and/or culture. Specimens that contained viral RNA (vRNA) were examined for the presence of subgenomic coronavirus RNA (sgRNA), a putative marker of infectivity. Culture methods were used to determine the thermal stability of SARS-CoV-2 in human milk.\n\nResultsBreast milk samples from 110 women (65 confirmed with a SARS-CoV-2 diagnostic test, 36 with symptoms but without tests, and 9 with symptoms but a negative SARS-CoV-2 diagnostic test) were tested by RT-PCR (285 samples) and/or viral culture (160 samples). Although vRNA of SARS-CoV-2 was detected in the milk of 7 of 110 (6%) women with either a confirmed infection or symptomatic illness, and in 6 of 65 (9%) of women with a positive SARS-CoV-2 diagnostic test, virus was not detected in any culture. None of the 7 milk specimens with detectable vRNA contained sgRNA. Notably, when artificially added to human milk in control experiments, infectious SARS-CoV-2 could be cultured despite several freeze-thaw cycles, as occurs in the storage and usage of human milk.\n\nConclusionsSARS-CoV-2 RNA can be found infrequently in the breastmilk of women with recent infection, but we found no evidence that breastmilk contains infectious virus or that breastfeeding represents a risk factor for transmission of infection to infants.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSSARS-CoV-2 RNA has been detected in a small number of human milk samples collected from recently infected women. The role of breastfeeding in transmission of the virus to infants has remained uncertain due to the small number of specimens analyzed in any study published thus far.\n\nFindingsIn a total study group of 110 women, SARS-CoV-2 RNA was detected in milk from 6 of 65 women (9.2%) with recent confirmed infection. Neither infectious virus nor subgenomic RNA (a marker of virus infectivity) were detected in any of the samples.\n\nMeaningWe found no evidence that infectious SARS-CoV-2 is present milk from recently infected women, even if SARS-CoV-2 PCR tests are positive, providing reassurance of the safety of breastfeeding.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Paul Krogstad", - "author_inst": "David Geffen School of Medicine at UCLA" - }, - { - "author_name": "Deisy Contreras", - "author_inst": "David Geffen School of Medicine at UCLA" - }, - { - "author_name": "Hwee Ng", - "author_inst": "David Geffen School of Medicine at UCLA" - }, - { - "author_name": "Nicole Tobin", - "author_inst": "David Geffen School of Medicine at UCLA" - }, - { - "author_name": "Christina Chambers", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Kerri Bertrand", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Lars Bode", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Grace Aldrovandi", - "author_inst": "David Geffen School of Medicine at UCLA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2021.04.03.21254639", "rel_title": "Energy Insecurity Influences Urban Outdoor Air Pollution Levels during COVID-19 Lockdown in South-Central Chile", @@ -854390,6 +852728,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.05.21253827", + "rel_title": "Sex and gender differences in COVID testing, hospital admission, presentation, and drivers of severe outcomes in the DC/Maryland region", + "rel_date": "2021-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.05.21253827", + "rel_abs": "Structured AbstractO_ST_ABSBackgroundC_ST_ABSRates of severe illness and mortality from SARS-CoV-2 are greater for males, but the mechanisms for this difference are unclear. Understanding the differences in outcomes between males and females across the age spectrum will guide both public health and biomedical interventions.\n\nMethodsRetrospective cohort analysis of SARS-CoV-2 testing and admission data in a health system. Patient-level data were assessed with descriptive statistics and logistic regression modeling was used to identify features associated with increased male risk of severe outcomes.\n\nResultsIn 213,175 SARS-CoV-2 tests, despite similar positivity rates (8.2%F vs 8.9%M), males were more frequently hospitalized (28%F vs 33%M). Of 2,626 hospitalized individuals, females had less severe presenting respiratory parameters and males had more fever. Comorbidity burden was similar, but with differences in specific conditions. Medications relevant for SARS-CoV-2 were used at similar frequency except tocilizumab (M>F). Males had higher inflammatory lab values. In a logistic regression model, male sex was associated with a higher risk of severe outcomes at 24 hours (odds ratio (OR) 3.01, 95%CI 1.75, 5.18) and at peak status (OR 2.58, 95%CI 1.78,3.74) among 18-49 year-olds. Block-wise addition of potential explanatory variables demonstrated that only the inflammatory labs substantially modified the OR associated with male sex across all ages.\n\nConclusionHigher levels of clinical inflammatory labs are the only features that are associated with the heightened risk of severe outcomes and death for males in COVID-19.\n\nTrial registrationNA\n\nFundingHopkins inHealth; COVID-19 Administrative Supplement (HHS Region 3 Treatment Center), Office of the ASPR; NIH/NCI U54CA260492 (SK), NIH/NIA U54AG062333 (SK).", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Eileen P. Scully", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Grant Schumock", + "author_inst": "The Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Martina Fu", + "author_inst": "The Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Guido Massaccesi", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "John Muschelli", + "author_inst": "The Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Joshua Betz", + "author_inst": "The Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Eili Y. Klein", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Natalie E. West", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Matthew L. Robinson", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Brian T Garibaldi", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Karen Bandeen- Roche", + "author_inst": "The Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Scott Zeger", + "author_inst": "The Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Sabra L. Klein", + "author_inst": "The Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Amita Gupta", + "author_inst": "Johns Hopkins School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.04.21254884", "rel_title": "Comparing between survived and deceased patients with Diabetes Mellitus and COVID-19 in Bangladesh: A cross- sectional study from COVID-19 dedicated hospital", @@ -854842,53 +853251,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.04.01.21254755", - "rel_title": "Rapid screening for variants of concern in routine SARS-CoV-2 PCR diagnostics", - "rel_date": "2021-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.01.21254755", - "rel_abs": "The emerging spread of variants of concern (VOC) of SARS-CoV-2 has been noted in several countries worldwide during last months. VOCs associated with increased transmissibility and morality. Sequencing is the gold standard for investigation of variants, however it is expensive and time-consuming. S-dropout routine monitoring in combination with VOC screening by RT-PCR is a useful tool for VOC surveillance.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Paul Naaber", - "author_inst": "SYNLAB Estonia" - }, - { - "author_name": "Andrio Lahesaare", - "author_inst": "SYNLAB Estonia" - }, - { - "author_name": "Laura Truu", - "author_inst": "SYNLAB Estonia" - }, - { - "author_name": "Andres Soojarv", - "author_inst": "SYNLAB Estonia" - }, - { - "author_name": "Ainika Adamson", - "author_inst": "SYNLAB Estonia" - }, - { - "author_name": "Kaido Beljaev", - "author_inst": "SYNLAB Estonia" - }, - { - "author_name": "Rainar Aamisepp", - "author_inst": "SYNLAB Estonia" - }, - { - "author_name": "Kaspar Ratnik", - "author_inst": "SYNLAB Estonia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.04.01.21254688", "rel_title": "Novel prognostic determinants of COVID-19-related mortality: a pilot study on severely-ill patients in Russia", @@ -856120,6 +854482,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2021.04.05.21254937", + "rel_title": "Increased vulnerability to SARS-CoV-2 infection among indigenous people living in the urban area of Manaus", + "rel_date": "2021-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.05.21254937", + "rel_abs": "BackgroundThe COVID-19 pandemic threatens indigenous peoples living in suburban areas of large Brazilian cities and has thus far intensified their pre-existing socio-economic inequalities. This study evaluated the epidemiological situation of SARS-CoV-2 infection among residents of the biggest urban multiethnic indigenous community of the Amazonas state, Brazil.\n\nMethodsBlood samples of 280 indigenous people who live in the urban community known as Parque das Tribos, which is located in the surrounding area of Manaus, were tested for the presence of anti- SARS-CoV-2 IgA or IgG antibodies using an enzyme-linked immunosorbent assay. An epidemiological standardized interviewer-administered questionnaire was applied to assess the risk factors and sociodemographic information of the study population.\n\nResultsWe found a total positivity rate of 64.64% (95% CI 59.01-70.28) for SARS-CoV-2 infection. IgA and IgG were detected in 55.71% (95% CI 49.89-61.54) and 60.71% (95% CI 54.98-66.45) of the individuals tested, respectively. From the total number (n=280), 80.11% of positive individuals (95%; CI 74.24-85.98) were positive for both IgA and IgG Abs. All individuals with COVID-19-related symptoms on the day of blood collection (n=11) were positive for IgG, while IgA was detected in 84.61% (n=55) of individuals who had presented symptoms several weeks before the blood collection. Individuals aged 30-39 were more susceptible to SARS-CoV-2 infection (prevalence ratio [PR] 0.77; 95% CI 0.58-1.03; p=0.033). People whose main source of information on COVID-19 was religious leaders or friends showed higher susceptibility to infection (PR 1.22; 95% CI 1.00-1.49; p=0.040). In addition, individuals who left home more frequently were at higher risk of infection (PR 1.22; 95% CI 1.00-1.49; p=0.048). Five or more individuals per household increased almost 5-fold the risk of virus transmission (Odds ratio [OR] 2.56; 95% CI; 1.09-6.01; p=0.019). Over 95% of the study population had no access to clean water and/or sanitation.\n\nConclusionsThe disproportionate dissemination of SARS-CoV-2 infection observed in the Parque das Tribos urban indigenous community might be driven by typical cultural behavior and socioeconomic inequalities. Despite the pandemic threat, this population is not being targeted by public policies and appears to be chronically invisible to the Brazilian authorities.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Gemilson Soares Pontes GSP", + "author_inst": "Instituto Nacional de Pesquisa da Amazonia (INPA); Universidade Federal do Amazonas (UFAM), Programa de Pos-graduacao em Imunologia Basica e Aplicada; Universid" + }, + { + "author_name": "Jean de Melo Silva JMS", + "author_inst": "Instituto Nacional de Pesquisa da Amazonia (INPA)" + }, + { + "author_name": "Renato Pinheiro-Silva RPS", + "author_inst": "Universidade do Estado do Amazonas, Programa de Pos-graduacao em Ciencias Aplicadas a Hematologia" + }, + { + "author_name": "Anderson Nogueira Barbosa ANB", + "author_inst": "Instituto Nacional de Pesquisa da Amazonia (INPA)" + }, + { + "author_name": "Luciano Cardenes Santos LCS", + "author_inst": "Universidade Federal do Mato Grosso, Campus do Araguaia" + }, + { + "author_name": "Antonio de Padua Quirino Ramalho APQR", + "author_inst": "Faculdade de Medicina, Departamento de Saude Coletiva, Universidade Federal do Amazonas (UFAM)" + }, + { + "author_name": "Carlos Eduardo de Castro Alves CECA", + "author_inst": "Universidade Federal do Amazonas (UFAM), Programa de Pos-graduacao em Imunologia Basica e Aplicada" + }, + { + "author_name": "Danielle Furtado da Silva DFS", + "author_inst": "Programa de Pos-graduacao em Biodiversidade e Biotecnologia da Amazonia Legal, PPG-BIONORTE" + }, + { + "author_name": "Leonardo Calheiros de Oliveira LCO", + "author_inst": "Universidade do Estado do Amazonas, Programa de Pos-graduacao em Ciencias Aplicadas a Hematologia" + }, + { + "author_name": "Allyson Guimaraes da Costa AGC", + "author_inst": "Universidade Federal do Amazonas (UFAM), Programa de Pos-graduacao em Imunologia Basica e Aplicada; Universidade do Estado do Amazonas, Programa de Pos-graduaca" + }, + { + "author_name": "Ana Carla Bruno ACB", + "author_inst": "Instituto Nacional de Pesquisa da Amazonia (INPA)" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.22.21254110", "rel_title": "Drug repositioning candidates identified using in-silico quasi-quantum molecular simulation demonstrate reduced COVID-19 mortality in 1.5M patient records", @@ -856580,41 +855001,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.04.05.438500", - "rel_title": "An Autoantigen-ome from HS-Sultan B-Lymphoblasts Offers a Molecular Map for Investigating Autoimmune Sequelae of COVID-19", - "rel_date": "2021-04-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.05.438500", - "rel_abs": "To understand how COVID-19 may induce autoimmune diseases, we have been compiling an atlas of COVID-autoantigens (autoAgs). Using dermatan sulfate (DS) affinity enrichment of autoantigenic proteins extracted from HS-Sultan lymphoblasts, we identified 362 DS-affinity proteins, of which at least 201 (56%) are confirmed autoAgs. Comparison with available multi-omic COVID data shows that 315 (87%) of the 362 proteins are affected in SARS-CoV-2 infection via altered expression, interaction with viral components, or modification by phosphorylation or ubiquitination, at least 186 (59%) of which are known autoAgs. These proteins are associated with gene expression, mRNA processing, mRNA splicing, translation, protein folding, vesicles, and chromosome organization. Numerous nuclear autoAgs were identified, including both classical ANAs and ENAs of systemic autoimmune diseases and unique autoAgs involved in the DNA replication fork, mitotic cell cycle, or telomerase maintenance. We also identified many uncommon autoAgs involved in nucleic acid and peptide biosynthesis and nucleocytoplasmic transport, such as aminoacyl-tRNA synthetases. In addition, this study found autoAgs that potentially interact with multiple SARS-CoV-2 Nsp and Orf components, including CCT/TriC chaperonin, insulin degrading enzyme, platelet-activating factor acetylhydrolase, and the ezrin-moesin-radixin family. Furthermore, B-cell-specific IgM-associated ER complex (including MBZ1, BiP, heat shock proteins, and protein disulfide-isomerases) is enriched by DS-affinity and up-regulated in B-cells of COVID-19 patients, and a similar IgH-associated ER complex was also identified in autoreactive pre-B1 cells in our previous study, which suggests a role of autoreactive B1 cells in COVID-19 that merits further investigation. In summary, this study demonstrates that virally infected cells are characterized by alterations of proteins with propensity to become autoAgs, thereby providing a possible explanation for infection-induced autoimmunity. The COVID autoantigen-ome provides a valuable molecular resource and map for investigation of COVID-related autoimmune sequelae and considerations for vaccine design.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Julia Y. Wang", - "author_inst": "Curandis" - }, - { - "author_name": "Wei Zhang", - "author_inst": "Guizhou Medical University" - }, - { - "author_name": "Victor B. Roehrl", - "author_inst": "Curandis" - }, - { - "author_name": "Michael W. Roehrl", - "author_inst": "Curandis" - }, - { - "author_name": "Michael H. Roehrl", - "author_inst": "Memorial Sloan Kettering Cancer Center" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.03.30.21254604", "rel_title": "Detection of SARS-CoV-2 antibodies formed in response to the BNT162b2 and mRNA-1237 mRNA vaccine by commercial antibody tests", @@ -858014,6 +856400,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical ethics" }, + { + "rel_doi": "10.1101/2021.03.31.21254731", + "rel_title": "Risk quantification for SARS-CoV-2 infection through airborne transmission in university settings", + "rel_date": "2021-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.31.21254731", + "rel_abs": "The COVID-19 pandemic has significantly impacted learning as many institutions switched to remote or hybrid instruction. An in-depth assessment of the risk of infection that takes into account environmental setting and mitigation strategies is needed to make safe and informed decisions regarding reopening university spaces. A quantitative model of infection probability that accounts for space-specific parameters is presented to enable assessment of the risk in reopening university spaces at given densities. The model uses local positivity rate, room capacity, mask filtration efficiency, air exchange rate, room volume, and time spent in the space as parameters to calculate infection probabilities in teaching spaces, dining halls, dorms, and shared bathrooms. The model readily calculates infection probabilities in various university spaces, with mask filtration efficiency and air exchange rate being among the dominant variables. When applied to university spaces, this model demonstrated that, under specific conditions that are feasible to implement, in-person classes could be held in large lecture halls with an infection risk over the semester < 1%. Meal pick-ups from dining halls and the use of shared bathrooms in residential dormitories among small groups of students could also be accomplished with low risk. The results of applying this model to spaces at Harvard University (Cambridge and Allston campuses) and Stanford University are reported. Finally, a user-friendly web application was developed using this model to calculate infection probability following input of space-specific variables. The successful development of a quantitative model and its implementation through a web application may facilitate accurate assessments of infection risk in university spaces. In light of the impact of the COVID-19 pandemic on universities, this tool could provide crucial insight to students, faculty, and university officials in making informed decisions.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Mythri Ambatipudi", + "author_inst": "Harvard University" + }, + { + "author_name": "Paola Carrillo Gonzalez", + "author_inst": "Harvard University" + }, + { + "author_name": "Kazi Tasnim", + "author_inst": "Harvard University" + }, + { + "author_name": "Jordan Daigle", + "author_inst": "Harvard University" + }, + { + "author_name": "Taisa Kulyk", + "author_inst": "Harvard University" + }, + { + "author_name": "Nicholas Jeffreys", + "author_inst": "Harvard University" + }, + { + "author_name": "Nishant Sule", + "author_inst": "Harvard University" + }, + { + "author_name": "Rafael Trevino", + "author_inst": "Harvard University" + }, + { + "author_name": "Emily M He", + "author_inst": "Harvard University" + }, + { + "author_name": "David Mooney", + "author_inst": "Harvard University" + }, + { + "author_name": "Esther E Koh", + "author_inst": "Harvard University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2021.03.31.21254699", "rel_title": "Tryptophan and arginine metabolism is significantly altered at the time of admission in hospital for severe COVID-19 patients: findings from longitudinal targeted metabolomics analysis", @@ -858462,33 +856907,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.04.05.438537", - "rel_title": "High-Potency Polypeptide-based Interference for Coronavirus Spike Glycoproteins", - "rel_date": "2021-04-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.05.438537", - "rel_abs": "Specific manipulation of proteins post-translationally remains difficult. Here we report results of a general approach that uses a partial sequence of a protein to efficiently modulate the expression level of the native protein. When applied to coronavirus, human immunodeficiency virus, Ebolavirus, respiratory syncytial virus and influenza virus, polypeptides containing highly conserved regions of the viral glycoproteins potently diminished expression of the respective native proteins. In the cases of coronavirus and influenza virus where multiple strains were tested, the polypeptides were equally effective against glycoproteins of other coronavirus and influenza strains with sequence identity as low as 27%, underscoring their high insensitivity to mutations. Thus, this method provides a platform for developing high-efficacy broad-spectrum anti-viral inhibitors, as well as a new way to alter expression of essentially any systems post-translationally.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Jianpeng Ma", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Adam Campos Acevedo", - "author_inst": "Baylor College of Medicine" - }, - { - "author_name": "Qinghua Wang", - "author_inst": "Baylor College of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.04.06.438630", "rel_title": "ADNKA overcomes SARS-CoV2-mediated NK cell inhibition through non-spike antibodies", @@ -859964,6 +858382,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.04.01.21254484", + "rel_title": "A Rapid SARS-CoV-2 Variant Detection by Molecular-Clamping Based RT-qPCR", + "rel_date": "2021-04-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.04.01.21254484", + "rel_abs": "We applied XNA-based Molecular Clamping Technology to develop a multiplex qPCR assay for rapid and accurate detection of SARS-CoV-2 mutations. A total of 278 previously tested SARS-COV-2 positive samples originating primarily from San Francisco Bay Area were tested, including 139 Samples collected in middle January and 139 samples collected at the end of February 2021, respectively. The SARS-CoV-2 Spike-gene D614G mutation was detected from 58 samples (41.7%) collected in January 2021 and, 78 samples (56.1%) collected in February. Notably, while there were no N501Y mutation detected in samples from January, seven of the February samples were tested positive for the N501Y and D614G mutations. The results suggest a relatively recent and speedy spreading of the UK variant (B.1.1.7) in Northern California. This new Molecular Clamping technology-based multiplex RT-qPCR assay is highly sensitive and specific and can help speed up large scale testing for SARS-CoV-2 variants.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Shuo Shen", + "author_inst": "Diacarta Inc" + }, + { + "author_name": "Andrew Y Fu", + "author_inst": "Diacarta Inc" + }, + { + "author_name": "Maidar Jamba", + "author_inst": "Diacarta Inc" + }, + { + "author_name": "Jonathan Li", + "author_inst": "Diacarta Inc" + }, + { + "author_name": "Mike J Powell", + "author_inst": "Diacarta Inc" + }, + { + "author_name": "Aiguo Zhang", + "author_inst": "Diacarta Inc" + }, + { + "author_name": "Chuanyi M Lu", + "author_inst": "University of California and VA Healthcare System, San Francisco, CA 94121" + }, + { + "author_name": "Michael Y Sha", + "author_inst": "Diacarta Inc" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.04.01.21254182", "rel_title": "Rapid, Affordable and Scalable SARS-CoV-2 Detection from Saliva", @@ -860516,25 +858981,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.04.04.438420", - "rel_title": "Rational Selection of PCR Primer/Probe Design Sites for SARS-CoV-2", - "rel_date": "2021-04-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.04.438420", - "rel_abs": "Various reports of decreased analytical sensitivities of real-time PCR-based detection of Coronavirus Disease 2019 (COVID-19) have been associated with occurrence of mutations in the target area of primer/probe binding. Knowledge about propensities of different genes to undergo mutation can inform researchers to select optimal genes to target for the qPCR design. We analyzed supplementary data from over 45 thousand SARS-CoV-2 genomes provided by Mercatelli et al to calculate the unique and prevalent mutations in different genes of SARS-CoV-2. We found that non-structural proteins in the ORF1ab region were more conserved compared to structural genes. Further factors which need to be relied upon for proper selection of genes for qPCR design are discussed.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Divya RSJB Rana", - "author_inst": "The Leprosy Mission Nepal" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2021.03.29.21254343", "rel_title": "Estimates and determinants of SARS-CoV-2 seroprevalence and infection fatality ratio using latent class analysis: the population-based Tirschenreuth study in the hardest-hit German county in spring 2020", @@ -861862,6 +860308,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.30.21254653", + "rel_title": "Differences in risk for SARS-CoV-2 infection among healthcare workers", + "rel_date": "2021-04-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.30.21254653", + "rel_abs": "Healthcare workers (HCWs) are a risk group for SARS-CoV-2 infection, but which healthcare work that conveys risk and to what extent such risk can be prevented is not clear. Starting on April 24th, 2020, all employees at work (n=15,300) at the Karolinska University Hospital, Stockholm, Sweden were invited and 92% consented to participate in a SARS-CoV-2 cohort study. Complete SARS-CoV-2 serology was available for n=12,928 employees and seroprevalences were analyzed by age, sex, profession, patient contact, and hospital department. Relative risks were estimated to examine the association between type of hospital department as a proxy for different working environment exposure and risk for seropositivity, adjusting for age, sex, sampling week, and profession. Wards that were primarily responsible for COVID-19 patients were at increased risk (adjusted OR 1.95 (95% CI 1.65-2.32) with the notable exception of the infectious diseases and intensive care units (adjusted OR 0.86 (95% CI 0.66-1.13)), that were not at increased risk despite being highly exposed. Several units with similar types of work varied greatly in seroprevalences. Among the professions examined, nurse assistants had the highest risk (adjusted OR 1.62 (95% CI 1.38-1.90)). Although healthcare workers, in particular nurse assistants, who attend to COVID-19 patients are a risk group for SARS-CoV-2 infection, several units caring for COVID-19 patients had no excess risk. Large variations in seroprevalences among similar units suggest that healthcare work-related risk of SARS-CoV-2 infection may be preventable.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "K. Miriam Elfstrom", + "author_inst": "Karolinska University Laboratory" + }, + { + "author_name": "Jonas Blomqvist", + "author_inst": "Karolinska University Hospital" + }, + { + "author_name": "Peter Nilsson", + "author_inst": "SciLifeLab" + }, + { + "author_name": "Sofia Hober", + "author_inst": "KTH Royal Institute of Technology" + }, + { + "author_name": "Elisa Pin", + "author_inst": "SciLifeLab" + }, + { + "author_name": "Anna Manberg", + "author_inst": "SciLifeLab" + }, + { + "author_name": "Ville Pimenoff", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Laila Sara Arroyo Muhr", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Kalle Conneryd-Lundgren", + "author_inst": "Karolinska University Hospital" + }, + { + "author_name": "Joakim Dillner", + "author_inst": "Karolinska University Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.30.21254591", "rel_title": "Genomic monitoring unveil the early detection of the SARS-CoV-2 B.1.351 lineage (20H/501Y.V2) in Brazil", @@ -862330,53 +860831,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.04.02.438204", - "rel_title": "Discovery and in-vitro evaluation of potent SARS-CoV-2 entry inhibitors", - "rel_date": "2021-04-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.04.02.438204", - "rel_abs": "SARS-CoV-2 infection initiates with the attachment of spike protein to the ACE2 receptor. While vaccines have been developed, no SARS-CoV-2 specific small molecule inhibitors have been approved. Herein, utilizing the crystal structure of the ACE2/Spike receptor binding domain (S-RBD) complex in computer-aided drug design (CADD) approach, we docked [~]8 million compounds within the pockets residing at S-RBD/ACE2 interface. Five best hits depending on the docking score, were selected and tested for their in vitro efficacy to block SARS-CoV-2 replication. Of these, two compounds (MU-UNMC-1 and MU-UNMC-2) blocked SARS-CoV-2 replication at sub-micromolar IC50 in human bronchial epithelial cells (UNCN1T) and Vero cells. Furthermore, MU-UNMC-2 was highly potent in blocking the virus entry by using pseudoviral particles expressing SARS-CoV-2 spike. Finally, we found that MU-UNMC-2 is highly synergistic with remdesivir (RDV), suggesting that minimal amounts are needed when used in combination with RDV, and has the potential to develop as a potential entry inhibitor for COVID-19.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Arpan Acharya", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Kabita Pandey", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Michellie Thurman", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Elizabeth Klug", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Jay Trivedi", - "author_inst": "University of Nebraska Medical Center" - }, - { - "author_name": "Christian L Lorson", - "author_inst": "University of Missouri, Columbia" - }, - { - "author_name": "Kamlendra Singh", - "author_inst": "University of Missouri" - }, - { - "author_name": "Siddappa N Byrareddy", - "author_inst": "University of Nebraska Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2021.04.01.438063", "rel_title": "COVIDOUTCOME - Estimating COVID Severity Based on Mutation Signatures in the SARS-CoV-2 Genome", @@ -863968,6 +862422,89 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.03.28.21254507", + "rel_title": "Efficacy and safety of convalescent plasma and intravenous immunoglobulin in critically ill COVID-19 patients. A controlled clinical trial.", + "rel_date": "2021-03-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.28.21254507", + "rel_abs": "BackgroundThe proportion of critically ill COVID-19 patients has collapsed hospital care worldwide. The need for alternative therapies for this group of patients is imperative. This study aims to compare the safety and efficacy of convalescent plasma (CP) compared with human immunoglobulin (IVIg) in patients requiring the administration of high oxygen levels or mechanical ventilation.\n\nMethodsThis is a controlled, randomized, open clinical trial of patients with pneumonia secondary to SARS-CoV-2 infection, that fulfilled criteria for severe or critical disease. They were randomized in a 1:2 ratio; group 1 was administered IVIg at a dose of 0.3 grams per kilogram of ideal weight, in an 8-hour infusion every 24 hours, for 5 days. Group 2 was administered 200 ml of CP infused in 2 hours, for 2 days. The primary outcomes were duration of hospitalization and mortality at 28 days.\n\nResultsOne hundred and ninety (190) patients were randomized; 130 to the CP group, and 60 to the IVIg group. Their average age was 58 years (IQR 47 - 72), and most were male (n= 119, 62.6 %). On inclusion, 85.2 % of patients (n=162) were on invasive mechanical ventilation therapy. Overall mortality in all included patients was 53 % (n= 102), with a median follow-up of 14 days (IQI 8 - 26). Mortality at 28 days was 45.2 % (n=86). In the intention-to-treat analysis, there was no difference between groups neither in mortality on follow-up (53.8 vs. 53.3, p =1.0) nor at 28 days (46.2 vs 43 %, p=0.75, Log Rank p = 0.83). Per-protocol analysis between treatment groups revealed no difference in mortality throughout hospitalization (51.5 vs 51.4 %, p=1.0) nor after 28 days (42.1 vs 42.87 %, p=0.92 Log Rank p = 0.54). Only 23 patients in the CP group received plasma with detectable anti-SARS-CoV-2 antibodies.\n\nConclusionsIn critically ill patients or on invasive mechanical ventilation for treatment of Covid-19, the use of CP is not superior to IVIg in terms of hospitalization duration or mortality. The use of CP is based on complex logistics and requires an assured level of antibodies if used therapeutically. IVIg does not appear to be useful in this group of patients.\n\nclinicaltrials.gov identifier: NCT04381858.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Jose Lenin Beltran Gonzalez", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Mario Gonzalez Gamez", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Emmanuel Antonio Mendoza Enciso", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Ramiro Josue Esparza Maldonado", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Daniel Hernandez Palacios", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Samuel Duenas Campos", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Itzel Ovalle Robles", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Mariana Jocelyn Macias Guzman", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Andrea Lucia Garcia Diaz", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Cesar Mauricio Gutierrez Pena", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Ana Lilia Reza Escalera", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Maria Teresa Tiscareno Gutierrez", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Elba Galvan Guerra", + "author_inst": "Laboratorio Clinico del Campestre" + }, + { + "author_name": "Maria del Rocio Dorantes Morales", + "author_inst": "Aguascalientes State Transfusion Center" + }, + { + "author_name": "Lucila Martinez Medina", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Victor Antonio Monroy Colin", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Jose Manuel Arreola Guerra", + "author_inst": "Centenario Hospital Miguel Hidalgo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.29.21254534", "rel_title": "Characterization of antibody response in asymptomatic and symptomatic SARS-CoV-2 infection", @@ -864480,61 +863017,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, - { - "rel_doi": "10.1101/2021.03.29.21254538", - "rel_title": "Half year longitudinal seroprevalence of SARS-CoV-2-antibodies and rule compliance in German hospital employees", - "rel_date": "2021-03-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.29.21254538", - "rel_abs": "IntroductionCOVID-19, caused by SARS-CoV-2, is an occupational health risk especially for healthcare employees. This study was designed to determine the longitudinal seroprevalence of specific immunglobolin-G (IgG)-antibodies in employees in a hospital setting.\n\nMethodsAll employees including healthcare and non-healthcare workers in a secondary care hospital were invited to participate in this single-center study. After an initial screening, a 6 months follow-up was done which included serological examination for SARS-CoV-2-IgG-antibodies and a questionnaire for self-reported symptoms, self-perception and thoughts about the local and national hygiene and pandemic plans.\n\nResultsThe seroprevalence of SARS-CoV-2-IgG-antibodies was 0.74% among 406 hospital employees (95% confidence interval) (0.75% in healthcare workers, 0.72% in non-healthcare workers), initially recruited in April 2020, in their follow-up blood specimen in October 2020.\n\nIn this study, 30.54% of the participants reported using the official German corona mobile application and the majority were content with the local and national rules in relation to Coronavirus restrictions.\n\nDiscussionAt the 6 months follow-up, the 0.74% seroprevalence was below the reported seroprevalence of 1.35% in the general German population. The prevalence in healthcare workers in direct patient care compared with those without direct patient contact did not differ significantly.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Jonas Herzberg", - "author_inst": "Department of Surgery, Krankenhaus Reinbek St. Adolf-Stift, Reinbek, Germany" - }, - { - "author_name": "Tanja Vollmer", - "author_inst": "Institute for Laboratory and Transfusion Medicine, Heart and Diabetes Centre NRW, Bad Oeynhausen, Ruhr University Bochum, Bochum, Germany" - }, - { - "author_name": "Bastian Fischer", - "author_inst": "Institute for Laboratory and Transfusion Medicine, Heart and Diabetes Centre NRW, Bad Oeynhausen, Ruhr University Bochum, Bochum, Germany" - }, - { - "author_name": "Heiko Becher", - "author_inst": "University Medical Center Hamburg-Eppendorf, Hamburg, Germany" - }, - { - "author_name": "Ann-Kristin Becker", - "author_inst": "Asklepios Klinik Harburg, Hamburg, Germany" - }, - { - "author_name": "Hany Sahly", - "author_inst": "Labor Lademannbogen MVZ Hamburg, Hamburg, Germany" - }, - { - "author_name": "Human Honarpisheh", - "author_inst": "Department of Surgery, Krankenhaus Reinbek St. Adolf-Stift, Reinbek, Germany" - }, - { - "author_name": "Salman Yousuf Guraya", - "author_inst": "Clinical Sciences Department, College of Medicine, University of Sharjah" - }, - { - "author_name": "Tim Strate", - "author_inst": "Department of Surgery, Krankenhaus Reinbek St. Adolf-Stift, Reinbek, Germany" - }, - { - "author_name": "Cornelius Knabbe", - "author_inst": "Institute for Laboratory and Transfusion Medicine, Heart and Diabetes Centre NRW, Bad Oeynhausen, Ruhr University Bochum, Bochum, Germany" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2021.03.29.21254529", "rel_title": "Psychological distress and resilience in a sample of Adolescents and Young Adults with cancer during the COVID-19 pandemic", @@ -865526,6 +864008,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.29.21254560", + "rel_title": "Innate immune deficiencies in patients with COVID-19", + "rel_date": "2021-03-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.29.21254560", + "rel_abs": "COVID-19 can cause acute respiratory distress syndrome (ARDS), leading to death in a significant number of individuals. Evidence of a strong role of the innate immune system is accumulating, but the precise cells and mechanism involved remain unclear. In this study, we investigated the links between circulating innate phagocyte phenotype and functions and severity in COVID-19 patients. Eighty-four consecutive patients were included, 44 of which were in intensive care units (ICU). We performed an in-depth phenotyping of neutrophil and monocyte subpopulations and measured soluble activation markers in plasma. Additionally, myeloid cell functions (phagocytosis, oxidative burst, and NETosis) were evaluated on fresh cells from patients. Resulting parameters were linked to disease severity and prognosis. Both ICU and non-ICU patients had circulating neutrophils and monocytes with an activated phenotype, as well as elevated concentrations of soluble activation markers (calprotectin, myeloperoxidase, neutrophil extracellular traps, MMP9, sCD14) in their plasma. ICU patients were characterized by increased CD10low CD13low immature neutrophils, LOX-1+ and CCR5+ immunosuppressive neutrophils, and HLA-DRlow CD14low downregulated monocytes. Markers of immature and immunosuppressive neutrophils were strongly associated with severity and poor outcome. Moreover, neutrophils and monocytes of ICU patients had impaired antimicrobial functions, which correlated with organ dysfunction, severe infections, and mortality. Our study reveals a marked dysregulation of innate immunity in COVID-19 patients, which was correlated with severity and prognosis. Together, our results strongly argue in favor of a pivotal role of innate immunity in COVID-19 severe infections and pleads for targeted therapeutic options.\n\nOne Sentence SummaryOur study reveals a marked dysregulation of innate immunity in COVID-19 patients, which correlates with severity and prognosis.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Marine Peyneau", + "author_inst": "AP-HP, Bichat Hospital, Autoimmunity and Hypersensitivity Laboratory; Paris, France" + }, + { + "author_name": "Vanessa Granger", + "author_inst": "AP-HP, Bichat Hospital, Autoimmunity and Hypersensitivity Laboratory; Paris, France" + }, + { + "author_name": "Paul-Henri Wicky", + "author_inst": "AP-HP, Bichat hospital Medial and infectious diseases ICU (MI2); Paris France" + }, + { + "author_name": "Dounia Khelifi-Touhami", + "author_inst": "AP-HP, Bichat Hospital, Autoimmunity and Hypersensitivity Laboratory; Paris, France" + }, + { + "author_name": "Jean-Francois Timsit", + "author_inst": "AP-HP, Bichat hospital Medial and infectious diseases ICU (MI2); Paris France" + }, + { + "author_name": "Francois-Xavier Lescure", + "author_inst": "AP-HP, Hopital Bichat, Infectious Diseases Department ; Paris, France" + }, + { + "author_name": "Yazdan Yazdanpanah", + "author_inst": "AP-HP, Hopital Bichat, Infectious Diseases Department ; Paris, France" + }, + { + "author_name": "Alexy Tran-Dihn", + "author_inst": "AP-HP, Bichat Hospital, Departement Anesthesie-Reanimation, DMU PARABOL, Universite de Paris; Paris France" + }, + { + "author_name": "Philippe Montravers", + "author_inst": "AP-HP, Bichat Hospital, Departement Anesthesie-Reanimation, DMU PARABOL, Universite de Paris; Paris France" + }, + { + "author_name": "Renato Monteiro", + "author_inst": "APHP, Bichat Hospital, Immunological Dysfunction Laboratory, Paris, France" + }, + { + "author_name": "Sylvie Chollet-Martin", + "author_inst": "AP-HP, Bichat Hospital, Autoimmunity and Hypersensitivity Laboratory; Paris, France" + }, + { + "author_name": "Margarita Hurtado-Nedelec", + "author_inst": "APHP, Bichat Hospital, Immunological Dysfunction Laboratory, Paris, France" + }, + { + "author_name": "Luc de Chaisemartin", + "author_inst": "AP-HP, Bichat Hospital, Autoimmunity and Hypersensitivity Laboratory; Paris, France" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.03.28.21254520", "rel_title": "Returning to the workplace during the COVID-19 pandemic: The concerns of Australian workers", @@ -866018,33 +864567,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.29.21254509", - "rel_title": "Genetic associations with severe COVID-19", - "rel_date": "2021-03-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.29.21254509", - "rel_abs": "Identification of host genetic factors that predispose individuals to severe COVID-19 is important, not only for understanding the disease and guiding the development of treatments, but also for risk prediction when combined to form a polygenic risk score (PRS). Using population controls, Pairo-Castineira et al. identified 12 SNPs (a panel of 8 SNPs and a panel of 6 SNPs, with two SNPs in both panels) associated with severe COVID-19. Using controls with asymptomatic or mild COVID-19, we were able to replicate the association with severe COVID-19 for only three of their SNPs and found marginal evidence for an association for one other. When combined as an 8-SNP PRS and a 6-SNP PRS, we found no evidence of association with severe COVID-19. The difference in our results and the results of Pairo-Castineira et al. might be the choice of controls: population controls vs controls with asymptomatic or mild COVID-19.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Nicholas M Murphy", - "author_inst": "Genetic Technologies Limited" - }, - { - "author_name": "Gillian S Dite", - "author_inst": "Genetic Technologies Ltd." - }, - { - "author_name": "Richard Allman", - "author_inst": "Genetic technologies Limited" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.30.21254578", "rel_title": "Muscle Strength and Muscle Mass as Predictors of Hospital Length of Stay in Patients with Moderate to Severe COVID-19: A Prospective Observational Study", @@ -867320,6 +865842,101 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2021.03.30.437173", + "rel_title": "Severity of SARS-CoV-2 infection as a function of the interferon landscape across the respiratory tract of COVID-19 patients.", + "rel_date": "2021-03-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.30.437173", + "rel_abs": "The COVID-19 outbreak driven by SARS-CoV-2 has caused more than 2.5 million deaths globally, with the most severe cases characterized by over-exuberant production of immune-mediators, the nature of which is not fully understood. Interferons of the type I (IFN-I) or type III (IFN-III) families are potent antivirals, but their role in COVID-19 remains debated. Our analysis of gene and protein expression along the respiratory tract shows that IFNs, especially IFN-III, are over-represented in the lower airways of patients with severe COVID-19, while high levels of IFN-III, and to a lesser extent IFN-I, characterize the upper airways of patients with high viral burden but reduced disease risk or severity; also, IFN expression varies with abundance of the cell types that produce them. Our data point to a dynamic process of inter- and intra-family production of IFNs in COVID-19, and suggest that IFNs play opposing roles at distinct anatomical sites.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Achille Broggi", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Laura Pandolfi", + "author_inst": "Fondazione IRCCS Policlinico San Matteo" + }, + { + "author_name": "Stefania Crotta", + "author_inst": "Francis Crick Institute" + }, + { + "author_name": "Roberto Ferrarese", + "author_inst": "San Raffaele Hospital" + }, + { + "author_name": "Sofia Sisti", + "author_inst": "San Raffaele Hospital" + }, + { + "author_name": "Nicola Clementi", + "author_inst": "Vita-Salute San Raffaele University" + }, + { + "author_name": "Alessandro Ambrosi", + "author_inst": "San Raffaele Hospital" + }, + { + "author_name": "Vanessa Frangipane", + "author_inst": "Fondazione IRCCS Policlinico San Matteo" + }, + { + "author_name": "Laura Saracino", + "author_inst": "Fondazione IRCCS Policlinico San Matteo" + }, + { + "author_name": "Laura Marongiu", + "author_inst": "university of Milano-Bicocca" + }, + { + "author_name": "Fabio Facchini", + "author_inst": "University of Milano-Bicocca" + }, + { + "author_name": "Andrea Bottazzi", + "author_inst": "Fondazione IRCCS Policlinico San Matteo" + }, + { + "author_name": "Tomaso Fossali", + "author_inst": "Sacco Hospital" + }, + { + "author_name": "Riccardo Colombo", + "author_inst": "Sacco Hospital" + }, + { + "author_name": "Massimo Clementi", + "author_inst": "Vita-Salute San Raffaele University" + }, + { + "author_name": "Elena Tagliabue", + "author_inst": "Multimedica" + }, + { + "author_name": "Antonio Pontiroli", + "author_inst": "University of Milano" + }, + { + "author_name": "Federica Meloni", + "author_inst": "Fondazione IRCCS Policlinico San Matteo" + }, + { + "author_name": "Andreas Wack", + "author_inst": "Francis Crick Institute" + }, + { + "author_name": "Nicasio Mancini", + "author_inst": "University Vita-Salute San Raffaele" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.03.29.437480", "rel_title": "COVID-19 and the abrupt shift to remote learning: Impact on grades and perceived learning for undergraduate biology students", @@ -867784,29 +866401,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.26.21254429", - "rel_title": "Forecasting the Spreading Trajectory of the COVID-19 Pandemic", - "rel_date": "2021-03-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.26.21254429", - "rel_abs": "Predictively forecasting future developments for the spread of the COVID-19 pandemic is extremely challenging. A recently published logistic mathematic model has achieved good predictions for infections weeks ahead. In this short communication, we summarize the Logistic spread model, which describes the dynamics of the pandemic evolution and the impacts of people social behavior in fighting against the pandemic. The new pandemic model has two parameters (i.e., transmission rate {gamma} and social distancing d) to be calibrated to the data from the pandemic regions in the early stage of the outbreak while the social distancing is put in place. The model is capable to make early predictions about the spreading trajectory in the communities of any size (countries, states, counties and cities) including the total infections, the date of peak daily infections and the date of the infections reaching a plateau if the testing is sufficient. The results are in good agreement with data and have important applications for ongoing outbreaks and similar infectious disease pandemics in the future.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Baolian Cheng", - "author_inst": "Los Alamos National Laboratory" - }, - { - "author_name": "Yi-Ming Wang", - "author_inst": "LANL Retiree" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.28.21254486", "rel_title": "Prohibit, protect, or adapt? The changing role of volunteers in palliative and hospice care services during the COVID-19 pandemic. A multinational survey (CovPall).", @@ -869142,6 +867736,45 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.03.26.21254369", + "rel_title": "Using Google Health Trends to investigate COVID19 incidence in Africa", + "rel_date": "2021-03-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.26.21254369", + "rel_abs": "The COVID-19 pandemic has caused over 350 million cases and over five million deaths globally. From these numbers, over 10 million cases and over 200 thousand deaths have occurred on the African continent as of 22 January 2022. Prevention and surveillance remain the cornerstone of interventions to halt the further spread of COVID-19. Google Health Trends (GHT), a free Internet tool, may be valuable to help anticipate outbreaks, identify disease hotspots, or understand the patterns of disease surveillance.\n\nWe collected COVID-19 case and death incidence for 54 African countries and obtained averages for four, five-month study periods in 2020-2021. Average case and death incidences were calculated during these four time periods to measure disease severity. We used GHT to characterize COVID-19 incidence across Africa, collecting numbers of searches from GHT related to COVID-19 using four terms: coronavirus, coronavirus symptoms, COVID19, and pandemic. The terms were related to weekly COVID-19 case incidences for the entire study period via multiple linear regression analysis and weighted linear regression analysis. We also assembled 72 predictors assessing Internet accessibility, demographics, economics, health, and others, for each country, to summarize potential mechanisms linking GHT searches and COVID-19 incidence.\n\nCOVID-19 burden in Africa increased steadily during the study period as in the rest of the world. Important increases for COVID-19 death incidence were observed for Seychelles and Tunisia over the study period. Our study demonstrated a weak correlation between GHT and COVID-19 incidence for most African countries. Several predictors were useful in explaining the pattern of GHT statistics and their relationship to COVID-19 including: log of average weekly cases, log of cumulative total deaths, and log of fixed total number of broadband subscriptions in a country. Apparently, GHT may best be used for surveillance of diseases that are diagnosed more consistently.\n\nGHT-based surveillance for an ongoing epidemic might be useful in specific situations, such as when countries have significant levels of infection with low variability. Overall, GHT-based surveillance showed little applicability in the studied countries. Future studies might assess the algorithm in different epidemic contexts.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Alex Fulk", + "author_inst": "University of Kansas" + }, + { + "author_name": "Daniel Romero-Alvarez", + "author_inst": "University of Kansas" + }, + { + "author_name": "Qays Abu Saymeh", + "author_inst": "University of Kansas" + }, + { + "author_name": "Jarron Saint Onge", + "author_inst": "University of Kansas" + }, + { + "author_name": "A. Townsend Peterson", + "author_inst": "University of Kansas" + }, + { + "author_name": "Folashade B Agusto", + "author_inst": "University of Kansas" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.29.437540", "rel_title": "SARS-CoV-2, a threat to marine mammals? A study from Italian seawaters", @@ -869594,41 +868227,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.27.21254471", - "rel_title": "Estimation of SARS-CoV-2 antibody prevalence through integration of serology and incidence data", - "rel_date": "2021-03-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.27.21254471", - "rel_abs": "Serology tests for SARS-CoV-2 provide a paradigm for estimating the number of individuals who have had infection in the past (including cases that are not detected by routine testing, which has varied over the course of the pandemic and between jurisdictions). Classical statistical approaches to such estimation do not incorporate case counts over time, and may be inaccurate due to uncertainty about the sensitivity and specificity of the serology test. In this work, we provide a joint Bayesian model for case counts and serological data, integrating uncertainty through priors on the sensitivity and specificity. We also model the Phases of the pandemic with exponential growth and decay. This model improves upon maximum likelihood estimates by conditioning on more data, and by taking into account the epidemiological trajectory. We apply our model to the greater Vancouver area, British Columbia, Canada with data acquired during Phase 1 of the pandemic.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Liangliang Wang", - "author_inst": "Simon Fraser University" - }, - { - "author_name": "Joosung Min", - "author_inst": "Simon Fraser University" - }, - { - "author_name": "Renny Doig", - "author_inst": "Simon Fraser University" - }, - { - "author_name": "Lloyd T Elliott", - "author_inst": "Simon Fraser University" - }, - { - "author_name": "Caroline Colijn", - "author_inst": "Simon Fraser University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.27.21254453", "rel_title": "How unequal vaccine distribution promotes the evolution of vaccine escape", @@ -870872,6 +869470,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.20.21254022", + "rel_title": "Supporting COVID-19 policy response with large-scale mobility-based modeling", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.20.21254022", + "rel_abs": "Social distancing measures, such as restricting occupancy at venues, have been a primary intervention for controlling the spread of COVID-19. However, these mobility restrictions place a significant economic burden on individuals and businesses. To balance these competing demands, policymakers need analytical tools to assess the costs and benefits of different mobility reduction measures.In this paper, we present our work motivated by our interactions with the Virginia Department of Health on a decision-support tool that utilizes large-scale data and epidemiological modeling to quantify the impact of changes in mobility on infection rates. Our model captures the spread of COVID-19 by using a fine-grained, dynamic mobility network that encodes the hourly movements of people from neighborhoods to individual places, with over 3 billion hourly edges. By perturbing the mobility network, we can simulate a wide variety of reopening plans and forecast their impact in terms of new infections and the loss in visits per sector. To deploy this model in practice, we built a robust computational infrastructure to support running millions of model realizations, and we worked with policymakers to develop an intuitive dashboard interface that communicates our models predictions for thousands of potential policies, tailored to their jurisdiction. The resulting decision-support environment provides policymakers with much-needed analytical machinery to assess the tradeoffs between future infections and mobility restrictions.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Serina Y Chang", + "author_inst": "Stanford University" + }, + { + "author_name": "Mandy L Wilson", + "author_inst": "Biocomplexity Institute & Initiative, University of Virginia" + }, + { + "author_name": "Bryan Lewis", + "author_inst": "Biocomplexity Institute & Initiative, University of Virginia" + }, + { + "author_name": "Zakaria Mehrab", + "author_inst": "Biocomplexity Institute & Initiative, University of Virginia" + }, + { + "author_name": "Komal K Dudakiya", + "author_inst": "Persistent Systems" + }, + { + "author_name": "Emma Pierson", + "author_inst": "Microsoft Research" + }, + { + "author_name": "Pang Wei Koh", + "author_inst": "Stanford University" + }, + { + "author_name": "Jaline Gerardin", + "author_inst": "Northwestern University" + }, + { + "author_name": "Beth Redbird", + "author_inst": "Northwestern University" + }, + { + "author_name": "David Grusky", + "author_inst": "Stanford University" + }, + { + "author_name": "Madhav Marathe", + "author_inst": "Biocomplexity Institute & Initiative, University of Virginia" + }, + { + "author_name": "Jure Leskovec", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.03.18.21253604", "rel_title": "A rapid assessment of wastewater for genomic surveillance of SARS-CoV-2 variants at sewershed scale in Louisville, KY", @@ -871532,109 +870193,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.21.21254061", - "rel_title": "Quantitative SARS-CoV-2 anti-spike responses to Pfizer-BioNTech and Oxford-AstraZeneca vaccines by previous infection status", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.21.21254061", - "rel_abs": "ObjectivesWe investigate determinants of SARS-CoV-2 anti-spike IgG responses in healthcare workers (HCWs) following one or two doses of Pfizer-BioNTech or Oxford-AstraZeneca vaccines.\n\nMethodsHCWs participating in regular SARS-CoV-2 PCR and antibody testing were invited for serological testing prior to first and second vaccination, and 4 weeks post-vaccination if receiving a 12-week dosing interval. Quantitative post-vaccination anti-spike antibody responses were measured using the Abbott SARS-CoV-2 IgG II Quant assay (detection threshold: [≥]50 AU/ml). We used multivariable logistic regression to identify predictors of seropositivity and generalised additive models to track antibody responses over time.\n\nResultsVaccine uptake was 80%, but less in lower-paid roles and Black, south Asian and minority ethnic groups. 3570/3610(98.9%) HCWs were seropositive >14 days post-first vaccination and prior to second vaccination, 2706/2720(99.5%) after Pfizer-BioNTech and 864/890(97.1%) following Oxford-AstraZeneca vaccines. Previously infected and younger HCWs were more likely to test seropositive post-first vaccination, with no evidence of differences by sex or ethnicity. All 470 HCWs tested >14 days after second vaccine were seropositive. Quantitative antibody responses were higher after previous infection: median(IQR) >21 days post-first Pfizer-BioNTech 14,604(7644-22,291) AU/ml vs. 1028(564-1985) AU/ml without prior infection (p<0.001). Oxford-AstraZeneca vaccine recipients had lower readings post-first dose compared to Pfizer-BioNTech, with and without previous infection, 10,095(5354-17,096) and 435(203-962) AU/ml respectively (both p<0.001 vs. Pfizer-BioNTech). Antibody responses post-second vaccination were similar to those after prior infection and one vaccine dose.\n\nConclusionsVaccination leads to detectable anti-spike antibodies in nearly all adult HCWs. Whether differences in response impact vaccine efficacy needs further study.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "David W Eyre", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sheila F Lumley", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jia Wei", - "author_inst": "University of Oxford" - }, - { - "author_name": "Stuart Cox", - "author_inst": "Oxford University Hospitals" - }, - { - "author_name": "Tim James", - "author_inst": "Oxford University Hospitals" - }, - { - "author_name": "Anita Justice", - "author_inst": "Oxford University Hospitals" - }, - { - "author_name": "Gerald Jesuthasan", - "author_inst": "Oxford University Hospitals" - }, - { - "author_name": "Alison Howarth", - "author_inst": "University of Oxford" - }, - { - "author_name": "Stephanie B Hatch", - "author_inst": "University of Oxford" - }, - { - "author_name": "Brian D Marsden", - "author_inst": "University of Oxford" - }, - { - "author_name": "E Yvonne Jones", - "author_inst": "University of Oxford" - }, - { - "author_name": "David I Stuart", - "author_inst": "University of Oxford" - }, - { - "author_name": "Daniel Ebner", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sarah Hoosdally", - "author_inst": "University of Oxford" - }, - { - "author_name": "Derrick Crook", - "author_inst": "University of Oxford" - }, - { - "author_name": "Tim EA Peto", - "author_inst": "University of Oxford" - }, - { - "author_name": "Timothy M Walker", - "author_inst": "University of Oxford" - }, - { - "author_name": "Nicole EA Stoesser", - "author_inst": "University of Oxford" - }, - { - "author_name": "Philippa C Matthews", - "author_inst": "University of Oxford" - }, - { - "author_name": "Koen B Pouwels", - "author_inst": "University of Oxford" - }, - { - "author_name": "A Sarah Walker", - "author_inst": "University of Oxford" - }, - { - "author_name": "Katie Jeffery", - "author_inst": "Oxford University Hospitals" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.21.21253498", "rel_title": "The 501Y.V2 SARS-CoV-2 variant has an intermediate viral load between the 501Y.V1 and the historical variants in nasopharyngeal samples from newly diagnosed COVID-19 patients", @@ -872966,6 +871524,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.22.21254121", + "rel_title": "Continuity of routine immunization programs in Canada during the COVID-19 pandemic", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.22.21254121", + "rel_abs": "IntroductionIn Canada, the COVID-19 pandemic has interrupted many routine health services, placed additional strain on the health care system, and resulted in many Canadians being either unable or unwilling to attend routine immunization appointments. We sought to capture and synthesize information about changes to routine immunization programs in response to the pandemic and plans to catch-up any missed immunizations.\n\nMethodsProvincial/territorial (P/T) public health leaders were interviewed via teleconference between August-October 2020 to collect information on the following topics: how routine immunization delivery was affected during and after initial lockdown periods, plans to catch-up missed doses, and major challenges and achievements in continuing routine immunization programs. Data were coded and categorized according to common responses and descriptive analysis was performed.\n\nResultsInterviews occurred with participants from 11 of 13 P/Ts. School immunization programs were reported to be most negatively affected by the pandemic (n=9). In the early pandemic period, infant, preschool, and maternal/prenatal programs were prioritized, with most P/Ts continuing these services with adaptations for COVID-19. After the initial lockdown period, all routine programs were continuing with adaptations in most P/Ts. Infant, preschool, and school programs were most often targeted for catch-up through measures such as appointment rebooking and making additional clinics and/or providers available. Major challenges included resource limitations (e.g., staff shortages, PPE shortages, limited infrastructure) (n=11), public health restrictions (n=8), and public hesitancy to attend appointments (n=5).\n\nConclusionsCanadian routine immunization programs faced some disruptions due to the COVID-19 pandemic, particularly the school, adult, and older adult programs. Further research is needed to determine the measurable impact of the pandemic on routine vaccine coverage levels.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Hannah Sell", + "author_inst": "University of Alberta" + }, + { + "author_name": "Ali Assi", + "author_inst": "University of Alberta" + }, + { + "author_name": "Michelle Driedger", + "author_inst": "University of Manitoba" + }, + { + "author_name": "Eve Dub\u00e9", + "author_inst": "Universit\u00e9 Laval" + }, + { + "author_name": "Arnaud Gagneur", + "author_inst": "Universit\u00e9 de Sherbrooke" + }, + { + "author_name": "Samantha B Meyer", + "author_inst": "University of Waterloo" + }, + { + "author_name": "Joan Robinson", + "author_inst": "University of Alberta" + }, + { + "author_name": "Manish Sadarangani", + "author_inst": "University of British Columbia" + }, + { + "author_name": "Matthew Tunis", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Shannon E MacDonald", + "author_inst": "University of Alberta" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.03.23.21253748", "rel_title": "Endogenous interferon-beta but not interferon-alpha or interferon-lambda levels in upper respiratory tract predict clinical outcome in critical COVID-19 patients independent of viral load", @@ -873518,81 +872131,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.23.21253460", - "rel_title": "Serological profiles of pan-coronavirus-specific responses in COVID-19 patients using a multiplexed electro-chemiluminescence-based testing platform", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.23.21253460", - "rel_abs": "Serological assessment of SARS-CoV-2 specific responses are an essential tool for determining the prevalence of past SARS-CoV-2 infections in the population especially when testing occurs after symptoms have developed and limited contact tracing is in place. The goal of our study was to test a new 10-plex electro-chemiluminescence-based assay to measure IgM and IgG responses to the spike proteins from multiple human coronaviruses including SARS-CoV-2, assess the epitope specificity of the SARS-CoV-2 antibody response against full-length spike protein, receptor-binding domain and N-terminal domain of the spike protein, and the nucleocapsid protein. We carried out the assay on samples collected from three sample groups: subjects diagnosed with COVID-19 from the U.S. Army hospital at Camp Humphreys in Pyeongtaek, South Korea; healthcare administrators from the same hospital but with no reported diagnosis of COVID-19; and pre-pandemic samples. We found that the new CoV-specific multiplex assay was highly sensitive allowing plasma samples to be diluted 1:30,000 with a robust signal. The reactivity of IgG responses to SARS-CoV-2 nucleocapsid protein and IgM responses to SARS-CoV-2 spike protein could distinguish COVID-19 samples from non-COVID-19 and pre-pandemic samples. The data from the three sample groups also revealed a unique pattern of cross-reactivity between SARS-CoV-2 and SARS-CoV-1, MERS-CoV, and seasonal coronaviruses HKU1 and OC43. Our findings show that the CoV-2 IgM response is highly specific while the CoV-2 IgG response is more cross-reactive across a range of human CoVs and also showed that IgM and IgG responses show distinct patterns of epitope specificity. In summary, this multiplex assay was able to distinguish samples by COVID-19 status and characterize distinct trends in terms of cross-reactivity and fine-specificity in antibody responses, underscoring its potential value in diagnostic or serosurveillance efforts.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Sidhartha Chaudhury", - "author_inst": "WRAIR" - }, - { - "author_name": "Jack N Hutter", - "author_inst": "WRAIR" - }, - { - "author_name": "Jessica S Bolton", - "author_inst": "WRAIR" - }, - { - "author_name": "Shilpa Hakre", - "author_inst": "WRAIR" - }, - { - "author_name": "Evelyn Mose", - "author_inst": "WRAIR" - }, - { - "author_name": "Amy I Wooten", - "author_inst": "Bryan D Allgood Army Community Hospital, Camp Humphrey" - }, - { - "author_name": "William D O'Connell", - "author_inst": "Bryan D Allgood Army Community Hospital, Camp Humphrey" - }, - { - "author_name": "Joseph Hudak", - "author_inst": "Bryan D Allgood Army Community Hospital, Camp Humphrey" - }, - { - "author_name": "Shelly J Krebs", - "author_inst": "WRAIR" - }, - { - "author_name": "Janice Darden", - "author_inst": "WRAIR" - }, - { - "author_name": "Jason A Regules", - "author_inst": "WRAIR" - }, - { - "author_name": "Clinton K Murray", - "author_inst": "Bryan D Allgood Army Community Hospital, Camp Humphrey" - }, - { - "author_name": "Kevin Mojarrad", - "author_inst": "WRAIR" - }, - { - "author_name": "Sheila A Peel", - "author_inst": "WRAIR" - }, - { - "author_name": "Elke S Bergmann-Leitner", - "author_inst": "WRAIR" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.23.21254201", "rel_title": "Toward Community Surveillance: Detecting Intact SARS-CoV-2 Using Exogeneous Oligonucleotide Labels", @@ -874608,6 +873146,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.25.21254326", + "rel_title": "Acute and longer-term psychological distress associated with testing positive for COVID-19: longitudinal evidence from a population-based study of US adults", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.25.21254326", + "rel_abs": "BackgroundThe novel coronavirus (SARS-CoV-2) has produced a considerable public health burden but the impact that contracting the disease has on mental health is unclear. In this observational population-based cohort study, we examined longitudinal changes in psychological distress associated with testing positive for COVID-19.\n\nMethodsParticipants (N = 8,002; Observations = 139,035) were drawn from 23 waves of the Understanding America Study, a nationally representative survey of American adults followed-up every two weeks from April 1 2020 to February 15 2021. Psychological distress was assessed using the standardized total score on the Patient Health Questionnaire-4 (PHQ-4).\n\nResultsOver the course of the study 576 participants reported testing positive for COVID-19. Using regression analysis including individual and time fixed effects we found that psychological distress increased by 0.29 standard deviations (p <.001) during the two-week period when participants first tested positive for COVID-19. Distress levels remained significantly elevated (d = 0.16, p <.01) for a further two weeks, before returning to baseline levels. Coronavirus symptom severity explained changes in distress attributable to COVID-19, whereby distress was more pronounced among those whose symptoms were more severe and were slower to subside.\n\nConclusionsThis study indicates that testing positive for COVID-19 is associated with an initial increase in psychological distress that diminishes quickly as symptoms subside. While COVID-19 may not produce lasting psychological distress among the majority of the general population it remains possible that a minority may suffer longer-term mental health consequences.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Michael Daly", + "author_inst": "Maynooth University" + }, + { + "author_name": "Eric Robinson", + "author_inst": "University of Liverpool" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2021.03.24.21254094", "rel_title": "Public Opinion about the UK Government during COVID-19 and Implications for Public Health: A Topic Modelling Analysis of Open-Ended Survey Response Data", @@ -875088,37 +873649,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2021.03.25.21254314", - "rel_title": "Automatic identification of risk factors for SARS-CoV-2 positivity and severe clinical outcomes of COVID-19 using Data Mining and Natural Language Processing", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.25.21254314", - "rel_abs": "ObjectivesSeveral risk factors have been identified for severe clinical outcomes of COVID-19 caused by SARS-CoV-2. Some can be found in structured data of patients Electronic Health Records. Others are included as unstructured free-text, and thus cannot be easily detected automatically. We propose an automated real-time detection of risk factors using a combination of data mining and Natural Language Processing (NLP).\n\nMaterial and methodsPatients were categorized as negative or positive for SARS-CoV-2, and according to disease severity (severe or non-severe COVID-19). Comorbidities were identified in the unstructured free-text using NLP. Further risk factors were taken from the structured data.\n\nResults6250 patients were analysed (5664 negative and 586 positive; 461 non-severe and 125 severe). Using NLP, comorbidities, i.e. cardiovascular and pulmonary conditions, diabetes, dementia and cancer, were automatically detected (error rate [≤]2%). Old age, male sex, higher BMI, arterial hypertension, chronic heart failure, coronary heart disease, COPD, diabetes, insulin only treatment of diabetic patients, reduced kidney and liver function were risk factors for severe COVID-19. Interestingly, the proportion of diabetic patients using metformin but not insulin was significantly higher in the non-severe COVID-19 cohort (p<0.05).\n\nDiscussion and conclusionOur findings were in line with previously reported risk factors for severe COVID-19. NLP in combination with other data mining approaches appears to be a suitable tool for the automated real-time detection of risk factors, which can be a time saving support for risk assessment and triage, especially in patients with long medical histories and multiple comorbidities.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Verena Schoening", - "author_inst": "University Hospital Bern" - }, - { - "author_name": "Evangelia Liakoni", - "author_inst": "University Hospital Bern" - }, - { - "author_name": "Juergen Drewe", - "author_inst": "University Hospital Basel" - }, - { - "author_name": "Felix Hammann", - "author_inst": "University Hospital Bern" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2021.03.25.21254375", "rel_title": "Predicting the Ophthalmic Surgical Backlog as a Result of the COVID-19 Pandemic: A population-based study and microsimulation model to inform surgical recovery plans", @@ -876210,6 +874740,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.26.21254259", + "rel_title": "Hemodialysis Patients Show a Highly Diminished Antibody Response after COVID-19 mRNA Vaccination Compared to Healthy Controls", + "rel_date": "2021-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.26.21254259", + "rel_abs": "1.1.1 Background and ObjectivesHemodialysis patients are prone to infection with SARS-COV2 and show a high probability of a severe course of disease and high mortality when infected. In many countries hemodialysis patients are prioritised in vaccination programs to protect this vulnerable community. However, no hemodialysis patients were included in efficacy trials of SARS CoV-2 vaccines and therefore efficacy and safety data for this patient group are lacking. These data would be critical, since hemodialysis patients showed decreased responses against various other vaccines and this could mean decreased response to SARS CoV-2 vaccines.\n\n1.2 Design, setting, participants, and measurementsWe conducted a prospective cohort study consisting of a group of 81 hemodialysis patients and 80 healthy controls who were vaccinated with mRNA vaccine BNT162b2 (BionTech/Pfizer, 2 doses with an interval of 21 days). Anti-SARS-COV-2 S antibody response in all participants was measured 21 days after the second dose. The groups were compared with univariate quantile regressions and a multiple analysis. Adverse events (AEs) of the vaccination were assessed with a standardized questionnaire. We also performed a correlation of HBs-Antibody response with the SARS-COV-2 antibody response in the hemodialysis patients.\n\n1.3 ResultsDialysis patients had significantly lower Anti-SARS-COV-2 S antibody titres than healthy control patients 21 days after vaccination with BNT162b2 (median dialysis Patients 171 U/ml versus median controls 2500 U/ml). Age also had a significant but less pronounced influence on antibody titres. Dialysis patients showed less AEs than the control group. No significant correlation was found for Hepatitis B vaccine antibody response and SARS CoV-2 vaccine antibody response.\n\n1.4 ConclusionsHemodialysis patients exhibit highly diminished SARS-COV-2 S antibody titres compared to a cohort of controls. Therefore these patients could be much less protected by SARS CoV-2 mRNA vaccination than expected. Alternative vaccination schemes must be considered and preventive measures must be maintained after vaccination.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Benedikt Simon", + "author_inst": "LKH Mistelbach" + }, + { + "author_name": "Harald Rubey", + "author_inst": "LK Mistelbach" + }, + { + "author_name": "Andreas Treipl", + "author_inst": "LK Mistelbach" + }, + { + "author_name": "Martin Gromann", + "author_inst": "LK Mistelbach" + }, + { + "author_name": "Boris Hemedi", + "author_inst": "LK Hainburg" + }, + { + "author_name": "Sonja Zehetmayer", + "author_inst": "Medical University of Vienna" + }, + { + "author_name": "Bernhard Kirsch", + "author_inst": "LK Mistelbach" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "nephrology" + }, { "rel_doi": "10.1101/2021.03.25.21253694", "rel_title": "From classic to rap: Airborne transmission of different singing styles, with respect to risk assessment of a SARS-CoV-2 infection", @@ -876566,49 +875139,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.24.21254254", - "rel_title": "Dental mitigation strategies to reduce aerosolization of SARS-CoV-2", - "rel_date": "2021-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.24.21254254", - "rel_abs": "Limiting infection transmission is central to the safety of all in dentistry, particularly during the current SARS-CoV-2 pandemic. Aerosol-generating procedures (AGPs) are crucial to the practise of dentistry; it is imperative to understand the inherent risks of viral dispersion associated with AGPs and the efficacy of available mitigation strategies.\n\nIn a dental surgery setting, crown preparation and root canal access procedures were performed with an air turbine or electric speed-controlled hand-piece, with mitigation via rubber dam or high-volume aspiration and a no mitigation control. A phantom head was used with a 1.5 mL flow of artificial saliva infected with {Phi}6 bacteriophage (a surrogate virus for SARS-CoV-2) at [~]108 plaque forming units mL-1, reflecting the upper limits of reported salivary SARS-CoV-2 levels. Bioaerosol dispersal was measured using agar settle plates lawned with the bacteriophages host, Pseudomonas syringae. Viral air concentrations were assessed using MicroBio MB2 air sampling, and particle quantities using Kanomax 3889 GEO particle counters.\n\nCompared to an air turbine, the electric hand-piece reduced settled bioaerosols by 99.72%, 100.00% and 100.00% for no mitigation, aspiration and rubber dam, respectively. Bacteriophage concentrations in the air were reduced by 99.98%, 100.00% and 100.00%, with the same mitigation strategies. Use of the electric hand-piece with high-volume aspiration, resulted in no detectable bacteriophage, both on settle plates and in air samples taken 6-10-minutes post-procedure.\n\nTo our knowledge, this study is the first to report the aerosolization of active virus as a marker for risk determination in the dental setting. Whilst this model represents a worst-case scenario for possible SARS-CoV-2 dispersal, these data showed that the use of electric hand-pieces can vastly reduce the risk of viral aerosolization, and therefore remove the need for clinic fallow time. Furthermore, our findings indicate that the use of particle analysis alone cannot provide sufficient insight to understand bioaerosol infection risk.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Jon J Vernon", - "author_inst": "University of Leeds" - }, - { - "author_name": "Emma V.I. Black", - "author_inst": "University of Leeds" - }, - { - "author_name": "Thomas Dennis", - "author_inst": "Leeds Dental Institute, Leeds Teaching Hospitals Trust" - }, - { - "author_name": "Deirdre A Devine", - "author_inst": "University of Leeds" - }, - { - "author_name": "Louise Fletcher", - "author_inst": "University of Leeds" - }, - { - "author_name": "David J Wood", - "author_inst": "University of Leeds" - }, - { - "author_name": "Brian R Nattress", - "author_inst": "University of Leeds" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "dentistry and oral medicine" - }, { "rel_doi": "10.1101/2021.03.26.21254327", "rel_title": "Prospective SARS-CoV-2 cohort study among general practitioners during the second COVID-19 wave in Flanders, Belgium", @@ -878048,6 +876578,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.24.436864", + "rel_title": "A public vaccine-induced human antibody protects against SARS-CoV-2 and emerging variants", + "rel_date": "2021-03-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.24.436864", + "rel_abs": "The emergence of antigenically distinct severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with increased transmissibility is a public health threat. Some of these variants show substantial resistance to neutralization by SARS-CoV-2 infection- or vaccination-induced antibodies, which principally target the receptor binding domain (RBD) on the virus spike glycoprotein. Here, we describe 2C08, a SARS-CoV-2 mRNA vaccine-induced germinal center B cell-derived human monoclonal antibody that binds to the receptor binding motif within the RBD. 2C08 broadly neutralizes SARS-CoV-2 variants with remarkable potency and reduces lung inflammation, viral load, and morbidity in hamsters challenged with either an ancestral SARS-CoV-2 strain or a recent variant of concern. Clonal analysis identified 2C08-like public clonotypes among B cell clones responding to SARS-CoV-2 infection or vaccination in at least 20 out of 78 individuals. Thus, 2C08-like antibodies can be readily induced by SARS-CoV-2 vaccines and mitigate resistance by circulating variants of concern.\n\nOne Sentence SummaryProtection against SARS-CoV-2 variants by a potently neutralizing vaccine-induced human monoclonal antibody.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Aaron J. Schmitz", + "author_inst": "Washington University School of Medicine in St. Louis" + }, + { + "author_name": "Jackson S. Turner", + "author_inst": "Washington University School of Medicine in St. Louis" + }, + { + "author_name": "Zhuoming Liu", + "author_inst": "Washington University School of Medicine in St. Louis" + }, + { + "author_name": "Ishmael D. Aziati", + "author_inst": "Washington University School of Medicine in St. Louis" + }, + { + "author_name": "Rita E. Chen", + "author_inst": "Washington University School of Medicine in St. Louis" + }, + { + "author_name": "Astha Joshi", + "author_inst": "Washington University School of Medicine in St. Louis" + }, + { + "author_name": "Traci L. Bricker", + "author_inst": "Washington University School of Medicine in St. Louis" + }, + { + "author_name": "Tamarand L. Darling", + "author_inst": "Washington University School of Medicine in St. Louis" + }, + { + "author_name": "Daniel C. Adelsberg", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Wafaa B. Al Soussi", + "author_inst": "Washington University School of Medicine in St. Louis" + }, + { + "author_name": "James Brett Case", + "author_inst": "Washington University School of Medicine in St. Louis" + }, + { + "author_name": "Tingting Lei", + "author_inst": "Washington University School of Medicine in St. Louis" + }, + { + "author_name": "Mahima Thapa", + "author_inst": "Washington University School of Medicine in St. Louis" + }, + { + "author_name": "Fatima Amanat", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Pei-Yong Shi", + "author_inst": "University of Texas Medical Branch at Galveston" + }, + { + "author_name": "Rachel M. Presti", + "author_inst": "Washington University School of Medicine in St. Louis" + }, + { + "author_name": "Florian Krammer", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Goran Bajic", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sean P.J. Whelan", + "author_inst": "Washington University School of Medicine in St. Louis" + }, + { + "author_name": "Michael S. Diamond", + "author_inst": "Washington University School of Medicine in St. Louis" + }, + { + "author_name": "Adrianus C.M. Boon", + "author_inst": "Washington University School of Medicine in St. Louis" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.03.24.436812", "rel_title": "Building alternative consensus trees and supertrees using k-means and Robinson and Foulds distance", @@ -878639,89 +877268,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2021.03.25.437046", - "rel_title": "Freely accessible ready to use global infrastructure for SARS-CoV-2 monitoring", - "rel_date": "2021-03-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.25.437046", - "rel_abs": "The COVID-19 pandemic is the first global health crisis to occur in the age of big genomic data.Although data generation capacity is well established and sufficiently standardized, analytical capacity is not. To establish analytical capacity it is necessary to pull together global computational resources and deliver the best open source tools and analysis workflows within a ready to use, universally accessible resource. Such a resource should not be controlled by a single research group, institution, or country. Instead it should be maintained by a community of users and developers who ensure that the system remains operational and populated with current tools. A community is also essential for facilitating the types of discourse needed to establish best analytical practices. Bringing together public computational research infrastructure from the USA, Europe, and Australia, we developed a distributed data analysis platform that accomplishes these goals. It is immediately accessible to anyone in the world and is designed for the analysis of rapidly growing collections of deep sequencing datasets. We demonstrate its utility by detecting allelic variants in high-quality existing SARS-CoV-2 sequencing datasets and by continuous reanalysis of COG-UK data. All workflows, data, and documentation is available at https://covid19.galaxyproject.org.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Wolfgang Maier", - "author_inst": "University of Freiburg" - }, - { - "author_name": "Simon Bray", - "author_inst": "University of Freiburg" - }, - { - "author_name": "Marius van den Beek", - "author_inst": "Penn State University" - }, - { - "author_name": "Dave Bouvier", - "author_inst": "Penn State University" - }, - { - "author_name": "Nathaniel Coraor", - "author_inst": "Penn State University" - }, - { - "author_name": "Milad Miladi", - "author_inst": "University of Freiburg" - }, - { - "author_name": "Babita Singh", - "author_inst": "Centre for Genomic Regulation" - }, - { - "author_name": "Jordi Rambla De Argila", - "author_inst": "Centre for Genomic Regulation" - }, - { - "author_name": "Dannon Baker", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Nathan Roach", - "author_inst": "GalaxyWorks, LLC" - }, - { - "author_name": "Simon Gladman", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Frederik Coppens", - "author_inst": "Ghent University" - }, - { - "author_name": "Darren Martin", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Andrew Lonie", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Bjorn Gruning", - "author_inst": "University of Freiburg" - }, - { - "author_name": "Sergei Kosakovsky Pond", - "author_inst": "Temple University" - }, - { - "author_name": "Anton Nekrutenko", - "author_inst": "Penn State University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.03.25.437060", "rel_title": "Sulforaphane exhibits in vitro and in vivo antiviral activity against pandemic SARS-CoV-2 and seasonal HCoV-OC43 coronaviruses", @@ -879821,6 +878367,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.16.21253669", + "rel_title": "The Case for Altruism in Institutional Diagnostic Testing", + "rel_date": "2021-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.16.21253669", + "rel_abs": "Amid COVID-19, many institutions deployed vast resources to test their members regularly for safe reopening. This self-focused approach, however, not only overlooks surrounding communities but also remains blind to community transmission that could breach the institution. To test the relative merits of a more altruistic strategy, we built an epidemiological model that assesses the differential impact on case counts when institutions instead allocate a proportion of their tests to members close contacts in the larger community. We found that testing outside the institution benefits the institution in all plausible circumstances, with the optimal proportion of tests to use externally landing at 45% under baseline model parameters. Our results were robust to local prevalence, secondary attack rate, testing capacity, and contact reporting level, yielding a range of optimal community testing proportions from 18% to 58%. The model performed best under the assumption that community contacts are known to the institution; however, it still demonstrated a significant benefit even without complete knowledge of the contact network.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Ivan Specht", + "author_inst": "The Broad Institute of MIT and Harvard; Harvard University" + }, + { + "author_name": "Kian Sani", + "author_inst": "The Broad Institute of MIT and Harvard; Harvard University" + }, + { + "author_name": "Yolanda Botti-Lodovico", + "author_inst": "The Broad Institute of MIT and Harvard; Howard Hughes Medical Institute" + }, + { + "author_name": "Michael Hughes", + "author_inst": "Colorado Mesa University" + }, + { + "author_name": "Kristin Heumann", + "author_inst": "Colorado Mesa University" + }, + { + "author_name": "Amy Bronson", + "author_inst": "Colorado Mesa University" + }, + { + "author_name": "John Marshall", + "author_inst": "Colorado Mesa University" + }, + { + "author_name": "Emily Baron", + "author_inst": "COVIDCheck Colorado" + }, + { + "author_name": "Eric Parrie", + "author_inst": "COVIDCheck Colorado" + }, + { + "author_name": "Olivia Glennon", + "author_inst": "Fathom Information Design" + }, + { + "author_name": "Ben Fry", + "author_inst": "Fathom Information Design" + }, + { + "author_name": "Andres Colubri", + "author_inst": "The Broad Institute of MIT and Harvard; Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School" + }, + { + "author_name": "Pardis C Sabeti", + "author_inst": "The Broad Institute or MIT and Harvard; Harvard University; Massachusetts Consortium on Pathogen Readiness; Howard Hughes Medical Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.14.21253554", "rel_title": "Improved Prediction of COVID-19 Transmission and Mortality Using Google Search Trends for Symptoms in the United States", @@ -880261,85 +878874,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.20.21253892", - "rel_title": "Intention of Healthcare Workers to Receive COVID-19 Vaccine: A Cross-Sectional Survey in 10 Countries in Eastern Mediterranean Region", - "rel_date": "2021-03-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.20.21253892", - "rel_abs": "BackgroundWillingness of healthcare workers to be vaccinated is an important factor to be consider for successful COVID-19 vaccination programme. Our study aimed to understand the willingness of health workers to receive COVID-19 vaccine and associated concerns across 10 countries in the Eastern Mediterranean Region (EMRO).\n\nMethodA cross-sectional study was conducted in January 2021 among healthcare workers using an online survey. A total of 2806 health workers (Physicians, Nurses and Pharmacists) completed and returned the informed consent along with the questionnaire electronically. Data were analyzed using IBM SPSS software package version 20.0. S\n\nResultsMore than half of the respondents (58.0%) were willing to receive COVID-19 vaccine, even if the vaccination is not mandatory for them. On the other hand, 25.7% of respondents were not willing to undertake COVID-19 vaccination while 16.3 % answered undecided. The top three reasons for not intending to be vaccinated were unreliability of COVID-19 vaccine clinical trials (62.0%), fear of the side effects of the vaccine (45.3%), and that COVID-19 vaccine will not give immunity for a long period of time (23.1%).\n\nConclusionOverall, our study revealed suboptimal acceptance of COVID-19 vaccine among our respondents in the EMRO region. Significant refusal of COVID-19 vaccine among healthcare professionals can reverse hard-won progress in building public trust in COVID-19 vaccination program. Our findings suggest the need to develop tailored strategies to address concerns identified in the study in order to ensure optimal vaccine acceptance among healthcare workers in the EMRO.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Yasir Ahmed Mohammed Elhadi", - "author_inst": "Department of Health Administration and Behavioral Sciences, High Institute of Public Health. Alexandria University, Alexandria, Egypt" - }, - { - "author_name": "Azza Mehanna", - "author_inst": "Department of Health Administration and Behavioral Sciences, High Institute of Public Health. Alexandria University, Alexandria, Egypt" - }, - { - "author_name": "Yusuff Adebayo Adebisi", - "author_inst": "University of Ibadan, Ibadan, Nigeria" - }, - { - "author_name": "Haider M El Saeh", - "author_inst": "Faculty of Medicine" - }, - { - "author_name": "Saddam Abdulhakeem Alnahari", - "author_inst": "Department of Health Administration and Behavioral Sciences, High Institute of Public Health. Alexandria University, Alexandria, Egypt" - }, - { - "author_name": "Omar Hassan Alenezi", - "author_inst": "Public Health Administration, Kuwait Ministry of Health, Kuwait" - }, - { - "author_name": "Diala El Chbib", - "author_inst": "Lebanese University, Faculty of Medical Sciences, Beirut, Lebanon" - }, - { - "author_name": "Zahraa Yahya", - "author_inst": "Department of Food Health and Nutrition, College of Food Science, Al-Qasim Green University, Babylon, Iraq." - }, - { - "author_name": "Eiman Ahmed", - "author_inst": "School of Global Public Health, New York University, New York, United States" - }, - { - "author_name": "Shoaib Ahmad", - "author_inst": "Punjab Medical College, Faisalabad, Pakistan" - }, - { - "author_name": "Saad Uakkas", - "author_inst": "Faculty of medicine, University Mohammed V, Rabat, Morocco" - }, - { - "author_name": "Majdi Mohammed Sabahelzain", - "author_inst": "Department of Public Health, School of Health Sciences, Ahfad University for Women, Sudan" - }, - { - "author_name": "Bushra Ahmed Alyamani", - "author_inst": "Department of Health Administration and Behavioral Sciences, High Institute of Public Health. Alexandria University, Alexandria, Egypt" - }, - { - "author_name": "Arash Nemat", - "author_inst": "Department of Microbiology, Kabul University of Medical Sciences, Kabul, Afghanistan" - }, - { - "author_name": "Don Eliseo Lucero-Prisno III", - "author_inst": "Department of Global health and Development, London School of Hygiene and Tropical Medicine, London, UK" - }, - { - "author_name": "Ashraf Zaghloul", - "author_inst": "Department of Health Administration and Behavioral Sciences, High Institute of Public Health. Alexandria University, Alexandria, Egypt" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.03.15.21253313", "rel_title": "Evaluation of the Panbio\u2122 COVID-19 Ag Rapid Test at an Emergency Room in a Hospital in Sao Paulo, Brazil", @@ -881421,6 +879955,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.23.21254203", + "rel_title": "Evaluation of the ROX index in SARS-CoV-2 Acute Respiratory failure treated with both High-Flow Nasal Oxygen (HFNO) and Continuous Positive Airway Pressure (CPAP)", + "rel_date": "2021-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.23.21254203", + "rel_abs": "BackgroundNon-invasive respiratory support including high-flow nasal oxygen (HFNO), and continuous positive airway pressure (CPAP) have been used to provide therapy in selected SARS-CoV-2 patients with acute respiratory failure (ARF). The value of the ROX index, a validated benchmark for outcomes in HFNO is unknown in CPAP.\n\nObjectiveCan the ROX, a validated benchmark in HFNO be used for measuring treatment outcomes of CPAP in SARS-COV-2 ARF?\n\nStudy Design and MethodsA non-randomised prospective protocol driven observational non-intensive care unit study in 130 SARS-COV-2 patients with ARF treated with non-invasive therapy from March 2020 to January 2021. The primary end point was failure of therapy (death or escalation). Secondary outcomes included time to failure including invasive mechanical ventilation (IMV) or death, the effect of escalation to CPAP from HFNO and the utility of ROX in ARF.\n\nResultsHFNO was better than CPAP in treating SARS-COV-2 ARF: 17/35 (48.5%) with successful HFNO therapy versus 24/95 (25.2%) with CPAP. The ROX index was more sensitive to outcomes with CPAP compared to HFNO and distinguished treatment failure early at 1, 4, 6, 12, and 24 hours with the highest sensitivity at 24 hours (ROX-24h). The AUC for the ROX-24h was 0.77 for HFNO (P<0.0001), and 0.84 for CPAP (P<0.0001). The ROX-24h cut-points predicted failure with HFNO when < 3.9 (PPV 71%, NPV 75%) and CPAP < 4.3 (PPV 75%, NPV 91%). For success, ROX-24h cut-points of 7.6 for HFNO (PPV 85%, NPV 48%) and 6.1 for CPAP (PPV 88%, NPV 62%) were observed. Escalation from HFNO to CPAP was mostly not successful.\n\nConclusionARF in SARS-COV-2 can be successfully managed by non-invasive support. The ROX index, validated for HFNO, provides a timely, low resource measure for both HFNO and CPAP avoiding delayed intubation.\n\nTrial registrationStudy approved by NHS HRAREC (20/HRA/2344;ethics 283888)\n\nKEY MESSAGEO_ST_ABSWhat is the key question?C_ST_ABSCan the ROX, a validated benchmark in high-flow nasal oxygen (HFNO) be used for measuring treatment outcomes of continuous positive airway pressure (CPAP) in SARS-COV-2 ARF?\n\nWhat is the bottom line?The ROX index, validated for HFNO, provides a timely, low resource measure for both HFNO and CPAP support avoiding delayed intubation.\n\nWhy read on?The present study compares the efficacy of HFNO and CPAP, two common globally used modalities of treatment for SARS-CoV-2 and notes the superior utility of the ROX-24h in CPAP to predict outcome, enabling timely escalation decisions.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Hakim Ghani", + "author_inst": "West Herts NHS Trust" + }, + { + "author_name": "Michael Shaw", + "author_inst": "West Herts NHS Trust" + }, + { + "author_name": "Phyoe Pyae", + "author_inst": "West Herts NHS Trust" + }, + { + "author_name": "Rigers Cama", + "author_inst": "West Herts NHS Trust" + }, + { + "author_name": "Meghna Prabhakar", + "author_inst": "West Herts NHS Trust" + }, + { + "author_name": "Alessio Navarra", + "author_inst": "West Herts NHS Trust" + }, + { + "author_name": "Janice Yu Ji Lee", + "author_inst": "Addenbrookes Hospital, Cambridge" + }, + { + "author_name": "Felix Chua", + "author_inst": "Royal Brompton & Harefield NHS Foundation Trust" + }, + { + "author_name": "Rahul Mogal", + "author_inst": "West Herts NHS Trust" + }, + { + "author_name": "Andrew Barlow", + "author_inst": "West Herts NHS Trust" + }, + { + "author_name": "Nazril Nordin", + "author_inst": "West Herts NHS Trust" + }, + { + "author_name": "Rama Vancheeswaran", + "author_inst": "West Herts NHS Trust" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2021.03.23.21254165", "rel_title": "Introducing the 4Ps Model of Transitioning to Distance Learning: a convergent mixed methods study conducted during the COVID-19 pandemic.", @@ -881929,45 +880526,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "endocrinology" }, - { - "rel_doi": "10.1101/2021.03.16.21253652", - "rel_title": "Within-Day Variability of SARS-CoV-2 RNA in Municipal Wastewater Influent During Periods of Varying COVID-19 Prevalence and Positivity", - "rel_date": "2021-03-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.16.21253652", - "rel_abs": "Wastewater surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA is being used to monitor Coronavirus Disease 2019 (COVID-19) trends in communities; however, within-day variation in primary influent concentrations of SARS-CoV-2 RNA remain largely uncharacterized. In the current study, grab sampling of primary influent was performed every 2 hours over two different 24-hour periods at two wastewater treatment plants (WWTPs) in northern Indiana, USA. In primary influent, uncorrected, recovery-corrected, and pepper mild mottle virus (PMMoV)-normalized SARS-CoV-2 RNA concentrations demonstrated ordinal agreement with increasing clinical COVID-19 positivity, but not COVID-19 cases. Primary influent SARS-CoV-2 RNA concentrations exhibited greater variation than PMMoV RNA concentrations as expected for lower shedding prevalence. The bovine respiratory syncytial virus (BRSV) process control recovery efficiency was low (mean: 0.91%) and highly variable (coefficient of variation: 51% - 206%) over the four sampling events with significant differences between the two WWTPs (p <0.0001). The process control recovery was similar to the independently assessed SARS-CoV-2 RNA recovery efficiency, which was also significantly different between the two WWTPs (p <0.0001). Recovery-corrected SARS-CoV-2 RNA concentrations better reflected within-day changes in primary influent flow rate and fecal content, as indicated by PMMoV concentrations. These observations highlight the importance of assessing the process recovery efficiency, which is highly variable, using an appropriate process control. Despite large variations, both recovery-corrected and PMMoV-normalized SARS-CoV-2 RNA concentrations in primary influent demonstrate potential for monitoring COVID-19 positivity trends in WWTPs serving peri-urban and rural areas.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Aaron Bivins", - "author_inst": "Ohio State University" - }, - { - "author_name": "Devin North", - "author_inst": "University of Notre Dame" - }, - { - "author_name": "Zhenyu Wu", - "author_inst": "University of Notre Dame" - }, - { - "author_name": "Marlee Shaffer", - "author_inst": "University of Notre Dame" - }, - { - "author_name": "Warish Ahmed", - "author_inst": "CSIRO" - }, - { - "author_name": "Kyle James Bibby", - "author_inst": "University of Notre Dame" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.17.21253626", "rel_title": "A SIRD model applied to COVID-19 dynamics and intervention strategies during the first wave in Kenya", @@ -883347,6 +881905,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.16.21253377", + "rel_title": "First and second SARS-CoV-2 waves in inner London: A comparison of admission characteristics and the effects of the B.1.1.7 variant", + "rel_date": "2021-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.16.21253377", + "rel_abs": "IntroductionA second wave of SARS-CoV-2 infection spread across the UK in 2020 linked with emergence of the more transmissible B.1.1.7 variant. The emergence of new variants, particularly during relaxation of social distancing policies and implementation of mass vaccination, highlights the need for real-time integration of detailed patient clinical data alongside pathogen genomic data. We linked clinical data with viral genome sequence data to compare cases admitted during the first and second waves of SARS-CoV-2 infection.\n\nMethodsClinical, laboratory and demographic data from five electronic health record (EHR) systems was collected for all cases with a positive SARS-CoV-2 RNA test between March 13th 2020 and February 17th 2021. SARS-CoV-2 viral sequencing was performed using Oxford Nanopore Technology. Descriptive data are presented comparing cases between waves, and between cases of B.1.1.7 and non-B.1.1.7 variants.\n\nResultsThere were 5810 SARS-CoV-2 RNA positive cases comprising inpatients (n=2341), healthcare workers (n=1549), outpatients (n=874), emergency department (ED) attenders not subsequently admitted (n=532), inter-hospital transfers (n=281) and nosocomial cases (n=233). There were two dominant waves of hospital admissions, with wave one starting from March 13th (n=838) and wave two from October 20th (n=1503), both with a temporally aligned rise in nosocomial cases (n=96 in wave one, n=137 in wave two). 1470 SARS-CoV-2 isolates were successfully sequenced, including 216/838 (26%) admitted cases from wave one, 472/1503 (31%) admitted cases in wave two and 121/233 (52%) nosocomial cases. The first B.1.1.7 variant was identified on 15th November 2020 and increased rapidly such that it comprised 400/472 (85%) of sequenced isolates from admitted cases in wave two. Females made up a larger proportion of admitted cases in wave two (47.3% vs 41.8%, p=0.011), and in those infected with the B.1.1.7 variant compared to non-B.1.1.7 variants (48.0% vs 41.8%, p=0.042). A diagnosis of frailty was less common in wave two (11.5% v 22.8%, p<0.001) and in the group infected with B.1.1.7 (14.5% v 22.4%, p=0.001). There was no difference in severity on admission between waves, as measured by hypoxia at admission (wave one: 64.3% vs wave two: 65.5%, p=0.67). However, a higher proportion of cases infected with the B.1.1.7 variant were hypoxic on admission compared to other variants (70.0% vs 62.5%, p=0.029).\n\nConclusionsAutomated EHR data extraction linked with SARS-CoV-2 genome sequence data provides valuable insight into the evolving characteristics of cases admitted to hospital with COVID-19. The proportion of cases with hypoxia on admission was greater in those infected with the B.1.1.7 variant, which supports evidence the B.1.1.7 variant is associated with more severe disease. The number of nosocomial cases was similar in both waves despite introduction of many infection control interventions before wave two, an observation requiring further investigation.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Luke B Snell", + "author_inst": "King's College London" + }, + { + "author_name": "Wenjuan Wang", + "author_inst": "School of Population Health and Environmental Sciences, King's College London, London, UK" + }, + { + "author_name": "Adela Alcolea-Medina", + "author_inst": "Viapath, London, UK" + }, + { + "author_name": "Themoula Charalampous", + "author_inst": "Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK" + }, + { + "author_name": "Gaia Nebbia", + "author_inst": "Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK" + }, + { + "author_name": "Rahul Batra", + "author_inst": "Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK" + }, + { + "author_name": "Leonardo de Jongh", + "author_inst": "NIHR Biomedical Research Centre, Guy's and St Thomas' NHS Foundation Trust" + }, + { + "author_name": "Finola Higgins", + "author_inst": "NIHR Biomedical Research Centre, Guy's and St Thomas' NHS Foundation Trust" + }, + { + "author_name": "Yanzhong Wang", + "author_inst": "School of Population Health and Environmental Sciences, King's College London, London, UK" + }, + { + "author_name": "Jonathan D Edgeworth", + "author_inst": "Centre for Clinical Infection and Diagnostics Research, School of Immunology and Microbial Sciences, King's College London, London, UK" + }, + { + "author_name": "Vasa Curcin", + "author_inst": "School of Population Health and Environmental Sciences, King's College London, London, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.14.21253557", "rel_title": "Mortality and Severity in COVID-19 Patients on ACEIs & ARBs - A Meta-Regression Analysis", @@ -883859,33 +882476,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.21.21254068", - "rel_title": "Determinants of COVID-19 outcomes: A systematic review.", - "rel_date": "2021-03-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.21.21254068", - "rel_abs": "BackgroundThe current pandemic, COVID-19, caused by a novel coronavirus SARS-CoV-2, has claimed over a million lives worldwide in a year, warranting the need for more research into the wider determinants of COVID-19 outcomes to support evidence-based policies.\n\nObjectiveThis study aimed to investigate what factors determined the mortality and length of hospitalisation in individuals with COVID-19.\n\nData SourceThis is a systematic review with data from four electronic databases: Scopus, Google Scholar, CINAHL and Web of Science.\n\nEligibility CriteriaStudies were included in this review if they explored determinants of COVID-19 mortality or length of hospitalisation, were written in the English Language, and had available full-text.\n\nStudy appraisal and data synthesisThe authors assessed the quality of the included studies with the Newcastle{square}Ottawa Scale and the Agency for Healthcare Research and Quality checklist, depending on their study design. Risk of bias in the included studies was assessed with risk of bias assessment tool for non-randomised studies. A narrative synthesis of the evidence was carried out. The review methods were informed by the Joana Briggs Institute guideline for systematic reviews.\n\nResultsThe review included 22 studies from nine countries, with participants totalling 239,830. The included studies quality was moderate to high. The identified determinants were categorised into demographic, biological, socioeconomic and lifestyle risk factors, based on the Dahlgren and Whitehead determinant of health model. Increasing age (ORs 1.04-20.6, 95%CIs 1.01-22.68) was the common demographic determinant of COVID-19 mortality while living with diabetes (ORs 0.50-3.2, 95%CIs -0.2-0.74) was one of the most common biological determinants of COVID-19 length of hospitalisation.\n\nReview limitationMeta-analysis was not conducted because of included studies heterogeneity.\n\nConclusionCOVID-19 outcomes are predicted by multiple determinants, with increasing age and living with diabetes being the most common risk factors. Population-level policies that prioritise interventions for the elderly population and the people living with diabetes may help mitigate the outbreaks impact.\n\nPROSPERO registration numberCRD42021237063.\n\nStrength and limitations of this reviewO_LIThis is the first systematic review synthesising the evidence on determinants of COVID-19 LOS outcome.\nC_LIO_LIIt is also the first review to provide a comprehensive investigation of contextual determinants of COVID-19 outcomes, based on the determinants of health model; thus, presenting with crucial gaps in the literature on the determinants of COVID-19 outcomes that require urgent attention.\nC_LIO_LIThe review was restricted in conducting meta-analysis due to included studies heterogeneity.\nC_LIO_LIThe review focused on only papers published in the English Language; hence, other relevant papers written on other languages could have been omitted.\nC_LI", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Shirley Crankson", - "author_inst": "Brunel University London" - }, - { - "author_name": "Subhash Pokhrel", - "author_inst": "Brunel University London" - }, - { - "author_name": "Nana Kwame Anokye", - "author_inst": "Brunel University London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.03.19.21253005", "rel_title": "Corticosteroids and mortality in patients with severe Covid-19 who have autoantibodies", @@ -885549,6 +884139,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.19.21251426", + "rel_title": "T-cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibody titers and disease severity", + "rel_date": "2021-03-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21251426", + "rel_abs": "Measuring the adaptive immune response to SARS-CoV-2 can enable the assessment of past infection as well as protective immunity and the risk of reinfection. While neutralizing antibody (nAb) titers are one measure of protection, such assays are challenging to perform at a large scale and the longevity of the SARS-CoV-2 nAb response is not fully understood. Here, we apply a T-cell receptor (TCR) sequencing assay that can be performed on a small volume standard blood sample to assess the adaptive T-cell response to SARS-CoV-2 infection. Samples were collected from a cohort of 302 individuals recovered from COVID-19 up to 6 months after infection. Previously published findings in this cohort showed that two commercially available SARS-CoV-2 serologic assays correlate well with nAb testing. We demonstrate that the magnitude of the SARS-CoV-2-specific T-cell response strongly correlates with nAb titer, as well as clinical indicators of disease severity including hospitalization, fever, or difficulty breathing. While the depth and breadth of the T-cell response declines during convalescence, the T-cell signal remains well above background with high sensitivity up to at least 6 months following initial infection. Compared to serology tests detecting binding antibodies to SARS-CoV-2 spike and nucleoprotein, the overall sensitivity of the TCR-based assay across the entire cohort and all timepoints was approximately 5% greater for identifying prior SARS-CoV-2 infection. Notably, the improved performance of T-cell testing compared to serology was most apparent in recovered individuals who were not hospitalized and were sampled beyond 150 days of their initial illness, suggesting that antibody testing may have reduced sensitivity in individuals who experienced less severe COVID-19 illness and at later timepoints. Finally, T-cell testing was able to identify SARS-CoV-2 infection in 68% (55/81) of convalescent samples having nAb titers below the lower limit of detection, as well as 37% (13/35) of samples testing negative by all three antibody assays. These results demonstrate the utility of a TCR-based assay as a scalable, reliable measure of past SARS-CoV-2 infection across a spectrum of disease severity. Additionally, the TCR repertoire may be useful as a surrogate for protective immunity with additive clinical value beyond serologic or nAb testing methods.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Rebecca Elyanow", + "author_inst": "Adaptive Biotechnologies, Seattle, Washington, USA" + }, + { + "author_name": "Thomas M. Snyder", + "author_inst": "Adaptive Biotechnologies, Seattle, Washington, USA" + }, + { + "author_name": "Sudeb C. Dalai", + "author_inst": "Adaptive Biotechnologies, Seattle, Washington, USA; and Stanford University School of Medicine, Stanford, California, USA" + }, + { + "author_name": "Rachel M. Gittelman", + "author_inst": "Adaptive Biotechnologies, Seattle, Washington, USA" + }, + { + "author_name": "Jim Boonyaratanakornkit", + "author_inst": "Department of Medicine, University of Washington, Seattle, Washington, USA, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA" + }, + { + "author_name": "Anna Wald", + "author_inst": "Department of Medicine, University of Washington, Seattle, Washington, USA; Fred Hutchinson Cancer Research Center, Seattle, Washington, USA; Department of Epid" + }, + { + "author_name": "Stacy Selke", + "author_inst": "Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA" + }, + { + "author_name": "Mark H. Wener", + "author_inst": "Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA" + }, + { + "author_name": "Chihiro Morishima", + "author_inst": "Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA" + }, + { + "author_name": "Alex L. Greninger", + "author_inst": "Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA" + }, + { + "author_name": "Michael R. Holbrook", + "author_inst": "National Institute of Allergy and Infectious Diseases Integrated Research Facility, Frederick, Maryland, USA" + }, + { + "author_name": "Ian M. Kaplan", + "author_inst": "Adaptive Biotechnologies, Seattle, Washington, USA" + }, + { + "author_name": "H. Jabran Zahid", + "author_inst": "Microsoft Research, Redmond, Washington, USA" + }, + { + "author_name": "Jonathan M. Carlson", + "author_inst": "Microsoft Research, Redmond, Washington, USA" + }, + { + "author_name": "Lance Baldo", + "author_inst": "Adaptive Biotechnologies, Seattle, Washington, USA" + }, + { + "author_name": "Thomas Manley", + "author_inst": "Adaptive Biotechnologies, Seattle, Washington, USA" + }, + { + "author_name": "Harlan S. Robins", + "author_inst": "Adaptive Biotechnologies, Seattle, Washington, USA" + }, + { + "author_name": "David M. Koelle", + "author_inst": "Department of Medicine, University of Washington, Seattle, Washington, USA; Fred Hutchinson Cancer Research Center, Seattle, Washington, USA; Department of Labo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.20.21253976", "rel_title": "Weekly SARS-CoV-2 screening of asymptomatic students and staff to guide and evaluate strategies for safer in-person learning", @@ -885905,25 +884582,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.21.21254048", - "rel_title": "Factors informing healthcare workers' willingness to work during the COVID-19 pandemic", - "rel_date": "2021-03-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.21.21254048", - "rel_abs": "ObjectiveThe COVID-19 pandemic represents a substantial challenge to healthcare workers. Exploring the determinants of their willingness to work is crucial to ensuring hospital function during the outbreak. Hence, this study examines the factors affecting the motivation and hesitation of health workers in the face of the COVID-19 pandemic in Poland.\n\nStudy DesignAn online, anonymous survey was carried out among Polish healthcare workers during the COVID-19 pandemic.\n\nMethodThe respondents were asked about their demographic characteristics, stress-related factors, and their self-reported motivation and hesitation to work. The responses were gathered during September-December 2020.\n\nResults912 valid responses were obtained. Of these, 22.8% (N = 208) respondents reported being strongly motivated to work while 37.8% (N = 345) expressed strong hesitation. The participants demographic characteristics and their responses to the stress-related questions were assigned to four categories depending on the odds ratios of motivation and hesitation. While some factors were linked to enhanced motivation and reduced hesitation, others solely affected either motivation or hesitation, and yet others had a positive impact on both.\n\nConclusionOverall, the study indicates that in order to increase hospital workers motivation and decrease their hesitation, they must be made to feel protected by both their hospitals and local and national authorities.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Marta Malesza", - "author_inst": "University of Economics and Human Sciences in Warsaw" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.03.19.21253958", "rel_title": "Job stress among workers who telecommute during the coronavirus disease (COVID-19) pandemic in Japan: a cross-sectional study", @@ -887299,6 +885957,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2021.03.11.21253275", + "rel_title": "Effect of vaccination on transmission of COVID-19: an observational study in healthcare workers and their households", + "rel_date": "2021-03-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.11.21253275", + "rel_abs": "BackgroundThe effect of vaccination for COVID-19 on onward transmission is unknown.\n\nMethodsA national record linkage study determined documented COVID-19 cases and hospitalisations in unvaccinated household members of vaccinated and unvaccinated healthcare workers from 8th December 2020 to 3rd March 2021. The primary endpoint was COVID-19 14 days following the first dose.\n\nResultsThe cohort comprised of 194,362 household members (mean age 31{middle dot}1 {+/-} 20{middle dot}9 years) and 144,525 healthcare workers (mean age 44{middle dot}4 {+/-} 11{middle dot}4 years). 113,253 (78{middle dot}3%) of healthcare workers received at least one dose of the BNT162b2 mRNA or ChAdOx1 nCoV-19 vaccine and 36,227 (25{middle dot}1%) received a second dose. There were 3,123 and 4,343 documented COVID-19 cases and 175 and 177 COVID-19 hospitalisations in household members of healthcare workers and healthcare workers respectively. Household members of vaccinated healthcare workers had a lower risk of COVID-19 case compared to household members of unvaccinated healthcare worker (rate per 100 person-years 9{middle dot}40 versus 5{middle dot}93; HR 0{middle dot}70, 95% confidence interval [CI] 0{middle dot}63 to 0{middle dot}78). The effect size for COVID-19 hospitalisation was similar, with the confidence interval crossing the null (HR 0{middle dot}77 [95% CI 0{middle dot}53 to 1{middle dot}10]). The rate per 100 person years was lower in vaccinated compared to unvaccinated healthcare workers for documented (20{middle dot}13 versus 8{middle dot}51; HR 0{middle dot}45 [95% CI 0{middle dot}42 to 0{middle dot}49]) and hospitalized COVID-19 (0{middle dot}97 versus 0{middle dot}14; HR 0{middle dot}16 [95% CI 0{middle dot}09 to 0{middle dot}27]). Compared to the period before the first dose, the risk of documented COVID-19 case was lower at [≥] 14 days after the second dose for household members (HR 0{middle dot}46 [95% CI 0{middle dot}30to 0{middle dot}70]) and healthcare workers (HR 0{middle dot}08 [95% CI 0{middle dot}04 to 0{middle dot}17]).\n\nInterpretationVaccination of health care workers was associated with a substantial reduction in COVID-19 cases in household contacts consistent with an effect of vaccination on transmission.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Anoop Shah", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Ciara Gribben", + "author_inst": "Public Health Scotland" + }, + { + "author_name": "Jennifer Bishop", + "author_inst": "Public Health Scotland" + }, + { + "author_name": "Peter Hanlon", + "author_inst": "University of Glasgow" + }, + { + "author_name": "David Caldwell", + "author_inst": "Public Health Scotland" + }, + { + "author_name": "Rachael Wood", + "author_inst": "PublicHealth Scotland" + }, + { + "author_name": "Martin Reid", + "author_inst": "Public Health Scotland" + }, + { + "author_name": "Jim McMenamin", + "author_inst": "Public Health Scotland" + }, + { + "author_name": "David Goldberg", + "author_inst": "Public Health Scotland" + }, + { + "author_name": "Diane Stockton", + "author_inst": "Public Health Scotland" + }, + { + "author_name": "Sharon Hutchinson", + "author_inst": "Public Health Scotland" + }, + { + "author_name": "Chris Robertson", + "author_inst": "Public Health Scotland" + }, + { + "author_name": "Paul M McKeigue", + "author_inst": "Public Health Scotland" + }, + { + "author_name": "Helen M Colhoun", + "author_inst": "Public Health Scotland" + }, + { + "author_name": "David McAllister", + "author_inst": "University of Glasgow" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.03.20.436243", "rel_title": "A bispecific monomeric nanobody induces SARS-COV-2 spike trimer dimers", @@ -887843,213 +886576,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2021.03.18.21253881", - "rel_title": "A Prospective Study of Long-Term Outcomes Among Hospitalized COVID-19 Patients with and without Neurological Complications", - "rel_date": "2021-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.18.21253881", - "rel_abs": "BackgroundLittle is known regarding long-term outcomes of patients hospitalized with COVID-19.\n\nMethodsWe conducted a prospective study of 6-month outcomes of hospitalized COVID-19 patients. Patients with new neurological complications during hospitalization who survived were propensity score-matched to COVID-19 survivors without neurological complications hospitalized during the same period. The primary 6-month outcome was multivariable ordinal analysis of the modified Rankin Scale(mRS) comparing patients with or without neurological complications. Secondary outcomes included: activities of daily living (ADLs;Barthel Index), telephone Montreal Cognitive Assessment and Neuro-QoL batteries for anxiety, depression, fatigue and sleep.\n\nResultsOf 606 COVID-19 patients with neurological complications, 395 survived hospitalization and were matched to 395 controls; N=196 neurological patients and N=186 controls completed follow-up. Overall, 346/382 (91%) patients had at least one abnormal outcome: 56% had limited ADLs, 50% impaired cognition, 47% could not return to work and 62% scored worse than average on [≥]1 Neuro-QoL scale (worse anxiety 46%, sleep 38%, fatigue 36%, and depression 25%). In multivariable analysis, patients with neurological complications had worse 6-month mRS (median 4 vs. 3 among controls, adjusted OR 2.03, 95%CI 1.22-3.40, P=0.01), worse ADLs (aOR 0.38, 95%CI 0.29-0.74, P=0.01) and were less likely to return to work than controls (41% versus 64%, P=0.04). Cognitive and Neuro-QOL metrics were similar between groups.\n\nConclusionsAbnormalities in functional outcomes, ADLs, anxiety, depression and sleep occurred in over 90% of patients 6-months after hospitalization for COVID-19. In multivariable analysis, patients with neurological complications during index hospitalization had significantly worse 6-month functional outcomes than those without.", - "rel_num_authors": 48, - "rel_authors": [ - { - "author_name": "Jennifer A. Frontera", - "author_inst": "NYU Grossman School of Medicine" - }, - { - "author_name": "Dixon Yang", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Ariane Lewis", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Palak Patel", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Chaitanya Medicherla", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Vito Arena", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Taolin Fang", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Andres Andino", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Thomas Snyder", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Maya Madhavan", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Daniel Gratch", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Benjamin Fuchs", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Alexa Dessy", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Melanie Canizares", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Ruben Jauregui", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Betsy Thomas", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Kristie Bauman", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Anlys Olivera", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Dhristie Bhagat", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Michael Sonson", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "George Park", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Rebecca Stainman", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Brian Sunwoo", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Daniel Talmasov", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Michael Tamimi", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Yingrong Zhu", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Jonathan Rosenthal", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Levi Dygert", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Milan Rustic", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Haruki Ishii", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Eduard Valdes", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Mirza Omari", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Lindsey Gurin", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Joshua Huang", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Barry M Czseiler", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "D. Ethan Kahn", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Ting Zhou", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Jessica Lin", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Aaron Lord", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Kara Melmed", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Sharon Meropol", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Andrea Troxel", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Eva Petkova", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Thomas Wisniewski", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Laura Balcer", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Chris Morrison", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Shadi Yaghi", - "author_inst": "NYU Langone Hospitals" - }, - { - "author_name": "Steven Galetta", - "author_inst": "NYU Langone Hospitals" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.18.21253907", "rel_title": "Integrated immunovirological profiling validates plasma SARS-CoV-2 RNA as an early predictor of COVID-19 mortality", @@ -889401,6 +887927,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.19.21253982", + "rel_title": "Low levels of protective humoral immunity following mild or asymptomatic infection with SARS-CoV-2 in a community-based serological study", + "rel_date": "2021-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.19.21253982", + "rel_abs": "The degree of protective humoral immunity after mild or asymptomatic SARS-CoV-2 infection is not known. We measured antibody-mediated neutralization of spike protein-ACE2 receptor binding--a surrogate measure of protection against SARS-CoV-2 infection--in a large and diverse community-based seroprevalence study. Comparisons were made across three groups of seropositive participants that differed in the severity of infection and engagement with clinical care (N=790). The clinical group was seropositive for prior infection, symptomatic, and diagnosed with COVID-19 by a healthcare provider. The symptomatic group was seropositive and reported one or more symptoms of infection but received no clinical care. The asymptomatic group was seropositive but reported no symptoms. 86.2% of all infections were mild or asymptomatic; 13.8% received clinical care. Of the clinical cases, 96.3% were outpatient; only 3.7% required hospitalization. Moderate or high levels of neutralizing activity were detected following 27.5% of clinical infections, in comparison with 5.4% of symptomatic and 1.5% of asymptomatic infections. The majority of infections in the general population are mild or asymptomatic and likely result in low levels of antibody-mediated protective immunity.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Thomas W. McDade", + "author_inst": "Northwestern University" + }, + { + "author_name": "Amelia Sancilio", + "author_inst": "Northwestern University" + }, + { + "author_name": "Richard T. D'Aquila", + "author_inst": "Northwestern University" + }, + { + "author_name": "Brian Mustanski", + "author_inst": "Northwestern University" + }, + { + "author_name": "Lauren A. Vaught", + "author_inst": "Northwestern University" + }, + { + "author_name": "Nina L. Reiser", + "author_inst": "Northwestern University" + }, + { + "author_name": "Matt P. Velez", + "author_inst": "Northwestern University" + }, + { + "author_name": "Ryan R. Hsieh", + "author_inst": "Northwestern University" + }, + { + "author_name": "Daniel T. Ryan", + "author_inst": "Northwestern University" + }, + { + "author_name": "Rana Saber", + "author_inst": "Northwestern University" + }, + { + "author_name": "Elizabeth M. McNally", + "author_inst": "Northwestern University" + }, + { + "author_name": "Alexis R. Demonbreun", + "author_inst": "Northwestern University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.19.21254004", "rel_title": "Heterogeneous immunological recovery trajectories revealed in post-acute COVID-19", @@ -890349,25 +888938,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.18.21253931", - "rel_title": "A convergence based assessment of relative differences in age-stratified susceptibility and infectiousness for SARS-CoV-2 variants of B.1.1.7 lineage", - "rel_date": "2021-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.18.21253931", - "rel_abs": "We propose (a) a method for aggregating and processing age-stratified subregional time series data for positive tests of infection given partial sampling for variant-of-concern biomarkers, and (b) a simple model-based theoretical framework for interpreting these processed data, to assess whether observed heterogeneity in age-specific relative differences can be explained by environmental effects alone.\n\nWe then apply this strategy to public-domain subregional time series data with S-gene target failure (SGTF) sampling as a proxy for B.1.1.7 lineage, from weeks 45 to 50 of 2020 from England. For the time period in question, we observe convergence toward a 1.27 (95% CI 1.17-1.38) times higher ratio of SGTF to non-SGTF infection for 0-9-year-olds than for the total population, and a 1.16 (95% CI 1.09-1.23) times higher ratio for 10-19-year-olds. These are roughly comparable to previous findings, but this time we find high-significance evidence for adequate compatibility with our proposed modelling framework criteria to conclude that these relative elevations for 0-19-year-olds are very unlikely to be explained by environmental effects alone. We also find possible indications that 0-19-year-olds might experience a higher relative increase in infectiousness than susceptibility for B.1.1.7.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Sarah Dean Rasmussen", - "author_inst": "University of Cambridge" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.19.21253883", "rel_title": "Prevalence and determinants of serum antibodies to SARS-CoV-2 in the general population of the Gardena Valley", @@ -891463,6 +890033,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2021.03.18.21253443", + "rel_title": "Intensity of COVID-19 in care homes following Hospital Discharge in the early stages of the UK epidemic", + "rel_date": "2021-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.18.21253443", + "rel_abs": "BackgroundA defining feature of the COVID-19 pandemic in many countries was the tragic extent to which care home residents were affected, and the difficulty preventing introduction and subsequent spread of infection. Management of risk in care homes requires good evidence on the most important transmission pathways. One hypothesised route at the start of the pandemic, prior to widespread testing, was transfer of patients from hospitals, which were experiencing high levels of nosocomial events.\n\nMethodsWe tested the hypothesis that hospital discharge events increased the intensity of care home cases using a national individually linked health record cohort in Wales, UK. We monitored 186,772 hospital discharge events over the period March to July 2020, tracking individuals to 923 care homes and recording the daily case rate in the homes populated by 15,772 residents. We estimated the risk of an increase in cases rates following exposure to a hospital discharge using multi-level hierarchical logistic regression, and a novel stochastic Hawkes process outbreak model.\n\nFindingsIn regression analysis, after adjusting for care home size, we found no significant association between hospital discharge and subsequent increases in care home case numbers (odds ratio: 0.99, 95% CI 0.82, 1.90). Risk factors for increased cases included care home size, care home resident density, and provision of nursing care. Using our outbreak model, we found a significant effect of hospital discharge on the subsequent intensity of cases. However, the effect was small, and considerably less than the effect of care home size, suggesting the highest risk of introduction came from interaction with the community. We estimated approximately 1.8% of hospital discharged patients may have been infected.\n\nInterpretationThere is growing evidence in the UK that the risk of transfer of COVID-19 from the high-risk hospital setting to the high-risk care home setting during the early stages of the pandemic was relatively small. Although access to testing was limited to initial symptomatic cases in each care home at this time, our results suggest that reduced numbers of discharges, selection of patients, and action taken within care homes following transfer all may have contributed to mitigation. The precise key transmission routes from the community remain to be quantified.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Joe Hollinghurst", + "author_inst": "Swansea University" + }, + { + "author_name": "Laura North", + "author_inst": "Swansea University" + }, + { + "author_name": "Chris Emmerson", + "author_inst": "Public Health Wales" + }, + { + "author_name": "Ashley Akbari", + "author_inst": "Swansea University" + }, + { + "author_name": "Fatemeh Torabi", + "author_inst": "Swansea University" + }, + { + "author_name": "Ronan A Lyons", + "author_inst": "Swansea University" + }, + { + "author_name": "Alan G Hawkes", + "author_inst": "Swansea University" + }, + { + "author_name": "Ed Bennett", + "author_inst": "Swansea University" + }, + { + "author_name": "Mike B Gravenor", + "author_inst": "Swansea University" + }, + { + "author_name": "Richard Fry", + "author_inst": "Swansea University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2021.03.17.21253728", "rel_title": "Learning from the Experiences of COVID-19 Survivors: A Descriptive Study", @@ -891887,93 +890512,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.03.17.21252673", - "rel_title": "Detecting SARS-CoV-2 lineages and mutational load in municipal wastewater; a use-case in the metropolitan area of Thessaloniki, Greece", - "rel_date": "2021-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.17.21252673", - "rel_abs": "The SARS-CoV-2 pandemic represents an unprecedented global crisis necessitating novel approaches for, amongst others, early detection of emerging variants relating to the evolution and spread of the virus. Recently, the detection of SARS-CoV-2 RNA in wastewater has emerged as a useful tool to monitor the prevalence of the virus in the community. Here, we propose a novel methodology, called lineagespot, for the detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing. Our proposed method was tested and evaluated using NGS data produced by the sequencing of three wastewater samples from the municipality of Thessaloniki, Greece, covering three distinct time periods. The results showed a clear identification of trends in the presence of SARS-CoV-2 mutations in sewage data, and allowed for a robust inference between the variants evident through our approach and the variants observed in patients from the same area time periods. Lineagespot is an open-source tool, implemented in R, and is freely available on GitHub.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Nikolaos Pechlivanis", - "author_inst": "Institute of Applied Biosciences, Centre of Research and Technology Hellas / Dept of Genetics, Development and Molecular Biology, School of Biology, Aristotle U" - }, - { - "author_name": "Maria Tsagiopoulou", - "author_inst": "Institute of Applied Biosciences, Centre of Research and Technology Hellas" - }, - { - "author_name": "Maria Christina Maniou", - "author_inst": "Institute of Applied Biosciences, Centre of Research and Technology Hellas" - }, - { - "author_name": "Anastasis Togkousidis", - "author_inst": "Institute of Applied Biosciences, Centre of Research and Technology Hellas" - }, - { - "author_name": "Evangelia Mouchtaropoulou", - "author_inst": "Institute of Applied Biosciences, Centre of Research and Technology Hellas" - }, - { - "author_name": "Taxiarchis Chassalevris", - "author_inst": "School of Veterinary Medicine, Aristotle University of Thessaloniki" - }, - { - "author_name": "Serafeim Chaintoutis", - "author_inst": "School of Veterinary Medicine, Aristotle University of Thessaloniki" - }, - { - "author_name": "Chrysostomos Dovas", - "author_inst": "School of Veterinary Medicine, Aristotle University of Thessaloniki" - }, - { - "author_name": "Maria Petala", - "author_inst": "Dept. of Civil Engineering, Aristotle University of Thessaloniki" - }, - { - "author_name": "Margaritis Kostoglou", - "author_inst": "Dept. of Chemistry, Aristotle University of Thessaloniki" - }, - { - "author_name": "Thodoris Karapantsios", - "author_inst": "Dept. of Chemistry, Aristotle University of Thessaloniki" - }, - { - "author_name": "Stamatia Laidou", - "author_inst": "Institute of Applied Biosciences, Centre of Research and Technology Hellas / Dept of Genetics, Development and Molecular Biology, School of Biology, Aristotle U" - }, - { - "author_name": "Elisavet Vlachonikola", - "author_inst": "Institute of Applied Biosciences, Centre of Research and Technology Hellas / Dept of Genetics, Development and Molecular Biology, School of Biology, Aristotle U" - }, - { - "author_name": "Anastasia Chatzidimitriou", - "author_inst": "Institute of Applied Biosciences, Centre of Research and Technology Hellas" - }, - { - "author_name": "Agis Papadopoulos", - "author_inst": "EYATH S.A., Thessaloniki Water Supply and Sewerage Company S.A." - }, - { - "author_name": "Nikolaos Papaioannou", - "author_inst": "School of Veterinary Medicine, Aristotle University of Thessaloniki" - }, - { - "author_name": "Anagnostis Argiriou", - "author_inst": "Institute of Applied Biosciences, Centre of Research and Technology Hellas" - }, - { - "author_name": "Fotis Psomopoulos", - "author_inst": "Institute of Applied Biosciences, Centre of Research and Technology Hellas" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.16.21253759", "rel_title": "The indirect health impacts of COVID19 restrictions: a strong debate informed by weak evidence", @@ -893325,6 +891863,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.15.21253615", + "rel_title": "Safety of administering biologics to IBD patients at an outpatient infusion center In New York City during the COVID-19 pandemic: Sars-CoV-2 seroprevalence and clinical and social characteristics", + "rel_date": "2021-03-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.15.21253615", + "rel_abs": "Patients with immune-mediated inflammatory diseases (IMIDs) and acquired and genetic immunodeficiencies receiving therapeutic infusions are considered high risk for SARS-CoV-2 infection. However, the seroprevalance in this group and the safety of routine administrations at outpatient infusion centers are unknown. To determine the infection rate and clinical-social factors related to SARS-CoV-2 in asymptomatic patients with IMIDs and immunodeficiencies receiving routine non-cancer therapeutic infusions, we conducted a seroprevalence study at our outpatient infusion center. We report the first prospective SARS-CoV-2 sero-surveillance of 444 IBD/IMID, immunodeficiency, and immune competent patients at an outpatient infusion center in the U.S. showing lower seroprevalence in patients compared with the general population and provide clinical and social characteristics associated with seroprevalence in this group. These data suggest that patients can safely continue infusions at outpatient centers.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Serre-Yu Wong", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Stephanie Gold", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Emma K. Accorsi", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Tori L. Cowger", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Dean Wiseman", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Reema Navalurkar", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Rebekah Dixon", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Drew S. Helmus", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "- CiTI Study Group", + "author_inst": "" + }, + { + "author_name": "Adolfo Firpo-Betancourt", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Damodara Rao Mendu", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Susan Zolla-Pazner", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Ken Cadwell", + "author_inst": "New York University School of Medicine" + }, + { + "author_name": "Jean-Frederic Colombel", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "gastroenterology" + }, { "rel_doi": "10.1101/2021.03.15.21253625", "rel_title": "A proteome-wide genetic investigation identifies several SARS-CoV-2-exploited host targets of clinical relevance", @@ -893861,73 +892470,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.03.15.21253619", - "rel_title": "COVID-19 with early neurological and cardiac thromboembolic phenomena--timeline of incidence and clinical features", - "rel_date": "2021-03-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.15.21253619", - "rel_abs": "BackgroundAt our tertiary care public hospital, we saw COVID-19 presenting with thromboembolic phenomena, indicating a possible early thrombo-inflammatory pathology.\n\nObjectivesWe documented patients with cardiac and neurological thromboembolic phenomena as a primary presentation of COVID-19, and compared a subset of COVID associated strokes against COVID-19 patients without thrombotic manifestations.\n\nMethodsWe included all COVID-Stroke and COVID-ACS (COVID-19, with ischemic arterial stroke/Acute Coronary Syndrome presenting prior to/simultaneous with/within 72 hours of systemic/respiratory COVID manifestations) admitted from April to November 2020. In the nested case control analysis, we used unpaired T-test and chi-square test to study differences between COVID-Strokes (case group) and non-thrombotic COVID controls.\n\nResults and ConclusionsWe noted 68 strokes and 122 ACS associated with COVID-19. ACS peaked in May-June, while stroke admissions peaked later in September-October, possibly because severe strokes may have expired at home during the lockdown.\n\nIn the case-control analysis, cases (n=43; 12F:31M; mean age 51.5 years) had significantly higher D-Dimer values than controls (n=50; 9F:41M; mean age 51.6 years). Mortality was significantly higher in cases (51.2% vs. 26.0%; p = 0.018). We noted 7.5 times higher mortality in cases versus controls even among patients needing minimal oxygen support. Imaging in 37 patients showed both anterior and posterior circulation territories affected in seven, with almost half of Carotid territory strokes being large hemispherical strokes. Additionally, CT/MRI angiography in 28 strokes showed large vessel occlusions in 19 patients. Death in cases thus probably occurred before progression to intense respiratory support, due to severe central nervous system insult.\n\nBinary logistic regression analysis showed respiratory support intensity to be the sole independent predictor of mortality among cases. Respiratory distress could have been due to COVID-19 lung infection or aspiration pneumonia resulting from obtunded sensorium. In controls, mortality was predicted by increasing age, female sex, and respiratory support intensity.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Uma Sundar", - "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" - }, - { - "author_name": "Sanah Merchant", - "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" - }, - { - "author_name": "Meera Shah", - "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" - }, - { - "author_name": "Amita Mukhopadhyay", - "author_inst": "Dr Chandramma Dayananda Sagar Institute of Medical Education and Research, Kanakapura 562112, Ramanagara District, Karnataka, India" - }, - { - "author_name": "Shaonak Kolte", - "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" - }, - { - "author_name": "Pramod Darole", - "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" - }, - { - "author_name": "Sharvari Mahajan", - "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" - }, - { - "author_name": "Ashank Bansal", - "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" - }, - { - "author_name": "Satish Gosavi", - "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" - }, - { - "author_name": "Dnaneshwar Asole", - "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" - }, - { - "author_name": "Niteen Karnik", - "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" - }, - { - "author_name": "Ajay Mahajan", - "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" - }, - { - "author_name": "Anagha Joshi", - "author_inst": "Lokmanya Tilak Municipal Medical College and General Hospital (LTMMC&GH), Sion, Mumbai 400022, Maharashtra, India" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2021.03.16.21253534", "rel_title": "The course of the UK COVID 19 pandemic; no measurable impact of new variants.", @@ -895027,6 +893569,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.17.21253775", + "rel_title": "Estimating the increased transmissibility of the B.1.1.7 strain over previously circulating strains in England using fractions of GISAID sequences and the distribution of serial intervals", + "rel_date": "2021-03-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.17.21253775", + "rel_abs": "The B.1.1.7 strain, also referred to as Alpha variant, is a variant strain of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The Alpha variant is considered to possess higher transmissibility compared to the strains previously circulating in England. This paper proposes a new method to estimate the selective advantage of a mutant strain over another strain using the time course of strain frequencies and the distribution of the serial interval of infections. This method allows the instantaneous reproduction numbers of infections to vary over calendar time. The proposed method also assumes that the selective advantage of a mutant strain over previously circulating strains is constant. Applying the method to SARS-CoV-2 sequence data from England, the instantaneous reproduction number of the B.1.1.7 strain was estimated to be 26.6-45.9% higher than previously circulating strains in England. This result indicates that control measures should be strengthened by 26.6-45.9% when the B.1.1.7 strain is newly introduced to a country where viruses with similar transmissibility to the preexisting strain in England are predominant.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Chayada Piantham", + "author_inst": "Hokkaido University" + }, + { + "author_name": "Natalie M Linton", + "author_inst": "Graduate School of Medicine, Hokkaido University" + }, + { + "author_name": "Hiroshi Nishiura", + "author_inst": "Graduate School of Medicine, Kyoto University" + }, + { + "author_name": "Kimihito Ito", + "author_inst": "Hokkaido University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.11.21253409", "rel_title": "Metagenomic sequencing of municipal wastewater provides a near-complete SARS-CoV-2 genome sequence identified as the B.1.1.7 variant of concern from a Canadian municipality concurrent with an outbreak", @@ -895603,33 +894176,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2021.03.16.434488", - "rel_title": "SARS-CoV-2 Spike receptor-binding domain with a G485R mutation in complex with human ACE2", - "rel_date": "2021-03-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.16.434488", - "rel_abs": "Since SARS-CoV-2 emerged in 2019, genomic sequencing has identified mutations in the viral RNA including in the receptor-binding domain of the Spike protein. Structural characterisation of the Spike carrying point mutations aids in our understanding of how these mutations impact binding of the protein to its human receptor, ACE2, and to therapeutic antibodies. The Spike G485R mutation has been observed in multiple isolates of the virus and mutation of the adjacent residue E484 to lysine is known to contribute to antigenic escape. Here, we have crystallised the SARS-CoV-2 Spike receptor-binding domain with a G485R mutation in complex with human ACE2. The crystal structure shows that while the G485 residue does not have a direct interaction with ACE2, its mutation to arginine affects the structure of the loop made by residues 480-488 in the receptor-binding motif, disrupting the interactions of neighbouring residues with ACE2 and with potential implications for antigenic escape from vaccines, antibodies and other biologics directed against SARS-CoV-2 Spike.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Claire Marie Weekley", - "author_inst": "Bio21 Institute and Department of Biochemistry and Pharmacology, The University of Melbourne 3010 Victoria, Australia" - }, - { - "author_name": "Damian Francis John Purcell", - "author_inst": "Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne 3010 Victoria, Australia" - }, - { - "author_name": "Michael W Parker", - "author_inst": "Bio21 Institute and Department of Biochemistry and Pharmacology, The University of Melbourne 3010 Victoria, Australia and St. Vincents Institute of Medical Rese" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2021.03.16.435700", "rel_title": "SARS-CoV-2 spike protein induces inflammation via TLR2-dependent activation of the NF-\u03baB pathway", @@ -897293,6 +895839,61 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.03.15.435440", + "rel_title": "Rationally designed immunogens enable immune focusing to the SARS-CoV-2 receptor binding motif", + "rel_date": "2021-03-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.15.435440", + "rel_abs": "Eliciting antibodies to surface-exposed viral glycoproteins can lead to protective responses that ultimately control and prevent future infections. Targeting functionally conserved epitopes may help reduce the likelihood of viral escape and aid in preventing the spread of related viruses with pandemic potential. One such functionally conserved viral epitope is the site to which a receptor must bind to facilitate viral entry. Here, we leveraged rational immunogen design strategies to focus humoral responses to the receptor binding motif (RBM) on the SARS-CoV-2 spike. Using glycan engineering and epitope scaffolding, we find an improved targeting of the serum response to the RBM in context of SARS-CoV-2 spike imprinting. Furthermore, we observed a robust SARS-CoV-2-neutralizing serum response with increased potency against related sarbecoviruses, SARS-CoV, WIV1-CoV, RaTG13-CoV, and SHC014-CoV. Thus, RBM focusing is a promising strategy to elicit breadth across emerging sarbecoviruses and represents an adaptable design approach for targeting conserved epitopes on other viral glycoproteins.\n\nOne Sentence SummarySARS-CoV-2 immune focusing with engineered immunogens", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Blake M. Hauser", + "author_inst": "Ragon Institute of MGH, MIT and Harvard" + }, + { + "author_name": "Maya Sangesland", + "author_inst": "Ragon Institute of MGH, MIT and Harvard" + }, + { + "author_name": "Kerri J. St. Denis", + "author_inst": "Ragon Institute of MGH, MIT and Harvard" + }, + { + "author_name": "Ian W. Windsor", + "author_inst": "Ragon Institute of MGH, MIT and Harvard" + }, + { + "author_name": "Jared Feldman", + "author_inst": "Ragon Institute of MGH, MIT and Harvard" + }, + { + "author_name": "Evan C. Lam", + "author_inst": "Ragon Institute of MGH, MIT and Harvard" + }, + { + "author_name": "Ty Kannegieter", + "author_inst": "Ragon Institute of MGH, MIT and Harvard" + }, + { + "author_name": "Alejandro B. Balazs", + "author_inst": "Ragon Institute of MGH, MIT and Harvard" + }, + { + "author_name": "Daniel Lingwood", + "author_inst": "Ragon Institute of MGH, MIT and Harvard" + }, + { + "author_name": "Aaron G. Schmidt", + "author_inst": "Ragon Institute of MGH, MIT and Harvard; Department of Microbiology, Harvard Medical School" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.03.14.435337", "rel_title": "Shed the light on virus: virucidal effects of 405 nm visible light on SARS-CoV-2 and influenza A virus.", @@ -897805,81 +896406,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.12.21253000", - "rel_title": "Novel highly divergent SARS-CoV-2 lineage with the Spike substitutions L249S and E484K", - "rel_date": "2021-03-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.12.21253000", - "rel_abs": "COVID-19 pandemics has led to genetic diversification of SARS-CoV-2 and the appearance of variants with potential impact in transmissibility and viral escape from acquired immunity. We report a new lineage containing ten distinctive amino acid changes across the genome. Further studies are required for monitoring its epidemiologic impact.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Katherine Laiton-Donato", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Jose A. Usme-Ciro", - "author_inst": "Universidad Cooperativa de Colombia" - }, - { - "author_name": "Carlos Franco-Munoz", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Diego A. Alvarez-Diaz", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Hector Alejandro Ruiz-Moreno", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Jhonnatan Reales-Gonzalez", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Diego Andres Prada", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Sheryll Corchuelo", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Maria T Herrera-Sepulveda", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Julian Naizaque", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Gerardo Santamaria", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Magdalena Wiesner", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Diana Marcela Walteros", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Martha Lucia Ospina Martinez", - "author_inst": "Instituto Nacional de Salud" - }, - { - "author_name": "Marcela Marcela Mercado-Reyes", - "author_inst": "Instituto Nacional de Salud" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.12.21253463", "rel_title": "HIV service interruptions during the COVID-19 pandemic in China: the role of HIV service challenges and institutional response from healthcare professional's perspective", @@ -899715,6 +898241,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.12.21253410", + "rel_title": "Rapid review of social contact patterns during the COVID-19 pandemic", + "rel_date": "2021-03-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.12.21253410", + "rel_abs": "BackgroundPhysical distancing measures aim to reduce person-to-person contact, a key driver of transmission of respiratory infections such as SARS-CoV-2. In response to unprecedented restrictions on human contact during the COVID-19 pandemic, a number of studies measured social contact patterns under the implementation of physical distancing measures. This rapid review aims to synthesize empirical data on the changing social contact patterns during the COVID-19 pandemic.\n\nMethodWe conducted a systematic review using PubMed, Medline, Embase and Google Scholar following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. We descriptively compared the distribution of contacts observed during the pandemic to pre-COVID data across countries to explore changes in contact patterns during physical distancing measures.\n\nResultsWe identified 12 studies that reported social contact patterns during the COVID-19 pandemic. The majority of studies (11/12) collected data during the initial mitigation period in the spring of 2020 marked by government-declared lockdowns and the most stringent physical distancing measures. Some studies collected additional data after relaxation of initial mitigation. Most study settings reported a mean of between 2-5 contacts per person per day, a substantial reduction compared to pre-COVID rates which ranged from 7-26 contacts per day in similar settings. This reduction was particularly pronounced for contacts outside of the home. Consequently, levels of assortative mixing by age substantially declined. After relaxation of initial mitigation, mean contact rates subsequently increased but did not return to pre-COVID levels. Increases in contacts post-relaxation were driven by working-age adults.\n\nConclusionInformation on changes in contact patterns during physical distancing measures can guide more realistic representations of contact patterns in mathematical models for SARS-CoV-2 transmission.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Carol Y. Liu", + "author_inst": "Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA 30322, USA" + }, + { + "author_name": "Juliette Berlin", + "author_inst": "Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA 30322, USA" + }, + { + "author_name": "Moses C. Kiti", + "author_inst": "Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA 30322, USA" + }, + { + "author_name": "Emanuele Del Fava", + "author_inst": "Max Planck Institute for Demographic Research, Rostock, Germany" + }, + { + "author_name": "Andr\u00e9 Grow", + "author_inst": "Max Planck Institute for Demographic Research, Rostock, Germany" + }, + { + "author_name": "Emilio Zagheni", + "author_inst": "Max Planck Institute for Demographic Research, Rostock, Germany" + }, + { + "author_name": "Alessia Melegaro", + "author_inst": "Centre for Research on Social Dynamics and Public Policy & Covid Crisis Lab, Bocconi University, 20136 Milan, Italy" + }, + { + "author_name": "Samuel M. Jenness", + "author_inst": "Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA 30322, USA" + }, + { + "author_name": "Saad Omer", + "author_inst": "Yale Institute of Global Health, Yale University, Connecticut, USA" + }, + { + "author_name": "Benjamin Lopman", + "author_inst": "Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA 30322, USA" + }, + { + "author_name": "Kristin Nelson", + "author_inst": "Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA 30322, USA" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.12.21253470", "rel_title": "The efficacy and safety of remdesivir in the treatment of patients with COVID-19: a systematic review and meta-analysis", @@ -900143,221 +898728,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.12.21253493", - "rel_title": "Seroprevalence of Antibodies to SARS-CoV-2 among Health Care Workers in Kenya", - "rel_date": "2021-03-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.12.21253493", - "rel_abs": "BackgroundFew studies have assessed the seroprevalence of antibodies against SARS-CoV-2 among Health Care Workers (HCWs) in Africa. We report findings from a survey among HCWs in three counties in Kenya.\n\nMethodsWe recruited 684 HCWs from Kilifi (rural), Busia (rural) and Nairobi (urban) counties. The serosurvey was conducted between 30th July 2020 and 4th December 2020. We tested for IgG antibodies to SARS-CoV-2 spike protein using ELISA. Assay sensitivity and specificity were 93% (95% CI 88-96%) and 99% (95% CI 98-99.5%), respectively. We adjusted prevalence estimates using Bayesian modeling to account for assay performance.\n\nResultsCrude overall seroprevalence was 19.7% (135/684). After adjustment for assay performance seroprevalence was 20.8% (95% CI 17.5-24.4%). Seroprevalence varied significantly (p<0.001) by site: 43.8% (CI 35.8-52.2%) in Nairobi, 12.6% (CI 8.8-17.1%) in Busia and 11.5% (CI 7.2-17.6%) in Kilifi. In a multivariable model controlling for age, sex and site, professional cadre was not associated with differences in seroprevalence.\n\nConclusionThese initial data demonstrate a high seroprevalence of antibodies to SARS-CoV-2 among HCWs in Kenya. There was significant variation in seroprevalence by region, but not by cadre.", - "rel_num_authors": 50, - "rel_authors": [ - { - "author_name": "Anthony O. Etyang", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Ruth Lucinde", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Henry Karanja", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Catherine Kalu", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Daisy Mugo", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "James Nyagwange", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "John Gitonga", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "James Tuju", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Perpetual Wanjiku", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Angela Karani", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Shadrack Mutua", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Hosea Maroko", - "author_inst": "KEMRI Center for Infectious and Parasitic Diseases Control Research" - }, - { - "author_name": "Eddy Nzomo", - "author_inst": "Kilifi County Hospital" - }, - { - "author_name": "Eric Maitha", - "author_inst": "Department of Health, Kilifi County" - }, - { - "author_name": "Evanson Kamuri", - "author_inst": "Kenyatta National Hospital" - }, - { - "author_name": "Thuranira Kaugiria", - "author_inst": "Kenyatta National Hospital" - }, - { - "author_name": "Justus Weru", - "author_inst": "Kenyatta National Hospital" - }, - { - "author_name": "Lucy B. Ochola", - "author_inst": "Institute of Primate Research" - }, - { - "author_name": "Nelson Kilimo", - "author_inst": "Alupe Sub-County Hospital" - }, - { - "author_name": "Sande Charo", - "author_inst": "Kocholia sub-County Hospital" - }, - { - "author_name": "Namdala Emukule", - "author_inst": "Busia County Referral Hospital" - }, - { - "author_name": "Wycliffe Moracha", - "author_inst": "Department of Health, Busia County" - }, - { - "author_name": "David Mukabi", - "author_inst": "Department of Health, Busia County" - }, - { - "author_name": "Rosemary Okuku", - "author_inst": "Department of Health, Busia County" - }, - { - "author_name": "Monicah Ogutu", - "author_inst": "Department of Health, Busia County" - }, - { - "author_name": "Barrack Angujo", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Mark Otiende", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Christian Bottomley", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Edward Otieno", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Leonard Ndwiga", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Amek Nyaguara", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Shirine Voller", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Charles Agoti", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "David James Nokes", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Lynette Isabella Ochola-Oyier", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Rashid Aman", - "author_inst": "Ministry of Health, Government of Kenya" - }, - { - "author_name": "Patrick Amoth", - "author_inst": "Ministry of Health, Government of Kenya" - }, - { - "author_name": "Mercy Mwangangi", - "author_inst": "Ministry of Health, Government of Kenya" - }, - { - "author_name": "Kadondi Kasera", - "author_inst": "Ministry of Health, Government of Kenya" - }, - { - "author_name": "Wangari Nganga", - "author_inst": "Ministry of Health, Government of Kenya" - }, - { - "author_name": "Ifedayo Adetifa", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Wangeci Kagucia", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Katherine Gallagher", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Sophie Uyoga", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Benjamin Tsofa", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Edwine Barasa", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Philip Bejon", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "J. Anthony G. Scott", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Ambrose Agweyu", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "George Warimwe", - "author_inst": "KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.12.21253015", "rel_title": "Diurnal variation in SARS-CoV-2 PCR test results: Test accuracy may vary by time of day", @@ -901673,6 +900043,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "transplantation" }, + { + "rel_doi": "10.1101/2021.03.09.434696", + "rel_title": "Contribution of SARS-CoV-2 accessory proteins to viral pathogenicity in K18 hACE2 transgenic mice", + "rel_date": "2021-03-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.09.434696", + "rel_abs": "Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) is the viral pathogen responsible for the current coronavirus disease 2019 (COVID-19) pandemic. To date, it is estimated that over 113 million individuals have been infected with SARS-CoV-2 and over 2.5 million human deaths have been recorded worldwide. Currently, three vaccines have been approved by the Food and Drug Administration for emergency use only. However much of the pathogenesis observed during SARS-CoV-2 infection remains elusive. To gain insight into the contribution of individual accessory open reading frame (ORF) proteins in SARS-CoV-2 pathogenesis, we used our recently described reverse genetics system approach to successfully engineer recombinant (r)SARS-CoV-2, where we individually removed viral 3a, 6, 7a, 7b, and 8 ORF proteins, and characterized these recombinant viruses in vitro and in vivo. Our results indicate differences in plaque morphology, with ORF deficient ({Delta}ORF) viruses producing smaller plaques than those of the wild-type (rSARS-CoV-2/WT). However, growth kinetics of {Delta}ORF viruses were like those of rSARS-CoV-2/WT. Interestingly, infection of K18 human angiotensin converting enzyme 2 (hACE2) transgenic mice with the {Delta}ORF rSARS-CoV-2 identified ORF3a and ORF6 as the major contributors of viral pathogenesis, while {Delta}ORF7a, {Delta}ORF7b and {Delta}ORF8 rSARS-CoV-2 induced comparable pathology to rSARS-CoV-2/WT. This study demonstrates the robustness of our reverse genetics system to generate rSARS-CoV-2 and the major role for ORF3a and ORF6 in viral pathogenesis, providing important information for the generation of attenuated forms of SARS-CoV-2 for their implementation as live-attenuated vaccines for the treatment of SARS-CoV-2 infection and associated COVID-19.\n\nIMPORTANCEDespite great efforts put forward worldwide to combat the current coronavirus disease 2019 (COVID-19) pandemic, Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) continues to be a human health and socioeconomic threat. Insights into the pathogenesis of SARS-CoV-2 and contribution of viral proteins to disease outcome remains elusive. Our study aims to determine the contribution of SARS-CoV-2 accessory open reading frame (ORF) proteins in viral pathogenesis and disease outcome, and develop a synergistic platform combining our robust reverse genetics system to generate recombinant (r)SARS-CoV-2 with a validated rodent model of infection and disease. We demonstrated that SARS-CoV-2 ORF3a and ORF6 contribute to lung pathology and ultimately disease outcome in K18 hACE2 transgenic mice, while ORF7a, ORF7b, and ORF8 have little impact on disease outcome. Moreover, our combinatory platform serves as the foundation to generate attenuated forms of the virus to develop live-attenuated vaccines for the treatment of SARS-CoV-2.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Jesus Silvas", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Desarey Morales Vasquez", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Jun-Gyu Park", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Kevin Chiem", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Jordi Torrelles", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Roy Neal Platt", + "author_inst": "Texas Biomedical Research Instititue" + }, + { + "author_name": "Tim Anderson", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Chengjin Ye", + "author_inst": "Texas Biomedical Research Institute" + }, + { + "author_name": "Luis Mart\u00ednez-Sobrido", + "author_inst": "Texas Biomedical Research Institute" + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.03.09.21251364", "rel_title": "Optimization of magnetic bead-based nucleic acid extraction for SARS-CoV-2 testing using readily available reagents", @@ -902153,113 +900574,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.10.21252711", - "rel_title": "An In-House ELISA for SARS-CoV-2 RBD uncovers elevatedimmune response at higher altitudes", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.10.21252711", - "rel_abs": "The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) first reported in Wuhan has caused a global pandemic with dramatic health and socioeconomic consequences. The Coronavirus Disease 2019 (COVID-19) associated represents a challenge for health systems that had to quickly respond developing new diagnostic and therapeutic strategies. In the present work, we developed an \"In House\" ELISA with high sensitivity (92.2 %), specificity (100%) and precision (93.9%), with an area under the ROC curve (AUC) of 0.991, rendering the assay as an excellent serological test to correctly discriminate between SARS-COv-2 infected and non-infected individuals and study population seroprevalence. Among 758 patients evaluated for SARS-CoV-2 diagnosis in the province of Tucuman, Argentina, we found a Pearson correlation coefficient of 0.5048 between antibodies elicited against the RBD and the nucleocapsid (N) antigen. Additionally, 33.6% of individuals diagnosed with COVID-19 displayed mild levels of RBD-IgG antibodies, while 19% of the patients showed high antibody titers. Interestingly, patients with SARS-COV-2 infection over 60 years old elicited significantly higher levels of IgG antibodies against RBD compared to younger ones, while no difference was found between women and men. Surprisingly, individuals from a high altitude village displayed statistically significant higher and longer lasting anti-RBD antibodies compared to those from a city at a lower altitude, suggesting that a hypobaric hypoxia-adapted mechanism may act as a protective factor for COVID-19. To our knowledge, this is the first report correlating altitude with increased humoral immune response against SARS-Cov-2 infection.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Rodrigo Tomas Grau", - "author_inst": "Instituto de Medicina Molecular y Celular Aplicada - IMMCA (CONICET-UNT-SiProSa). Tucuman, Argentina." - }, - { - "author_name": "Diego Ploper", - "author_inst": "Instituto de Medicina Molecular y Celular Aplicada - IMMCA (CONICET-UNT-SiProSa). Tucuman, Argentina." - }, - { - "author_name": "Cesar Luis Avila", - "author_inst": "Instituto de Medicina Molecular y Celular Aplicada - IMMCA (CONICET-UNT-SiProSa). Tucuman, Argentina." - }, - { - "author_name": "Esteban Vera Pingitore", - "author_inst": "Instituto de Medicina Molecular y Celular Aplicada - IMMCA (CONICET-UNT-SiProSa). Tucuman, Argentina." - }, - { - "author_name": "Carolina Maldonado", - "author_inst": "Centro de Referencia para Lactobacilos. CERELA, CONICET. Tucuman, Argentina." - }, - { - "author_name": "Silvina Chaves", - "author_inst": "Instituto de Medicina Molecular y Celular Aplicada - IMMCA (CONICET-UNT-SiProSa). Tucuman, Argentina." - }, - { - "author_name": "Sergio Benjamin Socias", - "author_inst": "Instituto de Medicina Molecular y Celular Aplicada - IMMCA (CONICET-UNT-SiProSa). Tucuman, Argentina." - }, - { - "author_name": "Agustin Stagnetto", - "author_inst": "Instituto de Medicina Molecular y Celular Aplicada - IMMCA (CONICET-UNT-SiProSa). Tucuman, Argentina." - }, - { - "author_name": "Silvia Navarro", - "author_inst": "Instituto de Medicina Molecular y Celular Aplicada - IMMCA (CONICET-UNT-SiProSa). Tucuman, Argentina." - }, - { - "author_name": "Rossana Chahla", - "author_inst": "Hospital Nestor Kirchner, Laboratorio de Salud Publica, Sistema Provincial de Salud. LSP (SiProSa). Tucuman, Argentina." - }, - { - "author_name": "Monica Aguilar", - "author_inst": "Hospital Nestor Kirchner, Laboratorio de Salud Publica, Sistema Provincial de Salud. LSP (SiProSa). Tucuman, Argentina." - }, - { - "author_name": "Conrado Llapur", - "author_inst": "Direccion de Investigacion en Salud. Ministerio de Salud Publica, Tucuman, Argentina" - }, - { - "author_name": "Patricia Aznar", - "author_inst": "Hospital Nestor Kirchner, Laboratorio de Salud Publica, Sistema Provincial de Salud. LSP (SiProSa). Tucuman, Argentina." - }, - { - "author_name": "Malena Alcorta", - "author_inst": "Hospital Nestor Kirchner, Laboratorio de Salud Publica, Sistema Provincial de Salud. LSP (SiProSa). Tucuman, Argentina." - }, - { - "author_name": "Dardo Costas", - "author_inst": "Hospital Nestor Kirchner, Laboratorio de Salud Publica, Sistema Provincial de Salud. LSP (SiProSa). Tucuman, Argentina." - }, - { - "author_name": "Isolina Flores", - "author_inst": "Hospital Nestor Kirchner, Laboratorio de Salud Publica, Sistema Provincial de Salud. LSP (SiProSa). Tucuman, Argentina." - }, - { - "author_name": "Gabriela Apfelbaum", - "author_inst": "Facultad de Medicina. Universidad Nacional de Tucuman. Tucuman, Argentina" - }, - { - "author_name": "Dar Heinze", - "author_inst": "EDITAR Section of Gastroenterology, Department of Medicine, Center for Regenerative Medicine (CReM), Boston University School of Medicine, Boston, MA, USA." - }, - { - "author_name": "Raul Mostoslavsky", - "author_inst": "The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA, USA." - }, - { - "author_name": "Gustavo Mostoslavsky", - "author_inst": "Section of Gastroenterology, Department of Medicine, Center for Regenerative Medicine (CReM), Boston University School of Medicine, Boston, MA, USA" - }, - { - "author_name": "Gabriela Perdigon", - "author_inst": "Centro de Referencia para Lactobacilos. CERELA. CONICET. Tucuman, Argentina." - }, - { - "author_name": "Silvia Cazorla", - "author_inst": "Centro de Referencia para Lactobacilos. CERELA. CONICET. Tucuman, Argentina." - }, - { - "author_name": "Rosana Chehin", - "author_inst": "Instituto de Medicina Molecular y Celular Aplicada - IMMCA (CONICET-UNT-SiProSa). Tucuman, Argentina." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.09.21253193", "rel_title": "A Recovery Algorithm and Pooling Designs for One-Stage Noisy Group Testing under the Probabilistic Framework", @@ -903567,6 +901881,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.10.21253331", + "rel_title": "Disulfiram associated with lower risk of Covid-19: a retrospective cohort study", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.10.21253331", + "rel_abs": "In the global COVID-19 pandemic, there is a substantial need for effective, low-cost therapeutics. We investigated the potential effects of disulfiram on the incidence and outcomes of COVID-19 in an observational study in a large database of US Veterans Administration clinical records, the VA Corporate Data Warehouse (CDW). The study is motivated by the unique properties of disulfiram, which has been used as an anti-alcoholism drug since 1948, is non-toxic, easy to manufacture and inexpensive. Disulfiram reduces hyperinflammation in mammalian cells by inhibition of the gasdermin D pore. In a mouse model of sepsis, disulfiram reduced inflammatory cytokines and mortality. Disulfiram also is a low micromolar inhibitor of the Mpro and PLpro viral proteases of SARS-CoV-2.\n\nTo investigate the potential effects of disulfiram on the incidence and severity of COVID-19, we carried out an epidemiological study in the CDW. The VA dataset used has 944,127 patients tested for SARS-Cov-2, 167,327 with a positive test, and 2,233 on disulfiram, of which 188 had a positive SARS-Cov-2 test. A multivariable Cox regression adjusted for age, gender, race/ethnicity, region, a diagnosis of alcohol use disorders, and Charlson comorbidity score revealed a reduced incidence of COVID-19 with disulfiram use with a hazard ratio of 0.66 and 95% confidence interval of 0.57 to 0.76 (P < 0.001). There were no deaths among the 188 SARS-Cov-2 positive patients treated with disulfiram. The expected number of deaths would have been 5-6 according to the 3% death rate among the untreated (P-value 0.03).\n\nOur finding of a lower hazard ratio and less severe outcomes for COVID-19 in patients treated with disulfiram compared to those not treated is a statistical association and does not prove any causative effect of disulfiram. However, the results of this study suggest that there is a pharmacological contribution to the reduced incidence and severity of COVID-19 with the use of disulfiram. Given the known anti-inflammatory and viral anti-protease effects of disulfiram, it is reasonable and urgent to initiate accelerated clinical trials to assess whether disulfiram reduces SARS-CoV-2 infection, disease severity and death.\n\nSTRUCTURED OUTLINEO_ST_ABSImportanceC_ST_ABSIdentifying already approved medications with well characterized antiviral or anti-inflammatory properties supported by real world evidence as candidates for clinical trials for repurposing is an important strategy to manage the pandemic given the ongoing challenges with producing and administering vaccines, the emergence of more infectious viral mutants and the paucity of approved therapies.\n\nObjectiveTo investigate the potential effects of disulfiram on the incidence and severity of COVID-19.\n\nDesignRetrospective cohort study from February 20, 2020 to February 1, 2021.\n\nSettingVeterans Health Administration. Veterans who had visited a VA primary care provider in the 18 months before their first SARS-CoV-2 test.\n\nParticipants2,233 Veterans with at least one SARS-CoV-2 laboratory (positive or negative) test result on or after February 20, 2020 and at least one pharmacy record for disulfiram on or after February 20, 2019 and 941,894 Veterans without a pharmacy record for disulfiram.\n\nExposureTreatment with disulfiram\n\nMain OutcomePositive test result for SARS-CoV-2\n\nResultsA multivariable Cox regression analysis adjusted for age, gender, race/ethnicity, region, diagnosis of an alcohol use disorder, and Charlson comorbidity score resulted in a reduced hazard of COVID-19 infection with disulfiram use, with a hazard ratio of 0.66 and 95% confidence interval of 0.57 to 0.76 (P < 0.001).\n\nConclusions and RelevanceThe results of this study suggest that disulfiram use contributes to a reduced incidence of COVID-19. Given the known anti-inflammatory and anti-protease effects of disulfiram, its low cost, low side effects, and general availability, it is reasonable and urgent to initiate accelerated clinical trials to assess the effect of disulfiram on infection and the development of advanced disease.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Nathanael Fillmore", + "author_inst": "Boston VA Cooperative Studies Program (CSP) Center, VA Boston Healthcare System" + }, + { + "author_name": "Steven Bell", + "author_inst": "Department of Clinical Neurosciences, University of Cambridge, UK" + }, + { + "author_name": "Ciyue Shen", + "author_inst": "Department of Cell Biology, Harvard Medical School and Department of Data Sciences, Dana-Farber Cancer Institute, Boston" + }, + { + "author_name": "Vinh Nguyen", + "author_inst": "Boston VA Cooperative Studies Program (CSP) Center, VA Boston Healthcare System" + }, + { + "author_name": "Jennifer La", + "author_inst": "Boston VA Cooperative Studies Program (CSP) Center, VA Boston Healthcare System" + }, + { + "author_name": "Maureen Dubreuil", + "author_inst": "Section of Rheumatology, Boston University School of Medicine and Rheumatology, VA Boston Healthcare System" + }, + { + "author_name": "Judith Strymish", + "author_inst": "Department of Medicine, Harvard Medical School, Boston and Infection Disease, VA Boston Healthcare System" + }, + { + "author_name": "Mary Brophy", + "author_inst": "Boston VA Cooperative Studies Program (CSP) Center, VA Boston Healthcare System and Section of Hematology and Medical Oncology, Boston University School of Medi" + }, + { + "author_name": "Gautam Mehta", + "author_inst": "Institute for Liver and Digestive Health, University College London and Institute of Hepatology, Foundation for Liver Research, London" + }, + { + "author_name": "Hao Wu", + "author_inst": "Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Program in Cellular and Molecular Medicine, Boston Children's Hospital" + }, + { + "author_name": "Judy Lieberman", + "author_inst": "Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston" + }, + { + "author_name": "Nhan Do", + "author_inst": "Boston VA Cooperative Studies Program (CSP) Center, VA Boston Healthcare System and Section of General Internal Medicine, Boston University School of Medicine" + }, + { + "author_name": "Chris Sander", + "author_inst": "MSKCC" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.10.21253292", "rel_title": "Repeated Testing Necessary: Assessing Negative Predictive Value of SARS-CoV-2 qPCR in a Population of Young Adults", @@ -903935,29 +902316,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.10.21253259", - "rel_title": "Evaluation of Measles Surveillance System amidst Covid 19 pandemic in Asutifi North District, Ahafo Region, Ghana.", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.10.21253259", - "rel_abs": "BackgroundMeasles is a disease of public health importance earmarked for elimination by all WHO Regions. Globally, more than 140 000 people died from Measles in 2018 affecting mostly children under 5 years, despite the availability of safe and effective vaccine.\n\nMethodsA descriptive cross-sectional survey was conducted. Disease surveillance focal persons were interviewed using semi-structured questionnaire on the system operations and use of Measles case definitions. Measles case-based investigation forms from 2015 - 2020 were reviewed for its timeliness and data quality. CDC updated guidelines for surveillance system evaluation was used to assess its usefulness and attributes. Data was analyzed for frequencies and proportions and results presented in tables and graphs.\n\nResultsMeasles surveillance system was timely as 100% (69/69) of the suspected cases were reported on time. Also, the level of representativeness was good as all the 14 health facilities in the District were participating in the Measles Surveillance system. Majority 73.1 (44/60) of the case-based investigation forms filled were incomplete with some columns wrongly filled.\n\nConclusionDespite the outbreak of Covid - 19 with most districts battling with how to contain the virus, measles surveillance system was still meeting its objectives of early detection and prompt reporting but with poor data quality.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Stephen Owusu Sekyere", - "author_inst": "University of Health and Allied Sciences" - }, - { - "author_name": "Salaam Laar Dam-Park", - "author_inst": "Ghana Health Service" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.10.21253317", "rel_title": "Type I, II, and III interferon signatures correspond to COVID-19 disease severity", @@ -905137,6 +903495,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.11.21253395", + "rel_title": "Airborne Transmission of COVID-19 and Mitigation Using Box Fan Air Cleaners in a Poorly Ventilated Classroom", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.11.21253395", + "rel_abs": "Many indoor places, including aged classrooms and offices, prisons, homeless shelters, etc., are poorly ventilated but resource-limited to afford expensive ventilation upgrade or commercial air purification systems, raising concerns on the safety of opening activities in these places in the era of COVID-19 pandemic. To address this challenge, using computational fluid dynamics, we conducted a systematic investigation of airborne transmission in a classroom equipped with a single horizontal unit ventilator (HUV) and evaluate the performance of low-cost box fan air cleaner for risk mitigation. Our study shows that placing box fan air cleaners in the classroom results in a substantial reduction of airborne transmission risk across the entire space. The air cleaner can achieve optimal performance when placed near the asymptomatic patient. However, without knowing the location of the patient, the performance of the cleaner is optimal near the HUV with the air flowing downwards. In addition, we find that it is more efficient in reducing aerosol concentration and spread in the classroom by adding air cleaners in comparison with raising the flow rate of HUV alone. The number and placement of air cleaners need to be adjusted to maintain its efficacy for larger classrooms and to account for the thermal gradient associated with human thermal plume and hot ventilation air during cold seasons. Overall, our study shows that box fan air cleaners can serve as an effective low-cost alternative for mitigating airborne transmission risks in poorly ventilated spaces.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Ruichen He", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Wanjiao Liu", + "author_inst": "Research and Advanced Engineering, Ford Motor Company" + }, + { + "author_name": "John Elson", + "author_inst": "Research and Advanced Engineering, Ford Motor Company" + }, + { + "author_name": "Rainer Vogt", + "author_inst": "Ford-Werke GmbH, Research & Innovation Center" + }, + { + "author_name": "Clay Maranville", + "author_inst": "Research and Advanced Engineering, Ford Motor Company" + }, + { + "author_name": "Jiarong Hong", + "author_inst": "University of Minnesota" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.03.11.21253374", "rel_title": "Acceptability of COVID-19 vaccination among health care workers in Ghana", @@ -905501,165 +903898,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.09.21253218", - "rel_title": "An observational cohort study on the incidence of SARS-CoV-2 infection and B.1.1.7 variant infection in healthcare workers by antibody and vaccination status", - "rel_date": "2021-03-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.09.21253218", - "rel_abs": "BackgroundNatural and vaccine-induced immunity will play a key role in controlling the SARS-CoV-2 pandemic. SARS-CoV-2 variants have the potential to evade natural and vaccine-induced immunity.\n\nMethodsIn a longitudinal cohort study of healthcare workers (HCWs) in Oxfordshire, UK, we investigated the protection from symptomatic and asymptomatic PCR-confirmed SARS-CoV-2 infection conferred by vaccination (Pfizer-BioNTech BNT162b2, Oxford-AstraZeneca ChAdOx1 nCOV-19) and prior infection (determined using anti-spike antibody status), using Poisson regression adjusted for age, sex, temporal changes in incidence and role. We estimated protection conferred after one versus two vaccinations and from infections with the B.1.1.7 variant identified using whole genome sequencing.\n\nResults13,109 HCWs participated; 8285 received the Pfizer-BioNTech vaccine (1407 two doses) and 2738 the Oxford-AstraZeneca vaccine (49 two doses). Compared to unvaccinated seronegative HCWs, natural immunity and two vaccination doses provided similar protection against symptomatic infection: no HCW vaccinated twice had symptomatic infection, and incidence was 98% lower in seropositive HCWs (adjusted incidence rate ratio 0.02 [95%CI <0.01-0.18]). Two vaccine doses or seropositivity reduced the incidence of any PCR-positive result with or without symptoms by 90% (0.10 [0.02-0.38]) and 85% (0.15 [0.08-0.26]) respectively. Single-dose vaccination reduced the incidence of symptomatic infection by 67% (0.33 [0.21-0.52]) and any PCR-positive result by 64% (0.36 [0.26-0.50]). There was no evidence of differences in immunity induced by natural infection and vaccination for infections with S-gene target failure and B.1.1.7.\n\nConclusionNatural infection resulting in detectable anti-spike antibodies and two vaccine doses both provide robust protection against SARS-CoV-2 infection, including against the B.1.1.7 variant.\n\nSummaryNatural infection resulting in detectable anti-spike antibodies and two vaccine doses both provided [≥] 85% protection against symptomatic and asymptomatic SARS-CoV-2 infection in healthcare workers, including against the B.1.1.7 variant. Single dose vaccination reduced symptomatic infection by 67%.", - "rel_num_authors": 36, - "rel_authors": [ - { - "author_name": "Sheila F Lumley", - "author_inst": "University of Oxford" - }, - { - "author_name": "Gillian Rodger", - "author_inst": "University of Oxford" - }, - { - "author_name": "Bede Constantinides", - "author_inst": "University of Oxford" - }, - { - "author_name": "Nicholas Sanderson", - "author_inst": "University of Oxford" - }, - { - "author_name": "Kevin K Chau", - "author_inst": "University of Oxford" - }, - { - "author_name": "Teresa L Street", - "author_inst": "University of Oxford" - }, - { - "author_name": "Alison Howarth", - "author_inst": "University of Oxford" - }, - { - "author_name": "Stephanie B Hatch", - "author_inst": "University of Oxford" - }, - { - "author_name": "Brian D Marsden", - "author_inst": "University of Oxford" - }, - { - "author_name": "Stuart Cox", - "author_inst": "Oxford University Hospitals" - }, - { - "author_name": "Tim James", - "author_inst": "Oxford University Hospitals" - }, - { - "author_name": "Fiona Warren", - "author_inst": "Oxford University Hospitals" - }, - { - "author_name": "Liam J Peck", - "author_inst": "University of Oxford" - }, - { - "author_name": "Thomas G Ritter", - "author_inst": "University of Oxford" - }, - { - "author_name": "Zoe de Toledo", - "author_inst": "University of Oxford" - }, - { - "author_name": "Laura Warren", - "author_inst": "Oxford University Hospitals" - }, - { - "author_name": "David Axten", - "author_inst": "Oxford University Hospitals" - }, - { - "author_name": "Richard J Cornall", - "author_inst": "University of Oxford" - }, - { - "author_name": "E Yvonne Jones", - "author_inst": "University of Oxford" - }, - { - "author_name": "David I Stuart", - "author_inst": "University of Oxford" - }, - { - "author_name": "Gavin Screaton", - "author_inst": "University of Oxford" - }, - { - "author_name": "Daniel Ebner", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sarah Hoosdally", - "author_inst": "University of Oxford" - }, - { - "author_name": "Meera Chand", - "author_inst": "Public Health England" - }, - { - "author_name": "- Oxford University Hospitals Staff Testing Group", - "author_inst": "" - }, - { - "author_name": "Derrick Crook", - "author_inst": "University of Oxford" - }, - { - "author_name": "Christopher P Conlon", - "author_inst": "University of Oxford" - }, - { - "author_name": "Koen B Pouwels", - "author_inst": "University of Oxford" - }, - { - "author_name": "A Sarah Walker", - "author_inst": "University of Oxford" - }, - { - "author_name": "Tim EA Peto", - "author_inst": "University of Oxford" - }, - { - "author_name": "Susan Hopkins", - "author_inst": "Public Health England" - }, - { - "author_name": "Timothy M Walker", - "author_inst": "University of Oxford" - }, - { - "author_name": "Nicole EA Stoesser", - "author_inst": "University of Oxford" - }, - { - "author_name": "Philippa C Matthews", - "author_inst": "University of Oxford" - }, - { - "author_name": "Katie Jeffery", - "author_inst": "Oxford University Hospitals" - }, - { - "author_name": "David W Eyre", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.11.21253207", "rel_title": "Recovered not restored: Long-term health consequences after mild COVID-19 in non-hospitalized patients", @@ -906715,6 +904953,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.12.21253447", + "rel_title": "Impact of Vaccine Prioritization Strategies on Mitigating COVID-19: An Agent-Based Simulation Study using an Urban Region in the United States", + "rel_date": "2021-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.12.21253447", + "rel_abs": "BackgroundApproval of novel vaccines for COVID-19 had brought hope and expectations, but not without additional challenges. One central challenge was understanding how to appropriately prioritize the use of limited supply of vaccines. This study examined the efficacy of the various vaccine prioritization strategies using the vaccination campaign underway in the U.S.\n\nMethodsThe study developed a granular agent-based simulation model for mimicking community spread of COVID-19 under various social interventions including full and partial closures, isolation and quarantine, use of face mask and contact tracing, and vaccination. The model was populated with parameters of disease natural history, as well as demographic and societal data for an urban community in the U.S. with 2.8 million residents. The model tracks daily numbers of infected, hospitalized, and deaths for all census age-groups. The model was calibrated using parameters for viral transmission and level of community circulation of individuals. Published data from the Florida COVID-19 dashboard was used to validate the model. Vaccination strategies were compared using a hypothesis test for pairwise comparisons.\n\nResultsThree prioritization strategies were examined: a minor variant of CDCs recommendation, an age-stratified strategy, and a random strategy. The impact of vaccination was also contrasted with a no vaccination scenario. The study showed that the campaign against COVID-19 in the U.S. using vaccines developed by Pfizer/BioNTech and Moderna 1) reduced the cumulative number of infections by 10% and 2) helped the pandemic to subside below a small threshold of 100 daily new reported cases sooner by approximately a month when compared to no vaccination. A comparison of the prioritization strategies showed no significant difference in their impacts on pandemic mitigation.\n\nConclusionsEven though vaccines for COVID-19 were developed and approved much quicker than ever before, their impact on pandemic mitigation was small as the explosive spread of the virus had already infected a significant portion of the population, thus reducing the susceptible pool. A notable observation from the study is that instead of adhering strictly to a sequential prioritizing strategy, focus should perhaps be on distributing the vaccines among all eligible as quickly as possible, after providing for the most vulnerable. As much of the population worldwide is yet to be vaccinated, results from this study should aid public health decision makers in effectively allocating their limited vaccine supplies.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Hanisha Anand Tatapudi", + "author_inst": "University of South Florida" + }, + { + "author_name": "Rachita Das", + "author_inst": "Miller School of Medicine" + }, + { + "author_name": "Tapas K Das", + "author_inst": "University of South Florida" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.11.21253421", "rel_title": "Exposure to SARS-CoV-2 within the household is associated with greater symptom severity and stronger antibody responses in a community-based sample of seropositive adults", @@ -907214,61 +905479,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.03.11.434937", - "rel_title": "SARS-CoV-2 comprehensive receptor profiling: mechanistic insight to drive new therapeutic strategies", - "rel_date": "2021-03-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.11.434937", - "rel_abs": "Here we describe a hypothesis free approach to screen for interactions of SARS-CoV-2 spike (S) protein with human cell surface receptors. We used a library screening approach to detect binding interactions across one of the largest known panels of membrane-bound and soluble receptors, comprising 5845 targets, expressed recombinantly in human cells. We were able confirm and replicate SARS-CoV-2 binding to ACE2 and other putative coreceptors such as CD209 and CLEC4M. More significantly, we identified interactions with a number of novel SARS-CoV-2 S binding proteins. Three of these novel receptors, NID1, CNTN1 and APOA4 were specific to SARS-CoV-2, and not SARS-COV, with APOA4 binding the S-protein with equal affinity as ACE2. With this knowledge we may further understand the disease pathogenesis of COVID-19 patients and how infection by SARS-CoV-2 may lead to differences in pathology in specific organs or indeed the virulence observed in different ethnicities. Importantly we illustrate a methodology which can be used for rapid, unbiassed identification of cell surface receptors, to support drug screening and drug repurposing approaches for this and future pandemics.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Sarah MV Brockbank", - "author_inst": "Medicines Discovery Catapult" - }, - { - "author_name": "Raquel Faba-Rodriguez", - "author_inst": "Peak Proteins Limited" - }, - { - "author_name": "Lyn Rosenbrier Ribeiro", - "author_inst": "Medicines Discovery Catapult" - }, - { - "author_name": "Catherine Geh", - "author_inst": "Peak Proteins Limited" - }, - { - "author_name": "Helen Thomas", - "author_inst": "Retrogenix Ltd" - }, - { - "author_name": "Jenni Delight", - "author_inst": "Retrogenix Ltd" - }, - { - "author_name": "Lucy Coverley", - "author_inst": "Retrogenix Ltd" - }, - { - "author_name": "W Mark Abbott", - "author_inst": "Peak Proteins Limited" - }, - { - "author_name": "Jo Soden", - "author_inst": "Retrogenix Ltd" - }, - { - "author_name": "Jim Freeth", - "author_inst": "Retrogenix Ltd" - } - ], - "version": "1", - "license": "cc0_ng", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2021.03.11.434764", "rel_title": "Novel inhibition mechanism of SARS-CoV-2 main protease by ebselen and its derivatives", @@ -908507,6 +906717,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.08.21252958", + "rel_title": "Immune response to SARS-CoV-2 variants of concern in vaccinated individuals", + "rel_date": "2021-03-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.08.21252958", + "rel_abs": "The SARS-CoV-2 pandemic virus is consistently evolving with mutations within the receptor binding domain (RBD)1 being of particular concern2-4. To date, there is little research into protection offered following vaccination or infection against RBD mutants in emerging variants of concern (UK3, South African5, Mink6 and Southern California7). To investigate this, serum and saliva samples were obtained from groups of vaccinated (Pfizer BNT-162b28), infected and uninfected individuals. Antibody responses among groups, including salivary antibody response and antibody binding to RBD mutant strains were examined. The neutralization capacity of the antibody response against a patient-isolated South African variant was tested by viral neutralization tests and further verified by an ACE2 competition assay. We found that humoral responses in vaccinated individuals showed a robust response after the second dose. Interestingly, IgG antibodies were detected in large titers in the saliva of vaccinated subjects. Antibody responses showed considerable differences in binding to RBD mutants in emerging variants of concern. A substantial reduction in RBD binding and neutralization was detected for the South African variant. Taken together our data reinforces the importance of administering the second dose of Pfizer BNT-162b2 to acquire high levels of neutralizing antibodies. High antibody titers in saliva suggest that vaccinated individuals may have reduced transmission potential. Substantially reduced neutralization for the South African variant highlights importance of surveillance strategies to detect new variants and targeting these in future vaccines.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Matthias Becker", + "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany" + }, + { + "author_name": "Alex Dulovic", + "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany" + }, + { + "author_name": "Daniel Junker", + "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany" + }, + { + "author_name": "Natalia Ruetalo", + "author_inst": "Institute for Medical Virology and Epidemiology, University Hospital Tuebingen, Tuebingen, Germany" + }, + { + "author_name": "Philipp Kaiser", + "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany" + }, + { + "author_name": "Yudi Pinilla", + "author_inst": "Institute of Tropical Medicine, University of Tuebingen, Germany" + }, + { + "author_name": "Constanze Heinzel", + "author_inst": "Institute of Tropical Medicine, University of Tuebingen, Germany" + }, + { + "author_name": "Julia Haering", + "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany" + }, + { + "author_name": "Bjoern Traenkle", + "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany" + }, + { + "author_name": "Teresa Wagner", + "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany" + }, + { + "author_name": "Mirjam Layer", + "author_inst": "Institute for Medical Virology and Epidemiology, University Hospital Tuebingen, Tuebingen, Germany" + }, + { + "author_name": "Martin Mehrlaender", + "author_inst": "Department of Anaesthesiology and Intensive Care Medicine, University Hospital Tuebingen, Tuebingen, Germany" + }, + { + "author_name": "Valbona Mirakaj", + "author_inst": "Department of Anaesthesiology and Intensive Care Medicine, University Hospital Tuebingen, Tuebingen, Germany" + }, + { + "author_name": "Jana Held", + "author_inst": "Institute of Tropical Medicine, University of Tuebingen, Germany" + }, + { + "author_name": "Hannes Planatscher", + "author_inst": "Signatope GmbH, Reutlingen, Germany" + }, + { + "author_name": "Katja Schenke-Layland", + "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany" + }, + { + "author_name": "Gerard Krause", + "author_inst": "Helmholtz Centre for Infection Research, Braunschweig, Germany" + }, + { + "author_name": "Monika Strengert", + "author_inst": "Helmholtz Centre for Infection Research, Braunschweig, Germany" + }, + { + "author_name": "Tamam Bakchoul", + "author_inst": "Institute for Clinical and Experimental Transfusion Medicine, University Hospital Tuebingen, Tuebingen, Germany" + }, + { + "author_name": "Karina Althaus", + "author_inst": "Institute for Clinical and Experimental Transfusion Medicine, University Hospital Tuebingen, Tuebingen, Germany" + }, + { + "author_name": "Rolf Fendel", + "author_inst": "Institute of Tropical Medicine, University of Tuebingen, Germany" + }, + { + "author_name": "Andrea Kreidenweiss", + "author_inst": "Institute of Tropical Medicine, University of Tuebingen, Germany" + }, + { + "author_name": "Michael Koeppen", + "author_inst": "Department of Anaesthesiology and Intensive Care Medicine, University Hospital Tuebingen, Tuebingen, Germany" + }, + { + "author_name": "Ulrich Rothbauer", + "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany" + }, + { + "author_name": "Michael Schindler", + "author_inst": "Institute for Medical Virology and Epidemiology, University Hospital Tuebingen, Tuebingen, Germany" + }, + { + "author_name": "Nicole Schneiderhan-Marra", + "author_inst": "NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.09.21252401", "rel_title": "Agreement between commercially available ELISA and in-house Luminex SARS-CoV-2 antibody immunoassays", @@ -909079,77 +907408,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.03.08.21253141", - "rel_title": "COVID-19 is associated with multiple sclerosis exacerbations that are prevented by disease modifying therapies", - "rel_date": "2021-03-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.08.21253141", - "rel_abs": "BackgroundInfections can trigger exacerbations of multiple sclerosis (MS). The effects of the coronavirus disease 2019 (COVID-19) on MS are not known. The aim of this study was to understand the impact of COVID-19 on new and pre-existing symptoms of MS.\n\nMethodsThe COVID-19 and MS study is an ongoing community-based, prospective cohort study conducted as part of the United Kingdom MS Register. People with MS and COVID-19 were invited by email to complete a questionnaire about their MS symptoms during the infection. An MS exacerbation was defined as developing new MS symptoms and/or worsening of pre-existing MS symptoms.\n\nResultsFifty-seven percent (230/404) of participants had an MS exacerbation during their infection; 82 developed new MS symptoms, 207 experienced worsened pre-existing MS symptoms, and 59 reported both. Disease modifying therapies (DMTs) reduced the likelihood of developing new MS symptoms during the infection (OR 0.556, 95%CI 0.316-0.978). Participants with a higher pre-COVID-19 webEDSS (web-based Expanded Disability Status Scale) score (OR 1.251, 95%CI 1.060-1.478) and longer MS duration (OR 1.042, 95%CI 1.009-1.076) were more likely to experience worsening of their pre-existing MS symptoms during the infection.\n\nConclusionCOVID-19 infection was associated with exacerbation of MS. DMTs reduced the chance of developing new MS symptoms during the infection.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Afagh Garjani", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Rodden M Middleton", - "author_inst": "Swansea University Medical School" - }, - { - "author_name": "Rachael Hunter", - "author_inst": "Swansea University" - }, - { - "author_name": "Katherine A Tuite-Dalton", - "author_inst": "Swansea University Medical School" - }, - { - "author_name": "Alasdair Coles", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Ruth Dobson", - "author_inst": "Queen Mary University London" - }, - { - "author_name": "Martin Duddy", - "author_inst": "Newcastle upon Tyne Hospitals NHS Trust" - }, - { - "author_name": "Stella Hughes", - "author_inst": "Belfast Health and Social Care Trust" - }, - { - "author_name": "Owen R Pearson", - "author_inst": "Swansea Bay University Health Board" - }, - { - "author_name": "David Rog", - "author_inst": "Salford Royal NHS Foundation Trust" - }, - { - "author_name": "Emma C Tallantyre", - "author_inst": "Cardiff University" - }, - { - "author_name": "Roshan das Nair", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Richard Nicholas", - "author_inst": "Imperial College London" - }, - { - "author_name": "Nikos Evangelou", - "author_inst": "University of Nottingham" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2021.03.09.21253183", "rel_title": "Efficacy of remdesivir in Japanese patients hospitalised with COVID-19: A large observational study using the COVID-19 Registry Japan", @@ -911133,6 +909391,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.08.21252586", + "rel_title": "Categorizing the Status of COVID-19 Outbreaks Around the World", + "rel_date": "2021-03-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.08.21252586", + "rel_abs": "Although the SARS-CoV-19 virus spread rapidly around in world in early 2020, disease epidemics in different places evolved differently as the year progressed - and the state of the COVID-19 pandemic now varies significantly across different countries and territories. We have created a taxonomy of possible categories of disease dynamics, and used the evolution of reported COVID-19 cases relative to changes in disease control measures, together with total reported cases and deaths, to allocate most countries and territories among the possible categories. As of 31 January 2021, we find that the disease was (1) kept out or suppressed quickly through quarantines and testing & tracing in 39 countries with 29 million people, (2) suppressed on one or more occasions through control measures in 74 countries with 2.49 billion people, (3) spread slowly but not suppressed, with cases still increasing or just past a peak, in 31 countries with 1.45 billion people, (4) spread through the population, but slowed a result of control measures, leading to a \"flattened curve\" and fewer infections than if the epidemic were unmitigated, in 32 countries with 2.24 billion people, and (5) spread through the population with some but limited mitigation in 5 countries with 168 million people. In addition, several countries have experienced increases in cases after disease appeared to have finished spreading due to declining numbers of susceptible people. For some of these countries - for example Kenya, Pakistan and Afghanistan - the resurgences can be explained by the relaxation of control measures (and may have been enhanced by disease spread in population segments that experienced lower infection levels during the first waves). For other countries, the resurgences point to the effects of new virus variants with higher transmissibility or immunity resistance - including most countries in Southern Africa (where the B.1.351 variant has been identified) and several countries in West Africa (potentially due to the B.1.1.7 or other variants). These findings are consistent with mounting evidence of high infection rates in several low- and middle-income countries, both from seroprevalence studies and estimates of actual deaths from COVID-19 combined with estimates of expected mortality rates. We estimate that 1.3-3.0 billion people, or 17-39% of the global population, have been infected by SARS-CoV-2 to date, and that at least 4.5 million people have died from COVID-19 - much higher than reported cases and deaths. Disease control policies and vaccination strategies should be designed based on the state of the COVID-19 epidemic in the population - and consequently may need to be different in different countries.\n\nKey Points The state of the COVID-19 pandemic varies significantly in different countries and territories around the world - and policies for disease control and vaccination will need to be tailored accordingly.\nIn any epidemic, there are several possibilities for how the disease will spread over time - and our analysis finds that, in fact, as of 31 January 2021, there were many countries and territories in each of the main categories of COVID-19 epidemic dynamics that might have been expected:\nO_LIKept out or suppressed quickly through quarantines and testing & tracing - in 39 countries with 29 million people (0.4% of the global population), mostly small island states and a few countries in Southeast Asia. [Category H in the following map and table]\nC_LIO_LISuppressed through control measures (social distancing, hygiene and testing & tracing) -in 74 countries with 2.49 billion people (31.9% of global population), mostly in Europe, East Asia and the Pacific. [Categories F and G]\nC_LIO_LISpread slowly but not suppressed, with cases still increasing or just past a peak - in 31 countries with 1.45 billion people (18.6% of global population), including many countries in Latin America, Eastern Europe and the Middle East, as well as the United States and Russia. [Categories D and E]\nC_LIO_LISpread through the population, but slowed as a result of control measures, leading to a \"flattened curve\" and fewer infections than if the epidemic were unmitigated - in 32 countries with 2.24 billion people (28.8% of global population), mostly in South and Southeast Asia (including India) and Africa. [Category B]\nC_LIO_LISpread through the population with some but limited mitigation or \"flattening the curve\" -in 5 countries with 168 million people (2.2% of global population). [Category A]\nC_LIO_LIExperienced increases in cases after disease appeared to have finished spreading, which in some countries might have been solely due to relaxation of control measures (especially in wealthier population segments which experienced low infection levels during the first wave) - for example in Kenya and in Pakistan and some Central Asian countries - but which in some countries is likely to be due to new virus variants with higher transmissibility or immunity resistance - for example in most countries in Southern Africa and several in West Africa, and possibly also in parts of South and Central America. [Category J and many countries in Category K]\nC_LI\nThese findings are backed up by mounting evidence of high infection rates in several low- and middle-income countries. Seroprevalence studies in Kenya, Nigeria, Pakistan and South Africa have reported finding antibodies for SARS-CoV-2 in large percentages of the studied populations - and suggest that current infection levels are likely above 50% in each country. Studies of actual deaths due to COVID-19, combined with estimates of expected mortality rates, similarly suggest that SARS-CoV-2 has, by now, infected more than half of the populations in Bolivia, Ecuador, Peru, Mexico, South Africa, Sudan, Syria, Yemen and Zambia.\nCountries of all income levels, and from all regions, appear in each of the main disease dynamics categories; however, there are clear income and geographical patterns in states of COVID-19 epidemics around the world. Most high-income countries have controlled the spread of SARS-CoV-2 through measures. Middle-income countries are spread across all categories, and account for 45 of the 63 countries which have slowed the disease significantly but not fully suppressed it. Some low-income have experienced largely unmitigated susceptibility-driven dynamics, while others have \"flattened the curve\" to varying degrees.\nWe estimate that between one and two out of every five people globally has been infected by SARS-CoV-2 to date, and that at least 4.5 million people have died from COVID-19. Our estimate of total infections - 1.3-3.0 billion people, or 17-39% of the global population - is between 13 and 30 times the number of confirmed cases, and twice to four times as much as previous estimates of total infection numbers. We estimate that 4.6-10.0 million people have died from COVID-19, between 2.1 and 4.5 times the number of deaths attributed to COVID-19.\nAn estimated 8.9-12.5 million lives remained at risk from COVID-19 as of the end of January 2021, prior to vaccination efforts - mainly in high-income countries (2.4-2.9 million), China (2.1 million) and India (1.7-2.9 million). Vaccinations, of course, have already started to reduce these numbers substantially.\nOur analytical approach is simple but useful - providing insight into the epidemic status even in many low-income countries with limited disease monitoring, and with potential to provide early warnings of significant new variants. We compare the evolution of reported cases with changes in stringency of disease control measures, and check that infection levels are plausible given total reported cases and deaths and the income level of the country. Anomalies in which changes in the evolution of reported cases cannot be explained by changes in the stringency index provide indications of possible significant variants of the virus. Up to the end of January, the data provide indications of the presence of significant new variants in:\nO_LIMost countries in Southern Africa (where the B.1.351 variant, with higher transmissibility and some resistance to immunity, was first identified in South Africa)\nC_LIO_LISeveral countries in West Africa (likely with higher transmissibility and resistance to immunity, possibly the B.1.1.7 variant, which was first identified in the UK and has been found in Ghana and Nigeria, or possibly a different variant).\nC_LI\nThey also suggest, with less certainty, that the disease dynamics may be affected by new variants in several countries in South and Central America (perhaps the P.1 variant descended from the B.1.1.28 variant which was first identified as coming from the Brazilian Amazon).\nDifferent countries should adopt different disease control policies, according to the state of the COVID-19 epidemic in the population.\nO_LIFor countries that have kept the disease out or suppressed outbreaks through control measures, their measures need to be kept in place - and potentially strengthened especially in the face of higher-transmissibility variants - until vaccines have been widely administered.\nC_LIO_LIFor countries in which the disease is spreading slowly, full control measures should be maintained at least until new case numbers fully decline from the peak; later, it may be possible to relax some measures, but if measures are relaxed too soon or too much after cases peak, then significant further outbreaks can be expected (as has already happened in several such countries).\nC_LIO_LIFor countries in which cases have declined following a flattened curve, there may be room to relax control measures that have the greatest negative health, economic and social consequences - but the most effective control measures will need to be maintained (even when cases remain low for extended periods), and measures may need to be strengthened to tackle variants which higher transmissibility or ability to evade immune responses.\nC_LIO_LIFor countries in which the disease spread was largely unmitigated, many control measures could be relaxed for most people - although there may be risks if sizeable population segments have much lower infection levels than the general population or from variants with a high degree of immunity resistance.\nC_LI\nThese findings may have implications for the optimal distribution of early batches of vaccines within countries.\nO_LIFor countries that have kept the disease out or suppressed outbreaks through control measures, vaccinations should be given first to frontline healthcare and essential workers and to elderly and vulnerable groups (starting with the oldest and most vulnerable).\nC_LIO_LIFor countries in which the disease is spreading slowly, detailed modelling should be done to determine whether the optimal strategy is to vaccinate at-risk groups first or to vaccinate key transmitters to halt the outbreak and \"crush the curve\" while waiting for further vaccine supplies to arrive. For any country choosing the key transmitter strategy - as Indonesia has done and has been suggested for the United States - it will be essential to maintain control measures, and to keep higher transmissibility variants out, or otherwise the benefits of a key transmitter vaccination strategy could be lost.\nC_LIO_LIFor countries in which the cases declined following a flattened curve, vaccinations should probably be given first to elderly and vulnerable groups, but the optimal strategy may switch to vaccinating key transmitters if there are resurgences in cases due to higher-transmissibility or immunity-resistant variants.\nC_LIO_LIFor countries in which the disease spread was largely unmitigated, vaccination should concentrate on elderly and vulnerable people, because population-level immunity already exists, and the greatest danger lies in vulnerable people becoming infected due to endemic SARS-CoV-2 from variants that will likely circulate over many years.\nC_LI\nThese findings may also have implications for the optimal distribution of the first vaccines across countries. For most countries, the optimal allocation of vaccines doses is likely still to be according to population size - as current recommendations suggest. However, the global optimal allocation strategy might include providing somewhat greater supplies, during the next few months, to countries where using the vaccine to halt spread of the disease might be possible (provided that disease control measures are maintained in those countries).\nVaccination strategies will need to account for current and potential future virus variants as well as the likelihood that immunity from vaccination will wane over time. Higher-transmissibility variants of the SARS-CoV-2 virus increase the urgency of distributing vaccines in countries which have controlled the disease to date, and may alter the optimal strategy for countries deciding between vaccination first of elderly and vulnerable people or of key transmitters. Immunity-resistant variants of the virus may reduce the effectiveness of current vaccines, but are not likely to negate fully the protection they offer. Immunity acquired through vaccination is likely to wane over time - like immunity acquired through infection. In many, perhaps most, countries, the time to vaccinate the whole population will exceed the timeframe in which immunity from vaccination wanes or new immunity-resistant variants emerge. Looking to the longer term, therefore, new virus variants and waning immunity are likely to necessitate re-vaccination (with vaccines tailored to the latest variants) on a regular basis - and the optimal long-term strategies for ongoing vaccination will vary widely across countries and will depend on many factors.\n\n\nO_FIG O_LINKSMALLFIG WIDTH=154 HEIGHT=200 SRC=\"FIGDIR/small/21252586v3_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (46K):\norg.highwire.dtl.DTLVardef@c39b02org.highwire.dtl.DTLVardef@1f5ccceorg.highwire.dtl.DTLVardef@590b3dorg.highwire.dtl.DTLVardef@1f0f1c5_HPS_FORMAT_FIGEXP M_FIG C_FIG O_FIG O_LINKSMALLFIG WIDTH=151 HEIGHT=200 SRC=\"FIGDIR/small/21252586v3_ufig2.gif\" ALT=\"Figure 2\">\nView larger version (60K):\norg.highwire.dtl.DTLVardef@190e169org.highwire.dtl.DTLVardef@bec2a2org.highwire.dtl.DTLVardef@1dc3cf0org.highwire.dtl.DTLVardef@24d56b_HPS_FORMAT_FIGEXP M_FIG C_FIG SummaryThe state of the COVID-19 pandemic varies significantly in different countries and territories around the world - and policies for disease control and vaccination will need to be tailored accordingly. Although the SARS-CoV-19 virus spread rapidly around in world in early 2020, the state of disease epidemics in different countries diverged rapidly as the year progressed. Many high-income countries have had second or third waves; other countries have seen cases continue to increase gradually; still others have experienced declines in cases to low levels after peaks in mid-2020. Facing different situations, different countries might need to adopt different policies in the coming months, including different disease control measures and vaccination strategies.\n\nEach country needs to know its COVID-19 status. There are several possible courses that a disease epidemic can take in a population. The disease can spread rapidly until its runs out of people remaining to infect; the disease can be slowed with control measures but still spread until large numbers of people are infected and immune; the disease can be suppressed or \"crushed\" by control measures; or the disease can be kept out completely. More complex disease dynamics will occur when a virus mutates, if new variants evade immune responses in people already infected or spread faster than before, or if the disease spreads differently in different segments of a population. Our research suggests that different countries have experienced outbreaks in each of the main possible categories:\n\nO_LISusceptibility-Driven Dynamics with Limited Mitigation [Category A] - in which the disease spread until it infect most people and declined due to low susceptibility levels (i.e., low share of the population still able to be infected).\nC_LIO_LISusceptibility-Driven Dynamics Mitigated by Measures [Categories B and C] - in which the disease curve was \"flattened\" by control measures, but the disease still spread and declined after infecting large numbers of people (but fewer than if there were no mitigation).\nC_LIO_LISusceptibility-plus-Measures-Driven Dynamics [Categories D and E] - in which the disease was slowed significantly but not suppressed, i.e., the curve was \"flattened\" but not \"crushed\", and the disease is still spreading in the population.\nC_LIO_LIMeasures-Driven Dynamics [Categories F and G] - in which the disease has been constrained to date mainly through control measures (social distancing, hygiene and testing & tracing), but, of course, could spread again if measures are relaxed because only a minority of the population has been infected.\nC_LIO_LIIndex-Case-Control Dynamics [Category H] - in which the disease has been kept out or suppressed to date through strict control measures (especially quarantines and testing & tracing).\nC_LIO_LIComplex Disease Dynamics due to Differences Across Population Segments and/or New Variants [Categories I and J, and many countries in Category K] - in which the disease experienced an apparently susceptibility-driven curve but with low overall infection levels (i.e., share of population infected) because some segments of the population have not had many infections, or in which the disease later shows an unexpected resurgence, due to spreading within the previously less-affected population segments or due to the emergence of immunity-evading strains of the virus.\nC_LI\n\nFrom reported data on COVID-19 cases and disease control measures, we can categorize, for most countries and territories, the dynamics of the disease to date. First, we compare the timing of increases and/or decreases in reported new cases with the timing of changes in the \"Stringency Index\" of control measures compiled by the Oxford COVID-19 Government Response Tracker - and select the appropriate disease dynamics category. Second, we check if the infection levels expected for the category or categories indicated in the first step, are consistent with predicted ranges from the total numbers of reported cases and deaths using plausible ranges for the case detection rate, death detection rate and infection fatality ratio (IFR) given the countrys income level. This approach yields definitive categories for most countries and territories. COVID-19 disease dynamics are complicated in many countries, due to changes in control measures, seasonal patterns, geographical differences within countries, variability in case testing over time and emergence of new variants; such effects can be seen in the reported cases and deaths for many countries, but they do not obscure the basic drivers of disease dynamics - in other words, which of the categories applies - for most countries.\n\nThe results suggest that there is a wide variation in the state of the COVID-19 epidemic around the world - as of 31 January 2021 - as illustrated in the map and the table below. COVID-19 has been suppressed through control measures - Categories F, G and H - in 113 countries and territories with 2.52 billion people or about 32.3% of the global population. However, the rest of the world are in different situations. A total of 31 countries, with populations of 1.45 billion people (18.6% of global population), fall into Categories D and E, meaning that the disease spread has been slowed but not suppressed and cases are currently still increasing or just past their peak. In the 23 countries of Category B, home to 2.05 billion people (26.3%), the disease was slowed but not suppressed, and cases have declined fully from the peak. In a further 9 countries with 0.19 billion people (2.5%), the disease spread through the population after initial waves were suppressed. COVID-19 outbreaks in 5 countries with 0.17 billion people (2.2%) were only somewhat mitigated by control measures and the virus has likely infected most of the population, falling into Category A.\n\nFor several countries, which have apparent anomalies and fall outside the \"basic\" categories, the methodology provides important insights into epidemic status - pointing to situations where significant differences may exist across population segments or providing early warnings of new variants with higher transmissibility or resistance to immunity. For 5 Arabian Peninsula countries (3 of which are in Category I) and Singapore, it is likely that the virus has spread widely among migrant worker communities but has been controlled in the rest of the population. Categories J and K include 28 countries in which reported cases have surged after first waves which were likely or possibly susceptibility-driven, with curves flattened to various extents as a result of control measures which mitigated the epidemics. For some countries - including (1) Kenya, (2) Pakistan, Afghanistan, Kyrgyzstan and Kazakhstan, and (3) Egypt and Sudan - the second peaks are likely due to relaxation of measures but larger than might be expected due to disproportionate effects of the second waves on population segments (likely more affluent groups) which had lower infection levels during the first waves. For other countries - including (1) most countries in Southern Africa and (2) many countries in West Africa - the data suggest the presence of new virus variants with higher transmissibility and possible resistance to immunity, because resurgences or accelerations in cases happened in several neighbouring countries around the same time, and often without changes in control measures, and the second surges in cases usually involved faster increases than the first waves. The B.1.351 variant, with higher transmissibility and some resistance to immunity, was first identified in South Africa and is known to have caused most cases in the countrys second wave; the B.1.1.7 variant, which has higher transmissibility, has been found in Ghana and Nigeria. Several countries in South and Central America have experienced second waves or surges in cases: Surinames might be due to a higher-transmissibility variant (perhaps the P.1 variant that was first identified as coming from the Brazilian Amazon); Bolivias was large but could be explained by a significant decline in control measures; increases in Brazil and several other countries across South and Central America might simply be due to relaxation of social distancing behaviours over the Christmas and New Year holiday season although a role for virus variants cannot be discounted.\n\nCountries of all income levels appear in each of the main disease dynamics categories; however there are clear correlations between income groups and COVID-19 status categories. Most high-income countries have controlled the spread of SARS-CoV-2 through measures (and thus fall in Categories F, G and H). Middle-income countries are spread across all categories, and account for 45 of the 63 countries which have slowed the disease significantly but not fully suppressed it (Categories B, C, D and E). Some low-income countries have experienced largely unmitigated susceptibility-driven dynamics (Category A), while others have \"flattened the curve\" to varying degrees (Categories B, C, D and E). A mix of low- and middle-income countries are among the 34 countries in Categories J and K.\n\nClear geographical patterns have emerged in the states of COVID-19 epidemics. There was more diversity in the state of the epidemic within regions earlier in the pandemic, but regional patterns had become clear by the end of January 2021.\n\nO_LIIn the Americas, the disease has spread slowly but has not been suppressed (Categories D and E) in most countries, including those with the largest populations, while many (but not all) of the Caribbean islands have kept SARS-CoV-2 out or under control (Category H).\nC_LIO_LIWestern and Northern European countries have, for the most part, controlled the disease through social distancing and hygiene measures, through two or three waves, and fall in Categories F and G.\nC_LIO_LIAcross Eastern Europe, the Levant, the Caucuses and Iran, all countries have constrained growth of the disease significantly, but infection levels in most have grown to moderate levels: different countries in these regions are included in Categories C, D/E and F/G, although their infection levels may all be in the moderate range.\nC_LIO_LIIn South and Central Asia, the virus has spread widely in most countries and cases have declined. In India, Bangladesh, Nepal and Uzbekistan, the case curve was flattened considerably, and current infection levels are likely moderate (Category B). In Pakistan, Afghanistan, Kyrgyzstan, and Kazakhstan (all in Category J), there have been two peaks in cases. Bhutan has contained the outbreaks of the virus to date (Category F).\nC_LIO_LIMany countries in East and South-East Asia have largely kept the disease under control or kept it out (Categories F, G and H). However, Malaysia, Mongolia and Myanmar experienced widespread outbreaks in the second half of 2020, the Philippines appears to be past the peak of its epidemic (Category B), and Indonesia has had a continuous but very slow rise in cases since the start of the pandemic (Category E).\nC_LIO_LIIn Australia, New Zealand and most Pacific Island States, SARS-CoV-2 has been excluded through quarantines, together with testing and tracing and lockdowns when the virus has spread beyond quarantined individuals (Categories F and H).\nC_LIO_LIAfrican countries appear to have differed greatly in how the disease has spread. Many countries appear to have experienced widespread epidemics followed by declines in case numbers, with varying degrees of \"curve flattening\" due to control measures (Categories A and B). In some countries - Tunisia, Libya, Togo, Botswana and Mozambique - cases spread very slowly (Categories D and E). A few countries appear to have kept the disease out, and a few others appear to have experienced full outbreaks after having previously kept the virus largely out. As described earlier, most countries in Southern Africa and many in West Africa experienced rapid growth in case numbers in December and January (putting many in Categories J and K) - suggestive of the presence of one or more new variants with higher transmissibility and possible resistance to immunity.\nC_LI\n\nWe estimate that 1.3-3.0 billion people have been infected by SARS-CoV-2 to date, or about 17-39% of the global population. This estimate is between 13 and 30 times the number of confirmed cases, and perhaps twice to four times as much as previous estimates of total infection numbers. We estimate that 4.6-10.0 million people have died from COVID-19, between 2.1 and 4.5 times the number of deaths attributed to COVID-19.\n\nAn estimated 8.9-12.5 million lives remain at risk from COVID-19, which can be saved through appropriate disease control measures and effective deployment of vaccines. Of these estimated extra deaths, if 90% of the population were to contract SARS-CoV-2, high-income countries account for about 2.4-2.9 million, China for about 2.1 million, and India for about 1.7- 2.9 million. Vaccinations, of course, have already started to reduce these numbers substantially.\n\nThe findings of this report are backed up by mounting evidence of high infection rates in several low- and middle-income countries. Immunity testing provides direct evidence of the current state of the COVID-19 epidemic. Serological studies in several cities and regions in Brazil, India, Kenya, Pakistan, Qatar and South Africa have already reported finding antibodies for SARS-CoV-2 in large percentages of the studied populations. Note, however, that serological testing will underestimate the number of people who have been infected, due to waning of SARS-CoV-2 antibodies which affects significant numbers of people at about 4-6 months after infection. Consequently, serological testing might understate the actual degree of immunity in a population, because some people may have antibodies at levels below the detection threshold of the serology tests or may have memory B cell or T cell responses, either or both of which will likely reduce the severity of their illness if reinfected, and may reduce their vulnerability to reinfection and their likelihood to pass on the virus to other people if reinfected. In some places, reliable estimates of actual deaths due to COVID-19 may be a substitute for immunity testing to determine the share of population infected to date, at least approximately. Estimates, using a variety of methodologies, in Bolivia, Ecuador, Mexico, Peru, South Africa, Sudan, Syria, Yemen and Zambia all indicate that moderate to high shares of their populations have already been infected.\n\nDifferent countries should adopt different disease control policies, according to the state of the COVID-19 epidemic in the population. The following recommendations for countries in different categories take into account their current infection levels and the potential for additional infections if measures are relaxed or if new variants become common in a country.\n\n[tpltrtarr]Category A: Control measures should be relaxed for most people; such relaxation is not likely to lead to many more cases and deaths. In some low- and middle-income countries, wealthier population segments may have implemented greater degrees of social distancing during the epidemic to date, and have much lower infection levels than in the overall population; these segments should maintain social distancing, until vaccines arrive, because otherwise they could experience substantial outbreaks (which may have generated \"second waves\" in some countries). If and when new virus strains with higher transmissibility and/or resistance to immunity arrive, control measures should be strengthened again to avoid new outbreaks, if the new variants cause high mortality levels and if it seems likely that control measures will be more effective at controlling the new outbreaks than they were during the initial outbreaks.\n[tpltrtarr]Categories B and C: Control measures currently in place that have the greatest negative health, economic and social consequences could be relaxed. However, many control measures, especially the most effective in limiting virus spread, will need to be maintained, even though current case numbers are low; otherwise, significant resurgences can take place (as has happened, for instance, in Kenya and Bolivia). Population segments that may have maintained lower infection levels during the outbreak to date will need to maintain social distancing. If and when new virus strains with higher transmissibility and/or resistance to immunity arrive, control measures will likely have to be strengthened again to avoid new outbreaks.\n[tpltrtarr]Categories D and E: Control measures should be maintained at least until new case numbers fully decline from the peak; if measures are relaxed too soon after cases peak, then significant further outbreaks can be expected (as has happened, for instance, in Brazil, Colombia and Paraguay). Once cases fully decline from the peak - through further infections or as a result of vaccination programmes - then, and only then, some of the disease control measures with the greatest negative health, economic and social consequences could be relaxed. For some countries in Categories D and E, it may be possible to push R0_e below 1 and hence \"crush the curve\" by introducing some additional control measures or improving compliance with existing measures. New virus strains, especially with higher transmissibility, can generate resurgences or accelerations in growth of cases (as seen, for example, in Mozambique and Togo).\n[tpltrtarr]Categories F and G: COVID-19 control measures, put in place by governments and implemented by citizens, have saved perhaps 13.1-14.2 million lives. To continue to protect these lives, control measures need to be maintained until vaccines become widely available - and strengthened, if necessary, to compensate for new virus variants with higher transmissibility.\n[tpltrtarr]Category H: Measures to keep the disease out - mainly strict quarantines for new arrivals and testing & tracing of suspected cases - should be maintained until vaccines become widely available.\n\n\nThe findings of this report may have implications for the optimal distribution of early batches of vaccines within countries. Current policies in several countries call for deployment of vaccines first to healthcare workers and then by age cohort, starting with the oldest. These plans are aligned with the results of modelling (by Imperial College London and others) which suggest that, when the supply of vaccines is limited, the optimal strategy is to target the elderly and other high-risk groups. However, the models indicate that, if the supply is sufficient to stop transmission of the virus, the optimal strategy switches to targeting key transmitters (e.g., working age people and potentially children) to indirectly protect the elderly and vulnerable. Consequently, the optimal strategy may vary according to the disease status category for each country:\n\n[tpltrtarr]Category A: Vaccination should concentrate on elderly and vulnerable people, starting with the oldest and most vulnerable. There is no alternative strategy to consider because population-level immunity already exists, and the greatest danger lies in vulnerable people becoming infected due to endemic SARS-CoV-2.\n[tpltrtarr]Categories B and C: Vaccinations should probably be given first to elderly and vulnerable groups, and to frontline healthcare and other essential workers. However, if there are resurgences in cases across the population due to higher-transmissibility or immunity-resistant variants, then the optimal strategy may switch to targeting key transmitters, similar to some countries in Categories D and E.\n[tpltrtarr]Categories D and E: In some of these countries, the optimal strategy may to be vaccinate key transmitters - while maintaining current disease control measures - because it may be possible to halt the outbreak and \"crush the curve\", while waiting for further vaccine supplies to arrive (after which disease control measures could be released). This strategy is being pursued by Indonesia and was suggested for the United States of America in a recent paper. However, careful modelling and planning would be necessary, for any country considering such an approach, to determine if a key transmitter strategy would in fact be optimal and if it would be feasible to implement. Further, for such a strategy to work, it will be necessary to keep control measures in place and to keep high-transmissibility variants of the virus out, until enough people have been vaccinated.\n[tpltrtarr]Categories F, G and H: Vaccinations should be given first to frontline healthcare and other essential workers and to elderly and vulnerable groups (starting with the oldest and most vulnerable).\n\n\nThese findings may also have implications for the optimal distribution of the first vaccines across countries. Modelling by the Imperial College London COVID-19 Response Team suggests that the optimal allocation of vaccine doses among countries \"is sensitive to many assumptions and will vary depending both on the vaccine characteristics and the stage of the epidemic in each country at vaccine introduction,\" and concluded that, \"[g]iven this uncertainty, allocating vaccine doses according to population size appears to be the next most efficient approach.\" Our findings reinforce the uncertainty strongly: it is very likely that that stage of the epidemic varies greatly across countries. For most countries, the optimal allocation of vaccines doses is likely still to be according to population size - and then for those countries to give doses first to elderly and vulnerable people. However, the global optimal allocation strategy might include providing somewhat greater supplies, during the next few months, to Category D and E countries where using the vaccine to halt spread of the disease might be possible (provided that disease control measures are maintained in those countries). It is clear, in any case, that further modelling of vaccine allocation strategies is essential, taking into account the actual vaccine efficacies and projected available doses by month, as well as allowing for disease stage categories in different countries.\n\nVaccination strategies will need to account for current and potential future virus variants as well as the likelihood that immunity from vaccination will wane over time. Higher-transmissibility variants of the SARS-CoV-2 virus increase the urgency of distributing vaccines, especially in Category F and G countries which may struggle to keep the disease suppressed, and might cause vaccination of key transmitters to be a less effective strategy for Category D and E countries if higher-transmissibility variants mean that they cant suppress the disease fully with limited vaccinations. Immunity-resistant variants of the virus may reduce the effectiveness of current vaccines, but are not likely to negate fully the protection offered by existing vaccines. Immunity acquired through vaccination is likely to wane over time - like immunity acquired through infection. Looking to the longer term, new virus variants and waning immunity are likely to necessitate re-vaccination (with vaccines effective against the latest variants) on a regular basis. In many, perhaps most, countries, the time to vaccinate the whole population will exceed the timeframe in which immunity from vaccination wanes or new immunity-resistant variants emerge. In making long-term plans, therefore, countries may face a wide range of options for who to vaccinate (elderly and vulnerable populations, key transmitters or entire populations) and for frequency of vaccination (every 6 months, annual, or once if residual benefits are sufficient). Optimal strategies for each country will be complicated to determine, as the choice will depend on many factors, including vaccine effectiveness in reducing mortality and in reducing transmission, how effectiveness wanes over time, mortality rates and transmissibility of new variants (in general and in previously infected or vaccinated people), and, once the risks to life and health from \"endemic COVID\" decrease to the point where COVID-19 is not an overriding issue, comparison with other health and budgetary priorities.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "John Paul Callan", + "author_inst": "Personal Capacity" + }, + { + "author_name": "Carlijn J. A. Nouwen", + "author_inst": "Personal Capacity" + }, + { + "author_name": "Axel S. Lexmond", + "author_inst": "Personal Capacity" + }, + { + "author_name": "Othmane Fourtassi", + "author_inst": "Personal Capacity" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.03.05.21252990", "rel_title": "A quantitative risk estimation platform for indoor aerosol transmission of COVID-19", @@ -911617,57 +909906,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.08.21252200", - "rel_title": "Vaccine effectiveness after 1st and 2nd dose of the BNT162b2 mRNA Covid-19 Vaccine in long-term care facility residents and healthcare workers - a Danish cohort study", - "rel_date": "2021-03-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.08.21252200", - "rel_abs": "BackgroundAt the end of 2020, Denmark launched an immunization program against SARS-CoV-2. The Danish health authorities prioritized persons currently living in long-term care facilities (LTCF residents) and frontline healthcare workers (HCW) as the first receivers of vaccination. Here we present preliminary population based vaccine effectiveness (VE) estimates in these two target groups.\n\nMethodsThe study was designed as a retrospective registry- and population-based observational cohort study including all LTCF residents and all HWC. The outcome was a polymerase chain reaction confirmed SARS-CoV-2, and VE was estimated for different periods following first and second dose. We used Poisson and Cox regressions to estimate respectively crude and calendar time-adjusted VE for the BNT162b2 mRNA Covid-19 Vaccine from Pfizer/BioNTech with 95% confidence intervals (CI) for vaccinated versus unvaccinated.\n\nResultsA total of 39,040 LTCF residents (median age at first dose; 84 years, Interquartile range (IQR): 77-90) and 331,039 HCW (median age at first dose; 47 years, IQR: 36-57) were included. Among LTCF residents, 95.2% and 86.0% received first and second dose from 27 December 2020 until 18 February 2021, for HWC the proportion was 27.8% and 24.4%. During a median follow-up of 53 days, there were 488 and 5,663 confirmed SARS-CoV-2 cases in the unvaccinated groups, whereas there were 57 and 52 in LTCF residents and HCW within the first 7 days after the second dose and 27 and 10 cases beyond seven days of second dose. No protective effect was observed for LTCF residents after first dose. In HCW, VE was 17% (95% CI; 4-28) in the > 14 days after first dose (before second dose). Furthermore, the VE in LTCF residents at day 0-7 of second dose was 52% (95% CI; 27-69) and 46% (95% CI; 28-59) in HCW. Beyond seven days of second dose, VE increased to 64% (95% CI; 14-84) and 90% (95% CI; 82-95) in the two groups, respectively.\n\nConclusionThe results were promising regarding the VE both within and beyond seven days of second vaccination with the BNT162b2 mRNA Covid-19 Vaccine currently used in many countries to help mitigate the global SARS-CoV-2 pandemic.\n\nImpact of the researchSo far, observational studies of the real-word effectiveness of the mRNA Vaccine BNT162b2 has been limited to the period after the administration of the first dose. This is the first report to date to present vaccine effectiveness (VE) estimates after the second BNT162b2 mRNA Covid-19 Vaccine. We estimated a VE of 52% and 46% in LTCF residents and HCW within seven days, which increased to 64% and 90% in the two groups respectively beyond seven days of immunization. These findings supports maintaining a two-dose schedule of the BNT162b2 mRNA Covid-19 Vaccine.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Ida Rask Moustsen-Helms", - "author_inst": "Statens Serum Institut" - }, - { - "author_name": "Hanne-Dorthe Emborg", - "author_inst": "Statens Serum Institut" - }, - { - "author_name": "Jens Nielsen", - "author_inst": "Statens Serum Institut" - }, - { - "author_name": "Katrine Finderup Nielsen", - "author_inst": "Statens Serum Institut" - }, - { - "author_name": "Tyra Grove Krause", - "author_inst": "Statens Serum Institut" - }, - { - "author_name": "Kaare Molbak", - "author_inst": "Statens Serum Institut" - }, - { - "author_name": "Karina Lauenborg Moeller", - "author_inst": "Statens Serum Institut" - }, - { - "author_name": "Ann-Sofie Nicole Berthelsen", - "author_inst": "Statens Serum Institut" - }, - { - "author_name": "Palle Valentiner-Branth", - "author_inst": "Staten Serum Institut" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.02.21252722", "rel_title": "Beliefs about Mask Efficacy and the Effect of Social Norms on Mask Wearing Intentions for COVID-19 Risk Reduction", @@ -913563,6 +911801,121 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2021.03.08.434300", + "rel_title": "Pediatric nasal epithelial cells are less permissive to SARS-CoV-2 replication compared to adult cells", + "rel_date": "2021-03-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.08.434300", + "rel_abs": "Children typically experience more mild symptoms of COVID-19 when compared to adults. There is a strong body of evidence that children are also less susceptible to SARS-CoV-2 infection with the ancestral viral isolate. However, the emergence of SARS-CoV-2 variants of concern (VOCs) has been associated with an increased number of pediatric infections. Whether this is the result of widespread adult vaccination or fundamental changes in the biology of SARS-CoV-2 remains to be determined. Here, we use primary nasal epithelial cells from children and adults, differentiated at an air-liquid interface to show that the ancestral SARS-CoV-2 replicates to significantly lower titers in the nasal epithelial cells of children compared to those of adults. This was associated with a heightened antiviral response to SARS-CoV-2 in the nasal epithelial cells of children. Importantly, the Delta variant also replicated to significantly lower titres in the nasal epithelial cells of children. This trend was markedly less pronounced in the case of Omicron. It is also striking to note that, at least in terms of viral RNA, Omicron replicated better in pediatric NECs compared to both Delta and the ancestral virus. Taken together, these data show that the nasal epithelium of children supports lower infection and replication of ancestral SARS-CoV-2, although this may be changing as the virus evolves.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Yanshan Zhu", + "author_inst": "School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia" + }, + { + "author_name": "Keng Yih Chew", + "author_inst": "School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia" + }, + { + "author_name": "Melanie Wu", + "author_inst": "School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia" + }, + { + "author_name": "Anjana C. Karawita", + "author_inst": "School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia" + }, + { + "author_name": "Georgina McCallum", + "author_inst": "School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia" + }, + { + "author_name": "Lauren E Steele", + "author_inst": "School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia" + }, + { + "author_name": "Ayaho Yamamoto", + "author_inst": "Child Health Research Centre, The University of Queensland, South Brisbane, QLD 4101, Australia" + }, + { + "author_name": "Larisa L. Labzin", + "author_inst": "Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Australia" + }, + { + "author_name": "Tejasri Yarlagadda", + "author_inst": "Centre for Immunology and Infection Control, Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane Queensland 4000, Au" + }, + { + "author_name": "Alexander A. Khromykh", + "author_inst": "School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia; Australian Infectious Diseases Research Centre, Global Virus N" + }, + { + "author_name": "Xiaohui Wang", + "author_inst": "Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia" + }, + { + "author_name": "Julian Sng", + "author_inst": "School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia" + }, + { + "author_name": "Claudia J. Stocks", + "author_inst": "Institute for Molecular Bioscience (IMB), The University of Queensland, Brisbane, Australia" + }, + { + "author_name": "Yao Xia", + "author_inst": "School of Science, Edith Cowan University; School of Biomedical Science, University of Western Australia, Perth, Australia" + }, + { + "author_name": "Tobias R. Kollmann", + "author_inst": "Wal-yan Respiratory Research Centre, Telethon Kids Institute, The University of Western Australia, Perth, Australia" + }, + { + "author_name": "David Martino", + "author_inst": "Wal-yan Respiratory Research Centre, Telethon Kids Institute, The University of Western Australia, Perth, Australia" + }, + { + "author_name": "Merja Joensuu", + "author_inst": "Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia; Queensland Brain Institute, " + }, + { + "author_name": "Frederic A Meunier", + "author_inst": "Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia; Queensland Brain Institute, " + }, + { + "author_name": "Giuseppe Balistreri", + "author_inst": "Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia; Department of Virology, Faculty of Medicine, University of Helsinki, Finland" + }, + { + "author_name": "Helle Bielefeldt-Ohmann", + "author_inst": "School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia" + }, + { + "author_name": "Asha C. Bowen", + "author_inst": "Wal-yan Respiratory Research Centre, Telethon Kids Institute, The University of Western Australia, Perth, Australia" + }, + { + "author_name": "Anthony Kicic", + "author_inst": "Wal-yan Respiratory Research Centre, Telethon Kids Institute, The University of Western Australia, Perth, Australia" + }, + { + "author_name": "Peter D. Sly", + "author_inst": "Child Health Research Centre, The University of Queensland, South Brisbane, QLD 4101, Australia; Australian Infectious Diseases Research Centre, Global Virus Ne" + }, + { + "author_name": "Kirsten M. Spann", + "author_inst": "Centre for Immunology and Infection Control, Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane Queensland 4000, Au" + }, + { + "author_name": "Kirsty R. Short", + "author_inst": "School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Australia; Australian Infectious Diseases Research Centre, Global Virus N" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.03.06.434226", "rel_title": "Experimental susceptibility of North American raccoons (Procyon lotor) and striped skunks (Mephitis mephitis) to SARS-CoV-2", @@ -913967,73 +912320,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2021.03.08.434390", - "rel_title": "Identification of novel bat coronaviruses sheds light on the evolutionary origins of SARS-CoV-2 and related viruses", - "rel_date": "2021-03-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.08.434390", - "rel_abs": "Although a variety of SARS-CoV-2 related coronaviruses have been identified, the evolutionary origins of this virus remain elusive. We describe a meta-transcriptomic study of 411 samples collected from 23 bat species in a small (~1100 hectare) region in Yunnan province, China, from May 2019 to November 2020. We identified coronavirus contigs in 40 of 100 sequencing libraries, including seven representing SARS-CoV-2-like contigs. From these data we obtained 24 full-length coronavirus genomes, including four novel SARS-CoV-2 related and three SARS-CoV related genomes. Of these viruses, RpYN06 exhibited 94.5% sequence identity to SARS-CoV-2 across the whole genome and was the closest relative of SARS-CoV-2 in the ORF1ab, ORF7a, ORF8, N, and ORF10 genes. The other three SARS-CoV-2 related coronaviruses were nearly identical in sequence and clustered closely with a virus previously identified in pangolins from Guangxi, China, although with a genetically distinct spike gene sequence. We also identified 17 alphacoronavirus genomes, including those closely related to swine acute diarrhea syndrome virus and porcine epidemic diarrhea virus. Ecological modeling predicted the co-existence of up to 23 Rhinolophus bat species in Southeast Asia and southern China, with the largest contiguous hotspots extending from South Lao and Vietnam to southern China. Our study highlights both the remarkable diversity of bat viruses at the local scale and that relatives of SARS-CoV-2 and SARS-CoV circulate in wildlife species in a broad geographic region of Southeast Asia and southern China. These data will help guide surveillance efforts to determine the origins of SARS-CoV-2 and other pathogenic coronaviruses.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Hong Zhou", - "author_inst": "Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of" - }, - { - "author_name": "Jingkai Ji", - "author_inst": "Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of" - }, - { - "author_name": "Xing Chen", - "author_inst": "Landscape Ecology Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences,Menglun, Mengla, Yunnan 66630" - }, - { - "author_name": "Yuhai Bi", - "author_inst": "CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, CAS Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS" - }, - { - "author_name": "Juan Li", - "author_inst": "Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of" - }, - { - "author_name": "Tao Hu", - "author_inst": "Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of" - }, - { - "author_name": "Hao Song", - "author_inst": "Research Network of Immunity and Health (RNIH), Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China" - }, - { - "author_name": "Yanhua Chen", - "author_inst": "Landscape Ecology Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences,Menglun, Mengla, Yunnan 66630" - }, - { - "author_name": "Mingxue Cui", - "author_inst": "Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of" - }, - { - "author_name": "Yanyan Zhang", - "author_inst": "Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of" - }, - { - "author_name": "Alice C. Hughes", - "author_inst": "Landscape Ecology Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences,Menglun, Mengla, Yunnan 66630" - }, - { - "author_name": "Edward C. Holmes", - "author_inst": "Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydn" - }, - { - "author_name": "Weifeng Shi", - "author_inst": "Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, Shandong First Medical University & Shandong Academy of" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.03.08.434363", "rel_title": "Genome-Wide Covariation in SARS-CoV-2", @@ -915025,6 +913311,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.03.04.21252084", + "rel_title": "Factors associated with increased mortality in critically ill COVID-19 patients in a Mexican public hospital: the other faces of health system oversaturation.", + "rel_date": "2021-03-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.04.21252084", + "rel_abs": "BACKGROUNDThe lethality rate of COVID-19 in Mexico is one of the highest worldwide, but in-hospital factors associated with this increased rate have yet to be explored. This study aims to evaluate those factors that could be associated with mortality at 28-days in critically ill COVID-19 patients in Mexico.\n\nMETHODSThis is a retrospective analysis of the patients included in the clinical trial (NCT04381858) which recruited patients with severe COVID-19 with high oxygen requirement or mechanical ventilation from May to October 2020. The primary outcome, death at 28, was analyzed.\n\nRESULTSBetween May and October 2020, 196 predominantly male patients (n=122, 62.2%) with an average of 58.1 years ({+/-} 15.5), were included in the cohort. Mortality at 28 days was 44.3 % (n= 84). Patients included in the second trimester had a greater mortality rate when compared with those recruited in the first trimester (54.1 vs 32.1, p< 0.01). On multivariate analysis, the detected protective factors were the use of fentanyl HR 0.51 (95%CI 0.31 - 0.85, p=0.01), the use of antibiotics HR 0.22 (95% CI 0.13 - 0.36, p<0.01), and a previously healthy state (no comorbidities other than obesity) HR 0.58 (95%CI 0.35 - 0.94, p =0.03); risk factors were severe kidney injury (AKIN3) HR 1.74 (95%CI 1.04 - 2.9, p=0.035), elevated D-Dimer levels HR 1.02 (95%CI 1.007 - 1.04, p=0.005), shock OR 5.8 (2.4 - 13.8, p<0.01), and recruitment in the second trimester OR 2.3 ((1.1 - 4.8, p=0.02).\n\nCONCLUSIONSIn-hospital mortality in critically ill COVID-19 patients has increased in our center. The appropriate use of antibiotics, the type of sedation, and AKIN3 are modifiable factors directly related to this increased mortality. The increase in mortality observed in the second trimester is explained by hospital overcrowding that began in August 2020.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Mariana Jocelyn Macias Guzman", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Alejandro Castillo Gonzalez", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Jose Lenin Beltran Gonzalez", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Mario Gonzalez Gamez", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Emmanuel Antonio Mendoza Enciso", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Itzel Ovalle Robles", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Andrea Lucia Garcia Diaz", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Cesar Mauricio Gutierrez Pena", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Lucila Martinez Medina", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Victor Antonio Monroy Colin", + "author_inst": "Centenario Hospital Miguel Hidalgo" + }, + { + "author_name": "Jose Manuel Arreola Guerra", + "author_inst": "Centenario Hospital Miguel Hidalgo" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.04.21252532", "rel_title": "Serological reconstruction of COVID-19 epidemics through analysis of antibody kinetics to SARS-CoV-2 proteins", @@ -915525,165 +913870,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.04.21252528", - "rel_title": "Case fatality risk of the SARS-CoV-2 variant of concern B.1.1.7 in England", - "rel_date": "2021-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.04.21252528", - "rel_abs": "The B.1.1.7 variant of concern (VOC) is increasing in prevalence across Europe. Accurate estimation of disease severity associated with this VOC is critical for pandemic planning. We found increased risk of death for VOC compared with non-VOC cases in England (HR: 1.67 (95% CI: 1.34 - 2.09; P<.0001). Absolute risk of death by 28-days increased with age and comorbidities. VOC has potential to spread faster with higher mortality than the pandemic to date.", - "rel_num_authors": 36, - "rel_authors": [ - { - "author_name": "Daniel J Grint", - "author_inst": "Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK" - }, - { - "author_name": "Kevin Wing", - "author_inst": "Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK" - }, - { - "author_name": "Elizabeth Williamson", - "author_inst": "Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK" - }, - { - "author_name": "Helen I McDonald", - "author_inst": "Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK" - }, - { - "author_name": "Krishnan Bhaskaran", - "author_inst": "Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK" - }, - { - "author_name": "David Evans", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK" - }, - { - "author_name": "Stephen JW Evans", - "author_inst": "Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK" - }, - { - "author_name": "Alex J Walker", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK" - }, - { - "author_name": "George Hickman", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK" - }, - { - "author_name": "Emily Nightingale", - "author_inst": "Faculty of Public Health and Policy, London School of Hygiene & Tropical Medicine, UK" - }, - { - "author_name": "Anna Schultze", - "author_inst": "Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK" - }, - { - "author_name": "Christopher T Rentsch", - "author_inst": "Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK" - }, - { - "author_name": "Chris Bates", - "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, UK" - }, - { - "author_name": "Jonathan Cockburn", - "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, UK" - }, - { - "author_name": "Helen J Curtis", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK" - }, - { - "author_name": "Caroline E Morton", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK" - }, - { - "author_name": "Sebastian Bacon", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK" - }, - { - "author_name": "Simon Davy", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK" - }, - { - "author_name": "Angel YS Wong", - "author_inst": "Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK" - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK" - }, - { - "author_name": "Laurie Tomlinson", - "author_inst": "Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK" - }, - { - "author_name": "Ian J Douglas", - "author_inst": "Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK" - }, - { - "author_name": "Rohini Mathur", - "author_inst": "Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK" - }, - { - "author_name": "Paula Blomquist", - "author_inst": "COVID-19 Outbreak Surveillance Team, Public Health England, London, UK" - }, - { - "author_name": "Brian MacKenna", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK" - }, - { - "author_name": "Peter Ingelsby", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK" - }, - { - "author_name": "Richard Croker", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK" - }, - { - "author_name": "John Parry", - "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, UK" - }, - { - "author_name": "Frank Hester", - "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, UK" - }, - { - "author_name": "Sam Harper", - "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, UK" - }, - { - "author_name": "Nicolas J DeVito", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK" - }, - { - "author_name": "Will Hulme", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK" - }, - { - "author_name": "John Tazare", - "author_inst": "Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK" - }, - { - "author_name": "Ben Goldacre", - "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, UK" - }, - { - "author_name": "Liam Smeeth", - "author_inst": "Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK" - }, - { - "author_name": "Rosalind M Eggo", - "author_inst": "Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, UK" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.04.21252945", "rel_title": "The COVIDome Explorer Researcher Portal", @@ -916863,6 +915049,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.05.21252709", + "rel_title": "A Simple RT-PCR Melting temperature Assay to Rapidly Screen for Widely Circulating SARS-CoV-2 Variants.", + "rel_date": "2021-03-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.05.21252709", + "rel_abs": "BackgroundThe increased transmission of SARS-CoV-2 variants of concern (VOC) which originated in the United Kingdom (B.1.1.7), South Africa (B1.351), Brazil (P.1) and in United States (B.1.427/429) requires a vigorous public health response, including real time strain surveillance on a global scale. Although genome sequencing is the gold standard for identifying these VOCs, it is time consuming and expensive. Here, we describe a simple, rapid and high-throughput reverse-transcriptase PCR (RT-PCR) melting temperature (Tm) screening assay that identifies these three major VOCs.\n\nMethodsRT-PCR primers and four sloppy molecular beacon (SMB) probes were designed to amplify and detect the SARS-CoV-2 N501Y (A23063T) and E484K (G23012A) mutations and their corresponding wild type sequences. After RT-PCR, the VOCs were identified by a characteristic Tm of each SMB. Assay optimization and testing was performed with RNA from SARS-CoV-2 USA WA1/2020 (WT), a B.1.17 and a B.1.351 variant strains. The assay was then validated using clinical samples.\n\nResultsThe limit of detection (LOD) for both the WT and variants was 4 and 10 genomic copies/reaction for the 501 and 484 codon assays, respectively. The assay was 100% sensitive and 100% specific for identifying the N501Y and E484K mutations in cultured virus and in clinical samples as confirmed by Sanger sequencing.\n\nConclusionWe have developed an RT-PCR melt screening test for the three major VOCs which can be used to rapidly screen large numbers of patient samples providing an early warning for the emergence of these variants and a simple way to track their spread.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Padmapriya P. Banada", + "author_inst": "Rutgers Biomedical and Health Sciences" + }, + { + "author_name": "Raquel Green", + "author_inst": "New Jersey Medical School-RBHS" + }, + { + "author_name": "Sukalyani Banik", + "author_inst": "Rutgers Biomedical and Health Sciences" + }, + { + "author_name": "Abby Chopoorian", + "author_inst": "Rutgers New Jersey Medical School-RBHS" + }, + { + "author_name": "Deanna Streck", + "author_inst": "Institute of Genomic Medicine, Rutgers New Jersey Medical School-RBHS" + }, + { + "author_name": "Robert Jones", + "author_inst": "Craic computing LLC" + }, + { + "author_name": "Soumitesh Chakravorty", + "author_inst": "Rutgers New Jersey Medical School-RBHS and Cepheid" + }, + { + "author_name": "David Alland", + "author_inst": "New Jersey Medical School - RBHS" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.03.06.21253035", "rel_title": "Value-based pricing of a COVID-19 vaccine", @@ -917431,53 +915664,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2021.03.06.21252964", - "rel_title": "Estimating the impact of reopening schools on the reproduction number of SARS-CoV-2 in England, using weekly contact survey data", - "rel_date": "2021-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.06.21252964", - "rel_abs": "BackgroundSchools have been closed in England since the 4th of January 2021 as part of the national restrictions to curb transmission of SARS-CoV-2. The UK Government plans to reopen schools on the 8th of March. Although there is evidence of lower individual-level transmission risk amongst children compared to adults, the combined effects of this with increased contact rates in school settings are not clear.\n\nMethodsWe measured social contacts when schools were both open or closed, amongst other restrictions. We combined these data with estimates of the susceptibility and infectiousness of children compared with adults to estimate the impact of reopening schools on the reproduction number.\n\nResultsOur results suggest that reopening all schools could increase R from an assumed baseline of 0.8 to between 1.0 and 1.5, or to between 0.9 and 1.2 reopening primary or secondary schools alone.\n\nConclusionOur results suggest that reopening schools is likely to halt the fall in cases observed in recent months and risks returning to rising infections, but these estimates rely heavily on the current estimates or reproduction number and the current validity of the susceptibility and infectiousness profiles we use.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "James D Munday", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Christopher I Jarvis", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Amy Gimma", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Kerry LM Wong", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Kevin van Zandvoort", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "- CMMID COVID-19 Working Group", - "author_inst": "" - }, - { - "author_name": "Sebastian Funk", - "author_inst": "London School of Hygiene & Tropical Medicine" - }, - { - "author_name": "W. John Edmunds", - "author_inst": "London School of Hygiene and Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.03.07.21252972", "rel_title": "COVID-19 vaccine hesitancy in care home staff: a survey of Liverpool care homes", @@ -919085,6 +917271,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.28.21252608", + "rel_title": "Association between SARS-CoV-2 Transmission Risk, Viral Load, and Age: A Nationwide Study in Danish Households", + "rel_date": "2021-03-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.28.21252608", + "rel_abs": "AimThe objective of this nationwide study was to investigate the association between SARS-CoV-2 transmissibility, viral load, and age of primary cases in Danish households.\n\nBackgroundSpread in households represents a major mode of transmission of SARS-CoV-2. In order to take proper action against the spread of the disease, it is important to have a better understanding of transmission in the household domain--including the role of viral load of primary cases.\n\nMethodsThe study was designed as an observational cohort study, using detailed administrative register data. We included the full population of Denmark and all SARS-CoV-2 tests (August 25, 2020 to February 10, 2021) to estimate transmissibility in house-holds comprising 2-6 people. RT-PCR Cycle threshold (Ct) values were used as a proxy for viral load.\n\nResultsWe identified 63,657 primary cases and 139,882 household members of which 21% tested positive by RT-PCR within a 1-14 day period after the primary case. There was an approximately linear association between Ct value of the sample and transmissibility, implying that cases with samples having a higher viral load were more transmissible than cases with samples having a lower viral load. However, even for primary cases with relatively high sample Ct values, the transmissibility was not negligible, e.g., for primary cases with a sample Ct value of 38, we found that 13% of the primary cases had at least one secondary household case. Moreover, 34% of all secondary cases were found in households with primary cases having sample Ct values >30. An increasing transmissibility with age of the primary cases for adults ([≥]20 years) and a decreasing transmissibility with age for children (<20 years) were found.\n\nConclusionsAlthough primary cases with sample high viral loads (low Ct values) were associated with higher SARS-CoV-2 transmissibility, we found no obvious cut-off for sample Ct values to eliminate transmissibility and a substantial amount of household transmission occurred in households where the primary cases had high sample Ct values (low viral load), The study further showed that transmissibility increases with age. These results have important public health implications, as they suggest that contact tracing should prioritize cases according to Ct values and age, and underline the importance of quick identification and isolation of cases. Furthermore, the study highlights that households can serve as a transmission bridge by creating connections between otherwise separate domains.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Frederik Plesner Lyngse", + "author_inst": "University of Copenhagen" + }, + { + "author_name": "K\u00e5re M\u00f8lbak", + "author_inst": "Statens Serum Institut" + }, + { + "author_name": "Kristina Tr\u00e6holt Franck", + "author_inst": "Statens Serum Institut" + }, + { + "author_name": "Claus Nielsen", + "author_inst": "Statens Serum Institut" + }, + { + "author_name": "Robert Leo Skov", + "author_inst": "Statens Serum Institut" + }, + { + "author_name": "Marianne Voldstedlund", + "author_inst": "Statens Serum Institut" + }, + { + "author_name": "Arieh S. Cohen", + "author_inst": "Statens Serum Institut" + }, + { + "author_name": "Carsten Thure Kirkeby", + "author_inst": "University of Copenhagen" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.03.03.21252014", "rel_title": "COVID-19 test positivity: predictive value of various symptoms in a large community-based testing program in California", @@ -919545,57 +917778,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.03.03.21252809", - "rel_title": "Sharing positive changes made during COVID-19 national lockdown: a multi-method co-production study", - "rel_date": "2021-03-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.03.21252809", - "rel_abs": "ObjectiveA multi-method co-production study was designed to share psychosocial insights into the adoption of positive changes made during COVID-19 national lockdown in Scotland. We examined: i) the psychosocial patterning of positive changes, ii) the psychosocial processes by which positive change was realised, and worked with partner organizations to share our insights.\n\nMethodsA sequential multi-method design included an online survey (n=2445) assessing positive changes in sleep and physical activity patterns, socio-demographics, mood, social support, coping, and resilience, with multivariate logistic regression analysis. We also employed interviews with a purposive diverse sub-sample of people self-reporting high levels of positive change (n=48) and used thematic analysis. Finally, partnership work translated insights into positive change-sharing targeted resources.\n\nResultsThe survey identified positive change was significantly patterned by age, gender and vulnerability to COVID-19. Higher positive reframing and higher active coping were associated with higher levels of cross-domain positive change. Higher symptoms of depression, planning, and self-distraction were associated with less cross-domain positive change. Thematic analysis showed the centrality of perceptions of time, opportunities to self-reflect and engage with the natural world, access support in diverse ways, actively build routine and purposefully build self-efficacy and a sense of control were key to initiating positive change. Our partner organizations focused on the rapid co-production of a series of online resources that shared study insights.\n\nConclusionsOur study, based around a salutogenic ethos and the constraints of COVID-19, sought to identify and share insights into achieving positive changes at a time of international crisis.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Lynn Williams", - "author_inst": "University of Strathclyde" - }, - { - "author_name": "Bradley MacDonald", - "author_inst": "University of Strathclyde" - }, - { - "author_name": "Lesley Rollins", - "author_inst": "University of Strathclyde" - }, - { - "author_name": "Xanne Janssen", - "author_inst": "University of Strathclyde" - }, - { - "author_name": "Leanne Fleming", - "author_inst": "University of Strathclyde" - }, - { - "author_name": "Madeleine Grealy", - "author_inst": "University of Strathclyde" - }, - { - "author_name": "Alison Kirk", - "author_inst": "University of Strathclyde" - }, - { - "author_name": "David Young", - "author_inst": "University of Strathclyde" - }, - { - "author_name": "Paul Flowers", - "author_inst": "University of Strathclyde" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.03.02.21252777", "rel_title": "Schooling amidst a pandemic: parents' perceptions about reopening schools and anticipated challenges during COVID-19", @@ -920803,6 +918985,33 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.03.04.433970", + "rel_title": "Molecular strategies for antibody binding and escape of SARS-CoV-2 and its mutations", + "rel_date": "2021-03-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.04.433970", + "rel_abs": "The COVID19 pandemic, caused by SARS-CoV-2, has infected more than 100 million people worldwide. Due to the rapid spreading of SARS-CoV-2 and its impact, it is paramount to find effective treatments against it. Human neutralizing antibodies are an effective method to fight viral infection. However, the recent discovery of new strains that substantially change the S-protein sequence has raised concern about vaccines and antibodies effectiveness. Here, we investigated the binding mechanisms between the S-protein and several antibodies. Multiple mutations were included to understand the strategies for antibody escape in new variants. We found that the combination of mutations K417N and E484K produced higher binding energy to ACE2 than the wild type, suggesting higher efficiency to enter host cells. The mutations effect depends on the antibody class. While Class I enhances the binding avidity in the presence of N501Y mutation, class II antibodies showed a sharp decline in the binding affinity. Our simulations suggest that Class I antibodies will remain effective against the new strains. In contrast, Class II antibodies will have less affinity to the S-protein, potentially affecting these antibodies efficiency.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Mohamed Hendy", + "author_inst": "The University of British Columbia" + }, + { + "author_name": "Samuel Kaufman", + "author_inst": "The University of British Columbia" + }, + { + "author_name": "Mauricio Ponga", + "author_inst": "University of British Columbia" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2021.03.02.21249552", "rel_title": "Modeling transmission dynamics and effectiveness of worker screening programs for SARS-CoV-2 in pork processing plants", @@ -921323,29 +919532,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.03.05.434119", - "rel_title": "SARS-CoV-2-host chimeric RNA-sequencing reads do not necessarily signify virus integration into the host DNA", - "rel_date": "2021-03-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.03.05.434119", - "rel_abs": "The human genome bears evidence of extensive invasion by retroviruses and other retroelements, as well as by diverse RNA and DNA viruses. High frequency of somatic integration of the RNA virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into the DNA of infected cells was recently suggested, partly based on the detection of chimeric RNA-sequencing (RNA-seq) reads between SARS-CoV-2 RNA and RNA transcribed from human host DNA. Here, we examined the possible origin of human-SARS-CoV-2 chimeric reads in RNA-seq libraries and provide alternative explanations for their origin. Chimeric reads were frequently detected also between SARS-CoV-2 RNA and RNA transcribed from mitochondrial DNA or episomal adenoviral DNA present in transfected cell lines, which was unlikely the result of SARS-CoV-2 integration. Furthermore, chimeric reads between SARS-CoV-2 RNA and RNA transcribed from nuclear DNA was highly enriched for host exonic, than intronic or intergenic sequences and often involved the same, highly expressed host genes. These findings suggest that human-SARS-CoV-2 chimeric reads found in RNA-seq data may arise during library preparation and do not necessarily signify SARS-CoV-2 reverse transcription, integration in to host DNA and further transcription.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Anastasiya Kazachenka", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "George Kassiotis", - "author_inst": "The Francis Crick Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.03.03.433675", "rel_title": "Ribosome-profiling reveals restricted post transcriptional ex-pression of antiviral cytokines and transcription factors during SARS-CoV-2 infection", @@ -922785,6 +920971,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.03.01.21252678", + "rel_title": "COVID-19 Mortality in California Based on Death Certificates: Disproportionate Impacts Across Racial/Ethnic Groups and Nativity", + "rel_date": "2021-03-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.01.21252678", + "rel_abs": "PurposeTo examine characteristics of coronavirus disease 2019 (COVID-19) decedents in California (CA) and evaluate for disproportionate mortality across race/ethnicity and ethnicity/nativity.\n\nMethodsCOVID-19 deaths were identified from death certificates. Age-adjusted mortality rate ratios (MRR) were compared across race/ethnicity. Proportionate mortality rates (PMR) were compared across race/ethnicity and by ethnicity/nativity.\n\nResultsWe identified 10,200 COVID-19 deaths in CA occurring February 1 through July 31, 2020. Decedents tended to be older, male, Hispanic, foreign-born, and have lower educational attainment. MRR indicated elevated COVID-19 morality rates among Asian/Pacific Islander, Black, and Hispanic groups compared with the White group, with Black and Hispanic groups having the highest MRR at 2.75 (95%CI:2.54-2.97) and 4.18 (95%CI: 3.99-4.37), respectively. Disparities were larger at younger ages. Similar results were observed with PMR, which remained in analyses stratified by education. Elevated PMR were observed in all ethnicity/nativity groups, especially foreign-born Hispanic individuals, relative to U.S.-born non-Hispanic individuals, were generally larger at younger ages, and persisted after stratifying by education.\n\nConclusionsDifferential COVID-19 mortality was observed in California across racial/ethnic groups and by ethnicity/nativity groups with evidence of greater disparities among younger age groups. Identifying COVID-19 disparities is an initial step towards mitigating disease impacts in vulnerable communities.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Erika Garcia", + "author_inst": "University of Southern California" + }, + { + "author_name": "Sandrah P Eckel", + "author_inst": "University of Southern California" + }, + { + "author_name": "Zhanghua Chen", + "author_inst": "University of Southern California" + }, + { + "author_name": "Kenan Li", + "author_inst": "University of Southern California" + }, + { + "author_name": "Frank Gilliland", + "author_inst": "University of Southern California" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.03.01.21252457", "rel_title": "Recent changes in COVID-19 Vaccine Hesitancy among Healthcare Workers", @@ -923389,33 +921610,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.03.01.21252243", - "rel_title": "On the Environmental Determinants of COVID-19 Seasonality", - "rel_date": "2021-03-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.01.21252243", - "rel_abs": "Viral respiratory diseases (VRDs), such as influenza and COVID-19, are thought to spread faster over winter than during summer. It has been previously argued that cold and dry conditions were more conducive to the transmission of VRD than warm and humid climates, although this relationship appears restricted to temperate regions, and the causal relationship is not well understood. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing COVID-19 has emerged as a serious global public health problem after the first COVID-19 reports in Wuhan, China, in late 2019. It is still unclear whether this novel respiratory disease will ultimately prove to be a seasonal endemic disease. Here, we suggest that Air Drying Capacity (ADC; an atmospheric state-variable known to control the fate/evolution of the virus-laden droplets) and ultraviolet radiation (UV) are probable environmental determinants in shaping the transmission of COVID-19 at the seasonal time scale. These variables, unlike temperature and humidity, provide a physically-based framework consistent with the apparent seasonal variability in COVID-19 prevalence across a broad range of climates (e.g., Germany and India). Since this disease is known to be influenced by the compounding effect of social, biological, and environmental determinants, this study does not claim that these environmental determinants exclusively shape the seasonality of COVID-19. However, we argue that ADC and UV play a significant role in COVID-19 dynamics at the seasonal scale. These findings could help guide the development of a sound adaptation strategy against the pandemic over the coming seasons.\n\nPlain Language SummaryThere is growing scientific interest in the potential seasonality of COVID-19 and its links to climate variables. This study aims to determine whether four environmental variables, namely temperature, humidity, Air Drying Capacity (ADC), and ultraviolet radiation (UV), are probable environmental determinants for the observed seasonal dynamics of COVID-19 prevalence, based on extensive country-level data spanning the first year of the pandemic. Although the influence of socio-economic factors may be dominant, we here suggest that ADC and UV are key environmental determinants of COVID-19 and can potentially affect the transmission and seasonality of the disease across a wide range of climates.\n\nKey PointsO_LIThe seasonality of COVID-19 appears to follow seasonality of some environmental variables.\nC_LIO_LISeasonality of air drying capacity and ultraviolet radiation consistently match seasonality of COVID-19, across climatic zones.\nC_LIO_LISeasonality of air humidity and temperature, match seasonality of COVID-19 in temperate climates, but not in tropical monsoon climates.\nC_LI", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Yeon-Woo Choi", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Alexandre Tuel", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Elfatih A. B. Eltahir", - "author_inst": "Massachusetts Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.03.01.21252698", "rel_title": "Towards Understanding the COVID-19 Case Fatality Rate", @@ -925071,6 +923265,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.03.02.21252768", + "rel_title": "Impact of COVID-19 pre-test probability on positive predictive value of high cycle threshold SARS-CoV-2 real-time reverse transcription PCR test results", + "rel_date": "2021-03-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.02.21252768", + "rel_abs": "BackgroundPerformance characteristics of SARS-CoV-2 nucleic acid detection assays are understudied within contexts of low pre-test probability, including screening asymptomatic persons without epidemiological links to confirmed cases, or asymptomatic surveillance testing. SARS-CoV-2 detection without symptoms may represent resolved infection with persistent RNA shedding, presymptomatic or asymptomatic infection, or a false positive test. This study assessed clinical specificity of SARS-CoV-2 real-time reverse transcription polymerase chain reaction (rRT-PCR) assays by retesting positive specimens from five pre-test probability groups ranging from high to low with an alternate assay.\n\nMaterials and MethodsA total of 122 rRT-PCR positive specimens collected from unique patients between March and July 2020 were retested using a laboratory-developed nested RT-PCR assay targeting the RNA-dependent RNA polymerase (RdRp) gene followed by Sanger sequencing.\n\nResultsSignificantly less positive results in the lowest pre-test probability group (facilities with institution-wide screening having [≤] 3 positive asymptomatic cases) were reproduced with the nested RdRp gene RT-PCR assay than in all other groups combined (5/32, 15{middle dot}6% vs 61/90, 68%; p <0{middle dot}0001), and in each subgroup with higher pre-test probability (individual subgroup range 50{middle dot}0% to 85{middle dot}0%).\n\nConclusionsA higher proportion of false-positive test results are likely with lower pre-test probability. Positive SARS-CoV-2 PCR results should be interpreted within the context of patient history, clinical setting, known exposure, and estimated community disease prevalence. Large-scale SARS-CoV-2 screening testing initiatives among low pre-test probability populations should be evaluated thoroughly prior to implementation given the risk of false positives and consequent potential for harm at the individual and population level.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Jonathan B Gubbay", + "author_inst": "Ontario Agency for Health Protection and Promotion" + }, + { + "author_name": "Heather Rilkoff", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Heather L. Kristjanson", + "author_inst": "Ontario Agency For Health Protection and Promotion" + }, + { + "author_name": "Jessica D. Forbes", + "author_inst": "Ontario Agency for Health Protection and Promotion" + }, + { + "author_name": "Michelle Murti", + "author_inst": "Ontario Agency for Health Protection and Promotion" + }, + { + "author_name": "AliReza Eshaghi", + "author_inst": "Ontario Agency for Health Protection and Promotion" + }, + { + "author_name": "George Broukhanski", + "author_inst": "University of Toronto" + }, + { + "author_name": "Antoine Corbeil", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Nahuel Fittipaldi", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Jessica Hopkins", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Erik Kristjanson", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Julianne V Kus", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Liane Macdonald", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Anna Majury", + "author_inst": "Public Health Ontario, Ontario, Canada" + }, + { + "author_name": "Gustavo V Mallo", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Tony Mazzulli", + "author_inst": "Mt Sinai Hospital, and University Health Network" + }, + { + "author_name": "Roberto G Melano", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Romy Olsha", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Stephen J Perusini", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Vanessa Tran", + "author_inst": "Ontario Public Health Laboratory" + }, + { + "author_name": "Vanessa Gray Allen", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Samir N Patel", + "author_inst": "Public Health Ontario" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.02.21252734", "rel_title": "Relation of severe COVID-19 in Scotland to transmission-related factors and risk conditions eligible for shielding support: REACT-SCOT case-control study", @@ -925531,45 +923828,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.26.21252555", - "rel_title": "Introductions and evolutions of SARS-CoV-2 strains in Japan", - "rel_date": "2021-03-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.26.21252555", - "rel_abs": "COVID-19 caused by SARS-CoV-2 was first identified in Japan on January 15th, 2020, soon after the pandemic originated in Wuhan, China. Subsequently, Japan experienced three distinct waves of the outbreak in the span of a year and has been attributed to new exogenous strains and evolving existing strains. Japan engaged very early on in tracking different COVID-19 sub-strains and have sequenced approximately 5% of all confirmed cases. While Japan has enforced stringent airport surveillance on cross-border travelers and returnees, some carriers appear to have advanced through the quarantine stations undetected. In this study, 17112 genomes sampled in Japan were analyzed to understand the strains, heterogeneity and temporal evolution of different SARS-CoV-2 strains. We identified 11 discrete strains with a substantial number of cases with most strains possessing the spike (S) D614G and nucleocapsid (N) 203_204delinsKR mutations. Besides these variants, ORF1ab P3371S, A4815V, S1361P, and N P151L were also detected in nearly half the samples constituting the most common strain in Japan. 115 distinct strains have been introduced into Japan and 12 of them were introduced after strict quarantine policy was implemented. In particular, the B.1.1.7 strain, that emerged in the United Kingdom (UK) in September 2020, has been circulating in Japan since late 2020 after eluding cross-border quarantine stations. Similarly, the B.1.351 strain dubbed the South African variant, P.1 Brazilian strain and R.1 strain with the spike E484K mutation have been detected in Japan. At least four exogenous B.1.1.7 sub-strains have been independently introduced in Japan as of late January 2021, and these strains carry mutations that give selective advantage including N501Y, H69_V70del, and E484K that confer increased transmissibility, reduced efficacy to vaccines and possible increased virulence. It is imperative that the quarantine policy be revised, cross-border surveillance reinforced, and new public health measures implemented to mitigate further transmission of this deadly disease and to identify strains that may engender resistance to vaccines.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Reitaro Tokumasu", - "author_inst": "IBM Research - Tokyo" - }, - { - "author_name": "Dilhan Weeraratne", - "author_inst": "IBM Watson Health" - }, - { - "author_name": "Jane Snowdon", - "author_inst": "IBM Watson Health" - }, - { - "author_name": "Laxmi Parida", - "author_inst": "IBM TJ Watson Research Center" - }, - { - "author_name": "Michiharu Kudo", - "author_inst": "IBM Research - Tokyo" - }, - { - "author_name": "Takahiko Koyama", - "author_inst": "IBM TJ Watson Research Center" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.26.21251848", "rel_title": "Clinical course and outcomes of critically ill COVID-19 patients in two successive pandemic waves", @@ -926869,6 +925127,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.28.21252181", + "rel_title": "Impact of COVID-19 on healthcare workers at a cancer care centre", + "rel_date": "2021-03-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.28.21252181", + "rel_abs": "BackgroundThe services of front-line health care workers (HCWs) have been paramount in the management of novel coronavirus disease 2019 (COVID-19). Health care professionals have been at high occupational risk of getting disease and even dying of the disease, however; they have been the subject of very limited studies in terms of COVID-19. The objectives of this study are to examine the incidence and the impact of COVID-19 infection among HCWs in terms of recovery, productivity, quality of life (QOL) and post-COVID complications.\n\nMaterials and MethodsThis was a retrospective, questionnaire based study including demographic details, workplace characteristics, symptoms, source/ spread of infection, details of recovery and the consequences of COVID-19 comprising impaired productivity/ QOL, post-COVID-19 complications and others. The data were analyzed by using IBM SPSS software (Version 23, SPSS Inc., Chicago, IL, USA).\n\nResults and ConclusionsOut of a total of 1482 employees, 18.3% (271) were laboratory confirmed to have contracted novel contagion during the study period of 5 months. The median age at diagnosis was 29 (range, 21-62) years. Front-line workers and female workers were the most infected personnel with COVID-19. Flu-like symptoms were the most frequently experienced symptoms. The median time for recovery was 20 (range, 2-150) days. The relationship between pre-existing comorbidities and age was highly significant. The QOL and productivity were associated with pre-existing comorbidities, severity of the disease, time for recovery and post-COVID syndrome. More than a half (51.8%) of all HCWs had suffered from post-COVID complications. There was no fatality reported due to COVID-19. The post-COVID complications were related to pre-existing comorbidities, severity of disease, time for recovery and status of recovery. Further research to explore the consequences of COVID-19 is warranted. The general public needs to be aware of symptoms and management of the post-COVID syndrome.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Atika Dogra", + "author_inst": "Rajiv Gandhi Cancer Institute and Research Centre" + }, + { + "author_name": "ANUJ PARKASH", + "author_inst": "RAJIV GANDHI CANCER INSTITUTE AND RESEARCH CENTRE" + }, + { + "author_name": "Anurag Mehta", + "author_inst": "Rajiv Gandhi Cancer Institute and Research Centre" + }, + { + "author_name": "Meenu Bhatia", + "author_inst": "Rajiv Gandhi Cancer Institute and Research Centre" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.03.02.433434", "rel_title": "High-content screening of coronavirus genes for innate immune suppression revealsenhanced potency of SARS-CoV-2 proteins", @@ -927533,29 +925822,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2021.03.01.21252330", - "rel_title": "Does Telemedicine Reduce health disparities? Longitudinal Evidence during the COVID-19 Pandemic in the US", - "rel_date": "2021-03-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.03.01.21252330", - "rel_abs": "ObjectiveThe COVID-19 pandemic could be a significant health issue for the elderly population and those with pre-excising chronic condition. In response to the pandemic health care services have increased the use of telehealth medicine. The propose of this study is to examine factors associated with access to telemedicine before and after COVID-19 based on sociodemographic factors and type of chronic disease.\n\nMethodWe have used data from the Research and Development Survey (RANDS) at two different time points Data collection for the first wave occurred between June 9, 2020 and July 6, 2020 (n= 6786), second wave was between August 3, 2020 and August 20, 2020 (n=5972). Three questions have been asked from the participant: 1) did the provider offer telemedicine before the pandemic? 2) does the provider offer telemedicine during the pandemic? And 3) have the participants schedule telemedicine appointments?\n\nResultIn both waves, 62 % of the participants reported providers did not have telemedicine services prior to the COVID-19 pandemic. However, we found a 22% increase in offering telemedicine in six first month of the COVID-19 pandemic. The finding shows almost no change in providing telemedicine between June and August. The data indicates just a 0.5% and 0.1% increase in accessing telemedicine, and scheduling in August than June, respectively. Patients older than 65 had higher access to telemedicine and had higher scheduling frequencies than other age groups, while they had the lowest access prior to the COVID-19. Blacks had the highest access to telemedicine services than other races (40%). Additionally, females, higher education, and living in metropolitan areas were associated with higher access and scheduling during the pandemic. There was a variation of access and scheduling in different chronic diseases, however, providers offered more remote services for those who diagnosed by diabetes.\n\nConclusionThe aim of telemedicine is to reduce disparities in healthcare access. The findings of this study show telemedicine has reduced racial disparities and provided greater accessibility for older groups. However, spatial and educational disparities are still noticeable. Research is necessary to examine how healthcare must address the socioeconomic heterogeneity in telemedicine by avoiding further disparities.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ali Roghani", - "author_inst": "University of Utah" - }, - { - "author_name": "Samin Panahi", - "author_inst": "University of Utah" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health systems and quality improvement" - }, { "rel_doi": "10.1101/2021.03.02.21252362", "rel_title": "High Initial Titres of Anti-Spike Antibodies following SARS-CoV-2 Infection is Associated with Faster Decay Rates at Four Months Follow-Up", @@ -928687,6 +926953,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.09.21251427", + "rel_title": "A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19).", + "rel_date": "2021-03-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.09.21251427", + "rel_abs": "The Coronavirus Disease 2019 (COVID-19) global pandemic has had a profound, lasting impact on the worlds population. A key aspect to providing care for those with COVID-19 and checking its further spread is early and accurate diagnosis of infection, which has been generally done via methods for amplifying and detecting viral RNA molecules. Detection and quantitation of peptides using targeted mass spectrometry-based strategies has been proposed as an alternative diagnostic tool due to direct detection of molecular indicators from non-invasively collected samples as well as the potential for high-throughput analysis in a clinical setting; many studies have revealed the presence of viral peptides within easily accessed patient samples. However, evidence suggests that some viral peptides could serve as better indicators of COVID-19 infection status than others, due to potential misidentification of peptides derived from human host proteins, poor spectral quality, high limits of detection etc. In this study we have compiled a list of 639 peptides identified from Sudden Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) samples, including from in vitro and clinical sources. These datasets were rigorously analyzed using automated, Galaxy-based workflows containing tools such as PepQuery, BLAST-P, and the Multi-omic Visualization Platform as well as the open-source tools MetaTryp and Proteomics Data Viewer (PDV). Using PepQuery for confirming peptide spectrum matches, we were able to narrow down the 639 peptide possibilities to 87 peptides which were most robustly detected and specific to the SARS-CoV-2 virus. The specificity of these sequences to coronavirus taxa was confirmed using Unipept and BLAST-P. Applying stringent statistical scoring thresholds, combined with manual verification of peptide spectrum match quality, 4 peptides derived from the nucleocapsid phosphoprotein and membrane protein were found to be most robustly detected across all cell culture and clinical samples, including those collected non-invasively. We propose that these peptides would be of the most value for clinical proteomics applications seeking to detect COVID-19 from a variety of sample types. We also contend that samples taken from the upper respiratory tract and oral cavity have the highest potential for diagnosis of SARS-CoV-2 infection from easily collected patient samples using mass spectrometry-based proteomics assays.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Andrew T Rajczewski", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Subina Mehta", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Dinh Duy An Ngyuen", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Bj\u00f6rn Andreas Gr\u00fcning", + "author_inst": "Uni-Freiburg" + }, + { + "author_name": "James E Johnson", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Thomas F McGowan", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Timothy Griffin", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Pratik Jagtap", + "author_inst": "University of Minnesota" + } + ], + "version": "2", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.27.433054", "rel_title": "Mice immunized with the vaccine candidate HexaPro spike produce neutralizing antibodies against SARS-CoV-2", @@ -929331,93 +927644,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.02.27.433180", - "rel_title": "Negligible impact of SARS-CoV-2 variants on CD4+ and CD8+ T cell reactivity in COVID-19 exposed donors and vaccinees.", - "rel_date": "2021-03-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.27.433180", - "rel_abs": "The emergence of SARS-CoV-2 variants highlighted the need to better understand adaptive immune responses to this virus. It is important to address whether also CD4+ and CD8+ T cell responses are affected, because of the role they play in disease resolution and modulation of COVID-19 disease severity. Here we performed a comprehensive analysis of SARS-CoV-2-specific CD4+ and CD8+ T cell responses from COVID-19 convalescent subjects recognizing the ancestral strain, compared to variant lineages B.1.1.7, B.1.351, P.1, and CAL.20C as well as recipients of the Moderna (mRNA-1273) or Pfizer/BioNTech (BNT162b2) COVID-19 vaccines. Similarly, we demonstrate that the sequences of the vast majority of SARS-CoV-2 T cell epitopes are not affected by the mutations found in the variants analyzed. Overall, the results demonstrate that CD4+ and CD8+ T cell responses in convalescent COVID-19 subjects or COVID-19 mRNA vaccinees are not substantially affected by mutations found in the SARS-CoV-2 variants.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Alison Tarke", - "author_inst": "La Jolla Institute for immunology" - }, - { - "author_name": "John Sidney", - "author_inst": "La Jolla Institute for immunology" - }, - { - "author_name": "Nils Methot", - "author_inst": "La Jolla Institute for immunology" - }, - { - "author_name": "Yun Zhang", - "author_inst": "J. Craig Venter Institute" - }, - { - "author_name": "Jennifer M Dan", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Benjamin Goodwin", - "author_inst": "La Jolla Institute for immunology" - }, - { - "author_name": "Paul Rubiro", - "author_inst": "La Jolla Institute for immunology" - }, - { - "author_name": "Aaron Sutherland", - "author_inst": "La Jolla Institute for immunology" - }, - { - "author_name": "Ricardo da Silva Antunes", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "April Fraizer", - "author_inst": "La Jolla Institute for immunology" - }, - { - "author_name": "Stephen A. Rawlings", - "author_inst": "University of California San Diego (UCSD)" - }, - { - "author_name": "Davey M. Smith", - "author_inst": "University of California San Diego (UCSD)" - }, - { - "author_name": "Bjoern Peters", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Richard H. Scheuermann", - "author_inst": "J. Craig Venter Institute" - }, - { - "author_name": "Daniela Weiskopf", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Shane Crotty", - "author_inst": "La Jolla Institute for immunology" - }, - { - "author_name": "Alba Grifoni", - "author_inst": "La Jolla Institute for Immunology" - }, - { - "author_name": "Alessandro Sette", - "author_inst": "La Jolla Institute for immunology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.03.01.433431", "rel_title": "Systematic analysis of SARS-CoV-2 infection of an ACE2-negative human airway cell", @@ -930433,6 +928659,197 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.25.21252433", + "rel_title": "Predicting COVID-19 related death using the OpenSAFELY platform", + "rel_date": "2021-03-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.25.21252433", + "rel_abs": "ObjectivesTo compare approaches for obtaining relative and absolute estimates of risk of 28-day COVID-19 mortality for adults in the general population of England in the context of changing levels of circulating infection.\n\nDesignThree designs were compared. (A) case-cohort which does not explicitly account for the time-changing prevalence of COVID-19 infection, (B) 28-day landmarking, a series of sequential overlapping sub-studies incorporating time-updating proxy measures of the prevalence of infection, and (C) daily landmarking. Regression models were fitted to predict 28-day COVID-19 mortality.\n\nSettingWorking on behalf of NHS England, we used clinical data from adult patients from all regions of England held in the TPP SystmOne electronic health record system, linked to Office for National Statistics (ONS) mortality data, using the OpenSAFELY platform.\n\nParticipantsEligible participants were adults aged 18 or over, registered at a general practice using TPP software on 1st March 2020 with recorded sex, postcode and ethnicity. 11,972,947 individuals were included, and 7,999 participants experienced a COVID-19 related death. The study period lasted 100 days, ending 8th June 2020.\n\nPredictorsA range of demographic characteristics and comorbidities were used as potential predictors. Local infection prevalence was estimated with three proxies: modelled based on local prevalence and other key factors; rate of A&E COVID-19 related attendances; and rate of suspected COVID-19 cases in primary care.\n\nMain outcome measuresCOVID-19 related death.\n\nResultsAll models discriminated well between patients who did and did not experience COVID-19 related death, with C-statistics ranging from 0.92-0.94. Accurate estimates of absolute risk required data on local infection prevalence, with modelled estimates providing the best performance.\n\nConclusionsReliable estimates of absolute risk need to incorporate changing local prevalence of infection. Simple models can provide very good discrimination and may simplify implementation of risk prediction tools in practice.", + "rel_num_authors": 44, + "rel_authors": [ + { + "author_name": "Elizabeth J Williamson", + "author_inst": "London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT" + }, + { + "author_name": "John Tazare", + "author_inst": "London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT" + }, + { + "author_name": "Krishnan Bhaskaran", + "author_inst": "London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT" + }, + { + "author_name": "Helen I McDonald", + "author_inst": "London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT; NIHR Health Protection Research Unit (HPRU) in Immunisation" + }, + { + "author_name": "Alex J Walker", + "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" + }, + { + "author_name": "Laurie Tomlinson", + "author_inst": "London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT" + }, + { + "author_name": "Kevin Wing", + "author_inst": "London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT" + }, + { + "author_name": "Sebastian Bacon", + "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" + }, + { + "author_name": "Chris Bates", + "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX" + }, + { + "author_name": "Helen J Curtis", + "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" + }, + { + "author_name": "Harriet Forbes", + "author_inst": "London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT" + }, + { + "author_name": "Caroline Minassian", + "author_inst": "London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT" + }, + { + "author_name": "Caroline E Morton", + "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" + }, + { + "author_name": "Emily Nightingale", + "author_inst": "London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT" + }, + { + "author_name": "Amir Mehrkar", + "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" + }, + { + "author_name": "Dave Evans", + "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" + }, + { + "author_name": "Brian D Nicholson", + "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" + }, + { + "author_name": "Dave Leon", + "author_inst": "London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT" + }, + { + "author_name": "Peter Inglesby", + "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" + }, + { + "author_name": "Brian MacKenna", + "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" + }, + { + "author_name": "Nicholas G Davies", + "author_inst": "London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT" + }, + { + "author_name": "Nicholas J DeVito", + "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" + }, + { + "author_name": "Henry Drysdale", + "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" + }, + { + "author_name": "Jonathan Cockburn", + "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX" + }, + { + "author_name": "William J Hulme", + "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" + }, + { + "author_name": "Jessica Morley", + "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" + }, + { + "author_name": "Ian Douglas", + "author_inst": "London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT" + }, + { + "author_name": "Christopher T Rentsch", + "author_inst": "London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT" + }, + { + "author_name": "Rohini Mathur", + "author_inst": "London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT" + }, + { + "author_name": "Angel Wong", + "author_inst": "London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT" + }, + { + "author_name": "Anna Schultze", + "author_inst": "London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT" + }, + { + "author_name": "Richard Croker", + "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" + }, + { + "author_name": "John Parry", + "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX" + }, + { + "author_name": "Frank Hester", + "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX" + }, + { + "author_name": "Sam Harper", + "author_inst": "TPP, TPP House, 129 Low Lane, Horsforth, Leeds, LS18 5PX" + }, + { + "author_name": "Richard Grieve", + "author_inst": "London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT" + }, + { + "author_name": "David A Harrison", + "author_inst": "Intensive Care National Audit & Research Centre (ICNARC), 24 High Holborn, Holborn, London WC1V 6AZ" + }, + { + "author_name": "Ewout W Steyerberg", + "author_inst": "Leiden University Medical Center, Leiden, the Netherlands" + }, + { + "author_name": "Rosalind M Eggo", + "author_inst": "London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT" + }, + { + "author_name": "Karla Diaz-Ordaz", + "author_inst": "London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT" + }, + { + "author_name": "Ruth Keogh", + "author_inst": "London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT" + }, + { + "author_name": "Stephen JW Evans", + "author_inst": "London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT" + }, + { + "author_name": "Liam Smeeth", + "author_inst": "London School of Hygiene & Tropical Medicine, Keppel Street, WC1E 7HT" + }, + { + "author_name": "Ben Goldacre", + "author_inst": "The DataLab, Nuffield Department of Primary Care Health Sciences, University of Oxford, OX26GG" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.25.21252445", "rel_title": "Emergent effects of contact tracing robustly stabilize outbreaks", @@ -930761,37 +929178,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sports medicine" }, - { - "rel_doi": "10.1101/2021.02.26.21252552", - "rel_title": "The Charitable Feeding System helps Food Insecure Participants maintain Fruit and Vegetable intake during COVID-19.", - "rel_date": "2021-03-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.26.21252552", - "rel_abs": "Charitable food services, including food banks and pantries, support individual and households food access, potentially maintaining food security and diet quality during emergencies. During the COVID-19 pandemic, the use of food banks and pantries has increased in the US. Here we examine perceptions of the charitable food system and its relationship to food security and dietary quality, specifically fruit and vegetable (FV) intake during the first six months of the COVID-19 pandemic, using a statewide representative survey (n=600) of residents of Vermont. We find that demand for charitable food services increased by 68%. The utilization of food pantries was more common among food insecure households and households with children. Among food insecure respondents, those who used the charitable food system were less likely to reduce their FV intake during the pandemic than those who did not use the charitable food system. Further, we find significant interactions between food pantry use and food insecure households, suggesting that, for food, insecure households, utilizing a food pantry since the onset of the COVID-19 pandemic was associated with higher fruit consumption. These results indicate that these services may support food access and diet quality for at-risk populations during emergencies.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Farryl MW Bertmann", - "author_inst": "University of Vermont" - }, - { - "author_name": "Katherine Rogomentich", - "author_inst": "University of Vermont" - }, - { - "author_name": "Emily H Belarmino", - "author_inst": "University of Vermont" - }, - { - "author_name": "Meredith T. Niles", - "author_inst": "University of Vermont" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "nutrition" - }, { "rel_doi": "10.1101/2021.02.27.21252569", "rel_title": "COVID-19 Vaccination Priority Evaluation", @@ -931831,6 +930217,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.21.21252168", + "rel_title": "Early Antibody Responses Associated with Survival in COVID19 Patients", + "rel_date": "2021-02-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.21.21252168", + "rel_abs": "Neutralizing antibodies to the SARS CoV-2 spike proteins have been issued Emergency Use Authorizations and are a likely mechanism of vaccines to prevent COVID-19. However, benefit of treatment with monoclonal antibodies has only been observed in clinical trials in outpatients with mild to moderate COVID-19 but not in patients who are hospitalized and/or have advanced disease. To address this observation, we evaluated the timing of anti SARS-CoV-2 antibody production in hospitalized patients with the use of a highly sensitive multiplexed bead-based immunoassay allowing for early detection of antibodies to SARS-CoV-2. We found that significantly lower levels of antibodies to the SARS-CoV-2 spike protein in the first week after symptom onset were associated with patients who expired as compared to patients who were discharged. We also developed a model, based on antibody level trajectory, to predict COVID 19 outcome that is compatible with greater antibody benefit earlier in COVID 19 disease.\n\nAuthor SummaryWe evaluated antibodies to SARS-CoV-2 over time in patients that were hospitalized with COVID 19. Early detection of Anti-SARS-CoV-2 antibodies was associated with survival in patients hospitalized with COVID 19. Early antibody levels predicted outcome in our study. This result is consistent with the benefit of therapeutic antibodies early in the course of COVID 19 disease. With additional study, early antibody levels may be helpful in deciding on appropriate therapies.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Zhao-hua Zhou", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Sai Dharmarajan", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Mari Lehtimaki", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Susan L Kirshner", + "author_inst": "US Food and Drug Administration" + }, + { + "author_name": "Steven Kozlowski", + "author_inst": "US Food and Drug Administration" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.22.21252228", "rel_title": "Hydroxychloroquine for SARS-CoV-2 positive patients quarantined at home: The first interim analysis of a remotely conducted randomized clinical trial", @@ -932335,85 +930756,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.23.21252299", - "rel_title": "The Public Health Impact of Delaying a Second Dose of the BNT162b2 or mRNA-1273 COVID-19 Vaccine", - "rel_date": "2021-02-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.23.21252299", - "rel_abs": "ObjectivesTo estimate population health outcomes under delayedsecond dose versus standard schedule SARS-CoV-2 mRNA vaccination.\n\nDesignAgent-based modeling on a simulated population of 100,000 based on a real-world US county. The simulation runs were replicated 10 times. To test the robustness of these findings, simulations were performed under different estimates for single-dose efficacy and vaccine administration rates, and under the possibility that a vaccine prevents only symptoms but not asymptomatic spread.\n\nSettingpopulation level simulation.\n\nParticipants100,000 agents are included in the simulation, with a representative distribution of demographics and occupations. Networks of contacts are established to simulate potentially infectious interactions though occupation, household, and random interactions\n\nInterventionswe simulate standard Covid-19 vaccination, versus delayed-second-dose vaccination prioritizing first dose. Sensitivity analyses include first-dose vaccine efficacy of 70%, 80% and 90% after day 12 post-vaccination; vaccination rate of 0.1%, 0.3%, and 1% of population per day; assuming the vaccine prevents only symptoms but not asymptomatic spread; and an alternative vaccination strategy that implements delayed-second-dose only for those under 65 years of age.\n\nMain outcome measurescumulative Covid-19 mortality over 180 days, cumulative infections and hospitalizations.\n\nResultsOver all simulation replications, the median cumulative mortality per 100,000 for standard versus delayed second dose was 226 vs 179; 233 vs 207; and 235 vs 236; for 90%, 80% and 70% first-dose efficacy, respectively. The delayed-second-dose strategy was optimal for vaccine efficacies at or above 80%, and vaccination rates at or below 0.3% population per day, both under sterilizing and non-sterilizing vaccine assumptions, resulting in absolute cumulative mortality reductions between 26 and 47 per 100,000. The delayed-second-dose for those under 65 performed consistently well under all vaccination rates tested.\n\nConclusionsA delayed-second-dose vaccination strategy, at least for those under 65, could result in reduced cumulative mortality under certain conditions.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Santiago Romero-Brufau", - "author_inst": "Mayo Clinic, Harvard T. H. Chan School of Public Health" - }, - { - "author_name": "Ayush Chopra", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Alex J Ryu", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Esma Gel", - "author_inst": "Arizona State University" - }, - { - "author_name": "Ramesh Raskar", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Walter Kremers", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Karen Anderson", - "author_inst": "Mayo Clinic, Arizona State University" - }, - { - "author_name": "Jayakumar Subramanian", - "author_inst": "Adobe Systems" - }, - { - "author_name": "Balaji Krishnamurthy", - "author_inst": "Adobe Systems" - }, - { - "author_name": "Abhishek Singh", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Kalyan Pasupathy", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Yue Dong", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "John C O'Horo", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Walter R Wilson", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Oscar Mitchell", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Thomas C Kingsley", - "author_inst": "Mayo Clinic" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.24.21252145", "rel_title": "Virtual handover of patients in the pediatric intensive care unit during COVID-19 crisis", @@ -934057,6 +932399,29 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.02.19.21252117", + "rel_title": "A Comprehensive County Level Framework to Identify Factors Affecting Hospital Capacity and Predict Future Hospital Demand", + "rel_date": "2021-02-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.19.21252117", + "rel_abs": "BackgroundAs of February 19, 2021, our review yielded a small number of studies that investigated high resolution hospitalization demand data from a public health planning perspective. The earlier studies compiled were conducted early in the pandemic and do not include any analysis of the hospitalization trends in the last 3 months when the US experienced a substantial surge in hospitalization and ICU demand. The earlier studies also focused on COVID 19 transmission influence on COVID 19 hospitalization rates. While this emphasis is understandable, there is evidence to suggest that non COVID hospitalization demand is being displaced due to the hospitalization and ICU surge. Further, with the discovery of multiple mutated variants of COVID 19, it is important to remain vigilant in an effort to control the pandemic. Given these circumstances, the development of a high resolution framework that examines overall hospitalizations and ICU usage rate for COVID and non COVID patients would allow us to build a prediction system that can identify potential vulnerable locations for hospitalization capacity in the nation so that appropriate remedial measures can be planned.\n\nMethodThe current study recognizes that COVID 19 has affected overall hospitalizations - not only COVID 19 hospitalizations. Drawing from the recently released Department of Health and Human services (DHH) weekly hospitalization data (or the time period August 28th, 2020 to January 22nd, 2021.), we study the overall hospitalization and ICU usage as two components: COVID 19 hospitalization and ICU per capita rates; and non COVID hospitalization and ICU per capita rates. A mixed linear mixed model is adopted to study the response variables in our study. The estimated models are subsequently employed to generate predictions for county level hospitalization and ICU usage rates in the future under a host of COVID 19 transmission scenarios considering the new variants of COVID 19 and vaccination impacts.\n\nFindingsWe find a significant association of the virus transmissibility with COVID (positive) and non COVID (negative) hospitalization and ICU usage rates. Several county level factors including demographics, mobility and health indicators are also found to be strongly associated with the overall hospitalization and ICU demand. Among the various scenarios considered, the results indicate a small possibility of a new wave of infections that can substantially overload hospitalization and ICU usage. In the scenario where vaccinations proceed as expected reducing transmission, our results indicate that hospitalizations and ICU usage rates are likely to reduce significantly.\n\nInterpretationThe research exercise presents a framework to predict evolving hospitalization and ICU usage trends in response to COVID 19 transmission rates while controlling for other factors. Our work highlights how future hospitalization demand varies by location and time in response to a range of pessimistic and optimistic scenarios. Further, the exercise allows us to identify vulnerable counties and regions under stress with high hospitalization and ICU rates that can be assisted with remedial measures. The model will also allow hospitals to understand evolving displaced non COVID hospital demand.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Tanmoy Bhowmik", + "author_inst": "University of Central Florida" + }, + { + "author_name": "Naveen Eluru", + "author_inst": "University of Central Florida" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.18.21251999", "rel_title": "Practical strategies for SARS-CoV-2 RT-PCR testing in resource-constrained settings", @@ -934485,37 +932850,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, - { - "rel_doi": "10.1101/2021.02.23.21251915", - "rel_title": "Clinical evaluation of the molecular-based BD SARS-CoV-2/Flu for the BD MAX\u2122 System", - "rel_date": "2021-02-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.23.21251915", - "rel_abs": "Efficient and accurate assays for the differential diagnosis of COVID-19 and/or influenza (flu) could facilitate optimal treatment for both diseases. Diagnostic performance related to SARS-CoV-2 and Flu A/B detection was characterized for the BD SARS-CoV-2/Flu for BD MAX System (\"MAX SARS-CoV-2/Flu\") multiplex assay in comparison with BD BioGx SARS-CoV-2 Reagents for BD MAX System (\"BioGx SARS-CoV-2\") and the Cepheid Xpert(R) Xpress Flu/RSV (\"Xpert Flu\"). Two hundred and thirty-five nasopharyngeal specimens were obtained from external vendors. MAX SARS-CoV-2/Flu had positive percent agreement (PPA) and negative percent agreement (NPA) values for SARS-CoV-2 and Flu A/B that met FDA-EUA acceptance criteria of >95%.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Sonia Paradis", - "author_inst": "BD" - }, - { - "author_name": "Elizabeth Lockamy", - "author_inst": "BD" - }, - { - "author_name": "Charles K Cooper", - "author_inst": "BD" - }, - { - "author_name": "Stephen Young", - "author_inst": "TriCore Reference Laboratories" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.23.21252309", "rel_title": "Vaccine Rollout Strategies: The Case for Vaccinating Essential Workers Early", @@ -935991,6 +934325,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.23.21252277", + "rel_title": "Impact of the Tier system on SARS-CoV-2 transmission in the UK between the first and second national lockdowns", + "rel_date": "2021-02-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.23.21252277", + "rel_abs": "ObjectiveMeasure the effects of the Tier system on the COVID-19 pandemic in the UK between the first and second national lockdowns, before the emergence of the B.1.1.7 variant of concern.\n\nDesignModelling study combining estimates of the real-time reproduction number Rt (derived from UK case, death and serological survey data) with publicly available data on regional non-pharmaceutical interventions. We fit a Bayesian hierarchical model with latent factors using these quantities, to account for broader national trends in addition to subnational effects from Tiers.\n\nSettingThe UK at Lower Tier Local Authority (LTLA) level.\n\nPrimary and secondary outcome measuresReduction in real-time reproduction number Rt.\n\nResultsNationally, transmission increased between July and late September, regional differences notwithstanding. Immediately prior to the introduction of the tier system, Rt averaged 1.3 (0.9 - 1.6) across LTLAs, but declined to an average of 1.1 (0.86 - 1.42) two weeks later. Decline in transmission was not solely attributable to Tiers. Tier 1 had negligible effects. Tiers 2 and 3 respectively reduced transmission by 6% (5%-7%) and 23% (21%-25%). 93% of LTLAs would have begun to suppress their epidemics if every LTLA had gone into Tier 3 by the second national lockdown, whereas only 29% did so in reality.\n\nConclusionsThe relatively small effect sizes found in this analysis demonstrate that interventions at least as stringent as Tier 3 are required to suppress transmission, especially considering more transmissible variants, at least until effective vaccination is widespread or much greater population immunity has amassed.\n\nStrengths and limitations of this studyO_LIFirst study to measure effects of UK Tier system for SARS-CoV-2 control at national and regional level.\nC_LIO_LIModel makes minimal assumptions and is primarily data driven.\nC_LIO_LIInsufficient statistical power to estimate effects of individual interventions that comprise Tiers, or their interaction.\nC_LIO_LIEstimates show that Tiers 1 and 2 are insufficient to suppress transmission, at least until widespread population immunity has amassed. Emergence of more transmissible variants of concern unfortunately supports this conclusion.\nC_LI", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Daniel J Laydon", + "author_inst": "Imperial College London" + }, + { + "author_name": "Swapnil Mishra", + "author_inst": "Imperial College London" + }, + { + "author_name": "Wes R Hinsley", + "author_inst": "Imperial College London" + }, + { + "author_name": "Pantelis Samartsidis", + "author_inst": "MRC Biostatistics Unit, Cambridge Institute of Public Health" + }, + { + "author_name": "Seth Flaxman", + "author_inst": "Imperial College London" + }, + { + "author_name": "Axel Gandy", + "author_inst": "Imperial College London" + }, + { + "author_name": "Neil M Ferguson", + "author_inst": "Imperial College London" + }, + { + "author_name": "Samir Bhatt", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.22.21252255", "rel_title": "An integrated framework for building trustworthy data-driven epidemiological models: Application to the COVID-19 outbreak in New York City", @@ -936479,61 +934860,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.23.21252230", - "rel_title": "Prior COVID-19 Infection and Antibody Response to Single Versus Double Dose mRNA SARS-CoV-2 Vaccination", - "rel_date": "2021-02-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.23.21252230", - "rel_abs": "The double dose regimen for mRNA vaccines against SARS-CoV-2 presents both a hope and a challenge for global efforts to curb the COVID-19 pandemic. With supply chain logistics impacting the rollout of population-scale vaccination programs, increasing attention has turned to the potential efficacy of single versus double dose vaccine administration for select individuals. To this end, we examined response to Pfizer-BioNTech mRNA vaccine in a large cohort of healthcare workers including those with versus without prior COVID-19 infection. For all participants, we quantified circulating levels of SARS-CoV-2 anti-spike (S) protein IgG at baseline prior to vaccine, after vaccine dose 1, and after vaccine dose 2. We observed that the anti-S IgG antibody response following a single vaccine dose in persons who had recovered from confirmed prior COVID-19 infection was similar to the antibody response following two doses of vaccine in persons without prior infection (P[≥]0.58). Patterns were similar for the post-vaccine symptoms experienced by infection recovered persons following their first dose compared to the symptoms experienced by infection naive persons following their second dose (P=0.66). These results support the premise that a single dose of mRNA vaccine could provoke in COVID-19 recovered individuals a level of immunity that is comparable to that seen in infection naive persons following a double dose regimen. Additional studies are needed to validate our findings, which could allow for public health programs to expand the reach of population wide vaccination efforts.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Joseph E. Ebinger", - "author_inst": "Cedars-Sinai Medical Center" - }, - { - "author_name": "Justyna Fert-Bober", - "author_inst": "Cedars-Sinai Medical Center" - }, - { - "author_name": "Ignat Printsev", - "author_inst": "Cedars-Sinai Medical Center" - }, - { - "author_name": "Min Wu", - "author_inst": "Cedars-Sinai Medical Center" - }, - { - "author_name": "Nancy Sun", - "author_inst": "Cedars-Sinai Medical Center" - }, - { - "author_name": "Jane C. Figueiredo", - "author_inst": "Cedars-Sinai Medical Center" - }, - { - "author_name": "Jennifer Van Eyk", - "author_inst": "Cedars-Sinai Medical Center" - }, - { - "author_name": "Jonathan Braun", - "author_inst": "Cedars-Sinai Medical Center" - }, - { - "author_name": "Susan Cheng", - "author_inst": "Cedars-Sinai Medical Center" - }, - { - "author_name": "Kimia Sobhani", - "author_inst": "Cedars-Sinai Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.22.21252262", "rel_title": "COVID-19 in New York state: Effects of demographics and air quality on infection and fatality", @@ -937821,6 +936147,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.19.21252093", + "rel_title": "The Association of Opioid Use Disorder and COVID-19 in Shahroud, Iran", + "rel_date": "2021-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.19.21252093", + "rel_abs": "BackgroundCOVID-19 quickly spread to the world, causing a pandemic. While some studies have found no link between Opioid Use Disorder (OUD) and COVID-19, the role of the opioid on COVID-19 is challenging. The present study aimed to determine the relationship between OUD and COVID-19.\n\nMethodsThis was a prospective cohort study. We used data from the third phase of the Shahroud eye cohort study on 4394 participants which started in September 2019 and ended before the COVID-19 epidemic in Shahroud in February 2020. The participants were followed for 10.5 months till November 2020. COVID-19 was detected by RT-PCR on swap samples from the oropharynx and nasopharynx. The incidence of COVID-19 compared in OUD and Non-OUD participants, and relative risk was calculated in Log Binomial Regression model.\n\nResultsAmong the 4394 participants with a mean age of 61.1 years, 120 people had OUD. The incidence of COVID-19 in participants with OUD and Non-OUD were 3.3% and 4.5%, respectively. The relative risk of OUD for COVID-19 was 0.75 (95% Confidence intervals: 0.28 - 1.98; P= 0.555).\n\nConclusionsOpioid use disorder was not associated with COVID-19. The claim that people with OUD are less likely to develop COVID-19 is not supported by this data.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Zhaleh Jamali", + "author_inst": "Student Research Committee, School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran" + }, + { + "author_name": "Mohammad Hassan Emamian", + "author_inst": "Ophthalmic Epidemiology Research Center, Shahroud University of Medical Sciences, Shahroud, Iran" + }, + { + "author_name": "Hassan Hashemi", + "author_inst": "Noor Ophthalmology Research Center, Noor Eye Hospital, Tehran, Iran" + }, + { + "author_name": "Akbar Fotouhi", + "author_inst": "Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "addiction medicine" + }, { "rel_doi": "10.1101/2021.02.18.21251504", "rel_title": "Efferocytosis of SARS-CoV-2-infected dying cells impairs macrophage anti-inflammatory programming and continual clearance of apoptotic cells", @@ -938405,73 +936762,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.02.20.21251855", - "rel_title": "Transmission of SARS-CoV-2 Considering Shared Chairs in Outpatient Dialysis: A Real-World Case-Control Study", - "rel_date": "2021-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.20.21251855", - "rel_abs": "BackgroundSARS-CoV-2 is primarily transmitted through aerosolized droplets; however, the virus can remain transiently viable on surfaces.\n\nObjectiveWe examined transmission within hemodialysis facilities, with a specific focus on the possibility of indirect patient-to-patient transmission through shared dialysis chairs.\n\nDesignWe used real-world data from hemodialysis patients treated between February 1st and June 8th, 2020 to perform a case-control study matching each SARS-CoV-2 positive patient (case) to a non-SARS-CoV-2 patient (control) in the same dialysis shift and traced back 14 days to capture possible exposure from chairs sat in by SARS-CoV-2 patients. Cases and controls were matched on age, sex, race, facility, shift date, and treatment count.\n\nSetting2,600 hemodialysis facilities in the United States.\n\nPatientsAdult (age [≥]18 years) hemodialysis patients.\n\nMeasurementsConditional logistic regression models tested whether chair exposure after a positive patient conferred a higher risk of SARS-CoV-2 infection to the immediate subsequent patient.\n\nResultsAmong 170,234 hemodialysis patients, 4,782 (2.8%) tested positive for SARS-CoV-2 (mean age 64 years, 44% female). Most facilities (68.5%) had 0 to 1 positive SARS-CoV-2 patient. We matched 2,379 SARS-CoV-2 positive cases to 2,379 non-SARS-CoV-2 controls; 1.30% (95%CI 0.90%, 1.87%) of cases and 1.39% (95%CI 0.97%, 1.97%) of controls were exposed to a chair previously sat in by a shedding SARS-CoV-2 patient. Transmission risk among cases was not significantly different from controls (OR=0.94; 95%CI 0.57 to 1.54; p=0.80). Results remained consistent in adjusted and sensitivity analyses.\n\nLimitationAnalysis used real-world data that could contain errors and only considered vertical transmission associated with shared use of dialysis chairs by symptomatic patients.\n\nConclusionsThe risk of indirect patient-to-patient transmission of SARS-CoV-2 infection from dialysis chairs appears to be low.\n\nPrimary Funding SourceFresenius Medical Care North America; National Institute of Diabetes and Digestive and Kidney Diseases (R01DK130067)", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Ravi Thadhani", - "author_inst": "Partners HealthCare" - }, - { - "author_name": "Joanna Willetts", - "author_inst": "Fresenius Medical Care, Global Medical Office" - }, - { - "author_name": "Catherine Wang", - "author_inst": "University of California-Santa Barbara" - }, - { - "author_name": "John W Larkin", - "author_inst": "Fresenius Medical Car, Global Medical Office" - }, - { - "author_name": "Hanjie Zhang", - "author_inst": "Renal Research Institute" - }, - { - "author_name": "Lemuel Rivera Fuentes", - "author_inst": "Renal Research Institute" - }, - { - "author_name": "Len Usvyat", - "author_inst": "Fresenius Medical Care, Global Medical Office" - }, - { - "author_name": "Kathleen Belmonte", - "author_inst": "Fresenius Kidney Care" - }, - { - "author_name": "Yuedong Wang", - "author_inst": "University of California-Santa Barbara" - }, - { - "author_name": "Robert Kossmann", - "author_inst": "Fresenius Medical Care North America" - }, - { - "author_name": "Jeffrey Hymes", - "author_inst": "Fresenius Medical Care, Global Medical Office" - }, - { - "author_name": "Peter Kotanko", - "author_inst": "Renal Research Institute" - }, - { - "author_name": "Franklin W Maddux", - "author_inst": "Fresenius Medical Care AG & Co. KGaA" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "nephrology" - }, { "rel_doi": "10.1101/2021.02.19.21252101", "rel_title": "SARS-CoV-2 disinfection in aqueous solution by UV222 from a krypton chlorine excilamp", @@ -939799,6 +938089,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.20.21251520", + "rel_title": "Wastewater Monitoring of SARS-CoV-2 from Acute Care Hospitals Identifies Nosocomial Transmission and Outbreaks", + "rel_date": "2021-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.20.21251520", + "rel_abs": "BackgroundSARS-CoV-2 has been detected in wastewater and its abundance correlated with community COVID-19 cases, hospitalizations and deaths. We sought to use wastewater-based detection of SARS-CoV-2 to assess the epidemiology of SARS-CoV-2 in hospitals.\n\nMethodsBetween August and December 2020, twice-weekly wastewater samples from three tertiary-care hospitals (totaling >2100 dedicated inpatient beds) were collected. Wastewater samples were concentrated and cleaned using the 4S-silica column method and assessed for SARS-CoV-2 gene-targets (N1, N2 and E) and controls using RT-qPCR. Wastewater SARS-CoV-2 as measured by quantification cycle (Cq), genome copies and genomes normalized to the fecal biomarker PMMoV were compared to the total daily number of patients hospitalized with active COVID-19, confirmed cases of hospital-acquired infection, and the occurrence of unit-specific outbreaks.\n\nResultsOf 165 wastewater samples collected, 159 (96%) were assayable. The N1-gene from SARS-CoV-2 was detected in 64.1% of samples, N2 in 49.7% and E in 10%. N1 and N2 in wastewater increased over time both in terms of amount of detectable virus and the proportion of samples that were positive, consistent with increasing hospitalizations (Pearsons r=0.679, P<0.0001, Pearsons r=0.728, P<0.0001, respectively). Despite increasing hospitalizations through the study period, wastewater analysis was able to identify incident nosocomial-acquired cases of COVID-19 (Pearsons r =0.389, P<0.001) and unit-specific outbreaks by increases in detectable SARS-CoV-2 N1-RNA (median 112 copies/ml) versus outbreak-free periods (0 copies/ml; P<0.0001).\n\nConclusionsWastewater-based monitoring of SARS-CoV-2 represents a promising tool for SARS-CoV-2 passive surveillance and case identification, containment, and mitigation in acute-care medical facilities.\n\nSupplemental Material includedO_ST_ABSKey-points summaryC_ST_ABSSAS-CoV-2 RNA is detectable in hospital wastewater. Wastewater SARS-CoV-2 RNA increases in conjunction with COVID-19-related hospitalizations. Spikes in SARS-CoV-2 wastewater signal correspond to incident hospital-acquired cases and outbreaks, suggesting passive surveillance via wastewater has great promise for COVID-19 monitoring.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Nicole Acosta", + "author_inst": "University of Calgary" + }, + { + "author_name": "Maria Bautista", + "author_inst": "University of Calgary" + }, + { + "author_name": "Jordan Hollman", + "author_inst": "University of Calgary" + }, + { + "author_name": "Janine McCalder", + "author_inst": "University of Calgary" + }, + { + "author_name": "Alexander Buchner Beaudet", + "author_inst": "University of Calgary" + }, + { + "author_name": "Lawrence Man", + "author_inst": "University of Calgary" + }, + { + "author_name": "Barbara J Waddell", + "author_inst": "University of Calgary" + }, + { + "author_name": "Jianwei Chen", + "author_inst": "University of Calgary" + }, + { + "author_name": "Carmen Li", + "author_inst": "University of Calgary" + }, + { + "author_name": "Darina Kuzma", + "author_inst": "University of Calgary" + }, + { + "author_name": "Srijak Bhatnagar", + "author_inst": "University of Calgary" + }, + { + "author_name": "Jenine Leal", + "author_inst": "Alberta Health Services" + }, + { + "author_name": "Jon Meddings", + "author_inst": "University of Calgary" + }, + { + "author_name": "Jia Hu", + "author_inst": "Alberta Health Services" + }, + { + "author_name": "Jason Cabaj", + "author_inst": "Alberta Health Services" + }, + { + "author_name": "Norma J Ruecker", + "author_inst": "City of Calgary" + }, + { + "author_name": "Christopher Naugler", + "author_inst": "University of Calgary" + }, + { + "author_name": "Dylan R Pillai", + "author_inst": "University of Calgary" + }, + { + "author_name": "Gopal Achari", + "author_inst": "University of Calgary" + }, + { + "author_name": "M. Cathryn Ryan", + "author_inst": "University of Calgary" + }, + { + "author_name": "John M Conly", + "author_inst": "University of Calgary" + }, + { + "author_name": "Kevin Frankowski", + "author_inst": "University of Calgary; Advancing Canadian Wastewater Assets (ACWA)" + }, + { + "author_name": "Casey RJ Hubert", + "author_inst": "University of Calgary" + }, + { + "author_name": "Michael D Parkins", + "author_inst": "University of Calgary" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.19.21251340", "rel_title": "Multicenter cohort study of children hospitalized with SARS-CoV-2 infection", @@ -940259,45 +938660,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.22.21252208", - "rel_title": "Vaccination efforts in Brazil: scenarios and perspectives under a mathematical modeling approach", - "rel_date": "2021-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.22.21252208", - "rel_abs": "An agent-based model is proposed to access the impact of vaccination strategies to halt the COVID-19 spread. The model is parameterized using data from Sao Paulo State, Brazil. It was considered the two vaccines that are already approved for emergency use in Brazil, the CoronaVac vaccine developed by the Chinese bio-pharmaceutical company Sinovac and the Oxford-AstraZeneca vaccine (ChadOx1) developed by Oxford University and the British laboratory AstraZeneca. Both of them are two-dose schemes, but the efficacy and the interval between doses are different. We found that even in the worst scenario, in which the vaccine does not prevent infection either severe symptoms, the number of deaths decreases from 122 to 99 for CoronaVac application and to 80 for ChadOx1 administration. The same patterns have been seen in hospitalizations. Nevertheless, we show that when a low risk perception occurs, the reduction values decrease between 2% to 4%. Moreover, the increase of disease prevalence also jeopardizes immunization, showing the importance of the mitigation measures maintenance. On the other hand, doubling the vaccination rate would be able to significantly decrease the disease outcomes, reducing deaths by up to 74.4%. In conclusion, vaccination, along with non-pharmaceutical measures, is key to the control of COVID-19 in Brazil.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Thomas Nogueira Vilches", - "author_inst": "IMECC-UNICAMP" - }, - { - "author_name": "Felipe Alves Rubio", - "author_inst": "University of Campinas" - }, - { - "author_name": "Rafael Forti Perroni", - "author_inst": "UNESP" - }, - { - "author_name": "Gabriel Berg de Almeida", - "author_inst": "Faculdade de Medicina de Botucatu" - }, - { - "author_name": "Claudia Pio Ferreira", - "author_inst": "Institute of Bioscience - UNESP" - }, - { - "author_name": "Carlos Magno Castelo Branco Fortaleza", - "author_inst": "Botucatu Medical School, S\u00e3o Paulo State University (UNESP)" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.22.21252219", "rel_title": "Factors Associated with Timely Test Seeking, Test Turnaround, and Public Reporting of COVID-19: a retrospective analysis in Ontario, Canada", @@ -941637,6 +939999,61 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.02.23.432569", + "rel_title": "Inhalable Nanobody (PiN-21) prevents and treats SARS-CoV-2 infections in Syrian hamsters at ultra-low doses", + "rel_date": "2021-02-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.23.432569", + "rel_abs": "Globally there is an urgency to develop effective, low-cost therapeutic interventions for coronavirus disease 2019 (COVID-19). We previously generated the stable and ultrapotent homotrimeric Pittsburgh inhalable Nanobody 21 (PiN-21). Using Syrian hamsters that model moderate to severe COVID-19 disease, we demonstrate the high efficacy of PiN-21 to prevent and treat SARS-CoV-2 infection. Intranasal delivery of PiN-21 at 0.6 mg/kg protects infected animals from weight loss and substantially reduces viral burdens in both lower and upper airways compared to control. Aerosol delivery of PiN-21 facilitates deposition throughout the respiratory tract and dose minimization to 0.2 mg/kg. Inhalation treatment quickly reverses animals weight loss post-infection and decreases lung viral titers by 6 logs leading to drastically mitigated lung pathology and prevents viral pneumonia. Combined with the marked stability and low production cost, this novel therapy may provide a convenient and cost-effective option to mitigate the ongoing pandemic.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Sham Nambulli", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Yufei Xiang", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Natasha L Tilston-Lunel", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Linda J Rennick", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Zhe Sang", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "William B Klimstra", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Douglas S Reed", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Nicholas A Crossland", + "author_inst": "Boston University School of Medicine" + }, + { + "author_name": "Yi Shi", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Paul W Duprex", + "author_inst": "University of Pittsburgh" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.02.20.21251927", "rel_title": "Rapid SARS-CoV-2 variants spread detected in France using specific RT-PCR testing", @@ -942177,77 +940594,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.02.20.432110", - "rel_title": "A novel glucocorticoid and androgen receptor modulator reduces viral entry and innate immune inflammatory responses in the Syrian Hamster model of SARS-CoV-2", - "rel_date": "2021-02-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.20.432110", - "rel_abs": "Since its initial discovery in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of COVID19, has spread worldwide and despite significant research efforts, treatment options remain limited. Replication of SARS-CoV-2 in lung is associated with marked infiltration of macrophages and activation of innate immune inflammatory responses triggered, in part, by heightened production of interleukin-6 (IL-6) that recruits lymphocytes to the site of infection that amplify tissue injury. Antagonists of the glucocorticoid and androgen receptors have shown promise in experimental models of COVID19 and in clinical studies, because cell surface proteins required for viral entry, angiotensin converting enzyme 2 (ACE2) and the transmembrane serine protease 2 (TMPRSS2), are transcriptionally regulated by these receptors. We therefore postulated that the glucocorticoid (GR) and androgen receptor (AR) antagonist, PT150, would reduce infectivity of SARS-CoV-2 and prevent inflammatory lung injury in the Syrian golden hamster model of COVID19. Animals were infected intranasally with 2.5 x 104 TCID50/ml equivalents of SARS-CoV-2 (strain 2019-nCoV/USA-WA1/ 2020) and PT150 was administered by oral gavage at 30 and 100 mg/Kg/day for a total of 7 days. Animals were then examined at days 3, 5 and 7 post-infection (DPI) for lung histopathology, viral load and production of proteins regulating the initiation and progression of SARS-CoV-2 infection. Results of these studies indicated that oral administration of PT150 decreased replication of SARS-CoV-2 in lung, as well as expression of ACE2 and TMPRSS2 protein. Hypercellularity and inflammatory cell infiltration driven by macrophage responses were dramatically decreased in PT150-treated animals, as was tissue damage and expression of IL-6. Molecular modeling suggested that PT150 binds to the co-activator interface of the ligand binding domain of both AR and GR and thereby acts as an allosteric modulator and transcriptional repressor of these receptors. Phylogenetic analysis of AR and GR across multiple species permissive to SARS-CoV-2 infection revealed a high degree of sequence identity maintained across species, including human, suggesting that the mechanism of action and therapeutic efficacy observed in Syrian hamsters would likely be predictive of positive outcomes in patients. PT150 is therefore a strong candidate for further clinical development for the treatment of COVID19 across variants of SARS-CoV-2.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Savannah M. Rocha", - "author_inst": "Colorado State University" - }, - { - "author_name": "Anna C. Fagre", - "author_inst": "Colorado State University" - }, - { - "author_name": "Amanda S. Latham", - "author_inst": "Colorado State University" - }, - { - "author_name": "Katriana A. Popichak", - "author_inst": "Colorado State University" - }, - { - "author_name": "Casey P. McDermott", - "author_inst": "Colorado State University" - }, - { - "author_name": "Clinton C. Dawson", - "author_inst": "Colorado State University" - }, - { - "author_name": "Juliette Lewis", - "author_inst": "Colorado State University" - }, - { - "author_name": "Phillip Reigan", - "author_inst": "University of Colorado Denver Anschutz Medical Campus" - }, - { - "author_name": "Tawfik A. Aboellail", - "author_inst": "Colorado State University" - }, - { - "author_name": "Rebekah C. Kading", - "author_inst": "Colorado State University" - }, - { - "author_name": "Tony Schountz", - "author_inst": "Colorado State University" - }, - { - "author_name": "Neil D. Theise", - "author_inst": "New York University-Grossman School of Medicine" - }, - { - "author_name": "Richard A. Slayden", - "author_inst": "Colorado State University" - }, - { - "author_name": "Ronald B. Tjalkens", - "author_inst": "Colorado State University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.02.17.431683", "rel_title": "Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016", @@ -943379,6 +941725,53 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2021.02.18.21252032", + "rel_title": "The COVID-19 Incarceration Model: a tool for corrections staff to analyze outbreaks of COVID-19", + "rel_date": "2021-02-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.18.21252032", + "rel_abs": "Correctional facilities are at high risk of COVID-19 outbreaks due to the inevitable close contacts in the environment. Such facilities are a high priority in the public health response to the epidemic. We developed a user-friendly Excel spreadsheet model (building on the previously developed Recidiviz model) to analyze COVID-19 outbreaks in correctional facilities and the potential impact of prevention strategies -the COVID-19 Incarceration Model. The model requires limited inputs and can be used by non-modelers. The impact of a COVID-19 outbreak and mitigation strategies is illustrated for an example prison setting.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Jisoo Amy Kwon", + "author_inst": "The Kirby Institute, University of New South Wales" + }, + { + "author_name": "Neil A Bretana", + "author_inst": "UniSA Online, University of South Australia, Australia" + }, + { + "author_name": "Luke Grant", + "author_inst": "Corrective Services NSW, Australia" + }, + { + "author_name": "Jennifer Galouzis", + "author_inst": "Corrective Services NSW, Australia" + }, + { + "author_name": "Wendy Hoey", + "author_inst": "Justice Health Forensic Mental Health Network NSW, Australia" + }, + { + "author_name": "James Blogg", + "author_inst": "Justice Health Forensic Mental Health Network NSW, Australia" + }, + { + "author_name": "Andrew R Lloyd", + "author_inst": "Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia" + }, + { + "author_name": "Richard T Gray", + "author_inst": "Kirby Institute, UNSW Sydney, Sydney, New South Wales, Australia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.15.21251752", "rel_title": "Predicting mortality, duration of treatment, pulmonary embolism and required ceiling of ventilatory support for COVID-19 inpatients: A Machine-Learning Approach", @@ -943847,33 +942240,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.18.21251939", - "rel_title": "Applicability of Neighborhood and Building Scale Wastewater-Based Genomic Epidemiology to Track the SARS-CoV-2 Pandemic and other Pathogens.", - "rel_date": "2021-02-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.18.21251939", - "rel_abs": "The benefits of wastewater-based epidemiology (WBE) for tracking the viral load of SARS-CoV-2, the causative agent of COVID-19, have become apparent since the start of the pandemic. However, most sampling occurs at the wastewater treatment plant influent and therefore can only monitor SARS-CoV-2 concentration and spread within the entire catchment, which can encompass multiple municipalities. Furthermore, most WBE only quantifies the virus, and therefore miss crucial information that can be gained by sequencing SARS-CoV-2. Here we demonstrate feasibility of sampling at the neighborhood or building complex level using a mix of quantitative polymerase chain reaction (qPCR) and targeted sequencing to provide a more refined understanding of the local dynamics of SARS-CoV-2 strains. When coupled with the higher-level treatment plant samples, this creates an opportunity for health officials to monitor the spread of the virus at different spatial and temporal scales to inform policy decisions.\n\nHere we demonstrate the feasibility of tracking SARS-CoV-2 at the neighborhood, hospital, and nursing home level with the ability to detect one COVID-19 positive out of 60 nursing home residents. The viral load obtained was correlative with the number of COVID-19 patients being treated in the hospital. Sequencing of the samples over time demonstrated that nonsynonymous mutations fluctuate in the viral population, and wastewater-based sequencing could be an efficient approach to monitor for vaccine or convalescent plasma escape mutants, as well as mutations that could reduce the efficacy of diagnostics. Furthermore, while SARS-CoV-2 was detected by untargeted RNA sequencing, qPCR and targeted whole genome amplicon sequencing were more reliable methods for tracking the pandemic. From our sequencing data, clades and shifts in mutation profiles within the community were traceable and could be used to determine if vaccine or diagnostics need to be adapted to ensure continued efficacy.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=75 SRC=\"FIGDIR/small/21251939v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (20K):\norg.highwire.dtl.DTLVardef@110f217org.highwire.dtl.DTLVardef@185d3f0org.highwire.dtl.DTLVardef@11d3a8corg.highwire.dtl.DTLVardef@1eef33d_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LINeighborhood or building level wastewater analysis accurately detects SARS-CoV-2\nC_LIO_LISARS-CoV-2 was detected in wastewater from one infected person out of 60 residents\nC_LIO_LITotal RNAseq did not accurately detect SARS-CoV-2 in wastewater samples.\nC_LIO_LITargeted whole genome sequencing of wastewater samples identified Spike mutations.\nC_LI", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Rachel R Spurbeck", - "author_inst": "Battelle Memorial Institute" - }, - { - "author_name": "Lindsay A Catlin", - "author_inst": "Battelle Memorial Institute" - }, - { - "author_name": "Angela T Minard-Smith", - "author_inst": "Battelle Memorial Institutes" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.18.21252000", "rel_title": "Estimates of the COVID-19 pandemic dynamics in Ukraine based on two data sets", @@ -944889,6 +943255,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.09.21251326", + "rel_title": "Lockdown and non-COVID-19 deaths: Cause-specific mortality during the first wave of the 2020 pandemic in Norway. A population-based register study", + "rel_date": "2021-02-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.09.21251326", + "rel_abs": "ObjectiveTo explore the potential impact of the first wave of COVID-19 pandemic on all cause and cause-specific mortality in Norway.\n\nDesignPopulation based register study.\n\nSettingThe Norwegian cause of Death Registry and the National Population Register of Norway.\n\nParticipantsAll recorded deaths in Norway during March to May from 2010 to 2020.\n\nMain outcome measuresRate (per 100 000) of all-cause mortality and causes of death in the EU Shortlist for Causes of Death March to May 2020. The rates were age-standardised and adjusted to a 100% register coverage and compared with a 95% prediction interval (PI) based on corresponding rates for 2010-2019.\n\nResults113 710 deaths were included, of which 10 226 from 2020. We did not observe any deviation from predicted total mortality. There were fewer than predicted deaths from chronic lower respiratory diseases excluding asthma (11.4, 95% PI 11.8 to 15.2) and from other non-ischemic, non-rheumatic heart diseases (13.9, 95% PI 14.5 to 20.2). The death rates were higher than predicted for Alzheimers disease (7.3, 95% PI 5.5 to 7.3) and diabetes mellitus (4.1, 95% PI 2.1 to 3.4).\n\nConclusionsThere was no significant difference in the frequency of the major causes of death in the first wave of the 2020 COVID-19 pandemic in Norway. An increase in diabetes mellitus deaths and reduced mortality due to some heart and lung conditions may be linked to infection control measures.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Guttorm Raknes", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Marianne Sorlie Strom", + "author_inst": "Norwegian Institute of Public Health, Bergen, Norway" + }, + { + "author_name": "Gerhard Sulo", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Simon Nygaard Overland", + "author_inst": "Norwegian Institute of Public Health" + }, + { + "author_name": "Mathieu Roelants", + "author_inst": "KU Leuven - University of Leuven, Leuven, Belgium" + }, + { + "author_name": "Petur Benedikt Juliusson", + "author_inst": "Norwegian Institute of Public Health" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.15.21251745", "rel_title": "The Effect of NFL and NCAA Football Games on the Spread of COVID-19 in the United States: An Empirical Analysis", @@ -945241,41 +943646,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.16.21251844", - "rel_title": "An exploratory study on the correlation of population SARS-CoV-2 cycle threshold values to local disease dynamics", - "rel_date": "2021-02-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.16.21251844", - "rel_abs": "IntroductionDespite limitations on the use of cycle threshold (CT) values for individual patient care, population distributions of CT values may be useful indicators of local outbreaks.\n\nMethodsSpecimens from the greater El Paso area were processed in the Dascena COVID-19 Laboratory. Daily median CT value, daily transmission rate R(t), daily count of COVID-19 hospitalizations, daily change in percent positivity, and rolling averages of these features were plotted over time. Two-way scatterplots and linear regression evaluated possible associations between daily median CT and outbreak measures. Cross-correlation plots determined whether a time delay existed between changes in the daily median CT value and measure of community disease dynamics.\n\nResultsDaily median CT was negatively correlated with the daily R(t), the daily COVID-19 hospitalization count (with a time delay), and the daily change in percent positivity among testing samples. Despite visual trends suggesting time delays in the plots for median CT and outbreak measures, a statistically significant delay was only detected between changes in median CT and COVID-19 hospitalization count.\n\nConclusionsThis study adds to the literature by analyzing samples collected from an entire geographical area, and contextualizing the results with other research investigating population CT values.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Chak Foon Tso", - "author_inst": "Dascena, Inc" - }, - { - "author_name": "Anurag Garikipati", - "author_inst": "Dascena, Inc" - }, - { - "author_name": "Abigail Green-Saxena", - "author_inst": "Dascena, Inc" - }, - { - "author_name": "Qingqing Mao", - "author_inst": "Dascena, Inc" - }, - { - "author_name": "Ritankar Das", - "author_inst": "Dascena, Inc" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.16.21251521", "rel_title": "SARS-CoV-2 detection by rRT-PCR on self-collected anterior nares swabs or saliva compared with clinician-collected nasopharyngeal swabs--Denver and Atlanta, August--November, 2020", @@ -946335,6 +944705,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.16.21251769", + "rel_title": "Associations of Race/Ethnicity and Other Demographic and Socioeconomic Factors with Vaccination During the COVID-19 Pandemic in the United States", + "rel_date": "2021-02-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.16.21251769", + "rel_abs": "BackgroundTo date, there has been limited data available to understand the associations between race/ethnicity and socioeconomic and related characteristics with novel coronavirus disease (COVID-19) vaccine initiation and planned vaccination in the United States.\n\nMethodsTo better characterize COVID-19 vaccinations nationally, we leveraged large cross-sectional surveys conducted between January and March 2021 with relatively complete race/ethnicity and socioeconomic data and nationally-representative of U.S. households to estimate trends in levels of COVID-19 vaccine initiation and vaccine intention. We further used survey data from January and March 2021 in adults aged 18-85 years to analyze the associations between race/ethnicity, education, pre-pandemic household income, and financial hardship during the pandemic and the adjusted odds of: 1) receipt of [≥]1 dose of a COVID-19 vaccine; and 2) among those unvaccinated, the definite intention to receive a vaccine, controlling for other demographic and socioeconomic factors.\n\nResultsWe observed persistent disparities in vaccine initiation for non-Hispanic Blacks, Hispanics, and non-Hispanic multiracial persons, and in vaccine intention for Blacks and multiracial persons, compared to non-Hispanic Whites and non-Hispanic Asians. In late March 2021, the prevalence estimates of Hispanics and Blacks receiving a vaccine were 12 percentage points and 8 percentage points lower than for Whites, respectively. Moreover, both education and income levels exhibited positive dose-response relationships with vaccine initiation (P for trend[≤]01 and <.001, respectively). Substantial financial hardship was linked to 35-44% lower odds of vaccination (P<.001). The most common reasons for vaccine hesitancy were concerns about side effects and safety, with evidence of higher levels of concerns about vaccine safety among Blacks vs. Whites.\n\nConclusionsIn this large, nationally-representative study with relatively complete race/ethnicity and socioeconomic data, we find that being Black non-Hispanic and having the least education and income were each independently associated with a markedly lower likelihood of definitely planning to get vaccinated or having been vaccinated. In the ensuing months of the pandemic, addressing the persevering racial/ethnic and socioeconomic inequities in vaccination due to differential access and vaccine hesitancy is essential to mitigate the pandemics higher risks of infection and adverse health outcomes in Hispanic, Black, and socioeconomically-disadvantaged communities.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Daniel Kim", + "author_inst": "Northeastern University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.02.17.21251929", "rel_title": "COVID-BioB Cohort Study: the neutralizing antibody response to SARS-CoV-2 in symptomatic COVID-19 is persistent and critical for virus control and survival.", @@ -946911,93 +945300,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.16.21251849", - "rel_title": "Convalescent plasma for preventing critical illness in COVID-19: A phase 2 trial and immune profile", - "rel_date": "2021-02-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.16.21251849", - "rel_abs": "RationaleThe COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an unprecedented event requiring rapid adaptation to changing clinical circumstances. Convalescent immune plasma (CIP) is a promising treatment that can be mobilized rapidly in a pandemic setting.\n\nObjectivesWe tested whether administration of SARS-CoV-2 CIP at hospital admission could reduce the rate of ICU transfer or 28 day mortality.\n\nMethodsIn a single-arm phase II study, patients >18 years-old with respiratory symptoms documented with COVID-19 infection who were admitted to a non-ICU bed were administered two units of CIP within 72 hours of admission. Detection of respiratory tract SARS-CoV-2 by polymerase chain reaction and circulating anti-SARS-CoV-2 antibody titers were measured before and at time points after CIP transfusion.\n\nMeasurements and Main ResultsTwenty-nine patients were transfused CIP and forty-eight contemporaneous controls were identified with comparable baseline characteristics. Levels of anti-SARS-CoV-2 IgG, IgM, and IgA anti-spike, anti-receptor-binding domain, and anti-nucleocapsid significantly increased from baseline to post-transfusion for all proteins tested. In patients transfused with CIP, the rate of ICU transfer was 13.8% compared to 27.1% for controls with a hazard ratio 0.506 (95% CI 0.165-1.554), and 28-day mortality was 6.9% compared to 10.4% for controls, hazard ratio 0.640 (95% CI 0.124-3.298).\n\nConclusionsTransfusion of high-titer CIP to patients early after admission with COVID-19 respiratory disease was associated with reduced ICU transfer and 28-day mortality but was not statistically significant. Follow up randomized trials may inform the use of CIP for COVID-19 or future coronavirus pandemics.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Jeffrey Michael Sturek", - "author_inst": "University of Virginia School of Medicine" - }, - { - "author_name": "Tania A Thomas", - "author_inst": "University of Virginia School of Medicine" - }, - { - "author_name": "James D Gorham", - "author_inst": "University of Virginia School of Medicine" - }, - { - "author_name": "Chelsea A Sheppard", - "author_inst": "University of Virginia School of Medicine" - }, - { - "author_name": "Allison E Raymond", - "author_inst": "University of Virginia School of Medicine" - }, - { - "author_name": "Kristen Petros De Guex", - "author_inst": "University of Virginia School of Medicine" - }, - { - "author_name": "William B Harrington", - "author_inst": "University of Virginia School of Medicine" - }, - { - "author_name": "Andrew J Barros", - "author_inst": "University of Virginia School of Medicine" - }, - { - "author_name": "Gregory R Madden", - "author_inst": "University of Virginia School of Medicine" - }, - { - "author_name": "Yosra M Alkabab", - "author_inst": "University of Virginia School of Medicine" - }, - { - "author_name": "David Lu", - "author_inst": "Cornell University" - }, - { - "author_name": "Qin Liu", - "author_inst": "The Wistar Institute" - }, - { - "author_name": "Melinda D Poulter", - "author_inst": "University of Virginia School of Medicine" - }, - { - "author_name": "Amy J Mathers", - "author_inst": "University of Virginia School of Medicine" - }, - { - "author_name": "Archana Thakur", - "author_inst": "University of Virginia School of Medicine" - }, - { - "author_name": "Ewa M Kubicka", - "author_inst": "University of Virginia School of Medicine" - }, - { - "author_name": "Lawrence G Lum", - "author_inst": "University of Virginia School of Medicine" - }, - { - "author_name": "Scott K Heysell", - "author_inst": "University of Virginia School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.17.21251556", "rel_title": "Clinical performance of oral sponge sampling for detection by RT-PCR of SARS-CoV-2", @@ -948153,6 +946455,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.19.431972", + "rel_title": "Antiviral activity of influenza A virus defective interfering particles against SARS-CoV-2 replication in vitro through stimulation of innate immunity", + "rel_date": "2021-02-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.19.431972", + "rel_abs": "SARS-CoV-2 causing COVID-19 emerged in late 2019 and resulted in a devastating pandemic. Although the first approved vaccines were already administered by the end of 2020, worldwide vaccine availability is still limited. Moreover, immune escape variants of the virus are emerging against which the current vaccines may confer only limited protection. Further, existing antivirals and treatment options against COVID-19 only show limited efficacy. Influenza A virus (IAV) defective interfering particles (DIPs) were previously proposed not only for antiviral treatment of the influenza disease but also for pan-specific treatment of interferon (IFN)-sensitive respiratory virus infections. To investigate the applicability of IAV DIPs as an antiviral for the treatment of COVID-19, we conducted in vitro co-infection experiments with cell culture-derived DIPs and the IFN-sensitive SARS-CoV-2 in human lung cells. We show that treatment with IAV DIPs leads to complete abrogation of SARS-CoV-2 replication. Moreover, this inhibitory effect was dependent on janus kinase/signal transducers and activators of transcription (JAK/STAT) signaling. Further, our results suggest boosting of IFN-induced antiviral activity by IAV DIPs as a major contributor in suppressing SARS-CoV-2 replication. Thus, we propose IAV DIPs as an effective antiviral agent for treatment of COVID-19, and potentially also for suppressing the replication of new variants of SARS-CoV-2.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Ulfert Rand", + "author_inst": "Helmholtz Centre for Infection Research" + }, + { + "author_name": "Sascha Young Kupke", + "author_inst": "Max Planck Institute for Dynamics of Complex Technical Systems" + }, + { + "author_name": "Hanna Shkarlet", + "author_inst": "Helmholtz Centre for Infection Research and Otto von Guericke University Magdeburg" + }, + { + "author_name": "Marc Dominique Hein", + "author_inst": "Otto von Guericke University Magdeburg" + }, + { + "author_name": "Tatjana Hirsch", + "author_inst": "Helmholtz Centre for Infection Research" + }, + { + "author_name": "Pavel Marichal-Gallardo", + "author_inst": "Max Planck Institute for Dynamics of Complex Technical Systems" + }, + { + "author_name": "Luka Cicin-Sain", + "author_inst": "Helmholtz Centre for Infection Research and German Centre for Infection Research" + }, + { + "author_name": "Udo Reichl", + "author_inst": "Max Planck Institute for Dynamics of Complex Technical Systems and Otto von Guericke University Magdeburg" + }, + { + "author_name": "Dunja Bruder", + "author_inst": "Helmholtz Centre for Infection Research and Otto von Guericke University Magdeburg" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.02.19.431311", "rel_title": "SARS-CoV-2 variant evolution in the United States: High accumulation of viral mutations over time likely through serial Founder Events and mutational bursts.", @@ -948709,33 +947062,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.02.13.21251670", - "rel_title": "Excess Mortality in Suicide caused by COVID-19 in Japan", - "rel_date": "2021-02-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.13.21251670", - "rel_abs": "BackgroundCountermeasures against COVID-19 outbreak such as lockdown and voluntary restrictions against going out adversely affect human stress and economic activity. Particularly, this stress might lead to suicide.\n\nObjectWe examined excess mortality attributable to suicide caused by COVID-19. Method: We applied the NIID model to suicide deaths from October 2009 through September, 2021 for the whole of Japan by gender. Effects of the great earthquake that struck in eastern Japan on March 11, 2011 were incorporated into the estimation model. Results: Significant excess mortality in suicide was found between July, 2020 and July, 2021 for both genders. However, in August and September, 2021, excess mortality in suicide was detected only in female. It was greater among females than among males. In total, 2950 excess cases of mortality were identified.\n\nDiscussion and ConclusionExcess mortality during the four months was more than two times greater than the number of COVID-19 deaths confirmed by PCR testing. Countermeasures against COVID-19 should be chosen carefully in light of suicide effects.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Junko Kurita", - "author_inst": "Tokiwa University, Ibaraki, Japan" - }, - { - "author_name": "Tamie Sugawara", - "author_inst": "Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan" - }, - { - "author_name": "Yasushi Ohkusa", - "author_inst": "Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Shinjuku, Tokyo, Japan" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.02.15.21251150", "rel_title": "Development and validation of a dynamic 48-hour in-hospital prognostic risk stratification for COVID-19 in a UK teaching hospital: a retrospective cohort study", @@ -949955,6 +948281,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.15.21251771", + "rel_title": "Interrogating structural inequalities in COVID-19 Mortality in England and Wales", + "rel_date": "2021-02-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.15.21251771", + "rel_abs": "BackgroundNumerous observational studies have highlighted structural inequalities in COVID-19 mortality in the UK. Such studies often fail to consider the complex spatial nature of such inequalities in their analysis, leading to the potential for bias and an inability to reach conclusions about the most appropriate structural levels for policy intervention.\n\nMethodsWe use publicly available population data on COVID-19 related- and all-cause mortality between March and July 2020 in England and Wales to investigate the spatial scale of such inequalities. We propose a multiscale approach to simultaneously consider four spatial scales at which processes driving inequality may act and apportion inequality between these.\n\nResultsAdjusting for population age structure, number of care homes and residing in the North we find highest regional inequality in March and June/July. We find finer-grained within-region increased steadily from March until July. The importance of spatial context increases over the study period. No analogous pattern is visible for non-COVID mortality. Higher relative deprivation is associated with increased COVID-19 mortality at all stages of the pandemic but does not explain structural inequalities.\n\nConclusionsResults support initial stochastic viral introduction in the South, with initially high inequality decreasing before the establishment of regional trends by June and July, prior to reported regionality of the \"second-wave\". We outline how this framework can help identify structural factors driving such processes, and offer suggestions for a long-term, locally-targeted model of pandemic relief in tandem with regional support to buffer the social context of the area.\n\nKey MessagesO_LIRegional inequality in COVID-19 mortality declined from an initial peak in April, before increasing again in June/July.\nC_LIO_LIWithin-region inequality increased steadily from March until July.\nC_LIO_LIStrong regional trends are evident in COVID-19 mortality in June/July, prior to wider reporting of regional differences in \"second wave\".\nC_LIO_LIAnalogous spatial inequalities are not present in non-COVID related mortality over the study period.\nC_LIO_LIThese inequalities are not explained by age structure, care homes, or deprivation.\nC_LI", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Gareth J Griffith", + "author_inst": "University of Bristol" + }, + { + "author_name": "George Davey Smith", + "author_inst": "University of Bristol" + }, + { + "author_name": "David Manley", + "author_inst": "University of Bristol, School of Geographical Sciences" + }, + { + "author_name": "Laura D Howe", + "author_inst": "University of Bristol" + }, + { + "author_name": "Gwilym Owen", + "author_inst": "University of Liverpool" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.15.21251726", "rel_title": "Are we back to normal yet? The impact of the COVID-19 pandemic on mental health with a specific focus on schizotypal traits in the general population of Germany and the UK, comparing responses from April/May vs. September/October", @@ -950555,25 +948916,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.02.15.21251788", - "rel_title": "COVID-19 European Regional Tracker", - "rel_date": "2021-02-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.15.21251788", - "rel_abs": "This Tracker presents data on daily COVID-19 cases at the sub-national level for 26 European countries from January 2020 till present. Country-level data sources are identified and processed to form a homogenized panel at the NUTS 3 or NUTS 2 level, the two lowest standardized administrative units of Europe. The strengths and weaknesses of each country dataset are discussed in detail. The raw data, spatial layers, the code, and the final homogenized files are provided in an online repository for replication. The data highlights the spatial distribution of cases both within and across countries that can be utilized for a disaggregated analysis on the impacts of the pandemic. The Tracker is updated monthly to expand its coverage.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Asjad Naqvi", - "author_inst": "International Institute for Applied Systems Analysis (IIASA)" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.13.21251652", "rel_title": "Should We Delay the Second COVID-19 Vaccine Dose?", @@ -951836,6 +950178,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.09.21251149", + "rel_title": "A multi-centre service evaluation of the impact of the COVID-19 pandemic on presentation of newly diagnosed cancers and type 1 diabetes in children in the UK", + "rel_date": "2021-02-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.09.21251149", + "rel_abs": "BackgroundThe COVID-19 pandemic led to changes in patterns of presentation to Emergency Departments (ED). Child health professionals were concerned that this could contribute to the delayed diagnosis of life-threatening conditions, including childhood cancer (CC) and type 1 diabetes (T1DM). Our multicentre, UK-based service evaluation assessed diagnostic intervals and disease severity for these conditions.\n\nMethodsWe collected presentation route, timing and disease severity for children with newly diagnosed CC in three principal treatment centres, and T1DM in four centres between 1stJanuary - 31st July 2020 and the corresponding period in 2019. We assessed the impact of lockdown on total diagnostic interval (TDI), patient interval (PI), system interval (SI) and disease severity.\n\nFindingsFor CCs and T1DM, the route to diagnosis and severity of illness at presentation were unchanged across all time periods. Diagnostic intervals for CCs during lockdown were comparable to that in 2019 (TDI 4.6, PI 1.1 and SI 2.1 weeks), except for an increased PI in Jan-Mar 2020 (median 2.7 weeks). Diagnostic intervals for T1DM during lockdown were similar to that in 2019 (TDI 16 vs 15 and PI 14 vs 14 days), except for an increased PI in Jan-Mar 2020 (median 21 days).\n\nInterpretationThere is no evidence of diagnostic delay or increased illness severity for CC or T1DM, during the first phase of the pandemic across the participating centres. This provides reassuring data for children and families with these life-changing conditions.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSThis project was initiated after the first national lockdown in March 2020 during COVID-19 pandemic in the UK. At the design stage, Medline was searched (with no language limit), using the keywords ((Cancer) OR (neoplasm) OR (Type 1 diabetes mellitus)) AND ((Covid-19) OR (SARS-CoV-2) OR (Pandemics)) AND ((Emergency department attendances) OR (diabetes ketoacidosis) OR (Delayed diagnosis) OR (interval) OR (wait)) to identify publications reporting the impact of the pandemic and public health measures on both overall and paediatric healthcare services. Significant changes in service utilisation in the UK were reported following the commencement of the first lockdown, including a 49% reduction in emergency department attendances in the week following the lockdown; and two adult studies reported that referral via the urgent two-week wait cancer referral diagnoses decreased by 84% from Mar-May and 60% in June 2020. As for Type 1 diabetes (T1DM), a 30 patient UK-study reported an increase in newly diagnosed T1DM during the first six weeks of lockdown. Increased proportions of severe diabetic ketoacidosis (DKA) at presentation were also reported in an Italian survey involving 53 paediatric diabetes centres. Through the search we identified a need for multi-centre, more thorough assessment on referral pathways, time taken from symptom onset to diagnosis, and its association with severity at presentation for children diagnosed with life-changing conditions during the national lockdown.\n\nAdded value of this studyOur findings suggest that the first national lockdown in the UK were not associated with delayed diagnosis of childhood cancer or type 1 diabetes at participating centres. This provides reassuring information for children and families with these life-changing conditions.\n\nImplicationWe believe that our study can play a key role in allaying parental and professional concern. it is important to establish whether subsequent public health measures have impacted the diagnostic interval in the context of an evolving backlog of patient referrals across the UK.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "- COVID-19 Pandemic UK-based Interest Group of Childhood Cancer and Diabetes", + "author_inst": "" + }, + { + "author_name": "Gemma Williams", + "author_inst": "Leeds Children's Hospital" + }, + { + "author_name": "Ross McLean", + "author_inst": "University Hospital Wishaw, Lanarkshire" + }, + { + "author_name": "Jo-Fen Liu", + "author_inst": "Children's Brain Tumour Research Centre, University of Nottingham" + }, + { + "author_name": "Timothy Ritzmann", + "author_inst": "Children's Brain Tumour Research Centre, University of Nottingham & Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Madhumita Dandapani", + "author_inst": "Children's Brain Tumour Research Centre, University of Nottingham & Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Dhurgshaarna Shanmugavadivel", + "author_inst": "Children's Brain Tumour Research Centre, University of Nottingham" + }, + { + "author_name": "Pooja Sachdev", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Mark Brougham", + "author_inst": "Royal Hospital for Sick Children, Edinburgh" + }, + { + "author_name": "Rod Mitchell", + "author_inst": "University of Edinburgh & Royal Hospital for Sick Children" + }, + { + "author_name": "Nicholas T Conway", + "author_inst": "Tayside Children's Hospital & University of Dundee" + }, + { + "author_name": "James Law", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Alice Cunnington", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Gbemi Ogunnaike", + "author_inst": "Nottingham University Hospitals NHS Trust" + }, + { + "author_name": "Karen Brougham", + "author_inst": "Royal Hospital for Sick Children, Edinburgh" + }, + { + "author_name": "Elizabeth Bayman", + "author_inst": "Royal Hospital for Sick Children, Edinburgh" + }, + { + "author_name": "David A Walker", + "author_inst": "Children's Brain Tumour Research Centre, University of Nottingham" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2021.02.15.21250916", "rel_title": "SARS-CoV-2 antibody immunoassays in serial samples reveal earlier seroconversion in acutely ill COVID-19 patients developing ARDS", @@ -952408,73 +950833,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.02.15.430863", - "rel_title": "Live attenuated SARS-CoV-2 vaccine candidate: Protective immunity without serious lung lesions in Syrian hamsters", - "rel_date": "2021-02-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.15.430863", - "rel_abs": "Live attenuated vaccines are generally highly effective. Here, we aimed to develop one against SARS-CoV-2, based on the identification of three types of temperature-sensitive (TS) strains with mutations in nonstructural proteins (nsp), impaired proliferation at 37-39{degrees}C, and the capacity to induce protective immunity in Syrian hamsters. To develop a live-attenuated vaccine, we generated a virus that combined all these TS-associated mutations (rTS-all), which showed a robust TS phenotype in vitro and high attenuation in vivo. The vaccine induced an effective cross-reactive immune response and protected hamsters against homologous or heterologous viral challenges. Importantly, rTS-all rarely reverted to the wild-type phenotype. By combining these mutations with an Omicron spike protein to construct a recombinant virus, protection against the Omicron strain was obtained. We show that immediate and effective live-attenuated vaccine candidates against SARS-CoV-2 variants may be developed using rTS-all as a backbone to incorporate the spike protein of the variants.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Akiho Yoshida", - "author_inst": "Virus vaccine group, BIKEN Innovative Vaccine Research Alliance Laboratories, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, S" - }, - { - "author_name": "Shinya Okamura", - "author_inst": "Virus vaccine group, BIKEN Innovative Vaccine Research Alliance Laboratories, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, S" - }, - { - "author_name": "Shiho Torii", - "author_inst": "Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan" - }, - { - "author_name": "Sayuri Komatsu", - "author_inst": "Virus Vaccine Group, BIKEN Innovative Vaccine Research Alliance Laboratories, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, S" - }, - { - "author_name": "Paola Miyazato", - "author_inst": "Virus vaccine group, BIKEN Innovative Vaccine Research Alliance Laboratories, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, S" - }, - { - "author_name": "Shiori Ueno", - "author_inst": "Department of Infectious Diseases and Host Defense, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan" - }, - { - "author_name": "Hidehiko Suzuki", - "author_inst": "Virus vaccine group, BIKEN Innovative Vaccine Research Alliance Laboratories, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, S" - }, - { - "author_name": "Wataru Kamitani", - "author_inst": "Department of Infectious Diseases and Host Defense, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan" - }, - { - "author_name": "Chikako Ono", - "author_inst": "Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan" - }, - { - "author_name": "Yoshiharu Matsuura", - "author_inst": "Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan" - }, - { - "author_name": "Shiro Takekawa", - "author_inst": "The Research Foundation for Microbial Diseases of Osaka University, Suita, Osaka, Japan" - }, - { - "author_name": "Koichi Yamanishi", - "author_inst": "The Research Foundation for Microbial Diseases of Osaka University, Suita, Osaka, Japan" - }, - { - "author_name": "Hirotaka Ebina", - "author_inst": "Virus vaccine group, BIKEN Innovative Vaccine Research Alliance Laboratories, Research institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan." - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.02.16.431305", "rel_title": "501Y.V2 and 501Y.V3 variants of SARS-CoV-2 lose binding to Bamlanivimab in vitro", @@ -953457,6 +951815,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.13.21251683", + "rel_title": "Learning Where to Look for COVID-19 Growth: Multivariate Analysis of COVID-19 Cases Over Time using Explainable Convolution-LSTM", + "rel_date": "2021-02-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.13.21251683", + "rel_abs": "Determinant factors which contribute to the prediction should take into account multivariate analysis for capturing coarse-to-fine contextual information. From the preliminary descriptive analysis, it shows that environmental factor such as UV (ultraviolet) is one of the essential factors that should be considered to observe the COVID-19 epidemic drivers, During summer, UV can inactivate viruses that live in the air and on the surface of the objects especially at noon in tropical or subtropical countries. However, it may not be significant in closed spaces like workspace and areas with the intensive human-to-human transmission, especially in densely populated areas. Different COVID-19 pandemic growth patterns in northern subtropical, southern subtropical and tropical countries occur over time. Moreover, there are education, government, morphological, health, economic, and behavioral factors contributing to the growth of COVID-19. Multivariate analysis via visual attribution of explainable Convolution-LSTM is utilized to see high contributing factors responsible for the growth of daily COVID-19 cases. For future works, data to be analyzed should be more detailed in terms of the region and the period where the time-series sample is acquired. The explainable Convolution-LSTM code is available here: https://github.com/cbasemaster/time-series-attribution", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Novanto Yudistira", + "author_inst": "Brawijaya University" + }, + { + "author_name": "Sutiman Bambang Sumitro", + "author_inst": "Brawijaya University" + }, + { + "author_name": "Alberth Christian Nahas", + "author_inst": "INDONESIAN AGENCY FOR METEOROLOGY, CLIMATOLOGY, AND GEOPHYSICS (BMKG)" + }, + { + "author_name": "Nelly Florida Riama", + "author_inst": "INDONESIAN AGENCY FOR METEOROLOGY, CLIMATOLOGY, AND GEOPHYSICS (BMKG)" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2021.02.10.21251350", "rel_title": "C-reactive protein guided use of procalcitonin in COVID-19", @@ -954049,37 +952438,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.02.12.431026", - "rel_title": "Jumper Enables Discontinuous Transcript Assembly in Coronaviruses", - "rel_date": "2021-02-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.12.431026", - "rel_abs": "Genes in SARS-CoV-2 and, more generally, in viruses in the order of Nidovirales are expressed by a process of discontinuous transcription mediated by the viral RNA-dependent RNA polymerase. This process is distinct from alternative splicing in eukaryotes, rendering current transcript assembly methods unsuitable to Nidovirales sequencing samples. Here, we introduce the DO_SCPLOWISCONTINUOUSC_SCPLOW TO_SCPLOWRANSCRIPTC_SCPLOW AO_SCPLOWSSEMBLYC_SCPLOW problem of finding transcripts [Formula] and their abundances c given an alignment [Formula] under a maximum likelihood model that accounts for varying transcript lengths. Underpinning our approach is the concept of a segment graph, a directed acyclic graph that, distinct from the splice graph used to characterize alternative splicing, has a unique Hamiltonian path. We provide a compact characterization of solutions as subsets of non-overlapping edges in this graph, enabling the formulation of an efficient mixed integer linear program. We show using simulations that our method, JO_SCPLOWUMPERC_SCPLOW, drastically outperforms existing methods for classical transcript assembly. On short-read data of SARS-CoV-1 and SARS-CoV-2 samples, we find that JO_SCPLOWUMPERC_SCPLOW not only identifies canonical transcripts that are part of the reference transcriptome, but also predicts expression of non-canonical transcripts that are well supported by direct evidence from long-read data, presence in multiple, independent samples or a conserved core sequence. JO_SCPLOWUMPERC_SCPLOW enables detailed analyses of Nidovirales transcriptomes.\n\nCode availabilitySoftware is available at https://github.com/elkebir-group/Jumper", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Palash Sashittal", - "author_inst": "University of Illinois, Urbana-Champaign" - }, - { - "author_name": "Chuanyi Zhang", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Jian Peng", - "author_inst": "University of Illinois at Urbana-Champaign" - }, - { - "author_name": "Mohammed El-Kebir", - "author_inst": "UIUC" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.02.11.430757", "rel_title": "SARS CoV-2 nucleoprotein enhances the infectivity of lentiviral spike particles", @@ -955147,6 +953505,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nursing" }, + { + "rel_doi": "10.1101/2021.02.09.21251443", + "rel_title": "Evaluation of Facial Protection Against Close-Contact Droplet Transmission", + "rel_date": "2021-02-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.09.21251443", + "rel_abs": "BackgroundFace shields are used as an alternative to facemasks, but their effectiveness in mitigating the spread of SARS-CoV-2 is unclear. The goal of this study is to compare the performance of face shields, surgical facemasks, and cloth facemasks for mitigation of droplet transmission during close contact conditions.\n\nMethodsA novel test system was developed to simulate droplet transmission during close contact conditions using two breathing headforms (transmitter and receiver) placed 4 feet apart with one producing droplets containing a DNA marker. Sampling coupons were placed throughout the test setup and subsequently analyzed for presence of DNA marker using quantitative PCR.\n\nResultsAll PPE donned on the transmitter headform provided a significant reduction in transmission of DNA marker to the receiver headform: cloth facemask (78.5%), surgical facemask (89.4%), and face shield (96.1%). All PPE resulted in increased contamination of the eye region of the transmitter headform (9,525.4% average for facemasks and 765.8% for the face shield). Only the face shield increased contamination of the neck region (207.4%), with the cloth facemask and surgical facemask resulting in reductions of 85.9% and 90.2%, respectively.\n\nConclusionsThis study demonstrates face shields can provide similar levels of protection against direct droplet exposure compared to surgical and cloth masks. However, all PPE tested resulted in release of particles that contaminated surfaces. Contamination caused by deflection of the users exhalation prompts concerns for contact transmission via surfaces in exhalation flow path (e.g., face, eyeglasses, etc.).", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Thomas B Stephenson", + "author_inst": "Applied Research Associates, Engineering Science Division" + }, + { + "author_name": "Courtney Cumberland", + "author_inst": "Applied Research Associates, Engineering Science Division" + }, + { + "author_name": "Geoff Kibble", + "author_inst": "Applied Research Associates, Engineering Science Division" + }, + { + "author_name": "Christopher Church", + "author_inst": "Applied Research Associates, Engineering Science Division" + }, + { + "author_name": "Sheila Nogueira-Prewitt", + "author_inst": "Applied Research Associates, Engineering Science Division" + }, + { + "author_name": "Sebastian MacNamara", + "author_inst": "Applied Research Associates, Engineering Science Division" + }, + { + "author_name": "Delbert A Harnish", + "author_inst": "Applied Research Associates, Engineering Science Division" + }, + { + "author_name": "Brian K Heimbuch", + "author_inst": "Applied Research Associates, Engineering Science Division" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2021.02.12.21249710", "rel_title": "Risk of Corona virus disease 2019 (COVID-19) among spectacles wearing population of Northern India", @@ -955631,33 +954036,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2021.02.11.21251581", - "rel_title": "A genetically-informed study disentangling the relationships between tobacco smoking, cannabis use, alcohol consumption, substance use disorders and respiratory infections, including COVID-19", - "rel_date": "2021-02-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.11.21251581", - "rel_abs": "BackgroundObservational studies suggest smoking, cannabis use, alcohol consumption, cannabis use, and substance use disorders (SUDs) may play a role in the susceptibility for respiratory infections and disease, including coronavirus 2019 (COVID-2019). However, causal inference is challenging due to comorbid substance use.\n\nMethodsUsing genome-wide association study data of European ancestry (data from >1.7 million individuals), we performed single-variable and multivariable Mendelian randomization to evaluate relationships between smoking, cannabis use, alcohol consumption, SUDs, and respiratory infections.\n\nResultsGenetically predicted lifetime smoking was found to be associated with increased risk for hospitalized COVID-19 (odds ratio (OR)=4.039, 95% CI 2.335-6.985, P-value=5.93x10-7) and very severe hospitalized COVID-19 (OR=3.091, 95% CI, 1.883-5.092, P-value=8.40x10-6). Genetically predicted lifetime smoking was also associated with increased risk pneumoniae (OR=1.589, 95% CI, 1.214-2.078, P-value=7.33x10-4), lower respiratory infections (OR=2.303, 95% CI, 1.713-3.097, P-value=3.40x10-8), and several others. Genetically predicted cannabis use disorder (CUD) was associated with increased bronchitis risk (OR=1.078, 95% CI, 1.020-1.128, P-value=0.007).\n\nConclusionsWe provide strong genetic evidence showing smoking increases the risk for respiratory infections and diseases even after accounting for other substance use and abuse. Additionally, we provide find CUD may increase the risk for bronchitis, which taken together, may guide future research SUDs and respiratory outcomes.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "DANIEL B Rosoff", - "author_inst": "NIAAA/NIH Oxford-Cambridge Scholars Program" - }, - { - "author_name": "Joyce Yoo", - "author_inst": "Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA" - }, - { - "author_name": "Falk W Lohoff", - "author_inst": "Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "addiction medicine" - }, { "rel_doi": "10.1101/2021.02.11.21251585", "rel_title": "CD8+ T cell responses in COVID-19 convalescent individuals target conserved epitopes from multiple prominent SARS-CoV-2 circulating variants", @@ -956977,6 +955355,32 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.09.21251288", + "rel_title": "Epidemic transmission with quarantine measures: application to COVID-19", + "rel_date": "2021-02-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.09.21251288", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Sergey A Trigger", + "author_inst": "Joint Institute for High Temperatures Russian Academy of Sciences" + }, + { + "author_name": "Eugeny Borisovich Czerniawski", + "author_inst": "Joint Institute for High Temperatures" + }, + { + "author_name": "Alexander Mikhailovich Ignatov", + "author_inst": "Prokhorov General Physics Institute, Russian Academy of Sciences" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.09.21251404", "rel_title": "Temporal trends of SARS-CoV-2 seroprevalence in transfusion blood donors during the first wave of the COVID-19 epidemic in Kenya", @@ -957569,32 +955973,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.10.21251392", - "rel_title": "COVID-19 and Influenza: Vaccination Before and During the Pandemic among the Lebanese Adult Population", - "rel_date": "2021-02-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.10.21251392", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Anthony Elia", - "author_inst": "Lebanese American University" - }, - { - "author_name": "Nedal Taha", - "author_inst": "Lebanese American University" - }, - { - "author_name": "Sima T Tokajian", - "author_inst": "Lebanese American University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.10.21251461", "rel_title": "Correcting excess mortality for pandemic-associated population decreases", @@ -959059,6 +957437,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.08.21251359", + "rel_title": "Country specific mutational profile of SARS-CoV-2 in pre- and post-international travel ban: Effect on vaccine efficacy", + "rel_date": "2021-02-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.08.21251359", + "rel_abs": "In order to curb the rapid transmission of SARS-CoV-2, nation-wide lockdowns were implemented as a preliminary measure. Since most countries enforced travel-bans during end of March 2020, the country-specific patterns should be discernible in the subsequent months. We identified frequently mutated non-synonymous mutations in 2,15,000 SARS-CoV-2 sequences during pre and post-travel-ban periods in 35 countries. We further investigated the mutational profile on a bi-monthly basis and traced the progress over the time. Several new mutations have emerged post-travel-ban and on the rise in specific countries, chief among them being A222V and S477N in Spike, and A220V in Nucleocapsid protein. Consequently, we examined the Spike protein epitopes to inspect whether any of these country-specific mutations overlapped with these epitopes. Several mutations were found to be contained within one or more epitopes, including the highly mutated residues of Spike protein, advocating the requirement of active monitoring of vaccine efficacies in respective countries.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Sayantan Laha", + "author_inst": "Indian Statistical institute" + }, + { + "author_name": "Raghunath Chatterjee", + "author_inst": "Indian Statistical institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.08.21251386", "rel_title": "How much do superspreaders matter? Epidemic dynamics in inhomogeneous populations", @@ -959403,153 +957804,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, - { - "rel_doi": "10.1101/2021.02.10.430668", - "rel_title": "Data-driven analysis of COVID-19 reveals specific severity patterns distinct from the temporal immune response", - "rel_date": "2021-02-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.10.430668", - "rel_abs": "Key immune signatures of SARS-CoV-2 infection may associate with either adverse immune reactions (severity) or simply an ongoing anti-viral response (temporality); how immune signatures contribute to severe manifestations and/or temporal progression of disease and whether longer disease duration correlates with severity remain unknown. Patient blood was comprehensively immunophenotyped via mass cytometry and multiplex cytokine arrays, leading to the identification of 327 basic subsets that were further stratified into more than 5000 immunotypes and correlated with 28 plasma cytokines. Low-density neutrophil abundance was closely correlated with hepatocyte growth factor levels, which in turn correlated with disease severity. Deep analysis also revealed additional players, namely conventional type 2 dendritic cells, natural killer T cells, plasmablasts and CD16+ monocytes, that can influence COVID-19 severity independent of temporal progression. Herein, we provide interactive network analysis and data visualization tools to facilitate data mining and hypothesis generation for elucidating COVID-19 pathogenesis.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Jackwee Lim", - "author_inst": "Singapore Immunology Network (A*STAR)" - }, - { - "author_name": "Guillaume Carissimo", - "author_inst": "Agency for Science, Technology and Research, Singapore" - }, - { - "author_name": "Yi-Hao Chan", - "author_inst": "Agency for Science, Technology and Research, Singapore" - }, - { - "author_name": "Siew-Wai Fong", - "author_inst": "Agency for Science, Technology and Research, Singapore" - }, - { - "author_name": "Wendy WL Lee", - "author_inst": "Singapore Immunology Network" - }, - { - "author_name": "Seow-Yen Tan", - "author_inst": "Changi General Hospital" - }, - { - "author_name": "David C Lye", - "author_inst": "National Centre for Infectious Diseases, Singapore" - }, - { - "author_name": "Barnaby E Young", - "author_inst": "National Centre for Infectious Diseases, Singapore" - }, - { - "author_name": "Laurent Renia", - "author_inst": "Agency for Science, Technology and Research (A*STAR)" - }, - { - "author_name": "Lisa Fong-Poh NG", - "author_inst": "Singapore Immunology Network, Agency for Science, Technology and Research, Singapore." - }, - { - "author_name": "Olaf Rotzschke", - "author_inst": "Singapore Immunology Network (A*STAR)" - }, - { - "author_name": "Kia Joo Puan", - "author_inst": "Singapore Immunology Network (A*STAR)" - }, - { - "author_name": "Liang Wei Wang", - "author_inst": "Singapore Immunology Network (A*STAR)" - }, - { - "author_name": "Karen Wei Weng Teng", - "author_inst": "Singapore Immunology Network (A*STAR)" - }, - { - "author_name": "Chiew Yee Loh", - "author_inst": "Singapore Immunology Network (A*STAR)" - }, - { - "author_name": "Kim Peng Tan", - "author_inst": "Singapore Immunology Network (A*STAR)" - }, - { - "author_name": "Chek Meng Poh", - "author_inst": "Agency for Science, Technology and Research, Singapore" - }, - { - "author_name": "Cheryl Yi-Pin Lee", - "author_inst": "Agency for Science, Technology and Research, Singapore" - }, - { - "author_name": "Nicholas Kim-Wah Yeo", - "author_inst": "Agency for Science, Technology and Research, Singapore" - }, - { - "author_name": "Rhonda Sin-Ling Chee", - "author_inst": "Agency for Science, Technology and Research, Singapore" - }, - { - "author_name": "Siti Naqiah Amrun", - "author_inst": "Agency for Science, Technology and Research, Singapore" - }, - { - "author_name": "Zi Wei Chang", - "author_inst": "Agency for Science, Technology and Research, Singapore" - }, - { - "author_name": "Matthew Zirui Tay", - "author_inst": "Agency for Science, Technology and Research (A*STAR)" - }, - { - "author_name": "Anthony Torres-Ruesta", - "author_inst": "Agency for Science, Technology and Research, Singapore" - }, - { - "author_name": "Norman Leo Fernandez", - "author_inst": "Singapore Immunology Network (A*STAR)" - }, - { - "author_name": "Wilson How", - "author_inst": "Singapore Immunology Network (A*STAR)" - }, - { - "author_name": "Anand K. Andiappan", - "author_inst": "Singapore Immunology Network (A*STAR)" - }, - { - "author_name": "Kaibo Duan", - "author_inst": "Singapore Immunology Network (A*STAR)" - }, - { - "author_name": "Gabriel Yan", - "author_inst": "National University Hospital" - }, - { - "author_name": "Shirin Kalimuddin", - "author_inst": "Singapore General Hospital" - }, - { - "author_name": "Yee-Sin Leo", - "author_inst": "National Centre for Infectious Diseases" - }, - { - "author_name": "Sean W. X. Ong", - "author_inst": "National Centre for Infectious Diseases" - }, - { - "author_name": "Bernett Lee", - "author_inst": "Singapore Immunology Network (A*STAR)" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.02.11.430787", "rel_title": "SARS-CoV-2 variants B.1.351 and B.1.1.248: Escape from therapeutic antibodies and antibodies induced by infection and vaccination", @@ -961089,6 +959343,137 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.02.10.430499", + "rel_title": "Bifurcated monocyte states are predictive of mortality in severe COVID-19", + "rel_date": "2021-02-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.10.430499", + "rel_abs": "Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 infection presents with varied clinical manifestations1, ranging from mild symptoms to acute respiratory distress syndrome (ARDS) with high mortality2,3. Despite extensive analyses, there remains an urgent need to delineate immune cell states that contribute to mortality in severe COVID-19. We performed high-dimensional cellular and molecular profiling of blood and respiratory samples from critically ill COVID-19 patients to define immune cell genomic states that are predictive of outcome in severe COVID-19 disease. Critically ill patients admitted to the intensive care unit (ICU) manifested increased frequencies of inflammatory monocytes and plasmablasts that were also associated with ARDS not due to COVID-19. Single-cell RNAseq (scRNAseq)-based deconvolution of genomic states of peripheral immune cells revealed distinct gene modules that were associated with COVID-19 outcome. Notably, monocytes exhibited bifurcated genomic states, with expression of a cytokine gene module exemplified by CCL4 (MIP-1{beta}) associated with survival and an interferon signaling module associated with death. These gene modules were correlated with higher levels of MIP-1{beta} and CXCL10 levels in plasma, respectively. Monocytes expressing genes reflective of these divergent modules were also detectable in endotracheal aspirates. Machine learning algorithms identified the distinctive monocyte modules as part of a multivariate peripheral immune system state that was predictive of COVID-19 mortality. Follow-up analysis of the monocyte modules on ICU day 5 was consistent with bifurcated states that correlated with distinct inflammatory cytokines. Our data suggests a pivotal role for monocytes and their specific inflammatory genomic states in contributing to mortality in life-threatening COVID-19 disease and may facilitate discovery of new diagnostics and therapeutics.", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Anthony R Cillo", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Ashwin Somasundaram", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Feng Shan", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Carly Cardello", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Creg J Workman", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Georgios D Kitsios", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Ayana Ruffin", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Sheryl Kunning", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Caleb Lampenfeld", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Sayali Onkar", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Stephanie Grebinowski", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Gaurav Deshmukh", + "author_inst": "Meso Scale Discovery" + }, + { + "author_name": "Barbara Methe", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Chang Liu", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Sham Nambulli", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Lawrence Andrews", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "W. Paul Duprex", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Alok J Joglekar", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Panayiotis V Benos", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Prabir Ray", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Anuradha Ray", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Bryan J McVerry", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Yingze Zhang", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Janet S Lee", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Jishnu Das", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Harinder Singh", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Alison Morris", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Tullia C Bruno", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Dario AA Vignali", + "author_inst": "University of Pittsburgh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2021.02.08.430146", "rel_title": "SARS-CoV-2 RBD-Tetanus toxoid conjugate vaccine induces a strong neutralizing immunity in preclinical studies", @@ -961645,57 +960030,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.07.21251309", - "rel_title": "The effect of respiratory activity, ventilatory therapy and facemasks on total aerosol emissions", - "rel_date": "2021-02-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.07.21251309", - "rel_abs": "Background Exhaled respirable aerosols (<5 m diameter) present a high risk of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) transmission. Many guidelines recommend using aerosol precautions during \"aerosol generating procedures\" (AGPs) and droplet (>5 m) precautions at other times. However, there is emerging evidence that respiratory activities such as cough and not AGPs are the important source of aerosols. Methods We used a novel chamber with an optical particle counter sampling at 100 L/min to count and size-fractionate all exhaled particles (0.5-25 m). We compared emissions from ten healthy subjects during respiratory \"activities\" (quiet breathing, talking, shouting, forced expiratory maneuvers, exercise and coughing) with respiratory \"therapies\" designated as AGPs: high flow nasal oxygen (HFNO) and single or dual circuit non-invasive positive pressure ventilation, NIPPV-S and NIPPV-D, respectively. Activities were repeated wearing facemasks. Results Compared to quiet breathing, respiratory activities increased particle counts between 34.6-fold (95% confidence interval [CI], 15.2 to 79.1) during talking, to 370.8-fold (95% CI, 162.3 to 847.1) during coughing (p<0.001). During quiet breathing, HFNO at 60 L/min increased counts 2.3-fold (95% CI, 1.2 to 4.4) (p=0.03) and NIPPV-S and NIPPV-D at 25/10 cm H2O increased counts by 2.6-fold (95% CI, 1.7 to 4.1) and 7.8-fold (95% CI, 4.4 to 13.6) respectively (p<0.001). During activities, respiratory therapies and facemasks reduced emissions compared to activities alone. Conclusion Talking, exertional breathing and coughing generate substantially more aerosols than the respiratory therapies HFNO and NIPPV which can reduce total emissions. The risk of aerosol exposure is underappreciated and warrants widespread targeted interventions.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Nicholas Wilson", - "author_inst": "Prince of Wales Hospital" - }, - { - "author_name": "Guy Marks", - "author_inst": "University of New South Wales, Sydney, Australia" - }, - { - "author_name": "Andrew Eckhardt", - "author_inst": "Department of Intensive Care Medicine, Prince of Wales Hospital, Sydney, Australia" - }, - { - "author_name": "Alyssa Clarke", - "author_inst": "Department of Intensive Care, Royal Prince Alfred Hospital, Camperdown, NSW, Australia" - }, - { - "author_name": "Francis Young", - "author_inst": "Department of Intensive Care Medicine, Prince of Wales Hospital, Sydney, Australia" - }, - { - "author_name": "Frances Garden", - "author_inst": "South Western Sydney Clinical School, University of New South Wales, Sydney, Australia" - }, - { - "author_name": "Warren Stewart", - "author_inst": "Department of Intensive Care Medicine, Prince of Wales Hospital, Sydney, Australia" - }, - { - "author_name": "Tim Cook", - "author_inst": "Department of Anaesthesia and Intensive Care Medicine, Royal United Hospital NHS Trust, Bath, UK" - }, - { - "author_name": "Euan Tovey", - "author_inst": "Woolcock Institute of Medical Research, University of Sydney, Glebe, NSW, Australia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.07.21251081", "rel_title": "How to decide which COVID-19 patient with myocardial infarction to send to the Cath Lab? - A case series of COVID-19 patients with myocardial infarction", @@ -962731,6 +961065,57 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2021.02.04.21251127", + "rel_title": "SARS-CoV-2 Transmission Risk from sports Equipment (STRIKE)", + "rel_date": "2021-02-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.04.21251127", + "rel_abs": "OBJECTIVESTo investigate the potential of shared sporting equipment as transmission vectors of SARS-CoV-2 during the reintroduction of sports such as soccer, rugby, cricket, tennis, golf and gymnastics.\n\nSETTINGLaboratory based live SARS-CoV-2 virus study\n\nINTERVENTIONSTen different types of sporting equipment were inoculated with 40l droplets containing clinically relevant high and low concentrations of live SARS-CoV-2 virus. Materials were then swabbed at time points relevant to sports (1, 5, 15, 30, 90 minutes). The amount of live SARS-CoV-2 recovered at each time point was enumerated using viral plaque assays, and viral decay and half-life was estimated through fitting linear models to log transformed data from each material.\n\nMAIN OUTCOME MEASUREThe primary outcome measure was quantification of retrievable SARS-CoV-2 virus from each piece of equipment at pre-determined time points.\n\nRESULTSAt one minute, SARS-CoV-2 virus was recovered in only seven of the ten types of equipment with the low dose inoculum, one at five minutes and none at 15 minutes. Retrievable virus dropped significantly for all materials tested using the high dose inoculum with mean recovery of virus falling to 0.74% at 1 minute, 0.39% at 15 minutes and 0.003% at 90 minutes. Viral recovery, predicted decay, and half-life varied between materials with porous surfaces limiting virus transmission.\n\nCONCLUSIONSThis study shows that there is an exponential reduction in SARS-CoV-2 recoverable from a range of sports equipment after a short time period, and virus is less transferrable from materials such as a tennis ball, red cricket ball and cricket glove. Given this rapid loss of viral load and the fact that transmission requires a significant inoculum to be transferred from equipment to the mucous membranes of another individual it seems unlikely that sports equipment is a major cause for transmission of SARS-CoV-2. These findings have important policy implications in the context of the pandemic and may promote other infection control measures in sports to reduce the risk of SARS-CoV-2 transmission and urge sports equipment manufacturers to identify surfaces that may or may not be likely to retain transferable virus.\n\nO_TEXTBOXWHAT IS ALREADY KNOWN ON THIS TOPICO_LITransmission of SARS-CoV-2 between individuals playing sport may be via respiratory droplets when in close proximity to an infected person.\nC_LIO_LISARS-CoV-2 remains viable on a variety of surfaces resulting in recommendations to reduce the sharing of sports equipment such as tennis balls when sports were re-opened.\nC_LI\n\nWHAT THIS STUDY ADDSO_LIThe recoverable SARS-CoV-2 viral load reduces exponentially with mean viral load of all materials less than 1% of the original inoculum after 1 minute.\nC_LIO_LIThe type of material has a significant effect on SARS-CoV-2 transfer, with less virus transferred from porous materials such as bovine leather or nylon woven cloth.\nC_LIO_LIPolicies on infection control measures in sport may be better directed towards areas other than reducing the sharing of sports equipment.\nC_LIO_LISports equipment manufacturers may consider using materials that absorb or retain virus as a way of reducing viral transmission from sports equipment.\nC_LI\n\nC_TEXTBOX", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Thomas Edwards", + "author_inst": "Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA" + }, + { + "author_name": "Grant A Kay", + "author_inst": "Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA" + }, + { + "author_name": "Ghaith Aljayyoussi", + "author_inst": "Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA" + }, + { + "author_name": "Sophie I Owen", + "author_inst": "Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA" + }, + { + "author_name": "Andy R Harland", + "author_inst": "Wolfson School of Mechanical, Manufacturing and Electrical Engineering, Loughborough University, Ashby Road, Loughborough, LE11 3TU" + }, + { + "author_name": "Nicholas S Pierce", + "author_inst": "England and Wales Cricket Board and National Centre for Sport and Exercise Medicine, Loughborough University, LE11 3TU" + }, + { + "author_name": "James D F Calder", + "author_inst": "Department of Bioengineering, Imperial College London, London, SW7 2AZ" + }, + { + "author_name": "Tom Fletcher", + "author_inst": "Department of Clinical Sciences, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA" + }, + { + "author_name": "Emily R Adams", + "author_inst": "Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.03.21250823", "rel_title": "Implementation of an in-house real-time reverse transcription-PCR assay for the rapid detection of the SARS-CoV-2 Marseille-4 variant", @@ -963267,73 +961652,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.04.21251170", - "rel_title": "Symptoms of COVID-19 infection and magnitude of antibody response in a large community-based study", - "rel_date": "2021-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.04.21251170", - "rel_abs": "BackgroundThe majority of COVID-19 cases are asymptomatic, or minimally symptomatic with management in the home. Little is known about the frequency of specific symptoms in the general population, and how symptoms predict the magnitude of antibody response to SARS-CoV-2 infection.\n\nMethodsWe quantified IgG antibodies against the SARS-CoV-2 receptor binding domain (RBD) in home-collected dried blood spot samples from 3,365 adults participating in a community-based seroprevalence study in the city of Chicago, USA, collected between June 24 and November 11, 2020.\n\nResults17.8% of the sample was seropositive for SARS-CoV-2. A cluster of symptoms (loss of sense of smell or taste, fever, shortness of breath, muscle or body aches, cough, fatigue, diarrhea, headache) was associated with stronger anti-RBD IgG responses among the seropositives. 39.2% of infections were asymptomatic, and 2 or fewer symptoms were reported for 66.7% of infections. Total number of symptoms was positively but weakly associated with IgG response: Median anti-RBD IgG was 0.95 ug/mL for individuals with 3 or more symptoms, in comparison with 0.61 ug/mL for asymptomatic infections.\n\nConclusionWe document high rates of asymptomatic and mild infection in a large community-based cohort, and relatively low levels of anti-SARS-CoV-2 IgG antibody in the general population of previously exposed individuals.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Thomas W McDade", - "author_inst": "Northwestern University" - }, - { - "author_name": "Joshua Schrock", - "author_inst": "Northwestern University" - }, - { - "author_name": "Richard D'Aquila", - "author_inst": "Northwestern University" - }, - { - "author_name": "Brian Mustanski", - "author_inst": "Northwestern University" - }, - { - "author_name": "Nanette Benbow", - "author_inst": "Northwestern University" - }, - { - "author_name": "Lauren Vaught", - "author_inst": "Northwestern University" - }, - { - "author_name": "Nina Reiser", - "author_inst": "Northwestern University" - }, - { - "author_name": "Matt Velez", - "author_inst": "Northwestern University" - }, - { - "author_name": "Ryan Hsieh", - "author_inst": "Northwestern University" - }, - { - "author_name": "Daniel Ryan", - "author_inst": "Northwestern University" - }, - { - "author_name": "Rana Saber", - "author_inst": "Northwestern University" - }, - { - "author_name": "ELIZABETH MCNALLY", - "author_inst": "Northwestern University Feinberg School of Medicine" - }, - { - "author_name": "Alexis R. Demonbreun", - "author_inst": "Northwestern University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.02.04.21251140", "rel_title": "Longitudinal serology in SARS-CoV-2 infected individuals in India - a prospective cohort study", @@ -964325,6 +962643,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.05.21250572", + "rel_title": "Modeling the Effect of Population-Wide Vaccination on the Evolution of COVID-19 Epidemic in Canada", + "rel_date": "2021-02-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.05.21250572", + "rel_abs": "Population-wide vaccination is critical for containing the COVID-19 pandemic when combined with effective testing and prevention measures. Since the beginning of the COVID-19 outbreak, several companies worked tirelessly for the development of an efficient vaccine that would put an end to this pandemic. Today, a number of COVID-19 vaccines have been approved for use by a number of national regulatory organizations. Vaccination campaigns have already started in several countries with different daily-vaccination rates depending on the countrys vaccination capacity. Therefore, we find it timely and extremely important to conduct a study on the effect of population-wide vaccination campaigns on the evolution of the COVID-19 epidemic. To this end, we propose a new deterministic mathematical model to forecast the COVID-19 epidemic evolution under the effect of vaccination and vaccine efficacy. This model, referred to as SIRV, consists of a compartmental SIR (susceptible, infectious and removed) model augmented with an additional state V representing the effectively vaccinated population as well as two inputs representing the daily-vaccination rate and the vaccine efficacy. Using our SIRV model, we predict the evolution of the COVID-19 epidemic in Canada and its most affected provinces (Ontario, Quebec, British Columbia, Alberta, Saskatchewan, and Manitoba), for different daily vaccination rates and vaccine efficacy. Projections suggest that, without vaccination, 219, 000 lives could be lost across Canada by the end of 2021 due to COVID-19. The ongoing vaccination campaign across Canada seems to unfold relatively slowly at an average daily rate close to 1/2 vaccine per 1, 000 population. At this pace, we could be saving more than 77, 496 lives by the end of the year. Doubling the current vaccination efforts (1 vaccine per day per 1, 000 population) could be sufficient to save 125, 839 lives in Canada during the current year 2021. We would like to point out that our study assumes that the vaccine is perfectly safe without any short or long term side-effects. This study has been conducted independently at arms length from vaccine manufacturers, using the available data from Canada health services. This study can be easily adapted to other places in the world.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Soulaimane Berkane", + "author_inst": "University of Quebec in Outaouais" + }, + { + "author_name": "Intissar Harizi", + "author_inst": "Ottawa" + }, + { + "author_name": "Abdelhamid Tayebi", + "author_inst": "Lakehead University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.02.05.21250127", "rel_title": "Engagement with COVID-19 Public Health Measures in the United States: A Cross-Sectional Social Media Analysis from June to November 2020", @@ -965269,33 +963614,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2021.02.05.21251085", - "rel_title": "Molecular Mechanism of Parosmia", - "rel_date": "2021-02-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.05.21251085", - "rel_abs": "The molecular stimuli that trigger a parosmic response have been identified. Parosmia is a debilitating disease in which familiar smells become distorted and unpleasant. Often a result of post infectious smell loss, incidences are increasing as the number of COVID-19 cases escalates worldwide. Little is understood of its pathophysiology, but the prevailing hypothesis for the underlying mechanism is a mis-wiring of olfactory sensory neurons. We identified 15 different molecular triggers in coffee using GC-Olfactometry as a relatively rapid screening tool for assessment of both quantitative olfactory loss and parosmia. This provides evidence for peripheral causation, but places constraints on the mis-wiring theory.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Jane K Parker", - "author_inst": "University of Reading" - }, - { - "author_name": "Christine E Kelly", - "author_inst": "AbScent" - }, - { - "author_name": "Simon B Gane", - "author_inst": "Royal National Ear, Nose and Throat and Eastman Dental Hospitals" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "otolaryngology" - }, { "rel_doi": "10.1101/2021.02.06.21251271", "rel_title": "Automated Detection of COVID-19 through Convolutional Neural Network using Chest x-ray images", @@ -966631,6 +964949,85 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.02.05.429959", + "rel_title": "Targeting CTP Synthetase 1 to Restore Interferon Induction and Impede Nucleotide Synthesis in SARS-CoV-2 Infection", + "rel_date": "2021-02-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.05.429959", + "rel_abs": "The newly emerged SARS-CoV-2 caused a global pandemic with astonishing mortality and morbidity. The mechanisms underpinning its highly infectious nature remain poorly understood. We report here that SARS-CoV-2 exploits cellular CTP synthetase 1 (CTPS1) to promote CTP synthesis and suppress interferon (IFN) induction. Screening a SARS-CoV-2 expression library identified ORF7b and ORF8 that suppressed IFN induction via inducing the deamidation of interferon regulatory factor 3 (IRF3). Deamidated IRF3 fails to bind the promoters of classic IRF3-responsible genes, thus muting IFN induction. Conversely, a shRNA-mediated screen focused on cellular glutamine amidotransferases corroborated that CTPS1 deamidates IRF3 to inhibit IFN induction. Functionally, ORF7b and ORF8 activate CTPS1 to promote de novo CTP synthesis while shutting down IFN induction. De novo synthesis of small-molecule inhibitors of CTPS1 enabled CTP depletion and IFN induction in SARS-CoV-2 infection, thus impeding SARS-CoV-2 replication. Our work uncovers a strategy that a viral pathogen couples immune evasion to metabolic activation to fuel viral replication. Inhibition of the cellular CTPS1 offers an attractive means for developing antiviral therapy that would be resistant to SARS-CoV-2 mutation.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Youliang Rao", + "author_inst": "University of Southern California" + }, + { + "author_name": "Ting-Yu Wang", + "author_inst": "University of Southern California" + }, + { + "author_name": "Chao Qin", + "author_inst": "University of Southern California" + }, + { + "author_name": "Bianca Espinosa", + "author_inst": "University of Southern California" + }, + { + "author_name": "Qizhi Liu", + "author_inst": "University of Southern California" + }, + { + "author_name": "Arunika Ekanayake", + "author_inst": "University of Southern California" + }, + { + "author_name": "Jun Zhao", + "author_inst": "University of Southern California" + }, + { + "author_name": "Ali Can Savas", + "author_inst": "University of Southern California" + }, + { + "author_name": "Shu Zhang", + "author_inst": "University of Southern California" + }, + { + "author_name": "Mehrnaz Zarinfar", + "author_inst": "University of Southern California" + }, + { + "author_name": "Yongzhen Liu", + "author_inst": "University of Southern California" + }, + { + "author_name": "Wenjie Zhu", + "author_inst": "Chinese Academy of Medical Sciences & Peking Union Medical College" + }, + { + "author_name": "Nicholas Alexander Graham", + "author_inst": "University of Southern California" + }, + { + "author_name": "Taijiao Jiang", + "author_inst": "Suzhou Institute of Systems Medicine" + }, + { + "author_name": "Chao Zhang", + "author_inst": "University of Southern California" + }, + { + "author_name": "Pinghui Feng", + "author_inst": "university of Southern California" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.02.06.430094", "rel_title": "The local topological free energy of the SARS-CoV-2 Spike protein", @@ -967019,29 +965416,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.02.04.21250932", - "rel_title": "The systemic inflammatory response and clinicopathological characteristics in patients admitted to hospital with COVID-19 infection: Comparison of 2 consecutive cohorts", - "rel_date": "2021-02-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.04.21250932", - "rel_abs": "BackgroundIn order to manage the COVID-19 systemic inflammatory response, it is important to identify clinicopathological characteristics across multiple cohorts.\n\nMethodsElectronic patient records for 2 consecutive cohorts of patients admitted to two urban teaching hospitals with COVID-19 during two 7-week periods of the COVID-19 pandemic in Glasgow, U.K. (cohort 1: 17th March 2020 - 1st May 2020) and (cohort 2: 18th May 2020 - 6th July 2020) were examined for routine clinical, laboratory and clinical outcome data.\n\nResultsCompared with cohort 1, cohort 2 were older (p<0.001), more likely to be female (p<0.05) and have less independent living circumstances (p<0.001). More patients in cohort 2 were PCR positive, CXR negative (both p<0.001) and had low serum albumin concentrations (p<0.001). 30-day mortality was similar between both cohorts (23% and 22%). Over the 2 cohorts, age [≥]70 (p<0.001), male gender (p<0.05), hypertension (p<0.01), heart failure (p<0.05), cognitive impairment (p<0.001), frailty (p<0.001), COPD (p<0.05), delirium (p<0.001), elevated perioperative Glasgow Prognostic Score (p[≤]0.001), elevated neutrophil-lymphocyte ratio (p<0.001), low haematocrit (p<0.01), elevated urea (p<0.001), creatinine (p<0.001), glucose (p<0.05) and lactate (p<0.01); and the 4C score were associated with 30-day mortality. When compared with the 4C score, greater frailty (OR 10.2, 95% C.I. 3.4 - 30.6, p<0.01) and low albumin (OR 5.6, 95% C.I. 2.0 - 15.6, p<0.01) were strongly independently associated with 30-day mortality.\n\nConclusionIn addition to the 4C mortality score, frailty score and a low albumin were strongly independently associated with 30-day mortality in two consecutive cohorts of patients admitted to hospital with COVID-19.\n\nArticle summaryO_LIIn two consecutive cohorts of patients with COVID-19 infection admitted to two urban teaching hospitals in Glasgow, UK, there were variations in a number of clinicopathological characteristics despite similar mortality (23 and 22%).\nC_LIO_LIIn these two cohorts, in a multivariate analysis that included the 4C mortality score, clinical frailty score >3, low serum albumin concentration (<35 g/L), high neutrophil-lymphocyte ratio ([≥]5), and abnormal serum sodium concentration (<133/>145 mmol/L) remained independently associated with 30-day mortality.\nC_LI", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Donogh Maguire", - "author_inst": "Glasgow Royal Infirmary" - }, - { - "author_name": "Donald McMillan", - "author_inst": "Academic Unit of Surgery, University of Glasgow, Glasgow Royal Infirmary" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2021.02.04.21251126", "rel_title": "Assessing the performance of a serological point-of-care test in measuring detectable antibodies against SARS-CoV-2", @@ -968449,6 +966823,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.02.21250799", + "rel_title": "Infection and mRNA-1273 vaccine antibodies neutralize SARS-CoV-2 UK variant", + "rel_date": "2021-02-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.02.21250799", + "rel_abs": "Antibody responses against the SARS-CoV-2 Spike protein correlate with protection against COVID-19. Serum neutralizing antibodies appear early after symptom onset following SARS-CoV-2 infection and can last for several months. Similarly, the messenger RNA vaccine, mRNA-1273, generates serum neutralizing antibodies that are detected through at least day 119. However, the recent emergence of the B.1.1.7 variant has raised significant concerns about the breadth of these neutralizing antibody responses. In this study, we used a live virus neutralization assay to compare the neutralization potency of sera from infected and vaccinated individuals against a panel of SARS-CoV-2 variants, including SARS-CoV-2 B.1.1.7. We found that both infection- and vaccine-induced antibodies were effective at neutralizing the SARS-CoV-2 B.1.1.7 variant. These findings support the notion that in the context of the UK variant, vaccine-induced immunity can provide protection against COVID-19. As additional SARS-CoV-2 viral variants continue to emerge, it is crucial to monitor their impact on neutralizing antibody responses following infection and vaccination.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Venkata Viswanadh Edara", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Katharine Floyd", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Lilin Lai", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Meredith Gardner", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "William Hudson", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Anne Piantadosi", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Jesse Waggoner", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Ahmed Babiker", + "author_inst": "Emory University" + }, + { + "author_name": "Rafi Ahmed", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Xuping Xie", + "author_inst": "Emory University School of Medcine" + }, + { + "author_name": "Kumari Lokugamage", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Vineet Menachery", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Pei-Yong Shi", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "- COVID-19 Neutralization Study Group", + "author_inst": "" + }, + { + "author_name": "Mehul S Suthar", + "author_inst": "Emory University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.02.02.21250988", "rel_title": "SARS-CoV-2 specific T cell responses are lower in children and increase with age and time after infection", @@ -968833,113 +967282,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2021.02.03.21251011", - "rel_title": "GPS-estimated foot traffic data and venue selection for COVID-19 serosurveillance studies", - "rel_date": "2021-02-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.03.21251011", - "rel_abs": "The initial phase of the COVID-19 pandemic in the US was marked by limited diagnostic testing, resulting in the need for seroprevalence studies to estimate cumulative incidence and define epidemic dynamics. In lieu of systematic representational surveillance, venue-based sampling was often used to rapidly estimate a communitys seroprevalence. However, biases and uncertainty due to site selection and use of convenience samples are poorly understood. Using data from a SARS-CoV-2 serosurveillance study we performed in Somerville, Massachusetts, we found that the uncertainty in seroprevalence estimates depends on how well sampling intensity matches the known or expected geographic distribution of seropositive individuals in the study area. We use GPS-estimated foot traffic to measure and account for these sources of bias. Our results demonstrated that study-site selection informed by mobility patterns can markedly improve seroprevalence estimates. Such data should be used in the design and interpretation of venue-based serosurveillance studies.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Tyler S Brown", - "author_inst": "Harvard T.H. Chan School of Public Health, Massachusetts General Hospital" - }, - { - "author_name": "Pablo Martinez de Salazar Munoz", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Abhishek Bhatia", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Bridget Bunda", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Ellen K Williams", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "David Bor", - "author_inst": "Cambridge Health Alliance" - }, - { - "author_name": "James S Miller", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Amir Mohareb", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Julia Thierauf", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Wenxin Yang", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Julian Villalba", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Vivek Naranbai", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Wilfredo Garcia Beltran", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Tyler E Miller", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Doug Kress", - "author_inst": "City of Somerville Board of Health" - }, - { - "author_name": "Kristen Stelljes", - "author_inst": "City of Somerville SomerStat" - }, - { - "author_name": "Keith Johnson", - "author_inst": "City of Somerville SomerStat" - }, - { - "author_name": "Daniel B Larremore", - "author_inst": "University of Colorado Boulder" - }, - { - "author_name": "Jochen Lennerz", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "A. John Iafrate", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Satchit Balsari", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Caroline O Buckee", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Yonatan H Grad", - "author_inst": "Harvard T.H. Chan School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.02.02.21251028", "rel_title": "COVID19-related and all-cause mortality among middle-aged and older adults across the first epidemic wave of SARS-COV-2 infection in the region of Tarragona, Spain: results from the COVID19 TARRACO Cohort Study, March-June 2020.", @@ -971251,6 +969593,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.02.02.429486", + "rel_title": "The mutation profile of SARS-CoV-2 is primarily shaped by the host antiviral defense", + "rel_date": "2021-02-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.02.429486", + "rel_abs": "Understanding SARS-CoV-2 evolution is a fundamental effort in coping with the COVID-19 pandemic. The virus genomes have been broadly evolving due to the high number of infected hosts world-wide. Mutagenesis and selection are the two inter-dependent mechanisms of virus diversification. However, which mechanisms contribute to the mutation profiles of SARS-CoV-2 remain under-explored. Here, we delineate the contribution of mutagenesis and selection to the genome diversity of SARS-CoV-2 isolates. We generated a comprehensive phylogenetic tree with representative genomes. Instead of counting mutations relative to the reference genome, we identified each mutation event at the nodes of the phylogenetic tree. With this approach, we obtained the mutation events that are independent of each other and generated the mutation profile of SARS-CoV-2 genomes. The results suggest that the heterogeneous mutation patterns are mainly reflections of host (i) antiviral mechanisms that are achieved through APOBEC, ADAR, and ZAP proteins and (ii) probable adaptation against reactive oxygen species.\n\nImportanceSARS-CoV-2 genomes are evolving worldwide. Revealing the evolutionary characteristics of SARS-CoV-2 is essential to understand host-virus interactions. Here, we aim to understand whether mutagenesis or selection is the primary driver of SARS-CoV-2 evolution. This study provides an unbiased computational method for profiling and analyzing independently occurring SARS-CoV-2 mutations. The results point out three host antiviral mechanisms shaping the mutational profile of SARS-CoV-2 through APOBEC, ADAR, and ZAP proteins. Besides, reactive oxygen species might have an impact on the SARS-CoV-2 mutagenesis.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Cem Azgari", + "author_inst": "Sabanci University" + }, + { + "author_name": "Zeynep Kilinc", + "author_inst": "Sabanci University" + }, + { + "author_name": "Berk Turhan", + "author_inst": "Sabanci University" + }, + { + "author_name": "Defne Circi", + "author_inst": "Sabanci University" + }, + { + "author_name": "Ogun Adebali", + "author_inst": "Sabanci University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2021.02.03.429670", "rel_title": "The SARS-CoV-2 transcriptome and the dynamics of the S gene furin cleavage site in primary human airway epithelia", @@ -971683,37 +970060,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2021.02.04.429819", - "rel_title": "Codon arrangement modulates MHC-I peptides presentation: implications for a SARS-CoV-2 peptide-based vaccine", - "rel_date": "2021-02-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.04.429819", - "rel_abs": "Among various vaccination strategies, peptide-based vaccines appear as excellent candidates because they are cheap to produce, are highly stable and harbor low toxicity. However, predicting which MHC-I Associated Peptide (MAP) will ultimately reach cell surface remains challenging, due to high false discovery rates. Previously, we demonstrated that synonymous codon arrangement (usage and placement) is predictive of, and modulates MAP presentation. Here, we apply CAMAP (Codon Arrangement MAP Predictor), the artificial neural network we used to unveil the role of codon arrangement in MAP presentation, to predict SARS-CoV MAPs. We report that experimentally identified SARS-CoV-1 and SARS-CoV-2 MAPs are associated with significantly higher CAMAP scores. Based on CAMAP scores and binding affinity, we identified 48 non-overlapping MAP candidates for a peptide-based vaccine, ensuring coverage for a high proportion of HLA haplotypes in the US population (>78%) and SARS-CoV-2 strains (detected in >98% of SARS-CoV-2 strains present in the GISAID database). Finally, we built an interactive web portal (https://www.epitopes.world) where researchers can freely explore CAMAP predictions for SARS-CoV-1/2 viruses. Collectively, we present an analysis framework that can be generalizable to empower the rapid identification of virus-specific MAPs, including in the context of an emergent virus, to help accelerate target identification for peptide-based vaccine designs that could be critical in safely attaining group immunity in the context of a global pandemic.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Tariq Daouda", - "author_inst": "Broad Institute of MIT and Harvard; Center for Cancer Research, Massachusetts General Hospital; Department of Medicine, Harvard Medical School; Center for Immu" - }, - { - "author_name": "Maude Dumont-Lagac\u00e9", - "author_inst": "Institute for Research in Immunology and Cancer; Universit\u00e9 de Montr\u00e9al" - }, - { - "author_name": "Albert Feghaly", - "author_inst": "Institute for Research in Immunology and Cancer; Universit\u00e9 de Montr\u00e9al" - }, - { - "author_name": "Alexandra-Chloe Villani", - "author_inst": "Broad Institute of MIT and Harvard; Center for Cancer Research, Massachusetts General Hospital; Department of Medicine, Harvard Medical School; Center for Immu" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.02.04.429711", "rel_title": "Follow-up of a hospital cohort during the first 3,530 suspected cases of COVID-19 in Sao Jose do Rio Preto, Sao Paulo, Brazil", @@ -973185,6 +971531,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2021.02.02.21250979", + "rel_title": "Vaccinating Australia: How long will it take?", + "rel_date": "2021-02-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.02.21250979", + "rel_abs": "The Australian Governments COVID-19 vaccine rollout strategy is scheduled to commence in late February 2021 and aims to vaccinate the Australian adult population by the end of October 2021. The task of vaccinating some 20 million people within this timeframe presents considerable logistical challenges. Key to meeting this target is the rate of vaccine delivery: the number of vaccine doses that can be administered per day. In the opening phase, high priority groups will receive the Pfizer/BioNTech vaccine through hospital hubs at an initial rate of 80,000 doses per week. However, pending regulatory approval, the currently announced plan appears to be to distribute the AstraZeneca vaccine to the bulk of the popluation through a combination of general practices and community pharmacies. Here, we run a series of projections to estimate how long it will take to vaccinate the Australian population under different assumptions about the rate of vaccine administration as well as the schedule for second doses and prevalence of vaccine hesitancy. Our analysis highlights the ambitious rate of vaccine administration that will be neccessary to meet the Australian Government completion target of October 2021. A rate of 200,000 doses per day would comfortably meet that target; 80,000 doses a day would see roll-out extended until mid-2022. Speed is of the essence when it comes to vaccine rollout: protecting the population quickly will minimise the risk of sporadic and costly lockdowns lockdowns and the potential for small, local clusters getting out of control and sparking new epidemic waves. The government should gather all its resources to maximise the daily vaccination rate, ideally aiming to ramp up administration to at least 200,000 doses per day as quickly as possible. Quickly achieving and maintaining this pace will likely require dedicated large-scale vaccination sites that are capable of delivering thousands of doses a week in addition to the enthusiastic participation of GP practices and community pharmacies around the country. Lessons on the neccessary logistical planning, including coordination of delivery, ultra-cold-chain storage and staffing, can potentially be learned from Israel, where between 7,000 and 20,000 vaccinations per million population have been delivered daily throughout January.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Mark J Hanly", + "author_inst": "Centre for Big Data Research in Health, UNSW Australia" + }, + { + "author_name": "Tim Churches", + "author_inst": "South Western Sydney Clinical School, Faculty of Medicine & Health, UNSW Sydney & Ingham Institute for Applied Medical Research" + }, + { + "author_name": "Oisin Fitzgerald", + "author_inst": "Centre for Big Data Research in Health, UNSW Sydney" + }, + { + "author_name": "Chandini Raina MacIntyre", + "author_inst": "University of New South Wales" + }, + { + "author_name": "Louisa Jorm", + "author_inst": "Centre for Big Data Research in Health, UNSW Sydney" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.02.01.21250959", "rel_title": "Increased hazard of death in community-tested cases of SARS-CoV-2 Variant of Concern 202012/01", @@ -973645,105 +972026,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2021.02.01.21250943", - "rel_title": "Seroprevalence of SARS-CoV-2 during pregnancy and associated outcomes: results from an ongoing prospective cohort study, New York City", - "rel_date": "2021-02-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.02.01.21250943", - "rel_abs": "BackgroundIn May-July 2020 in the New York City area, up to 16% of pregnant women had reportedly been infected with SARS-CoV-2. Prior studies found associations between SARS-CoV-2 infection during pregnancy and certain adverse outcomes (e.g., preterm birth, cesarean delivery). These studies relied on reverse transcription polymerase chain reaction (RT-PCR) testing to establish SARS-CoV-2 infection. This led to overrepresentation of symptomatic or acutely ill cases in scientific studies.\n\nObjectiveTo expand our understanding of the effects of SARS-CoV-2 infection during pregnancy on pregnancy outcomes, regardless of symptomatology and stage of infection, by using serological tests to measure IgG antibody levels.\n\nStudy DesignThe Generation C Study is an ongoing prospective cohort study conducted at the Mount Sinai Health System. All pregnant women receiving obstetrical care at the Mount Sinai Hospital and Mount Sinai West Hospital from April 20, 2020 onwards are eligible for participation. For the current analysis, we included participants who had given birth to a liveborn singleton infant on or before August 15, 2020. Blood was drawn as part of routine clinical care; for each woman, we tested the latest sample available to establish seropositivity using a SARS-CoV-2 serologic enzyme-linked immunosorbent assay. Additionally, RT-PCR testing was performed on a nasopharyngeal swab taken during labor and delivery. Pregnancy outcomes of interest (i.e., gestational age at delivery, birth weight, mode of delivery, Apgar score, ICU/NICU admission, and neonatal hospital length of stay) and covariates were extracted from electronic medical records. Among all Generation C participants who had given birth by August 15, 2020 (n=708), we established the SARS-CoV-2 seroprevalence. Excluding women who tested RT-PCR positive at delivery, we conducted crude and adjusted linear and logistic regression models to compare antibody positive women without RT-PCR positivity at delivery with antibody negative women without RT-PCR positivity at delivery. We stratified analyses by race/ethnicity to examine potential effect modification.\n\nResultsThe SARS-CoV-2 seroprevalence based on IgG measurement was 16.4% (n=116, 95% CI 13.7-19.3). Twelve women (1.7%) were SARS-CoV-2 RT-PCR positive at delivery (11 of these women were seropositive). Seropositive women were generally younger, more often Black or Hispanic, and more often had public insurance and higher pre-pregnancy BMI compared with seronegative women. SARS-CoV-2 seropositivity without RT-PCR positivity at delivery was associated with decreased odds of caesarean delivery (aOR 0.48, 95%CI 0.27; 0.84) compared with seronegative women without RT-PCR positivity at delivery. Stratified by race/ethnicity, the association between seropositivity and decreased odds of caesarean delivery remained for non-Hispanic Black/African-American and Hispanic women, but not for non-Hispanic White women. No other pregnancy outcomes differed by seropositivity, overall or stratified by race/ethnicity.\n\nConclusionSeropositivity for SARS-CoV-2 without RT-PCR positivity at delivery, suggesting that infection occurred earlier during pregnancy, was not associated with selected adverse maternal or neonatal outcomes among live births in a cohort sample of women from New York City. While non-Hispanic Black and Latina women in our cohort had a higher rate of SARS-CoV-2 seropositivity compared with non-Hispanic White women, we found no increase in adverse maternal or neonatal outcomes among these groups due to infection.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Nina M Molenaar", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Anna-Sophie Rommel", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Lotje de Witte", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Siobhan Dolan", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Whitney Lieb", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Erona Ibroci", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Sophie Ohrn", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Jezelle Lynch", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Christina Capuano", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Daniel Stadlbauer", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Florian Krammer", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Lauren Zapata", - "author_inst": "Centers for Disease Control" - }, - { - "author_name": "Rachel Brody", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Rhoda Sperling", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Omara Afzal", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Roy Missall", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Amy Balbierz", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Teresa Janevic", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Joanne Stone", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Elizabeth Howell", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Veerle Bergink", - "author_inst": "Icahn School of Medicine at Mount Sinai" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2021.02.01.21250952", "rel_title": "Wastewater surveillance for SARS-CoV-2 on college campuses: Initial efforts, lessons learned and research needs", @@ -974863,6 +973145,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.02.03.429601", + "rel_title": "Bacterial expression and purification of functional recombinant SARS-CoV-2 spike receptor binding domain", + "rel_date": "2021-02-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.03.429601", + "rel_abs": "The COVID-19 pandemic caused by SARS-CoV-2 has applied significant pressure on overtaxed healthcare around the world, underscoring the urgent need for rapid diagnosis and treatment. We have developed a bacterial strategy for the expression and purification of the SARS-CoV-2 spike protein receptor binding domain using the CyDisCo system to create and maintain the correct disulfide bonds for protein integrity and functionality. We show that it is possible to quickly and inexpensively produce functional, active antigen in bacteria capable of recognizing and binding to the ACE2 (angiotensin-converting enzyme) receptor as well as antibodies in COVID-19 patient sera.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Janani Prahlad", + "author_inst": "University of Nebraska Medical Center" + }, + { + "author_name": "Lucas Struble", + "author_inst": "University of Nebraska Medical Center" + }, + { + "author_name": "William E Lutz", + "author_inst": "University of Nebraska Medical Center" + }, + { + "author_name": "Savanna A Wallin", + "author_inst": "University of Nebraska Medical Center" + }, + { + "author_name": "Surender Khurana", + "author_inst": "University of Nebraska Medical Center" + }, + { + "author_name": "Andy Schnaubelt", + "author_inst": "University of Nebraska Medical Center" + }, + { + "author_name": "Mara J Broadhurst", + "author_inst": "University of Nebraska Medical Center" + }, + { + "author_name": "Ken Bayles", + "author_inst": "University of Nebraska Medical Center" + }, + { + "author_name": "Gloria E. O. Borgstahl", + "author_inst": "University of Nebraska Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2021.02.03.429146", "rel_title": "CovRadar: Continuously tracking and filtering SARS-CoV-2 mutations for molecular surveillance", @@ -975519,53 +973852,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2021.02.03.429355", - "rel_title": "Impact of the B.1.1.7 variant on neutralizing monoclonal antibodies recognizing diverse epitopes on SARS-CoV-2 Spike", - "rel_date": "2021-02-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.03.429355", - "rel_abs": "The interaction of the SARS-CoV-2 Spike receptor binding domain (RBD) with the ACE2 receptor on host cells is essential for viral entry. RBD is the dominant target for neutralizing antibodies and several neutralizing epitopes on RBD have been molecularly characterized. Analysis of circulating SARS-CoV-2 variants has revealed mutations arising in the RBD, the N-terminal domain (NTD) and S2 subunits of Spike. To fully understand how these mutations affect the antigenicity of Spike, we have isolated and characterized neutralizing antibodies targeting epitopes beyond the already identified RBD epitopes. Using recombinant Spike as a sorting bait, we isolated >100 Spike-reactive monoclonal antibodies from SARS-CoV-2 infected individuals. ~45% showed neutralizing activity of which ~20% were NTD-specific. None of the S2-specific antibodies showed neutralizing activity. Competition ELISA revealed that NTD-specific mAbs formed two distinct groups: the first group was highly potent against infectious virus, whereas the second was less potent and displayed glycan-dependant neutralization activity. Importantly, mutations present in B.1.1.7 Spike frequently conferred resistance to neutralization by the NTD-specific neutralizing antibodies. This work demonstrates that neutralizing antibodies targeting subdominant epitopes need to be considered when investigating antigenic drift in emerging variants.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Luke Muir", - "author_inst": "UCL" - }, - { - "author_name": "Weng M Ng", - "author_inst": "University of Oxford" - }, - { - "author_name": "Helen M. E. Duyvesteyn", - "author_inst": "University of Oxford" - }, - { - "author_name": "Yuguang Zhao", - "author_inst": "University of Oxford" - }, - { - "author_name": "Thomas A. Bowden", - "author_inst": "University of Oxford" - }, - { - "author_name": "Annachiara Rosa", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Peter Cherepanov", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Laura E McCoy", - "author_inst": "UCL" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.02.03.429164", "rel_title": "Multi-specific DARPin(R) therapeutics demonstrate very high potency against mutated SARS-CoV-2 variants in vitro", @@ -977021,6 +975307,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.02.01.429283", + "rel_title": "A Thermostable, Flexible RNA Vaccine Delivery Platform for Pandemic Response", + "rel_date": "2021-02-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.02.01.429283", + "rel_abs": "Current RNA vaccines against SARS-CoV-2 are limited by instability of both the RNA and the lipid nanoparticle delivery system, requiring storage at -20{degrees}C or -70{degrees}C and compromising universally accessible vaccine distribution. This study demonstrates the thermostability and adaptability of a nanostructured lipid carrier (NLC) RNA vaccine delivery system for use in pandemic preparedness and pandemic response. Liquid NLC is stable at refrigerated temperatures for [≥] 1 year, enabling stockpiling and rapid deployment by point-of-care mixing with any vaccine RNA. Alternatively, NLC complexed with RNA may be readily lyophilized and stored at room temperature for [≥] 8 months or refrigerated temperature for [≥] 21 months. This thermostable RNA vaccine platform could significantly improve distribution of current and future pandemic response vaccines, particularly in low-resource settings.\n\nOne Sentence SummaryAn RNA vaccine delivery system stable at room temperature for 8+ months and refrigerated for 21+ months.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Alana Gerhardt", + "author_inst": "Infectious Disease Research Institute" + }, + { + "author_name": "Emily Voigt", + "author_inst": "Infectious Disease Research Institute" + }, + { + "author_name": "Michelle Archer", + "author_inst": "Infectious Disease Research Institute" + }, + { + "author_name": "Sierra Reed", + "author_inst": "Infectious Disease Research Institute" + }, + { + "author_name": "Elise Larson", + "author_inst": "Infectious Disease Research Institute" + }, + { + "author_name": "Neal Van Hoeven", + "author_inst": "Infectious Disease Research Institute" + }, + { + "author_name": "Ryan Kramer", + "author_inst": "Infectious Disease Research Institute" + }, + { + "author_name": "Christopher Fox", + "author_inst": "Infectious Disease Research Institute" + }, + { + "author_name": "Corey Casper", + "author_inst": "Infectious Disease Research Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioengineering" + }, { "rel_doi": "10.1101/2021.02.02.428995", "rel_title": "Therapeutic antibodies, targeting the SARS-CoV-2 spike N-terminal domain, protect lethally infected K18-hACE2 mice", @@ -977433,81 +975770,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2021.01.31.429001", - "rel_title": "Identification of anti-severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) oxysterol derivatives in vitro", - "rel_date": "2021-02-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.31.429001", - "rel_abs": "Development of effective antiviral drugs targeting the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) are urgently needed to combat the coronavirus disease 2019 (COVID-19). Oxysterols, defined as oxidized derivatives of cholesterol, include endogenous (naturally occurring) cholesterol metabolites as well as semi-synthetic oxysterol derivatives. We have previously studied the use of semi-synthetic oxysterol derivatives as drug candidates for inhibition of cancer, fibrosis, and bone regeneration. In this study, we have screened a panel of naturally occurring and semi-synthetic oxysterol derivatives for anti-SARS-CoV-2 activity, using a cell culture infection assay. We show that the natural oxysterols, 7-ketocholesterol, 22(R)-hydroxycholesterol, 24(S)-hydroxycholesterol, and 27-hydroxycholesterol, substantially inhibited SARS-CoV-2 propagation in cultured cells. Among semi-synthetic oxysterols, Oxy186 displayed antiviral activity comparable to natural oxysterols. In addition, related oxysterol analogues Oxy210 and Oxy232 displayed more robust anti-SARS-CoV-2 activities, reducing viral replication more than 90% at 10 M and 99% at 15 M, respectively. When orally administered in mice, peak plasma concentrations of Oxy210 fall into a therapeutically relevant range (19 M), based on the dose-dependent curve for antiviral activity in our cell culture infection assay. Mechanistic studies suggest that Oxy210 reduced replication of SARS-CoV-2 with disrupting the formation of double membrane vesicles (DMVs), intracellular membrane compartments associated with viral replication. Oxy210 also inhibited the replication of hepatitis C virus, another RNA virus whose replication is associated with DMVs, but not the replication of the DMV-independent hepatitis D virus. Our study warrants further evaluation of Oxy210 and Oxy232 as a safe and reliable oral medication, which could help protect vulnerable populations with increased risk developing COVID-19.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Hirofumi Ohashi", - "author_inst": "National Institute for Infectious Diseases" - }, - { - "author_name": "Feng Wang", - "author_inst": "MAX BioPharma, Inc." - }, - { - "author_name": "Frank Stappenbeck", - "author_inst": "MAX BioPharma, Inc." - }, - { - "author_name": "Kana Tsuchimoto", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Chisa Kobayashi", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Wakana Saso", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Michiyo Kataoka", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Kouji Kuramochi", - "author_inst": "Tokyo University of Science" - }, - { - "author_name": "Masamichi Muramatsu", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Tadaki Suzuki", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Camille Sureau", - "author_inst": "Institut National de la Transfusion Sanguine (INTS)" - }, - { - "author_name": "Makoto Takeda", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Takaji Wakita", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Farhad Parhami", - "author_inst": "MAX BioPharma, Inc." - }, - { - "author_name": "Koichi Watashi", - "author_inst": "National Institute of Infectious Diseases" - } - ], - "version": "1", - "license": "", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.02.01.429110", "rel_title": "Sequential delivery of LAIV and SARS-CoV-2 in the ferret model can reduce SARS-CoV-2 shedding and does not result in enhanced lung pathology.", @@ -978643,6 +976905,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.28.21250717", + "rel_title": "Comparative performance of multiplex salivary and commercially available serologic assays to detect SARS-CoV-2 IgG and neutralization titers", + "rel_date": "2021-02-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.28.21250717", + "rel_abs": "Oral fluid (hereafter saliva) offers a non-invasive sampling method for the detection of SARS-CoV-2 antibodies. However, data comparing performance of salivary tests against commercially-available serologic and neutralizing antibody (nAb) assays are lacking. This study compared the performance of a multiplex salivary SARS-CoV-2 IgG assay targeting antibodies to nucleocapsid (N), receptor binding domain (RBD) and spike (S) antigens to three commercially-available SARS-CoV-2 serology enzyme immunoassays (EIAs) (Ortho Vitros, Euroimmun, and BioRad) and nAb. Paired saliva and plasma samples were collected from 101 eligible COVID-19 convalescent plasma (CCP) donors >14 days since PCR+ confirmed diagnosis. Concordance was evaluated using positive (PPA) and negative (NPA) percent agreement, overall percent agreement (PA), and Cohens kappa coefficient. The range between salivary and plasma EIAs for SARS-CoV-2-specific N was PPA: 54.4-92.1% and NPA: 69.2-91.7%, for RBD was PPA: 89.9-100% and NPA: 50.0-84.6%, and for S was PPA: 50.6-96.6% and NPA: 50.0-100%. Compared to a plasma nAb assay, the multiplex salivary assay PPA ranged from 62.3% (N) and 98.6% (RBD) and NPA ranged from 18.8% (RBD) to 96.9% (S). Combinations of N, RBD, and S and a summary algorithmic index of all three (N/RBD/S) in saliva produced ranges of PPA: 87.6-98.9% and NPA: 50-91.7% with the three EIAs and ranges of PPA: 88.4-98.6% and NPA: 21.9-34.4% with the nAb assay. A multiplex salivary SARS-CoV-2 IgG assay demonstrated comparable performance to three commercially-available plasma EIAs and a nAb assay, and may be a viable alternative to assist in screening CCP donors and monitoring population-based seroprevalence and vaccine antibody response.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Christopher D Heaney", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Nora Pisanic", + "author_inst": "Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA" + }, + { + "author_name": "Pranay R Randad", + "author_inst": "Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA" + }, + { + "author_name": "Kate Kruczynski", + "author_inst": "Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA" + }, + { + "author_name": "Tyrone Howard", + "author_inst": "Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA" + }, + { + "author_name": "Xianming Zhu", + "author_inst": "Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA" + }, + { + "author_name": "Kirsten Littlefield", + "author_inst": "Johns Hopkins Bloomberg School of Public Health," + }, + { + "author_name": "Eshan Patel", + "author_inst": "NIAID" + }, + { + "author_name": "Ruchee Shrestha", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Oliver Laeyendecker", + "author_inst": "NIAID & JHMI" + }, + { + "author_name": "Shmuel Shoham", + "author_inst": "The Johns Hopkins Hospital, , MD" + }, + { + "author_name": "David J Sullivan", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Kelly Gebo", + "author_inst": "Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA" + }, + { + "author_name": "Daniel Hanley", + "author_inst": "Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA" + }, + { + "author_name": "Andrew Redd", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Thomas Quinn", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Arturo Casadevall", + "author_inst": "Johns Hopkins School of Public Health" + }, + { + "author_name": "Jonathan M Zenilman", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Andrew Pekosz", + "author_inst": "Johns Hopkins Bloomberg School of Public Health" + }, + { + "author_name": "Evan M Bloch", + "author_inst": "Johns Hopkins Medicine" + }, + { + "author_name": "Aaron AR Tobian", + "author_inst": "Johns Hopkins Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.28.21250721", "rel_title": "Significance of SARS-CoV-2 Specific Antibody Testing during COVID-19 Vaccine Allocation", @@ -979135,93 +977496,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2021.01.28.21250129", - "rel_title": "Application of a 27-protein candidate cardiovascular surrogate endpoint to track risk ascendancy and resolution in COVID-19.", - "rel_date": "2021-02-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.28.21250129", - "rel_abs": "BackgroundThere is an urgent need for tools allowing the early prognosis and subsequent monitoring of individuals with heterogeneous COVID-19 disease trajectories. Pre-existing cardiovascular (CV) disease is a leading risk factor for COVID-19 susceptibility and poor outcomes, and cardiac involvement is prevalent in COVID-19 patients both during the acute phase as well as in convalescence. The utility of traditional CV risk biomarkers in mild COVID-19 disease or across disease course is poorly understood. We sought to determine if a previously validated 27-protein predictor of CV outcomes served a purpose in COVID-19.\n\nMethodsThe 27-protein test of residual CV (RCV) risk was applied without modification to n=860 plasma samples from hospitalized and non-hospitalized SARS-CoV-2 infected individuals at disease presentation from three independent cohorts to predict COVID-19 severity and mortality. The same test was applied to an additional n=991 longitudinal samples to assess sensitivity to change in CV risk throughout the course of infection into convalescence.\n\nResultsIn each independent cohort, RCV predictions were significantly related to maximal subsequent COVID-19 severity and to mortality. At the baseline blood draw, the mean protein-predicted likelihood of an event in subjects who died during the study period ranged from 88-99% while it ranged from 8-36% in subjects who were not admitted to hospital. Additionally, the test outperformed existing risk predictors based on commonly used laboratory chemistry values or presence of comorbidities. Application of the RCV test to sequential samples showed dramatic increases in risk during the first few days of infection followed by risk reduction in the survivors; a period of catastrophically high cardiovascular risk (above 50%) typically lasted 8-12 days and had not resolved to normal levels in most people within that timescale.\n\nConclusionsThe finding that a 27-protein candidate CV surrogate endpoint developed in multi-morbid patients prior to the pandemic is both prognostic and acutely sensitive to the adverse effects of COVID-19 suggests that this disease activates the same biologic risk-related mechanisms. The test may be useful for monitoring recovery and drug response.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Clare Paterson", - "author_inst": "SomaLogic Inc. Boulder, CO, USA" - }, - { - "author_name": "Yolanda Hagar", - "author_inst": "SomaLogic Inc. Boulder, CO, USA" - }, - { - "author_name": "Michael A Hinterberg", - "author_inst": "SomaLogic Inc. Boulder, CO, USA" - }, - { - "author_name": "Alexander W Charney", - "author_inst": "Icahn School of Medicine at Mount Sinai, New York, NY, USA" - }, - { - "author_name": "Diane M Del Valle", - "author_inst": "Icahn School of Medicine at Mount Sinai, New York, NY, USA" - }, - { - "author_name": "Michael R Filbin", - "author_inst": "Department of Emergency Medicine, Massachusetts General Hospital, Boston, MA, USA" - }, - { - "author_name": "Sacha Gnjatic", - "author_inst": "Icahn School of Medicine at Mount Sinai, New York, NY, USA" - }, - { - "author_name": "Jason D Goldman", - "author_inst": "Swedish Center for Research and Innovation, Swedish Medical Center, Seattle, WA, USA" - }, - { - "author_name": "Nir Hacohen", - "author_inst": "Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA" - }, - { - "author_name": "James R Heath", - "author_inst": "Institute for Systems Biology, Seattle, WA, USA" - }, - { - "author_name": "Rainer Hillenbrand", - "author_inst": "Novartis Institutes for BioMedical Research, Basel, Switzerland" - }, - { - "author_name": "Lori L Jennings", - "author_inst": "Novartis Institutes for BioMedical Research, Cambridge, MA, USA" - }, - { - "author_name": "Seunghee Kim-Schulze", - "author_inst": "Icahn School of Medicine at Mount Sinai, New York, NY, USA" - }, - { - "author_name": "Andrew T Magis", - "author_inst": "Institute for Systems Biology, Seattle, WA, USA" - }, - { - "author_name": "Miriam Merad", - "author_inst": "Icahn School of Medicine at Mount Sinai, New York, NY, USA" - }, - { - "author_name": "Konstantinos Mouskas", - "author_inst": "Icahn School of Medicine at Mount Sinai, New York, NY, USA" - }, - { - "author_name": "Nicole W Simons", - "author_inst": "Icahn School of Medicine at Mount Sinai, New York, NY, USA" - }, - { - "author_name": "Stephen A Williams", - "author_inst": "SomaLogic Inc. Boulder, CO, USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2021.01.29.20248797", "rel_title": "High variability in transmission of SARS-CoV-2 within households and implications for control", @@ -980405,6 +978679,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.29.21250552", + "rel_title": "Aerosol emission from the respiratory tract: an analysis of relative risks from oxygen delivery systems", + "rel_date": "2021-02-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.29.21250552", + "rel_abs": "BackgroundRisk of aerosolisation of SARS-CoV-2 directly informs organisation of acute healthcare and PPE guidance. Continuous positive airways pressure (CPAP) and high-flow nasal oxygen (HFNO) are widely used modes of oxygen delivery and respiratory support for patients with severe COVID-19, with both considered as high risk aerosol generating procedures. However, there are limited high quality experimental data characterising aerosolisation during oxygen delivery and respiratory support.\n\nMethodsHealthy volunteers were recruited to breathe, speak, and cough in ultra-clean, laminar flow theatres followed by using oxygen and respiratory support systems. Aerosol emission was measured using two discrete methodologies, simultaneously. Hospitalised patients with COVID-19 were also recruited and had aerosol emissions measured during breathing, speaking, and coughing.\n\nFindingsIn healthy volunteers (n = 25 subjects; 531 measures), CPAP (with exhalation port filter) produced less aerosols than breathing, speaking and coughing (even with large >50L/m facemask leaks). HFNO did emit aerosols, but the majority of these particles were generated from the HFNO machine, not the patient. HFNO-generated particles were small (<1m), passing from the machine through the patient and to the detector without coalescence with respiratory aerosol, thereby unlikely to carry viral particles. Coughing was associated with the highest aerosol emissions with a peak concentration at least 10 times greater the mean concentration generated from speaking or breathing. Hospitalised patients with COVID-19 (n = 8 subjects; 56 measures) had similar size distributions to healthy volunteers.\n\nInterpretationIn healthy volunteers, CPAP is associated with less aerosol emission than breathing, speaking or coughing. Aerosol emission from the respiratory tract does not appear to be increased by HFNO. Although direct comparisons are complex, cough appears to generate significant aerosols in a size range compatible with airborne transmission of SARS-CoV-2. As a consequence, the risk of SARS-CoV-2 aerosolisation is likely to be high in all areas where patients with Covid-19 are coughing. Guidance on personal protective equipment policy should reflect these updated risks.\n\nFundingNIHR-UKRI Rapid COVID call (COV003), Wellcome Trust GW4-CAT Doctoral Training Scheme (FH), MRC CARP Fellowship(JD, MR/T005114/1). Natural Environment Research Council grant (BB, NE/P018459/1)\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSPubMed was searched from inception until 10/1/21 using the terms aerosol, and variations of non-invasive positive pressure ventilation and high-flow nasal oxygen therapy. Studies were included if they measured aerosol generated from volunteers or patients receiving non-invasive positive pressure ventilation (NIV) or high flow nasal oxygen therapy (HFNO), or provided experimental evidence on a simulated human setting. One study was identified (Gaeckle et al, 2020) which measured aerosol emission with one methodology (APS) but was limited by high background concentration of aerosol and a low number of participants (n = 10).\n\nAdded value of this studyThis study used multiple methodologies to measure aerosol emission from the respiratory tract before and during CPAP and high-flow nasal oxygen, in an ultra-clean, laminar flow theatre with near-zero background aerosol and recruited patients with COVID-19 to ensure similar aerosol distributions. We conclude that there is negligible aerosol generation with CPAP, that aerosol emission from HFNO is from the machine and not the patient, coughing emits aerosols consistent with airborne transmission of SARS CoV2 and that healthy volunteers are a reasonable proxy for COVID-19 patients.\n\nImplications of all the available evidenceCPAP and HFNO should not be considered high risk aerosol generating procedures, based on our study and that of Gaeckle et al. Recorded aerosol emission from HFNO stems from the machine. Cough remains a significant aerosol risk. PPE guidance should be updated to ensure medical staff are protected with appropriate PPE in situations when patients with suspected or proven COVID-19 are likely to cough.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Fergus W Hamilton", + "author_inst": "University of Bristol" + }, + { + "author_name": "Florence Gregson", + "author_inst": "University of Bristol" + }, + { + "author_name": "David T Arnold", + "author_inst": "University of Bristol" + }, + { + "author_name": "Sadiyah Sheikh", + "author_inst": "University of Bristol" + }, + { + "author_name": "Kirsty Ward", + "author_inst": "North Bristol NHS Trust" + }, + { + "author_name": "Jules Brown", + "author_inst": "North Bristol NHS Trust" + }, + { + "author_name": "Ed Moran", + "author_inst": "North Bristol NHS Trust" + }, + { + "author_name": "Carrie White", + "author_inst": "North Bristol NHS Trust" + }, + { + "author_name": "Anna Morley", + "author_inst": "North Bristol NHS Trust" + }, + { + "author_name": "- AERATOR Group", + "author_inst": "" + }, + { + "author_name": "Bryan R Bzdek", + "author_inst": "University of Bristol" + }, + { + "author_name": "Jonathan Reid", + "author_inst": "University of Bristol" + }, + { + "author_name": "Nick Maskell", + "author_inst": "University of Bristol" + }, + { + "author_name": "James W Dodd", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.29.21250655", "rel_title": "Impact of public sentiments on the transmission of COVID-19 across a geographical gradient", @@ -980757,65 +979102,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.30.21250830", - "rel_title": "Estimated SARS-CoV-2 Seroprevalence in Healthy Children and Those with Chronic Illnesses in The Washington Metropolitan Area as of October 2020", - "rel_date": "2021-02-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.30.21250830", - "rel_abs": "The estimated SARS-CoV-2 seroprevalence in children was found to be 9.46% for the Washington Metropolitan area. Hispanic/Latinx individuals were found to have higher odds of seropositivity. While chronic medical conditions were not associated with having antibodies, previous fever and body aches were predictive symptoms.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Burak Bahar", - "author_inst": "Children's National Hospital" - }, - { - "author_name": "Joelle N Simpson", - "author_inst": "Children's National Hospital" - }, - { - "author_name": "Cara Biddle", - "author_inst": "Children's National Hospital" - }, - { - "author_name": "Andrew Campbell", - "author_inst": "Children's National Hospital" - }, - { - "author_name": "Jeffrey S Dome", - "author_inst": "Children's National Hospital" - }, - { - "author_name": "Roberta L DeBiasi", - "author_inst": "Children's National Hospital" - }, - { - "author_name": "Catriona Mowbray", - "author_inst": "Children's National Hospital" - }, - { - "author_name": "Stefanie Marguilies", - "author_inst": "Children's National Hospital" - }, - { - "author_name": "Adrienne Sherman", - "author_inst": "DC Department of Health" - }, - { - "author_name": "Jacqueline Reuben", - "author_inst": "DC Department of Health" - }, - { - "author_name": "Meghan Delaney", - "author_inst": "Children's National Hospital" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.30.21250822", "rel_title": "Understanding soaring coronavirus cases and the effect of contagion policies in the UK", @@ -981979,6 +980265,93 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.28.21250598", + "rel_title": "Nationwide Seroprevalence of SARS-CoV-2 in Saudi Arabia", + "rel_date": "2021-01-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.28.21250598", + "rel_abs": "BackgroundEstimated seroprevalence of Coronavirus Infectious Disease 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) is a critical evidence for a better evaluation of the virus spread and monitoring the progress of the COVID-19 pandemic in a population. In the Kingdom of Saudi Arabia (KSA), SARS-CoV-2 seroprevalence has been reported in specific regions, but an extensive nationwide study has not been reported. Here, we report a nationwide study to determine the prevalence of SARS-CoV-2 in the population of KSA during the pandemic, using serum samples from healthy blood donors, non-COVID patients and healthcare workers (HCWs) in six different regions of the kingdom, with addition samples from COVID-19 patients.\n\nMethodsA total of 11703 serum samples were collected from different regions of the KSA including; 5395 samples from residual healthy blood donors (D); 5877 samples from non-COVID patients collected through residual sera at clinical biochemistry labs from non-COVID patients (P); and 400 samples from consented HCWs. To determine the seroprevalence of SARS-CoV-2, all serum samples, in addition to positive control sera from RT-PCR confirmed COVID-19 patients, were subjected to in-house ELISA with a sample pooling strategy, which was further validated by testing individual samples that make up some of the pools, with a statistical estimation method to report seroprevalence estimates\n\nResultsOverall (combining D and P groups) seroprevalence estimate was around 11% in Saudi Arabia; and was 5.1% (Riyadh), 1.5% (Jazan), 18.4% (Qassim), 20.8% (Hail), 14.7% (ER; Alahsa), and 18.8% in Makkah. Makkah samples were only D group and had a rate of 24.4% and 12.8% in the cities of Makkah and Jeddah, respectively. The seroprevalence in Saudi Arabia across the sampled areas would be 12 times the COVID-19 infection rate. Among HCWs, 7.5% (4.95-10.16 CI 95%) had reactive antibodies to SARS-CoV-2 without reporting any previously confirmed infection. This was higher in HCWs with hypertension. The study also presents the demographics and prevalence of co-morbidities in HCWs and subset of non-COVID-19 population.\n\nConclusionOur study estimates the overall national serological prevalence of COVID-19 in Saudi Arabia to be 11%, with an apparent disparity between regions.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Naif Khalaf Alharbi", + "author_inst": "King Abdullah International Medical Research Center, Riyadh, Saudi Arabia. King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia." + }, + { + "author_name": "Suliman Alghnam", + "author_inst": "King Abdullah International Medical Research Center, Riyadh, Saudi Arabia. King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia." + }, + { + "author_name": "Abdullah Algaissi", + "author_inst": "Department of Medical Laboratories Technology, College of Applied Medical Sciences, Medical Research Center, Jazan University, Jazan 45142, Saudi Arabia" + }, + { + "author_name": "Hind Albalawi", + "author_inst": "King Abdullah International Medical Research Center, Riyadh, Kingdom of Saudi Arabia" + }, + { + "author_name": "Mohammed W Alenazi", + "author_inst": "King Abdullah International Medical Research Center, Riyadh, Kingdom of Saudi Arabia" + }, + { + "author_name": "Areeb M Albargawi", + "author_inst": "King Abdullah International Medical Research Center, Riyadh, Kingdom of Saudi Arabia" + }, + { + "author_name": "Abdullah G Alharbi", + "author_inst": "King Fahad Specialized Hospital, Qassim, Saudi Arabia." + }, + { + "author_name": "Abdulaziz Alhazmi", + "author_inst": "Department of Medical Laboratories Technology, College of Applied Medical Sciences, Medical Research Center, Jazan University, Jazan 45142, Saudi Arabia" + }, + { + "author_name": "Ali Al Qarni", + "author_inst": "King Abdulaziz Hospital, Ministry of National Guard Health Affairs, Alahsa, Saudi Arabia" + }, + { + "author_name": "Ali Alfarhan", + "author_inst": "King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia" + }, + { + "author_name": "Hossam M. Zowawi", + "author_inst": "King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia" + }, + { + "author_name": "Hind Alhatmi", + "author_inst": "King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia" + }, + { + "author_name": "Jahad Alghamdi", + "author_inst": "King Abdullah International Medical Research Center, Riyadh, Saudi Arabia. King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia." + }, + { + "author_name": "Fayhan Alroqi", + "author_inst": "King Abdullah International Medical Research Center, Riyadh, Kingdom of Saudi Arabia. King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arab" + }, + { + "author_name": "Yaseen M. Arabi", + "author_inst": "King Abdullah International Medical Research Center, Riyadh, Kingdom of Saudi Arabia. King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arab" + }, + { + "author_name": "Anwar M. Hashem", + "author_inst": "Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia. Vaccines and Immunotherapy Unit, King" + }, + { + "author_name": "Mohammed Bosaeed", + "author_inst": "King Abdullah International Medical Research Center, Riyadh, Kingdom of Saudi Arabia. King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arab" + }, + { + "author_name": "Omar Aldibasi", + "author_inst": "King Abdullah International Medical Research Center, Riyadh, Saudi Arabia. King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia." + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.27.21250637", "rel_title": "Evidence for SARS-CoV-2 Spike Protein in the Urine of COVID-19 patients", @@ -982551,57 +980924,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.29.428890", - "rel_title": "Recombinant production of a functional SARS-CoV-2 spike receptor binding domain in the green algae Chlamydomonas reinhardtii", - "rel_date": "2021-01-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.29.428890", - "rel_abs": "Recombinant production of viral proteins can be used to produce vaccine antigens or reagents to identify antibodies in patient serum. Minimally, these proteins must be correctly folded and have appropriate post-translation modifications. Here we report the production of the SARS-CoV-2 spike protein Receptor Binding Domain (RBD) in the green algae Chlamydomonas. RBD fused to a fluorescent reporter protein accumulates as an intact protein when targeted for ER-Golgi retention or secreted from the cell, while a chloroplast localized version is truncated, lacking the amino terminus. The ER-retained RBD fusion protein was able to bind the human ACE2 receptor, the host target of SARS-CoV-2, and was specifically out-competed by mammalian cell-produced recombinant RBD, suggesting that the algae produced proteins are sufficiently post-translationally modified to act as authentic SARS-CoV-2 antigens. Because algae can be grown at large scale very inexpensively, this recombinant protein may be a low cost alternative to other expression platforms.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Anthony J Berndt", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Tressa N Smalley", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Bijie Ren", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Amr Badary", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Ashley Sproles", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Francis Fields", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Yasin Torres-Tiji", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Vanessa Heredia", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Stephen P Mayfield", - "author_inst": "University of California, San Diego" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "synthetic biology" - }, { "rel_doi": "10.1101/2021.01.30.428921", "rel_title": "SARS-CoV-2 binding and neutralizing antibody levels after vaccination with Ad26.COV2.S predict durable protection in rhesus macaques", @@ -984041,6 +982363,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nutrition" }, + { + "rel_doi": "10.1101/2021.01.28.21250547", + "rel_title": "Ownership and COVID-19 in care homes for older people: A living systematic review of outbreaks, infections, and mortalities", + "rel_date": "2021-01-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.28.21250547", + "rel_abs": "BackgroundThe adult social care sector is increasingly outsourced to for-profit providers, who constitute the largest provider of care homes in many developed countries. During the COVID-19 pandemic, for-profit providers have been accused of failing their residents by prioritising profits over care, prevention, and caution, which has been reported to result in a higher prevalence of COVID-19 infections and deaths in for-profit care homes. Although many of these reports are anecdotal or based on news reports, there is a growing body of academic research investigating ownership variation across COVID-19 outcomes, which has not been systematically appraised and synthesised.\n\nObjectivesTo identify, appraise, and synthesise the available research on ownership variation in COVID-19 outcomes (outbreaks, infections, deaths, shortage of personal protective equipment (PPE) and staff) across for-profit, public, and non-profit care homes for older people, and to update our findings as new research becomes available.\n\nDesignLiving systematic review.\n\nMethodsThis review was prospectively registered with Prospero (CRD42020218673). We searched 17 databases and performed forward and backward citation tracking of all included studies. Search results were screened and reviewed in duplicate. Risk of bias (RoB) was assessed in duplicate according to the COSMOS-E guidance. Data was extracted by ABM and independently validated. The results were synthesised by country, RoB, and model adjustments, and visualised using harvest plots.\n\nResultsTwenty-nine studies across five countries were included, with 75% of included studies conducted in the Unites States. For-profit ownership was not consistently associated with a higher probability of a COVID-19 outbreak. However, there was compelling evidence of worse COVID-19 outcomes following an outbreak, with for-profit care homes having higher rates of accumulative infections and deaths. For-profit providers were also associated with shortages in PPE, which may have contributed to the higher incidence of infections and deaths in the early stages of the pandemic. Chain affiliation was often correlated with an increased risk of outbreak but was usually not reported to be associated with higher rates of deaths and infections.\n\nConclusionFor-profit ownership was a consistent risk factor for higher cumulative COVID-19 infections and deaths in the first wave of the pandemic. Thus, ownership and the characteristics associated with FP care home providers may present key regulatable factors that can be addressed to improve health outcomes in vulnerable populations and reduce health disparities. This review will be updated as new research becomes published, which may change the conclusion of our synthesis.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Anders M Bach-Mortensen", + "author_inst": "University of Oxford" + }, + { + "author_name": "Ani Movsisyan", + "author_inst": "LMU, Munich" + }, + { + "author_name": "Ben Verboom", + "author_inst": "University of Oxford" + }, + { + "author_name": "Michelle Degli Esposti", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2021.01.27.21250617", "rel_title": "More than 50 Long-term effects of COVID-19: a systematic review and meta-analysis", @@ -984397,41 +982750,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.27.21250048", - "rel_title": "A Rapid and Low-Cost protocol for the detection of B.1.1.7 lineage of SARS-CoV-2 by using SYBR Green-Based RT-qPCR", - "rel_date": "2021-01-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.27.21250048", - "rel_abs": "BackgroundThe new SARS-CoV-2 variant VUI (202012/01), identified recently in the United Kingdom (UK), exhibits a higher transmissibility rate compared to other variants, and a reproductive number 0.4 higher. In the UK, scientists were able to identify the increase of this new variant through the rise of false negative results for the spike (S) target using a three-target RT-PCR assay (TaqPath kit).\n\nMethodsTo control and study the current coronavirus pandemic, it is important to develop a rapid and low-cost molecular test to identify the aforementioned variant. In this work, we designed primer sets specific to SARS-CoV-2 variant VUI (202012/01) to be used by SYBR Green-based RT-PCR. These primers were specifically designed to confirm the deletion mutations {Delta}69/{Delta}70 in the spike and the {Delta}106/{Delta}107/{Delta}108 in the NSP6 gene. We studied 20 samples from positive patients, 16 samples displayed an S-negative profile (negative for S target and positive for N and ORF1ab targets) and four samples with S, N and ORF1ab positive profile.\n\nResultsOur results emphasized that all S-negative samples harbored the mutations {Delta}69/{Delta}70 and {Delta}106/{Delta}107/{Delta}108. This protocol could be used as a second test to confirm the diagnosis in patients who were already positive to COVID-19 but showed false negative results for S-gene.\n\nConclusionsThis technique may allow to identify patients carrying the VUI (202012/01) variant or a closely related variant, in case of shortage in sequencing.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Fadi Abdel-Sater", - "author_inst": "Laboratory of Molecular Biology and Cancer Immunology (Covid 19 Unit), FACULTY OF SCIENCE I, Lebanese University, HADATH, Beirut, LB 1003" - }, - { - "author_name": "Mahmoud Younes", - "author_inst": "Research Department, Beirut Cardiac institute, Old airport road, Beirut, Lebanon" - }, - { - "author_name": "Hassan Nassar", - "author_inst": "Bahman Hospital, Beirut, Lebanon" - }, - { - "author_name": "Paul Nguewa", - "author_inst": "University of Navarra, ISTUN Instituto de Salud Tropical, Department of Microbiology and Parasitology. IdiSNA (Navarra Institute for Health Research). c/ Irunla" - }, - { - "author_name": "Kassem Hamze", - "author_inst": "Laboratory of Molecular Biology and Cancer Immunology (Covid 19 Unit), FACULTY OF SCIENCE I, Lebanese University, HADATH, Beirut, LB 1003" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.27.21250551", "rel_title": "A prediction model for COVID-19 prevalence based on demographic and healthcare parameters in Iran", @@ -985523,6 +983841,57 @@ "type": "contradictory results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.01.29.428847", + "rel_title": "Information retrieval in an infodemic: the case of COVID-19 publications", + "rel_date": "2021-01-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.29.428847", + "rel_abs": "The COVID-19 pandemic has led to an exponential surge and an enormous amount of published literature, both accurate and inaccurate, a term usually coined as an infodemic. In the context of searching for COVID-19 related scientific literature, we present an information retrieval methodology for effectively finding relevant publications for different information needs. Our multi-stage information retrieval architecture combines probabilistic weighting models and re-ranking algorithms based on neural masked language models. The methodology was evaluated in the context of the TREC-COVID challenge, achieving competitive results with the top ranking teams participating in the competition. Particularly, the ranking combination of bag-of-words and language models significantly outperformed a BM25-based baseline model (16 percentage points for the NDCG@20 metric), correctly retrieving more than 16 out of the top 20 documents retrieved. The proposed pipeline could thus support the effective search and discovery of relevant information in the case of an infodemic.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Douglas Teodoro", + "author_inst": "HES-SO - University of Applied Sciences and Arts of Western Switzerland" + }, + { + "author_name": "Sohrab Ferdowsi", + "author_inst": "HES-SO - University of Applied Sciences and Arts of Western Switzerland" + }, + { + "author_name": "Nikolay Borissov", + "author_inst": "Riskclik AG, Bern, Switzerland" + }, + { + "author_name": "Elaham Kashani", + "author_inst": "Institute of Pathology, University of Bern, Bern, Switzerland" + }, + { + "author_name": "David Vicente Alvarez", + "author_inst": "HES-SO - University of Applied Sciences and Arts of Western Switzerland" + }, + { + "author_name": "Jenny Copara", + "author_inst": "HES-SO - University of Applied Sciences and Arts of Western Switzerland" + }, + { + "author_name": "Racha Gouareb", + "author_inst": "HES-SO - University of Applied Sciences and Arts of Western Switzerland" + }, + { + "author_name": "Nona Naderi", + "author_inst": "HES-SO University of Applied Sciences and Arts of Western Switzerland" + }, + { + "author_name": "Poorya Amini", + "author_inst": "Riskclik AG, Bern, Switzerland" + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2021.01.29.428808", "rel_title": "The evolutionary making of SARS-CoV-2", @@ -986127,81 +984496,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.01.27.428534", - "rel_title": "Unbiased interrogation of memory B cells from convalescent COVID-19 patients reveals a broad antiviral humoral response targeting SARS-CoV-2 antigens beyond the spike protein", - "rel_date": "2021-01-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.27.428534", - "rel_abs": "Patients who recover from SARS-CoV-2 infections produce antibodies and antigen-specific T cells against multiple viral proteins. Here, an unbiased interrogation of the anti-viral memory B cell repertoire of convalescent patients has been performed by generating large, stable hybridoma libraries and screening thousands of monoclonal antibodies to identify specific, high-affinity immunoglobulins (Igs) directed at distinct viral components. As expected, a significant number of antibodies were directed at the Spike (S) protein, a majority of which recognized the full-length protein. These full-length Spike specific antibodies included a group of somatically hypermutated IgMs. Further, all but one of the six COVID-19 convalescent patients produced class-switched antibodies to a soluble form of the receptor-binding domain (RBD) of S protein. Functional properties of anti-Spike antibodies were confirmed in a pseudovirus neutralization assay. Importantly, more than half of all of the antibodies generated were directed at non-S viral proteins, including structural nucleocapsid (N) and membrane (M) proteins, as well as auxiliary open reading frame-encoded (ORF) proteins. The antibodies were generally characterized as having variable levels of somatic hypermutations (SHM) in all Ig classes and sub-types, and a diversity of VL and VH gene usage. These findings demonstrated that an unbiased, function-based approach towards interrogating the COVID-19 patient memory B cell response may have distinct advantages relative to genomics-based approaches when identifying highly effective anti-viral antibodies directed at SARS-CoV-2.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Jillian M DiMuzio", - "author_inst": "Immunome, Inc." - }, - { - "author_name": "Baron C Heimbach", - "author_inst": "Immunome, Inc." - }, - { - "author_name": "Raymond J Howanski", - "author_inst": "Immunome, Inc." - }, - { - "author_name": "John P Dowling", - "author_inst": "Immunome, Inc." - }, - { - "author_name": "Nirja B Patel", - "author_inst": "Immunome, Inc." - }, - { - "author_name": "Noeleya Henriquez", - "author_inst": "Immunome, Inc." - }, - { - "author_name": "Chris Nicolescu", - "author_inst": "Immunome, Inc." - }, - { - "author_name": "Mitchell Nath", - "author_inst": "Immunome, Inc." - }, - { - "author_name": "Antonio Polley", - "author_inst": "Immunome, Inc." - }, - { - "author_name": "Jamie L Bingaman", - "author_inst": "Immunome, Inc." - }, - { - "author_name": "Todd Smith", - "author_inst": "Immunome, Inc." - }, - { - "author_name": "Benjamin C Harman", - "author_inst": "Immunome, Inc." - }, - { - "author_name": "Matthew K Robinson", - "author_inst": "Immunome, Inc." - }, - { - "author_name": "Michael J Morin", - "author_inst": "Immunome, Inc." - }, - { - "author_name": "Pavel A Nikitin", - "author_inst": "Immunome, Inc." - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2021.01.27.428541", "rel_title": "D614G Substitution of SARS-CoV-2 Spike Protein Increases Syncytium Formation and Viral Transmission via Enhanced Furin-mediated Spike Cleavage", @@ -987573,6 +985867,77 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.01.27.427998", + "rel_title": "Neutralization of spike 69/70 deletion, E484K, and N501Y SARS-CoV-2 by BNT162b2 vaccine-elicited sera", + "rel_date": "2021-01-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.27.427998", + "rel_abs": "We engineered three SARS-CoV-2 viruses containing key spike mutations from the newly emerged United Kingdom (UK) and South African (SA) variants: N501Y from UK and SA; 69/70-deletion+N501Y+D614G from UK; and E484K+N501Y+D614G from SA. Neutralization geometric mean titers (GMTs) of twenty BTN162b2 vaccine-elicited human sera against the three mutant viruses were 0.81- to 1.46-fold of the GMTs against parental virus, indicating small effects of these mutations on neutralization by sera elicited by two BNT162b2 doses.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Xuping Xie", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Yang Liu", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Jianying Liu", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Xianwen Zhang", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Jing Zou", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Camila R. Fontes-Garfias", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Hongjie Xia", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Kena A. Swanson", + "author_inst": "Pfizer" + }, + { + "author_name": "Mark Cutler", + "author_inst": "Pfizer" + }, + { + "author_name": "David Cooper", + "author_inst": "Pfizer" + }, + { + "author_name": "Vineet D Menachery", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Scott Weaver", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Philip Dormitzer", + "author_inst": "Pfizer" + }, + { + "author_name": "Pei-Yong Shi", + "author_inst": "University of Texas Medical Branch" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.01.26.426655", "rel_title": "An Updated Investigation Prior To COVID-19 Vaccination Program In Indonesia: Full-Length Genome Mutation Analysis Of SARS-CoV-2", @@ -987869,69 +986234,6 @@ "type": "new results", "category": "scientific communication and education" }, - { - "rel_doi": "10.1101/2021.01.21.21250249", - "rel_title": "Evaluation of six commercial SARS-CoV-2 Enzyme-Linked Immunosorbent assays for clinical testing and serosurveillance.", - "rel_date": "2021-01-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.21.21250249", - "rel_abs": "BackgroundSerological testing for SARS-CoV-2 complements nucleic acid tests for patient diagnosis and enables monitoring of population susceptibility to inform the COVID-19 pandemic response. As we move into the era of vaccines, the detection of neutralising antibody will become increasingly important. Many serological tests have been developed under emergency use authorization, but their reliability remains unclear.\n\nMethodsWe evaluated the performance of six commercially-available Enzyme-linked Immunosorbent Assays (ELISAs), including a surrogate virus neutralization test, for detection of SARS-CoV-2 immunoglobulins (IgA, IgM, IgG), total or neutralising antibodies and a subset of results were compared to microneutralisation.\n\nResultsFor sera collected > 14 days post-symptom onset the Wantai total Ab performed best with highest sensitivity 100% (95% confidence interval: 94.6-100) followed by 93.1% for Euroimmun NCP-IgG,93.1% for GenScript Surrogate Virus Neutralization Test, 90.3% for Euroimmun S1-IgG, 88.9% for Euroimmun S1-IgA and 83.3% for Wantai IgM. Specificity for the best performing assay was 99.5% and for the lowest 97.1%.\n\nConclusionWantai ELISA, detecting total immunoglobulins against SARS-CoV-2 receptor binding domain, had the best performance. Antibody target, timing and longevity of the immune response, and the objectives of testing should be considered in test choice. ELISAs should be used within a confirmatory testing algorithm to ensure reliable results. ELISAs provide high quality results, with flexibility for test numbers without the need for manufacturer specific analyzers.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Suellen R Nicholson", - "author_inst": "The Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Aust" - }, - { - "author_name": "Theo Karapanagiotidis", - "author_inst": "The Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Aust" - }, - { - "author_name": "Arseniy Khvorov", - "author_inst": "WHO Collaborating Centre for Reference and Research on Influenza at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia" - }, - { - "author_name": "Celia Douros", - "author_inst": "The Victorian Infectious Diseases Reference Laboratory, The Royal Melbourne Hospital, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Aust" - }, - { - "author_name": "Francesca Mordant", - "author_inst": "Department of Microbiology and Immunology, The University of Melbourne, WHO Collaborating Centre for Reference and Research on Influenza at The Peter Doherty In" - }, - { - "author_name": "Katherine Bond", - "author_inst": "Department of Microbiology, Royal Melbourne Hospital, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for " - }, - { - "author_name": "Deborah A Williamson", - "author_inst": "Department of Microbiology, Royal Melbourne Hospital, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for " - }, - { - "author_name": "Damian Francis John Purcell", - "author_inst": "Peter Doherty Institute for Infection and Immunity" - }, - { - "author_name": "Sharon Lewin", - "author_inst": "The Peter Doherty Institute for Infection and Immunity, Victorian Infectious Diseases Service, Royal Melbourne Hospital, Department of Infectious Diseases, Alfr" - }, - { - "author_name": "Sheena Sullivan", - "author_inst": "WHO Collaborating Centre for Reference and Research on Influenza at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia" - }, - { - "author_name": "Kanta Subbarao", - "author_inst": "Department of Microbiology and Immunology, WHO Collaborating Centre for Reference and Research on Influenza The University of Melbourne at The Peter Doherty In" - }, - { - "author_name": "Mike Catton", - "author_inst": "Victorian Infectious Diseases Reference Laboratory at the Peter Doherty Institute for Infection and Immunity, Melbourne" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.21.21249203", "rel_title": "SARS-CoV-2 recruits a haem metabolite to evade antibody immunity", @@ -989043,6 +987345,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.23.21250375", + "rel_title": "Preliminary Evidence on Long COVID in children", + "rel_date": "2021-01-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.23.21250375", + "rel_abs": "There is increasing evidence that adult patients diagnosed with acute COVID-19 suffer from Long COVID initially described in Italy.\n\nTo date, data on Long COVID in children are lacking.\n\nWe assessed persistent symptoms in pediatric patients previously diagnosed with COVID-19. More than a half reported at least one persisting symptom even after 120 days since COVID-19, with 42.6% being impaired by these symptoms during daily activities. Symptoms like fatigue, muscle and joint pain, headache, insomnia, respiratory problems and palpitations were particularly frequent, as also described in adults.\n\nThe evidence that COVID-19 can have long-term impact children as well, including those with asymptomatic/paucisymptomatic COVID-19, highlight the need for pediatricians, mental health experts and policy makers of implementing measures to reduce impact of the pandemic on childs health.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "danilo buonsenso", + "author_inst": "Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy" + }, + { + "author_name": "Daniel Munblit", + "author_inst": "Department of Paediatrics and Paediatric Infectious Diseases, Institute of Child's Health, Sechenov First Moscow State Medical University (Sechenov University)," + }, + { + "author_name": "Cristina De Rose", + "author_inst": "Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy" + }, + { + "author_name": "Dario Sinatti", + "author_inst": "Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy" + }, + { + "author_name": "Antonia Ricchiuto", + "author_inst": "Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy" + }, + { + "author_name": "Angelo Carfi", + "author_inst": "Geriatric Department, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy" + }, + { + "author_name": "Piero Valentini", + "author_inst": "Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2021.01.22.21249865", "rel_title": "Longevity of SARS-CoV-2 immune responses in haemodialysis patients and protection against reinfection", @@ -989643,85 +987988,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.21.21249906", - "rel_title": "Genomic Epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil", - "rel_date": "2021-01-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.21.21249906", - "rel_abs": "Brazil is the third country most affected by Covid-19 pandemic. In spite of this, viral evolution in municipality resolution is poorly understood in Brazil and it is crucial to understand the epidemiology of viral spread. We identified four main circulating lineages in Esteio (Southern Brazil) and their relationship with global, national and regional lineages using phylogenetics and phylodynamics inferences from 21 SARS-CoV-2 genome sequences. We provided a comprehensive view of viral mutations from a time- and age-representative sampling from May to October 2020, in Esteio (RS, Brazil), highlighting two frequent mutations in Spike glycoprotein (D614G and V1176F), an emergent mutation (E484K) in Spike Receptor Binding Domain (RBD) characteristic of the South African lineage B.1.351, and the adjacent replacement of 2 amino acids in Nucleocapsid phosphoprotein (R203K and G204R). A significant viral diversity was evidenced with the identification of 80 different SNPs. The E484K replacement was found in two genomes (9.5%) from samples obtained in mid-October, which is to our best knowledge the earliest description of E484K harboring SARS-CoV-2 in South Brazil. This mutation identified in a small municipality from the RS state demonstrates that it was probably widely distributed in the Brazilian territory, but went unnoticed so far by the lack of genomic surveillance in Brazil. The introduction of E484K mutants shows temporal correlation with later increases in new cases in our state. Importantly, since it has been associated with immune evasion and enhanced interaction with hACE-2, lineages containing this substitution must be the subject of intense surveillance. Our date demonstrates multiple introductions of the most prevalent lineages (B.1.1.33 and B.1.1.248) and the major role of community transmission in viral spreading and the establishment of Brazilian lineages. This represents an important contribution to the epidemiology of SARS-CoV-2.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Vinicius Bonetti Franceschi", - "author_inst": "Universidade Federal do Rio Grande do Sul" - }, - { - "author_name": "Gabriel Dickin Caldana", - "author_inst": "Universidade Federal de Ciencias da Saude de Porto Alegre" - }, - { - "author_name": "Amanda de Menezes Mayer", - "author_inst": "Universidade Federal do Rio Grande do Sul" - }, - { - "author_name": "Gabriela Bettella Cybis", - "author_inst": "Universidade Federal do Rio Grande do Sul" - }, - { - "author_name": "Carla Andretta Moreira Neves", - "author_inst": "Universidade Federal de Ciencias da Saude de Porto Alegre" - }, - { - "author_name": "Patricia Aline Grohs Ferrareze", - "author_inst": "Universidade Federal de Ciencias da Saude de Porto Alegre" - }, - { - "author_name": "Meriane Demoliner", - "author_inst": "Universidade Feevale" - }, - { - "author_name": "Paula Rodrigues de Almeida", - "author_inst": "Universidade Feevale" - }, - { - "author_name": "Juliana Schons Gularte", - "author_inst": "Universidade Feevale" - }, - { - "author_name": "Alana Witt Hansen", - "author_inst": "Universidade Feevale" - }, - { - "author_name": "Matheus Nunes Weber", - "author_inst": "Universidade Feevale" - }, - { - "author_name": "Juliane Deise Fleck", - "author_inst": "Universidade Feevale" - }, - { - "author_name": "Ricardo Ariel Zimerman", - "author_inst": "Irmandade Santa Casa de Misericordia de Porto Alegre" - }, - { - "author_name": "Livia Kmetzsch", - "author_inst": "Universidade Federal do Rio Grande do Sul" - }, - { - "author_name": "Fernando Rosado Spilki", - "author_inst": "Universidade Feevale" - }, - { - "author_name": "Claudia Elizabeth Thompson", - "author_inst": "Universidade Federal de Ciencias da Saude de Porto Alegre" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.22.21249812", "rel_title": "Magnitude and timing of the antiviral response determine SARS-CoV-2 replication early in infection", @@ -991213,6 +989479,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.26.21249544", + "rel_title": "COVID-19 Test Positivity Rate as a marker for hospital overload", + "rel_date": "2021-01-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.26.21249544", + "rel_abs": "The use of antigen tests for the diagnosis of COVID-19 in Italy has risen sharply in autumn 2020. Although, Italian regions like Alto Adige, Veneto, Toscana, Lazio, Piemonte and Marche did a large use of these tests for screening and surveillance purposes or for implementing diagnosis protocols, in addition to molecular tests, they were not reported in the statistics in the last months of 2020. As a consequence of this situation the test positivity rate (TPR) index, defined as the number of new positive cases divided by the number of tests, has lost in accuracy. Only in the recent days, starting from the 15th of January 2021, antigen tests have become part of the statistics for all the Italian regions. Despite the lack of data, we have noticed that TPR has a strong correlation with the number of patients admitted in hospitals, and that TPR peaks in general precede the peaks of hospitalized people which occur on average about 15 days later.\n\nIn this paper, we have deepened this intuition, analysing the TPR course and its relationship with the number of hospitalized people. To conduct the study we have defined a novel version of the TPR index which takes into account the number of tests done with respect to the population (considering both molecular and antigen tests), the number of infected individuals, and the number of patients healed. Successively, starting from a limited set of data which were made available in November 2020, we have reconstructed the antigen tests time series of four Italian regions, and we computed the TPR index for them.\n\nThe results show that TPR peaks precede peaks of hospitalized people in both the first and the second phases of the pandemic in Italy, provided that antigen tests are considered. Moreover, the TPR index trend, can be used to deduct important information on the course of the epidemic, and on the impact of COVID-19 in the health care system, which can be monitored in advance.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Mauro Gaspari", + "author_inst": "University of Bologna" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.23.21250242", "rel_title": "Super-Spreaders Out, Super-Spreading In: The Effects of Infectiousness Heterogeneity and Lockdowns on Herd Immunity", @@ -991581,57 +989866,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.25.21250505", - "rel_title": "Community structured model for vaccine strategies to control COVID19 spread: a mathematical study", - "rel_date": "2021-01-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.25.21250505", - "rel_abs": "Efforts to mitigate the COVID-19 pandemic have relied heavily on non-pharmaceutical interventions (NPIs), including physical distancing, hand hygiene, and mask-wearing. However, an effective vaccine is essential to containing the spread of the virus. The first doses were distributed at the end of 2020, but the efficacy, period of immunity it will provide, and percentage of coverage still remain unclear. We developed a compartment model to examine different vaccine strategies for controlling the spread of COVID-19. Our framework accounts for testing rates, test-turnaround times, and vaccination waning immunity. Using reported case data from the city of Toronto, Canada between Mar-Dec, 2020 we defined epidemic phases of infection using contact rates, which depend on individuals duration of time spent within the household, workplace/school, or community settings, as well as the probability of transmission upon contact. We investigated the impact of vaccine distribution by comparing different permutations of waning immunity, vaccine coverage and efficacy throughout various stages of NPIs relaxation in terms of cases, deaths, and household transmission, as measured using the basic reproduction number (R0). We observed that widespread vaccine coverage substantially reduced the number of cases and deaths. In order for NPIs to be relaxed 8 months after vaccine distribution, infection spread can be kept under control with either 60% vaccine coverage, no waning immunity, and 70% efficacy, or with 60% coverage with a 12-month waning immunity and 90% vaccine efficacy. Widespread virus resurgence can result when the immunity wanes under 3 months and/or when NPIs are relaxed in concomitance with vaccine distribution. In addition to vaccination, our analysis of R0 showed that the basic reproduction number is reduced by decreasing the tests turnaround time and transmission in the household. While we found that household transmission can decrease following the introduction of a vaccine, public health efforts to reduce test turnaround times remain important for virus containment. Our findings suggest that vaccinating two-thirds of the population with a vaccine that is at least 70% effective may be sufficient for controlling COVID-19 spread, as long as NPIs are not immediately relaxed.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Elena Aruffo", - "author_inst": "York University" - }, - { - "author_name": "Pei Yuan", - "author_inst": "York University" - }, - { - "author_name": "Yi Tan", - "author_inst": "York University" - }, - { - "author_name": "Evgenia Gatov", - "author_inst": "Toronto Public Health" - }, - { - "author_name": "Effie Gournis", - "author_inst": "Toronto Public Health" - }, - { - "author_name": "Sarah Collier", - "author_inst": "Toronto Public Health" - }, - { - "author_name": "Nick Ogden", - "author_inst": "Public Health Agency of Canada" - }, - { - "author_name": "Jacques B\u00e9lair", - "author_inst": "Universit\u00e9 de Montr\u00e9al" - }, - { - "author_name": "Huaiping Zhu", - "author_inst": "York University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.25.21250489", "rel_title": "Health impact of routine immunisation service disruptions and mass vaccination campaign suspensions caused by the COVID-19 pandemic: Multimodel comparative analysis of disruption scenarios for measles, meningococcal A, and yellow fever vaccination in 10 low- and lower middle-income countries", @@ -992883,6 +991117,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2021.01.20.21250145", + "rel_title": "Impact of COVID-19 Pandemic on Inpatient Rehabilitation and the Original Infection Control Measures for Rehabilitation Team", + "rel_date": "2021-01-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.20.21250145", + "rel_abs": "ObjectiveThis study aimed to investigate the impact of the coronavirus disease 2019 (COVID-19) pandemic on inpatient rehabilitation, and to determine the effectiveness of the original infection control measures implemented for the rehabilitation team.\n\nMethodsIn this single-center, retrospective, observational study, we calculated multiple rehabilitation indices of patients discharged from our rehabilitation ward between February 28 and May 25, 2020 when Hokkaido was initially affected by COVID-19, and compared them with those calculated during the same period in 2019. Fishers exact test and the Mann-Whitney U test were used for statistical analysis. We also verified the impact of implementing the original infection control measures for the rehabilitation team on preventing nosocomial infections.\n\nResultsA total of 93 patients (47 of 2020 group, 46 of 2019 group) were included. The median age was 87 and 88 years, respectively, with no differences in age, sex, and main disease between the groups. Training time per day in the ward in 2020 was significantly lower than that in 2019 (p = 0.013). No significant differences were found in the qualitative evaluation indices of Functional Independence Measure (FIM) score at admission, FIM gain, length of ward stay, FIM efficiency, and rate of discharge to home. None of the patients or staff members had confirmed COVID-19 during the study period.\n\nConclusionsEarly COVID-19 pandemic in Hokkaido affected the quantitative index for inpatient rehabilitation but not the qualitative indices. No symptomatic nosocomial COVID-19 infections were observed with our infection control measures.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Yukimasa Igawa", + "author_inst": "Aizen hospital" + }, + { + "author_name": "Takahiro Sugimoto", + "author_inst": "Aizen hospital" + }, + { + "author_name": "Hiromasa Horimoto", + "author_inst": "Aizen hospital" + }, + { + "author_name": "Yusuke Moriya", + "author_inst": "Aizen hospital" + }, + { + "author_name": "Masaki Okada", + "author_inst": "Aizen hospital" + }, + { + "author_name": "Yasuyuki Yamada", + "author_inst": "Aizen hospital" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "rehabilitation medicine and physical therapy" + }, { "rel_doi": "10.1101/2021.01.21.21249764", "rel_title": "Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil", @@ -993319,49 +991592,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.22.21249716", - "rel_title": "An interactive COVID-19 virus Mutation Tracker (CovMT) with a particular focus on critical mutations in the Receptor Binding Domain (RBD) region of the Spike protein", - "rel_date": "2021-01-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.22.21249716", - "rel_abs": "Almost one year has passed since the appearance of SARS-CoV-2, causing the COVID-19 pandemic. The number of confirmed SARS-Cov-2 cases worldwide has now reached [~]92 million, with 2 million reported deaths (https://covid19.who.int). Nearly 400,000 SARS-Cov-2 genomes were sequenced from COVID-19 samples and added to public resources such as GISAID (https://gisaid.org). With the vaccines becoming available or entering trials (https://covid19.trackvaccines.org), it is vital to keep track of mutations in the genome of SARS-CoV-2, especially in the Spike proteins Receptor Binding Domain (RBD) region, which could have a potential impact on disease severity and treatment strategies.1-3 In the wake of a recent increase in cases with a potentially more infective RBD mutation (N501Y) in the United Kingdom, countries worldwide are concerned about the spread of this or similar variants. Impressive sampling and timely increase in sequencing efforts related to COVID-19 in the United Kingdom (UK) helped detect and monitor the spread of the new N501Y variant. Similar sequencing efforts are needed in other countries for timely tracking of this or different variants. To track geographic sequencing efforts and mutations, with a particular focus on RBD region of the Spike protein, we present our daily updated COVID-19 virus Mutation Tracker system, see https://www.cbrc.kaust.edu.sa/covmt.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Intikhab Alam", - "author_inst": "Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah, Saudi Arabia." - }, - { - "author_name": "Aleksandar Radovanovic", - "author_inst": "Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah, Saudi Arabia." - }, - { - "author_name": "Roberto Incitti", - "author_inst": "Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah, Saudi Arabia." - }, - { - "author_name": "Allan Kamau", - "author_inst": "Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah, Saudi Arabia." - }, - { - "author_name": "Muhammed Alarawi", - "author_inst": "Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah, Saudi Arabia." - }, - { - "author_name": "Esam I. Azhar", - "author_inst": "Special Infectious Agent Unit (SIAU), King Fahd Medical Research Center (KFMRC), and Medical Laboratory Technology Department, Faculty of Applied Medical Scienc" - }, - { - "author_name": "Takashi Gojobori", - "author_inst": "Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Makkah, Saudi Arabia." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.22.21249945", "rel_title": "Acute and persistent symptoms in non-hospitalized PCR-confirmed COVID-19 patients", @@ -994893,6 +993123,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.21.21250045", + "rel_title": "Mental health and wellbeing amongst people with informal caring responsibilities across different time points during the COVID-19 pandemic: A population-based propensity score matching analysis", + "rel_date": "2021-01-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.21.21250045", + "rel_abs": "AimsDue to a prolonged period of national and regional lockdown measures during the coronavirus (COVID-19) pandemic, there has been an increase reliance on informal care and a consequent increase in care intensity for informal carers. In light of this, the current study compared the experiences of carers and non-carers on various mental health and wellbeing measures across 5 key time points during the pandemic.\n\nMethodsData analysed were from the UCL COVID -19 Social Study. Our study focused on 5 time points in England: (i) the first national lockdown (March-April 2020; N=12,053); (ii) the beginning of lockdown rules easing (May 2020; N=24,374); (iii) further easing (July 2020; N=21,395); (iv) new COVID-19 restrictions (September 2020; N=4,792); and (v) the three-tier system restrictions (October 2020; N=4,526). We considered 5 mental health and wellbeing measures-depression, anxiety, loneliness, life satisfaction and sense of worthwhile. Propensity score matching were applied for the analyses.\n\nResultsWe found that informal carers experienced higher levels of depressive symptoms and anxiety than non-carers across all time points. During the first national lockdown, carers also experienced a higher sense of life being worthwhile. No association was found between informal caring responsibilities and levels of loneliness and life satisfaction.\n\nConclusionGiven that carers are an essential national health care support, especially during a pandemic, it is crucial to integrate carers needs into healthcare planning and delivery. These results highlight there is a pressing need to provide adequate and targeted mental health support for carers during and following this pandemic.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Hei Wan Mak", + "author_inst": "University College London" + }, + { + "author_name": "Feifei Bu", + "author_inst": "University College London" + }, + { + "author_name": "Daisy Fancourt", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2021.01.22.21250320", "rel_title": "High-throughput sequencing of SARS-CoV-2 in wastewater provides insights into circulating variants", @@ -995393,25 +993650,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.01.25.428122", - "rel_title": "Profiling transcription factor sub-networks in type I interferon signaling and in response to SARS-CoV-2 infection", - "rel_date": "2021-01-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.25.428122", - "rel_abs": "Type I interferons (IFN /{beta}) play a central role in innate immunity to respiratory viruses, including coronaviruses. Genetic defects in type I interferon signaling were reported in a significant proportion of critically ill COVID-19 patients. Extensive studies on interferon-induced intracellular signal transduction pathways led to the elucidation of the Jak-Stat pathway. Furthermore, advances in gene expression profiling by microarrays have revealed that type I interferon rapidly induced multiple transcription factor mRNA levels. In this study, transcription factor profiling in the transcriptome was used to gain novel insights into the role of inducible transcription factors in response to type I interferon signaling in immune cells and in lung epithelial cells after SARS-CoV-2 infection. Modeling the interferon-inducible transcription factor mRNA data in terms of distinct sub-networks based on biological functions such as antiviral response, immune modulation, and cell growth revealed enrichment of specific transcription factors in mouse and human immune cells. The evolutionarily conserved core type I interferon gene expression consists of the inducible transcriptional factor mRNA of the antiviral response sub-network and enriched in granulocytes. Analysis of the type I interferon-inducible transcription factor sub-networks as distinct protein-protein interaction pathways revealed insights into the role of critical hubs in signaling. Interrogation of multiple microarray datasets revealed that SARS-CoV-2 induced high levels of IFN-beta and interferon-inducible transcription factor mRNA in human lung epithelial cells. Transcription factor mRNA of the three major sub-networks regulating antiviral, immune modulation, and cell growth were differentially regulated in human lung epithelial cell lines after SARS-CoV-2 infection and in the tissue samples of COVID-19 patients. A subset of type I interferon-inducible transcription factors and inflammatory mediators were specifically enriched in the lungs and neutrophils of COVID-19 patients. The emerging complex picture of type I IFN transcriptional regulation consists of a rapid transcriptional switch mediated by the Jak-Stat cascade and a graded output of the inducible transcription factor activation that enables temporal regulation of gene expression.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Ramana Chilakamarti", - "author_inst": "Dartmouth-Hitchcock Medical Center, Dartmouth Med School, Lebanon, New Hampshire" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.01.25.428097", "rel_title": "Longitudinal analysis of humoral immunity against SARS-CoV-2 Spike in convalescent individuals up to 8 months post-symptom onset", @@ -996511,6 +994749,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.20.21249905", + "rel_title": "A cross-sectional analysis of demographic and behavioral risk factors of SARS-CoV-2 antibody positivity among a sample of U.S. college students", + "rel_date": "2021-01-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.20.21249905", + "rel_abs": "BackgroundColleges and universities across the United States are developing and implementing data-driven prevention and containment measures against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Identifying risk factors for SARS-CoV-2 seropositivity could help to direct these efforts.\n\nObjectiveTo estimate the associations between demographic factors and social behaviors and SARS-CoV-2 seropositivity and self-reported positive SARS-CoV-2 diagnostic test.\n\nMethodsIn September 2020, we randomly sampled Indiana University Bloomington (IUB) undergraduate students. Participants completed a cross-sectional, online survey about demographics, SARS-CoV-2 testing history, relationship status, and risk behaviors. Additionally, during a subsequent appointment, participants were tested for SARS-CoV-2 antibodies using a fingerstick procedure and SARS-CoV-2 IgM/IgG rapid assay kit. We used unadjusted modified Poisson regression models to evaluate the associations between predictors of both SARS-CoV-2 seropositivity and self-reported positive SARS-CoV-2 infection history.\n\nResultsOverall, 1,076 students were included in the serological testing analysis, and 1,239 students were included in the SARS-CoV-2 infection history analysis. Current seroprevalence of SARS-CoV-2 was 4.6% (95% CI: 3.3%, 5.8%). Prevalence of self-reported SARS-CoV-2 infection history was 10.3% (95% CI: 8.6%, 12.0%). Greek membership, having multiple romantic partners, knowing someone in ones immediate environment with SARS-CoV-2 infection, drinking alcohol more than 1 day per week, and hanging out with more than 4 people when drinking alcohol increased both the likelihood of seropositivity and SARS-CoV-2 infection history.\n\nConclusionOur findings have implications for American colleges and universities and could be used to inform SARS-C0V-2 prevention and control strategies on such campuses.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Sina Kianersi", + "author_inst": "Indiana University School of Public Health-Bloomington" + }, + { + "author_name": "Christina Ludema", + "author_inst": "Indiana University School of Public Health-Bloomington" + }, + { + "author_name": "Jonathan T. Macy", + "author_inst": "Indiana University School of Public Health-Bloomington" + }, + { + "author_name": "Edlin Garcia", + "author_inst": "Indiana University School of Public Health-Bloomington" + }, + { + "author_name": "Chen Chen", + "author_inst": "Indiana University School of Public Health-Bloomington" + }, + { + "author_name": "Maya Luetke", + "author_inst": "Indiana University School of Public Health-Bloomington" + }, + { + "author_name": "Mason H. Lown", + "author_inst": "Indiana University School of Public Health-Bloomington" + }, + { + "author_name": "Molly Rosenberg", + "author_inst": "Indiana University School of Public Health-Bloomington" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.21.21250228", "rel_title": "Simulating the impact of different vaccination policies on the COVID-19 pandemic in New York City", @@ -996883,49 +995168,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2021.01.21.21250261", - "rel_title": "Using body temperature and variables commonly available in the EHR to predict acute infection: A proof-of-concept study showing improved pretest probability estimates for acute COVID-19 infection among discharged emergency department patients", - "rel_date": "2021-01-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.21.21250261", - "rel_abs": "ObjectivesObtaining body temperature is a quick and easy method to screen for acute infection such as COVID-19. Currently, the predictive value of body temperature for acute infection is inhibited by failure to account for other readily available variables that affect temperature values. In this proof-of-concept study, we sought to improve COVID-19 pretest probability estimation by incorporating covariates known to be associated with body temperature, including patient age, sex, comorbidities, month, time of day.\n\nMethodsFor patients discharged from an academic hospital emergency department after testing for COVID-19 in March and April of 2020, we abstracted clinical data. We reviewed physician documentation to retrospectively generate estimates of pretest probability for COVID-19. Using patients COVID-19 PCR test results as a gold standard, we compared AUCs of logistic regression models predicting COVID-19 positivity that used: 1) body temperature alone; 2) body temperature and pretest probability; 3) body temperature, pretest probability, and body temperature-relevant covariates. Calibration plots and bootstrap validation were used to assess predictive performance for model #3.\n\nResultsData from 117 patients were included. The models AUCs were: 1) 0.69 2) 0.72, and 3) 0.76, respectively. The absolute difference in AUC was 0.029 (95%CI -0.057 to 0.114, p=0.25) between model 2 and 1 and 0.038 (95%CI -0.021 to 0.097, p=0.10) between model 3 and 2.\n\nConclusionsBy incorporating covariates known to affect body temperature, we demonstrated improved pretest probability estimates of acute COVID-19 infection. Future work should be undertaken to further develop and validate our model in a larger, multi-institutional sample.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Carl T Berdahl", - "author_inst": "Cedars-Sinai Medical Center; Departments of Medicine and Emergency Medicine: Los Angeles, CA, US" - }, - { - "author_name": "An T Nguyen", - "author_inst": "Cedars-Sinai Medical Center; Department of Physical Medicine and Rehabilitation: Los Angeles, CA, US" - }, - { - "author_name": "Marcio A Diniz", - "author_inst": "Cedars-Sinai Health System; Biostatistics and Bionformatics Research Center: Los Angeles, CA, US" - }, - { - "author_name": "Andrew J Henreid", - "author_inst": "Cedars-Sinai Medical Center; Department of Medicine: Los Angeles, CA, US" - }, - { - "author_name": "Teryl K Nuckols", - "author_inst": "Cedars-Sinai Medical Center; Department of Medicine: Los Angeles, CA, US" - }, - { - "author_name": "Christopher P Libby", - "author_inst": "Cedars-Sinai Medical Center; EIS: Los Angeles, CA, US" - }, - { - "author_name": "Joshua M Pevnick", - "author_inst": "Cedars-Sinai Medical Center; Department of General Internal Medicine: Los Angeles, CA, US" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2021.01.21.21250264", "rel_title": "Abrupt increase in the UK coronavirus death-case ratio in December 2020", @@ -998157,6 +996399,93 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.01.21.427657", + "rel_title": "High-throughput screening of the ReFRAME, Pandemic Box, and COVID Box drug repurposing libraries against SARS-CoV2 nsp15 endoribonuclease to identify small-molecule inhibitors of viral activity.", + "rel_date": "2021-01-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.21.427657", + "rel_abs": "SARS-CoV-2 has caused a global pandemic, and has taken over 1.7 million lives as of mid-December, 2020. Although great progress has been made in the development of effective countermeasures, with several pharmaceutical companies approved or poised to deliver vaccines to market, there is still an unmet need of essential antiviral drugs with therapeutic impact for the treatment of moderate-to-severe COVID-19. Towards this goal, a high-throughput assay was used to screen SARS-CoV-2 nsp15 uracil-dependent endonuclease (endoU) function against 13 thousand compounds from drug and lead repurposing compound libraries. While over 80% of initial hit compounds were pan-assay inhibitory compounds, three hits were confirmed as nsp15 endoU inhibitors in the 1-20 M range in vitro. Furthermore, Exebryl-1, a {beta}-amyloid anti-aggregation molecule for Alzheimers therapy, was shown to have antiviral activity between 10 to 66 M, in VERO, Caco-2, and Calu-3 cells. Although the inhibitory concentrations determined for Exebryl-1 exceed those recommended for therapeutic intervention, our findings show great promise for further optimization of Exebryl-1 as an nsp15 endoU inhibitor and as a SARS-CoV-2 antiviral.\n\nAuthor summaryDrugs to treat COVID-19 are urgently needed. To address this, we searched libraries of drugs and drug-like molecules for inhibitors of an essential enzyme of the virus that causes COVID-19, SARS-CoV-2 nonstructural protein (nsp)15. We found several molecules that inhibited the nsp15 enzyme function and one was shown to be active in inhibiting the SARS-CoV-2 virus. This demonstrates that searching for SARS-CoV-2 nsp15 inhibitors can lead inhibitors of SARS-CoV-2, and thus therapeutics for COVID-19. We are currently working to see if these inhibitors could be turned into a drug to treat COVID-19.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Ryan Choi", + "author_inst": "Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington" + }, + { + "author_name": "Mowei Zhou", + "author_inst": "Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL)" + }, + { + "author_name": "Roger Shek", + "author_inst": "Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington" + }, + { + "author_name": "Jesse W Wilson", + "author_inst": "Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL)" + }, + { + "author_name": "Logan Tillery", + "author_inst": "Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington" + }, + { + "author_name": "Justin K Craig", + "author_inst": "Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington" + }, + { + "author_name": "Indraneel A Salukhe", + "author_inst": "Department of Microbiology, University of Washington" + }, + { + "author_name": "Sarah E Hickson", + "author_inst": "Department of Microbiology, University of Washington" + }, + { + "author_name": "Neeraj Kumar", + "author_inst": "Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL)" + }, + { + "author_name": "Rhema M James", + "author_inst": "Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL)" + }, + { + "author_name": "Garry W Buchko", + "author_inst": "Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory (PNNL), School of Molecular Bioscience, Washington State University" + }, + { + "author_name": "Ruilian Wu", + "author_inst": "Bioenergy and Biome Sciences, Los Alamos National Laboratory (LANL)" + }, + { + "author_name": "Sydney Huff", + "author_inst": "Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington" + }, + { + "author_name": "Tu-Trinh Nguyen", + "author_inst": "Calibr, a division of The Scripps Research Institute" + }, + { + "author_name": "Brett L Hurst", + "author_inst": "Institute for Antiviral Research, Utah State University" + }, + { + "author_name": "Sara Cherry", + "author_inst": "Department of Pathology and Laboratory Medicine, University of Pennsylvania" + }, + { + "author_name": "Lynn K Barrett", + "author_inst": "Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington" + }, + { + "author_name": "Wesley C Van Voorhis", + "author_inst": "Center for Emerging and Reemerging Infectious Diseases (CERID), University of Washington" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.01.20.427043", "rel_title": "Design of Specific Primer Sets for the Detection of B.1.1.7, B.1.351 and P.1 SARS-CoV-2 Variants using Deep Learning", @@ -998493,37 +996822,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.15.20249089", - "rel_title": "Physician Perceptions of Catching COVID-19", - "rel_date": "2021-01-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.15.20249089", - "rel_abs": "BackgroundRisk perception, influenced and biased by multiple factors, can affect behavior.\n\nObjectiveTo assess the variability of physician perceptions of catching COVID-19.\n\nDesignCross sectional, random stratified sample of physicians registered with Sermo, a global networking platform open to verified and licensed physicians.\n\nMain outcome measuresThe survey asked: \"What is your likelihood of catching COVID-19 in the next three months?\" The physicians were asked to give their best estimate as an exact percentage.\n\nResultsThe survey was completed by 1004 physicians (40 countries, 67 specialties, 49% frontline [e.g. ER, infectious disease, internal medicine]) with a mean (SD) age of 49.14 (12) years. Mean (SD) self-risk estimate was 32.3% {+/-} 26% with a range from 0% to 100% (Figure 1a). Risk estimates were higher in younger (<50 years) doctors and in non-US doctors versus their older and US counterparts (p<0.05 for all) (Figure 1b). Risk estimates were higher among front line versus non-frontline doctors (p<0.05). Risk estimates were higher for women than men (p<0.05) among respondents (60%) reporting gender.\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC=\"FIGDIR/small/20249089v2_fig1A.gif\" ALT=\"Figure 1A\">\nView larger version (17K):\norg.highwire.dtl.DTLVardef@7dd844org.highwire.dtl.DTLVardef@17241org.highwire.dtl.DTLVardef@f43cb2org.highwire.dtl.DTLVardef@bcd7f1_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1A.C_FLOATNO Distribution of risk prediction for overall sample (N=1004). Upper panel is a line box whisker and bottom panel shows the frequency distribution.\n\nC_FIG O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC=\"FIGDIR/small/20249089v2_fig1B.gif\" ALT=\"Figure 1B\">\nView larger version (21K):\norg.highwire.dtl.DTLVardef@51be7org.highwire.dtl.DTLVardef@16ae5fcorg.highwire.dtl.DTLVardef@12118a2org.highwire.dtl.DTLVardef@1d848c6_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure1B.C_FLOATNO Mean (SD) risk estimates by age, frontline status, and geographic region.\n\nC_FIG ConclusionsTo our knowledge, this is the first global study to document physician risk perceptions for catching COVID-19 and how it is impacted by age, gender, practice specialty and geography. Accurate calibration of risk perception is vital since both over- and underestimation of risk could impact physician behavior and have implications for public health.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "P. Murali Doraiswamy", - "author_inst": "Duke University School of Medicine" - }, - { - "author_name": "Mohan Chilukuri", - "author_inst": "University of North Carolina School of Medicine" - }, - { - "author_name": "Dan Ariely", - "author_inst": "Duke University" - }, - { - "author_name": "Alexandra Rose Linares", - "author_inst": "Duke University School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.17.21249912", "rel_title": "Electronic Computer-Based Model of Combined Ventilation Using a New Medical Device", @@ -999471,6 +997769,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.18.21250044", + "rel_title": "Blood transcriptional biomarkers of acute viral infection for detection of pre-symptomatic SARS-CoV 2 infection", + "rel_date": "2021-01-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.18.21250044", + "rel_abs": "We hypothesised that host-response biomarkers of viral infections may contribute to early identification of SARS-CoV-2 infected individuals, critical to breaking chains of transmission. We identified 20 candidate blood transcriptomic signatures of viral infection by systematic review and evaluated their ability to detect SARS-CoV-2 infection, compared to the gold-standard of virus PCR tests, among a prospective cohort of 400 hospital staff subjected to weekly testing when fit to attend work. The transcriptional signatures had limited overlap, but were mostly co-correlated as components of type 1 interferon responses. We reconstructed each signature score in blood RNA sequencing data from 41 individuals over sequential weeks spanning a first positive SARS-CoV-2 PCR, and after 6-month convalescence. A single blood transcript for IFI27 provided the highest accuracy for discriminating individuals at the time of their first positive viral PCR result from uninfected controls, with area under the receiver operating characteristic curve (AUROC) of 0.95 (95% confidence interval 0.91-0.99), sensitivity 0.84 (0.7-0.93) and specificity 0.95 (0.85-0.98) at a predefined test threshold. The test performed equally well in individuals with and without symptoms, correlated with viral load, and identified incident infections one week before the first positive viral PCR with sensitivity 0.4 (0.17-0.69) and specificity 0.95 (0.85-0.98). Our findings strongly support further urgent evaluation and development of blood IFI27 transcripts as a biomarker for early phase SARS-CoV-2 infection, for screening individuals such as contacts of index cases, in order to facilitate early case isolation and early antiviral treatments as they emerge.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Rishi K Gupta", + "author_inst": "Institute of Global Health, University College London, London, UK" + }, + { + "author_name": "Joshua Rosenheim", + "author_inst": "Division of Infection and Immunity, University College London, London, UK" + }, + { + "author_name": "Lucy C K Bell", + "author_inst": "University College London" + }, + { + "author_name": "Aneesh Chandran", + "author_inst": "Division of Infection and Immunity, University College London, London, UK" + }, + { + "author_name": "Jose Afonso Guerra-Assuncao", + "author_inst": "Division of Infection and Immunity, University College London, London, UK" + }, + { + "author_name": "Gabriele Pollara", + "author_inst": "Division of Infection and Immunity, University College London, London, UK" + }, + { + "author_name": "Matthew Whelan", + "author_inst": "Division of Infection and Immunity, University College London, London, UK" + }, + { + "author_name": "Jessica Artico", + "author_inst": "Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, UK, London, UK" + }, + { + "author_name": "George Joy", + "author_inst": "Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, UK, London, UK" + }, + { + "author_name": "Hibba Kurdi", + "author_inst": "Barts Heart Centre, St Bartholomew's Hospital, Barts Health NHS Trust, London, UK, London, UK" + }, + { + "author_name": "Daniel M Altmann", + "author_inst": "Department of Immunology and Inflammation, Imperial College London, London, UK" + }, + { + "author_name": "Rosemary Boyton", + "author_inst": "Lung Division, Royal Brompton & Harefield NHS Foundation Trust, London, UK" + }, + { + "author_name": "Mala Maini", + "author_inst": "Division of Infection and Immunity, University College London, London, UK" + }, + { + "author_name": "Aine McKnight", + "author_inst": "Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK." + }, + { + "author_name": "Jonathan Lambourne", + "author_inst": "Department of Infection, Barts Health NHS Trust, London, UK" + }, + { + "author_name": "Teresa Cutino-moguel", + "author_inst": "Department of Virology, Barts Health NHS Trust, London, UK" + }, + { + "author_name": "Charlotte Manisty", + "author_inst": "Institute of Cardiovascular Sciences, University College London, London, UK" + }, + { + "author_name": "Thomas Alexander Treibel", + "author_inst": "Institute of Cardiovascular Sciences, University College London, London, UK" + }, + { + "author_name": "James Moon", + "author_inst": "Institute of Cardiovascular Sciences, University College London, London, UK" + }, + { + "author_name": "Benjamin Chain", + "author_inst": "Division of Infection and Immunity, University College London, London, UK" + }, + { + "author_name": "Mahdad Noursadeghi", + "author_inst": "Division of Infection and Immunity, University College London, London, UK" + }, + { + "author_name": "- The COVIDsortium Investigators", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.15.21249756", "rel_title": "Factors associated with deaths due to COVID-19 versus other causes: population-based cohort analysis of UK primary care data and linked national death registrations within the OpenSAFELY platform", @@ -999819,33 +998220,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.18.21249998", - "rel_title": "The Association between Early Country-level Testing Capacity and Later COVID-19 Mortality Outcomes", - "rel_date": "2021-01-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.18.21249998", - "rel_abs": "BackgroundThe COVID-19 pandemic has overrun hospital systems while exacerbating economic hardship and food insecurity on a global scale. In an effort to understand how early action to find and control the virus is associated with cumulative outcomes, we explored how country-level testing capacity affects later COVID-19 mortality.\n\nMethodsWe used the Our World in Data database to explore testing and mortality records in 27 countries from December 31, 2019 to September 30, 2020; we applied ordinary-least squares regression with clustering on country to determine the association between early COVID-19 testing capacity (cumulative tests per case) and later COVID-19 mortality (time to specified mortality thresholds), adjusting for country-level confounders, including median age, GDP, hospital bed capacity, population density, and non-pharmaceutical interventions.\n\nResultsHigher early testing implementation, as indicated by more cumulative tests per case when mortality was still low, was associated with longer accrual time for higher per capita deaths. For instance, a higher cumulative number of tests administered per case at the time of 6 deaths per million persons was positively predictive of a longer time to reach 15 deaths per million, after adjustment for all confounders ({beta}=0.659; P=0.001).\n\nConclusionsCountries that developed stronger COVID-19 testing capacity at early timepoints, as measured by tests administered per case identified, experienced a slower increase of deaths per capita. Thus, this study operationalizes the value of testing and provides empirical evidence that stronger testing capacity at early timepoints is associated with reduced mortality and better pandemic control.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Sneha Kannoth", - "author_inst": "Columbia University, Mailman School of Public Health" - }, - { - "author_name": "Sasikiran Kandula", - "author_inst": "Columbia University, Mailman School of Public Health" - }, - { - "author_name": "Jeffrey Shaman", - "author_inst": "Columbia University, Mailman School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.17.21249837", "rel_title": "Modeling and Simulation: A study on predicting the outbreak of COVID- 19 in Saudi Arabia", @@ -1001357,6 +999731,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.01.19.427330", + "rel_title": "Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts", + "rel_date": "2021-01-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.19.427330", + "rel_abs": "Analysis of SARS-CoV-2 genetic diversity within infected hosts can provide insight into the generation and spread of new viral variants and may enable high resolution inference of transmission chains. However, little is known about temporal aspects of SARS-CoV-2 intrahost diversity and the extent to which shared diversity reflects convergent evolution as opposed to transmission linkage. Here we use high depth of coverage sequencing to identify within-host genetic variants in 325 specimens from hospitalized COVID-19 patients and infected employees at a single medical center. We validated our variant calling by sequencing defined RNA mixtures and identified a viral load threshold that minimizes false positives. By leveraging clinical metadata, we found that intrahost diversity is low and does not vary by time from symptom onset. This suggests that variants will only rarely rise to appreciable frequency prior to transmission. Although there was generally little shared variation across the sequenced cohort, we identified intrahost variants shared across individuals who were unlikely to be related by transmission. These variants did not precede a rise in frequency in global consensus genomes, suggesting that intrahost variants may have limited utility for predicting future lineages. These results provide important context for sequence-based inference in SARS-CoV-2 evolution and epidemiology.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Andrew L. Valesano", + "author_inst": "University of Michigan" + }, + { + "author_name": "Kalee E. Rumfelt", + "author_inst": "University of Michigan" + }, + { + "author_name": "Derek E. Dimcheff", + "author_inst": "University of Michigan" + }, + { + "author_name": "Christopher N. Blair", + "author_inst": "University of Michigan" + }, + { + "author_name": "William J. Fitzsimmons", + "author_inst": "University of Michigan" + }, + { + "author_name": "Joshua G. Petrie", + "author_inst": "University of Michigan" + }, + { + "author_name": "Emily Toth Martin", + "author_inst": "University of Michigan" + }, + { + "author_name": "Adam S. Lauring", + "author_inst": "University of Michigan" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.01.19.21249790", "rel_title": "COVID-19: making the best out of a forced transition to online medical teaching. A mixed methods study", @@ -1001733,77 +1000154,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2021.01.20.427105", - "rel_title": "Use Of Canine Olfactory Detection For COVID-19 Testing Study On U.A.E. Trained Detection Dog Sensitivity", - "rel_date": "2021-01-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.20.427105", - "rel_abs": "This study aimed to evaluate the sensitivity of 21 dogs belonging to different United Arab Emirates (UAE) Ministry of Interior (MOI), trained for COVID-19 olfactory detection.\n\nThe study involved 17 explosives detection dogs, two cadaver detection dogs and two dogs with no previous detection training. Training lasted two weeks before starting the validation protocol. Sequential five and seven-cone line-ups were used with axillary sweat samples from symptomatic COVID-19 individuals (SARS-CoV-2 PCR positive) and from asymptomatic COVID-19 negative individuals (SARS-CoV-2 PCR negative). A total of 1368 trials were performed during validation, including 151 positive and 110 negative samples. Each line-up had one positive sample and at least one negative sample. The dog had to mark the positive sample, randomly positioned behind one of the cones. The dog, handler and data recorder were blinded to the positive sample location.\n\nThe calculated overall sensitivities were between 71% and 79% for three dogs, between83% and 87% for three other dogs, and equal to or higher than 90% for the remaining 15 dogs (more than two thirds of the 21 dogs).\n\nAfter calculating the overall sensitivity for each dog using all line-ups, \"matched\" sensitivities were calculated only including line-ups containing COVID-19 positive and negative samples strictly comparable on confounding factors such as diabetes, anosmia, asthma, fever, body pain, diarrhoea, sex, hospital, method of sweat collection and sampling duration. Most of the time, the sensitivities increased after matching.\n\nPandemic conditions in the U.A.E., associated with the desire to use dogs as an efficient mass-pretesting tool has already led to the operational deployment of the study dogs.\n\nFuture studies will focus on comparatives fields-test results including the impact of the main COVID-19 comorbidities and other respiratory tract infections.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Dana H Al Marzooqi", - "author_inst": "Ministry of Interior. International affairs bureau. UAE" - }, - { - "author_name": "Clothilde Lecoq-Julien", - "author_inst": "Ecole Nationale Veterinaire Alfort. France" - }, - { - "author_name": "Hamad K Al Hammadi", - "author_inst": "Ministry of Interior. International affairs bureau. UAE" - }, - { - "author_name": "Guillaume Alvergnat", - "author_inst": "Ministry of Interior. International affairs bureau. UAE" - }, - { - "author_name": "Kalthoom M Al Blooshi", - "author_inst": "Ministry of Health and Prevention. Director of hospitals dept. UAE" - }, - { - "author_name": "Salah K Al Mazrooei", - "author_inst": "General Dept of Protective Security and Emergency. Director Dubai K9 Unit. UAE" - }, - { - "author_name": "Mohammed S Alhmoudi", - "author_inst": "Ministry of Interior of the U.A.E. International Affairs Bureau" - }, - { - "author_name": "Faisal M Al Ahbabi", - "author_inst": "Infectious Diseases Programs. Abu Dhabi Health Center. UAE" - }, - { - "author_name": "Yasser S Mohammed", - "author_inst": "Dubai Health Authority. UAE" - }, - { - "author_name": "Nasser M Al Falasi", - "author_inst": "General Dept of Protective Security and Emergency. Dubai K9 Unit. UAE" - }, - { - "author_name": "Noor M Almheiri", - "author_inst": "Head of Medical Services Unit Hospital Dpt. Ministry of Health and Prevention. UAE" - }, - { - "author_name": "Sumaya M Al Blooshi", - "author_inst": "Director of Nursing Department, Hospital Sector, Ministry of Health and Prevention. UAE" - }, - { - "author_name": "Quentin Muzzin", - "author_inst": "Ecole Nationale Veterinaire Alfort. France" - }, - { - "author_name": "Loic Desquilbet", - "author_inst": "Ecole Nationale Veterinaire Alfort. France" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "animal behavior and cognition" - }, { "rel_doi": "10.1101/2021.01.20.427368", "rel_title": "GRP78 binds SARS-CoV-2 Spike protein and ACE2 and GRP78 depleting antibody blocks viral entry and infection in vitro", @@ -1002991,6 +1001341,37 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2021.01.15.426908", + "rel_title": "Interferon-regulated genetic programs and JAK/STAT pathway activate the intronic promoter of the short ACE2 isoform in renal proximal tubules", + "rel_date": "2021-01-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.15.426908", + "rel_abs": "Recently, a short, interferon-inducible isoform of Angiotensin-Converting Enzyme 2 (ACE2), dACE2 was identified. ACE2 is a SARS-Cov-2 receptor and changes in its renal expression have been linked to several human nephropathies. These changes were never analyzed in context of dACE2, as its expression was not investigated in the kidney. We used Human Primary Proximal Tubule (HPPT) cells to show genome-wide gene expression patterns after cytokine stimulation, with emphasis on the ACE2/dACE2 locus. Putative regulatory elements controlling dACE2 expression were identified using ChIP-seq and RNA-seq. qRT-PCR differentiating between ACE2 and dACE2 revealed 300- and 600-fold upregulation of dACE2 by IFN and IFN{beta}, respectively, while full length ACE2 expression was almost unchanged. JAK inhibitor ruxolitinib ablated STAT1 and dACE2 expression after interferon treatment. Finally, with RNA-seq, we identified a set of genes, largely immune-related, induced by cytokine treatment. These gene expression profiles provide new insights into cytokine response of proximal tubule cells.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jakub Jankowski", + "author_inst": "Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, U.S. National Institutes of Health, Bethesda, MD 20892," + }, + { + "author_name": "Hye Kyung Lee", + "author_inst": "Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, U.S. National Institutes of Health, Bethesda, MD 20892," + }, + { + "author_name": "Julia Wilflingseder", + "author_inst": "Department of Physiology and Pathophysiology, University of Veterinary Medicine, Veterinarplatz 1, 1210, Vienna, Austria" + }, + { + "author_name": "Lothar Hennighausen", + "author_inst": "Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, U.S. National Institutes of Health, Bethesda, MD 20892," + } + ], + "version": "1", + "license": "", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2021.01.19.427256", "rel_title": "An all-solid-state heterojunction oxide transistor for the rapid detection of biomolecules and SARS-CoV-2 spike S1 protein", @@ -1003583,61 +1001964,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2021.01.19.427250", - "rel_title": "COVID-19 Knowledge, Attitudes, and Practices of United Arab Emirates Medical and Health Sciences Students: A Cross Sectional Study", - "rel_date": "2021-01-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.19.427250", - "rel_abs": "COVID-19 pandemic is the largest unprecedented viral pandemic of the 21st century. We aimed to study the COVID-19 knowledge, attitudes, and practices (KAP) among medical and health sciences students in the United Arab Emirates (UAE). We performed a cross-sectional study between 2nd June and 19th August 2020. The survey was developed using online Survey Monkey. The link was distributed via UAE University to all students and via WhatsApp(C) groups. The self-administered questionnaire was conducted in English and comprised of two parts: socio-demographic characteristics and KAP towards COVID-19. A total of 712 responses to the questionnaire were collected. 90% (n=695) were under-graduate, while 10% (n=81) were post-graduate students. Majority (87%, n=647) stated that they obtained COVID-19 information from multiple reliable sources. They were highly knowledgeable about COVID-19 pandemic but 76% (n=539) did not recognize its routes of transmission. 63% (n=431) were worried of getting COVID-19, while 92% (n=633)) were worried that a family member could get infected with the virus. 97% (n=655) took precautions when accepting home deliveries, 94% (n=637) had been washing their hands more frequently, and 95% (n=643) had been wearing face masks. In conclusion, participants showed high levels of knowledge and awareness about COVID-19. They were worried about getting infected themselves or their family members, and had good practices against COVID-19.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Noura Baniyas", - "author_inst": "College of Medicine" - }, - { - "author_name": "Mohamud M Sheek-Hussein", - "author_inst": "UAE University: United Arab Emirates University" - }, - { - "author_name": "Nouf Al Kaabi", - "author_inst": "College of Medicine" - }, - { - "author_name": "Maitha Al Shamsi", - "author_inst": "College of Medicine" - }, - { - "author_name": "Maitha M Al Neyadi", - "author_inst": "College of Medicine" - }, - { - "author_name": "Rauda Al Khoori", - "author_inst": "College of Medicine" - }, - { - "author_name": "Suad Ajab", - "author_inst": "College of Medicine" - }, - { - "author_name": "Muhammad Abid", - "author_inst": "College of Medicine" - }, - { - "author_name": "Michael Grivna", - "author_inst": "College of Medicine" - }, - { - "author_name": "Fikri M Abu Zidan", - "author_inst": "UAE University: United Arab Emirates University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "scientific communication and education" - }, { "rel_doi": "10.1101/2021.01.16.21249632", "rel_title": "Acute Endotheliitis (Type 3 Hypersensitivity Vasculitis) in Ten COVID-19 Autopsy Brains", @@ -1005765,6 +1004091,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2021.01.14.21249797", + "rel_title": "Modelling the Spreading of the SARS-CoV-2 in Presence of the Lockdown and Quarantine Measures by a \"Kinetic-Type Reactions\" Approach", + "rel_date": "2021-01-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.14.21249797", + "rel_abs": "We propose a realistic model for the evolution of the COVID-19 pandemic subject to the lockdown and quarantine measures, which takes into account the time-delay for recovery or death processes. The dynamic equations for the entire process are derived by adopting a kinetic-type reactions approach. More specifically, the lockdown and the quarantine measures are modelled by some kind of inhibitor reactions where susceptible and infected individuals can be trapped into inactive states. The dynamics for the recovered people is obtained by accounting people who are only traced back to hospitalised infected people. To get the evolution equation we take inspiration from the Michaelis-Mentens enzyme-substrate reaction model (the so-called MM reaction) where the enzyme is associated to the available hospital beds, the substrate to the infected people, and the product to the recovered people, respectively. In other words, everything happens as if the hospitals beds act as a catalyzer in the hospital recovery process. Of course, in our case the reverse MM reactions has no sense in our case and, consequently, the kinetic constant is equal to zero. Finally, the O.D.E.s for people tested positive to COVID-19 is simply modelled by the following kinetic scheme S + I {Rightarrow} 2I with I {Rightarrow} R or I {Rightarrow} D, with S, I, R, and D denoting the compartments Susceptible, Infected, Recovered, and Deceased people, respectively. The resulting kinetic-type equations provide the O.D.E.s, for elementary reaction steps, describing the number of the infected people, the total number of the recovered people previously hospitalised, subject to the lockdown and the quarantine measure, and the total number of deaths. The model foresees also the second wave of Infection by Coronavirus. The tests carried out on real data for Belgium, France and Germany confirmed the correctness of our model.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Giorgio SONNINO", + "author_inst": "Universite' Libre de Bruxelles (ULB), Department of Physics" + }, + { + "author_name": "Philippe PEETERS", + "author_inst": "Universite' Libre de Bruxelles (ULB), Department de Physique" + }, + { + "author_name": "Pasquale NARDONE", + "author_inst": "Universite' Libre de Bruxelles (ULB), Department of Physics" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.13.21249773", "rel_title": "Optimal piecewise constant vaccination and lockdown policies for COVID-19", @@ -1006088,61 +1004441,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2021.01.15.21249863", - "rel_title": "How to best test suspected cases of COVID-19: an analysis of the diagnostic performance of RT-PCR and alternative molecular methods for the detection of SARS-CoV-2", - "rel_date": "2021-01-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.15.21249863", - "rel_abs": "As COVID-19 testing is rolled out increasingly widely, the use of a range of alternative testing methods will be beneficial in ensuring testing systems are resilient and adaptable to different clinical and public health scenarios. Here, we compare and discuss the diagnostic performance of a range of different molecular assays designed to detect the presence of SARS-CoV-2 infection in people with suspected COVID-19. Using findings from a systematic review of 103 studies, we categorised COVID-19 molecular assays into 12 different test classes, covering point-of-care tests, various alternative RT-PCR protocols, and alternative methods such as isothermal amplification. We carried out meta-analyses to estimate the diagnostic accuracy and clinical utility of each test class. We also estimated the positive and negative predictive values of all diagnostic test classes across a range of prevalence rates. Using previously validated RT-PCR assays as a reference standard, 11 out of 12 classes showed a summary sensitivity estimate of at least 92% and a specificity estimate of at least 99%. Several diagnostic test classes were estimated to have positive predictive values of 100% throughout the investigated prevalence spectrum, whilst estimated negative predictive values were more variable and sensitive to disease prevalence. We also report the results of clinical utility models that can be used to determine the information gained from a positive and negative test result in each class, and whether each test is more suitable for confirmation or exclusion of disease. Our analysis suggests that several tests exist that are suitable alternatives to standard RT-PCR and we discuss scenarios in which these could be most beneficial, such as where time to test result is critical or, where resources are constrained. However, we also highlight methodological concerns with the design and conduct of many included studies, and also the existence of likely publication bias for some test classes. Our results should be interpreted with these shortcomings in mind. Furthermore, our conclusions on test performance are limited to their use in symptomatic populations: we did not identify sufficient suitable data to allow analysis of testing in asymptomatic populations.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Adrian Mironas", - "author_inst": "Health Technology Wales" - }, - { - "author_name": "David Jarrom", - "author_inst": "Health Technology Wales" - }, - { - "author_name": "Evan Campbell", - "author_inst": "Healthcare Improvement Scotland" - }, - { - "author_name": "Jennifer Washington", - "author_inst": "Health Technology Wales" - }, - { - "author_name": "Sabine Ettinger", - "author_inst": "HTA Austria - Austrian Institute for Health Technology Assessment GmbH" - }, - { - "author_name": "Ingrid Wilbacher", - "author_inst": "Federation of Social Insurances" - }, - { - "author_name": "Gottfried Endel", - "author_inst": "Federation of Social Insurances" - }, - { - "author_name": "Hrvoje Vrazic", - "author_inst": "Federation of Social Insurances" - }, - { - "author_name": "Susan Myles", - "author_inst": "Health Technology Wales" - }, - { - "author_name": "Matthew Prettyjohns", - "author_inst": "Health Technology Wales" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2021.01.15.21249868", "rel_title": "Antibiotic Prescribing Patterns at COVID-19 Dedicated Wards in Bangladesh: A Single Center Point-Prevalence Survey", @@ -1007550,6 +1005848,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.15.426787", + "rel_title": "Correlation of Computerized Tomography (CT) Severity Score for COVID-19 pneumonia with Clinical Outcomes", + "rel_date": "2021-01-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.15.426787", + "rel_abs": "IntroductionVarious CT severity scores have already been described in literature since the start of this pandemic. One pertinent issue with all of the previously described severity scores is their relative challenging calculation and variance in inter-observer agreement. The severity score proposed in our study is relatively simpler, easier to calculate and apart from a trained radiologist, can easily be calculated even by physicians with good inter-observer agreement. Therefore, a rapid CT severity score calculation can give a clue to physician about possible clinical outcome without being dependent on radiologist who may not be readily available especially in third world countries.\n\nObjectiveThe objective of this study is to develop a simple CT severity score (CT-SS) with good inter-observer agreement and access its correlation with clinical outcome.\n\nMethodsThis retrospective study was conducted by the Department of Radiology and Internal Medicine, at the Aga Khan University Hospital Karachi, from April 2020 to August 2020. Non-probability consecutive sampling was used to include all patients who were positive for COVID-19 on PCR, and underwent CT chest examination at AKUH. Severity of disease was calculated in each lobe on the basis of following proposed CT severity scoring system (CT-SS). For each lobe the percentage of involvement by disease was scored - 0% involvement was scored 0, <50% involvement was scored 1 and >50% involvement was scored 2. Maximum score for one lobe was 2 and hence total maximum overall score for all lobes was 10. Continuous data was represented using mean and standard deviation, and compared using independent sample t-tests. Categorical data was represented using frequencies and percentages, and compared using Chi-squared tests. Inter-observer reliability between radiologist and COVID intensivist for the 10 point CT-SS rated on 0-10 was assessed using the Kappa statistic. A p-value < 0.05 was considered significant for all analyses.\n\nResultsA total of 73 patients were included, the majority male (58.9%) with mean age 55.8 {+/-} 13.93 years. The CT-SS rated on 0-10 showed substantial inter-observer reliability between radiologist and intensivist with a Kappa statistic of 0.78. Patients with CT-SS 8-10 had a significantly higher ICU admission & intubation rate (53.8% vs. 23.5%) and mortality rate (35.9% vs. 11.8%; p = 0.017), as compared to those with CT-SS 0-7.\n\nConclusionWe conclude that the described CT severity score (CT-SS) is a quick, effective and easily reproducible tool for prediction of adverse clinical outcome in patients with COVID 19 pneumonia. The tool shows good inter-observer agreement when calculated by radiologist and physician independently.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Kiran Hilal", + "author_inst": "Aga Khan University Hospital" + }, + { + "author_name": "Jehanzeb Shahid", + "author_inst": "Aga Khan University Hospital" + }, + { + "author_name": "Abdullah Aameen", + "author_inst": "Aga Khan University Hospital" + }, + { + "author_name": "Russell Seth Martins", + "author_inst": "Aga Khan University Medical College Pakistan" + }, + { + "author_name": "Avinash Nankani", + "author_inst": "Dow University of Health Sciences" + }, + { + "author_name": "Ainan Arshad", + "author_inst": "Aga Khan University Hospital" + }, + { + "author_name": "Haq Tu", + "author_inst": "Aga Khan University Hospital" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2021.01.12.426407", "rel_title": "Distinct Patterns of Emergence of SARS-CoV-2 Spike Variants including N501Y in Clinical Samples in Columbus Ohio", @@ -1008018,89 +1006359,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.10.20248871", - "rel_title": "Emergence of multiple SARS-CoV-2 mutations in an immunocompromised host", - "rel_date": "2021-01-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.10.20248871", - "rel_abs": "Prolonged shedding of infectious SARS-CoV-2 has recently been reported in a number of immunosuppressed individuals with COVID-19. Here, we describe the detection of high levels of replication-competent SARS-CoV-2 in specimens taken from the respiratory tract of a B-cell depleted patient up to 154 days after initial COVID-19 diagnosis concomitant with the development of high mutation rate. In this patient, a total of 11 nonsynonymous mutations were detected in addition to the Y144 deletion in the spike protein of SARS-CoV-2.\n\nVirus evolution studies revealed a dramatic diversification in viral population coinciding with treatment with convalescent plasma and clinical respiratory deterioration. Our findings highlight the urgent need for continuous real-time surveillance of genetic changes of SARS-CoV-2 adaptation alongside immunological investigations in patients with severely compromised humoral responses who may shed infectious virus over prolonged periods of time.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Elham Khatamzas", - "author_inst": "Department of Medicine III, LMU Hospital Munich, Germany" - }, - { - "author_name": "Alexandra Rehn", - "author_inst": "Bundeswehr, Institute of Microbiology, Munich, Germany and German Center for Infection Research (DZIF), Partner Site Munich, Germany" - }, - { - "author_name": "Maximilian Muenchhoff", - "author_inst": "Max von Pettenkofer Institute and Gene Center, Virology, Faculty of Medicine, LMU Munich, Germany and COVID-19 Registry of the LMU Munich (CORKUM), University H" - }, - { - "author_name": "Johannes Hellmuth", - "author_inst": "Department of Medicine III, LMU Hospital Munich, Germany; COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU, Munich, Germany" - }, - { - "author_name": "Erik Gaitzsch", - "author_inst": "Department of Medicine III, LMU Hospital Munich, Germany" - }, - { - "author_name": "Tobias Weiglein", - "author_inst": "Department of Medicine III, LMU Hospital Munich, Germany" - }, - { - "author_name": "Enrico Georgi", - "author_inst": "Bundeswehr, Institute of Microbiology, Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Germany" - }, - { - "author_name": "Clemens Scherer", - "author_inst": "COVID-19 Registry of the LMU Munich (CORKUM), University Hospital, LMU, Munich, Germany; Department of Medicine I, LMU Hospital Munich, Germany" - }, - { - "author_name": "Stephanie Stecher", - "author_inst": "Department of Medicine II, LMU Hospital Munich, Germany" - }, - { - "author_name": "Oliver Weigert", - "author_inst": "Department of Medicine III, LMU Hospital Munich, Germany; German Cancer Consortium (DKTK), Munich, Germany; German Cancer Research Center (DKFZ), Heidelberg, Ge" - }, - { - "author_name": "Philipp Girl", - "author_inst": "Bundeswehr, Institute of Microbiology, Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Germany" - }, - { - "author_name": "Sabine Zange", - "author_inst": "German Center for Infection Research (DZIF), Partner Site Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Germany" - }, - { - "author_name": "Oliver T. Keppler", - "author_inst": "Max von Pettenkofer Institute and Gene Center, Virology, Faculty of Medicine, LMU Munich, Germany; German Center for Infection Research (DZIF), Partner Site Mun" - }, - { - "author_name": "Joachim Stemmler", - "author_inst": "Department of Medicine III, LMU Hospital Munich, Germany" - }, - { - "author_name": "Michael Bergwelt-Baildon", - "author_inst": "Department of Medicine III, LMU Hospital Munich, Germany; German Cancer Consortium (DKTK), Munich, Germany; German Cancer Research Center (DKFZ), Heidelberg, Ge" - }, - { - "author_name": "Roman Woelfel", - "author_inst": "Bundeswehr, Institute of Microbiology, Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Germany" - }, - { - "author_name": "Markus Antwerpen", - "author_inst": "Bundeswehr, Institute of Microbiology, Munich, Germany; German Center for Infection Research (DZIF), Partner Site Munich, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.11.20248606", "rel_title": "An optimised protocol for detection of SARS-COV-2 in stool", @@ -1009512,6 +1007770,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.14.21249690", + "rel_title": "Mapping SARS-CoV-2 Antibody Epitopes in COVID-19 Patients with a Multi-Coronavirus Protein Microarray", + "rel_date": "2021-01-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.14.21249690", + "rel_abs": "The emergence and rapid worldwide spread of SARS-CoV-2 has accelerated research and development for controlling the pandemic. A multi-coronavirus protein microarray was created containing full-length proteins, overlapping protein fragments of varying lengths and peptide libraries from SARS-CoV-2 and four other human coronaviruses. Sera from confirmed COVID-19 patients as well as unexposed individuals were applied to multi-coronavirus arrays to identify specific antibody reactivity. High level IgG, IgM and IgA reactivity to structural proteins S, M and N, as well as accessory proteins, of SARS-CoV-2 were observed that was specific to COVID-19 patients. Overlapping 100, 50 and 30 amino acid fragments of SARS-CoV-2 proteins identified antigenic regions. Numerous proteins of SARS-CoV, MERS-CoV and the endemic human coronaviruses, HCoV-NL63 and HCoV-OC43 were also more reactive with IgG, IgM and IgA in COVID-19 patient sera than in unexposed control sera, providing further evidence of immunologic cross-reactivity between these viruses. The multi-coronavirus protein microarray is a useful tool for mapping antibody reactivity in COVID-19 patients.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "David Camerini", + "author_inst": "Antigen Discovery Innc." + }, + { + "author_name": "Arlo Z Randall", + "author_inst": "Antigen Discovery Inc." + }, + { + "author_name": "Krista Trappl-Kimmons", + "author_inst": "Antigen Discovery Incorporated" + }, + { + "author_name": "Amit Oberai", + "author_inst": "Antigen Discovery Inc." + }, + { + "author_name": "Christopher Hung", + "author_inst": "Antigen Discovery Inc" + }, + { + "author_name": "Joshua Edgar", + "author_inst": "Antigen Discovery Inc." + }, + { + "author_name": "Adam Shandling", + "author_inst": "Antigen Discovery Inc." + }, + { + "author_name": "Vu Huynh", + "author_inst": "Antigen Discovery Inc." + }, + { + "author_name": "Andy A Teng", + "author_inst": "Antigen Discovery Inc." + }, + { + "author_name": "Gary Hermanson", + "author_inst": "Antigen Discovery Inc." + }, + { + "author_name": "Jozelyn V Pablo", + "author_inst": "Antigen Discovery Inc." + }, + { + "author_name": "Megan M Stumpf", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Sandra N Lester", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Jennifer Harcourt", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Azaibi Tamin", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Mohammed Rasheed", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Natalie J Thornburg", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Panayampalli S Satheshkumar", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Xiaowu Liang", + "author_inst": "Antigen Discovery Inc." + }, + { + "author_name": "Richard B Kennedy", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Angela Yee", + "author_inst": "Antigen Discovery Inc." + }, + { + "author_name": "Michael Townsend", + "author_inst": "Centers for Disease Control and Prevention" + }, + { + "author_name": "Joseph J Campo", + "author_inst": "Antigen Discovery Inc." + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.13.21249412", "rel_title": "Real-time optical analysis of a colorimetric LAMP assay for SARS-CoV-2 in saliva with a handheld instrument improves accuracy compared to endpoint assessment", @@ -1009972,153 +1008337,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2021.01.14.21249831", - "rel_title": "Increased peripheral blood neutrophil activation phenotypes and NETosis in critically ill COVID-19 patients", - "rel_date": "2021-01-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.14.21249831", - "rel_abs": "BackgroundIncreased inflammation is a hallmark of COVID-19, with pulmonary and systemic inflammation identified in multiple cohorts of patients. Definitive cellular and molecular pathways driving severe forms of this disease remain uncertain. Neutrophils, the most numerous leukocytes in blood circulation, can contribute to immunopathology in infections, inflammatory diseases and acute respiratory distress syndrome (ARDS), a primary cause of morbidity and mortality in COVID-19. Changes in multiple neutrophil functions and circulating cytokine levels over time during COVID-19 may help define disease severity and guide care and decision making.\n\nMethodsBlood was obtained serially from critically ill COVID-19 patients for 11 days. Neutrophil oxidative burst, neutrophil extracellular trap formation (NETosis), phagocytosis and cytokine levels were assessed ex vivo. Lung tissue was obtained immediately post-mortem for immunostaining.\n\nResultsElevations in neutrophil-associated cytokines IL-8 and IL-6, and general inflammatory cytokines IP-10, GM-CSF, IL-1b, IL-10 and TNF, were identified in COVID-19 plasma both at the first measurement and at multiple timepoints across hospitalization (p < 0.0001). Neutrophils had exaggerated oxidative burst (p < 0.0001), NETosis (p < 0.0001) and phagocytosis (p < 0.0001) relative to controls. Increased NETosis correlated with both leukocytosis and neutrophilia. Neutrophils and NETs were identified within airways and alveoli in the lung parenchyma of 40% of SARS-CoV-2 infected lungs. While elevations in IL-8 and ANC correlated to COVID-19 disease severity, plasma IL-8 levels alone correlated with death.\n\nConclusionsCirculating neutrophils in COVID-19 exhibit an activated phenotype with increased oxidative burst, NETosis and phagocytosis. Readily accessible and dynamic, plasma IL-8 and circulating neutrophil function may be potential COVID-19 disease biomarkers.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Jorge A. Masso-Silva PhD", - "author_inst": "VA San Diego Healthcare System" - }, - { - "author_name": "Alexander Moshensky BS", - "author_inst": "VA San Diego Healthcare System" - }, - { - "author_name": "Michael T. Y. Lam MD PhD", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Mazen Odish MD", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Arjun Patel MBBS", - "author_inst": "VA San Diego Healthcare System" - }, - { - "author_name": "Le Xu PhD", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Emily Hansen MS", - "author_inst": "Rady Childrens Hospital" - }, - { - "author_name": "Samantha Trescott BS", - "author_inst": "Rady Childrens Hospital" - }, - { - "author_name": "Celina Nguyen BS", - "author_inst": "Rady Childrens Hospital" - }, - { - "author_name": "Roy Kim BS", - "author_inst": "Rady Childrens Hospital" - }, - { - "author_name": "Katherine Perofsky MD", - "author_inst": "Rady Childrens Hospital" - }, - { - "author_name": "Samantha Perera N/A", - "author_inst": "VA San Diego Healthcare System" - }, - { - "author_name": "Lauren Ma BS", - "author_inst": "VA San Diego Healthcare System" - }, - { - "author_name": "Josephine Pham N/A", - "author_inst": "VA San Diego Healthcare System" - }, - { - "author_name": "Mark Rolfsen MD", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Jarod Olay MS", - "author_inst": "VA San Diego Healthcare System" - }, - { - "author_name": "John Shin BS", - "author_inst": "VA San Diego Healthcare System" - }, - { - "author_name": "Jennifer M. Dan MD PhD", - "author_inst": "La Jolla Institute of Allergy and Immunology" - }, - { - "author_name": "Robert Abbott PhD", - "author_inst": "La Jolla Institute of Allergy and Immunology" - }, - { - "author_name": "Sydney Ramirez MD PhD", - "author_inst": "La Jolla Institute of Allergy and Immunology" - }, - { - "author_name": "Thomas H. Alexander MD MHSc", - "author_inst": "Scripps Clinic" - }, - { - "author_name": "Grace Y. Lin MD", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Ana Lucia Fuentes MD", - "author_inst": "VA San Diego Healthcare System" - }, - { - "author_name": "Ira N. Advani BS", - "author_inst": "VA San Diego Healthcare System" - }, - { - "author_name": "Deepti Gunge BS", - "author_inst": "VA San Diego Healthcare System" - }, - { - "author_name": "Victor Pretorius MBChB MD", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Atul Malhotra MD", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Xin Sun PhD", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Jason Duran MD PhD", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Shane Crotty PhD", - "author_inst": "La Jolla Institute of Allergy and Immunology" - }, - { - "author_name": "Nicole G. Coufal MD PhD", - "author_inst": "Rady Childrens Hospital" - }, - { - "author_name": "Angela Meier MD PhD", - "author_inst": "VA San Diego Healthcare System" - }, - { - "author_name": "Laura E. Crotty Alexander MD", - "author_inst": "VA San Diego Healthcare System" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2021.01.13.21249429", "rel_title": "Elevated Angiopoietin-2 inhibits thrombomodulin-mediated anticoagulation in critically ill COVID-19 patients", @@ -1011454,6 +1009672,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2021.01.12.21249702", + "rel_title": "Diverse Humoral Immune Responses in Younger and Older Adult COVID-19 Patients", + "rel_date": "2021-01-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.12.21249702", + "rel_abs": "We sought to discover links between antibody responses to SARS-CoV-2 and patient clinical variables, cytokine profiles and antibodies to endemic coronaviruses. Serum from patients of varying ages and clinical severity were collected and used to probe a novel multi-coronavirus protein microarray containing SARS-CoV-2 proteins and overlapping protein fragments of varying length as well as SARS-CoV, MERS-CoV, HCoV-OC43 and HCoV-NL63 proteins. IgG, IgA and IgM antibody responses to specific epitopes within the spike (S), nucleocapsid (N) and membrane proteins (M) were higher in older adult patients. Moreover, the older age group displayed more consistent correlations of antibody reactivity with systemic cytokine and chemokine responses when compared to the younger adult group. A subset of patients, however, had little or no response to SARS-CoV-2 antigens and disproportionately severe clinical outcomes. Further characterization of these serosilent individuals with cytokine analysis revealed significant differences in IL-10, IL-15, IP-10, EGF and sCD40L levels when compared to seroreactive patients in the cohort.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Jennifer M Sasson", + "author_inst": "University of Virginia Health System" + }, + { + "author_name": "Joseph J Campo", + "author_inst": "Antigen Discovery Inc." + }, + { + "author_name": "Rebecca M Carpenter", + "author_inst": "University of Virginia Health System" + }, + { + "author_name": "Mary K Young", + "author_inst": "University of Virginia Health System" + }, + { + "author_name": "Arlo Z Randall", + "author_inst": "Antigen Discovery Inc." + }, + { + "author_name": "Krista Trappl-Kimmons", + "author_inst": "Antigen Discovery Inc." + }, + { + "author_name": "Amit Oberai", + "author_inst": "Antigen Discovery Inc." + }, + { + "author_name": "Christopher Hung", + "author_inst": "Antigen Discovery Inc." + }, + { + "author_name": "Joshua Edgar", + "author_inst": "Antigen Discovery Inc." + }, + { + "author_name": "Andy A Teng", + "author_inst": "Antigen Discovery Inc." + }, + { + "author_name": "Jozelyn V Pablo", + "author_inst": "Antigen Discovery Inc." + }, + { + "author_name": "Xiaowu Liang", + "author_inst": "Antigen Discovery Inc." + }, + { + "author_name": "Angela Yee", + "author_inst": "Antigen Discovery Inc." + }, + { + "author_name": "William A Petri Jr.", + "author_inst": "University of Virginia Health System" + }, + { + "author_name": "David Camerini", + "author_inst": "Antigen Discovery Inc." + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.11.21249549", "rel_title": "The Relationship between Democracy embracement and COVID-19 reported casualties worldwide", @@ -1011874,145 +1010167,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.11.21249564", - "rel_title": "The 2020 SARS-CoV-2 epidemic in England: key epidemiological drivers and impact of interventions", - "rel_date": "2021-01-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.11.21249564", - "rel_abs": "We fitted a model of SARS-CoV-2 transmission in care homes and the community to regional surveillance data for England. Among control measures implemented, only national lockdown brought the reproduction number below 1 consistently; introduced one week earlier it could have reduced first wave deaths from 36,700 to 15,700 (95%CrI: 8,900-26,800). Improved clinical care reduced the infection fatality ratio from 1.25% (95%CrI: 1.18%-1.33%) to 0.77% (95%CrI: 0.71%-0.84%). The infection fatality ratio was higher in the elderly residing in care homes (35.9%, 95%CrI: 29.1%-43.4%) than those residing in the community (10.4%, 95%CrI: 9.1%-11.5%). England is still far from herd immunity, with regional cumulative infection incidence to 1st December 2020 between 4.8% (95%CrI: 4.4%-5.1%) and 15.4% (95%CrI: 14.9%-15.9%) of the population.\n\nOne-sentence summaryWe fit a mathematical model of SARS-CoV-2 transmission to surveillance data from England, to estimate transmissibility, severity, and the impact of interventions", - "rel_num_authors": 31, - "rel_authors": [ - { - "author_name": "Edward S. Knock", - "author_inst": "Imperial College London" - }, - { - "author_name": "Lilith K. Whittles", - "author_inst": "Imperial College London" - }, - { - "author_name": "John A. Lees", - "author_inst": "Imperial College London" - }, - { - "author_name": "Pablo N. Perez-Guzman", - "author_inst": "Imperial College London" - }, - { - "author_name": "Robert Verity", - "author_inst": "Imperial College London" - }, - { - "author_name": "Richard G. FitzJohn", - "author_inst": "Imperial College London" - }, - { - "author_name": "Katy AM. Gaythorpe", - "author_inst": "Imperial College London" - }, - { - "author_name": "Natsuko Imai", - "author_inst": "Imperial College London" - }, - { - "author_name": "Wes Hinsley", - "author_inst": "Imperial College London" - }, - { - "author_name": "Lucy C. Okell", - "author_inst": "Imperial College London" - }, - { - "author_name": "Alicia Rosello", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Nikolas Kantas", - "author_inst": "Imperial College London" - }, - { - "author_name": "Caroline E. Walters", - "author_inst": "Imperial College London" - }, - { - "author_name": "Sangeeta Bhatia", - "author_inst": "Imperial College London" - }, - { - "author_name": "Oliver J. Watson", - "author_inst": "Imperial College London" - }, - { - "author_name": "Charles Whittaker", - "author_inst": "Imperial College London" - }, - { - "author_name": "Lorenzo Cattarino", - "author_inst": "Imperial College London" - }, - { - "author_name": "Adhiratha Boonyasiri", - "author_inst": "Imperial College London" - }, - { - "author_name": "Bimandra A. Djaafara", - "author_inst": "Imperial College London" - }, - { - "author_name": "Keith Fraser", - "author_inst": "Imperial College London" - }, - { - "author_name": "Han Fu", - "author_inst": "Imperial College London" - }, - { - "author_name": "Haowei Wang", - "author_inst": "Imperial College London" - }, - { - "author_name": "Xiaoyue Xi", - "author_inst": "Imperial College London" - }, - { - "author_name": "Christl A. Donnelly", - "author_inst": "Imperial College London" - }, - { - "author_name": "Elita Jauneikaite", - "author_inst": "Imperial College London" - }, - { - "author_name": "Daniel J. Laydon", - "author_inst": "Imperial College London" - }, - { - "author_name": "Peter J. White", - "author_inst": "Imperial College London" - }, - { - "author_name": "Azra C. Ghani", - "author_inst": "Imperial College London" - }, - { - "author_name": "Neil M. Ferguson", - "author_inst": "Imperial College London" - }, - { - "author_name": "Anne Cori", - "author_inst": "Imperial College London" - }, - { - "author_name": "Marc Baguelin", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.11.21249561", "rel_title": "Transmission dynamics and forecasts of the COVID-19 pandemic in Mexico, March 20-November 11, 2020.", @@ -1013148,6 +1011302,49 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.01.12.426404", + "rel_title": "Ineffectual AEC1 Differentiation from KRT8hi Transitional Cells without Fibrosis Associated with Fatal Acute Respiratory Failure in COVID-19 ARDS", + "rel_date": "2021-01-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.12.426404", + "rel_abs": "ARDS due to COVID-19 and other etiologies results from injury to the alveolar epithelial cell (AEC) barrier resulting in noncardiogenic pulmonary edema, which causes acute respiratory failure; clinical recovery requires epithelial regeneration. During physiologic regeneration in mice, AEC2s proliferate, exit the cell cycle, and transiently assume a transitional state before differentiating into AEC1s; persistence of the transitional state is associated with pulmonary fibrosis in humans. It is unknown whether transitional cells emerge and differentiate into AEC1s without fibrosis in human ARDS and why transitional cells differentiate into AEC1s during physiologic regeneration but persist in fibrosis. We hypothesized that incomplete but ongoing AEC1 differentiation from transitional cells without fibrosis may underlie persistent barrier permeability and fatal acute respiratory failure in ARDS. Immunostaining of postmortem ARDS lungs revealed abundant transitional cells in organized monolayers on alveolar septa without fibrosis. They were typically cuboidal or partially spread, sometimes flat, and occasionally expressed AEC1 markers. Immunostaining and/or interrogation of scRNAseq datasets revealed that transitional cells in mouse models of physiologic regeneration, ARDS, and fibrosis express markers of cell cycle exit but only in fibrosis express a specific senescence marker. Thus, in severe, fatal early ARDS, AEC1 differentiation from transitional cells is incomplete, underlying persistent barrier permeability and respiratory failure, but ongoing without fibrosis; senescence of transitional cells may be associated with pulmonary fibrosis.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Christopher Ting", + "author_inst": "University of Michigan" + }, + { + "author_name": "Mohit Aspal", + "author_inst": "University of Michigan" + }, + { + "author_name": "Neil Vaishampayan", + "author_inst": "University of Michigan" + }, + { + "author_name": "Steven K. Huang", + "author_inst": "University of Michigan" + }, + { + "author_name": "Fa Wang", + "author_inst": "University of Michigan" + }, + { + "author_name": "Carol Farver", + "author_inst": "University of Michigan" + }, + { + "author_name": "Rachel Lynne Zemans", + "author_inst": "University of Michigan" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2021.01.13.426553", "rel_title": "Distinct lung-homing receptor expression and activation profiles on NK cell and T cell subsets in COVID-19 and influenza", @@ -1013556,33 +1011753,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2021.01.06.20249030", - "rel_title": "Convergence of Comorbidity and COVID-19 Infection to Fatality: An Investigation Based on Concurrent Health Status Evaluation among the Elderly Population in Kerala", - "rel_date": "2021-01-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.06.20249030", - "rel_abs": "ObjectiveTo investigate the impact of age, comorbidity, and vaccination in the fatality of older COVID-19 patients in the state of Kerala, India, based on their comorbidity and vaccination status.\n\nMethodsIt is a cross sectional study adopting a mixed method approach conducted among the older population in Kerala. To study the health profile, 405 older people were surveyed, and 102 people were interviewed in-depth at their households, between June to November 2020. The results of the study were triangulated with elderly COVID-19 fatality data, available from the citizen-science dashboards of the research team and Department of Health, Kerala. Vaccination data was retrieved from cowin.gov.in to study its impact. The data was analysed using the IBM SPSS version 22.0.\n\nResultsAge is a predictor of COVID-19 fatality. Diabetes, hypertension, heart diseases, CKD and COPD are the significant predictors of elderly COVID-19 fatality. The current comorbidity profile of the total older population matches with the comorbidities of the COVID-19 elderly death cases. Vaccination has impacted COVID-19 mortality after vaccinating 65 percent (first dose) of the elderly.\n\nConclusionsAge and comorbidities can predict potential fatality among older COVID-19 patients. Timely and accurate health data and better knowledge of high-risk factors such as comorbidity can easily guide the healthcare system and authorities to efficient prevention and treatment methodologies. Knowledge on prevailing NCDs can drive early preparedness before it converges with an epidemic like the present zoonotic disease. Priority must be given for elderly vaccination to bring down the mortality rates.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Sindhu Joseph", - "author_inst": "Govinda Pai Memorial Government College" - }, - { - "author_name": "Jijo Pulickiyil Ulahannan", - "author_inst": "Government College Kasaragod" - }, - { - "author_name": "Parvathy AJ", - "author_inst": "Vellore Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2021.01.10.20249079", "rel_title": "Altered kidney function and acute kidney damage markers predict survival outcomes of COVID-19 patients: A prospective pilot study.", @@ -1014758,6 +1012928,85 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2021.01.10.20248831", + "rel_title": "Factors indicating intention to vaccinate with a COVID-19 vaccine among older U.S. Adults", + "rel_date": "2021-01-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.10.20248831", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSBACKGROUNDC_ST_ABSThe success of vaccination efforts to curb the COVID-19 pandemic will require broad public uptake of immunization and highlights the importance of understanding factors associated with willingness to receive a vaccine.\n\nMETHODSAdults enrolled in the Heartline clinical study were invited to complete a COVID-19 vaccine assessment through the Heartline mobile application between November 6-20, 2020. Factors associated with willingness to receive a COVID-19 vaccine were evaluated using an ordered logistic regression as well as a Random Forest classification algorithm.\n\nRESULTSAmong 9,106 study participants, 81.3% (n=7402) responded and had available demographic data. The majority (91.3%) reported a willingness to be vaccinated. Factors most strongly associated with vaccine willingness were beliefs about the safety and efficacy of COVID-19 vaccines and vaccines in general. Women and Black or African American respondents reported lower willingness to vaccinate. Among those less willing to get vaccinated, 66.2% said that they would talk with their health provider before making a decision. During the study, positive results from the first COVID-19 vaccine outcome study were released; vaccine willingness increased after this report.\n\nCONCLUSIONSEven among older adults at high-risk for COVID-19 complications who are participating in a longitudinal clinical study, 1 in 11 reported lack of willingness to receive COVID-19 vaccine in November 2020. Variability in vaccine willingness by gender, race, education, and income suggests the potential for uneven vaccine uptake. Education by health providers directed toward assuaging concerns about vaccine safety and efficacy can help improve vaccine acceptance among those less willing.\n\nClinicaltrials.gov NCT04276441", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Janeta Nikolovski", + "author_inst": "Janssen Pharmaceutical Companies of Johnson & Johnson" + }, + { + "author_name": "Martin Koldijk", + "author_inst": "Janssen Pharmaceutical Companies of Johnson & Johnson" + }, + { + "author_name": "Gerrit Jan Weverling", + "author_inst": "Janssen Pharmaceutical Companies of Johnson & Johnson" + }, + { + "author_name": "John Spertus", + "author_inst": "University of Missouri Kansas City School of Medicine" + }, + { + "author_name": "Mintu Turakhia", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Leslie Saxon", + "author_inst": "University of Southern California School of Medicine" + }, + { + "author_name": "Charles Michael Gibson", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "John Whang", + "author_inst": "Janssen Pharmaceutical Companies of Johnson & Johnson" + }, + { + "author_name": "Troy Sarich", + "author_inst": "Janssen Pharmaceutical Companies of Johnson & Johnson" + }, + { + "author_name": "Robert Zambon", + "author_inst": "Janssen Pharmaceutical Companies of Johnson & Johnson" + }, + { + "author_name": "Nnamdi Ezeanochie", + "author_inst": "Johnson & Johnson" + }, + { + "author_name": "Jennifer Turgiss", + "author_inst": "Johnson & Johnson" + }, + { + "author_name": "Robyn Jones", + "author_inst": "Johnson & Johnson" + }, + { + "author_name": "Jeff Stoddard", + "author_inst": "Janssen Pharmaceutical Companies of Johnson & Johnson" + }, + { + "author_name": "Paul Burton", + "author_inst": "Janssen Pharmaceutical Companies of Johnson & Johnson" + }, + { + "author_name": "Ann Marie Navar", + "author_inst": "UT Southwestern Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2021.01.06.21249342", "rel_title": "Indoor dust as a matrix for surveillance of COVID-19 outbreaks", @@ -1015202,109 +1013451,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.10.21249151", - "rel_title": "Robotic RNA extraction for SARS-CoV-2 surveillance using saliva samples", - "rel_date": "2021-01-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.10.21249151", - "rel_abs": "Saliva is an attractive specimen type for asymptomatic surveillance of COVID-19 in large populations due to its ease of collection and its demonstrated utility for detecting RNA from SARS-CoV-2. Multiple saliva-based viral detection protocols use a direct-to-RT-qPCR approach that eliminates nucleic acid extraction but can reduce viral RNA detection sensitivity. To improve test sensitivity while maintaining speed, we developed a robotic nucleic acid extraction method for detecting SARS-CoV-2 RNA in saliva samples with high throughput. Using this assay, the Free Asymptomatic Saliva Testing (IGI-FAST) research study on the UC Berkeley campus conducted 11,971 tests on supervised self-collected saliva samples and identified rare positive specimens containing SARS-CoV-2 RNA during a time of low infection prevalence. In an attempt to increase testing capacity, we further adapted our robotic extraction assay to process pooled saliva samples. We also benchmarked our assay against the gold standard, nasopharyngeal swab specimens. Finally, we designed and validated a RT-qPCR test suitable for saliva self-collection. These results establish a robotic extraction-based procedure for rapid PCR-based saliva testing that is suitable for samples from both symptomatic and asymptomatic individuals.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Jennifer R. Hamilton", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA. Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Elizabeth C. Stahl", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA. Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Connor A. Tsuchida", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA. Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Enrique Lin-Shiao", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA. Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "C. Kimberly Tsui", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Kathleen Pestal", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Holly K. Gildea", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Lea B. Witkowsky", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA. Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Erica A. Moehle", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA. Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Shana L. McDevitt", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA. Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Matthew McElroy", - "author_inst": "Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Amanda Keller", - "author_inst": "Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Iman Sylvain", - "author_inst": "Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Ariana Hirsh", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA. Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Alison Ciling", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA. Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Alexander J. Ehrenberg", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA. Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "- IGI SARS-CoV-2 consortium", - "author_inst": "" - }, - { - "author_name": "Bradley R. Ringeisen", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA. Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Garth Huberty", - "author_inst": "Washington Hospital Healthcare System Clinical Laboratory, Fremont, CA USA" - }, - { - "author_name": "Fyodor D. Urnov", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA. Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Petros Giannikopoulos", - "author_inst": "Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA" - }, - { - "author_name": "Jennifer A. Doudna", - "author_inst": "University of California, Berkeley, Berkeley, CA, USA. Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA. Howard Hughes Medic" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2021.01.10.21249528", "rel_title": "Characteristics of changes in circulating markers of alveolar epithelial and endothelial injury in acute respiratory distress syndrome with COVID-19", @@ -1017032,6 +1015178,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.08.21249445", + "rel_title": "COVID-19 seroprevalence among healthcare workers of a large COVID Hospital in Rome reveals strengths and limits of two different serological tests", + "rel_date": "2021-01-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.08.21249445", + "rel_abs": "In several hospitals worldwide, healthcare workers are currently at the forefront against coronavirus disease 2019 (COVID-19). Since Fondazione Policlinico Universitario A. Gemelli (FPG) IRCCS has been enlisted as a COVID hospital, healthcare workers deployed to COVID wards were separated from those with limited or no exposure, whereas administrative staff was destined to work-from-home.\n\nBetween June 4 and July 3 2020, an investigation was carried out to evaluate seroprevalence of SARS-CoV-2 IgG antibodies among employees of the FPG using point-of-care (POC) and venous blood tests. Sensitivity, specificity and predictive values were determined with reverse-transcription polymerase chain reaction (RT-PCR) on nasal/oropharyngeal swabs as gold standard.\n\nFour thousand, seven hundred seventy-seven participants were enrolled. Seroprevalence was 3.66% using the POC test and 1.19% using venous blood test, with a significant difference between the two (p < 0.05).\n\nPOC sensitivity and specificity were, respectively, 63.64% (95% confidence interval (CI): 62.20% to 65.04%) and 96.64% (95% CI: 96.05% to 97.13%), while those of the venous blood test were, respectively, 78.79% (95% CI: 77.58% to 79.94%) and 99.36% (95% CI: 99.07% to 99.55%). Among low-risk population, point-of-cares predictive values were 58.33% (positive) and 98.23% (negative) whereas venous blood tests were 92.86% (positive) and 98.53% (negative). In conclusion, point-of-care tests have low diagnostic accuracy, while venous blood tests seem to show an overall poor reliability.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Giuseppe Vetrugno", + "author_inst": "Risk Management Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy. Department of Health Care Surveillance and Bioethics, section of Legal" + }, + { + "author_name": "Daniele Ignazio La Milia", + "author_inst": "Hospital Health Management, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy." + }, + { + "author_name": "Floriana D'Ambrosio", + "author_inst": "Section of Hygiene, University Department of Health Sciences and Public Health, Universita' Cattolica del Sacro Cuore, Rome, Italy" + }, + { + "author_name": "Marcello Di Pumpo", + "author_inst": "Section of Hygiene, University Department of Health Sciences and Public Health, Universita' Cattolica del Sacro Cuore, Rome, Italy." + }, + { + "author_name": "Roberta Pastorino", + "author_inst": "Department of Woman and Child Health and Public Health - Public Health Area, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy." + }, + { + "author_name": "Stefania Boccia", + "author_inst": "Section of Hygiene, University Department of Health Sciences and Public Health, Universita' Cattolica del Sacro Cuore, Rome, Italy. Department of Woman and Chil" + }, + { + "author_name": "Rosalba Ricci", + "author_inst": "Department of laboratory and infectivological sciences, Fondazione Policlinico A. Gemelli IRCCS, Rome, Italy." + }, + { + "author_name": "Fabio De-Giorgio", + "author_inst": "Department of Health Care Surveillance and Bioethics, section of Legal Medicine, Universita' Cattolica del Sacro Cuore, Rome, Italy. Fondazione Policlinico Univ" + }, + { + "author_name": "Michela Cicconi", + "author_inst": "Risk Management Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy. Section of Hygiene, University Department of Health Sciences and Publi" + }, + { + "author_name": "Federica Foti", + "author_inst": "Risk Management Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy." + }, + { + "author_name": "Domenico Pascucci", + "author_inst": "Section of Hygiene, University Department of Health Sciences and Public Health, Universita' Cattolica del Sacro Cuore, Rome, Italy." + }, + { + "author_name": "Francesco Castrini", + "author_inst": "Section of Hygiene, University Department of Health Sciences and Public Health, Universita' Cattolica del Sacro Cuore, Rome, Italy." + }, + { + "author_name": "Elettra Carini", + "author_inst": "Hospital Health Management, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy. Section of Hygiene, University Department of Health Sciences and" + }, + { + "author_name": "Andrea Cambieri", + "author_inst": "Hospital Health Management, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy." + }, + { + "author_name": "Maria Elena D'Alfonso", + "author_inst": "Hospital Health Management, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy" + }, + { + "author_name": "Gennaro Capalbo", + "author_inst": "Hospital Health Management, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy." + }, + { + "author_name": "Massimo Fantoni", + "author_inst": "Department of laboratory and infectivological sciences, Fondazione Policlinico A. Gemelli IRCCS, Rome, Italy. Department of Health Care Surveillance and Bioethi" + }, + { + "author_name": "Umberto Moscato", + "author_inst": "Section of Hygiene, University Department of Health Sciences and Public Health, Universita' Cattolica del Sacro Cuore, Rome, Italy. Department of Woman and Chil" + }, + { + "author_name": "Domenico Staiti", + "author_inst": "Department of Woman and Child Health and Public Health-Public Health Area, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy. University Depart" + }, + { + "author_name": "Francesco Maria De Simone", + "author_inst": "Department of Woman and Child Health and Public Health-Public Health Area, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy." + }, + { + "author_name": "Filippo Berloco", + "author_inst": "Hospital Health Management, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy." + }, + { + "author_name": "Maurizio Zega", + "author_inst": "Director of Nursing Service Technician and Rehabilitation Administration (S.I.T.R.A.), Fondazione Policlinico Universitario Agostino Gemelli, Rome, Italy." + }, + { + "author_name": "Paola Cattani", + "author_inst": "Department of laboratory and infectivological sciences, Fondazione Policlinico A. Gemelli IRCCS, Rome, Italy." + }, + { + "author_name": "Brunella Posteraro", + "author_inst": "Department of Basic Biotechnological Sciences, Intensive and Perioperative Clinics, Universita' Cattolica del Sacro Cuore, Rome, Italy. Department of Medical an" + }, + { + "author_name": "Maurizio Sanguinetti", + "author_inst": "Department of laboratory and infectivological sciences, Fondazione Policlinico A. Gemelli IRCCS, Rome, Italy. Department of Basic Biotechnological Sciences, Int" + }, + { + "author_name": "Patrizia Laurenti", + "author_inst": "Section of Hygiene, University Department of Health Sciences and Public Health, Universita' Cattolica del Sacro Cuore, Rome, Italy. Department of Woman and Chil" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2021.01.08.21249432", "rel_title": "Levels of SARS-CoV-2 population exposure are considerably higher than suggested by seroprevalence surveys", @@ -1017480,65 +1015745,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2021.01.06.21249325", - "rel_title": "Pregnancy and neonatal outcomes of COVID-19, co-reporting of common outcomes from the PAN-COVID and AAP SONPM registry", - "rel_date": "2021-01-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.06.21249325", - "rel_abs": "BackgroundFew large, cohort studies report data on individuals maternal, fetal, perinatal, and neonatal outcomes associated with SARS-CoV-2 infection in pregnancy. We report outcomes from a collaboration formed early during the pandemic between the investigators of two registries, the UK and global Pregnancy and Neonatal outcomes in COVID-19 (PAN-COVID) study and the US American Academy of Pediatrics Section on Neonatal Perinatal Medicine (AAP SONPM) National Perinatal COVID-19 Registry.\n\nMethodsPAN-COVID (suspected or confirmed SARS-CoV-2 infection at any stage in pregnancy) and the AAP SONPM registry (positive maternal testing for SARS-CoV-2 from 14 days before delivery to 3 days after delivery) studies collected data on maternal, fetal, perinatal and neonatal outcomes. PAN-COVID results are presented as all inclusions and those with confirmed SARS-CoV-2 infection only.\n\nResultsWe report 4004 women in pregnancy affected by suspected or confirmed SARS-CoV-2 infection (1606 from PAN-COVID and 2398 from the AAP SONPM) from January 1st 2020 to July 25th 2020 (PAN-COVID) and August 8th (AAP SONPM). For obstetric outcomes in PAN-COVID and AAP SONPM, respectively, maternal death occurred in 0.5% and 0.17%, early neonatal death in 0.2% and 0.3%, and stillbirth in 0.50% and 0.65% of women. Delivery was pre-term (<37 weeks gestation) in 12% of all women in PAN-COVID, in 16.2% of those women with confirmed infection in PAN-COVID and 16.2% of women in AAP SONPM. Very preterm delivery (< 27 weeks gestation) occurred in 0.6% in PAN-COVID and 0.7% in AAP SONPM.\n\nNeonatal SARS-CoV-2 infection was reported in 0.8% of PAN-COVID all inclusions, 2.0% in PAN-COVID confirmed infections and 1.8% in the AAP SONPM study; the proportions of babies tested were 9.5%, 20.7% and 87.2% respectively.\n\nThe proportion of SGA babies was 8.2% in PAN-COVID all inclusions, 9.7% in PAN-COVID confirmed infection and 9.6% in AAP SONPM. Gestational age adjusted mean z-scores were -0.03 for PAN-COVID and -0.18 for AAP SONPM.\n\nConclusionsThe findings from the UK and US SARS-CoV-2 in pregnancy registries were remarkably concordant. Pre-term delivery affected a higher proportion of women in pregnancy than expected from historical and contemporaneous national data. The proportions of women affected by stillbirth, small for gestational age infants and early neonatal death were comparable to historical and contemporaneous UK and US data. Although maternal death was uncommon, the proportion was higher than expected from UK and US population data, likely explained by under-ascertainment of women affected by milder and asymptomatic infection in pregnancy. The data presented support strong guidance for enhanced precautions to prevent SARS-COV-2 infection in pregnancy, particularly in the context of increased risks of preterm delivery and maternal mortality, and for priority vaccination of women planning pregnancy.\n\nWhat is known about SARS-COV-2 infection in pregnancy and neonates?Cohort, population surveillance studies and living systematic reviews have included limited numbers of women in pregnancy affected by COVID-19 and report that most women and infants had good outcomes.\n\nWhat this study addsPreterm deliveries occurred in a high proportion of women participating in these two registries in comparison to contemporaneous and historical national data in the UK and US. The majority of preterm deliveries occurred late preterm (between 32+0 and 36+6 weeks gestation).\n\nSARS-COV-2 infection in pregnancy did not appear to be associated with a clinically significant effect on the rate of stillbirth, fetal growth, or neonatal outcomes.\n\nAlthough maternal death was uncommon, the proportion was higher than expected from UK and US population data, likely explained by under-ascertainment of women affected by milder and asymptomatic infection in pregnancy.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Edward Mullins", - "author_inst": "Imperial College" - }, - { - "author_name": "Mark Hudak", - "author_inst": "University of Florida, AAP SONPM" - }, - { - "author_name": "Jay Banerjee", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Trace Getzlaff", - "author_inst": "University of Florida" - }, - { - "author_name": "Julia Townson", - "author_inst": "Cardiff University" - }, - { - "author_name": "Kimberly Barnette", - "author_inst": "University of Florida Jacksonville Physicians Inc." - }, - { - "author_name": "Rebecca Playle", - "author_inst": "Cardiff University" - }, - { - "author_name": "Tom Bourne", - "author_inst": "Imperial College London" - }, - { - "author_name": "- PAN-COVID-investigators", - "author_inst": "-" - }, - { - "author_name": "- National Perinatal COVID-19 Registry Study Group", - "author_inst": "-" - }, - { - "author_name": "Christoph Lees", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "obstetrics and gynecology" - }, { "rel_doi": "10.1101/2021.01.04.20237578", "rel_title": "Zorro versus Covid-19: fighting the pandemic with face masks", @@ -1018734,6 +1016940,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.07.21249116", + "rel_title": "Multi-organ complement deposition in COVID-19 patients", + "rel_date": "2021-01-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.07.21249116", + "rel_abs": "BackgroundIncreased levels of circulating complement activation products have been reported in COVID-19 patients, but only limited information is available on complement involvement at tissue level. The mechanisms and pathways of local complement activation remain unclear.\n\nMethodsWe performed immunofluorescence analyses of autopsy specimens of lungs, kidney and liver from nine COVID-19 patients who died of acute respiratory failure. Snap-frozen samples embedded in OCT were stained with antibodies against complement components and activation products, IgG and spike protein of SARS-CoV-2.\n\nFindingsLung deposits of C1q, C4, C3 and C5b-9 were localized in the capillaries of the interalveolar septa and on alveolar cells. IgG displayed a similar even distribution, suggesting classical pathway activation. The spike protein is a potential target of IgG, but its uneven distribution suggests that other viral and tissue molecules may be targeted by IgG. Factor B deposits were also seen in COVID-19 lungs and are consistent with activation of the alternative pathway, whereas MBL and MASP-2 were hardly detectable. Analysis of kidney and liver specimens mirrored findings observed in the lung. Complement deposits were seen on tubules and vessels of the kidney with only mild C5b-9 staining in glomeruli, and on hepatic artery and portal vein of the liver.\n\nInterpretationComplement deposits in different organs of deceased COVID-19 patients caused by activation of the classical and alternative pathways support the multi-organ nature of the disease.\n\nFundingGrants from the Italian Ministry of Health (COVID-2020-12371808) to PLM and National Institutes of Health HL150146 to NP are gratefully acknowledged.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Paolo Macor", + "author_inst": "Department of Life Sciences, University of Trieste, Trieste, Italy" + }, + { + "author_name": "Paolo Durigutto", + "author_inst": "Istituto Auxologico Italiano, IRCCS, Laboratory of Immuno-Rheumatology, Milan, Italy" + }, + { + "author_name": "Alessandro Mangogna", + "author_inst": "Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy" + }, + { + "author_name": "Rossana Bussani", + "author_inst": "Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy" + }, + { + "author_name": "Stefano D'Errico", + "author_inst": "Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy" + }, + { + "author_name": "Martina Zanon", + "author_inst": "Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy" + }, + { + "author_name": "Nicola Pozzi", + "author_inst": "Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, US" + }, + { + "author_name": "Pier Luigi Meroni", + "author_inst": "Istituto Auxologico Italiano, IRCCS, Laboratory of Immuno-Rheumatology, Milan, Italy" + }, + { + "author_name": "Francesco Tedesco", + "author_inst": "Istituto Auxologico Italiano, IRCCS, Laboratory of Immuno-Rheumatology, Milan, Italy" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2021.01.06.20249026", "rel_title": "Recurrent dissemination of SARS-CoV-2 through the Uruguayan-Brazilian border", @@ -1019318,33 +1017575,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2021.01.07.21249392", - "rel_title": "Predicting severity of Covid-19 using standard laboratory parameters", - "rel_date": "2021-01-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.07.21249392", - "rel_abs": "BackgroundMore than 1.6 million people have already deceased due to a COVID-19 infection making it a major public health concern. A prediction of severe courses can enhance treatment quality and thus lower fatality and morbidity rates. The use of laboratory parameters has recently been established for a prediction. However, laboratory parameters have rarely been used in combination to predict severe outcomes.\n\nMethodWe used a retrospective case-control design to analyze risk factors derived from laboratory parameters. Patients treated for COVID-19 at an hospital in Krefeld, Germany, from March to May 2020 were included (n =42). Patients were classified into two categories based on their outcome (Mild course vs. treatment in intensive care unit). Laboratory parameters were compared across severity categories using non-parametric statistic. Identified laboratory parameters were used in a logistic regression model. The model was replicated using a) clinical standardized parameters b) aggregated factors derived from a factor analysis.\n\nResultsPatients in intensive care unit showed elevated ALT, CRP and LDH levels, a higher leukocyte and neutrophile count, a higher neutrophile ratio and a lowered lymphocyte ratio. We were able to classify 95.1% of all cases correctly (96.6% of mild and 91.7% of severe cases, p<.001).\n\nConclusionA number of routinely collected laboratory parameters is associated with a severe outcome of COVID-19. The combination of these parameters provides a powerful tool in predicting severity and can enhance treatment effectiveness.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Thimo Buchmueller", - "author_inst": "Alexianer Krefeld GmbH" - }, - { - "author_name": "Ingmar Groening", - "author_inst": "Alexianer Krefeld GmbH" - }, - { - "author_name": "Ralf Ihl", - "author_inst": "Alexianer Krefeld GmbH" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2021.01.07.21249419", "rel_title": "Competing Health Risks Associated with the COVID-19 Pandemic and Response: A Scoping Review", @@ -1020383,6 +1018613,29 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2021.01.07.21249390", + "rel_title": "Interleukin-6 Receptor Antagonists in Critically Ill Patients with Covid-19 - Preliminary report", + "rel_date": "2021-01-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.07.21249390", + "rel_abs": "BackgroundThe efficacy of interleukin-6 receptor antagonists in critically ill patients with coronavirus disease 2019 (Covid-19) is unclear.\n\nMethodsWe evaluated tocilizumab and sarilumab in an ongoing international, multifactorial, adaptive platform trial. Adult patients with Covid-19, within 24 hours of commencing organ support in an intensive care unit, were randomized to receive either tocilizumab (8mg/kg) or sarilumab (400mg) or standard care (control). The primary outcome was an ordinal scale combining in-hospital mortality (assigned -1) and days free of organ support to day 21. The trial uses a Bayesian statistical model with pre-defined triggers to declare superiority, efficacy, equivalence or futility.\n\nResultsTocilizumab and sarilumab both met the pre-defined triggers for efficacy. At the time of full analysis 353 patients had been assigned to tocilizumab, 48 to sarilumab and 402 to control. Median organ support-free days were 10 (interquartile range [IQR] -1, 16), 11 (IQR 0, 16) and 0 (IQR -1, 15) for tocilizumab, sarilumab and control, respectively. Relative to control, median adjusted odds ratios were 1.64 (95% credible intervals [CrI] 1.25, 2.14) for tocilizumab and 1.76 (95%CrI 1.17, 2.91) for sarilumab, yielding >99.9% and 99.5% posterior probabilities of superiority compared with control. Hospital mortality was 28.0% (98/350) for tocilizumab, 22.2% (10/45) for sarilumab and 35.8% (142/397) for control. All secondary outcomes and analyses supported efficacy of these IL-6 receptor antagonists.\n\nConclusionsIn critically ill patients with Covid-19 receiving organ support in intensive care, treatment with the IL-6 receptor antagonists, tocilizumab and sarilumab, improved outcome, including survival. (ClinicalTrials.gov number: NCT02735707)", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "- The REMAP-CAP Investigators", + "author_inst": "" + }, + { + "author_name": "Anthony C Gordon", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2021.01.07.425705", "rel_title": "Sequencing of SARS CoV2 in local transmission cases through oxford nanopore MinION platform from Karachi Pakistan", @@ -1020791,37 +1019044,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2021.01.04.21249235", - "rel_title": "Machine Learning Forecast of Growth in COVID-19 Confirmed Infection Cases with Non-Pharmaceutical Interventions and Cultural Dimensions: Algorithm Development and Validation", - "rel_date": "2021-01-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.04.21249235", - "rel_abs": "BackgroundNational governments have implemented non-pharmaceutical interventions to control and mitigate against the COVID-19 pandemic. A deep understanding of these interventions is required.\n\nObjectiveWe investigate the prediction of future daily national Confirmed Infection Growths - the percentage change in total cumulative cases across 14 days - using metrics representative of non-pharmaceutical interventions and cultural dimensions of each country.\n\nMethodsWe combine the OxCGRT dataset, Hofstedes cultural dimensions, and COVID-19 daily reported infection case numbers to train and evaluate five non-time series machine learning models in predicting Confirmed Infection Growth. We use three validation methods - in-distribution, out-of-distribution, and country-based cross-validation - for evaluation, each applicable to a different use case of the models.\n\nResultsOur results demonstrate high R2 values between the labels and predictions for the in-distribution, out-of-distribution, and country-based cross-validation methods (0.959, 0.513, and 0.574 respectively) using random forest and AdaBoost regression. While these models may be used to predict the Confirmed Infection Growth, the differing accuracies obtained from the three tasks suggest a strong influence of the use case.\n\nConclusionsThis work provides new considerations in using machine learning techniques with non-pharmaceutical interventions and cultural dimensions data for predicting the national growth of confirmed infections of COVID-19.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Arnold YS Yeung", - "author_inst": "University of Toronto" - }, - { - "author_name": "Francois Roewer-Despres", - "author_inst": "University of Toronto" - }, - { - "author_name": "Laura Rosella", - "author_inst": "University of Toronto" - }, - { - "author_name": "Frank Rudzicz", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2021.01.04.20232520", "rel_title": "Genomic epidemiology of the SARS-CoV-2 epidemic in Zimbabwe: Role of international travel and regional migration in spread", @@ -1022157,6 +1020379,41 @@ "type": "new results", "category": "developmental biology" }, + { + "rel_doi": "10.1101/2021.01.05.425339", + "rel_title": "Distinct mutations and lineages of SARS-CoV-2 virus in the early phase of COVID-19 global pandemic and subsequent global expansion", + "rel_date": "2021-01-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.05.425339", + "rel_abs": "A novel coronavirus, SARS-CoV-2, has caused over 190 million cases and over 4 million deaths worldwide since it occurred in December 2019 in Wuhan, China. Here we conceptualized the temporospatial evolutionary and expansion dynamics of SARS-CoV-2 by taking a series of cross-sectional view of viral genomes from early outbreak in January 2020 in Wuhan to early phase of global ignition in early April, and finally to the subsequent global expansion by late December 2020. Based on the phylogenetic analysis of the early patients in Wuhan, Wuhan/WH04/2020 is supposed to be a more appropriate reference genome of SARS-CoV-2, instead of the first sequenced genome Wuhan-Hu-1. By scrutinizing the cases from the very early outbreak, we found a viral genotype from the Seafood Market in Wuhan featured with two concurrent mutations (i.e. M type) had become the overwhelmingly dominant genotype (95.3%) of the pandemic one year later. By analyzing 4,013 SARS-CoV-2 genomes from different continents by early April, we were able to interrogate the viral genomic composition dynamics of initial phase of global ignition over a timespan of 14-week. 11 major viral genotypes with unique geographic distributions were also identified. WE1 type, a descendant of M and predominantly witnessed in western Europe, consisted a half of all the cases (50.2%) at the time. The mutations of major genotypes at the same hierarchical level were mutually exclusive, which implying that various genotypes bearing the specific mutations were propagated during human-to-human transmission, not by accumulating hot-spot mutations during the replication of individual viral genomes. As the pandemic was unfolding, we also used the same approach to analyze 261,323 SARS-CoV-2 genomes from the world since the outbreak in Wuhan (i.e. including all the publicly available viral genomes) in order to recapitulate our findings over one-year timespan. By 25 December 2020, 95.3% of global cases were M type and 93.0% of M-type cases were WE1. In fact, at present all the four variants of concern (VOC) are the descendants of WE1 type. This study demonstrates the viral genotypes can be utilized as molecular barcodes in combination with epidemiologic data to monitor the spreading routes of the pandemic and evaluate the effectiveness of control measures. Moreover, the dynamics of viral mutational spectrum in the study may help the early identification of new strains in patients to reduce further spread of infection, guide the development of molecular diagnosis and vaccines against COVID-19, and help assess their accuracy and efficacy in real world at real time.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Yan Chen", + "author_inst": "SeekIn Inc" + }, + { + "author_name": "Shiyong Li", + "author_inst": "SeekIn Inc" + }, + { + "author_name": "Wei Wu", + "author_inst": "SeekIn Inc" + }, + { + "author_name": "Shuaipeng Geng", + "author_inst": "Shenyou Bio" + }, + { + "author_name": "Mao Mao", + "author_inst": "Yonsei University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2021.01.06.20240903", "rel_title": "The spread of breathing air from wind instruments and singers using schlieren techniques", @@ -1022553,33 +1020810,6 @@ "type": "new results", "category": "scientific communication and education" }, - { - "rel_doi": "10.1101/2021.01.06.425544", - "rel_title": "Complex Systems Analysis Informs on the Spread of COVID-19", - "rel_date": "2021-01-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.06.425544", - "rel_abs": "The non-linear progression of new infection numbers in a pandemic poses challenges to the evaluation of its management. The tools of complex systems research may aid in attaining information that would be difficult to extract with other means. To study the COVID-19 pandemic, we utilize the reported new cases per day for the globe, nine countries and six US states through October 2020. Fourier and univariate wavelet analyses inform on periodicity and extent of change. Evaluating time-lagged data sets of various lag lengths, we find that the autocorrelation function, average mutual information and box counting dimension represent good quantitative readouts for the progression of new infections. Bivariate wavelet analysis and return plots give indications of containment versus exacerbation. Homogeneity or heterogeneity in the population response, uptick versus suppression, and worsening or improving trends are discernible, in part by plotting various time lags in three dimensions. The analysis of epidemic or pandemic progression with the techniques available for observed (noisy) complex data can aid decision making in the public health response.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Xia Wang", - "author_inst": "University of Cincinnati" - }, - { - "author_name": "Dorcas Washington", - "author_inst": "University of Cincinnati" - }, - { - "author_name": "Georg F. Weber", - "author_inst": "College of Pharmacy, University of Cincinnati Medical Center, 3225 Eden Avenue, Cincinnati, OH 45267-0004, USA" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2021.01.06.425542", "rel_title": "Incidence and Characteristics of Co-infection and Secondary Infection in Patients with COVID-19", @@ -1023487,6 +1021717,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2021.01.03.21249159", + "rel_title": "Pharmacokinetic modelling to estimate intracellular favipiravir ribofuranosyl-5'-triphosphate exposure to support posology for SARS-CoV-2", + "rel_date": "2021-01-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2021.01.03.21249159", + "rel_abs": "BackgroundThe role of favipiravir as a treatment for COVID-19 is unclear, with discrepant activity against SARS-CoV-2 in vitro, concerns about teratogenicity and pill burden, and an unknown optimal dose. In Vero-E6 cells, high concentrations are needed to inhibit SARS-CoV-2 replication. The purpose of this analysis was to use available data to simulate intracellular pharmacokinetics of favipiravir ribofuranosyl-5-triphosphate (FAVI-RTP) to better understand the putative applicability as a COVID-19 intervention.\n\nMethodsPreviously published in vitro data for the intracellular production and elimination of FAVI- RTP in MDCK cells incubated with parent favipiravir was fitted with a mathematical model to describe the time course of intracellular FAVI-RTP concentrations as a function of incubation concentration of parent favipiravir. Parameter estimates from this model fitting were then combined with a previously published population PK model for the plasma exposure of parent favipiravir in Chinese patients with severe influenza (the modelled free plasma concentration of favipiravir substituting for in vitro incubation concentration) to predict the human intracellular FAVI-RTP pharmacokinetics.\n\nResultsIn vitro FAVI-RTP data was adequately described as a function of in vitro incubation media concentrations of parent favipiravir with an empirical model, noting that the model simplifies and consolidates various processes and is used under various assumptions and within certain limits. Parameter estimates from the fittings to in vitro data predict a flatter dynamic range of peak to trough for intracellular FAVI-RTP when driven by a predicted free plasma concentration profile.\n\nConclusionThis modelling approach has several important limitations that are discussed in the main text of the manuscript. However, the simulations indicate that despite rapid clearance of the parent drug from plasma, sufficient intracellular FAVI-RTP may be maintained across the dosing interval because of its long intracellular half-life. Population average intracellular FAVI-RTP concentrations are estimated to maintain the Km for the SARS-CoV-2 polymerase for 3 days following 800 mg BID dosing and 9 days following 1200 mg BID dosing after a 1600 mg BID loading dose on day 1. Further evaluation of favipiravir as part of antiviral combinations for SARS-CoV-2 is warranted.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Henry Pertinez", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Rajith Rajoli", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Saye H Khoo", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Andrew Owen", + "author_inst": "University of Liverpool" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.29.20248991", "rel_title": "Prior Bariatric Surgery in COVID-19 Positive Patients May Be Protective", @@ -1023815,105 +1022076,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, - { - "rel_doi": "10.1101/2021.01.04.425336", - "rel_title": "SARS-CoV-2 susceptibility of cell lines and substrates commonly used in diagnosis and isolation of influenza and other viruses", - "rel_date": "2021-01-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.04.425336", - "rel_abs": "Coinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other viruses is inevitable as the COVID-19 pandemic continues. This study aimed to evaluate cell lines commonly used in virus diagnosis and isolation for their susceptibility to SARS-CoV-2. While multiple kidney cell lines from monkeys were susceptible and permissive to SARS-CoV-2, many cell types derived from human, dog, mink, cat, mouse, or chicken were not. Analysis of MDCK cells, which are most commonly used for surveillance and study of influenza viruses, demonstrated that they were insusceptible to SARS-CoV-2 and that the cellular barrier to productive infection was due to low expression level of the angiotensin converting enzyme 2 (ACE2) receptor and lower receptor affinity to SARS-CoV-2 spike, which could be overcome by over-expression of canine ACE2 in trans. Moreover, SARS-CoV-2 cell tropism did not appear to be affected by a D614G mutation in the spike protein.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Li Wang", - "author_inst": "Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Xiaoyu Fan", - "author_inst": "Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Gaston Bonenfant", - "author_inst": "Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA" - }, - { - "author_name": "Dan Cui", - "author_inst": "Battelle Memorial Institute, Atlanta, Georgia, USA" - }, - { - "author_name": "Jaber Hossain", - "author_inst": "Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Nannan Jiang", - "author_inst": "Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA" - }, - { - "author_name": "Gloria Larson", - "author_inst": "Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, USA" - }, - { - "author_name": "Michael Currier", - "author_inst": "Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Jimma Liddell", - "author_inst": "Battelle Memorial Institute, Atlanta, Georgia, USA" - }, - { - "author_name": "Malania Wilson", - "author_inst": "Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Azaibi Tamin", - "author_inst": "Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Jennifer Harcourt", - "author_inst": "Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Jessica Ciomperlik-Patton", - "author_inst": "Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Hong Pang", - "author_inst": "Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Naomi Dybdahl-Sissoko", - "author_inst": "Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Ray Campagnoli", - "author_inst": "Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Pei-Yong Shi", - "author_inst": "University of Texas Medical Branch, Galveston, Texas, USA" - }, - { - "author_name": "John R Barnes", - "author_inst": "Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Natalie J. Thornburg", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "David E Wentworth", - "author_inst": "Centers for Disease Control and Prevention, Atlanta, Georgia, USA" - }, - { - "author_name": "Bin Zhou", - "author_inst": "Centers for Disease Control and Prevention" - } - ], - "version": "1", - "license": "cc0", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2021.01.05.425331", "rel_title": "Synergistic interferon alpha-based drug combinations inhibit SARS-CoV-2 and other viral infections in vitro", @@ -1025009,6 +1023171,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2020.12.28.20248958", + "rel_title": "Lived experiences of pregnant and new mothers during COVID-19 pandemic: A narrative analysis of YouTube birth stories.", + "rel_date": "2021-01-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.28.20248958", + "rel_abs": "IntroductionThe COVID-19 pandemic has brought on unprecedented changes, not only to our daily lives but also to our healthcare system. The pandemic has particularly impacted pregnant women that must give birth with tight restrictions and significant uncertainties. Birth stories have frequently been used as a way for women to describe their experiences with the birthing process. In this uncertain time, birth stories can provide valuable insight into how pregnancy and birth stressors during a pandemic can impact the patients overall experience. This study sought to describe and understand pregnant and new mothers lived experiences during the COVID-19 pandemic.\n\nMethodsResearchers extracted relevant YouTube birth stories using predetermined search terms and inclusion criteria. The mothers birth stories were narrated in their second or third trimester or those who had recently given birth during the study period. Birth stories were analyzed using an inductive and deductive approach to capture different aspects of the birthing experience.\n\nResultsOverall, eighty-three birth stories were analyzed. Within these birth stories, four broad themes and twelve subthemes emerged. Key themes included a sense of loss, hospital experiences, experiences with healthcare providers, and unique experiences during birth and postpartum. The birth stories revealed negative and positive birth experiences. Particularly, mothers were frustrated with constantly changing policies within the healthcare setting that negatively affected their birthing experience. On the other hand, support from healthcare professionals, having their partners in the delivery room, and having a positive mindset was instrumental in having a positive birth experience.\n\nConclusionResults from this study provided a detailed description of womens lived experience with giving birth during the COVID-19 pandemic. Healthcare providers need to provide clear communication and compassionate patient-centered care to relieve womens anxiety about uncertain and unpredictable policy as the pandemic continues to evolve.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Kobi V Ajayi", + "author_inst": "Texas A&M University" + }, + { + "author_name": "Idethia S Harvey", + "author_inst": "Texas A&M University" + }, + { + "author_name": "Sonya Panjwani", + "author_inst": "Texas A&M University" + }, + { + "author_name": "Inyang Uwak", + "author_inst": "Texas A&M University" + }, + { + "author_name": "Whitney Garney", + "author_inst": "Texas A&M University" + }, + { + "author_name": "Robin L Page", + "author_inst": "Texas A&M University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "obstetrics and gynecology" + }, { "rel_doi": "10.1101/2020.12.29.20249005", "rel_title": "An Intrinsic and Extrinsic Evaluation of Learned COVID-19 Concepts using Open-Source Word Embedding Sources", @@ -1025521,37 +1023722,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.23.20248803", - "rel_title": "Clinical diagnosis of COVID-19: a prompt, feasible, and sensitive diagnostic tool for COVID-19 based on a 1,757-patient cohort (The AndroCoV Clinical Scoring for COVID-19 diagnosis).", - "rel_date": "2021-01-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.23.20248803", - "rel_abs": "ImportanceIn the COVID-19 pandemic, a limiting barrier for more successful approaches to COVID-19 is the lack of appropriate timing for its diagnosis, during the viral replication stage, when antiviral approaches could demonstrate efficacy, precluding progression to severe stages. Three major reasons that hamper the diagnosis earlier in the disease are the unspecific and mild symptoms in the first stage, the cost- and time-limitations of the rtPCR-SARS-CoV-2, and the insufficient sensitivity of this test as desired for screening purposes during the pandemic. More sensitive and earlier methods of COVID-19 detection should be considered as key for breakthrough changes in the disease course and response to specific therapeutic strategies. Our objective was to propose a clinical scoring for the diagnosis of COVID-19 (The AndroCoV Clinical Scoring for COVID-19 Diagnosis) that has been validated in a large population sample, aiming to encourage the management of patients with high pre-clinical likelihood of presenting COVID-19, at least during the pandemics, independent of a rtPCR-SARS-COV-2 test.\n\nMaterials and methodsThis is a compounded retrospective and prospective analysis of clinical data prospectively collected from the Pre-AndroCoV and AndroCov Trials that resulted in a clinical scoring for COVID-19 diagnosis based on likelihood of presenting COVID-19 according to the number of symptoms, presence of anosmia, and known positive household contact, in a variety of combinations of scoring criteria, aiming to the detect scorings that provided the highest pre-test probability and accuracy. Sensitivity, specificity, positive predictive value, negative predictive value, positive likelihood ratio, and accuracy were calculated for subjects screened in two different periods and altogether, for females, males, and both, in a total of nine different scenarios, for combinations between one, two, or three or more symptoms, or presence of anosmia in subjects without known positive household contacts, and no symptoms, one, two, or three or more symptoms, or presence of anosmia or ageusia in subjects with known positive household contacts.\n\nResults1,757 patients were screened for COVID-19. Among the multiple combinations, requiring two or more symptoms with or without anosmia or ageusia for subjects without known contact and one or more symptoms with or without anosmia or ageusia with known positive contacts presented the highest accuracy (80.4%), and higher pretest probability and accuracy than virtually all rtPCR-SARS-CoV-2 commercially available kit tests.\n\nConclusionThe AndroCoV Clinical Scoring for COVID-19 Diagnosis was demonstrated to be a feasible, quick, inexpensive and sensitive diagnostic tool for clinical diagnosis of COVID-19. A clinical diagnosis of COVID-19 should avoid delays and missed diagnosis, and reduce costs, and should therefore be recommended as a first-line option for COVID-19 diagnosis for public health policies, at least while SARS-CoV-2 is the prevailing circulating virus.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSIs a clinical diagnosis of COVID-19 sensitive, accurate, and feasible?\n\nFindingsThe present analysis of a 1,757-subject cohort of the AndroCoV trials demonstrated that clinical scoring for COVID-19 diagnosis can deliver a more sensitive and prompter diagnosis than the current gold-standard diagnostic method, rtPCR-SARS-CoV-2, with an accuracy above 80%.\n\nMeaningA clinical diagnosis of COVID-19 avoids missed diagnosis due to insufficient sensitivity or incorrect timing of the performance of rtPCR-SARS-CoV-2, reduces costs, avoid delays on specific managements, and allows the testing of potentially effective antiviral therapeutic approaches that should work if administered in the early stage of COVID-19", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Flavio A Cadegiani", - "author_inst": "Federal University of Sao Paulo" - }, - { - "author_name": "John A McCoy", - "author_inst": "Applied Biology, Inc." - }, - { - "author_name": "Carlos Gustavo Wambier", - "author_inst": "Warren Alpert Medical School of Brown University" - }, - { - "author_name": "Andy Goren", - "author_inst": "Applied Biology Inc." - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.28.20248965", "rel_title": "PREDICTORS OF UPTAKE OF A POTENTIAL COVID-19 VACCINE AMONG NIGERIAN ADULTS", @@ -1026459,6 +1024629,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.30.20248888", + "rel_title": "The Joint Impact of COVID-19 Vaccination and Non-Pharmaceutical Interventions on Infections, Hospitalizations, and Mortality: An Agent-Based Simulation", + "rel_date": "2021-01-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.30.20248888", + "rel_abs": "BackgroundVaccination against SARS-CoV-2 has the potential to significantly reduce transmission and morbidity and mortality due to COVID-19. This modeling study simulated the comparative and joint impact of COVID-19 vaccine efficacy and coverage with and without non-pharmaceutical interventions (NPIs) on total infections, hospitalizations, and deaths.\n\nMethodsAn agent-based simulation model was employed to estimate incident SARS-CoV-2 infections and COVID-19-associated hospitalizations and deaths over 18 months for the State of North Carolina, a population of roughly 10.5 million. Vaccine efficacy of 50% and 90% and vaccine coverage of 25%, 50%, and 75% (at the end of a 6-month distribution period) were evaluated. Six vaccination scenarios were simulated with NPIs (i.e., reduced mobility, school closings, face mask usage) maintained and removed during the period of vaccine distribution.\n\nResultsIn the worst-case vaccination scenario (50% efficacy and 25% coverage), 2,231,134 new SARS-CoV-2 infections occurred with NPIs removed and 799,949 infections with NPIs maintained. In contrast, in the best-case scenario (90% efficacy and 75% coverage), there were 450,575 new infections with NPIs maintained and 527,409 with NPIs removed. When NPIs were removed, lower efficacy (50%) and higher coverage (75%) reduced infection risk by a greater magnitude than higher efficacy (90%) and lower coverage (25%) compared to the worst-case scenario (absolute risk reduction 13% and 8%, respectively).\n\nConclusionSimulation results suggest that premature lifting of NPIs while vaccines are distributed may result in substantial increases in infections, hospitalizations, and deaths. Furthermore, as NPIs are removed, higher vaccination coverage with less efficacious vaccines can contribute to a larger reduction in risk of SARS-CoV-2 infection compared to more efficacious vaccines at lower coverage. Our findings highlight the need for well-resourced and coordinated efforts to achieve high vaccine coverage and continued adherence to NPIs before many pre-pandemic activities can be resumed.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Mehul D Patel", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Erik Rosenstrom", + "author_inst": "North Carolina State University" + }, + { + "author_name": "Julie S Ivy", + "author_inst": "North Carolina State University" + }, + { + "author_name": "Maria E Mayorga", + "author_inst": "North Carolina State University" + }, + { + "author_name": "Pinar Keskinocak", + "author_inst": "Georgia Institute of Technology" + }, + { + "author_name": "Ross M Boyce", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Kristen Hassmiller Lich", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Raymond L Smith", + "author_inst": "East Carolina University" + }, + { + "author_name": "Karl T Johnson", + "author_inst": "University of North Carolina at Chapel Hill" + }, + { + "author_name": "Julie L Swann", + "author_inst": "North Carolina State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.31.20249081", "rel_title": "THE INFLUENCE OF HLA GENOTYPE ON SUSCEPTIBILITY TO, AND SEVERITY OF, COVID-19 INFECTION", @@ -1026823,37 +1025048,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.30.20249066", - "rel_title": "Need of care in interpreting Google Trends-based COVID-19 infodemiological study results: potential risk of false-positivity", - "rel_date": "2021-01-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.30.20249066", - "rel_abs": "ObjectiveGoogle Trends (GT) is being used as an epidemiological tool to study coronavirus disease (COVID-19) by identifying keywords in search trends that are predictive for the COVID-19 epidemiological burden. However, many of the earlier GT-based studies include potential statistical fallacies by measuring the correlation between non-stationary time sequences without adjusting for multiple comparisons or the confounding of media coverage, leading to concerns about the increased risk of obtaining false-positive results. In this study, we aimed to apply statistically more favorable methods to validate the earlier GT-based COVID-19 study results.\n\nMethodsWe extracted the relative GT search volume for keywords associated with COVID-19 symptoms, and evaluated their Granger-causality to weekly COVID-19 positivity in eight English-speaking countries and Japan. In addition, the impact of media coverage on keywords with significant Granger-causality was further evaluated using Japanese regional data.\n\nResultsOur Granger causality-based approach largely decreased (by up to approximately one-third) the number of keywords identified as having a significant temporal relationship with the COVID-19 trend when compared to those identified by the Pearson correlation-based approach. \"Sense of smell\" and \"loss of smell\" were the most reliable GT keywords across all the evaluated countries; however, when adjusted with their media coverage, these keyword trends did not Granger-cause the COVID-19 positivity trends (in Japan).\n\nConclusionOur results suggest that some of the search keywords reported as candidate predictive measures in earlier GT-based COVID-19 studies may potentially be unreliable; therefore, caution is necessary when interpreting published GT-based study results.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Kenichiro Sato", - "author_inst": "University of Tokyo Hospital" - }, - { - "author_name": "Tatsuo Mano", - "author_inst": "University of Tokyo Hospital" - }, - { - "author_name": "Atsushi Iwata", - "author_inst": "Tokyo Metropolitan Geriatric Medical Center Hospital" - }, - { - "author_name": "Tatsushi Toda", - "author_inst": "University of Tokyo Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.31.20249076", "rel_title": "Divergences on expected pneumonia cases during the COVID-19 epidemic in Catalonia: A time-series analysis of primary care electronic health records covering about 6 million people.", @@ -1027989,6 +1026183,49 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2021.01.02.425099", + "rel_title": "Spike protein disulfide disruption as a potential treatment for SARS-CoV-2", + "rel_date": "2021-01-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2021.01.02.425099", + "rel_abs": "The coronaviral pandemic is exerting a tremendously detrimental impact on global health, quality of life and the world economy, emphasizing the need for effective medications for current and future coronaviral outbreaks as a complementary approach to vaccines. The Spike protein, responsible for cell receptor binding and viral internalization, possesses multiple disulfide bonds raising the possibility that disulfide-reducing agents might disrupt Spike function, prevent viral entry and serve as effective drugs against SARS-CoV-2. Here we show the first experimental evidence that reagents capable of reducing disulfide bonds can inhibit viral infection in cell-based assays. Molecular dynamics simulations of the Spike receptor-binding domain (RBD) predict increased domain flexibility when the four disulfide bonds of the domain are reduced. This flexibility is particularly prominent for the surface loop, comprised of residues 456-490, which interacts with the Spike cell receptor ACE2. Consistent with this finding, the addition of exogenous disulfide bond reducing agents affects the RBD secondary structure, lowers its melting temperature from 52 to 36-39{degrees}C and decreases its binding affinity to ACE2 by two orders of magnitude at 37{degrees}C. Finally, the reducing agents dithiothreitol (DTT) and tris(2-carboxyethyl)phosphine (TCEP) inhibit viral replication at high {micro}M - low mM levels with a negligible effect on cell viability at these concentrations. The antiviral effect of monothiol-based reductants N-Acetyl-L-cysteine (NAC) and reduced glutathione (GSH) was not observed due to decreases in cell viability. Our research demonstrates the clear potential for medications that disrupt Spike disulfides as broad-spectrum anticoronaviral agents and as a first-line defense against current and future outbreaks.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Andrey M. Grishin", + "author_inst": "University of Saskatchewan" + }, + { + "author_name": "Nataliya V. Dolgova", + "author_inst": "University of Saskatchewan" + }, + { + "author_name": "Shelby Harms", + "author_inst": "University of Saskatchewan" + }, + { + "author_name": "Ingrid J. Pickering", + "author_inst": "University of Saskatchewan" + }, + { + "author_name": "Graham N. George", + "author_inst": "University of Saskatchewan" + }, + { + "author_name": "Darryl Falzarano", + "author_inst": "University of Saskatchewan" + }, + { + "author_name": "Miroslaw Cygler", + "author_inst": "University of Saskatchewan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2021.01.03.425115", "rel_title": "The ancient cardioprotective mechanisms of ACE2 bestow SARS-CoV-2 with a wide host range", @@ -1028393,157 +1026630,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.31.424987", - "rel_title": "Paired heavy and light chain signatures contribute to potent SARS-CoV-2 neutralization in public antibody responses", - "rel_date": "2021-01-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.31.424987", - "rel_abs": "Understanding protective mechanisms of antibody recognition can inform vaccine and therapeutic strategies against SARS-CoV-2. We discovered a new antibody, 910-30, that targets the SARS-CoV-2 ACE2 receptor binding site as a member of a public antibody response encoded by IGHV3-53/IGHV3-66 genes. We performed sequence and structural analyses to explore how antibody features correlate with SARS-CoV-2 neutralization. Cryo-EM structures of 910-30 bound to the SARS-CoV-2 spike trimer revealed its binding interactions and ability to disassemble spike. Despite heavy chain sequence similarity, biophysical analyses of IGHV3-53/3-66 antibodies highlighted the importance of native heavy:light pairings for ACE2 binding competition and for SARS-CoV-2 neutralization. We defined paired heavy:light sequence signatures and determined antibody precursor prevalence to be ~1 in 44,000 human B cells, consistent with public antibody identification in several convalescent COVID-19 patients. These data reveal key structural and functional neutralization features in the IGHV3-53/3-66 public antibody class to accelerate antibody-based medical interventions against SARS-CoV-2.\n\nHighlightsO_LIA molecular study of IGHV3-53/3-66 public antibody responses reveals critical heavy and light chain features for potent neutralization\nC_LIO_LICryo-EM analyses detail the structure of a novel public antibody class member, antibody 910-30, in complex with SARS-CoV-2 spike trimer\nC_LIO_LICryo-EM data reveal that 910-30 can both bind assembled trimer and can disassemble the SARS-CoV-2 spike\nC_LIO_LISequence-structure-function signatures defined for IGHV3-53/3-66 class antibodies including both heavy and light chains\nC_LIO_LIIGHV3-53/3-66 class precursors have a prevalence of 1:44,000 B cells in healthy human antibody repertoires\nC_LI", - "rel_num_authors": 34, - "rel_authors": [ - { - "author_name": "Bailey B Banach", - "author_inst": "Bioengineering Graduate Program, University of Kansas, Lawrence, KS 66045, USA." - }, - { - "author_name": "Gabriele Cerutti", - "author_inst": "Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. Zuckerman Mind Brain Behavior Institute, Columbia University," - }, - { - "author_name": "Ahmed S Fahad", - "author_inst": "Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66045, USA." - }, - { - "author_name": "Chen-Hsiang Shen", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Matheus Oliveira de Souza", - "author_inst": "Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66045, USA." - }, - { - "author_name": "Phinikoula S Katsamba", - "author_inst": "Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. Zuckerman Mind Brain Behavior Institute, Columbia University," - }, - { - "author_name": "Yaroslav Tsybovsky", - "author_inst": "Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederi" - }, - { - "author_name": "Pengfei Wang", - "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA." - }, - { - "author_name": "Manoj S Nair", - "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA." - }, - { - "author_name": "Yaoxing Huang", - "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA." - }, - { - "author_name": "Irene M Francino Urdaniz", - "author_inst": "Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, 80305, USA." - }, - { - "author_name": "Paul J Steiner", - "author_inst": "Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, 80305, USA." - }, - { - "author_name": "Matias Gutierrez-Gonzalez", - "author_inst": "Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66045, USA." - }, - { - "author_name": "Lihong Liu", - "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA." - }, - { - "author_name": "Sheila N Lopez Acevedo", - "author_inst": "Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66045, USA." - }, - { - "author_name": "Alexandra Nazzari", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Jacy R Wolfe", - "author_inst": "Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66045, USA." - }, - { - "author_name": "Yang Luo", - "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA." - }, - { - "author_name": "Adam S Olia", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "I-Ting Teng", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Jian Yu", - "author_inst": "Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. Aaron Diamond AIDS Research Center, Columbia University Vagel" - }, - { - "author_name": "Tongqing Zhou", - "author_inst": "Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA." - }, - { - "author_name": "Eswar R Reddem", - "author_inst": "Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. Zuckerman Mind Brain Behavior Institute, Columbia University," - }, - { - "author_name": "Jude Bimela", - "author_inst": "Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. Zuckerman Mind Brain Behavior Institute, Columbia University," - }, - { - "author_name": "Xiaoli Pan", - "author_inst": "Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66045, USA." - }, - { - "author_name": "Bharat Madan", - "author_inst": "Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66045, USA." - }, - { - "author_name": "Amy D Laflin", - "author_inst": "Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66045, USA." - }, - { - "author_name": "Rajani Nimrania", - "author_inst": "Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66045, USA." - }, - { - "author_name": "Kwon-Tung Yuen", - "author_inst": "State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Carol Yu Centre for Infection, Li Ka Shing Faculty of Medicine, The Universit" - }, - { - "author_name": "Timothy A Whitehead", - "author_inst": "Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, 80305, USA." - }, - { - "author_name": "David D Ho", - "author_inst": "Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA." - }, - { - "author_name": "Peter D Kwong", - "author_inst": "Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. Vaccine Research Center, National Institute of Allergy and In" - }, - { - "author_name": "Lawrence Shapiro", - "author_inst": "Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. Aaron Diamond AIDS Research Center, Columbia University Vagel" - }, - { - "author_name": "Brandon J DeKosky", - "author_inst": "Bioengineering Graduate Program, University of Kansas, Lawrence, KS 66045, USA. Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, KS 66045" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.12.31.424729", "rel_title": "The functions of SARS-CoV-2 neutralizing and infection-enhancing antibodies in vitro and in mice and nonhuman primates", @@ -1029751,6 +1027837,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.27.20248905", + "rel_title": "Probability that an infection like Covid-19 stops without reaching herd immunity, calculated with a stochastic agent-based model.", + "rel_date": "2021-01-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.27.20248905", + "rel_abs": "The spread of an infection is simulated with a stochastic agent-based model. In a certain range of R0 values, the infection either rapidly comes to halt or a large proportion of the population is infected until herd immunity is achieved. Which of these two possibilities actually occurs is random. The probability of each case is determined quasi-empirically. This stochastic phenomenon may explain unexpected infection trajectories.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Manfred Karl Robert Eissler", + "author_inst": "Praxis Dres Eissler" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.26.20248883", "rel_title": "Covid-19, Lockdowns and Motor Vehicle Collisions: Empirical Evidence from Greece", @@ -1030083,33 +1028188,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.12.30.424801", - "rel_title": "Pharmacophore-based peptide biologics neutralize SARS-CoV-2 S1 and deter S1-ACE2 interaction in vitro", - "rel_date": "2020-12-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.30.424801", - "rel_abs": "Effective therapeutics and stable vaccine are the urgent need of the day to combat COVID-19 pandemic. SARS-CoV-2 spike protein has a pivotal role in cell-entry and host immune response, thus regarded as potential drug- and vaccine-target. As the virus utilizes the S1 domain of spike to initiate cell-attachment and S2 domain for membrane fusion, several attempts have been made to design viral-receptor and viral-fusion blockers. Here, by deploying interactive structure-based design and pharmacophore-based approaches, we designed short and stable peptide-biologics i.e. CoV-spike-neutralizing peptides (CSNPs) including CSNP1, CSNP2, CSNP3, CSNP4. We could demonstrate in cell culture experiments that CSNP2 binds to S1 at submicromolar concentration and abrogates the S1-hACE2 interaction. CSNP3, a modified and downsized form of CSNP2, could neither interfere with the S1-hACE2 interaction nor bind to S1. CSNP4 exhibited dose-dependent binding to both S1 and hACE2 and abolished the S1-hACE2 interaction in vitro. CSNP4 possibly enhance the mAb-based S1 neutralization by limiting the spontaneous movement of spike receptor-binding domain (RBD), whereas CSNP2 allowed RBD-mAb binding without any steric hindrance. Taken together, we suggest that CSNP2 and CSNP4 are potent and stable candidate peptides that can neutralize the SARS-CoV-2 spike and possibly pose the virus to host immune surveillance.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Hyun Goo Woo", - "author_inst": "Ajou University" - }, - { - "author_name": "Masaud Shah", - "author_inst": "Dept. Physiology. Biomedical School, Ajou University" - }, - { - "author_name": "Sung Ung Moon", - "author_inst": "Ajou University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.12.29.424779", "rel_title": "Engineering, production and characterization of Spike and Nucleocapsid structural proteins of SARS-CoV-2 in Nicotiana benthamiana as vaccine candidates against COVID-19", @@ -1031372,6 +1029450,81 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.12.29.424482", + "rel_title": "Structural basis for broad coronavirus neutralization", + "rel_date": "2020-12-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.29.424482", + "rel_abs": "Three highly pathogenic {beta}-coronaviruses crossed the animal-to-human species barrier in the past two decades: SARS-CoV, MERS-CoV and SARS-CoV-2. SARS-CoV-2 has infected more than 64 million people worldwide, claimed over 1.4 million lives and is responsible for the ongoing COVID-19 pandemic. We isolated a monoclonal antibody, termed B6, cross-reacting with eight {beta}-coronavirus spike glycoproteins, including all five human-infecting {beta}-coronaviruses, and broadly inhibiting entry of pseudotyped viruses from two coronavirus lineages. Cryo-electron microscopy and X-ray crystallography characterization reveal that B6 binds to a conserved cryptic epitope located in the fusion machinery and indicate that antibody binding sterically interferes with spike conformational changes leading to membrane fusion. Our data provide a structural framework explaining B6 cross-reactivity with {beta}-coronaviruses from three lineages along with proof-of-concept for antibody-mediated broad coronavirus neutralization elicited through vaccination. This study unveils an unexpected target for next-generation structure-guided design of a pan-coronavirus vaccine.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Maximilian Sauer", + "author_inst": "University of Washington" + }, + { + "author_name": "Young-Jun Park", + "author_inst": "University of Washington" + }, + { + "author_name": "M. Alejandra Tortorici", + "author_inst": "University of Washington" + }, + { + "author_name": "Alexandra C Walls", + "author_inst": "University of Washington" + }, + { + "author_name": "Leah Homad", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Oliver Acton", + "author_inst": "University of Washington" + }, + { + "author_name": "John E Bowen", + "author_inst": "University of Washington" + }, + { + "author_name": "Chunyan Wang", + "author_inst": "Utrecht University" + }, + { + "author_name": "Xiaoli Xiong", + "author_inst": "University of Washington" + }, + { + "author_name": "Willem de van der Schueren", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Joel Quispe", + "author_inst": "University of Washington" + }, + { + "author_name": "Berend-Jan Bosch", + "author_inst": "Utrecht University" + }, + { + "author_name": "Benjamin G Hoffstrom", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Andrew T McGuire", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "David Veesler", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.12.29.424733", "rel_title": "SARS-CoV-2 highly conserved s2m element dimerizes via a kissing complex and interacts with host miRNA-1307-3p", @@ -1031844,49 +1029997,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.12.29.424682", - "rel_title": "ACE2 peptide fragment interacts with several sites on the SARS-CoV-2 spike protein S1", - "rel_date": "2020-12-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.29.424682", - "rel_abs": "The influence of the peptide QAKTFLDKFNHEAEDLFYQ on the kinetics of the SARS-CoV-2 spike protein S1 binding to angiotensin-converting enzyme 2(ACE2) was studied to model the interaction of the virus with its host cell. This peptide corresponds to the sequence 24-42 of the ACE2 1 domain, which is the binding site for the S1 protein. The on-rate and off-rate of S1-ACE2 complex formation were measured in the presence of various peptide concentrations using Bio-Layer Interferometry (BLI). The formation of the S1-ACE2 complex was inhibited when the S1 protein was preincubated with the peptide, however, no significant inhibitory effect was observed in the absence of preincubation. Dissociation kinetics revealed that the peptide remained bound to the S1-ACE2 complex and stabilized this complex. Computational mapping of the S1 protein surface for peptide binding revealed two additional sites, located at some distance from the receptor binding domain (RBD) of S1. These additional binding sites affect the interaction between the peptide, the S1 protein, and ACE2.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Aleksei Kuznetsov", - "author_inst": "University of Tartu" - }, - { - "author_name": "Piret Arukuusk", - "author_inst": "University of Tartu" - }, - { - "author_name": "Heleri H\u00e4rk", - "author_inst": "University of Tartu" - }, - { - "author_name": "Erkki Juronen", - "author_inst": "Icosagen AS, Tartu" - }, - { - "author_name": "\u00dclo Langel", - "author_inst": "University of Tartu" - }, - { - "author_name": "Mart Ustav", - "author_inst": "University of Tartu" - }, - { - "author_name": "Jaak J\u00e4rv", - "author_inst": "University of Tartu" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.12.28.424630", "rel_title": "Structural dynamics of the SARS-CoV-2 frameshift-stimulatory pseudoknot reveal topologically distinct conformers", @@ -1032985,6 +1031095,101 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.12.23.20248598", + "rel_title": "Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil", + "rel_date": "2020-12-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.23.20248598", + "rel_abs": "In this study, we report the sequencing of 180 new viral genomes obtained from different municipalities of the state of Rio de Janeiro from April to December 2020. We identified a novel lineage of SARS-CoV-2, originated from B.1.1.28, distinguished by five single-nucleotide variants (SNVs): C100U, C28253U, G28628U, G28975U, and C29754U. The SNV G23012A (E484K), in the receptor-binding domain of Spike protein, was widely spread across the samples. This mutation was previously associated with escape from neutralizing antibodies against SARS-CoV-2. This novel lineage emerged in late July being first detected by us in late October and still mainly restricted to the capital of the state. However, as observed for other strains it can be rapidly spread in the state. The significant increase in the frequency of this lineage raises concerns about public health management and continuous need for genomic surveillance during the second wave of infections.\n\nArticle Summary LineWe identified a novel circulating lineage of SARS-CoV-2 in the state of Rio de Janeiro Brazil originated from B.1.1.28 lineage.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Carolina M Voloch", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Ronaldo da Silva Francisco Junior", + "author_inst": "Laboratorio Nacional de Computacao Cientifica" + }, + { + "author_name": "Luiz Gonzaga P de Almeida", + "author_inst": "Laboratorio Nacional de Computacao Cientifica" + }, + { + "author_name": "Cynthia C Cardoso", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Otavio J Brustolini", + "author_inst": "Laboratorio Nacional de Computacao Cientifica" + }, + { + "author_name": "Alexandra L Gerber", + "author_inst": "Laboratorio Nacional de Computacao Cientifica" + }, + { + "author_name": "Ana Paula de C Guimaraes", + "author_inst": "Laboratorio Nacional de Computacao Cientifica" + }, + { + "author_name": "Diana Mariani", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Raissa Mirella da Costa", + "author_inst": "Universidade Federal do Rio de Janeiro; Hospital Naval Marcilio Dias" + }, + { + "author_name": "Orlando Costa Ferreira Junior", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "- Covid19-UFRJ Workgroup", + "author_inst": "" + }, + { + "author_name": "- LNCC-Workgroup", + "author_inst": "" + }, + { + "author_name": "Adriana Cony Cavalcanti", + "author_inst": "Laboratorio Central de Saude Publica Noel Nutels, Rio de Janeiro, Brazil" + }, + { + "author_name": "Thiago Silva Frauches", + "author_inst": "Secretaria Municipal de Saude de Marica, Marica, Brazil" + }, + { + "author_name": "Claudia Maria Braga de Mello", + "author_inst": "Secretaria Estadual de Saude do Rio de Janeiro, Rio de Janeiro, Brazil." + }, + { + "author_name": "Rafael de Mello Galiez", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Debora Souza Faffe", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Terezinha M P P Castineira", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "AMILCAR TANURI", + "author_inst": "Universidade Federal do Rio de Janeiro" + }, + { + "author_name": "Ana Tereza Ribeiro de Vasconcelos", + "author_inst": "Universidade Federal do Rio de Janeiro" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2020.12.23.20231589", "rel_title": "Characteristics of SARS-CoV-2 Testing for Rapid Diagnosis of COVID-19 during the Initial Stages of a Global Pandemic", @@ -1033565,49 +1031770,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.23.20248784", - "rel_title": "The importance of continued non-pharmaceutical interventions during the upcoming SARS-COV-2 vaccination campaign", - "rel_date": "2020-12-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.23.20248784", - "rel_abs": "In this communication we assess the potential benefit of SARS-COV-2 pandemic vaccination in the US and show how continued use of non-pharmaceutical interventions (NPIs) will be crucial during implementation.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Marta Galanti", - "author_inst": "Columbia University" - }, - { - "author_name": "Sen Pei", - "author_inst": "Columbia University" - }, - { - "author_name": "Teresa K Yamana", - "author_inst": "Columbia University" - }, - { - "author_name": "Frederick J Angulo", - "author_inst": "Pfizer Vaccines" - }, - { - "author_name": "Apostolos Charos", - "author_inst": "Pfizer Vaccines" - }, - { - "author_name": "David L Swerdlow", - "author_inst": "Pfizer Vaccines" - }, - { - "author_name": "Jeffrey Shaman", - "author_inst": "Columbia University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.23.20247379", "rel_title": "Prognostic and predictive biomarkers in patients with COVID-19 treated with tocilizumab in a randomised controlled trial", @@ -1034643,6 +1032805,121 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.24.20248822", + "rel_title": "Estimated transmissibility and severity of novel SARS-CoV-2 Variant of Concern 202012/01 in England", + "rel_date": "2020-12-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.24.20248822", + "rel_abs": "A novel SARS-CoV-2 variant, VOC 202012/01 (lineage B.1.1.7), emerged in southeast England in November 2020 and is rapidly spreading towards fixation. Using a variety of statistical and dynamic modelling approaches, we estimate that this variant has a 43-90% (range of 95% credible intervals 38-130%) higher reproduction number than preexisting variants. A fitted two-strain dynamic transmission model shows that VOC 202012/01 will lead to large resurgences of COVID-19 cases. Without stringent control measures, including limited closure of educational institutions and a greatly accelerated vaccine roll-out, COVID-19 hospitalisations and deaths across England in 2021 will exceed those in 2020. Concerningly, VOC 202012/01 has spread globally and exhibits a similar transmission increase (59-74%) in Denmark, Switzerland, and the United States.", + "rel_num_authors": 25, + "rel_authors": [ + { + "author_name": "Nicholas G Davies", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Sam Abbott", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Rosanna C. Barnard", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Christopher I. Jarvis", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Adam J. Kucharski", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "James D Munday", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Carl A. B. Pearson", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Timothy Russell", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Damien Tully", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Alex D. Washburne", + "author_inst": "Selva Analytics LLC" + }, + { + "author_name": "Tom Wenseleers", + "author_inst": "KU Leuven" + }, + { + "author_name": "Amy Gimma", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "William Waites", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Kerry L. M. Wong", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Kevin van Zandvoort", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Justin D. Silverman", + "author_inst": "College of Information Science and Technology, Pennsylvania State University" + }, + { + "author_name": "- CMMID COVID-19 Working Group", + "author_inst": "" + }, + { + "author_name": "- The COVID-19 Genomics UK (COG-UK) Consortium", + "author_inst": "" + }, + { + "author_name": "Karla Diaz-Ordaz", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Ruth H Keogh", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Rosalind M Eggo", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Sebastian Funk", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Mark Jit", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Katherine E. Atkins", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "W. John Edmunds", + "author_inst": "London School of Hygiene and Tropical Medicine" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.23.423942", "rel_title": "SARS-CoV-2 infecting the inner ear results in potential hearing damage at the early stage or prognosis of COVID-19 in rodents", @@ -1035219,65 +1033496,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2020.12.23.424189", - "rel_title": "Berberine and obatoclax inhibit SARS-CoV-2 replication in primary human nasal epithelial cells in vitro", - "rel_date": "2020-12-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.23.424189", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged as a new human pathogen in late 2019 and has infected an estimated 10% of the global population in less than a year. There is a clear need for effective antiviral drugs to complement current preventive measures including vaccines. In this study, we demonstrate that berberine and obatoclax, two broad-spectrum antiviral compounds, are effective against multiple isolates of SARS-CoV-2. Berberine, a plant-derived alkaloid, inhibited SARS-CoV-2 at low micromolar concentrations and obatoclax, originally developed as an anti-apoptotic protein antagonist, was effective at sub-micromolar concentrations. Time-of-addition studies indicated that berberine acts on the late stage of the viral life cycle. In agreement, berberine mildly affected viral RNA synthesis, but strongly reduced infectious viral titers, leading to an increase in the particle-to-pfu ratio. In contrast, obatoclax acted at the early stage of the infection, in line with its activity to neutralize the acidic environment in endosomes. We assessed infection of primary human nasal epithelial cells cultured on an air-liquid interface and found that SARS-CoV-2 infection induced and repressed expression of a specific set of cytokines and chemokines. Moreover, both obatoclax and berberine inhibited SARS-CoV-2 replication in these primary target cells. We propose berberine and obatoclax as potential antiviral drugs against SARS-CoV-2 that could be considered for further efficacy testing.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Finny S. Varghese", - "author_inst": "Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands" - }, - { - "author_name": "Esther van Woudenbergh", - "author_inst": "Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, the Netherlands" - }, - { - "author_name": "Gijs J. Overheul", - "author_inst": "Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands" - }, - { - "author_name": "Marc J. Eleveld", - "author_inst": "Section Paediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijm" - }, - { - "author_name": "Lisa Kurver", - "author_inst": "Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands" - }, - { - "author_name": "Niels van Heerbeek", - "author_inst": "Department of Otolaryngology, Head and Neck Surgery, Radboudumc, Nijmegen, The Netherlands" - }, - { - "author_name": "Arjan van Laarhoven", - "author_inst": "Department of Internal Medicine, Radboud University Medical Center, Nijmegen, The Netherlands" - }, - { - "author_name": "Pascal Miesen", - "author_inst": "Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands" - }, - { - "author_name": "Gerco den Hartog", - "author_inst": "Centre for Immunology of Infectious Diseases and Vaccines, National Institute for Public Health and the Environment, Bilthoven, The Netherlands" - }, - { - "author_name": "Marien I. de Jonge", - "author_inst": "Section Paediatric Infectious Diseases, Laboratory of Medical Immunology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijm" - }, - { - "author_name": "Ronald P. van Rij", - "author_inst": "Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.12.23.424199", "rel_title": "Exploring epitope and functional diversity of anti-SARS-CoV2 antibodies using AI-based methods", @@ -1036557,6 +1034775,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.12.22.20248676", + "rel_title": "Acceptance and Attitudes Toward COVID-19 Vaccines: A Cross-Sectional Study from Jordan", + "rel_date": "2020-12-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.22.20248676", + "rel_abs": "BackgroundVaccines are effective interventions that can reduce the high burden of diseases globally. However, public vaccine hesitancy is a pressing problem for public health authorities. With the availability of COVID-19 vaccines, little information is available on the public acceptability and attitudes towards the COVID-19 vaccines in Jordan. This study aimed to investigate the acceptability of COVID-19 vaccines and its predictors in addition to the attitudes towards these vaccines among public in Jordan.\n\nMethodsAn online, cross-sectional, and self-administered questionnaire was instrumentalized to survey adult participants from Jordan on the acceptability of COVID-19 vaccines. Logistic regression analysis was used to find the predictors of COVID-19 vaccines acceptability.\n\nResultsA total of 3,100 participants completed the survey. The public acceptability of COVID-19 vaccines was fairly low (37.4%) in Jordan. Males (OR=2.488, 95CI%=1.834-3.375, p<.001) and those who took the seasonal influenza vaccine (OR=2.036, 95CI%=1.306-3.174, p=.002) were more likely to accept Covid-19 vaccines. Similarly, participants who believed that vaccines are generally safe (OR=9.258, 95CI%=6.020-14.237, p<.001) and those who were willing to pay for vaccines (OR=19.223, 95CI%=13.665-27.042, p<.001), once available, were more likely to accept the COVID-19 vaccines. However, those above 35 years old (OR=0.376, 95CI%=0.233-0.607, p<.001) and employed participants (OR=0.542, 95CI%=0.405-0.725, p<.001) were less likely to accept the COVID-19 vaccines. Moreover, participants who believed that there was a conspiracy behind COVID-19 (OR=0.502, 95CI%=0.356- 0.709, p<.001) and those who do not trust any source of information on COVID-19 vaccines (OR=0.271, 95CI%=0.183 - 0.400, p<.001), were less likely to have acceptance towards them. The most trusted sources of information on COVID-19 vaccines were healthcare providers.\n\nConclusionSystematic interventions are required by public health authorities to reduce the levels of vaccines hesitancy and improve their acceptance. We believe these results and specifically the low rate of acceptability is alarming to Jordanian health authorities and should stir further studies on the root causes and the need of awareness campaigns. These interventions should take the form of reviving the trust in national health authorities and structured awareness campaigns that offer transparent information about the safety and efficacy of the vaccines and the technology that was utilized in their production.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Tamam El-Elimat", + "author_inst": "Department of Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid 22110, Jordan" + }, + { + "author_name": "Mahmoud M. AbuAlSamen", + "author_inst": "Department of Family and Community Medicine, Faculty of Medicine, University of Jordan, Amman 11942, Jordan" + }, + { + "author_name": "Basima A. Almomani", + "author_inst": "Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid 22110, Jordan" + }, + { + "author_name": "Nour A. Al-Sawalha", + "author_inst": "Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid 22110, Jordan" + }, + { + "author_name": "Feras Q. Alali", + "author_inst": "Faculty of Pharmacy, QU Health, Qatar University, Doha 2713, Qatar and Biomedical and Pharmaceutical Research Unit, QU Health, Qatar University, Doha 2713, Qata" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.12.23.20248758", "rel_title": "Introduction into the Marseille geographical area of a mild SARS-CoV-2 variant originating from sub-Saharan Africa", @@ -1036937,33 +1035190,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.22.20248736", - "rel_title": "REAL-TIME MECHANISTIC BAYESIAN FORECASTS OF COVID-19 MORTALITY", - "rel_date": "2020-12-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.22.20248736", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWThe COVID-19 pandemic emerged in late December 2019. In the first six months of the global outbreak, the US reported more cases and deaths than any other country in the world. Effective modeling of the course of the pandemic can help assist with public health resource planning, intervention efforts, and vaccine clinical trials. However, building applied forecasting models presents unique challenges during a pandemic. First, case data available to models in real-time represent a non-stationary fraction of the true case incidence due to changes in available diagnostic tests and test-seeking behavior. Second, interventions varied across time and geography leading to large changes in transmissibility over the course of the pandemic. We propose a mechanistic Bayesian model (MechBayes) that builds upon the classic compartmental susceptible-exposed-infected-recovered (SEIR) model to operationalize COVID-19 forecasting in real time. This framework includes non-parametric modeling of varying transmission rates, non-parametric modeling of case and death discrepancies due to testing and reporting issues, and a joint observation likelihood on new case counts and new deaths; it is implemented in a probabilistic programming language to automate the use of Bayesian reasoning for quantifying uncertainty in probabilistic forecasts. The model has been used to submit forecasts to the US Centers for Disease Control, through the COVID-19 Forecast Hub. We examine the performance relative to a baseline model as well as alternate models submitted to the Forecast Hub. Additionally, we include an ablation test of our extensions to the classic SEIR model. We demonstrate a significant gain in both point and probabilistic forecast scoring measures using MechBayes when compared to a baseline model and show that MechBayes ranks as one of the top 2 models out of 10 submitted to the COVID-19 Forecast Hub. Finally, we demonstrate that MechBayes performs significantly better than the classical SEIR model.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Graham C Gibson", - "author_inst": "University of Massachusetts Amherst" - }, - { - "author_name": "Nicholas G Reich", - "author_inst": "University of Massachusetts Amherst" - }, - { - "author_name": "Daniel Sheldon", - "author_inst": "University of Massachusetts Amherst" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.22.20248744", "rel_title": "Unravelling the early warning capability of wastewater surveillance for COVID-19: A temporal study on SARS-CoV-2 RNA detection and need for the escalation", @@ -1038194,6 +1036420,41 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.12.22.423894", + "rel_title": "Ferritin nanoparticle based SARS-CoV-2 RBD vaccine induces persistent antibody response and long-term memory in mice", + "rel_date": "2020-12-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.22.423894", + "rel_abs": "Since the outbreak of COVID-19, over 200 vaccine candidates have been documented and some of them have advanced to clinical trials with encouraging results. However, the antibody persistence over 3 months post immunization and the long-term memory have been rarely reported. Here, we report that a ferritin nanoparticle based SARS-CoV-2 RBD vaccine induced in mice an efficient antibody response which lasts for at least 7 months post immunization. Significantly higher number of memory B cells were maintained and a significantly higher level of recall response was induced upon antigen challenge. Thus, we believe our current study provide the first information about the long-term antibody persistence and memory response of a COVID-19 vaccine. This information would be also timely useful for the development and evaluation of other vaccines.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Wenjun Wang", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Baoying Huang", + "author_inst": "National Institute for Viral Disease Control and Prevention, China CDC" + }, + { + "author_name": "Yanping Zhu", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + }, + { + "author_name": "Wenjie Tan", + "author_inst": "National Institute for Viral Disease Control and Prevention, China CDC" + }, + { + "author_name": "Mingzhao Zhu", + "author_inst": "Institute of Biophysics, Chinese Academy of Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.12.22.423965", "rel_title": "Development of a novel hybrid alphavirus-SARS-CoV-2 particle for rapid in vitro screening and quantification of neutralization antibodies, antiviral drugs, and viral mutations", @@ -1038590,293 +1036851,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.12.21.20248608", - "rel_title": "Adaptive immunity to SARS-CoV-2 in cancer patients: The CAPTURE study", - "rel_date": "2020-12-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.21.20248608", - "rel_abs": "There is a pressing need to characterise the nature, extent and duration of immune response to SARS-CoV-2 in cancer patients and inform risk-reduction strategies and preserve cancer outcomes. CAPTURE is a prospective, longitudinal cohort study of cancer patients and healthcare workers (HCWs) integrating longitudinal immune profiling and clinical annotation. We evaluated 529 blood samples and 1051 oronasopharyngeal swabs from 144 cancer patients and 73 HCWs and correlated with >200 clinical variables. In patients with solid cancers and HCWs, S1-reactive and neutralising antibodies to SARS-CoV-2 were detectable five months post-infection. SARS-CoV-2-specific T-cell responses were detected, and CD4+ T-cell responses correlated with S1 antibody levels. Patients with haematological malignancies had impaired but partially compensated immune responses. Overall, cancer stage, disease status, and therapies did not correlate with immune responses. These findings have implications for understanding individual risks and potential effectiveness of SARS-CoV-2 vaccination in the cancer population.", - "rel_num_authors": 68, - "rel_authors": [ - { - "author_name": "Annika Fendler", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Lewis Au", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Laura Amanda Boos", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Fiona Byrne", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Scott Thomas Colville Shepherd", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Ben Shum", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Camille L Gerard", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Barry Ward", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Wenyi Xie", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Maddalena Cerrone", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Georgina H Cornish", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Martin Pule", - "author_inst": "Autolus Limited, The MediaWorks" - }, - { - "author_name": "Leila Mekkaoui", - "author_inst": "Autolus Limited, The MediaWorks" - }, - { - "author_name": "Kevin Ng", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Richard Stone", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Camilla Gomes", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Helen R Flynn", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Ana Agua-Doce", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Phillip Hobson", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Simon Caidan", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Mike Howell", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Robert Goldstone", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Mike Gavrielides", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Emma Nye", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Bram Snijders", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "James Macrae", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Jerome Nicod", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Adrian Hayday", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Firza Gronthoud", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Christina Messiou", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "David Cunningham", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Ian Chau", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Naureen Starling", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Nicholas Turner", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Jennifer Rusby", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Liam Welsh", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Nicholas van As", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Robin Jones", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Joanne Droney", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Susana Banerjee", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Kate Tatham", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Shaman Jhanji", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Olivia Curtis", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Kevin Harrington", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Shreerang Bhide", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Tim Slattery", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Yasir Khan", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Zayd Tippu", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Isla Leslie", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Spyridon Gennatas", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Alicia Okines", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Alison Reid", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Kate Young", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Andrew Furness", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Lisa Pickering", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Sonia Ghandi", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Steve Gamblin", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Charles Swanton", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Emma Nicholson", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Sacheen Kumar", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Nadia Yousaf", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Katalin Andrea Wilkinson", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Anthony Swerdlow", - "author_inst": "The Institute of Cancer Research" - }, - { - "author_name": "Ruth Harvey", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "George Kassiotis", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Robert Wilkinson", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "James Larkin", - "author_inst": "The Royal Marsden NHS Foundation Trust" - }, - { - "author_name": "Samra Turajlic", - "author_inst": "The Francis Crick Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "oncology" - }, { "rel_doi": "10.1101/2020.12.22.20248392", "rel_title": "Dynamics of a dual SARS-CoV-2 strain co-infection on a prolonged viral shedding COVID-19 case: insights into clinical severity and disease duration", @@ -1040088,6 +1038062,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.21.20248383", + "rel_title": "Transmission risk of SARS-CoV-2 on airplanes and high-speed trains", + "rel_date": "2020-12-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.21.20248383", + "rel_abs": "Modern transportation plays a key role in the long-distance and rapid spread of SARS-CoV-2. However, little is known about the transmission risk of SARS-CoV-2 on confined vehicles, such as airplanes and trains. Based on the itinerary and epidemiological data of COVID-19 cases and close contacts among 9,265 airline passengers on 291 airplanes and 29,335 passengers on 830 high-speed trains in China from December 20, 2019 to March 17, 2020, we estimated that the upper bound of overall attack rate of COVID-19 among passengers was 0.60% (95% confidence interval: 0.43%-0.84%) for airplanes and 0.35% (0.28%-0.44%) for trains departing from Wuhan before its lockdown, respectively. The reproduction number during travel ranged from 0.12 to 0.19 on airplanes and from 0.07 to 0.12 on trains, with the risk varying by seat distance from the index case and joint travel time, but the difference in risk was not significant between the types of aircraft and train. Overall, the risk of SARS-CoV-2 transmission on planes and high-speed trains with high efficiency air filtration devices was relatively low. Our findings improve understanding of COVID-19 spread during travel and may inform response efforts, such as lifting travel restrictions, and resuming transportation in the pandemic.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Maogui Hu", + "author_inst": "Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, China" + }, + { + "author_name": "Jinfeng Wang", + "author_inst": "Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, China" + }, + { + "author_name": "Hui Lin", + "author_inst": "China Academy of Electronics and Information Technology, Beijing, China" + }, + { + "author_name": "Corrine W Ruktanonchai", + "author_inst": "WorldPop, School of Geography and Environmental Science, University of Southampton, UK" + }, + { + "author_name": "Chengdong Xu", + "author_inst": "Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, China" + }, + { + "author_name": "Bin Meng", + "author_inst": "Beijing Union University, Beijing, China" + }, + { + "author_name": "Xin Zhang", + "author_inst": "Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing, China" + }, + { + "author_name": "Alessandra Carioli", + "author_inst": "WorldPop, School of Geography and Environmental Science, University of Southampton, UK" + }, + { + "author_name": "Yuqing Feng", + "author_inst": "Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, China" + }, + { + "author_name": "Qian Yin", + "author_inst": "Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, China" + }, + { + "author_name": "Jessica R Floyd", + "author_inst": "WorldPop, School of Geography and Environmental Science, University of Southampton, UK" + }, + { + "author_name": "Nick W Ruktanonchai", + "author_inst": "WorldPop, School of Geography and Environmental Science, University of Southampton, UK" + }, + { + "author_name": "Zhongjie Li", + "author_inst": "Divisions of Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing, China" + }, + { + "author_name": "Weizhong Yang", + "author_inst": "School of Population Medicine and Public Health, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China" + }, + { + "author_name": "Andrew J Tatem", + "author_inst": "WorldPop, School of Geography and Environmental Science, University of Southampton, UK" + }, + { + "author_name": "Shengjie Lai", + "author_inst": "WorldPop, School of Geography and Environmental Science, University of Southampton, UK" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.19.20248374", "rel_title": "Airborne Transmission of Virus-Laden Aerosols inside a Music Classroom: Effects of Portable Purifiers and Aerosol Injection Rates", @@ -1040516,49 +1038569,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.22.20248622", - "rel_title": "Optimal strategies for combining vaccine prioritization and social distancing to reduce hospitalizations and mitigate COVID19 progression", - "rel_date": "2020-12-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.22.20248622", - "rel_abs": "Social distancing is an effective population-level mitigation strategy to prevent COVID19 propagation but it does not reduce the number of susceptible individuals and bears severe social consequences--a dire situation that can be overcome with the recently developed vaccines. Although a combination of these interventions should provide greater benefits than their isolated deployment, a mechanistic understanding of the interplay between them is missing. To tackle this challenge we developed an age-structured deterministic model in which vaccines are deployed during the pandemic to individuals who, in the eye of public health, are susceptible (do not show symptoms). The model allows for flexible and dynamic prioritization strategies with shifts between target groups. We find a strong interaction between social distancing and vaccination in their effect on the proportion of hospitalizations. In particular, prioritizing vaccines to elderly (60+) before adults (20-59) is more effective when social distancing is applied to adults or uniformly. In addition, the temporal reproductive number Rt is only affected by vaccines when deployed at sufficiently high rates and in tandem with social distancing. Finally, the same reduction in hospitalization can be achieved via different combination of strategies, giving decision makers flexibility in choosing public health policies. Our study provides insights into the factors that affect vaccination success and provides methodology to test different intervention strategies in a way that will align with ethical guidelines.\n\nAuthor summaryA major question in epidemiology is how to combine intervention methods in an optimal way. With the recent deployment of COVID19 vaccine, this question is now particularly relevant. Using a data-driven model in which vaccines are deployed during the pandemic and their prioritization can shift between target groups we show that there is a strong interplay between these interventions. For example, prioritizing vaccines to elderly--the common strategy worldwide--results in a larger reduction in hospitalizations when social distancing is applied to adults than to elderly. Importantly, reduction in hospitalizations can be achieved via multiple combination of intervention strategies, allowing for flexible public health policies.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Sharon Guerstein", - "author_inst": "Ben-Gurion University of the Negev" - }, - { - "author_name": "Victoria Romeo-Aznar", - "author_inst": "University of Chicago" - }, - { - "author_name": "Ma'ayan Dekel", - "author_inst": "Ben-Gurion University of the Negev" - }, - { - "author_name": "Oren Miron", - "author_inst": "Ben-Gurion University of the Negev" - }, - { - "author_name": "Nadav Davidovitch", - "author_inst": "Ben-Gurion University of the Negev" - }, - { - "author_name": "Rami Puzis", - "author_inst": "Ben-Gurion University of the Negev" - }, - { - "author_name": "Shai Pilosof", - "author_inst": "Ben Gurion University of the Negev" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.19.20248531", "rel_title": "COVID-19 control measure effects suggest excess winter mortality is more sensitive to infection control than warmer temperatures.", @@ -1041362,6 +1039372,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.12.21.20248662", + "rel_title": "Home confinement during COVID-19 pandemic reduced physical activity but not health-related quality of life in previously active older women", + "rel_date": "2020-12-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.21.20248662", + "rel_abs": "BackgroundTo investigate the effect of COVID-19 home confinement on levels of physical activity, sedentary behavior and health-related quality of life (HRQL) in older women previously participating in exercise and educational programs.\n\nMethods64 older women (age = 72{+/-}5 ys) who participated in a physical exercise/educational program and adhered to government home confinement recommendations have their levels of physical activity, sedentary behavior and HRQL assessed before and during (11 to 13 weeks after introduction of government recommendations to reduce virus transmission) COVID-19 pandemic.\n\nResultsThere were significant reductions in total physical activity (-259 METs/week, P = 0.02), as a result of a [~]17.0 % reduction in walking (-30.8 min/week, P = 0.004) and [~]41.8 % reduction in vigorous-intensity activity (-29.6 min/week, P < 0.001). Sedentary behavior also increased (2.24 h/week, P < 0.001; 1.07 h/week days, P < 0.001; and 1.54 h/weekend days, P < 0.001). However, no significant change occurred in moderate-intensity physical activity, and HRQL domains and facets, except for an improvement in environment domain.\n\nConclusionHome confinement due to COVID-19 pandemic decreased levels of physical activity and increased levels of sedentary behavior in previously active older women who participated in an educational program. However, there were no significant changes in HRQL. These results suggest that educational programs promoting healthy behaviors may attenuate the impact of home confinement in older women.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Vanessa Teixeira do Amaral", + "author_inst": "Sao Paulo State University" + }, + { + "author_name": "Isabela Roque Marcal", + "author_inst": "Sao Paulo State University" + }, + { + "author_name": "Thiago da Cruz Silva", + "author_inst": "Sao Paulo State University" + }, + { + "author_name": "Fernanda Bianchi Souza", + "author_inst": "Sao Paulo State University" + }, + { + "author_name": "Yacco Volpato Munhoz", + "author_inst": "Sao Paulo State University" + }, + { + "author_name": "Pedro Henrique Camprigher Witzler", + "author_inst": "Sao Paulo State University" + }, + { + "author_name": "Matheus Monge Soares Correa", + "author_inst": "Sao Paulo State University" + }, + { + "author_name": "Bianca Fernandes", + "author_inst": "Sao Paulo State University" + }, + { + "author_name": "Emmanuel Gomes Ciolac", + "author_inst": "Sao Paulo State University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "sports medicine" + }, { "rel_doi": "10.1101/2020.12.22.20248666", "rel_title": "When months matter; modelling the impact of the COVID-19 pandemic on the diagnostic pathway of Motor Neurone Disease (MND)", @@ -1041818,137 +1039879,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.19.20248559", - "rel_title": "Changes in UK hospital mortality in the first wave of COVID-19: the ISARIC WHO Clinical Characterisation Protocol prospective multicentre observational cohort study", - "rel_date": "2020-12-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.19.20248559", - "rel_abs": "BackgroundMortality rates of UK patients hospitalised with COVID-19 appeared to fall during the first wave. We quantify potential drivers of this change and identify groups of patients who remain at high risk of dying in hospital.\n\nMethodsThe International Severe Acute Respiratory and emerging Infection Consortium (ISARIC) WHO Clinical Characterisation Protocol UK recruited a prospective cohort admitted to 247 acute UK hospitals with COVID-19 in the first wave (March to August 2020). Outcome was hospital mortality within 28 days of admission. We performed a three-way decomposition mediation analysis using natural effects models to explore associations between week of admission and hospital mortality adjusting for confounders (demographics, comorbidity, illness severity) and quantifying potential mediators (respiratory support and steroids).\n\nFindingsUnadjusted hospital mortality fell from 32.3% (95%CI 31.8, 32.7) in March/April to 16.4% (95%CI 15.0, 17.8) in June/July 2020. Reductions were seen in all ages, ethnicities, both sexes, and in comorbid and non-comorbid patients. After adjustment, there was a 19% reduction in the odds of mortality per 4 week period (OR 0.81, 95%CI 0.79, 0.83). 15.2% of this reduction was explained by greater disease severity and comorbidity earlier in the epidemic. The use of respiratory support changed with greater use of non-invasive ventilation (NIV). 22.2% (OR 0.94, 95%CI 0.94, 0.96) of the reduction in mortality was mediated by changes in respiratory support.\n\nInterpretationThe fall in hospital mortality in COVID-19 patients during the first wave in the UK was partly accounted for by changes in case mix and illness severity. A significant reduction was associated with differences in respiratory support and critical care use, which may partly reflect improved clinical decision making. The remaining improvement in mortality is not explained by these factors, and may relate to community behaviour on inoculum dose and hospital capacity strain.\n\nFundingNIHR & MRC\n\nKey points / Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSRisk factors for mortality in patients hospitalised with COVID-19 have been established. However there is little literature regarding how mortality is changing over time, and potential explanations for why this might be. Understanding changes in mortality rates over time will help policy makers identify evolving risk, strategies to manage this and broader decisions about public health interventions.\n\nAdded value of this studyMortality in hospitalised patients at the beginning of the first wave was extremely high. Patients who were admitted to hospital in March and early April were significantly more unwell at presentation than patients who were admitted in later months. Mortality fell in all ages, ethnic groups, both sexes and in patients with and without comorbidity, over and above contributions from falling illness severity. After adjustment for these variables, a fifth of the fall in mortality was explained by changes in the use of respiratory support and steroid treatment, along with associated changes in clinical decision-making relating to supportive interventions. However, mortality was persistently high in patients who required invasive mechanical ventilation, and in those patients who received non-invasive ventilation outside of critical care.\n\nImplications of all the available evidenceThe observed reduction in hospital mortality was greater than expected based on the changes seen in both case mix and illness severity. Some of this fall can be explained by changes in respiratory care, including clinical learning. In addition, introduction of community policies including wearing of masks, social distancing, shielding of vulnerable patients and the UK lockdown potentially resulted in people being exposed to less virus.\n\nThe decrease in mortality varied depending on the level of respiratory support received. Patients receiving invasive mechanical ventilation have persistently high mortality rates, albeit with a changing case-mix, and further research should target this group.\n\nSevere COVID-19 disease has primarily affected older people in the UK. Many of these people, but not all have significant frailty. It is essential to ensure that patients and their families remain at the centre of decision-making, and we continue with an individualised approach to their treatment and care.", - "rel_num_authors": 29, - "rel_authors": [ - { - "author_name": "Annemarie B Docherty", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Rachel H Mulholland", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Nazir I Lone", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Christopher P Cheyne", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Daniela De Angelis", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Karla Diaz-Ordaz", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Cara Donoghue", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Thomas M Drake", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Jake Dunning", - "author_inst": "Imperial College, London" - }, - { - "author_name": "Sebastian Funk", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Marta Garcia-Finana", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Michelle Girvan", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Hayley E Hardwick", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Janet Harrison", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Antonia Ho", - "author_inst": "University of Glasgow" - }, - { - "author_name": "David M Hughes", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Ruth H Keogh", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Peter D Kirwan", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Gary Leeming", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Jonathan S Nguyen-Van-Tam", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Riinu Pius", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Clark D Russell", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Rebecca Spencer", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Brian DM Tom", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Lance Turtle", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Peter JM Openshaw", - "author_inst": "Imperial College London" - }, - { - "author_name": "J Kenneth Baillie", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Ewen M Harrison", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Malcolm G Semple", - "author_inst": "University of Liverpool" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.20.20248602", "rel_title": "Safety and immunogenicity of a recombinant tandem-repeat dimeric RBD protein vaccine against COVID-19 in adults: pooled analysis of two randomized, double-blind, placebo-controlled, phase 1 and 2 trials", @@ -1043692,6 +1041622,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.18.20248518", + "rel_title": "Impact of the COVID-19 Pandemic and Vaccine Hesitancy among Farmworkers from Monterey County, California", + "rel_date": "2020-12-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.18.20248518", + "rel_abs": "ObjectivesTo examine the impact of the COVID-19 pandemic on farmworkers from Monterey County, California.\n\nMethodsWe recruited adult farmworkers (n=1115) between July 16, 2020 and November 30, 2020. We collected information on sociodemographic characteristics, health behaviors, economic and social stressors experienced during COVID-19, and willingness to be vaccinated via interviews by phone.\n\nResultsStudy participants, particularly female farmworkers, reported adverse effects of the pandemic on their mental health and home environment (e.g., 24% overall reported depression and/or anxiety symptoms). The pandemic also resulted in greater financial burden for many farmworkers, with 37% food insecure and 51% unable to pay bills. Half of respondents reported that they were extremely likely to be vaccinated. Vaccine hesitancy was most common in participants who were women, younger, born in the United States, and living in more rural areas.\n\nConclusionsWe found that the pandemic has substantially impacted the mental and physical health and economic and food security of farmworkers.\n\nPublic Health ImplicationsThis study highlights the need to provide farmworkers with supplemental income, and increased mental and family health, and food support services.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Ana M Mora", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Joseph A Lewnard", + "author_inst": "University of California Berkeley" + }, + { + "author_name": "Katherine Kogut", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Stephen Rauch", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Norma Morga", + "author_inst": "Clinica de Salud del Valle de Salinas" + }, + { + "author_name": "Nicholas Jewell", + "author_inst": "University of California, Berkeley" + }, + { + "author_name": "Maximiliano Cuevas", + "author_inst": "Clinica de Salud del Valle de Salinas" + }, + { + "author_name": "Brenda Eskenazi", + "author_inst": "University of California, Berkeley" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.16.20245191", "rel_title": "Impact of housing conditions on changes in youth's mental health following the initial national COVID-19 lockdown: A cohort study", @@ -1044220,45 +1042197,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.12.22.423920", - "rel_title": "Evolutionary tracking of SARS-CoV-2 genetic variants highlights intricate balance of stabilizing and destabilizing mutations", - "rel_date": "2020-12-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.22.423920", - "rel_abs": "The currently ongoing COVID-19 pandemic caused by SARS-CoV-2 has accounted for millions of infections and deaths across the globe. Genome sequences of SARS-CoV-2 are being published daily in public databases and the availability of this genome datasets has allowed unprecedented access into the mutational patterns of SARS-CoV-2 evolution. We made use of the same genomic information for conducting phylogenetic analysis and identifying lineage-specific mutations. The catalogued lineage defining mutations were analysed for their stabilizing or destabilizing impact on viral proteins. We recorded persistence of D614G, S477N, A222V V1176F variants and a global expansion of the PANGOLIN variant B.1. In addition, a retention of Q57H (B.1.X), R203K/G204R (B.1.1.X), T85I (B.1.2-B.1.3), G15S+T428I (C.X) and I120F (D.X) variations was observed. Overall, we recorded a striking balance between stabilizing and destabilizing mutations, therefore well-maintained protein structures. With selection pressures in the form of newly developed vaccines and therapeutics to mount soon in coming months, the task of mapping of viral mutations and recording of their impact on key viral proteins would be crucial to pre-emptively catch any escape mechanism that SARS-CoV-2 may evolve for.\n\nSTUDY IMPORTANCEAs large numbers of the SARS CoV-2 genome sequences are shared in publicly accessible repositories, it enables scientists a detailed evolutionary analysis since its initial isolation in Wuhan, China. We investigated the evolutionarily associated mutational diversity overlaid on the major phylogenetic lineages circulating globally, using 513 representative genomes. We detailed phylogenetic persistence of key variants facilitating global expansion of the PANGOLIN variant B.1, including the recent, fast expanding, B.1.1.7 lineage. The stabilizing or destabilizing impact of the catalogued lineage defining mutations on viral proteins indicates their possible involvement in balancing the protein function and structure. A clear understanding of this mutational profile is of high clinical significance to catch any vaccine escape mechanism, as the same proteins make crucial components of vaccines recently approved and in development. In this direction, our study provides an imperative framework and baseline data upon which further analysis could be built as newer variants of SARS-CoV-2 continue to appear.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Jobin John Jacob", - "author_inst": "Christian Medical College,Vellore" - }, - { - "author_name": "Karthick Vasudevan", - "author_inst": "Christian Medical College, Vellore" - }, - { - "author_name": "Agila Kumari Pragasam", - "author_inst": "Christian Medical College, Vellore" - }, - { - "author_name": "Karthik Gunasekaran", - "author_inst": "Christian Medical College, Vellore" - }, - { - "author_name": "Balaji Veeraraghavan", - "author_inst": "Christian Medical College, Vellore" - }, - { - "author_name": "Ankur Mutreja", - "author_inst": "University of Cambridge" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.12.21.423850", "rel_title": "SARS-CoV-2 Genomic Surveillance in Costa Rica: Evidence of a Divergent Population and an Increased Detection of a Spike T1117I Mutation", @@ -1045558,6 +1043496,45 @@ "type": "new results", "category": "scientific communication and education" }, + { + "rel_doi": "10.1101/2020.12.18.20248478", + "rel_title": "The challenges of the coming mass vaccination and exit strategy in prevention and control of COVID-19, a modelling study", + "rel_date": "2020-12-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.18.20248478", + "rel_abs": "With success in the development of COVID-19 vaccines, it is urgent and challenging to analyse how the coming large-scale vaccination in the population and the growing public desire of relaxation of non-pharmaceutical interventions (NPIs) interact to impact the prevention and control of the COVID-19 pandemic. Using mathematical models, we focus on two aspects: 1) how the vaccination program should be designed to balance the dynamic exit of NPIs; 2) how much the vaccination coverage is needed to avoid a second wave of the epidemics when the NPIs exit in stages. We address this issue globally, and take six countries--China, Brazil, Indonesia, Russia, UK, and US--in our case study. We showed that a dynamic vaccination program in three stages can be an effective approach to balance the dynamic exit of the NPIs in terms of mitigating the epidemics. The vaccination rates and the accumulative vaccination coverage in these countries are estimated by fitting the model to the real data. We observed that the required effective vaccination coverages are greatly different to balance the dynamic exit of NPIs in these countries, providing a quantitative criterion for the requirement of an integrative package of NPIs. We predicted the epidemics under different vaccination rates for these countries, and showed that the vaccination can significantly decrease the peak value of a future wave. Furthermore, we found that a lower vaccination coverage can result in a subsequent wave once the NPIs exit. Therefore, there is a critical (minimum) vaccination coverage, depending on effectiveness of NPIs to avoid a subsequent wave. We estimated the critical vaccination coverages for China, Brazil, and Indonesia under different scenarios. In conclusion, we quantitatively showed that the dynamic vaccination program can be the effective approach to supplement or even eventually replace NPIs in mitigating the epidemics and avoiding future waves, and we suggest that country level-based exit strategies of the NPIs should be considered, according to the possible quarantine rate and testing ability, and the accessibility, affordability and efficiency of the vaccines.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Biao Tang", + "author_inst": "Xi'an Jiaotong University" + }, + { + "author_name": "Peiyu Liu", + "author_inst": "Shaanxi Normal University" + }, + { + "author_name": "Jie Yang", + "author_inst": "Shaanxi Normal University" + }, + { + "author_name": "Jianhong Wu", + "author_inst": "York University" + }, + { + "author_name": "Yanni Xiao", + "author_inst": "Xi'an Jiaotong University" + }, + { + "author_name": "Sanyi Tang", + "author_inst": "Shaanxi Normal University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.18.20248336", "rel_title": "Real-world data suggest antibody positivity to SARS-CoV-2 is associated with a decreased risk of future infection", @@ -1046093,45 +1044070,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.12.18.20248455", - "rel_title": "The impact of the first UK Covid-19 lockdown on carers and people living with low prevalence dementia: results from the Rare Dementia Support survey", - "rel_date": "2020-12-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.18.20248455", - "rel_abs": "IntroductionThe public health measures imposed to contain Covid-19 during the first UK lockdown resulted in significant changes in the provision of community support and care for people with dementia. People with low prevalence and young-onset dementias often experience non-memory, behavioural or neuropsychiatric symptoms that require specialised support.\n\nObjectiveWe explored the impact of the first Covid-19 lockdown on people living with low prevalence and young-onset dementia and their carers in the UK.\n\nMethodAn online survey, including eleven questions about the impact of the lockdown on both the person with dementia and their family caregivers was conducted. Participants were people living with dementia and caregivers who are members of the UK national-reach organisation Rare Dementia Support.\n\nResults184 carers and 24 people with dementia completed the survey. People with dementia experienced worsening of cognitive symptoms (70%), ability to do things (62%) and well-being (57%) according to their carers. Carers also reported a reduction in the support received for caring (55%). 93% of carers of people living in care homes reported a reduction in their ability to provide care. 26% of carers reported changes in the medication of the person with dementia during the lockdown. 74% of people with dementia reported decreased ability to connect with people socially.\n\nConclusionsPeople with dementia experienced a worsening of dementia symptoms, removal of support and increased difficulty to connect with other people socially during the 1st wave of Covid-19. Carers encountered barriers to both receiving and providing support and a decline in their own mental health and well-being.\n\nKey pointsO_LI70 % of carers reported cognitive symptoms getting worse during the lockdown (e.g., the person with dementia being more disoriented and finding it more difficult to communicate).\nC_LIO_LI26 % of carers reported a change (initiation or increase) in medication in the person with dementia during the lockdown.\nC_LIO_LI79 % carers reported their own physical or mental health getting worse due to the lockdown. This increased to 93% when considering responses only from family carers of people living in care homes.\nC_LIO_LI93 % of family carers of people living in care homes found it harder to continue providing care and support for their relative due to Covid-19.\nC_LI", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Aida Suarez Gonzalez", - "author_inst": "University College London" - }, - { - "author_name": "Emma Harding", - "author_inst": "UCL" - }, - { - "author_name": "Nicola Zimmerman", - "author_inst": "UCL" - }, - { - "author_name": "Zoe Hoare", - "author_inst": "UCL" - }, - { - "author_name": "Emilie Brotherhood", - "author_inst": "UCL" - }, - { - "author_name": "Sebastian J Crutch", - "author_inst": "UCL" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "neurology" - }, { "rel_doi": "10.1101/2020.12.18.20248319", "rel_title": "Genetic correlations between COVID-19 and a variety of diseases and other medically relevant traits", @@ -1047643,6 +1045581,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.17.20248389", + "rel_title": "Enhancing the estimation of compartmental model parameters for COVID-19 data with a high level of uncertainty", + "rel_date": "2020-12-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.17.20248389", + "rel_abs": "Reliable data is essential to obtain adequate simulations for forecasting the dynamics of epidemics. In this context, several political, economic, and social factors may cause inconsistencies in the reported data, which reflect the capacity for realistic simulations and predictions. In the case of COVID-19, for example, such uncertainties are mainly motivated by large-scale underreporting of cases due to reduced testing capacity in some locations. In order to mitigate the effects of noise in the data used to estimate parameters of models, we propose strategies capable of improving the ability to predict the spread of the diseases. Using a compartmental model in a COVID-19 study case, we show that the regularization of data by means of Gaussian Process Regression can reduce the variability of successive forecasts, improving predictive ability. We also present the advantages of adopting parameters of compartmental models that vary over time, in detriment to the usual approach with constant values.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Gustavo B Libotte", + "author_inst": "National Laboratory for Scientific Computing" + }, + { + "author_name": "Lucas Anjos", + "author_inst": "National Laboratory for Scientific Computing" + }, + { + "author_name": "Regina C Almeida", + "author_inst": "National Laboratory for Scientific Computing" + }, + { + "author_name": "Sandra M C Malta", + "author_inst": "National Laboratory for Scientific Computing" + }, + { + "author_name": "Renato S Silva", + "author_inst": "National Laboratory for Scientific Computing" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.17.20248424", "rel_title": "Assessing Global Covid-19 Cases Data through Compositional Data Analysis(CoDa)", @@ -1048091,53 +1046064,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.18.20248449", - "rel_title": "Coinfection with Respiratory Pathogens in COVID-19 in Korea", - "rel_date": "2020-12-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.18.20248449", - "rel_abs": "Detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in upper and lower respiratory specimens and coinfection with other respiratory pathogens in patients with coronavirus disease 2019 (COVID-19) were investigated. From the study subjects (N = 258) retrospectively enrolled when confirmed as SARS-CoV-2 positive, nasopharyngeal (NPS), oropharyngeal swabs (OPS), and sputum specimens were restored for retesting SARS-CoV-2 and detecting respiratory pathogens. Majority of the study subjects (95.7%, N = 247) were confirmed as SARS-CoV-2 positive using NPS/OPS specimens, suggesting that the upper respiratory specimen is most valuable in detecting SARS-CoV-2. Coinfection rates in COVID-19 patients (N = 258) with respiratory pathogens were 9.7% (N = 25); 8.5% (N = 22) respiratory viruses and 1.2% (N = 3) Mycoplasma pneumoniae, an atypical bacterium. Of the respiratory virus coinfection cases (N = 22), 20 (90.9%) were co-infected with a single respiratory virus and 2 (0.8%) (metapneumovirus/adenovirus and rhinovirus/bocavirus 1/2/3/4) with two viruses. Respiratory viruses in single viral coinfection cases with SARS-CoV-2 were as follows: non-SARS-CoV-2 coronaviruses (229E, NL63, and OC43, N = 5, 1.9%), rhinovirus (N = 4, 1.6%), metapneumovirus (N = 3, 1.2%), influenza A (N = 3, 1.2%), respiratory syncytial virus A and B (N = 3, 1.2%), and adenovirus (N = 2, 0.8%). No mixed coinfections with respiratory viruses and M. pneumoniae were found. In conclusion, the diagnostic value of utilizing NPS/OPS specimen is excellent, and, as the first report in Korea, coinfection with respiratory pathogens were detected at a rate of 9.7% in patients with COVID-19.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Kyung Ho Roh", - "author_inst": "Seegene Medical Foundation" - }, - { - "author_name": "Yu Kyung Kim", - "author_inst": "Kyungpook National University Hospital" - }, - { - "author_name": "Shin-Woo Kim", - "author_inst": "Kyungpook National University Hospital" - }, - { - "author_name": "Eun-Rim Kang", - "author_inst": "Seegene Medical Foundation" - }, - { - "author_name": "Yong-Jin Yang", - "author_inst": "Seegene Medical Foundation" - }, - { - "author_name": "Sun-Kyung Jung", - "author_inst": "Seegene Medical Foundation" - }, - { - "author_name": "Sun-Hwa Lee", - "author_inst": "Seegene Medical Foundation" - }, - { - "author_name": "Nackmoon Sung", - "author_inst": "Seegene Medical Foundation" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.17.20248362", "rel_title": "History of premorbid depression is a risk factor for COVID-related mortality: Analysis of a retrospective cohort of 1,387 COVID+ patients", @@ -1049513,6 +1047439,69 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.12.16.423178", + "rel_title": "Genomic and phylogenetic analyses of SARS-CoV-2 strains isolated in the city of Gwangju, South Korea", + "rel_date": "2020-12-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.16.423178", + "rel_abs": "Since the first identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in China in late December 2019, the coronavirus disease 2019 (COVID-19) has spread fast around the world. RNA viruses, including SARS-CoV-2, have higher gene mutations than DNA viruses during virus replication. Variations in SARS-CoV-2 genome could contribute to efficiency of viral spread and severity of COVID-19. In this study, we analyzed the locations of genomic mutations to investigate the genetic diversity among isolates of SARS-CoV-2 in Gwangju. We detected non-synonymous and frameshift mutations in various parts of SARS-CoV-2 genome. The phylogenetic analysis for whole genome showed that SARS-CoV-2 genomes in Gwangju isolates are clustered within clade V and G. Our findings not only provide a glimpse into changes of prevalent virus clades in Gwangju, South Korea, but also support genomic surveillance of SARS-CoV-2 to aid in the development of efficient therapeutic antibodies and vaccines against COVID-19.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Kim Min Ji", + "author_inst": "Health and Environmental Research Institution of Gwangju Metropolitan city" + }, + { + "author_name": "Lee Ji-eun", + "author_inst": "Health and Environmental Research Institution of Gwangju Metropolitan city" + }, + { + "author_name": "Chung Jae Keun", + "author_inst": "Health and Environmental Research Institution of Gwangju Metropolitan city" + }, + { + "author_name": "Kim Tae sun", + "author_inst": "Health and Environmental Research Institution of Gwangju Metropolitan city" + }, + { + "author_name": "Park Jungwook", + "author_inst": "Health and Environmental Research Institution of Gwangju Metropolitan city" + }, + { + "author_name": "Lim Mi hyeon", + "author_inst": "Health and Environmental Research Institution of Gwangju Metropolitan city" + }, + { + "author_name": "Hwang Da jeong", + "author_inst": "Health and Environmental Research Institution of Gwangju Metropolitan city" + }, + { + "author_name": "Jeong Jin", + "author_inst": "Health and Environmental Research Institution of Gwangju Metropolitan city" + }, + { + "author_name": "Yoon Ji-eun", + "author_inst": "Health and Environmental Research Institution of Gwangju Metropolitan city" + }, + { + "author_name": "Kee Hye young", + "author_inst": "Health and Environmental Research Institution of Gwangju Metropolitan city" + }, + { + "author_name": "Seo Jin jong", + "author_inst": "Health and Environmental Research Institution of Gwangju Metropolitan city" + }, + { + "author_name": "Kim Kwang gon", + "author_inst": "Health and Environmental Research Institution of Gwangju Metropolitan city" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "confirmatory results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.12.15.20248299", "rel_title": "Fundamental Limitations of Contact Tracing for COVID-19", @@ -1049985,81 +1047974,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.12.15.20247981", - "rel_title": "SIREN protocol: Impact of detectable anti-SARS-CoV-2 on the subsequent incidence of COVID-19 in 100,000 healthcare workers: do antibody positive healthcare workers have less reinfection than antibody negative healthcare workers?", - "rel_date": "2020-12-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.15.20247981", - "rel_abs": "BackgroundThe overall risk of reinfection in individuals who have previously had COVID-19 is unknown. To determine if prior SARS-CoV-2 infection (as determined by at least one positive commercial antibody test performed in a laboratory) in healthcare workers confers future immunity to reinfection, we are undertaking a large-scale prospective longitudinal cohort study of healthcare staff across the United Kingdom.\n\nMethodsPopulation and Setting: staff members of healthcare organisations working in hospitals in the UK\n\nAt recruitment, participants will have their serum tested for anti-SARS-CoV-2 at baseline and using these results will be initially allocated to either antibody positive or antibody negative cohorts. Participants will undergo antibody and viral RNA testing at 1-4 weekly intervals throughout the study period, and based on these results may move between cohorts. Any results from testing undertaken for other reasons (e.g. symptoms, contact tracing etc.) or prior to study entry will also be included. Individuals will complete enrolment and fortnightly questionnaires on exposures and symptoms. Follow-up will be for at least 12 months from study entry.\n\nOutcomeThe primary outcome of interest is a reinfection with SARS -CoV-2 during the study period. Secondary outcomes will include incidence and prevalence (both RNA and antibody) of SARS-CoV-2, viral genomics, viral culture, symptom history and antibody/neutralising antibody titres.\n\nConclusionThis large study will help us to understand the impact of the presence of antibodies on the risk of reinfection with SARS-CoV-2; the results will have substantial implications in terms of national and international policy, as well as for risk management of contacts of COVID-19 cases.\n\nTrial RegistrationIRAS ID 284460, HRA and Health and Care Research Wales approval granted 22 May 2020.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Sarah Wallace", - "author_inst": "Public Health England" - }, - { - "author_name": "Victoria Hall", - "author_inst": "COVID-19 response, Public Health England, London, UK" - }, - { - "author_name": "Andre Charlett", - "author_inst": "COVID-19 response, Public Health England, London, UK" - }, - { - "author_name": "Peter D Kirwan", - "author_inst": "COVID-19 response, Public Health England, London, UK and MRC Biostatistics Unit, University of Cambridge, Cambridge, UK" - }, - { - "author_name": "Michelle J Cole", - "author_inst": "COVID-19 response, Public Health England, London, UK" - }, - { - "author_name": "Madhumita Shrotri", - "author_inst": "COVID-19 response, Public Health England, London, UK" - }, - { - "author_name": "Sakib Rokadiya", - "author_inst": "COVID-19 response, Public Health England, London, UK" - }, - { - "author_name": "Blanche Oguti", - "author_inst": "COVID-19 response, Public Health England, London, UK" - }, - { - "author_name": "Amoolya Vusirikala", - "author_inst": "COVID-19 response, Public Health England, London, UK" - }, - { - "author_name": "Maria Zambon", - "author_inst": "COVID-19 response, Public Health England, London, UK" - }, - { - "author_name": "Tim Brooks", - "author_inst": "COVID-19 response, Public Health England, London, UK" - }, - { - "author_name": "Mary Ramsay", - "author_inst": "COVID-19 response, Public Health England, London, UK" - }, - { - "author_name": "Colin S Brown", - "author_inst": "COVID-19 response, Public Health England, London, UK" - }, - { - "author_name": "Meera A Chand", - "author_inst": "COVID-19 response, Public Health England, London, UK" - }, - { - "author_name": "Susan Hopkins", - "author_inst": "COVID-19 response, Public Health England, London, UK" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.12.16.20248358", "rel_title": "Interim evaluation of Google AI forecasting for COVID-19 compared with statistical forecasting by human intelligence in the first week", @@ -1051183,6 +1049097,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.12.14.20221937", + "rel_title": "QFEA - A Method for Assessing the Filtration Efficiency of Face Mask Materials for Early Design Prototypes and Home Mask Makers", + "rel_date": "2020-12-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.14.20221937", + "rel_abs": "The COVID-19 pandemic has led to a surge in the design and production of fabric face coverings. There are few published methods which enable mask designers, makers and purchasers to assess the relative filtration ability of mask making materials. Those methods which do exist are prohibitively expensive and difficult to conduct. As a result, mask makers, non-profits, and small-scale designers face difficult decisions when designing face coverings for personal and commercial use. In this paper, we propose a novel method, the Qualitative Filtration Efficiency Assessment (QFEA), for easily and inexpensively comparing the filtration efficiency of common materials. This method provides a highly affordable and readily available way to assess potential mask materials.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Eugenia O'Kelly", + "author_inst": "Cambridge University" + }, + { + "author_name": "Anmol Arora", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Corinne E O'Kelly", + "author_inst": "Independent Researcher" + }, + { + "author_name": "Charlotte Pearson", + "author_inst": "University of Oregon" + }, + { + "author_name": "James Ward", + "author_inst": "University of Cambridge" + }, + { + "author_name": "P John Clarkson", + "author_inst": "University of Cambridge" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.12.15.20248284", "rel_title": "Impact of COVID-19 related unemployment on increased cardiovascular disease in a high-income country: Modeling health loss, cost and equity", @@ -1051583,41 +1049536,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.12.16.423166", - "rel_title": "Molecular diversity analysis of the spike glycoprotein (S) gene from Hong Kong - China", - "rel_date": "2020-12-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.16.423166", - "rel_abs": "In this work, 37 haplotypes of spike glycoprotein of SARS-CoV-2 from Hong Kong, China, were used. All sequences were publicly available on the Platform of the National Center for Biotechnology Information (NCBI) and were analyzed for their Molecular Variance (AMOVA), haplotypic diversity, mismatch, demographic and spatial expansion, molecular diversity and time of evolutionary divergence. The results suggested that there was a low diversity among haplotypes, with very low numbers of transitions, transversions, indels-type mutations and with total absence of population expansion perceived in the neutrality tests. The estimators used in this study supported the uniformity among all the results found and confirm the evolutionary conservation of the gene, as well as its protein product, a fact that stimulates the use of therapies based on neutralizing antibodies, such as vaccines based on protein S.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Eduarda Doralice Alves Braz Da Silva", - "author_inst": "Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA" - }, - { - "author_name": "Dallynne Barbara Ramos Venancio", - "author_inst": "Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA" - }, - { - "author_name": "Rosane Maria de Albuquerque", - "author_inst": "Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA" - }, - { - "author_name": "Robson da Silva Ramos", - "author_inst": "Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA" - }, - { - "author_name": "Pierre Teodosio Felix Sr.", - "author_inst": "Laboratory of Population Genetics and Computational Evolutionary Biology - LaBECom, UNIVISA" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.12.15.422900", "rel_title": "The rapid, massive infection of the scientific literature and authors by COVID-19", @@ -1052561,6 +1050479,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.15.20248039", + "rel_title": "IMPACT OF A SARS-COV-2 INFECTION IN PATIENTS WITH CELIAC DISEASE", + "rel_date": "2020-12-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.15.20248039", + "rel_abs": "ObjectiveThe SARS-CoV-2 pandemic has spread across the world causing a dramatic number of infections and deaths. No data are available about the effects of an infection in patients affected by celiac disease (CD) in terms of the development of related symptoms and antibodies. We aimed to investigate the impact of the SARS-CoV-2 pandemic in celiac patients.\n\nDesignDuring a lockdown, the celiac patients living in the Milan area were contacted and interviewed about the development of COVID-19 symptoms as well as adherence to an anti-virus lifestyle and a gluten-free diet (GFD). They were also given a stress questionnaire to fill in. The development of anti-SARS-CoV-2 IgG and IgA (anti-RBD and N proteins) and the expression of the duodenal ACE2 receptor were investigated. When available, duodenal histology, anti-tissue transglutaminase IgA (tTGA), presence of immunologic comorbidities and adherence to the GFD were analysed as possible risk factors.\n\nResults362 celiac patients have been interviewed and 42 (11%) presented with COVID-19 symptoms. The presence of symptoms was not influenced by tTGA positivity, presence of duodenal atrophy or adherence to GFD. 37% of the symptomatic patients presented anti-SARS-CoV-2 immunoglobulins (Ig). Globally, 18% of celiac patients showed anti-SARS-CoV-2 Ig vs 25% of the non-celiac control (p=0.18). The values of anti-RBD IgG/IgA and anti-N IgG did not differ from the non-celiac controls. Celiac patients had a significant lower level of anti-N IgA. The ACE2 receptor was detected in the non-atrophic duodenal mucosa of celiac patients; atrophy was associated with a lower expression of the ACE2 receptor.\n\nConclusionCD patients have an anti-SARS-CoV-2 Ig positiveness and profile similar to non-celiac controls, except for anti-N IgA. The main celiac parameters and adherence to the GFD do not influence the development of a different Ig profile.\n\nWhat is already known about this subject?The SARS-CoV-2 pandemic has spread across the world causing infections and deaths. little is known about the possible relationship between autoimmune comorbidities and SARS-CoV-2 infection and COVID-19, and nothing it known about celiac disease.\n\nWhat are the new findings?In a large cohort of celiac patients living in a high SARS-CoV-2 incidence area in Northern Italy, no difference was observed evidenced in terms of the development of anti-SARS-CoV-2 Ig and their IgG and IgA profile compared with the normal population\n\nHow might it impact clinical practice in the foreseeable future?The absence of a relationship between celiac disease and SARS-CoV-2/COVID-19 has a relevant impact on health policy to control the pandemic by supporting an optimal resource location.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Luca Elli", + "author_inst": "Fondazione IRCCS Ca' Granda" + }, + { + "author_name": "Federica Facciotti", + "author_inst": "European Institute of Oncology IRCCS, Department of Experimental Oncology" + }, + { + "author_name": "Vincenza Lombardo", + "author_inst": "Fondazione IRCCS Ca' Granda" + }, + { + "author_name": "Alice Scricciolo", + "author_inst": "Fondazione IRCCS Ca' Granda" + }, + { + "author_name": "David S Sanders", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Valentina Vaira", + "author_inst": "University of Milan" + }, + { + "author_name": "Donatella Barisani", + "author_inst": "University of Milano-Bicocca" + }, + { + "author_name": "Maurizio Vecchi", + "author_inst": "University of Milan" + }, + { + "author_name": "Andrea Costantino", + "author_inst": "Fondazione IRCCS Ca' Granda" + }, + { + "author_name": "Lucia Scaramella", + "author_inst": "Fondazione IRCCS Ca' Granda" + }, + { + "author_name": "Bernardo Dell'Osso", + "author_inst": "University of Milan" + }, + { + "author_name": "Luisa Doneda", + "author_inst": "University of Milan" + }, + { + "author_name": "Leda Roncoroni", + "author_inst": "Fondazione IRCCS Ca' Granda" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "gastroenterology" + }, { "rel_doi": "10.1101/2020.12.15.20248237", "rel_title": "Mental and social health of children and adolescents with pre-existing mental or somatic problems during the COVID-19 pandemic lockdown", @@ -1053305,61 +1051290,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.15.20248279", - "rel_title": "Shared genetic etiology between idiopathic pulmonary fibrosis and COVID-19 severity", - "rel_date": "2020-12-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.15.20248279", - "rel_abs": "BackgroundIdiopathic pulmonary fibrosis (IPF) is a complex lung disease, characterized by progressive lung scarring. Severe COVID-19 is associated with substantial pneumonitis and has a number of shared major risk factors with IPF. This study aimed to determine the genetic correlation between IPF and severe COVID-19 and assess a potential causal role of genetically increased risk of IPF on COVID-19 severity.\n\nMethodsWe performed a Mendelian randomisation (MR) study for IPF causality in COVID-19. Genetic variants associated with IPF susceptibility (P<5x10-8) in previous genome-wide association studies (GWAS) were used as instrumental variables (IVs). Effect estimates of those IVs on COVID-19 severity were gathered from the GWAS meta-analysis by the COVID-19 Host Genetics Initiative. The genetic correlation between IPF and COVID-19 severity was estimated with linkage disequilibrium (LD) score regression.\n\nFindingsWe detected a positive genetic correlation of IPF with COVID-19 severity (rg=0.31 [95% CI 0.04-0.57], P = 0.023). The MR estimates for severe COVID-19 did not reveal any genetic association (OR 1.05, [95% CI 0.92-1.20], P = 0.43). However, outlier analysis revealed that the IPF risk allele rs35705950 at MUC5B had a different effect compared with the other variants. When rs35705950 was excluded, MR results provided evidence that genetically increased risk of IPF has a causal effect on COVID-19 severity (OR 1.21, [95% CI 1.06-1.38], P = 4.24x10-3). Furthermore, the IPF risk-allele at MUC5B showed an apparent protective effect against COVID-19 hospitalization only in older adults (OR 0.86, [95% CI 0.73-1.00], P = 2.99x10-2).\n\nInterpretationThe strongest genetic determinant of IPF, rs35705950 at MUC5B, seems to confer protection against COVID-19, whereas the combined effect of all other IPF risk loci seem to confer risk of COVID-19 severity. The observed effect of rs35705950 could either be due to protective effects of mucin over-production on the airways or a consequence of selection bias due to a patient group that is heavily enriched for the rs35705950 T undertaking strict self-isolation. Due to the diverse impact of IPF causal variants on SARS-CoV-2 infection, further investigation is needed to address this apparent paradox between variance at MUC5B and other IPF genetic risk factors.\n\nFundingNovo Nordisk Foundation and Oak Foundation.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Joao Fadista", - "author_inst": "Statens Serum Institut" - }, - { - "author_name": "Luke M. Kraven", - "author_inst": "University of Leicester" - }, - { - "author_name": "Juha Karjalainen", - "author_inst": "Institute for Molecular Medicine Finland (FIMM)" - }, - { - "author_name": "Shea J. Andrews", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Frank Geller", - "author_inst": "Statens Serum Institut" - }, - { - "author_name": "- The COVID-19 Host Genetics Initiative", - "author_inst": "-" - }, - { - "author_name": "J Kenneth Baillie", - "author_inst": "Roslin Institute" - }, - { - "author_name": "Louise V. Wain", - "author_inst": "University of Leicester" - }, - { - "author_name": "R. Gisli Jenkins", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Bjarke Feenstra", - "author_inst": "Statens Serum Institut" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2020.12.15.20248214", "rel_title": "Characteristics and Risk Factors for Hospitalization and Mortality among Persons with COVID-19 in Atlanta Metropolitan Area", @@ -1054443,6 +1052373,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.11.20210419", + "rel_title": "Safety and immunogenicity trial of an inactivated SARS-CoV-2 vaccine-BBV152: a phase 1, double-blind, randomised control trial", + "rel_date": "2020-12-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.11.20210419", + "rel_abs": "BackgroundBBV152 is a whole-virion inactivated SARS-CoV-2 vaccine formulated with a TLR 7/8 agonist molecule adsorbed to alum (Algel-IMDG).\n\nMethodsWe conducted a double-blind randomized controlled phase 1 clinical trial to evaluate the safety and immunogenicity of BBV152. A total of 375 participants were randomized equally to receive three vaccine formulations (n=100 each) prepared with 3 g with Algel-IMDG, 6 g with Algel-IMDG, and 6 g with Algel, and an Algel only control arm (n=75). Vaccines were administered on a two-dose intramuscular accelerated schedule on day 0 (baseline) and day 14. The primary outcomes were reactogenicity and safety. The secondary outcomes were immunogenicity based on the anti-IgG S1 response (detected with an enzyme-linked immunosorbent assay [ELISA] and wild-type virus neutralization [microneutralization and plaque reduction neutralization assays]). Cell-mediated responses were also evaluated.\n\nResultsReactogenicity was absent in the majority of participants, with mild events. The majority of adverse events were mild and were resolved. One serious adverse event was reported, which was found to be unrelated to vaccination. All three vaccine formulations resulted in robust immune responses comparable to a panel of convalescent serum. No significant differences were observed between the 3-g and 6-g Algel-IMDG groups. Neutralizing responses to homologous and heterologous SARS-CoV-2 strains were detected in all vaccinated individuals. Cell-mediated responses were biased to a Th-1 phenotype.\n\nConclusionsBBV152 induced binding and neutralising antibody responses and with the inclusion of the Algel-IMDG adjuvant, this is the first inactivated SARS-CoV-2 vaccine that has been reported to induce a Th1-biased response. Vaccine induced neutralizing antibody titers were reported with two divergent SARS-CoV-2 strains. BBV152 is stored between 2{degrees}C and 8{degrees}C, which is compatible with all national immunization program cold chain requirements. Both Algel-IMDG formulations were selected for the phase 2 immunogenicity trials. Further efficacy trials are underway.\n\nClinicaltrials.gov: NCT04471519", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Raches Ella", + "author_inst": "Bharat Biotech International Limited" + }, + { + "author_name": "Krishna Mohan", + "author_inst": "Bharat Biotech" + }, + { + "author_name": "Harsh Jogdand", + "author_inst": "Bharat Biotech" + }, + { + "author_name": "Sai Prasad", + "author_inst": "Bharat Biotech" + }, + { + "author_name": "Siddharth Reddy", + "author_inst": "Bharat Biotech" + }, + { + "author_name": "Vamshi Krishna Sarangi", + "author_inst": "Bharat Biotech" + }, + { + "author_name": "Brunda Ganneru", + "author_inst": "Bharat Biotech" + }, + { + "author_name": "Gajanan Sapkal", + "author_inst": "ICMR- National Institute of Virology" + }, + { + "author_name": "Pragya Yadav", + "author_inst": "ICMR-National Institute of Virology" + }, + { + "author_name": "Samiran Panda", + "author_inst": "Indian Council of Medical Research" + }, + { + "author_name": "Nivedita Gupta", + "author_inst": "Indian Council of Medical Research" + }, + { + "author_name": "Prabhakar Reddy", + "author_inst": "Nizam's Institute of Medical Sciences" + }, + { + "author_name": "Savita Verma", + "author_inst": "PGIMS-Rohtak" + }, + { + "author_name": "Sanjay Rai", + "author_inst": "All India Institute of Medical Sciences - New Delhi" + }, + { + "author_name": "Chandramani Singh", + "author_inst": "All India Institute of Medical Sciences - Patna" + }, + { + "author_name": "Sagar Redkar", + "author_inst": "Redkar Hospital" + }, + { + "author_name": "Chandra Sekhar Gillurkar", + "author_inst": "Gillurkar Hospital" + }, + { + "author_name": "Jitendra Singh Kushwaha", + "author_inst": "Prakhar Hospital" + }, + { + "author_name": "Venkat Rao", + "author_inst": "IMS SUM Hospital" + }, + { + "author_name": "Satyajit Mohapatra", + "author_inst": "SRM Hospital" + }, + { + "author_name": "Randeep Guleria", + "author_inst": "All India Institute of Medical Sciences - New Delhi" + }, + { + "author_name": "Krishna Ella", + "author_inst": "Bharat Biotech" + }, + { + "author_name": "Balram Bhargava", + "author_inst": "Indian Council of Medical Research" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.11.20246561", "rel_title": "Evolution of COVID-19 patients treated with a combination of nutraceuticals to reduce symptomatology and improve prognosis: a multi-centred, retrospective cohort study", @@ -1054891,157 +1052928,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.12.10.20245944", - "rel_title": "Azithromycin in Hospitalised Patients with COVID-19 (RECOVERY): a randomised, controlled, open-label, platform trial", - "rel_date": "2020-12-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.10.20245944", - "rel_abs": "BackgroundAzithromycin has been proposed as a treatment for COVID-19 on the basis of its immunomodulatory actions. We evaluated the efficacy and safety of azithromycin in hospitalised patients with COVID-19.\n\nMethodsIn this randomised, controlled, open-label, adaptive platform trial, several possible treatments were compared with usual care in patients hospitalised with COVID-19 in the UK. Eligible and consenting patients were randomly allocated to either usual standard of care alone or usual standard of care plus azithromycin 500 mg once daily by mouth or intravenously for 10 days or until discharge (or one of the other treatment arms). Patients were twice as likely to be randomised to usual care as to any of the active treatment groups. The primary outcome was 28-day mortality. The trial is registered with ISRCTN (50189673) and clinicaltrials.gov (NCT04381936).\n\nFindingsBetween 7 April and 27 November 2020, 2582 patients were randomly allocated to receive azithromycin and 5182 patients to receive usual care alone. Overall, 496 (19%) patients allocated to azithromycin and 997 (19%) patients allocated to usual care died within 28 days (rate ratio 1{middle dot}00; 95% confidence interval [CI] 0{middle dot}90-1{middle dot}12; p=0{middle dot}99). Consistent results were seen in all pre-specified subgroups of patients. There was no difference in duration of hospitalisation (median 12 days vs. 13 days) or the proportion of patients discharged from hospital alive within 28 days (60% vs. 59%; rate ratio 1{middle dot}03; 95% CI 0{middle dot}97-1{middle dot}10; p=0{middle dot}29). Among those not on invasive mechanical ventilation at baseline, there was no difference in the proportion meeting the composite endpoint of invasive mechanical ventilation or death (21% vs. 22%; risk ratio 0{middle dot}97; 95% CI 0{middle dot}89-1{middle dot}07; p=0{middle dot}54).\n\nInterpretationIn patients hospitalised with COVID-19, azithromycin did not provide any clinical benefit. Azithromycin use in patients hospitalised with COVID-19 should be restricted to patients where there is a clear antimicrobial indication.\n\nFundingUK Research and Innovation (Medical Research Council) and National Institute of Health Research (Grant ref: MC_PC_19056).", - "rel_num_authors": 34, - "rel_authors": [ - { - "author_name": "Peter W Horby", - "author_inst": "Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom" - }, - { - "author_name": "Alistair Roddick", - "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" - }, - { - "author_name": "Enti Spata", - "author_inst": "MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" - }, - { - "author_name": "Natalie Staplin", - "author_inst": "MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" - }, - { - "author_name": "Jonathan R Emberson", - "author_inst": "MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" - }, - { - "author_name": "Guilherme Pessoa-Amorim", - "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" - }, - { - "author_name": "Leon Peto", - "author_inst": "Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom" - }, - { - "author_name": "Mark Campbell", - "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" - }, - { - "author_name": "Christopher Brightling", - "author_inst": "Institute for Lung Health, Leicester NIHR Biomedical Research Centre, University of Leicester, Leicester, United Kingdom" - }, - { - "author_name": "Ben Prudon", - "author_inst": "Department of Respiratory Medicine, North Tees & Hartlepool NHS Foundation Trust, Stockton-on-Tees, United Kingdom" - }, - { - "author_name": "David Chadwick", - "author_inst": "Centre for Clinical Infection, James Cook University Hospital, Middlesbrough, United Kingdom" - }, - { - "author_name": "Andrew Ustianowski", - "author_inst": "North Manchester General Hospital & University of Manchester, Manchester, United Kingdom" - }, - { - "author_name": "Abdul Ashish", - "author_inst": "Wrightington Wigan and Leigh NHS Foundation Trust, Wigan, United Kingdom" - }, - { - "author_name": "Stacy Todd", - "author_inst": "Liverpool University Hospitals NHS Foundation Trust, Liverpool, United Kingdom" - }, - { - "author_name": "Bryan Yates", - "author_inst": "Northumbria Healthcare NHS Foundation Trust, North Tyneside, United Kingdom" - }, - { - "author_name": "Robert Buttery", - "author_inst": "North West Anglia NHS Foundation Trust, Peterborough, United Kingdom" - }, - { - "author_name": "Stephen Scott", - "author_inst": "The Countess of Chester Hospital NHS Foundation Trust, Chester, United Kingdom" - }, - { - "author_name": "Diego Maseda", - "author_inst": "Mid Cheshire Hospitals NHS Foundation Trust, Crewe, United Kingdom" - }, - { - "author_name": "J Kenneth Baillie", - "author_inst": "Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom" - }, - { - "author_name": "Maya H Buch", - "author_inst": "Centre for Musculoskeletal Research, University of Manchester, Manchester, United Kingdom" - }, - { - "author_name": "Lucy C Chappell", - "author_inst": "School of Life Sciences, King's College London, London, United Kingdom" - }, - { - "author_name": "Jeremy N Day", - "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom" - }, - { - "author_name": "Saul N Faust", - "author_inst": "NIHR Southampton Clinical Research Facility and Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust and University of Southampton, " - }, - { - "author_name": "Thomas Jaki", - "author_inst": "Department of Mathematics and Statistics, Lancaster University, Lancaster, United Kingdom; MRC Biostatistics Unit, University of Cambridge, Cambridge, United Ki" - }, - { - "author_name": "Katie Jeffery", - "author_inst": "Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom" - }, - { - "author_name": "Edmund Juszczak", - "author_inst": "School of Medicine, University of Nottingham, Nottingham, United Kingdom" - }, - { - "author_name": "Wei Shen Lim", - "author_inst": "Respiratory Medicine Department, Nottingham University Hospitals NHS Trust, Nottingham, United Kingdom" - }, - { - "author_name": "Alan Montgomery", - "author_inst": "School of Medicine, University of Nottingham, Nottingham, United Kingdom" - }, - { - "author_name": "Andrew Mumford", - "author_inst": "School of Cellular and Molecular Medicine, University of Bristol, Bristol, United kingdom" - }, - { - "author_name": "Kathryn Rowan", - "author_inst": "Intensive Care National Audit & Research Centre, London, United Kingdom" - }, - { - "author_name": "Guy Thwaites", - "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam, and Nuffield Department of Medicine, University of Oxford, United Kingdom" - }, - { - "author_name": "Marion Mafham", - "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" - }, - { - "author_name": "Richard Haynes", - "author_inst": "MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" - }, - { - "author_name": "Martin J Landray", - "author_inst": "Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.12.20248070", "rel_title": "Social Media Study of Public Opinions on Potential COVID-19 Vaccines: Informing Dissent, Disparities, and Dissemination", @@ -1056173,6 +1054059,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.10.20247403", + "rel_title": "Simulation-Based Study on the COVID-19 Airborne Transmission in a Restaurant", + "rel_date": "2020-12-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.10.20247403", + "rel_abs": "COVID-19 has shown a high potential of transmission via virus-carrying aerosols as supported by growing evidence. However, detailed investigations that draw direct links between aerosol transport and virus infection are still lacking. To fill in the gap, we conducted a systematic computational fluid dynamics (CFD)-based investigation of indoor air flow and the associated aerosol transport in a restaurant setting, where likely cases of airborne infection of COVID-19 caused by asymptomatic individuals were widely reported by the media. We employed an advanced in-house large eddy simulation (LES) solver and other cutting-edge numerical methods to resolve complex indoor processes simultaneously, including turbulence, flow-aerosol interplay, thermal effect, and the filtration effect by air conditioners. Using the aerosol exposure index derived from the simulation, we are able to provide a spatial map of the airborne infection risk under different settings. Our results have shown a remarkable direct linkage between regions of high aerosol exposure index and the reported infection patterns in the restaurant, providing strong support to the airborne transmission occurring in this widely-reported incidence. Using flow structure analysis and reverse-time tracing of aerosol trajectories, we are able to further pinpoint the influence of environmental parameters on the infection risks and highlight the needs for more effective preventive measures, e.g., placement of shielding according to the local flow patterns. Our research, thus, has demonstrated the capability and value of high-fidelity CFD tools for airborne infection risk assessment and the development of effective preventive measures.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Han Liu", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Sida He", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Lian Shen", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Jiarong Hong", + "author_inst": "University of Minnesota" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.12.20246934", "rel_title": "CD177, a specific marker of neutrophil activation, is a hallmark of COVID-19 severity and death", @@ -1056657,77 +1054574,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.11.20247262", - "rel_title": "COVID-19 in persons affected by Hansen's disease in Brazil", - "rel_date": "2020-12-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.11.20247262", - "rel_abs": "BackgroundHansens disease (HD) is endemic in Brazil, a country with the third highest number of COVID-19 cases in the world and the second highest number of COVID-19 deaths. COVID-19 in persons affected by HD has not been described at population level in this country.\n\nMethodsWe collated numbers of COVID-19 cases and deaths among patients who were receiving routine treatment for HD at six centres across Brazil (Belem, Bauru, Brasilia, Vitoria, Petrolina, Palmas) between 1st March and 10th December 2020.\n\nResultsOf 1,333 HD patients receiving treatment, 70 (5.2%) reported having had COVID-19. Almost all patients (97% (1,296/1,333)) including all but one of the COVID-19 cases were receiving MDT comprising rifampicin (600mg once per month), dapsone (100mg daily), and clofazimine (50 mg daily plus 300 mg once per month). Four patients died, including a patient in their 30s on MDT who had a severe type 2 HD reaction (erythema nodosum leprosum) and who was taking clofazimine 100mg daily.\n\nConclusionsWe cannot determine from these preliminary data whether persons affected by Hansens disease have a higher or lower risk of COVID-19 and related mortality compared with the general population. We will continue to monitor the effects of COVID-19 in persons affected by and treated for HD and extend this to monitor SARS-CoV-2 vaccine effectiveness in this group of patients.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Patr\u00edcia Deps", - "author_inst": "Universidade Federal do Esp\u00edrito Santo" - }, - { - "author_name": "Taynah Repsold", - "author_inst": "Universidade Federal do Esp\u00edrito Santo" - }, - { - "author_name": "Claudio Salgado", - "author_inst": "Universidade Federal do Par\u00e1" - }, - { - "author_name": "Raquel de Carvalho Bouth", - "author_inst": "Universidade Federal do Par\u00e1" - }, - { - "author_name": "Selma Regina Penha Silva Cerqueira", - "author_inst": "Universidade de Bras\u00edlia" - }, - { - "author_name": "Marisa Simon Brezinscki", - "author_inst": "Hospital da Santa Casa de Miseric\u00f3rdia de Vit\u00f3ria" - }, - { - "author_name": "Rebeca Ruppert Galarda Baptista Peixoto", - "author_inst": "Hospital da Santa Casa de Miseric\u00f3rdia de Vit\u00f3ria" - }, - { - "author_name": "Jaison Antonio Barreto", - "author_inst": "Instituto Lauro de Souza Lima" - }, - { - "author_name": "Andrea Fonseca", - "author_inst": "Servi\u00e7o de Infectologia de Petrolina" - }, - { - "author_name": "Marlene Peixoto", - "author_inst": "Secretaria Municipal de Sa\u00fade de Petrolina" - }, - { - "author_name": "Seyna Ueno Mendes", - "author_inst": "Secretaria Municipal de Sa\u00fade de Palmas" - }, - { - "author_name": "Rafael Pereira Rabelo Mendes", - "author_inst": "Secretaria Municipal de Sa\u00fade de Palmas" - }, - { - "author_name": "Pedro Paulo dos Santos Oliveira", - "author_inst": "Secretaria Municipal de Sa\u00fade de Palmas" - }, - { - "author_name": "Ciro Martins Gomes", - "author_inst": "Universidade de Bras\u00edlia" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.11.20247916", "rel_title": "Mathematical assessment of the roles of vaccination and non-pharmaceutical interventions on COVID-19 dynamics: a multigroup modeling approach", @@ -1057951,6 +1055797,49 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.12.12.422516", + "rel_title": "SARS-CoV-2 RNA reverse-transcribed and integrated into the human genome", + "rel_date": "2020-12-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.12.422516", + "rel_abs": "Prolonged SARS-CoV-2 RNA shedding and recurrence of PCR-positive tests have been widely reported in patients after recovery, yet these patients most commonly are non-infectious1-14. Here we investigated the possibility that SARS-CoV-2 RNAs can be reverse-transcribed and integrated into the human genome and that transcription of the integrated sequences might account for PCR-positive tests. In support of this hypothesis, we found chimeric transcripts consisting of viral fused to cellular sequences in published data sets of SARS-CoV-2 infected cultured cells and primary cells of patients, consistent with the transcription of viral sequences integrated into the genome. To experimentally corroborate the possibility of viral retro-integration, we describe evidence that SARS-CoV-2 RNAs can be reverse transcribed in human cells by reverse transcriptase (RT) from LINE-1 elements or by HIV-1 RT, and that these DNA sequences can be integrated into the cell genome and subsequently be transcribed. Human endogenous LINE-1 expression was induced upon SARS-CoV-2 infection or by cytokine exposure in cultured cells, suggesting a molecular mechanism for SARS-CoV-2 retro-integration in patients. This novel feature of SARS-CoV-2 infection may explain why patients can continue to produce viral RNA after recovery and suggests a new aspect of RNA virus replication.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Liguo Zhang", + "author_inst": "Whitehead Institute for Biomedical Research, Cambridge, MA, USA" + }, + { + "author_name": "Alexsia Richards", + "author_inst": "Whitehead Institute for Biomedical Research, Cambridge, MA, USA" + }, + { + "author_name": "Andrew Khalil", + "author_inst": "Whitehead Institute for Biomedical Research, Cambridge, MA, USA" + }, + { + "author_name": "Emile Wogram", + "author_inst": "Whitehead Institute for Biomedical Research, Cambridge, MA, USA" + }, + { + "author_name": "Haiting Ma", + "author_inst": "Whitehead Institute for Biomedical Research, Cambridge, MA, USA" + }, + { + "author_name": "Richard A. Young", + "author_inst": "Whitehead Institute for Biomedical Research, Cambridge, MA, USA" + }, + { + "author_name": "Rudolf Jaenisch", + "author_inst": "Whitehead Institute for Biomedical Research, Cambridge, MA, USA" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.12.13.422550", "rel_title": "Identification of four linear B-cell epitopes on the SARS-CoV-2 spike protein able to elicit neutralizing antibodies", @@ -1058402,37 +1056291,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2020.12.08.20246140", - "rel_title": "How detection ranges and usage stops impact digital contact tracing effectiveness for COVID-19", - "rel_date": "2020-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.08.20246140", - "rel_abs": "To combat the COVID-19 pandemic, many countries have adopted digital contact tracing apps. Various technologies exist to trace contacts that are potentially prone to different types of tracing errors. Here, we study the impact of different proximity detection ranges on the effectiveness and efficiency of digital contact tracing apps. Furthermore, we study a usage stop effect induced by a false positive quarantine. Our results reveal that policy makers should adjust digital contact tracing apps to the behavioral characteristics of a society. Based on this, the proximity detection range should at least cover the range of a disease spread, and be much wider in certain cases. The widely used Bluetooth Low Energy protocol may not necessarily be the most effective option in its current setting.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Konstantin D Pandl", - "author_inst": "Karlsruhe Institute of Technology" - }, - { - "author_name": "Scott Thiebes", - "author_inst": "Karlsruhe Institute of Technology" - }, - { - "author_name": "Manuel Schmidt-Kraepelin", - "author_inst": "Karlsruhe Institute of Technology" - }, - { - "author_name": "Ali Sunyaev", - "author_inst": "Karlsruhe Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.12.08.20246132", "rel_title": "Routine asymptomatic testing strategies for airline travel during the COVID-19 pandemic: a simulation analysis", @@ -1059816,6 +1057674,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.12.08.20246231", + "rel_title": "Artificial intelligence-enabled analysis of UK and US public attitudes on Facebook and Twitter towards COVID-19 vaccinations", + "rel_date": "2020-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.08.20246231", + "rel_abs": "BackgroundGlobal efforts towards the development and deployment of a vaccine for SARS-CoV-2 are rapidly advancing. We developed and applied an artificial-intelligence (AI)-based approach to analyse social-media public sentiment in the UK and the US towards COVID-19 vaccinations, to understand public attitude and identify topics of concern.\n\nMethodsOver 300,000 social-media posts related to COVID-19 vaccinations were extracted, including 23,571 Facebook-posts from the UK and 144,864 from the US, along with 40,268 tweets from the UK and 98,385 from the US respectively, from 1st March - 22nd November 2020. We used natural language processing and deep learning based techniques to predict average sentiments, sentiment trends and topics of discussion. These were analysed longitudinally and geo-spatially, and a manual reading of randomly selected posts around points of interest helped identify underlying themes and validated insights from the analysis.\n\nResultsWe found overall averaged positive, negative and neutral sentiment in the UK to be 58%, 22% and 17%, compared to 56%, 24% and 18% in the US, respectively. Public optimism over vaccine development, effectiveness and trials as well as concerns over safety, economic viability and corporation control were identified. We compared our findings to national surveys in both countries and found them to correlate broadly.\n\nConclusionsAI-enabled social-media analysis should be considered for adoption by institutions and governments, alongside surveys and other conventional methods of assessing public attitude. This could enable real-time assessment, at scale, of public confidence and trust in COVID-19 vaccinations, help address concerns of vaccine-sceptics and develop more effective policies and communication strategies to maximise uptake.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Amir Hussain", + "author_inst": "Edinburgh Napier University, UK" + }, + { + "author_name": "Ahsen Tahir", + "author_inst": "Edinburgh Napier University, UK" + }, + { + "author_name": "Zain Hussain", + "author_inst": "Edinburgh Medical School, College of Medicine and Veterinary Medicine, University of Edinburgh, UK" + }, + { + "author_name": "Zakariya Sheikh", + "author_inst": "Edinburgh Medical School, College of Medicine and Veterinary Medicine, University of Edinburgh, UK" + }, + { + "author_name": "Mandar Gogate", + "author_inst": "Edinburgh Napier University, UK" + }, + { + "author_name": "Kia Dashtipour", + "author_inst": "Edinburgh Napier University, UK" + }, + { + "author_name": "Azhar Ali", + "author_inst": "NHS Forth Medical Group, UK & Harvard T.H. Chan School of Public Health, USA" + }, + { + "author_name": "Aziz Sheikh", + "author_inst": "Usher Institute, Edinburgh Medical School, University of Edinburgh, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.12.09.20242396", "rel_title": "Through The Back Door: Expiratory Accumulation of SARS-Cov-2 in the Olfactory Mucosa as Mechanism for CNS Penetration", @@ -1060320,37 +1058225,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.09.20246363", - "rel_title": "Risk of adverse outcomes with COVID-19 in the Republic of Ireland", - "rel_date": "2020-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.09.20246363", - "rel_abs": "AimsTo compare the risk of adverse outcomes (i.e. hospital/intensive care admission, death) in population sub-groups during two periods of the COVID-19 pandemic in the Republic of Ireland.\n\nMethodsWe analysed routinely-collected, publicly-available data on 67,900 people with laboratory confirmed COVID-19 infection between 29th Feb to 14th Nov 2020. This period encompassed two waves of infection and two corresponding national lockdowns. For two observational periods covering each wave (W1, W2), each ending 17-19 days before implementation of high-level national restrictions, we segmented the population based on age and underlying clinical conditions.\n\nResultsThe prevalence of laboratory confirmed COVID-19 was 1.4%. The risk of admission to hospital, admission to intensive care, and death was 7.2%, 0.9%, and 2.5%, respectively. Compared to younger confirmed cases, those aged [≥]65 y had increased risk of hospital admission (RR 5.61), ICU admission (RR 3.56), and death (RR 60.8). W2 was associated with more cases and fewer adverse events than W1. The risk of all adverse outcomes was reduced in W2 than in W1.\n\nConclusionsOngoing responses should consider the variation in risk of adverse outcomes between specific sub-groups. These findings indicate the need to sustain the prevention, identification and management of noncommunicable diseases to reduce the burden of COVID-19.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Mark Roe", - "author_inst": "University College Dublin" - }, - { - "author_name": "Patrick Wall", - "author_inst": "University College Dublin" - }, - { - "author_name": "Patrick Mallon", - "author_inst": "University College Dublin" - }, - { - "author_name": "Mary Horgan", - "author_inst": "University College Cork" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.10.20247007", "rel_title": "Kinetics of SARS-CoV-2 antibody responses pre- and post- COVID-19 convalescent plasma transfusion in patients with severe respiratory failure: an observational case-control study", @@ -1061410,6 +1059284,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.12.10.20247130", + "rel_title": "Airborne magnetic nanoparticles: environmental risk factors for the transmission of SARS-CoV-2", + "rel_date": "2020-12-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.10.20247130", + "rel_abs": "ObjectivesTo examine the impact of concentrations of ambient fine particulate matter (PM2.5) air pollution on the incidence of COVID-19.\n\nMethodsPublicly available data of COVID-19 deaths in March/October 2020 were compared with concentrations of PM2.5 measured in previous years at urban and suburban areas in Thessaloniki. Similar publicly available data of PM2.5 concentrations from Tehran were gathered for comparison. Cross-correlation and Granger causality analysis were performed in order to assess linkage.\n\nResultsOn the one hand, the mean PM2.5 concentrations in Thessaloniki were significantly higher in the winter, however the magnetic fraction of particulate matter in the autumn is twice its annual average, suggesting that traffic-related emissions alone may not explain the entire variability of PM2.5. On the other hand, it is implied that changes in coronavirus-related deaths follow changes in airborne magnetite, with the correlation between the two data sets being maximized at the lag time of one-month. Further insight is provided by the monthly pattern of PM2.5 mass concentrations in Tehran. We find that air pollution Granger causes COVID-19 deaths (p<0.05).\n\nConclusionsA significant association has been found between PM2.5 values and the impact of the COVID-19 pandemic on a bunch of regions. Reported links between pollution levels, climate conditions and other factors affecting vulnerability to COVID-19 may instead reflect inhalation exposure to magnetic nanoparticles. A hypothesis has been set that ubiquitous airborne magnetite pollution, together with certain climatic conditions, may promote a longer permanence of the viral particles in the air, thus favoring transmission.\n\nKey messagesO_ST_ABSWhat is already known about this subject?C_ST_ABS{blacktriangleright}{blacktriangleright} Due to their small dimensions, airborne particles are able to penetrate through inhalation into many human organs, from the lungs to the cardiovascular system and the brain, which can threaten our health. Research has shown that air pollution is an important cofactor increasing the risk of mortality from coronaviruses.\n\n\nWhat are the new findings?{blacktriangleright}{blacktriangleright} Evidence exists that the magnetic fraction of PM has modulated the transmission of SARS-CoV-2 in Thessaloniki, and potentially in any other region in the world.\n\n\nHow might this impact on policy or clinical practice in the foreseeable future?{blacktriangleright}{blacktriangleright} Policymakers should take care not to overestimate the effect of social distancing interventions and should consider the impact of air pollution in current or future epidemic waves.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Carlos Martinez-Boubeta", + "author_inst": "Ecoresources P.C" + }, + { + "author_name": "Konstantinos Simeonidis", + "author_inst": "Department of Chemical Engineering, Aristotle University of Thessaloniki, Greece" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2020.12.11.20247304", "rel_title": "Predictors of Physical and Mental Health in Healthcare Teams Working with COVID-19 patients: a scoping review protocol.", @@ -1062026,65 +1059923,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.10.20247247", - "rel_title": "Mathematical modelling projections versus the actual course of the COVID-19 epidemic following the nationwide lockdown in Kyrgyzstan", - "rel_date": "2020-12-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.10.20247247", - "rel_abs": "Kyrgyzstan was placed under a two-month, nationwide lockdown due to the COVID-19 epidemic, starting on March 25, 2020. Given the highly disruptive effects of the lockdown on the national economy and peoples lives, the government decided not to extend lockdown beyond the initially planned date of May 10, 2020. The strategy chosen by the government was close to the input parameters of our models baseline scenario, full lockdown release, which we presented to policymakers in April 2020, along with various other hypothetical scenarios with managed lockdown release options. To explore whether our model could accurately predict the actual course of the epidemic following the release of lockdown, we compared the outputs of the baseline scenario, such as new cases, deaths, and demand for and occupancy of hospital beds, with actual official reports. Our analysis revealed that the model could accurately predict the timing of the epidemic peak, with a difference of just two weeks, although the magnitude of the peak was overestimated compared with the official statistics. However, it is important to note that the accuracy of the official reports remains debatable, so outputs relating to the size of the epidemic and related pressures on the health system will need to be updated if new evidence becomes available.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Ainura Moldokmatova", - "author_inst": "Univeristy of Oxford" - }, - { - "author_name": "Aida Estebesova", - "author_inst": "USAID Mission in the Kyrgyz Republic" - }, - { - "author_name": "Aizhan Dooronbekova", - "author_inst": "Public Fund Institution of Social Development in the Kyrgyz Republic" - }, - { - "author_name": "Chynar Zhumalieva", - "author_inst": "Public Fund Institution of Social Development in the Kyrgyz Republic" - }, - { - "author_name": "Aibek Mukambetov", - "author_inst": "Soros Foundation in the Kyrgyz Republic" - }, - { - "author_name": "Talant Abdyldaev", - "author_inst": "Kyrgyz Medical Academy in the Kyrgyz Republic" - }, - { - "author_name": "Aisuluu Kubatova", - "author_inst": "Public Fund Institution of Social Development in the Kyrgyz Republic" - }, - { - "author_name": "Shamil Ibragimov", - "author_inst": "Soros Foundation in the Kyrgyz Republic" - }, - { - "author_name": "Nurbolot Usenbaev", - "author_inst": "Ministry of Health of the Kyrgyz Republic" - }, - { - "author_name": "Ainura Kutmanova", - "author_inst": "Ministry of Health of the Kyrgyz Republic" - }, - { - "author_name": "Lisa J White", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.12.11.20246694", "rel_title": "Did people really drink bleach to prevent COVID-19? A tale of problematic respondents and a guide for measuring rare events in survey data", @@ -1063816,6 +1061654,69 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.12.09.417121", + "rel_title": "An interactive viral genome evolution network analysis system enabling rapid large-scale molecular tracing of SARS-CoV-2", + "rel_date": "2020-12-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.09.417121", + "rel_abs": "Comprehensive analyses of viral genomes can provide a global picture on SARS-CoV-2 transmission and help to predict the oncoming trends of pandemic. This molecular tracing is mainly conducted through extensive phylogenetic network analyses. However, the rapid accumulation of SARS-CoV-2 genomes presents an unprecedented data size and complexity that has exceeded the capacity of existing methods in constructing evolution network through virus genotyping. Here we report a Viral genome Evolution Network Analysis System (VENAS), which uses Hamming distances adjusted by the minor allele frequency to construct viral genome evolution network. The resulting network was topologically clustered and divided using community detection algorithm, and potential evolution paths were further inferred with a network disassortativity trimming algorithm. We also employed parallel computing technology to achieve rapid processing and interactive visualization of >10,000 viral genomes, enabling accurate detection and subtyping of the viral mutations through different stages of Covid-19 pandemic. In particular, several core viral mutations can be independently identified and linked to early transmission events in Covid-19 pandemic. As a general platform for comprehensive viral genome analysis, VENAS serves as a useful computational tool in the current and future pandemics.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Yunchao Ling", + "author_inst": "Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and H" + }, + { + "author_name": "Ruifang Cao", + "author_inst": "Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and H" + }, + { + "author_name": "Jiaqiang Qian", + "author_inst": "Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and H" + }, + { + "author_name": "Jiefu Li", + "author_inst": "Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and H" + }, + { + "author_name": "Haokui Zhou", + "author_inst": "Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences" + }, + { + "author_name": "Liyun Yuan", + "author_inst": "Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and H" + }, + { + "author_name": "Zhen Wang", + "author_inst": "Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and H" + }, + { + "author_name": "Guangyong Zheng", + "author_inst": "Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and H" + }, + { + "author_name": "Guoping Zhao", + "author_inst": "Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and H" + }, + { + "author_name": "Yixue Li", + "author_inst": "Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and H" + }, + { + "author_name": "Zefeng Wang", + "author_inst": "Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and H" + }, + { + "author_name": "Guoqing Zhang", + "author_inst": "Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and H" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2020.12.10.419440", "rel_title": "Coiled-coil heterodimers with increased stability for cellular regulation and sensing SARS-CoV-2 spike protein-mediated cell fusion", @@ -1064136,93 +1062037,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2020.12.09.417741", - "rel_title": "Characterization of protease activity of Nsp3 from SARS-CoV-2 and its in vitro inhibition by nanobodies", - "rel_date": "2020-12-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.09.417741", - "rel_abs": "Of the 16 non-structural proteins (Nsps) encoded by SARS CoV-2, Nsp3 is the largest and plays important roles in the viral life cycle. Being a large, multidomain, transmembrane protein, Nsp3 has been the most challenging Nsp to characterize. Encoded within Nsp3 is the papain-like protease PLpro domain that cleaves not only the viral protein but also polyubiquitin and the ubiquitin-like modifier ISG15 from host cells. We here compare the interactors of PLpro and Nsp3 and find a largely overlapping interactome. Intriguingly, we find that near full length Nsp3 is a more active protease compared to the minimal catalytic domain of PLpro. Using a MALDI-TOF based assay, we screen 1971 approved clinical compounds and identify five compounds that inhibit PLpro with IC50s in the low micromolar range but showed cross reactivity with other human deubiquitinases and had no significant antiviral activity in cellular SARS-CoV-2 infection assays. We therefore looked for alternative methods to block PLpro activity and engineered competitive nanobodies that bind to PLpro at the substrate binding site with nanomolar affinity thus inhibiting the enzyme. Our work highlights the importance of studying Nsp3 and provides tools and valuable insights to investigate Nsp3 biology during the viral infection cycle.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Lee Armstrong", - "author_inst": "MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, Dow Street, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland" - }, - { - "author_name": "Sven M Lange", - "author_inst": "MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, Dow Street, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland" - }, - { - "author_name": "Virginia de Cesare", - "author_inst": "MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, Dow Street, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland" - }, - { - "author_name": "Stephen P Matthews", - "author_inst": "MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, Dow Street, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland" - }, - { - "author_name": "Raja Sekar Nirujogi", - "author_inst": "MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, Dow Street, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland" - }, - { - "author_name": "Isobel Cole", - "author_inst": "MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, Dow Street, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland" - }, - { - "author_name": "Anthony Hope", - "author_inst": "Drug Discovery Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK" - }, - { - "author_name": "Fraser Cunningham", - "author_inst": "Drug Discovery Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK" - }, - { - "author_name": "Rachel Toth", - "author_inst": "MRC Reagents and Services, University of Dundee, Dundee DD1 5EH, Scotland, UK" - }, - { - "author_name": "Rukmini Mukherjee", - "author_inst": "Institute of Biochemistry II, Faculty of Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany. Buchmann Institute for Molecular " - }, - { - "author_name": "Denisa Bojkova", - "author_inst": "Institute of Medical Virology, University Hospital Frankfurt, Frankfurt am Main, Germany" - }, - { - "author_name": "Franz Gruber", - "author_inst": "National Phenotypic Screening Centre, University of Dundee, Dundee DD1 5EH, Scotland, UK" - }, - { - "author_name": "David Gray", - "author_inst": "Drug Discovery Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK" - }, - { - "author_name": "Paul G Wyatt", - "author_inst": "Drug Discovery Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK" - }, - { - "author_name": "Jindrich Cinatl", - "author_inst": "Institute of Medical Virology, University Hospital Frankfurt, Frankfurt am Main, Germany" - }, - { - "author_name": "Ivan Dikic", - "author_inst": "Institute of Biochemistry II, Faculty of Medicine, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany. Buchmann Institute for Molecular " - }, - { - "author_name": "Paul Davies", - "author_inst": "MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, Dow Street, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland" - }, - { - "author_name": "Yogesh Kulathu", - "author_inst": "MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, Dow Street, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.12.08.417022", "rel_title": "The D614G Mutation Enhances the Lysosomal Trafficking of SARS-CoV-2 Spike", @@ -1065474,6 +1063288,41 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.12.07.20245043", + "rel_title": "Particle-Based COVID-19 Simulator with Contact Tracing and Testing", + "rel_date": "2020-12-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.07.20245043", + "rel_abs": "GoalThe COVID-19 pandemic has emerged as the most severe public health crisis in over a century. As of January 2021, there are more than 100 million cases and 2.1 million deaths. For informed decision making, reliable statistical data and capable simulation tools are needed. Our goal is to develop an epidemic simulator that can model the effects of random population testing and contact tracing.\n\nMethodsOur simulator models individuals as particles with the position, velocity, and epidemic status states on a 2D map and runs an SEIR epidemic model with contact tracing and testing modules. The simulator is available on GitHub under the MIT license.\n\nResultsThe results show that the synergistic use of contact tracing and massive testing is effective in suppressing the epidemic (the number of deaths was reduced by 72%).\n\nConclusionsThe Particle-based COVID-19 simulator enables the modeling of intervention measures, random testing, and contact tracing, for epidemic mitigation and suppression.\n\nImpact StatementOur particle-based epidemic simulator, calibrated with COVID-19 data, models each individual as a unique particle with a location, velocity, and epidemic state, enabling the consideration of contact tracing and testing measures.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Askat Kuzdeuov", + "author_inst": "Institute of Smart Systems and Artificial Intelligence, Nazarbayev University" + }, + { + "author_name": "Aknur Karabay", + "author_inst": "Institute of Smart Systems and Artificial Intelligence, Nazarbayev University" + }, + { + "author_name": "Daulet Baimukashev", + "author_inst": "Institute of Smart Systems and Artificial Intelligence, Nazarbayev University" + }, + { + "author_name": "Bauyrzhan Ibragimov", + "author_inst": "Institute of Smart Systems and Artificial Intelligence, Nazarbayev University" + }, + { + "author_name": "Huseyin Atakan Varol", + "author_inst": "Institute of Smart Systems and Artificial Intelligence, Nazarbayev University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.12.07.20230235", "rel_title": "A 6-mRNA host response whole-blood classifier trained using patients with non-COVID-19 viral infections accurately predicts severity of COVID-19", @@ -1065917,29 +1063766,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.06.20244756", - "rel_title": "Comparing Decision Tree-Based Ensemble Machine Learning Models for COVID-19 Death Probability Profiling", - "rel_date": "2020-12-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.06.20244756", - "rel_abs": "We compare the performance of major decision tree-based ensemble machine learning models on the task of COVID-19 death probability prediction, conditional on three risk factors: age group, sex and underlying comorbidity or disease, using the US Centers for Disease Control and Prevention (CDC)s COVID-19 case surveillance dataset. To evaluate the impact of the three risk factors on COVID-19 death probability, we extract and analyze the conditional probability profile produced by the best performer. The results show the presence of an exponential rise in death probability from COVID-19 with the age group, with males exhibiting a higher exponential growth rate than females, an effect that is stronger when an underlying comorbidity or disease is present, which also acts as an accelerator of COVID-19 death probability rise for both male and female subjects. The results are discussed in connection to healthcare and epidemiological concerns and in the degree to which they reinforce findings coming from other studies on COVID-19.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Carlos Pedro Goncalves", - "author_inst": "Lusofona University of Humanities and Technologies" - }, - { - "author_name": "Jose Rouco", - "author_inst": "Lusofona University of Humanities and Technologies" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.07.20245506", "rel_title": "Model-based evaluation of school- and non-school-related measures to control the COVID-19 pandemic", @@ -1067074,6 +1064900,81 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.12.04.20242115", + "rel_title": "Lipid storm within the lungs of severe COVID-19 patients: Extensive levels of cyclooxygenase and lipoxygenase-derived inflammatory metabolites.", + "rel_date": "2020-12-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.04.20242115", + "rel_abs": "BACKGROUNDSevere Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) is the infectious agent responsible for Coronavirus disease 2019 (COVID-19). While SARS-CoV-2 infections are often benign, there are also severe COVID-19 cases, characterized by severe bilobar pneumonia that can decompensate to an acute respiratory distress syndrome, notably characterized by increased inflammation and a cytokine storm. While there is no cure against severe COVID-19 cases, some treatments significantly decrease the severity of the disease, notably aspirin and dexamethasone, which both directly or indirectly target the biosynthesis (and effects) of numerous bioactive lipids.\n\nOBJECTIVEOur working hypothesis was that severe COVID-19 cases necessitating mechanical ventilation were characterized by increased bioactive lipid levels modulating lung inflammation. We thus quantitated several lung bioactive lipids using liquid chromatography combined to tandem mass spectrometry.\n\nRESULTSWe performed an exhaustive assessment of the lipid content of bronchoalveolar lavages from 25 healthy controls and 33 COVID-19 patients necessitating mechanical ventilation. Severe COVID-19 patients were characterized by increased fatty acid levels as well as an accompanying inflammatory lipid storm. As such, most quantified bioactive lipids were heavily increased. There was a predominance of cyclooxygenase metabolites, notably TXB2 >> PGE2 [~] 12-HHTrE > PGD2. Leukotrienes were also increased, notably LTB4, 20-COOH-LTB4, LTE4, and eoxin E4. 15-lipoxygenase metabolites derived from linoleic, arachidonic, eicosapentaenoic and docosahexaenoic acids were also increased. Finally, yet importantly, specialized pro-resolving mediators, notably lipoxin A4 and the D-series resolvins, were also found at important levels, underscoring that the lipid storm occurring in severe SARS-CoV-2 infections involves pro- and anti-inflammatory lipids.\n\nCONCLUSIONSOur data unmask the important lipid storm occurring in the lungs of patients afflicted with severe COVID-19. We discuss which clinically available drugs could be helpful at modulating the lipidome we observed in the hope of minimizing the deleterious effects of pro-inflammatory lipids and enhancing the effects of anti-inflammatory and/or pro-resolving lipids.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Anne-Sophie Archambault", + "author_inst": "Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Quebec - Universite Laval, Faculty of medicine, Quebec City, Canada" + }, + { + "author_name": "Younes Zaid", + "author_inst": "Biology Department, Faculty of Sciences, Mohammed V University, Rabat, Morocco" + }, + { + "author_name": "Volatiana Rakotoarivelo", + "author_inst": "Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Quebec - Universite Laval, Faculty of medicine, Quebec City, Canada" + }, + { + "author_name": "Etienne Dore", + "author_inst": "Centre de Recherche du Centre Hospitalier Universitaire de Quebec - Universite Laval, Quebec City, Canada" + }, + { + "author_name": "Isabelle Dubuc", + "author_inst": "Centre de Recherche du Centre Hospitalier Universitaire de Quebec - Universite Laval, Quebec City, Canada" + }, + { + "author_name": "Cyril Martin", + "author_inst": "Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Quebec - Universite Laval, Faculty of medicine, Quebec City, Canada" + }, + { + "author_name": "Youssef Amar", + "author_inst": "Moroccan Foundation for Advanced Science, Innovation & Research (MAScIR), Rabat, Morocco" + }, + { + "author_name": "Amine Cheikh", + "author_inst": "Cheikh Zaid Hospital, Abulcasis University of Health Sciences, Rabat, Morocco" + }, + { + "author_name": "Hakima Fares", + "author_inst": "Cheikh Zaid Hospital, Abulcasis University of Health Sciences, Rabat, Morocco" + }, + { + "author_name": "Amine El Hassani", + "author_inst": "Cheikh Zaid Hospital, Abulcasis University of Health Sciences, Rabat, Morocco" + }, + { + "author_name": "Youssef Tijani", + "author_inst": "Faculty of Medicine, Mohammed VI University of Health Sciences, Casablanca, Morocco" + }, + { + "author_name": "Michel Laviolette", + "author_inst": "Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Quebec - Universite Laval, Faculty of medicine, Quebec City, Canada" + }, + { + "author_name": "Eric Boilard", + "author_inst": "Centre de Recherche du Centre Hospitalier Universitaire de Quebec - Universite Laval, department of microbiology-infectiology-immunology, Quebec City, Canada" + }, + { + "author_name": "Louis Flamand", + "author_inst": "Centre de Recherche du Centre Hospitalier Universitaire de Quebec - Universite Laval, department of microbiology-infectiology-immunology, Quebec City, Canada" + }, + { + "author_name": "Nicolas Flamand", + "author_inst": "Centre de recherche de l'Institut universitaire de cardiologie et de pneumologie de Quebec - Universite Laval, Faculty of medicine, Quebec City, Canada" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.04.20244137", "rel_title": "Predicting Hospital Utilization and Inpatient Mortality of Patients Tested for COVID-19", @@ -1067386,41 +1065287,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pharmacology and therapeutics" }, - { - "rel_doi": "10.1101/2020.12.04.20244327", - "rel_title": "COVID-19 RELATED IMMUNIZATION DISRUPTIONS IN RAJASTHAN, INDIA: A RETROSPECTIVE OBSERVATIONAL STUDY", - "rel_date": "2020-12-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.04.20244327", - "rel_abs": "IntroductionGovernments around the world suspended immunization outreach to control COVID-19 spread. Many have since resumed services with an emphasis on catch-up vaccinations to reach children with missed vaccinations. This paper evaluated immunization disruptions during Indias March-May 2020 lockdown and the extent to which subsequent catch-up efforts reversed them in Rajasthan, India.\n\nMethodsIn this retrospective observational study, we conducted phone surveys to collect immunization details for 2,144 children that turned one year old between January and October 2020. We used logistic regressions to compare differences in immunization timeliness and completed first-year immunization status among children that were due immunizations just before (unexposed), during (heavily exposed), and after (post-exposure) the lockdown.\n\nResultsRelative to unexposed children, heavily exposed children were significantly less likely to be immunized at or before 9 months (OR 0.550; 95%CI 0.367-0.824; p=0.004), but more likely to be immunized at 10-12 months (OR 1.761; 95%CI 1.196-2.591; p=0.004). They were also less likely to have completed their key first-year immunizations (OR 0.624; 95%CI 0.478-0.816; p=0.001) by the time of survey. In contrast, post-exposure children showed no difference in timeliness or completed first-year immunizations relative to unexposed children, and their immunization coverage was 6.9pp above heavily exposed children despite their younger age. Declines in immunization coverage were larger among children in households that were poorer, less educated, lower caste, and residing in COVID red zones, although subgroup comparisons were not statistically significant.\n\nConclusionDisruptions to immunization services resulted in children missing immunization during the lockdown, but catch-up efforts after it was eased ensured many children were reached at later ages. Nevertheless, catch-up was incomplete and children due their immunizations during the lockdown remained less likely to be fully immunized 4-5 months after it lifted, even as younger cohorts due immunizations in June or later returned to pre-lockdown schedules.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Radhika Jain", - "author_inst": "Stanford University" - }, - { - "author_name": "Ambika Chopra", - "author_inst": "J-PAL South Asia at IFMR" - }, - { - "author_name": "Camille Falezan", - "author_inst": "Stanford University" - }, - { - "author_name": "Mustufa Patel", - "author_inst": "J-PAL South Asia at IFMR" - }, - { - "author_name": "Pascaline Dupas", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.12.05.20244657", "rel_title": "Antibacterial consumption in the context of COVID-19 in Pakistan: an analysis of national pharmaceutical sales data for 2019-20", @@ -1068464,6 +1066330,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.12.04.20244129", + "rel_title": "Self-harm and the COVID-19 pandemic: a study of factors contributing to self-harm during lockdown restrictions", + "rel_date": "2020-12-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.04.20244129", + "rel_abs": "IntroductionThe COVID-19 pandemic and resulting public health measures may have major impacts on mental health, including on self-harm. We have investigated what factors related to the pandemic influenced hospital presentations following self-harm during lockdown in England.\n\nMethodMental health clinicians assessing individuals aged 18 years and over presenting to hospitals in Oxford and Derby following self-harm during the period March 23rd to 17th May 2020 recorded whether the self-harm was related to the impact of COVID- 19 and, if so, what specific factors were relevant. These factors were organized into a classification scheme. Information was also collected on patients demographic characteristics, method of self-harm and suicide intent.\n\nResultsOf 228 patients assessed, in 46.9% (N=107) COVID-19 and lockdown restrictions were identified as influencing self-harm. This applied more to females than males (53.5%, N=68/127 v 38.6%, N=39/101, {chi}2 = 5.03, p=0.025), but there were no differences in age, methods of self-harm or suicide intent between the two groups. The most frequent COVID-related factors were mental health issues, including new and worsening disorders, and cessation or reduction of services (including absence of face-to-face support), isolation and loneliness, reduced contact with key individuals, disruption to normal routine, and entrapment. Multiple, often inter- connected COVID-related factors were identified in many patients.\n\nConclusionsCOVID-related factors were identified as influences in nearly half of individuals presenting to hospitals following self-harm in the period following introduction of lockdown restrictions. Females were particularly affected. The fact that mental health problems, including issues with delivery of care, predominated has implications for organisation of services during such periods. The contribution of isolation, loneliness and sense of entrapment highlight the need for relatives, friends and neighbours to be encouraged to reach out to others, especially those living alone. The classification of COVID-related factors can be used as an aide-memoire for clinicians.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Keith Hawton", + "author_inst": "University of Oxford" + }, + { + "author_name": "Karen Lascelles", + "author_inst": "University of Oxford" + }, + { + "author_name": "Fiona Brand", + "author_inst": "University of Oxford" + }, + { + "author_name": "Deborah Casey", + "author_inst": "University of Oxford" + }, + { + "author_name": "Elizabeth Bale", + "author_inst": "Univeristy of Oxford" + }, + { + "author_name": "Jennifer Ness", + "author_inst": "Derbyshire Healthcare NHS Foundation Trust" + }, + { + "author_name": "Samantha Kelly", + "author_inst": "Derbyshire Healthcare NHS Foundation Trust" + }, + { + "author_name": "Keith Waters", + "author_inst": "Derbyshire Helathcare NHS Foundation Trust" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.12.05.20244590", "rel_title": "Aripiprazole as a candidate treatment of COVID-19 identified through genomic analysis", @@ -1068864,57 +1066777,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.12.06.412759", - "rel_title": "The new generation hDHODH inhibitor MEDS433 hinders the in vitro replication of SARS-CoV-2", - "rel_date": "2020-12-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.06.412759", - "rel_abs": "Identification and development of effective drugs active against SARS-CoV-2 are urgently needed. Here, we report on the anti-SARS-CoV-2 activity of MEDS433, a novel inhibitor of human dihydroorotate dehydrogenase (hDHODH), a key cellular enzyme of the de novo pyrimidines biosynthesis. MEDS433 inhibits in vitro virus replication in the low nanomolar range, and through a mechanism that stems from its ability to block hDHODH activity. MEDS433 thus represents an attractive candidate to develop novel anti-SARS-CoV-2 agents.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Arianna Calistri", - "author_inst": "University of Padova" - }, - { - "author_name": "Anna Luganini", - "author_inst": "University of Turin" - }, - { - "author_name": "Valeria Conciatori", - "author_inst": "University of Padua" - }, - { - "author_name": "Claudia Del Vecchio", - "author_inst": "University of Padova" - }, - { - "author_name": "Stefano Sainas", - "author_inst": "University of Turin" - }, - { - "author_name": "Donatella Boschi", - "author_inst": "University of Turin" - }, - { - "author_name": "Marco Lucio Lolli", - "author_inst": "Department of Sciences and Drug Technology" - }, - { - "author_name": "Giorgio Gribaudo", - "author_inst": "University of Turin" - }, - { - "author_name": "Cristina Parolin", - "author_inst": "University of Padova" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.12.07.414292", "rel_title": "A framework for predicting potential host ranges of pathogenic viruses based on receptor ortholog analysis", @@ -1070286,6 +1068148,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.12.02.20238907", + "rel_title": "Functional profile, homing and residency of protective T cell immune responses against SARS-CoV-2", + "rel_date": "2020-12-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.02.20238907", + "rel_abs": "Considering that SARS-CoV-2 interacts with the host at the respiratory tract mucosal interface, T cells strategically placed within these surfaces, namely resident memory T cells, will be essential to limit viral spread and disease. Importantly, these cells are mostly non-recirculating, which reduces the window of opportunity to examine circulating lymphocytes in blood as they home to the lung parenchyma. Here, we demonstrate that viral specific T cells can migrate and establish in the lung as resident memory T cells remaining detectable up to 10 months after initial infection. Moreover, focusing on the acute phase of the infection, we identified virus-specific T cell responses in blood with functional, migratory and apoptotic patterns modulated by viral proteins and associated with clinical outcome. Our study highlights IL-10 secretion by virus-specific T cells associated to a better outcome and the persistence of resident memory T cells as key players for future protection against SARS-CoV-2 infection.", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Judith Grau-Exp\u00f3sito", + "author_inst": "Vall d'Hebron Research Institute (VHIR)" + }, + { + "author_name": "Nerea S\u00e1nchez-Gaona", + "author_inst": "Vall Hebron Institut de Recerca (VHIR)" + }, + { + "author_name": "N\u00faria Massana", + "author_inst": "Vall Hebron Institut de Recerca (VHIR)" + }, + { + "author_name": "Marina Suppi", + "author_inst": "Vall Hebron Institut de Recerca (VHIR)" + }, + { + "author_name": "Antonio Astorga-Gamaza", + "author_inst": "Vall Hebron Institut de Recerca (VHIR)" + }, + { + "author_name": "David Perea", + "author_inst": "Vall Hebron Institut de Recerca (VHIR)" + }, + { + "author_name": "Joel Rosado", + "author_inst": "Vall Hebron Hospital Universitari" + }, + { + "author_name": "Anna Falc\u00f3", + "author_inst": "Vall Hebron Hospital Universitari" + }, + { + "author_name": "Cristina Kirkegaard", + "author_inst": "Vall Hebron Hospital Universitari" + }, + { + "author_name": "Ariadna Torrella", + "author_inst": "Vall Hebron Hospital Universitari," + }, + { + "author_name": "Bibiana Planas", + "author_inst": "Vall Hebron Hospital Universitari" + }, + { + "author_name": "Jordi Navarro", + "author_inst": "Vall Hebron Hospital Universitari" + }, + { + "author_name": "Paula Suanzes", + "author_inst": "Vall Hebron Hospital Universitari" + }, + { + "author_name": "Daniel Alvarez-de la Sierra", + "author_inst": "Vall Hebron Hospital Universitari" + }, + { + "author_name": "Alfonso Ayora", + "author_inst": "Vall Hebron Hospital Universitari" + }, + { + "author_name": "Irene Sansano", + "author_inst": "Vall Hebron Hospital Universitari" + }, + { + "author_name": "Juliana Esperalba", + "author_inst": "Vall Hebron Hospital Universitari" + }, + { + "author_name": "Cristina Andr\u00e9s", + "author_inst": "Vall Hebron Hospital Universitari" + }, + { + "author_name": "Andr\u00e9s Ant\u00f3n", + "author_inst": "Vall Hebron Hospital Universitari" + }, + { + "author_name": "Santiago Ram\u00f3n y Cajal", + "author_inst": "Vall Hebron Hospital Universitari" + }, + { + "author_name": "Benito Almirante", + "author_inst": "Vall Hebron Hospital Universitari" + }, + { + "author_name": "Ricardo Pujol-Borrell", + "author_inst": "Vall Hebron Hospital Universitari" + }, + { + "author_name": "Vicen\u00e7 Falc\u00f3", + "author_inst": "Vall Hebron Hospital Universitari" + }, + { + "author_name": "Joaqu\u00edn Burgos", + "author_inst": "Vall Hebron Hospital Universitari" + }, + { + "author_name": "Mar\u00eda J. Buz\u00f3n", + "author_inst": "Vall Hebron Institut de Recerca (VHIR)" + }, + { + "author_name": "Meritxell Genesc\u00e0", + "author_inst": "Vall Hebron Research Institute (VHIR)" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.12.02.20242354", "rel_title": "COVID-19 as cause of viral sepsis: A Systematic Review and Meta-Analysis", @@ -1070690,61 +1068671,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.02.20242958", - "rel_title": "Longitudinal lab test analysis confirms pre-existing anemia as a severe risk factor for post-viral clearance hospitalization in COVID-19 patients", - "rel_date": "2020-12-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.02.20242958", - "rel_abs": "BackgroundAs the number of new and recovering COVID-19 cases continues to rise, it has become evident that patients can experience symptoms and complications after viral clearance. Clinical biomarkers characterizing patients who are likely to experience these prolonged effects are unknown.\n\nMethodsWe conducted a retrospective study to compare longitudinal lab test measurements (hemoglobin, hematocrit, estimated glomerular filtration rate, serum creatinine, and blood urea nitrogen) in patients rehospitalized after PCR-confirmed SARS-CoV-2 clearance (n=104) versus patients not rehospitalized after viral clearance (n=278).\n\nFindingsCompared to patients who were not rehospitalized after PCR-confirmed viral clearance, those who were rehospitalized had lower median hemoglobin levels in the year prior to COVID-19 diagnosis (cohens D = -0.50; p=1.2x10-3) and during the active infection window (cohens D = -0.71; p=4.6x10-8). Patients hospitalized after viral clearance were also more likely to be diagnosed with moderate or severe anemia during the active infection window (OR = 2.18; p = 4.99x10-9).\n\nConclusionsThe occurrence of moderate or severe anemia in hospitalized COVID-19 patients is strongly associated with rehospitalization after viral clearance. Whether interventions to mitigate anemia can improve long term outcomes of COVID-19 patients should be further investigated.\n\nFundingThis study was funded by nference.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Patrick Lenehan", - "author_inst": "nference" - }, - { - "author_name": "Eshwan Ramudu", - "author_inst": "nference" - }, - { - "author_name": "AJ Venkatakrishnan", - "author_inst": "nference" - }, - { - "author_name": "Gabriela Berner", - "author_inst": "nference" - }, - { - "author_name": "Reid McMurry", - "author_inst": "nference" - }, - { - "author_name": "John O'Horo", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Andrew D Badley", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "William G Morice", - "author_inst": "Mayo Clinic Laboratories" - }, - { - "author_name": "John Halamka", - "author_inst": "Mayo Clinic" - }, - { - "author_name": "Venky Soundararajan", - "author_inst": "nference" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.12.02.20242909", "rel_title": "Treatment of Severe COVID-19 with Convalescent Plasma in the Bronx, NYC", @@ -1072060,6 +1069986,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.12.03.20243717", + "rel_title": "Covid-19 Will Reduce US Life Expectancy at Birth by More Than One Year in 2020", + "rel_date": "2020-12-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.03.20243717", + "rel_abs": "On December 3rd, 2020, the cumulative number of U.S. Covid-19 deaths tallied by Johns Hopkins University (JHU) online dashboard reached 275,000, surpassing the number at which life table calculations show Covid-19 mortality will lower the U.S. life expectancy at birth (LEB) for 2020 by one full year. Such an impact on the U.S. LEB is unprecedented since the end of World War II. With additional deaths by the year end, the reduction in 2020 LEB induced by Covid-19 deaths will inexorably exceed one year. Factoring the expected continuation of secular gains against other causes of mortality, the U.S. LEB should still drop by more than a full year between 2019 and 2020. By comparison, the opioid-overdose crisis led to a decline in U.S. LEB averaging .1 year annually, from 78.9 years in 2014 to 78.6 years in 2017. At its peak, the HIV epidemic reduced the U.S. LEB by .3 year in a single year, from 75.8 years in 1992 to 75.5 years in 1993. As of now, the US LEB is expected to fall back to the level it first reached in 2010. In other words, the impact of Covid-19 on U.S. mortality can be expected to cancel a decade of gains against all other causes of mortality combined.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Patrick Heuveline", + "author_inst": "UCLA" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.12.04.20243840", "rel_title": "How do the public interpret COVID-19 swab test results? Comparing the impact of official information about results and reliability used in the UK, US and New Zealand: a randomised, controlled trial", @@ -1072356,157 +1070301,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.12.03.20243535", - "rel_title": "OpenSAFELY: impact of national guidance on switching from warfarin to direct oral anticoagulants (DOACs) in early phase of COVID-19 pandemic in England", - "rel_date": "2020-12-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.03.20243535", - "rel_abs": "BackgroundEarly in the COVID-19 pandemic the NHS recommended that appropriate patients anticoagulated with warfarin should be switched to direct acting oral anticoagulants (DOACs), requiring less frequent blood testing. Subsequently, a national safety alert was issued regarding patients being inappropriately co-prescribed two anticoagulants following a medication change, and associated monitoring.\n\nObjectiveTo describe which people were switched from warfarin to DOACs; identify potentially unsafe co-prescribing of anticoagulants; and assess whether abnormal clotting results have become more frequent during the pandemic.\n\nMethodsWorking on behalf of NHS England we conducted a population cohort based study using routine clinical data from >17 million adults in England.\n\nResults20,000 of 164,000 warfarin patients (12.2%) switched to DOACs between March and May 2020, most commonly to edoxaban and apixaban. Factors associated with switching included: older age, recent renal function test, higher number of recent INR tests recorded, atrial fibrillation diagnosis and care home residency. There was a sharp rise in co-prescribing of warfarin and DOACs from typically 50-100 per month to 246 in April 2020, 0.06% of all people receiving a DOAC or warfarin. INR testing fell by 14% to 506.8 patients tested per 1000 warfarin patients each month. We observed a very small increase in elevated INRs (n=470) during April compared with January (n=420).\n\nConclusionsIncreased switching of anticoagulants from warfarin to DOACs was observed at the outset of the COVID-19 pandemic in England following national guidance. There was a small but substantial number of people co-prescribed warfarin and DOACs during this period. Despite a national safety alert on the issue, a widespread rise in elevated INR test results was not found. Primary care has responded rapidly to changes in patient care during the COVID-19 pandemic.", - "rel_num_authors": 34, - "rel_authors": [ - { - "author_name": "Helen J Curtis", - "author_inst": "University of Oxford" - }, - { - "author_name": "Brian MacKenna", - "author_inst": "University of Oxford" - }, - { - "author_name": "Alex J Walker", - "author_inst": "University of Oxford" - }, - { - "author_name": "Richard Croker", - "author_inst": "University of Oxford" - }, - { - "author_name": "Amir Mehrkar", - "author_inst": "University of Oxford" - }, - { - "author_name": "Caroline E Morton", - "author_inst": "University of Oxford" - }, - { - "author_name": "Seb Bacon", - "author_inst": "University of Oxford" - }, - { - "author_name": "George Hickman", - "author_inst": "University of Oxford" - }, - { - "author_name": "Peter Inglesby", - "author_inst": "University of Oxford" - }, - { - "author_name": "Chris Bates", - "author_inst": "TPP" - }, - { - "author_name": "David Evans", - "author_inst": "University of Oxford" - }, - { - "author_name": "Tom Ward", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jonathan Cockburn", - "author_inst": "TPP" - }, - { - "author_name": "Simon Davy", - "author_inst": "University of Oxford" - }, - { - "author_name": "Krishnan Bhaskaran", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Anna Schultze", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Christopher T Rentsch", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Elizabeth Williamson", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "William Hulme", - "author_inst": "University of Oxford" - }, - { - "author_name": "Helen I McDonald", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Laurie Tomlinson", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Rohini Mathur", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Henry Drysdale", - "author_inst": "University of Oxford" - }, - { - "author_name": "Rosalind M Eggo", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Kevin Wing", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Angel Wong", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Harriet Forbes", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "John Parry", - "author_inst": "TPP" - }, - { - "author_name": "Frank Hester", - "author_inst": "TPP" - }, - { - "author_name": "Sam Harper", - "author_inst": "TPP" - }, - { - "author_name": "Stephen JW Evans", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Ian J Douglas", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Liam Smeeth", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Ben Goldacre", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2020.12.04.410340", "rel_title": "First-described recently discovered non-toxic vegetal-derived furocoumarin preclinical efficacy against SARS-CoV-2: a promising antiviral herbal drug.", @@ -1073518,6 +1071312,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.12.01.20241612", + "rel_title": "Impact of COVID-19 restrictions on pre-school children's eating, activity and sleep behaviours: a qualitative study", + "rel_date": "2020-12-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.01.20241612", + "rel_abs": "BackgroundIn spring 2020, the COVID-19 lockdown placed unprecedented restrictions on the behaviour and movements of the UK population. Citizens were ordered to stay at home, only allowed to leave their houses to buy essential supplies, attend medical appointments or exercise once a day. This qualitative study explored how lockdown and its subsequent easing changed young childrens everyday activities, eating and sleep habits to gain insight into the impact for health and wellbeing.\n\nMethodsIn summer 2020 we interviewed 20 parents of children due to start school in September 2020 (aged 3-5 years) by phone or video call to explore their experiences of lockdown and its easing. We recruited participants through nurseries and local Facebook community groups in the South West and West Midlands of England. Half the sample were from Black, Asian or Minority Ethnic backgrounds and half lived in the most deprived quintile. We analysed interviews using thematic analysis.\n\nResultsChildrens activity, screen time, eating, and sleep routines had some level of disruption. Parents reported children ate more snacks during lockdown, but also spent more time preparing meals and eating as a family. Most parents reported a reduction in their childrens physical activity and an increase in screen time, which some linked to difficulties in getting their child to sleep. Parents sometimes expressed guilt about changes in activity, screen time and snacking over lockdown. Most felt these changes would be temporary with no lasting impact, though others worried about re-establishing healthy routines.\n\nConclusionsThe spring COVID-19 lockdown negatively impacted on pre-school childrens eating, activity and sleep routines. While some positive changes were reported, there were wide-spread reports of lack of routines, habits and boundaries which, at least in the short-term, were likely to have been detrimental for child health and development. Guidance and support for families during times of COVID-19 restrictions could be valuable to help them maintain healthy activity, eating, screen-time and sleeping routines to protect child health and ensure unhealthy habits are not adopted.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Joanne L Clarke", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Ruth Kipping", + "author_inst": "University of Bristol" + }, + { + "author_name": "Stephanie Chambers", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Kate Willis", + "author_inst": "University of Bristol" + }, + { + "author_name": "Hilary Taylor", + "author_inst": "University of Bristol" + }, + { + "author_name": "Rachel Brophy", + "author_inst": "University of Bristol" + }, + { + "author_name": "Kimberly J Hannam", + "author_inst": "University of Bristol" + }, + { + "author_name": "Sharon Simpson", + "author_inst": "University of Glasgow" + }, + { + "author_name": "Beki Langford", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.12.01.20241836", "rel_title": "No current evidence for risk of vaccine-driven virulence evolution in SARS-CoV-2", @@ -1073890,41 +1071735,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.12.01.20242289", - "rel_title": "The COVID-19 herd immunity threshold is not low: A re-analysis of European data from spring of 2020", - "rel_date": "2020-12-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.12.01.20242289", - "rel_abs": "The recent publication of the Great Barrington Declaration (GBD), which calls for relaxing all public health interventions on young, healthy individuals, has brought the question of herd immunity to the forefront of COVID-19 policy discussions, and is partially based on unpublished research that suggests low herd immunity thresholds (HITs) of 10-20%. We re-evaluate these findings and correct a flawed assumption leading to COVID-19 HIT estimates of 60-80%. If policymakers were to adopt a herd immunity strategy, in which the virus is allowed to spread relatively unimpeded, we project that cumulative COVID-19 deaths would be five times higher than the initial estimates suggest. Our re-estimates of the COVID-19 HIT corroborate strong signals in the data and compelling arguments that most of the globe remains far from herd immunity, and suggest that abandoning community mitigation efforts would jeopardize the welfare of communities and integrity of healthcare systems.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Spencer J Fox", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Pratyush Potu", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Ravi Srinivasan", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Michael Lachmann", - "author_inst": "The Santa Fe Institute" - }, - { - "author_name": "Lauren Ancel Meyers", - "author_inst": "The University of Texas at Austin" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.12.01.20242149", "rel_title": "Variants in SARS-CoV-2 Associated with Mild or Severe Outcome", @@ -1075028,6 +1072838,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.30.20229732", + "rel_title": "Validation of a combined ELISA to detect IgG, IgA and IgM antibody responses to SARS-CoV-2 in mild or moderate non-hospitalised patients", + "rel_date": "2020-12-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.30.20229732", + "rel_abs": "BackgroundFrequently SARS-CoV-2 results in mild or moderate disease with potentially lower concentrations of antibodies compared to those that are hospitalised. Here, we validated an ELISA using SARS-CoV-2 trimeric spike glycoprotein, with targeted detection of IgG, IgA and IgM (IgGAM) using serum and dried blood spots (DBS) from adults with mild or moderate disease.\n\nMethodsTargeting the SARS-CoV-2 trimeric spike, a combined anti-IgG, IgA and IgM serology ELISA assay was developed using 62 PCR-confirmed non-hospitalised, mild or moderate COVID-19 samples, [≥]14 days post symptom onset and 624 COVID-19 negative samples. The assay was validated using 73 PCR-confirmed non-hospitalised COVID-19 and 359 COVID-19 negative serum samples with an additional 81 DBSs, and further validated in 226 PCR-confirmed non-hospitalised COVID-19 and 426 COVID-19 negative clinical samples.\n\nResultsA sensitivity and specificity of 98.6% (95% CI, 92.6-100.0), 98.3% (95% CI, 96.4-99.4), respectively, was observed following validation of the SARS-CoV-2 ELISA. No cross-reactivities with endemic coronaviruses or other human viruses were observed, and no change in results were recorded for interfering substances. The assay was stable at temperature extremes and components were stable for 15 days once opened. A matrix comparison showed DBS to correlate with serum results. Clinical validation of the assay reported a sensitivity of 94.7% (95% CI, 90.9-97.2%) and a specificity of 98.4% (95% CI, 96.6-99.3%).\n\nConclusionsThe human anti-IgGAM SARS-CoV-2 ELISA provides accurate and sensitive detection of SARS-CoV-2 antibodies in non-hospitalised adults with mild or moderate disease. The use of dried blood spots makes the assay accessible to the wider community.\n\nSupplementary MaterialNo", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Alex M Cook", + "author_inst": "The Binding Site Group Ltd, 8 Calthorpe Road, Birmingham, B15 1QT, UK." + }, + { + "author_name": "Sian E Faustini", + "author_inst": "Clinical Immunology Service, University of Birmingham College of Medical and Dental Sciences, Birmingham, B15 2TT, UK." + }, + { + "author_name": "Leigh J Williams", + "author_inst": "The Binding Site Group Ltd, 8 Calthorpe Road, Birmingham, B15 1QT, UK." + }, + { + "author_name": "Adam F Cunningham", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK." + }, + { + "author_name": "Mark T Drayson", + "author_inst": "Clinical Immunology Service, University of Birmingham College of Medical and Dental Sciences, Birmingham, B15 2TT, UK." + }, + { + "author_name": "Adrian Shields", + "author_inst": "Clinical Immunology Service, University of Birmingham College of Medical and Dental Sciences, Birmingham, B15 2TT, UK & University Hospitals Birmingham NHS Foun" + }, + { + "author_name": "Dale Kay", + "author_inst": "The Binding Site Group Ltd, 8 Calthorpe Road, Birmingham, B15 1QT, UK." + }, + { + "author_name": "Lorna Taylor", + "author_inst": "The Royal Wolverhampton NHS trust, Wolverhampton Road, Wolverhampton, West Midlands, WV10 0QP, UK." + }, + { + "author_name": "Tim Plant", + "author_inst": "Clinical Immunology Service, University of Birmingham College of Medical and Dental Sciences, Birmingham, B15 2TT, UK." + }, + { + "author_name": "Aarnoud Huissoon", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK & University Hospitals Birmingham NHS Foundation Trust, Birmingham," + }, + { + "author_name": "Gregg Wallis", + "author_inst": "The Binding Site Group Ltd, 8 Calthorpe Road, Birmingham, B15 1QT, UK." + }, + { + "author_name": "Sarah Beck", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust, Birmingham, B15 2GW, UK." + }, + { + "author_name": "Sian E Jossi", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK." + }, + { + "author_name": "Marisol Perez-Toledo", + "author_inst": "Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, B15 2TT, UK." + }, + { + "author_name": "M L Newby", + "author_inst": "School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK." + }, + { + "author_name": "Joel D Allen", + "author_inst": "School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK." + }, + { + "author_name": "Max Crispin", + "author_inst": "School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK." + }, + { + "author_name": "Stephen Harding", + "author_inst": "The Binding Site Group Ltd, 8 Calthorpe Road, Birmingham, B15 1QT, UK" + }, + { + "author_name": "Alex G Richter", + "author_inst": "Clinical Immunology Service, University of Birmingham College of Medical and Dental Sciences, Birmingham, B15 2TT, UK & University Hospitals Birmingham NHS Foun" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.29.20240440", "rel_title": "Model-based evaluation of the impact of noncompliance with public health measures on COVID-19 disease control", @@ -1075324,41 +1073225,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2020.11.30.20240986", - "rel_title": "A Net Benefit Approach for the Optimal Allocation of a COVID-19 Vaccine", - "rel_date": "2020-12-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.30.20240986", - "rel_abs": "OBJECTIVEWe implement a model-based approach to identify the optimal allocation of a COVID-19 vaccine in the province of Alberta, Canada.\n\nMETHODSWe develop an epidemiologic model to evaluate allocation strategies defined by age and risk target groups, coverage, effectiveness, and cost of vaccine. The model simulates hypothetical immunization scenarios within a dynamic context, capturing concurrent public health strategies and population behaviour changes.\n\nRESULTSIn a scenario with 80% vaccine effectiveness, 40% population coverage, and prioritisation of those over the age of 60 at high-risk of poor outcomes, active cases are reduced by 17% and net monetary benefit increased by $263 million dollars, relative to no vaccine. Concurrent implementation of policies such as school closure and senior contact reductions have similar impacts on incremental net monetary benefit ($352 vs. 292 million, respectively) when there is no prioritisation given to any age or risk group. When older age groups are given priority, the relative benefit of school closures is much larger ($214 vs. 118 million). Results demonstrate that the rank ordering of different prioritisation options varies by prioritisation criteria, vaccine effectiveness and coverage, and concurrently implemented policies.\n\nCONCLUSIONSOur results have three implications: (i) optimal vaccine allocation will depend on the public health policies in place at the time of allocation and the impact of those policies on population behaviour; (ii) outcomes of vaccine allocation policies can be greatly supported with interventions targeting contact reduction in critical sub-populations; and (iii) identification of the optimal strategy depends on which outcomes are prioritised.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Erin Kirwin", - "author_inst": "University of Manchester, Institute of Health Economics" - }, - { - "author_name": "Ellen Rafferty", - "author_inst": "Institute of Health Economics" - }, - { - "author_name": "Kate Harback", - "author_inst": "Institute of Health Economics" - }, - { - "author_name": "Jeff Round", - "author_inst": "Institute of Health Economics, University of Alberta" - }, - { - "author_name": "Christopher McCabe", - "author_inst": "Institute of Health Economics, University of Alberta" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.11.30.20241414", "rel_title": "Predicting patients with false negative SARS-CoV-2 testing at hospital admission: A retrospective multi-center study", @@ -1076458,6 +1074324,53 @@ "type": "contradictory results", "category": "pathology" }, + { + "rel_doi": "10.1101/2020.12.02.408153", + "rel_title": "LL-37 fights SARS-CoV-2: The Vitamin D-Inducible Peptide LL-37 Inhibits Binding of SARS-CoV-2 Spike Protein to its Cellular Receptor Angiotensin Converting Enzyme 2 In Vitro", + "rel_date": "2020-12-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.12.02.408153", + "rel_abs": "ObjectiveSevere acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the pathogen accountable for the coronavirus disease 2019 (COVID-19) pandemic. Viral entry via binding of the receptor binding domain (RBD) located within the S1 subunit of the SARS-CoV-2 Spike (S) protein to its target receptor angiotensin converting enzyme (ACE) 2 is a key step in cell infection. The efficient transition of the virus is linked to a unique protein called open reading frame (ORF) 8. As SARS-CoV-2 infections can develop into life-threatening lower respiratory syndromes, effective therapy options are urgently needed. Several publications propose vitamin D treatment, although its mode of action against COVID-19 is not fully elucidated. It is speculated that vitamin Ds beneficial effects are mediated by up-regulating LL-37, a well-known antimicrobial peptide with antiviral effects.\n\nMethodsRecombinantly expressed SARS-CoV-2 S protein, the extended S1 subunit (S1e), the S2 subunit (S2), the receptor binding domain (RBD), and ORF8 were used for surface plasmon resonance (SPR) studies to investigate LL-37s ability to bind to SARS-CoV-2 proteins and to localize its binding site within the S protein. Binding competition studies were conducted to confirm an inhibitory action of LL-37 on the attachment of SARS-CoV-2 S protein to its entry receptor ACE2.\n\nResultsWe could show that LL-37 binds to SARS-CoV-2 S protein (LL-37/SStrep KD = 410 nM, LL-37/SHis KD = 410 nM) with the same affinity, as SARS-CoV-2 binds to hACE2 (hACE2/SStrep KD = 370 nM, hACE2/SHis KD = 370 nM). The binding is not restricted to the RBD of the S protein, but rather distributed along the entire length of the protein. Interaction between LL-37 and ORF8 was detected with a KD of 290 nM. Further, inhibition of the binding of SStrep (IC50 = 740 nM), S1e (IC50 = 170 nM), and RBD (IC50 = 130 nM) to hACE2 by LL-37 was demonstrated.\n\nConclusionsWe have revealed a biochemical link between vitamin D, LL-37, and COVID-19 severity. SPR analysis demonstrated that LL-37 binds to SARS-CoV-2 S protein and inhibits binding to its receptor hACE2, and most likely viral entry into the cell. This study supports the prophylactic use of vitamin D to induce LL-37 that protects from SARS-CoV-2 infection, and the therapeutic administration of vitamin D for the treatment of COVID-19 patients. Further, our results provide evidence that the direct use of LL-37 by inhalation and systemic application may reduce the severity of COVID-19.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Annika Roth", + "author_inst": "Institute for Clinical Chemistry, Medical Faculty, University of Cologne" + }, + { + "author_name": "Steffen Luetke", + "author_inst": "Institute for Biochemistry II, Clinic for Pediatric and Adolescent Medicine, Medical Faculty, University of Cologne" + }, + { + "author_name": "Denise Meinberger", + "author_inst": "Institute for Clinical Chemistry, Medical Faculty, University of Cologne" + }, + { + "author_name": "Gabriele Hermes", + "author_inst": "Institute for Clinical Chemistry, Medical Faculty, University of Cologne" + }, + { + "author_name": "Gerhard Sengle", + "author_inst": "Institute for Biochemistry II, Clinic for Pediatric and Adolescent Medicine, Medical Faculty, University of Cologne" + }, + { + "author_name": "Manuel Koch", + "author_inst": "Institute for Biochemistry II, Institute for Dental Research and Oral Musculoskeletal Biology, Center for Molecular Medicine Cologne, University of Cologne" + }, + { + "author_name": "Thomas Streichert", + "author_inst": "Institute for Clinical Chemistry, Medical Faculty, University of Cologne" + }, + { + "author_name": "Andreas R. Klatt", + "author_inst": "University of Cologne" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.12.01.407015", "rel_title": "Shared B cell memory to coronaviruses and other pathogens varies in human age groups and tissues", @@ -1077034,37 +1074947,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.11.30.405340", - "rel_title": "Role of Long-range Allosteric Communication in Determining the Stability and Disassembly of SARS-COV-2 in Complex with ACE2", - "rel_date": "2020-12-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.30.405340", - "rel_abs": "Severe acute respiratory syndrome (SARS) and novel coronavirus disease (COVID-19) are caused by two closely related beta-coronaviruses, SARS-CoV and SARS-CoV-2, respectively. The envelopes surrounding these viruses are decorated with spike proteins, whose receptor binding domains (RBDs) initiate invasion by binding to the human angiotensin-converting enzyme 2 (ACE2). Subtle changes at the interface with ACE2 seem to be responsible for the enhanced affinity for the receptor of the SARS-CoV-2 RBD compared to SARS-CoV RBD. Here, we use Elastic Network Models (ENMs) to study the response of the viral RBDs and ACE2 upon dissassembly of the complexes. We identify a dominant detachment mode, in which the RBD rotates away from the surface of ACE2, while the receptor undergoes a conformational transition which stretches the active-site cleft. Using the Structural Perturbation Method, we determine the network of residues, referred to as the Allostery Wiring Diagram (AWD), which drives the large-scale motion activated by the detachment of the complex. The AWD for SARS-CoV and SARS-CoV-2 are remarkably similar, showing a network that spans the interface of the complex and reaches the active site of ACE2, thus establishing an allosteric connection between RBD binding and receptor catalytic function. Informed in part by the AWD, we used Molecular Dynamics simulations to probe the effect of interfacial mutations in which SARS-CoV-2 residues are replaced by their SARS-CoV counterparts. We focused on a conserved glycine (G502 in SARS-CoV-2, G488 in SARS-CoV) because it belongs to a region that initiates the dissociation of the complex along the dominant detachment mode, and is prominent in the AWD. Molecular Dynamics simulations of SARS-CoV-2 wild-type and G502P mutant show that the affinity for the human receptor of the mutant is drastically diminished. Our results suggest that in addition to residues that are in direct contact with the interface those involved in long range allosteric communication are also a determinant of the stability of the RBD-ACE2 complex.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Mauro Lorenzo Mugnai", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Clark Templeton", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Ron Elber", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Dave Thirumalai", - "author_inst": "University of Texas at Austin" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.11.30.405472", "rel_title": "Prospective mapping of viral mutations that escape antibodies used to treat COVID-19", @@ -1078720,6 +1076602,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.25.20235366", + "rel_title": "Clinical characteristics and mortality associated with COVID-19 in Jakarta, Indonesia: a hospital-based retrospective cohort study", + "rel_date": "2020-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.25.20235366", + "rel_abs": "BackgroundData on COVID-19-related mortality and associated factors from low-resource settings are scarce. This study examined clinical characteristics and factors associated with in-hospital mortality of COVID-19 patients in Jakarta, Indonesia, from March 2 to July 31, 2020.\n\nMethodsThis retrospective cohort included all hospitalised patients with PCR-confirmed COVID-19 in 55 hospitals. We extracted demographic and clinical data, including hospital outcomes (discharge or death). We used Cox regression to examine factors associated with mortality.\n\nFindingsOf 4265 patients with a definitive outcome by July 31, 3768 (88%) were discharged and 497 (12%) died. The median age was 46 years (IQR 32-57), 5% were children, and 31% had at least one comorbidity. Age-specific mortalities were 11% (7/61) for <5 years; 4% (1/23) for 5-9; 2% (3/133) for 10-19; 2% (8/638) for 20-29; 3% (26/755) for 30-39; 7% (61/819) for 40-49; 17% (155/941) for 50-59; 22% (132/611) for 60-69; and 34% (96/284) for [≥]70. Risk of death was associated with higher age; pre-existing hypertension, cardiac disease, chronic kidney disease or liver disease; clinical diagnosis of pneumonia; multiple (>3) symptoms; and shorter time from symptom onset to admission. Patients <50 years with >1 comorbidity had a nearly six-fold higher risk of death than those without (adjusted hazard ratio 5{middle dot}50, 95% CI 2{middle dot}72-11{middle dot}13; 27% vs 3% mortality).\n\nInterpretationOverall mortality was lower than reported in high-income countries, probably due to younger age distribution and fewer comorbidities. However, deaths occurred across all ages, with >10% mortality among children <5 years and adults >50 years.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Henry Surendra", + "author_inst": "Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia" + }, + { + "author_name": "Iqbal RF Elyazar", + "author_inst": "Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia" + }, + { + "author_name": "Bimandra A Djaafara", + "author_inst": "Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia" + }, + { + "author_name": "Lenny L Ekawati", + "author_inst": "Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia" + }, + { + "author_name": "Kartika Saraswati", + "author_inst": "Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia" + }, + { + "author_name": "Verry Adrian", + "author_inst": "Jakarta Provincial Health Office, Jakarta, Indonesia" + }, + { + "author_name": "Widyastuti Widyastuti", + "author_inst": "Jakarta Provincial Health Office, Jakarta, Indonesia" + }, + { + "author_name": "Dwi Oktavia", + "author_inst": "Jakarta Provincial Health Office, Jakarta, Indonesia" + }, + { + "author_name": "Ngabila Salama", + "author_inst": "Jakarta Provincial Health Office, Jakarta, Indonesia" + }, + { + "author_name": "Rosa N Lina", + "author_inst": "Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia" + }, + { + "author_name": "Adhi Andrianto", + "author_inst": "Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia" + }, + { + "author_name": "Karina D Lestari", + "author_inst": "Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia" + }, + { + "author_name": "Erlina Burhan", + "author_inst": "Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia" + }, + { + "author_name": "Anuraj H Shankar", + "author_inst": "Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia" + }, + { + "author_name": "Guy Thwaites", + "author_inst": "Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam" + }, + { + "author_name": "J. Kevin Baird", + "author_inst": "Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia" + }, + { + "author_name": "Raph L Hamers", + "author_inst": "Eijkman-Oxford Clinical Research Unit, Jakarta, Indonesia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.25.20238899", "rel_title": "Universities and COVID-19 Growth at the Start of the 2020 Academic Year", @@ -1079032,49 +1076997,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.11.25.20238741", - "rel_title": "I dont feel safe sitting in my own yard: Chicago resident experiences with urban rats during a COVID-19 stay-at-home order", - "rel_date": "2020-11-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.25.20238741", - "rel_abs": "BackgroundEncounters with rats in urban areas increase risk of human exposure to rat-associated zoonotic pathogens and act as a stressor associated with psychological distress. The frequency and nature of human-rat encounters may be altered by social distancing policies to mitigate the COVID-19 pandemic. For example, restaurant closures may reduce food availability for rats and promote rat activity in nearby residential areas, thus increasing public health risks during a period of public health crisis. In this study, we aimed to identify factors associated with increased perceived exposure to rats during a stay-at-home order, describe residents encounters with rats relevant to their health and well-being, and identify factors associated with increased use of rodent control.\n\nMethodsUrban residents in Chicago, a large city with growing concerns about rats and health disparities, completed an online questionnaire including fixed response and open-ended questions during the spring 2020 stay-at-home order. Analyses included ordinal multivariate regression, spatial analysis, and thematic analysis for open-ended responses.\n\nResultsOverall, 21% of respondents (n=835) reported an increase in rat sightings around their homes during the stay-at-home order and increased rat sightings was positively associated with proximity to restaurants, low-rise apartment buildings, and rat feces in the home (p[≤]0.01). Many respondents described feeling unsafe using their patio or yard, and afraid of rats entering their home or spreading disease. Greater engagement with rodent control was associated with property ownership, information about rat control, and lower incomes (p[≤]0.01).\n\nConclusionsMore frequent rat encounters may be an unanticipated public health concern during periods of social distancing, especially in restaurant-dense areas or in low-rise apartment buildings. Rat presence may also limit residents ability to enjoy nearby outdoor spaces, which otherwise might buffer stress experienced during a stay-at-home order. Proactive rat control may be needed to mitigate rat-associated health risks during future stay-at-home orders.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Maureen H Murray", - "author_inst": "Lincoln Park Zoo" - }, - { - "author_name": "Kaylee A Byers", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Jacqueline Buckley", - "author_inst": "Lincoln Park Zoo" - }, - { - "author_name": "Seth B Magle", - "author_inst": "Lincoln Park Zoo" - }, - { - "author_name": "Dorothy Maffei", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Preeya Waite", - "author_inst": "DePaul University" - }, - { - "author_name": "Danielle German", - "author_inst": "Johns Hopkins University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.11.25.20238998", "rel_title": "What do we Know about smell and taste dysfunction by SARS-CoV-2.Predictive value of the Venezuelan Olfactory test and RT-PCR analysis in viral infection diagnosis", @@ -1080142,6 +1078064,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.27.20237966", + "rel_title": "Predicting critical illness on initial diagnosis of COVID-19: Development and validation of the PRIORITY model for outpatient applicability.", + "rel_date": "2020-11-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.27.20237966", + "rel_abs": "ObjectivesCurrently available COVID-19 prognostic models have focused on laboratory and radiological data obtained following admission. However, these tests are not available on initial assessment or in resource-limited settings. We aim to develop and validate a prediction model, based on clinical history and examination findings on initial diagnosis of COVID-19, to identify patients at risk of critical outcomes.\n\nMethodsWe used data from the SEMI-COVID-19 Registry, a nationwide multicenter cohort of consecutive patients hospitalized for COVID-19 from 132 centers in Spain. Clinical signs and symptoms, demographic variables, and medical history ascertained at hospital admission were screened using Least Absolute Shrinkage and Selection Operator (LASSO) and logistic regression to construct a predictive model. We externally validated the final model in a separate cohort of patients admitted at less-complex hospitals (< 300 beds).We undertook decision curve analysis to assess the clinical usefulness of the predictive model. The primary outcome was a composite of in-hospital death, mechanical ventilation or admission to intensive care unit.\n\nResultsThere were 10,433 patients, 7,850 (primary outcome 25.1%) in the development cohort and 2,583 (primary outcome 27.0%) in the validation cohort. Variables in the final model included: age, cardiovascular disease, chronic kidney disease, dyspnea, tachypnea, confusion, systolic blood pressure, and SpO2[≤]93% or oxygen requirement.The C-statistic in the development cohort was 0.823 (95% CI,0.813-0.834). On external validation, the C-statistic was 0.792 (95% CI,0.772-0.812). The model showed a positive net benefit for threshold probabilities between 3% and 79%.\n\nConclusionsAmong patients presenting with COVID-19, the model based on easily-obtained clinical information had good discrimination and generalizability for identifying patients at risk of critical outcomes without the need of additional testing. The online calculator provided would facilitate triage of patients during the pandemic. This study could provide a useful tool for decision-making in health systems under pandemic pressure and resource-limited settings.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Miguel Martinez-Lacalzada", + "author_inst": "Hospital Universitario Ramon y Cajal" + }, + { + "author_name": "Adri\u00e1n Viteri-Noel", + "author_inst": "Hospital Universitario Ramon y Cajal" + }, + { + "author_name": "Luis Manzano", + "author_inst": "Hospital Universitario Ramon y Cajal" + }, + { + "author_name": "Martin Fabregate-Fuente", + "author_inst": "Hospital Universitario Ramon y Cajal" + }, + { + "author_name": "Manuel Rubio-Rivas", + "author_inst": "Bellvitge University Hospital" + }, + { + "author_name": "Sara Luis Garcia", + "author_inst": "Gregorio Mara\u00f1on University Hospital" + }, + { + "author_name": "Francisco Arnalich Fern\u00e1ndez", + "author_inst": "La Paz University Hospital" + }, + { + "author_name": "Jos\u00e9 Luis Beato P\u00e9rez", + "author_inst": "Albacete University Hospital Complex" + }, + { + "author_name": "Elpidio Calvo Manuel", + "author_inst": "San Carlos Clinical Hospital" + }, + { + "author_name": "Alexia Constanza Espi\u00f1o", + "author_inst": "La Princesa University Hospital" + }, + { + "author_name": "Santiago J Freire Castro", + "author_inst": "A Coru\u00f1a University Hospital" + }, + { + "author_name": "Jose Loureiro-Amigo", + "author_inst": "Mois\u00e8s Broggi Hospital" + }, + { + "author_name": "Maria Pesqueira Fontan", + "author_inst": "Santiago Clinical Hospital" + }, + { + "author_name": "Adela Pina", + "author_inst": "Dr. Peset University Hospital" + }, + { + "author_name": "Ana Mar\u00eda \u00c1lvarez Su\u00e1rez", + "author_inst": "Cabue\u00f1es Hospital" + }, + { + "author_name": "Andrea Silva Asiain", + "author_inst": "Nuestra Se\u0148ora del Prado Hospital" + }, + { + "author_name": "Beatriz Garc\u00eda L\u00f3pez", + "author_inst": "Zamora Hospital Complex" + }, + { + "author_name": "Jairo Luque del Pino", + "author_inst": "Costa del Sol Hospital" + }, + { + "author_name": "Jaime Sanz C\u00e1novas", + "author_inst": "Regional University Hospital of M\u00e1laga" + }, + { + "author_name": "Paloma Chazarra P\u00e9rez", + "author_inst": "San Juan de Alicante University Hospital" + }, + { + "author_name": "Gema Mar\u00eda Garc\u00eda Garc\u00eda", + "author_inst": "Badajoz University Hospital Complex" + }, + { + "author_name": "Jes\u00fas Mill\u00e1n N\u00fa\u00f1ez-Cort\u00e9s", + "author_inst": "Gregorio Mara\u00f1on University Hospital" + }, + { + "author_name": "Jos\u00e9 Manuel Casas Rojo", + "author_inst": "Infanta Cristina University Hospital" + }, + { + "author_name": "Ricardo G\u00f3mez Huelgas", + "author_inst": "Regional University Hospital of M\u00e1laga" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.27.20237032", "rel_title": "Proteo-genomic analysis of SARS-CoV-2: A clinical landscape of SNPs, COVID-19 proteome and host responses", @@ -1080606,45 +1078639,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.27.20240036", - "rel_title": "Rapid disappearance of influenza following the implementation of COVID-19 mitigation measures in Hamilton, Ontario", - "rel_date": "2020-11-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.27.20240036", - "rel_abs": "BackgroundPublic health measures, such as social distancing and closure of schools and non-essential services, were rapidly implemented in Canada to interrupt the spread of the novel coronavirus disease 2019 (COVID-19).\n\nObjectiveWe sought to investigate the impact of mitigation measures during the spring wave of COVID-19 on the incidence of other laboratory-confirmed respiratory viruses in Hamilton, Ontario.\n\nMethodsAll nasopharyngeal swab specimens (n = 57,503) submitted for routine respiratory virus testing at a regional laboratory serving all acute-care hospitals in Hamilton, Ontario between January 2010 and June 2020 were reviewed. Testing for influenza A/B, respiratory syncytial virus, human metapneumovirus, parainfluenza I-III, adenovirus and rhinovirus/enterovirus was done routinely using a laboratory-developed polymerase chain reaction multiplex respiratory viral panel. A Bayesian linear regression model was used to determine the trend of positivity rates of all influenza samples for the first 26 weeks of each year from 2010 to 2019. The mean positivity rate of Bayesian inference was compared with the weekly reported positivity rate of influenza samples in 2020.\n\nResultsThe positivity rate of influenza in 2020 diminished sharply following the population-wide implementation of COVID-19 interventions. Weeks 12-26 reported 0% positivity for influenza, with the exception of 0.1% reported in week 13.\n\nConclusionsPublic health measures implemented during the COVID-19 pandemic were associated with a reduced incidence of other respiratory viruses and should be considered to mitigate severe seasonal influenza and other respiratory virus pandemics.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Kevin Zhang", - "author_inst": "University of Toronto" - }, - { - "author_name": "Avika Misra", - "author_inst": "University of Ottawa" - }, - { - "author_name": "Patrick J. Kim", - "author_inst": "McMaster University" - }, - { - "author_name": "Seyed M. Moghadas", - "author_inst": "York University" - }, - { - "author_name": "Joanne M. Langley", - "author_inst": "Dalhousie University" - }, - { - "author_name": "Marek Smieja", - "author_inst": "McMaster University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.27.20240044", "rel_title": "Routine saliva testing for the identification of silent COVID-19 infections in healthcare workers", @@ -1081516,6 +1079510,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.30.403824", + "rel_title": "First computational design of Covid-19 coronavirus vaccine using lambda superstrings", + "rel_date": "2020-11-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.30.403824", + "rel_abs": "In this work we have developed, by employing lambda superstrings, a map of candidate vaccines against SARS-CoV-2 with lengths between 9 and 200, based on estimations of the immunogenicity of the epitopes and the binding affinity of epitopes to MHC class I molecules using tools from the IEDB Analysis Resource, as well as the overall predictions obtained using the VaxiJen tool. We have synthesized one of the peptides, specifically the one of length 22, and we have carried out an immunogenicity assay and a cytokine assay, which has given positive results in both cases.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Luis Mart\u00ednez", + "author_inst": "University of the Basque Country (UPV/EHU)" + }, + { + "author_name": "Iker Malaina", + "author_inst": "University of the Basque Country (UPV/EHU)" + }, + { + "author_name": "David Salcines", + "author_inst": "Instituto de Investigaci\u00f3n Marqu\u00e9s de Valdecilla" + }, + { + "author_name": "H\u00e9ctor Ter\u00e1n", + "author_inst": "Instituto de Investigaci\u00f3n Marqu\u00e9s de Valdecilla" + }, + { + "author_name": "Santos Alegre", + "author_inst": "University of the Basque Country (UPV/EHU)" + }, + { + "author_name": "Ildefonso Mart\u00cdnez de la Fuente", + "author_inst": "CEBAS-CSIC" + }, + { + "author_name": "Elena Gonz\u00e1lez", + "author_inst": "Hospital Universitario Marqu\u00e9s de Valdecilla" + }, + { + "author_name": "Gonzalo Ocejo", + "author_inst": "Hospital Universitario Marqu\u00e9s de Valdecilla" + }, + { + "author_name": "Carmen \u00c1lvarez", + "author_inst": "Universidad Internacional de La Rioja" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.11.29.402339", "rel_title": "Recombinant Fc-fusion vaccine of RBD induced protection against SARS-CoV-2 in non-human primate and mice", @@ -1082096,57 +1080141,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.11.25.20234914", - "rel_title": "The efficacy and safety of hydroxychloroquine in COVID19 patients : a multicenter national retrospective cohort", - "rel_date": "2020-11-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.25.20234914", - "rel_abs": "BackgroundHydroxychloroquine is an antimalarial drug that received worldwide news and media attention in the treatment of COVID-19 patients. This drug was used based on its antimicrobial and antiviral properties despite lack of definite evidence of clinical efficacy. In this study, we aim to assess the efficacy and safety of using Hydroxychloroquine in treatment of COVID-19 patients who are admitted in acute care hospitals in Bahrain.\n\nMethodologyWe conducted retrospective cohort study on a random sample of admitted COVID19 patients between 24 February and 31 July 2020. The study was conducted in four acute care COVID19 hospitals in Bahrain. Data was extracted from the medical records. The primary endpoint was the requirement of non-invasive ventilation, intubation or death. Secondary endpoint was length of hospitalization for survivors. Three methods of analysis were used to control for confounding factors: logistic multivariate regression, propensity score adjusted regression and matched propensity score analysis.\n\nResultsA random sample of 1571 patients were included, 440 of which received HCQ (treatment group) and 1131 did not receive it (control group). Our results showed that HCQ did not have a significant effect on primary outcomes due to COVID-19 infection when compared to controls after adjusting for confounders (OR 1.43 95% CI 0.85 to 2.37, P value=0.17). Co-administration of azithromycin had no effect on primary outcomes (OR 2.7 95% CI 0.82 to 8.85 P value =0.10). HCQ was found to be associated with increased risk of hypoglycemia (OR 10.9 95% CI 1.72 - 69.49, P value =0.011) and diarrhea(OR 2.8, 95% CI 1.4-5.5, P value =0.003), but not QT prolongation(OR=1.92, 95% CI 0.95-3.9, P value =0.06) or cardiac arrhythmia.(OR=1.06, 95% CI 0.55-2.05, P value =0.85).\n\nConclusionOur results showed no significant beneficial effect of using hydroxychloroquine on the outcome of COVID-19 patients. Moreover, the risk of hypoglycemia due to hydroxychloroquine would possess a significant risk for out of hospital use.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Abdulkarim Abdulrahman", - "author_inst": "National Taskforce for Combating the Coronavirus (COVID-19), Bahrain ; Mohammed Bin Khalifa Cardiac Centre, Bahrain" - }, - { - "author_name": "Islam AlSayed", - "author_inst": "King Hamad University Hospital, Bahrain" - }, - { - "author_name": "Marwa AlMadhi", - "author_inst": "School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom" - }, - { - "author_name": "Jumana AlArayedh", - "author_inst": "Ministry of Health, Bahrain" - }, - { - "author_name": "Sara Jaafar Mohamed", - "author_inst": "King Hamad University Hospital, Bahrain" - }, - { - "author_name": "Aesha Khalid Sharif", - "author_inst": "Ministry of Health, Bahrain" - }, - { - "author_name": "Khadija Alansari", - "author_inst": "King Hamad University Hospital, Bahrain" - }, - { - "author_name": "Abdulla Ismael AlAwadhi", - "author_inst": "National Taskforce for Combating the Coronavirus (COVID-19), Bahrain ; Bahrain Defence Force hospital, Bahrain" - }, - { - "author_name": "Manaf AlQahtani", - "author_inst": "Royal College of Surgeons in Ireland, Bahrain ; National Taskforce for Combating the Coronavirus (COVID-19), Bahrain ; Bahrain Defence Force hospital, Bahrain" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.30.402487", "rel_title": "Clade GR and Clade GH Isolates in Asia Show Highest Amount of SNPs", @@ -1083118,6 +1081112,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.25.20235457", + "rel_title": "EXPLORING THE HEALTHY BEHAVIORS OF NIGERIANS DURING THE COVID-19 PANDEMIC.", + "rel_date": "2020-11-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.25.20235457", + "rel_abs": "Healthy behaviors remain important for staying safe during the coronavirus disease 2019 (COVID-19) pandemic. This study, therefore, explored the healthy behaviors of Nigerians during the COVID-19 pandemic and the impact of COVID-19 related news on healthy behaviors. Thirty-three (17 females and 16 males) participants from the general Nigerian population with age range of 23-64 years were recruited via social media using the snowball technique. Responses were elicited using semi-structured questions and subjected to thematic analysis. The healthy behaviors identified included; \"social distancing\", \"changes in nutrition\", \"hand washing or sanitizing\", \"exercise\", \"increased vigilance from those with comorbidities\", and \"use of facemask\". In another analysis, the impacts of COVID-19 related news on healthy behaviors were; \"behavior modification\", \"anxious impacts\", and \"fake news about COVID-19 caused people to stop listening to COVID-19 related news\". Findings generated practical implications for enhancing healthy behaviors during the COVID-19 pandemic. The role of the media in strengthening healthy behaviors during the pandemic was also highlighted.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Ifeanyichukwu Meek Eyisi", + "author_inst": "Covenant University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.11.24.20237909", "rel_title": "Psychological distress among people with probable COVID-19 infection: analysis of the UK Household Longitudinal Study", @@ -1083390,57 +1081403,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.25.20237776", - "rel_title": "Body mass index and risk of COVID-19 diagnosis, hospitalisation, and death: a population-based multi-state cohort analysis including 2,524,926 people in Catalonia, Spain", - "rel_date": "2020-11-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.25.20237776", - "rel_abs": "ObjectiveTo investigate associations between body mass index (BMI) and risk of COVID-19 diagnosis, hospitalisation with COVID-19, and COVID-19-related death, accounting for potential effect modification by age and sex.\n\nDesignPopulation-based cohort study.\n\nSettingPrimary care records covering >80% of the Catalonian population (Spain), linked to region-wide testing, hospital, and mortality records from March to May 2020.\n\nParticipantsPeople aged [≥]18 years with at least one measurement of weight and height from the general population and with at least one year of prior medical history available.\n\nMain outcome measuresCause-specific hazard ratios (HR) with 95% confidence intervals for each outcome.\n\nResultsOverall, 2,524,926 participants were followed up for a median of 67 days. A total of 57,443 individuals were diagnosed with COVID-19, 10,862 were hospitalised with COVID-19, and 2,467 had a COVID-19-related death. BMI was positively associated with being diagnosed as well as hospitalised with COVID-19. Compared to a BMI of 22kg/m2, the HR (95%CI) of a BMI of 31kg/m2 was 1.22 (1.19-1.24) for COVID-19 diagnosis, and 1.88 (1.75-2.03) and 2.01 (1.86-2.18) for hospitalisation without and with a prior outpatient diagnosis, respectively. The relation between BMI and risk of COVID-19 related death was J-shaped. There was a modestly higher risk of death among individuals with BMIs[≤]19 kg/m2 and a more pronounced increasing risk for BMIs [≥]37 kg/m2 and [≥]40 kg/m2 among those who were previously hospitalised with COVID-19 and diagnosed with COVID-19 in outpatient settings, respectively. The increase in risk for COVID-19 outcomes was particularly pronounced among younger patients.\n\nConclusionsThere is a monotonic association between BMI and COVID-19 infection and hospitalisation risks, but a J-shaped one with mortality. More research is needed to unravel the mechanisms underlying these relationships.\n\nSummary boxesO_ST_ABSSection 1: What is already known on this topicC_ST_ABSO_LIA high body mass index (BMI) has previously been associated in a linear and non-linear fashion with an increased risk of multiple health outcomes; these associations may vary by individual factors such as age and sex.\nC_LIO_LIObesity has been identified as a risk factor for COVID-19 severity and mortality. However, the role of general adiposity in relation to COVID-19 outcomes has mostly been studied by dichotomizing BMI (below or above 30 kg/m2) or by a diagnostic code indicating obesity.\nC_LIO_LITwo studies have investigated BMI (as a continuous variable) in relation to COVID-19 outcomes, accounting for non-linearity: one conducted in a tested population sample of the UK Biobank found BMI is related in a dose-response manner with the risk of testing positive for COVID-19; another conducted in a hospital setting in New York reported a J-shaped association between BMI and the risk of intubation or death. These studies were limited in sample size and were prone to collider bias due to the participants restriction to tested and hospitalised patients. No studies have described the association between BMI and COVID-19 outcomes across the natural history of the disease (from no disease to symptomatic disease, hospitalisation, and mortality) using data from diverse health settings.\nC_LI\n\nSection 2: What this study addsO_LIWe provide a comprehensive analysis of the association between BMI and the course of the COVID-19 disease in the general population of a Spanish region during the first wave of the pandemic, using linked data capturing outpatient clinical diagnoses, RT-PCR test results, hospitalisations, and mortality (inside and outside of the hospital setting).\nC_LIO_LIWe found that BMI is positively associated with being diagnosed as well as hospitalised with COVID-19, and is linked in a J-shaped fashion with the risk of COVID-19 related death.\nC_LIO_LIThe association between BMI and COVID-19 related outcomes is modified by age and sex; particularly, the risk of COVID-19 outcomes related to increased BMI is higher for those aged between 18 and 59 years, compared to those in older age groups.\nC_LI", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Martina Recalde", - "author_inst": "1) Fundacio Institut Universitari per a la recerca a l Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain; 2) Universitat Autonoma de Ba" - }, - { - "author_name": "Andrea Pistillo", - "author_inst": "1) Fundacio Institut Universitari per a la recerca a l Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain" - }, - { - "author_name": "Sergio Fernandez-Bertolin", - "author_inst": "1) Fundacio Institut Universitari per a la recerca a l Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain" - }, - { - "author_name": "Elena Roel", - "author_inst": "1) Fundacio Institut Universitari per a la recerca a l Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain; 2) Universitat Autonoma de Ba" - }, - { - "author_name": "Maria Aragon", - "author_inst": "1) Fundacio Institut Universitari per a la recerca a l Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain" - }, - { - "author_name": "Heinz Freisling", - "author_inst": "1) International Agency for Research on Cancer (IARC-WHO), 150 Cours Albert Thomas, 69008 Lyon, France" - }, - { - "author_name": "Daniel Prieto-Alhambra", - "author_inst": "1) Centre for Statistics in Medicine (CSM), Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS), University of Oxford, UK" - }, - { - "author_name": "Edward Burn", - "author_inst": "1) Fundacio Institut Universitari per a la recerca a l Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain; 2) Centre for Statistics in M" - }, - { - "author_name": "Talita Duarte-Salles", - "author_inst": "1) Fundacio Institut Universitari per a la recerca a l Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol), Barcelona, Spain" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.24.20237818", "rel_title": "County Demographics and COVID-19 Death Rates: Comparison of relationship in the first and current stage of the pandemic in the United States of America", @@ -1084868,6 +1082830,133 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.11.25.399139", + "rel_title": "Highly functional virus-specific cellular immune response in asymptomatic SARS-CoV-2 infection", + "rel_date": "2020-11-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.25.399139", + "rel_abs": "The efficacy of virus-specific T cells in clearing pathogens involves a fine balance between their antiviral and inflammatory features. SARS-CoV-2-specific T cells in individuals who clear SARS-CoV-2 infection without symptoms or disease could reveal non-pathological yet protective characteristics. We therefore compared the quantity and function of SARS-CoV-2-specific T cells in a cohort of asymptomatic individuals (n=85) with that of symptomatic COVID-19 patients (n=76), at different time points after antibody seroconversion. We quantified T cells reactive to structural proteins (M, NP and Spike) using ELISpot assays, and measured the magnitude of cytokine secretion (IL-2, IFN-{gamma}, IL-4, IL-6, IL-1{beta}, TNF- and IL-10) in whole blood following T cell activation with SARS-CoV-2 peptide pools as a functional readout. Frequencies of T cells specific for the different SARS-CoV-2 proteins in the early phases of recovery were similar between asymptomatic and symptomatic individuals. However, we detected an increased IFN-{gamma} and IL-2 production in asymptomatic compared to symptomatic individuals after activation of SARS-CoV-2-specific T cells in blood. This was associated with a proportional secretion of IL-10 and pro-inflammatory cytokines (IL-6, TNF- and IL-1{beta}) only in asymptomatic infection, while a disproportionate secretion of inflammatory cytokines was triggered by SARS-CoV-2-specific T cell activation in symptomatic individuals. Thus, asymptomatic SARS-CoV-2 infected individuals are not characterized by a weak antiviral immunity; on the contrary, they mount a robust and highly functional virus-specific cellular immune response. Their ability to induce a proportionate production of IL-10 might help to reduce inflammatory events during viral clearance.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Nina Le Bert", + "author_inst": "Duke-NUS Medical School" + }, + { + "author_name": "Hannah E Clapham", + "author_inst": "Saw Swee Hock School of Public Health, National University of Singapore" + }, + { + "author_name": "Anthony T Tan", + "author_inst": "Duke-NUS Medical School" + }, + { + "author_name": "Wan Ni Chia", + "author_inst": "Duke-NUS Medical School" + }, + { + "author_name": "Christine YL Tham", + "author_inst": "Duke-NUS Medical School" + }, + { + "author_name": "Jane M Lim", + "author_inst": "Saw Swee Hock School of Public Health, National University of Singapore" + }, + { + "author_name": "Kamini Kunasegaran", + "author_inst": "Duke-NUS Medical School" + }, + { + "author_name": "Linda Tan", + "author_inst": "Saw Swee Hock School of Public Health, National University of Singapore" + }, + { + "author_name": "Charles-Antoine Dutertre", + "author_inst": "Gustave Roussy" + }, + { + "author_name": "Nivedita Shankar", + "author_inst": "Saw Swee Hock School of Public Health, National University of Singapore" + }, + { + "author_name": "Joey ME Lim", + "author_inst": "Duke-NUS Medical School" + }, + { + "author_name": "Louisa Jin Sun", + "author_inst": "Alexandra Hospital, National University Health System" + }, + { + "author_name": "Marina Zahari", + "author_inst": "Saw Swee Hock School of Public Health, National University of Singapore" + }, + { + "author_name": "Zaw M Tun", + "author_inst": "Saw Swee Hock School of Public Health, National University of Singapore" + }, + { + "author_name": "Vishakha Kumar", + "author_inst": "Saw Swee Hock School of Public Health, National University of Singapore" + }, + { + "author_name": "Beng Lee Lim", + "author_inst": "Duke-NUS Medical School" + }, + { + "author_name": "Siew Hoon Lim", + "author_inst": "Singapore General Hospital" + }, + { + "author_name": "Adeline Chia", + "author_inst": "Duke-NUS Medical School" + }, + { + "author_name": "Yee-Joo Tan", + "author_inst": "Yong Loo Lin School of Medicine, National University of Singapore" + }, + { + "author_name": "Paul Anantharajah Tambyah", + "author_inst": "National University Hospital" + }, + { + "author_name": "Shirin Kalimuddin", + "author_inst": "Singapore General Hospital" + }, + { + "author_name": "David CB Lye", + "author_inst": "National Centre of Infectious Diseases" + }, + { + "author_name": "Jenny GH Low", + "author_inst": "Singapore General Hospital" + }, + { + "author_name": "Lin-Fa Wang", + "author_inst": "Duke-NUS Medical School" + }, + { + "author_name": "Wei Yee Wan", + "author_inst": "Singapore General Hospital" + }, + { + "author_name": "Li Yang Hsu", + "author_inst": "Saw Swee Hock School of Public Health, National University of Singapore" + }, + { + "author_name": "Antonio Bertoletti", + "author_inst": "Duke-NUS Medical School" + }, + { + "author_name": "Clarence C Tam", + "author_inst": "Saw Swee Hock School of Public Health, National University of Singapore" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.11.27.400788", "rel_title": "Unheeded SARS-CoV-2 protein? Look deep into negative-sense RNA", @@ -1085260,65 +1083349,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.11.26.399436", - "rel_title": "Host-directed FDA-approved drugs with antiviral activity against SARS-CoV-2 identified by hierarchical in silico/in vitro screening methods", - "rel_date": "2020-11-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.26.399436", - "rel_abs": "The unprecedent situation generated by the COVID-19 global emergency prompted us to actively work to fight against this pandemic by searching for repurposable agents among FDA approved drugs to shed light into immediate opportunities for the treatment of COVID-19 patients.\n\nIn the attempt to proceed toward a proper rationalization of the search for new antivirals among approved drugs, we carried out a hierarchical in silico/in vitro protocol which successfully combines virtual and biological screening to speed up the identification of host-directed therapies against COVID-19 in an effective way.\n\nTo this end a multi-target virtual screening approach focused on host-based targets related to viral entry followed by the experimental evaluation of the antiviral activity of selected compounds has been carried out. As a result, five different potentially repurposable drugs interfering with viral entry, cepharantine, clofazimine, metergoline, imatinib and efloxate, have been identified.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Tiziana Ginez", - "author_inst": "CIB-CSIC" - }, - { - "author_name": "Urtzi Garaigorta", - "author_inst": "CNB-CSIC" - }, - { - "author_name": "David Ramirez", - "author_inst": "Universidad Autonoma de Chile" - }, - { - "author_name": "Victoria Castro", - "author_inst": "CNB-CSIC" - }, - { - "author_name": "Vanesa Nozal", - "author_inst": "CIB-CSIC" - }, - { - "author_name": "Ines Maestro", - "author_inst": "CIB-CSIC" - }, - { - "author_name": "Javier Garcia-Carceles", - "author_inst": "CIB-CSIC" - }, - { - "author_name": "Nuria E Campillo", - "author_inst": "CIB-CSIC" - }, - { - "author_name": "Ana Martinez", - "author_inst": "CSIC" - }, - { - "author_name": "Pablo Gastaminza", - "author_inst": "CNB-CSIC" - }, - { - "author_name": "Carmen Gil", - "author_inst": "CSIC" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.11.25.398859", "rel_title": "Pharmacologic profiling reveals lapatinib as a novel antiviral against SARS-CoV-2 in vitro", @@ -1086538,6 +1084568,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, + { + "rel_doi": "10.1101/2020.11.23.20237172", + "rel_title": "Effect of hot zone infection outbreaks on the dynamics of SARS-CoV-2 spread in the community at large", + "rel_date": "2020-11-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.23.20237172", + "rel_abs": "Transmission of SARS-CoV-2 appears especially effective in \"hot zone\" locations where individuals interact in close proximity. We present mathematical models describing two types of hot zones. First, we consider a metapopulation model of infection spread where transmission hot zones are explicitly described by independent demes in which the same people repeatedly interact (referred to as \"static\" hot zones, e.g. nursing homes, food processing plants, prisons, etc.). These are assumed to exists in addition to a \"community at large\" compartment in which virus transmission is less effective. This model yields a number of predictions that are relevant to interpreting epidemiological patterns in COVID19 data. Even if the rate of community virus spread is assumed to be relatively slow, outbreaks in hot zones can temporarily accelerate initial community virus growth, which can lead to an overestimation of the viral reproduction number in the general population. Further, the model suggests that hot zones are a reservoir enabling the prolonged persistence of the virus at \"infection plateaus\" following implementation of non-pharmaceutical interventions, which has been frequently observed in data. The second model considers \"dynamic\" hot zones, which can repeatedly form by drawing random individuals from the community, and subsequently dissolve (e.g. restaurants, bars, movie theaters). While dynamic hot zones can accelerate the average rate of community virus spread and can provide opportunities for targeted interventions, they do not predict the occurrence of infection plateaus or other atypical epidemiological dynamics. The models therefore identify two types of transmission hot zones with very different effects on the infection dynamics, which warrants further epidemiological investigations.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Dominik Wodarz", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Natalia L. Komarova", + "author_inst": "University of California Irvine" + }, + { + "author_name": "Luis M. Schang", + "author_inst": "Cornell University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.23.20237024", "rel_title": "COVID-19: Short term prediction model using daily incidence data", @@ -1086990,77 +1085047,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.24.20237560", - "rel_title": "Demography, social contact patterns and the COVID-19 burden in different settings of Ethiopia: a modeling study", - "rel_date": "2020-11-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.24.20237560", - "rel_abs": "BackgroundCOVID-19 spread may have a dramatic impact in countries with vulnerable economies and limited availability of, and access to, healthcare resources and infrastructures. However, in sub-Saharan Africa a low prevalence and mortality have been observed so far.\n\nMethodsWe collected data on individuals social contacts in Ethiopia across geographical contexts characterized by heterogeneous population density, work and travel opportunities, and access to primary care. We assessed how socio-demographic factors and observed mixing patterns can influence the COVID-19 disease burden, by simulating SARS-CoV-2 transmission in remote settlements, rural villages, and urban neighborhoods, under the current school closure mandate.\n\nResultsFrom national surveillance data, we estimated a net reproduction number of 1.62 (95%CI 1.55-1.70). We found that, at the end of an epidemic mitigated by school closure alone, 10-15% of the overall population would have been symptomatic and 0.3-0.4% of the population would require mechanical ventilation and/or possibly result in a fatal outcome. Higher infection attack rates are expected in more urbanized areas, but the highest incidence of critical disease is expected in remote subsistence farming settlements.\n\nConclusionsThe relatively low burden of COVID-19 in Ethiopia can be explained by the estimated mixing patterns, underlying demography and the enacted school closures. Socio-demographic factors can also determine marked heterogeneities across different geographical contexts within the same country. Our findings can contribute to understand why sub-Saharan Africa is experiencing a relatively lower attack rate of severe cases compared to high income countries.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Filippo Trentini", - "author_inst": "Bruno Kessler Foundation" - }, - { - "author_name": "Giorgio Guzzetta", - "author_inst": "Bruno Kessler Foundation" - }, - { - "author_name": "Margherita Galli", - "author_inst": "Bruno Kessler Foundation" - }, - { - "author_name": "Agnese Zardini", - "author_inst": "Bruno Kessler Foundation" - }, - { - "author_name": "Fabio Manenti", - "author_inst": "Doctors with Africa CUAMM" - }, - { - "author_name": "Giovanni Putoto", - "author_inst": "Doctors with Africa CUAMM" - }, - { - "author_name": "Valentina Marziano", - "author_inst": "Bruno Kessler Foundation" - }, - { - "author_name": "Worku Gamshie Nigussa", - "author_inst": "Doctors with Africa CUAMM" - }, - { - "author_name": "Ademe Tsegaye", - "author_inst": "Doctors with Africa CUAMM" - }, - { - "author_name": "Alessandro Greblo", - "author_inst": "Doctors with Africa CUAMM" - }, - { - "author_name": "Alessia Melegaro", - "author_inst": "Bocconi University" - }, - { - "author_name": "Marco Ajelli", - "author_inst": "Indiana University School of Public Health" - }, - { - "author_name": "Stefano Merler", - "author_inst": "Bruno Kessler Foundation" - }, - { - "author_name": "Piero Poletti", - "author_inst": "Bruno Kessler Foundation" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.24.20235952", "rel_title": "Severity of COVID-19 is inversely correlated with increased number counts of non-synonymous mutations in Tokyo", @@ -1088152,6 +1086138,57 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.11.24.389627", + "rel_title": "The rocaglate CR-31-B (-) inhibits SARS-CoV-2 replication at non-cytotoxic, low nanomolar concentrations in vitro and ex vivo", + "rel_date": "2020-11-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.24.389627", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a betacoronavirus in the subgenus Sarbecovirus causes a respiratory disease with varying symptoms referred to as coronavirus disease 2019 (COVID-19) and is responsible for a pandemic that started in early 2020. With no vaccines or effective antiviral treatments available, and infection and fatality numbers continuing to increase globally, the quest for novel therapeutic solutions remains an urgent priority. Rocaglates, a class of plant-derived cyclopenta[b]benzofurans, exhibit broad-spectrum antiviral activity against positive- and negative-sense RNA viruses. This compound class inhibits eukaryotic initiation factor 4A (eIF4A)-dependent mRNA translation initiation, resulting in strongly reduced viral RNA translation. The synthetic rocaglate CR-31-B (-) has previously been shown to inhibit the replication of human coronaviruses, such as HCoV-229E and MERS-CoV, as well as Zika-, Lassa-, Crimean Congo hemorrhagic fever virus in primary cells. Here, we assessed the antiviral activity of CR-31-B (-) against SARS-CoV-2 using both in vitro and ex vivo cell culture models. In African green monkey Vero E6 cells, CR-31-B (-) inhibited SARS-CoV-2 replication with an EC50 of ~1.8 nM. In line with this, viral protein accumulation and replication/transcription complex formation were found to be strongly reduced by this compound. In an ex vivo infection system using human airway epithelial cells, CR-31-B (-) was found to cause a massive reduction of SARS-CoV-2 titers by about 4 logs to nearly non-detectable levels. The data reveal a potent anti-SARS-CoV-2 activity by CR-31-B (-), corroborating previous results obtained for other coronaviruses and supporting the idea that rocaglates may be used in first-line antiviral intervention strategies against novel and emerging RNA virus outbreaks.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Christin Mueller", + "author_inst": "Justus-Liebig University Giessen" + }, + { + "author_name": "Wiebke Obermann", + "author_inst": "Philipps University Marburg" + }, + { + "author_name": "Nadja Karl", + "author_inst": "Justus-Liebig University Giessen" + }, + { + "author_name": "Hans G. Wendel", + "author_inst": "Sloan-Kettering Institute" + }, + { + "author_name": "Gaspar Taroncher-Oldenburg", + "author_inst": "Gaspar Taroncher Consulting, Philadelphia" + }, + { + "author_name": "Stephan Pleschka", + "author_inst": "Justus-Liebig University Giessen" + }, + { + "author_name": "Roland K. Hartmann", + "author_inst": "Philipps University Marburg" + }, + { + "author_name": "Arnold Gruenweller", + "author_inst": "Philipps University Marburg" + }, + { + "author_name": "John Ziebuhr", + "author_inst": "Justus Liebig University Giessen" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.11.17.386714", "rel_title": "Mutations in SARS-CoV-2 spike protein and RNA polymerase complex are associated with COVID-19 mortality risk", @@ -1088752,29 +1086789,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.20.20220749", - "rel_title": "Community Transmission of SARS-CoV-2 by Fomites: Risks and Risk Reduction Strategies", - "rel_date": "2020-11-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.20.20220749", - "rel_abs": "SARS-CoV-2, the virus responsible for the COVID-19 pandemic, is perceived to be primarily transmitted via person-to-person contact, through droplets produced while talking, coughing, and sneezing. Transmission may also occur through other routes, including contaminated surfaces; nevertheless, the role that surfaces have on the spread of the disease remains contested. Here we use the Quantitative Microbial Risk Assessment framework to examine the risks of community transmission of SARS-CoV-2 through contaminated surfaces and to evaluate the effectiveness of hand and surface disinfection as potential interventions. The risks posed by contacting surfaces in communities are low (average of the median risks 1.6x10-4 - 5.6x10-9) for community infection prevalence rates ranging from 0.2-5%. Hand disinfection substantially reduces relative risks of transmission independently of the diseases prevalence and the frequency of contact, even with low (25% of people) or moderate (50% of people) compliance. In contrast, the effectiveness of surface disinfection is highly dependent on the prevalence and the frequency of contacts. The work supports the current perception that contaminated surfaces are not a primary mode of transmission of SARS-CoV-2 and affirms the benefits of making hand disinfectants widely available.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ana K Pitol", - "author_inst": "Imperial College London" - }, - { - "author_name": "Timothy R Julian", - "author_inst": "Eawag, Swiss Federal Institute of Aquatic Science and Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.11.21.20236067", "rel_title": "Commitment of medical students during the COVID-19-pandemic in Germany", @@ -1089802,6 +1087816,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.11.20.20235812", + "rel_title": "Psychosocial Health of School-aged Children during the Initial COVID-19 Safer-At-Home School Mandates in Florida: A cross-sectional study", + "rel_date": "2020-11-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.20.20235812", + "rel_abs": "BackgroundGiven the emerging literature regarding the impacts of lockdown measures on mental health, this study aims to identify risk factors in school-aged children for being at risk for psychosocial disorders during the COVID-19 Safer-at-Home School mandates in Florida\n\nMethodsA cross-sectional study was conducted in April 2020 (n=280). Bivariate analysis and logistic and multinomial logistic regression models are used to examine socio-demographic and knowledge, attitude, and practice (KAP) predictors of anxiety, depression, and obsessive- compulsive disorder (OCD).\n\nResultsLoss of household income was associated with being at risk for depression [aOR=3.130, 95% CI= (1.41-6.97)], anxiety [aOR=2.531, 95%CI= (1.154-5.551)], and OCD [aOR=2.90, 95%CI= (1.32-6.36)]. Being female was associated with risk for depression [aOR=1.72, 95% CI=(1.02-2.93)], anxiety [aOR=1.75, 95% CI=(1.04-2.97)], and OCD[aOR=1.764, 95%CI= (1.027-3.028)]. Parental practices that are protective against COVID-19 were associated with children being at risk of depression [aOR=1.55, 95% CI= (1.04-2.31)]. Being at a lower school level was risk factor for anxiety and OCD.\n\nConclusionsEfforts to address mental health risk in children, as a result schools should prioritize girls, younger children, and children of families who lose income. Limiting the spread of COVID-19 through school closure may exacerbate the risk of psychosocial disorders in children, thus school administrators should move quickly to target those at greatest risk.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Sarah Lindley McKune", + "author_inst": "University of Florida" + }, + { + "author_name": "Daniel E Acosta", + "author_inst": "University of Florida" + }, + { + "author_name": "Nick Diaz", + "author_inst": "University of Florida" + }, + { + "author_name": "Kaitlin Brittain", + "author_inst": "University of Florida" + }, + { + "author_name": "Diana Joyce Beaulieu", + "author_inst": "University of Florida" + }, + { + "author_name": "Anthony Thomas Maurelli", + "author_inst": "University of Florida" + }, + { + "author_name": "Eric J. Nelson", + "author_inst": "University of Florida" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.11.21.20236034", "rel_title": "Role of asymptomatic COVID-19 cases in viral transmission: Findings from a hierarchical community contact network model", @@ -1090162,45 +1088219,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2020.11.21.392670", - "rel_title": "A repurposed, blood gene signature is associated with poor outcomes in SARS-CoV-2", - "rel_date": "2020-11-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.21.392670", - "rel_abs": "Poor outcomes after SARS-CoV-2 infection are difficult to predict. Survivors may develop pulmonary fibrosis. We previously identified a 52-gene signature in peripheral blood, predictive of mortality in Idiopathic Pulmonary Fibrosis. In this study, we analyzed this signature in SARS-CoV-2 infected individuals and identified genomic risk profiles with significant differences in outcomes. Analysis of single cell expression data shows that monocytes, red blood cells, neutrophils and dendritic cells are the cellular source of the high risk gene signature.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Brenda M Juan-Guardela", - "author_inst": "NCH Healthcare System, University of South Florida" - }, - { - "author_name": "Jiehuan Sun", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Tong Zhang", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Bing Xu", - "author_inst": "University of Illinois at Chicago" - }, - { - "author_name": "Gaetane Michaud", - "author_inst": "University of South Florida" - }, - { - "author_name": "Jose D. Herazo-Maya", - "author_inst": "NCH Healthcare System, University of South Florida" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.11.21.392407", "rel_title": "N439K variant in spike protein may alter the infection efficiency and antigenicity of SARS-CoV-2 based on molecular dynamics simulation", @@ -1091404,6 +1089422,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.18.20232892", + "rel_title": "A follow-up study shows no new infections caused by patients with repeat positive of COVID-19 in Wuhan", + "rel_date": "2020-11-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.18.20232892", + "rel_abs": "BackgroundIt has been reported that a few recovered COVID-19 patients could suffer repeat positive, testing positive for the SARS-CoV-2 virus again after they were discharged from hospital. Understanding the epidemiological characteristics of patients with repeat positive is vital in preventing a second wave of COVID-19.\n\nMethodsIn this study, the epidemiological and clinical features for 20,280 COVID-19 patients from multiple centers between 31 December 2019 and 4 August 2020 in Wuhan were collected and followed. In addition, the RT-qPCR testing results for 4,079 individuals who had close contact with the patients suffering repeat positive were also obtained.\n\nResults2,466 (12.16%) of 20,280 patients presented with a repeat positive of SARS-CoV-2 after they were discharged from hospital. 4,079 individuals had close contact with them. The PCR result were negative for the 4,079 individuals.\n\nConclusionsBy a follow-up study in Wuhan, we show the basic characteristics of patients with repeat positive and no new infections caused by patients with repeat positive of COVID-19.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Xiaomin Wu", + "author_inst": "Wuhan Center for Disease Control and Prevention, Wuhan, China" + }, + { + "author_name": "Zengmiao Wang", + "author_inst": "State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China" + }, + { + "author_name": "Zhenyu He", + "author_inst": "Wuhan Center for Disease Control and Prevention, Wuhan, China" + }, + { + "author_name": "Yapin Li", + "author_inst": "Central Theater Center for Disease Control and Prevention of PLA, Beijing, China" + }, + { + "author_name": "Yating Wu", + "author_inst": "Wuhan Center for Disease Control and Prevention, Wuhan, China" + }, + { + "author_name": "Huaiji Wang", + "author_inst": "Wuhan Center for Disease Control and Prevention, Wuhan, China" + }, + { + "author_name": "Yonghong Liu", + "author_inst": "State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China" + }, + { + "author_name": "Fanghua Hao", + "author_inst": "Central China Normal University, Wuhan, China" + }, + { + "author_name": "Huaiyu Tian", + "author_inst": "State Key Laboratory of Remote Sensing Science, College of Global Change and Earth System Science, Beijing Normal University, Beijing, China" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.19.20233437", "rel_title": "Viruses such as SARS-CoV-2 can be partially shielded from UV radiation when in particles generated by sneezing or coughing: Numerical simulations", @@ -1091912,65 +1089981,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.21.392639", - "rel_title": "Anti-COVID-19 efficacy of ivermectin in the golden hamster", - "rel_date": "2020-11-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.21.392639", - "rel_abs": "The devastating coronavirus disease 2019 (COVID-19) pandemic, due to SARS-CoV-2, has caused more than 47 million confirmed cases and more than 1.2 million human deaths around the globe1, and most of the severe cases of COVID-19 in humans are associated with neurological symptoms such as anosmia and ageusia, and uncontrolled inflammatory immune response2-5. Among therapeutic options6-8, the use of the anti-parasitic drug ivermectin (IVM), has been proposed, given its possible anti-SARS-CoV-2 activity9. Ivermectin is a positive allosteric modulator of the -7 nicotinic acetylcholine receptor10, which has been suggested to represent a target for the control of Covid-19 infection11, with a potential immunomodulatory activity12. We assessed the effects of IVM in SARS-CoV-2-intranasally-inoculated golden Syrian hamsters. Even though ivermectin had no effect on viral load, SARS-Cov-2-associated pathology was greatly attenuated. IVM had a sex-dependent and compartmentalized immunomodulatory effect, preventing clinical deterioration and reducing olfactory deficit in infected animals. Importantly, ivermectin dramatically reduced the Il-6/Il-10 ratio in lung tissue, which likely accounts for the more favorable clinical presentation in treated animals. Our data support IVM as a promising anti-COVID-19 drug candidate.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Guilherme Dias de Melo", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Fran\u00e7oise Lazarini", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Florence Larrous", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Lena Feige", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Lauriane Kergoat", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Agnes Marchio", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Pascal Pineau", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Marc Lecuit", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Pierre-Marie Lledo", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Jean-Pierre Changeux", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Herve Bourhy", - "author_inst": "Institut Pasteur" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.11.20.392381", "rel_title": "Transmission and protection against re-infection in the ferret model with the SARS-CoV-2 USA-WA1/2020 reference isolate", @@ -1093790,6 +1091800,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.18.20230649", + "rel_title": "A network modelling approach to assess non-pharmaceutical disease controls in a worker population: An application to SARS-CoV-2", + "rel_date": "2020-11-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.18.20230649", + "rel_abs": "BackgroundAs part of a concerted pandemic response to protect public health, businesses can enact non-pharmaceutical controls to minimise exposure to pathogens in workplaces and premises open to the public. Amendments to working practices can lead to the amount, duration and/or proximity of interactions being changed, ultimately altering the dynamics of disease spread. These modifications could be specific to the type of business being operated.\n\nMethodsWe use a data-driven approach to parameterise an individual-based network model for transmission of SARS-CoV-2 amongst the working population, stratified into work sectors. The network is comprised of layered contacts to consider the risk of spread in multiple encounter settings (workplaces, households, social and other). We analyse several interventions targeted towards working practices: mandating a fraction of the population to work from home; using temporally asynchronous work patterns; and introducing measures to create COVID-secure workplaces. We also assess the general role of adherence to (or effectiveness of) isolation and test and trace measures and demonstrate the impact of all these interventions across a variety of relevant metrics.\n\nResultsThe progress of the epidemic can be significantly hindered by instructing a significant proportion of the workforce to work from home. Furthermore, if required to be present at the workplace, asynchronous work patterns can help to reduce infections when compared with scenarios where all workers work on the same days, particularly for longer working weeks. When assessing COVID-secure workplace measures, we found that smaller work teams and a greater reduction in transmission risk reduced the probability of large, prolonged outbreaks. Finally, following isolation guidance and engaging with contact tracing without other measures is an effective tool to curb transmission, but is highly sensitive to adherence levels.\n\nConclusionsIn the absence of sufficient adherence to non-pharmaceutical interventions, our results indicate a high likelihood of SARS-CoV-2 spreading widely throughout a worker population. Given the heterogeneity of demographic attributes across worker roles, in addition to the individual nature of controls such as contact tracing, we demonstrate the utility of a network model approach to investigate workplace-targeted intervention strategies and the role of test, trace and isolation in tackling disease spread.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Edward M Hill", + "author_inst": "University of Warwick" + }, + { + "author_name": "Benjamin D Atkins", + "author_inst": "University of Warwick" + }, + { + "author_name": "Matt J Keeling", + "author_inst": "University of Warwick" + }, + { + "author_name": "Louise Dyson", + "author_inst": "University of Warwick" + }, + { + "author_name": "Michael J Tildesley", + "author_inst": "University of Warwick" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.18.20234104", "rel_title": "Clinical evaluation of the Roche/SD Biosensor rapid antigen test with symptomatic, non-hospitalized patients in a municipal health service drive-through testing site.", @@ -1094418,69 +1092463,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.18.388140", - "rel_title": "Detecting SARS-CoV-2 variants with SNP genotyping", - "rel_date": "2020-11-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.18.388140", - "rel_abs": "Tracking genetic variations from positive SARS-CoV-2 samples yields crucial information about the number of variants circulating in an outbreak and the possible lines of transmission but sequencing every positive SARS-CoV-2 sample would be prohibitively costly for population-scale test and trace operations. Genotyping is a rapid, high-throughput and low-cost alternative for screening positive SARS-CoV-2 samples in many settings. We have designed a SNP identification pipeline to identify genetic variation using sequenced SARS-CoV-2 samples. Our pipeline identifies a minimal marker panel that can define distinct genotypes. To evaluate the system we developed a genotyping panel to detect variants-identified from SARS-CoV-2 sequences surveyed between March and May 2020- and tested this on 50 stored qRT-PCR positive SARS-CoV-2 clinical samples that had been collected across the South West of the UK in April 2020. The 50 samples split into 15 distinct genotypes and there was a 76% probability that any two randomly chosen samples from our set of 50 would have a distinct genotype. In a high throughput laboratory, qRT-PCR positive samples pooled into 384-well plates could be screened with our marker panel at a cost of < {pound}1.50 per sample. Our results demonstrate the usefulness of a SNP genotyping panel to provide a rapid, cost-effective, and reliable way to monitor SARS-CoV-2 variants circulating in an outbreak. Our analysis pipeline is publicly available and will allow for marker panels to be updated periodically as viral genotypes arise or disappear from circulation.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Helen Harper", - "author_inst": "University of Bristol" - }, - { - "author_name": "Amanda J Burridge", - "author_inst": "University of Bristol" - }, - { - "author_name": "Mark Winfield", - "author_inst": "University of Bristol" - }, - { - "author_name": "Adam Finn", - "author_inst": "University of Bristol" - }, - { - "author_name": "Andrew D Davidson", - "author_inst": "University of Bristol" - }, - { - "author_name": "David Matthews", - "author_inst": "University of Bristol" - }, - { - "author_name": "Stephanie Hutchings", - "author_inst": "Public Health England South West" - }, - { - "author_name": "Barry Vipond", - "author_inst": "Public Health England South West" - }, - { - "author_name": "Nisha Jain", - "author_inst": "3CR Biosciences" - }, - { - "author_name": "Keith J Edwards", - "author_inst": "University of Bristol" - }, - { - "author_name": "Gary Barker", - "author_inst": "University of Bristol" - }, - { - "author_name": "- The COVID-19 Genomics UK (COG-UK) consortium", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.11.18.388850", "rel_title": "SARS-CoV-2 infection suppresses ACE2 function and antiviral immune response in the upper respiratory tract of infected patients", @@ -1095664,6 +1093646,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "geriatric medicine" }, + { + "rel_doi": "10.1101/2020.11.16.20232512", + "rel_title": "5-Alpha-Reductase Inhibitors Reduce Remission Time of COVID-19: Results From a Randomized Double Blind Placebo Controlled Interventional Trial in 130 SARS-CoV-2 Positive Men", + "rel_date": "2020-11-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.16.20232512", + "rel_abs": "BackgroundSARS-CoV-2 entry into type II pneumocytes is depended on the TMPRSS2 proteolytic enzyme. The only known promoter of TMPRSS2 in humans is an androgen response element. As such, androgen sensitivity may be a risk factor for COVID-19. Previously, we have reported a retrospective cohort analysis demonstrating the protective effect of 5-alpha-reductase inhibitors (5ARis) in COVID-19. Men using 5ARis were less likely to be admitted to the ICU than men not taking 5ARis. Additionally, men using 5ARis had drastically reduced frequency of symptoms compared to men not using 5ARis in an outpatient setting. Here we aim to determine if 5ARis will be a beneficial treatment if given after SARS-CoV-2 infection.\n\nMethodsA double-blinded, randomized, prospective, investigational study of dutasteride for the treatment of COVID-19 (NCT04446429). Subjects confirmed positive for SARS-CoV-2 were treated in an outpatient setting. Endpoints for the study were remission times for a predetermined set of symptoms: fever or feeling feverish, cough, shortness of breath, sore throat, body pain or muscle pain/ache, fatigue, headache, nasal congestion, nasal discharge (runny nose), nausea or vomiting, diarrhea, loss of appetite, and loss of taste or smell (Ageusia or Anosmia).\n\nResultsA total of 130 SARS-CoV-2 positive men were included in the study, 64 subjects in the dutasteride arm and 66 subjects in the placebo-controlled group. The differences in the average remission times for fatigue and anosmia or ageusia was statistically different between the groups (5.8 versus 10.1 days for fatigue and 7.3 versus 13.4 days for anosmia or ageusia, in dutasteride and placebo groups, respectively), however, the total remission time was significantly reduced for the men given dutasteride; 9.0 days versus 15.6 days in the placebo group (p < 0.001). Excluding loss of taste and smell the average total remission time was 7.3 days in the dutasteride group versus 11.7 in the placebo arm (p < 0.001).\n\nConclusionThe total remission time for men using 5ARis was significantly reduced compared to men not taking 5ARis.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Flavio A Cadegiani", + "author_inst": "Federal University of Sao Paulo" + }, + { + "author_name": "John McCoy", + "author_inst": "Applied Biology, Inc. Irvine, CA, USA" + }, + { + "author_name": "Carlos Gustavo Wambier", + "author_inst": "Department of Dermatology, Alpert Medical School of Brown University, Providence, RI, USA." + }, + { + "author_name": "Andy Goren", + "author_inst": "Applied Biology, Inc. Irvine, CA, USA." + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.16.20231514", "rel_title": "Low Dose Radiation Therapy for COVID-19 Pneumonia: A Pilot Study", @@ -1096044,41 +1094057,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2020.11.16.20227389", - "rel_title": "Designing Efficient Contact Tracing Through Risk-Based Quarantining", - "rel_date": "2020-11-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.16.20227389", - "rel_abs": "Contact tracing for COVID-19 is especially challenging because transmission often occurs in the absence of symptoms and because a purported 20% of cases cause 80% of infections, resulting in a small risk of infection for some contacts and a high risk for others. Here, we introduce risk-based quarantine, a system for contact tracing where each cluster (a group of individuals with a common source of exposure) is observed for symptoms when tracing begins, and clusters that do not display them are released from quarantine. We show that, under our assumptions, risk-based quarantine reduces the amount of quarantine time served by more than 30%, while achieving a reduction in transmission similar to standard contact tracing policies where all contacts are quarantined for two weeks. We compare our proposed risk-based quarantine approach against test-driven release policies, which fail to achieve a comparable level of transmission reduction due to the inability of tests to detect exposed people who are not yet infectious but will eventually become so. Additionally, test-based release policies are expensive, limiting their effectiveness in low-resource environments, whereas the costs imposed by risk-based quarantine are primarily in terms of labor and organization.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Andrew Perrault", - "author_inst": "Center for Research on Computation and Society, Harvard University, Cambridge, MA" - }, - { - "author_name": "Marie Charpignon", - "author_inst": "Institute for Data, Systems, and Society, MIT, Cambridge, MA" - }, - { - "author_name": "Jonathan Gruber", - "author_inst": "Department of Economics, MIT, Cambridge, MA" - }, - { - "author_name": "Milind Tambe", - "author_inst": "Center for Research on Computation and Society, Harvard University, Cambridge, MA" - }, - { - "author_name": "Maimuna S. Majumder", - "author_inst": "Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA and Department of Pediatrics, Harvard Medical School, Boston, MA, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.11.16.20232488", "rel_title": "Scientific output on coronavirus and WHO's Solidarity Project: a science-based choice?", @@ -1097130,6 +1095108,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, + { + "rel_doi": "10.1101/2020.11.17.20231498", + "rel_title": "Impact of a public policy restricting staff mobility between long-term care homes in Ontario, Canada during the COVID-19 pandemic", + "rel_date": "2020-11-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.17.20231498", + "rel_abs": "ObjectivesTo assess changes in the mobility of staff between long-term care homes in Ontario, Canada before and after enactment of public policy restricting staff from working at multiple homes.\n\nDesignPre-post observational study.\n\nSetting and Participants623 long-term cares homes in Ontario, Canada between March 2020 and June 2020.\n\nMethodsWe used anonymized mobile device location data to approximate connectivity between all 623 long-term care homes in Ontario during the 7 weeks before (March 1 - April 21) and after (April 22 - June 13) the policy restricting staff movement was implemented. We visualized connectivity between long-term care homes in Ontario using an undirected network and calculated the number of homes that had a connection with another long-term care home and the average number of connections per home in each period. We calculated the relative difference in these mobility metrics between the two time periods and compared within-home changes using McNemars test and the Wilcoxon rank-sum test.\n\nResultsIn the period preceding restrictions, 266 (42.7%) long-term care homes had a connection with at least one other home, compared to 79 (12.7%) homes during the period after restrictions, a drop of 70.3% (p <0.001). The average number of connections in the before period was 3.90 compared to 0.77 in after period, a drop of 80.3% (p < 0.001). In both periods, mobility between long-term care homes was higher in homes located in larger communities, those with higher bed counts, and those part of a large chain.\n\nConclusions and ImplicationsMobility between long-term care homes in Ontario fell sharply after an emergency order by the Ontario government limiting long-term care staff to a single home, though some mobility persisted. Reducing this residual mobility should be a focus of efforts to reduce risk within the long-term care sector during the COVID-19 pandemic.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Aaron Jones", + "author_inst": "McMaster University" + }, + { + "author_name": "Alexander G Watts", + "author_inst": "BlueDot" + }, + { + "author_name": "Salah Uddin Khan", + "author_inst": "BlueDot" + }, + { + "author_name": "Jack Forsyth", + "author_inst": "BlueDot" + }, + { + "author_name": "Kevin A Brown", + "author_inst": "Public Health Ontario" + }, + { + "author_name": "Andrew P Costa", + "author_inst": "McMaster University" + }, + { + "author_name": "Isaac I Bogoch", + "author_inst": "BlueDot" + }, + { + "author_name": "Nathan M Stall", + "author_inst": "University of Toronto" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "geriatric medicine" + }, { "rel_doi": "10.1101/2020.11.17.20232983", "rel_title": "COHD-COVID: Columbia Open Health Data for COVID-19 Research", @@ -1097438,105 +1095463,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.17.20233080", - "rel_title": "COVID-19: more than a little flu? Insights from the Swiss hospital-based surveillance of Influenza and COVID-19", - "rel_date": "2020-11-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.17.20233080", - "rel_abs": "BackgroundCoronavirus disease 19 (COVID-19) has frequently been colloquially compared to the seasonal influenza, but comparisons based on empirical data are scarce.\n\nAimsTo compare in-hospital outcomes for patients admitted with community-acquired COVID-19 to patients with community-acquired influenza in Switzerland.\n\nMethodsPatients >18 years, who were admitted with PCR proven COVID-19 or influenza A/B infection to 14 participating Swiss hospitals were included in a prospective surveillance. Primary and secondary outcomes were the in-hospital mortality and intensive care unit (ICU) admission between influenza and COVID-19 patients. We used Cox regression (cause-specific models, and Fine & Gray subdistribution) to account for time-dependency and competing events with inverse probability weighting to account for confounders.\n\nResultsIn 2020, 2843 patients with COVID-19 were included from 14 centers and in years 2018 to 2020, 1361 patients with influenza were recruited in 7 centers. Patients with COVID-19 were predominantly male (n=1722, 61% vs. 666 influenza patients, 48%, p<0.001) and were younger than influenza patients (median 67 years IQR 54-78 vs. median 74 years IQR 61-84, p<0.001). 363 patients (12.8%) died in-hospital with COVID-19 versus 61 (4.4%) patients with influenza (p<0.001). The final, adjusted subdistribution Hazard Ratio for mortality was 3.01 (95% CI 2.22-4.09, p<0.001) for COVID-19 compared to influenza, and 2.44 (95% CI, 2.00-3.00, p<0.001) for ICU admission.\n\nConclusionEven in a national healthcare system with sufficient human and financial resources, community-acquired COVID-19 was associated with worse outcomes compared to community-acquired influenza, as the hazards of in-hospital death and ICU admission were [~]3-fold higher.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Georg Froehlich", - "author_inst": "HeartClinic Lucerne, St. Annastrasse 32, 6006 Lucerne, Switzerland and Charite Universitaetsmedizin Berlin, Berlin, Germany" - }, - { - "author_name": "Marlieke De Kraker", - "author_inst": "Geneva University Hospitals and Faculty of Medicine, Infection Control program,Gabrielle-Perret-Gentil4, 1205 Geneva, Switzerland" - }, - { - "author_name": "Mohammed Abbas", - "author_inst": "Geneva University Hospitals and Faculty of Medicine, Infection Control program,Gabrielle-Perret-Gentil4, 1205 Geneva, Switzerland" - }, - { - "author_name": "Olivia Keiser", - "author_inst": "Geneva University Hospitals and Faculty of Medicine, Infection Control program,Gabrielle-Perret-Gentil4, 1205 Geneva, Switzerland" - }, - { - "author_name": "Amaury Thiabaud", - "author_inst": "Geneva University Hospitals and Faculty of Medicine, Infection Control program,Gabrielle-Perret-Gentil4, 1205 Geneva, Switzerland" - }, - { - "author_name": "Maroussia Roulens", - "author_inst": "Geneva University Hospitals and Faculty of Medicine, Infection Control program,Gabrielle-Perret-Gentil4, 1205 Geneva, Switzerland" - }, - { - "author_name": "Alexia Cusini", - "author_inst": "Kantonsspital Graubuenden, Department for General Medicine, Loestrasse 170, CH-7000 Chur" - }, - { - "author_name": "Domenica Flury", - "author_inst": "Kantonsspital St. Gallen, Rorschacher Strasse 95, CH-9007 St. Gallen, Switzerland" - }, - { - "author_name": "Peter Schreiber", - "author_inst": "University Hospital Zurich, Department of Infectious Diseases and Hospital Epidemiology, Raemistrasse 100, 8091 Zuerich" - }, - { - "author_name": "Michael Buettcher", - "author_inst": "Cantonal Hospital Lucerne, Pediatric Infectious Diseases, Spitalstrasse, 6000 Luzern, Switzerland" - }, - { - "author_name": "Natascia Corti", - "author_inst": "Department for General Medicine, Klinik Hirslanden, Witellikerstrasse 40, 8032 Zuerich, Switzerland" - }, - { - "author_name": "Danielle Vuichard-Gysin", - "author_inst": "Department for General Medicine, Spital Thurgau, Waldeggstrasse 8A, 8501 Frauenfeld" - }, - { - "author_name": "Nicolas Troillet", - "author_inst": "Department for Infectious Diseases, Hopital du Valais, Av. Grand-Champsec 80, 1951 Sion" - }, - { - "author_name": "Julien Sauser", - "author_inst": "Geneva University Hospitals and Faculty of Medicine, Infection Control program,Gabrielle-Perret-Gentil4, 1205 Geneva, Switzerland" - }, - { - "author_name": "Roman Gaudenz", - "author_inst": "Department for General Medicine, Kantonsspital Nidwalden, Ennetmooserstrasse 19, 6370 Stans" - }, - { - "author_name": "Lauro Damonti", - "author_inst": "Department of Infectious Diseases, Bern University Hospital, Freiburgstrasse, 3010 Bern" - }, - { - "author_name": "Carlo Balmelli", - "author_inst": "Ente Ospedaliero Cantonale Ticino, Division of Infection control and Hospital Epidemiology, CH-6500 Bellinzona, Switzerland" - }, - { - "author_name": "Anne Iten", - "author_inst": "Geneva University Hospitals and Faculty of Medicine, Infection Control program,Gabrielle-Perret-Gentil4, 1205 Geneva, Switzerland" - }, - { - "author_name": "Andreas Widmer", - "author_inst": "Department for Infectious Diseases, University Hospital Basel, Spitalstrasse 21/Petersgraben 4, 4031 Basel, Switzerland" - }, - { - "author_name": "Stephan Harbarth", - "author_inst": "Geneva University Hospitals and Faculty of Medicine, Infection Control program,Gabrielle-Perret-Gentil4, 1205 Geneva, Switzerland" - }, - { - "author_name": "Rami Sommerstein", - "author_inst": "Bern University Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.17.20233692", "rel_title": "The decrease in hospitalizations for transient ischemic attack and ischemic stroke, especially in mild cases, during the COVID-19 epidemic in Japan.", @@ -1098640,6 +1096566,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.11.17.387571", + "rel_title": "In-vitro virucidal activity of hypothiocyanite and hypothiocyanite/lactoferrin mix against SARS-CoV-2", + "rel_date": "2020-11-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.17.387571", + "rel_abs": "SARS-CoV-2 replicates efficiently in the upper airway during prodromal stage with resulting viral shedding into the environment from patients with active disease as well as from asymptomatic individuals. So far, virus spread has been exclusively contained by non-pharmacological interventions (social distancing, face masks, hand washing and several measures limiting business activities or movement of individuals)1,2. There is a need to find pharmacological interventions to mitigate the viral spread, supporting yet limiting the existing health protection measures while an effective and safe vaccine will hopefully become available. Hypothiocyanite and lactoferrin as part of the innate human immune system were shown to have a large spectrum of cidal activity against bacteria, fungi and viruses2,3. To test their virucidal activity against SARS-CoV-2 we conducted an in-vitro study. Here we show a dose-dependent virucidal activity of hypothiocyanite at micromolar concentrations, slightly improved by the presence of lactoferrin. The two substances are devoid of any cytotoxicity and may be administered combined by aerosol to exploit their antiviral activity at the port of entry (mouth, nasal cavity, conjunctiva) or exit (mouth, through emission of respiratory droplets) of SARS-CoV-2 in the human body. Furthermore, aerosol with hypothiocyanite and lactoferrin combined could also have a therapeutic effect in the lower respiratory tract, at the level of gas exchange units of the lung, preventing the devastating infection of alveolar type II cells where ACE2 is highly expressed. An in-vivo validation of in-vitro results is urgently required.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Luca Cegolon", + "author_inst": "Local Health Unit N.2 \"Marca Trevigiana\", Public Health Department, Treviso, Italy" + }, + { + "author_name": "Mattia Mirandola", + "author_inst": "Padua University, Department of Molecular Medicine, Padua, Italy" + }, + { + "author_name": "Claudio Salaris", + "author_inst": "Padua University, Department of Molecular Medicine, Padua, Italy" + }, + { + "author_name": "Maria Vittoria Salvati", + "author_inst": "Padua University, Department of Molecular Medicine, Padua, Italy" + }, + { + "author_name": "Cristiano Salata", + "author_inst": "Padua University, Department of Molecular Medicine, Padua, Italy" + }, + { + "author_name": "Giuseppe Mastrangelo", + "author_inst": "Padua University, Department of Cardiac, Thoracic, Vascular Sciences & Public Health, Padua, Italy" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.11.18.388645", "rel_title": "Formulation of a composite nasal spray enabling enhanced surface coverage and prophylaxis of SARS-COV-2", @@ -1099076,49 +1097041,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "geriatric medicine" }, - { - "rel_doi": "10.1101/2020.11.16.20232009", - "rel_title": "The total number and mass of SARS-CoV-2 virions in an infected person", - "rel_date": "2020-11-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.16.20232009", - "rel_abs": "Quantitatively describing the time course of the SARS-CoV-2 infection within an infected individual is important for understanding the current global pandemic and possible ways to combat it. Here we integrate the best current knowledge about the typical viral load of SARS-CoV-2 in bodily fluids and host tissues to estimate the total number and mass of SARS-CoV-2 virions in an infected person. We estimate that each infected person carries 109-1011 virions during peak infection, with a total mass in the range of 1-100 g, which curiously implies that all SARS-CoV-2 virions currently circulating within human hosts have a collective mass of only 0.1-10 kg. We combine our estimates with the available literature on host immune response and viral mutation rates to demonstrate how antibodies markedly outnumber the spike proteins and the genetic diversity of virions in an infected host covers all possible single nucleotide substitutions.\n\nSignificanceKnowing the absolute numbers of virions in an infection promotes better understanding of the disease dynamics and the response of the immune system. Here we use the best current knowledge on the concentrations of virions in infected individuals to estimate the total number and mass of SARS-CoV-2 virions in an infected person. Although each infected person carries an estimated 1-100 billion virions during peak infection, their total mass is no more than 0.1 mg. This curiously implies that all SARS-CoV-2 virions currently in all human hosts have a mass of between 100 gram and 10 kilogram. Combining the known mutation rate and our estimate of the number of infectious virions we quantify the formation rate of genetic variants.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Ron Sender", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Yinon Moise Bar-On", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Shmuel Gleizer", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Biana Bernsthein", - "author_inst": "Ragon Institute of MGH, MIT and Harvard" - }, - { - "author_name": "Avi Flamholz", - "author_inst": "University of California" - }, - { - "author_name": "Rob Phillips", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Ron Milo", - "author_inst": "Weizmann Institute of Science" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.16.20230003", "rel_title": "Nasopharyngeal Panbio COVID-19 antigen performed at point-of-care has a high sensitivity in symptomatic and asymptomatic patients with higher risk for transmission and older age", @@ -1100686,6 +1098608,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.11.13.20231431", + "rel_title": "Racial and Ethnic Differentials in COVID-19-Related Job Exposures by Occupational Status in the US", + "rel_date": "2020-11-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.13.20231431", + "rel_abs": "Researchers and journalists have argued that work-related factors may be partly responsible for disproportionate COVID-19 infection and death rates among vulnerable groups. We evaluate these claims by examining racial and ethnic differences in the likelihood of work-related exposure to COVID-19. We extend previous studies by considering 12 racial and ethnic groups and five types of potential occupational exposure to the virus: exposure to infection, physical proximity to others, face-to-face discussions, interactions with external customers and the public, and working indoors. Most importantly, we stratify our results by occupational standing, defined as the proportion of workers within each occupation with at least some college education. This measure serves as a proxy for whether workplaces and workers employ significant COVID-19-related risk reduction strategies. We use the 2018 American Community Survey to identify recent workers by occupation, and link 409 occupations to information on work context from the Occupational Information Network to identify potential COVID-related risk factors. We then examine the racial/ethnic distribution of all frontline workers and frontline workers at highest potential risk of COVID-19, by occupational standing and by sex. The results indicate that, contrary to expectation, White frontline workers are often overrepresented in high-risk jobs while Black and Latino frontline workers are generally underrepresented in these jobs. However, disaggregation of the results by occupational standing shows that, in contrast to Whites and several Asian groups, Latino and Black frontline workers are overrepresented in lower status occupations overall and in lower status occupations associated with high risk, and are thus less likely to have adequate COVID-19 protections. Our findings suggest that greater work exposures likely contribute to a higher prevalence of COVID-19 among Latino and Black adults and underscore the need for measures to reduce potential exposure for workers in low status occupations and for the development of programs outside the workplace.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Noreen Goldman", + "author_inst": "Princeton University" + }, + { + "author_name": "Anne R Pebley", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Keunbok Lee", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Theresa Andrasfay", + "author_inst": "University of Southern California" + }, + { + "author_name": "Boriana Pratt", + "author_inst": "Princeton University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.13.20231217", "rel_title": "Intra-host evolution during SARS-CoV-2 persistent infection", @@ -1101218,65 +1099175,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.12.20230656", - "rel_title": "Development and validation of a highly sensitive and specific electrochemical assay to quantify anti-SARS-CoV-2 IgG antibodies to facilitate pandemic surveillance and monitoring of vaccine response", - "rel_date": "2020-11-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.12.20230656", - "rel_abs": "Amperial is a novel assay platform that uses immobilized antigen in a conductive polymer gel followed by an electrochemical detection. A highly specific and sensitive assay was developed to quantify levels of IgG antibodies to SARS-CoV-2 in saliva. After establishing linearity and limit of detection we established a reference range of 5 standard deviations above the mean. There were no false positives in 667 consecutive saliva samples obtained prior to 2019. Saliva was obtained from 34 patients who had recovered from documented COVID-19 or had documented positive serologies. All of the patients with symptoms severe enough to seek medical attention had positive antibody tests and 88% overall had positive results.\n\nWe obtained blinded paired saliva and plasma samples from 14 individuals. The plasma was analyzed using an EUA-FDA cleared ELISA kit and the saliva was analyzed by our Amperial assay. All 5 samples with negative plasma titers were negative in saliva testing. Eight of the 9 positive plasma samples were positive in saliva and 1 had borderline results. A CLIA validation was performed as a laboratory developed test in a high complexity laboratory.\n\nA quantitative non-invasive saliva based SARSCoV-2 antibody test was developed and validated with sufficient specificity to be useful for population-based monitoring and monitoring of individuals following vaccination.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Samantha H. Chiang", - "author_inst": "UCLA School of Dentistry" - }, - { - "author_name": "Michael Tu", - "author_inst": "Liquid Diagnostics, LLC" - }, - { - "author_name": "Jordan Cheng", - "author_inst": "UCLA School of Dentistry" - }, - { - "author_name": "Fang Wei", - "author_inst": "UCLA School of Dentistry" - }, - { - "author_name": "Feng Li", - "author_inst": "UCLA School of Dentistry" - }, - { - "author_name": "David Chia", - "author_inst": "UCLA Health" - }, - { - "author_name": "Omai B Garner", - "author_inst": "University of California Los Angeles" - }, - { - "author_name": "Sukantha Chandrasekaran", - "author_inst": "UCLA Department of Pathology and Laboratory Medicine" - }, - { - "author_name": "Richard Bender", - "author_inst": "Liquid Diagnostics LLC" - }, - { - "author_name": "Charles Strom", - "author_inst": "UCLA" - }, - { - "author_name": "David T. W. Wong", - "author_inst": "University of California Los Angeles School of Dentistry" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.12.20230417", "rel_title": "Specific immune-regulatory transcriptional signatures reveal sex and age differences in SARS-CoV-2 infected patients", @@ -1102408,6 +1100306,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.13.20230862", + "rel_title": "Lack of immune homology with vaccine preventable pathogens suggests childhood immunizations do not protect against SARS-CoV-2 through adaptive cross-immunity", + "rel_date": "2020-11-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.13.20230862", + "rel_abs": "Abstract (Summary)Recent epidemiological studies have investigated the potential effects of childhood immunization history on COVID-19 severity. Specifically, prior exposure to Bacillus Calmette-Guerin (BCG) vaccine, oral poliovirus vaccine (OPV), or measles vaccine have been postulated to reduce COVID-19 severity - putative mechanism is via stimulation of the innate immune system to provide broader protection against non-specific pathogens. While these epidemiological results remain inconclusive, we sought to investigate the potential role of adaptive immunity via cross-reactivity between vaccine preventable diseases (VPDs) with SARS-CoV-2. We implemented a comprehensive exploration of immune homology (including sequence homology, immune epitopes, and glycosylation patterns) between SARS-CoV-2 and all pathogens with FDA-approved vaccines. Sequence homology did not reveal significant alignments of protein sequences between SARS-CoV-2 with any VPD pathogens, including BCG-related strains. We also could not identify any shared T or B cell epitopes between SARS-CoV-2 and VPD pathogens among either experimentally validated epitopes or predicted immune epitopes. For N-glycosylation (N-glyc), while sites with the same tripeptides could be found between SARS-CoV-2 and certain VPD pathogens, their glycosylation potentials and positions were different. In summary, lack of immune homology between SARS-CoV-2 and VPD pathogens suggests that childhood immunization history (i.e., BCG vaccination or others) does not provide protection from SARS-CoV-2 through adaptive cross-immunity.\n\nHighlightsO_LIComprehensive exploration of immune homology for SARS-CoV-2 with 34 vaccine preventable pathogens covering all FDA-approved vaccines.\nC_LIO_LILittle to no immune homology between SARS-CoV-2 and VPD pathogens: insignificant aligned protein sequences, unmapped immune epitopes, or matched N-glycosylation sites with different glycosylation potentials and positions.\nC_LIO_LIBCG vaccination is unlikely to confer SARS-CoV-2 protection through adaptive cross-immunity.\nC_LI\n\nGraphic summary\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC=\"FIGDIR/small/20230862v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (53K):\norg.highwire.dtl.DTLVardef@1f07e88org.highwire.dtl.DTLVardef@316caorg.highwire.dtl.DTLVardef@cd4794org.highwire.dtl.DTLVardef@11664bb_HPS_FORMAT_FIGEXP M_FIG C_FIG", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Weihua Guo", + "author_inst": "City of Hope Cancer Center" + }, + { + "author_name": "Kyle O. Lee", + "author_inst": "NA" + }, + { + "author_name": "Peter P. Lee", + "author_inst": "City of Hope Cancer Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.13.20231373", "rel_title": "Dysregulated immunity in SARS-CoV-2 infected pregnant women", @@ -1102872,41 +1100797,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.11.14.20229096", - "rel_title": "Chest CT features of COVID-19 in the region of Abu Dhabi, UAE- A single institute study", - "rel_date": "2020-11-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.14.20229096", - "rel_abs": "OBJECTIVEOur aim is to investigate high resolution CT features of COVID-19 infection in Abu Dhabi, UAE, and to compare the diagnostic performance of CT scan with RT-PCR test.\n\nMETHODSData of consecutive patients who were suspected to have COVID-19 infection and presented to our hospital, was collected from March 2, 2020, until April 12, 2020. All patients underwent RT-PCR test; out of which 53.8% had chest CT scan done. Using RT-PCR as a standard reference, the sensitivity and specify of CT scan was calculated. We also analyzed the most common imaging findings in patients with positive RT-PCR results.\n\nRESULTSThe typical HRCT findings were seen in 50 scans (65.8%) out of total positive ones; 44 (77.2%) with positive RT-PCR results and 6 (31.6%) with negative results. The peripheral disease distribution was seen in 86%, multilobe involvement in 70%, bilateral in 82%, and posterior in 82% of the 50 scans.\n\nThe ground glass opacities were seen in 50/74 (89.3%) of positive RT-PCR group. The recognized GGO patterns in these scans were: rounded 50%, linear 38%, and crazy-paving 24%.\n\nUsing RT-PCR as a standard of reference, chest HRCT scan revealed sensitivity of 68.8% and specificity of 70%.\n\nCONCLUSIONThe commonest HRCT findings in patients with COVID-19 pneumonia were peripheral, posterior, bilateral, multilobe rounded ground glass opacities.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Ghufran Saeed", - "author_inst": "Sheikh Khalifa Medical City" - }, - { - "author_name": "Abeer Al Helali", - "author_inst": "SKMC" - }, - { - "author_name": "Safaa Almazrouei", - "author_inst": "SKMC" - }, - { - "author_name": "Asad Shah", - "author_inst": "SKMC" - }, - { - "author_name": "Luai Ahmed", - "author_inst": "UAEU" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.11.15.20231795", "rel_title": "Evaluation of two RT-PCR techniques for SARS-CoV-2 RNA detection in serum for microbiological diagnosis", @@ -1104086,6 +1101976,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.12.20229823", + "rel_title": "COVID-19 COGNITIVE DEFICITS AFTER RESPIRATORY ASSISTANCE IN THE SUBACUTE PHASE:A COVID-REHABILITATION UNIT EXPERIENCE", + "rel_date": "2020-11-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.12.20229823", + "rel_abs": "IntroductionCOVID-19 complications can include neurological, psychiatric, psychological, and psychosocial impairments. Little is known on the consequences of SARS-COV-2 on cognitive functions of patients in the sub-acute phase of the disease. We aimed to investigate the impact of COVID-19 on cognitive functions of patients admitted to the COVID-19 Rehabilitation Unit of the San Raffaele Hospital (Milan, Italy).\n\nMaterial and Methods87 patients admitted to the COVID-19 Rehabilitation Unit from March 27th to June 20th 2020 were included. Patients underwent Mini Mental State Evaluation (MMSE), Montreal Cognitive Assessment (MoCA), Hamilton Rating Scale for Depression, and Functional Independence Measure (FIM). Data were divided in 4 groups according to the respiratory assistance in the acute phase: Group1 (orotracheal intubation), Group2 (non-invasive ventilation using Biphasic Positive Airway Pressure), Group3 (Venturi Masks), Group4 (no oxygen therapy). Follow-ups were performed at one month after home-discharge.\n\nResultsOut of the 87 patients (62 Male, mean age 67.23 {+/-} 12.89 years), 80% had neuropsychological deficits (MoCA and MMSE) and 40% showed mild-to-moderate depression. Group1 had higher scores than Group3 for visuospatial/executive functions (p=0.016), naming (p=0.024), short- and long-term memory (p=0.010, p=0.005), abstraction (p=0.024), and orientation (p=0.034). Group1 was younger than Groups2 and 3. Cognitive impairments correlated with patients age. Only 18 patients presented with anosmia. Their data did not differ from the other patients. FIM (<100) did not differ between groups. Patients partly recovered at one-month follow-up and 43% showed signs of post-traumatic stress disorder.\n\nConclusionPatients with severe functional impairments had important cognitive and emotional deficits which might have been influenced by the choice of ventilatory therapy, but mostly appeared to be related to aging, independently of FIM scores. These findings should be integrated for decision-making in respiratory and neuropsychiatric assistance of COVID-19 patients in the subacute phase of the disease, and show the need for long-term support and psychological treatment of post-COVID-19 patients.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Federica Alemanno", + "author_inst": "IRCCS Ospedale San Raffaele" + }, + { + "author_name": "Elise Houdayer", + "author_inst": "IRCCS San Raffaele Hospital" + }, + { + "author_name": "Anna Parma", + "author_inst": "IRCCS Ospedale San Raffaele" + }, + { + "author_name": "Alfio Spina", + "author_inst": "IRCCS Ospedale San Raffaele" + }, + { + "author_name": "Alessandra Del Forno", + "author_inst": "IRCCS Ospedale San Raffaele" + }, + { + "author_name": "Alessandra Scatolini", + "author_inst": "IRCCS Ospedale San Raffaele" + }, + { + "author_name": "Sara Angelone", + "author_inst": "IRCCS Ospedale San Raffaele" + }, + { + "author_name": "Luigia Brugliera", + "author_inst": "IRCCS Ospedale San Raffaele" + }, + { + "author_name": "Andrea Tettamanti", + "author_inst": "IRCCS Ospedale San Raffaele" + }, + { + "author_name": "Luigi Beretta", + "author_inst": "IRCCS Ospedale San Raffaele" + }, + { + "author_name": "Sandro Iannaccone", + "author_inst": "IRCCS Ospedale San Raffaele" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.11.12.20229955", "rel_title": "Mobile consulting (mConsulting) as an option for accessing healthcare services for communities in remote rural areas and urban slums in low- and middle- income countries: A mixed methods study", @@ -1104790,37 +1102739,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.11.11.20229393", - "rel_title": "Using Convergent Sequential Design for Rapid Complex Case Study Descriptions: Example of Public Health Briefings During the Onset of the COVID-19 Pandemic", - "rel_date": "2020-11-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.11.20229393", - "rel_abs": "Conceptualizing the public health response to the COVID-19 pandemic response as a complex adaptive system is useful to study its key features of emergence, interdependency, and adaptation yet practical guidance for mixed methods researchers remains limited. This study contributes an illustrative example and discussion for guiding how a mixed methods convergent sequential research design, informed by complexity theory and drawing upon open-access datasets, can rapidly generate complex case study descriptions. This article serves as an essential reference for identifying points of integration within a sequential convergent design using text mining to manage large data volumes and studying complex phenomena using a complexity-informed case study-mixed methods approach to generate novel public health insights.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Cheryl Poth", - "author_inst": "University of Alberta" - }, - { - "author_name": "Okan Bulut", - "author_inst": "University of Alberta" - }, - { - "author_name": "Alexandra M. Aquilina", - "author_inst": "University of Alberta" - }, - { - "author_name": "Simon J G Otto", - "author_inst": "University of Alberta" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.11.10.20229146", "rel_title": "Awareness, knowledge and trust in the Greek authorities towards COVID-19 pandemic: results from the Epirus Health Study cohort", @@ -1106044,6 +1103962,45 @@ "type": "new results", "category": "cell biology" }, + { + "rel_doi": "10.1101/2020.11.13.381319", + "rel_title": "Plasma irradiation efficiently inactivates the coronaviruses mouse hepatitis virus and SARS-CoV-2", + "rel_date": "2020-11-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.13.381319", + "rel_abs": "Many inactivation methods have been shown to inactivate SARS-CoV-2 for safe and efficient diagnostic methods. COVID-19 is caused by airborne infection of SARS-CoV-2, and therefore, methods of inactivating the virus efficiently and safely are crucial for reducing the risk of airborne infection. In this regard, the effect of plasma discharge on the infectivity of the coronaviruses mouse hepatitis virus (MHV) and SARS-CoV-2 was tested. Plasma discharge efficiently reduced the infectivity of both coronaviruses. Treatment of SARS-CoV-2 in culture medium with a plasma discharge resulted in 95.17% viral inactivation after plasma irradiation after 1 hour (hr), 99.54% inactivation after 2 hrs and 99.93% inactivation after 3 hrs. Similar results were obtained for MHV. The results indicated that plasma discharge effectively and safely inactivated the airborne coronaviruses and may be useful in minimizing the risk of airborne infection of SARS-CoV-2.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Shigeru Morikawa", + "author_inst": "Okayama University of Science" + }, + { + "author_name": "Shunpei Watanabe", + "author_inst": "Okayama University of Science" + }, + { + "author_name": "Hikaru Fujii", + "author_inst": "Okayama University of Science: Okayama Rika Daigaku" + }, + { + "author_name": "Toshio Tanaka", + "author_inst": "Daikin Industries, Ltd." + }, + { + "author_name": "Junichirou Arai", + "author_inst": "Daikin Industries, Ltd." + }, + { + "author_name": "Shigeru Kyuwa", + "author_inst": "The University of Tokyo: Tokyo Daigaku" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.11.13.381335", "rel_title": "A Whole Virion Vaccine for COVID-19 Produced Via a Novel Inactivation Method: Results from Animal Challenge Model Studies", @@ -1106568,45 +1104525,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.10.20228973", - "rel_title": "Comparison of SARS-COV-2 nasal antigen test to nasopharyngeal RT-PCR in mildly symptomatic patients", - "rel_date": "2020-11-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.10.20228973", - "rel_abs": "IntroductionCOVID 19 has been vastly spreading since December 2019 and the medical teams worldwide are doing their best to limit its spread. In the absence of a vaccine the best way to fight it is by detecting infected cases early and isolate them to prevent its spread. Therefore, a readily available, rapid, and cost-effective test with high specificity and sensitivity for early detection of COVID 19 is required. In this study, we are testing the diagnostic performance of a rapid antigen detection test in mildly symptomatic cases. (RADT).\n\nMethodsThe study included 4183 patients who were mildly symptomatic. A nasal sample for the rapid antigen test and a nasopharyngeal sample was taken from each patient. Statistical analysis was conducted to calculate the sensitivity, specificity, positive predictive value, negative predictive value and kappa coefficient of agreement.\n\nResultsThe prevalence of COVID 19 in the study population was 17.5% (733/4183). The calculated sensitivity and specificity were 82.1% and 99.1% respectively. Kappas coefficient of agreement between the rapid antigen test and RT-PCR was 0.859 (p < 0.001). A stratified analysis was performed and it showed that the sensitivity of the test improved significantly with lowering the cutoff Ct value to 24.\n\nConclusionThe results of the diagnostic assessment of nasal swabs in the RADT used in our study are promising regarding the potential benefit of using them as a screening tool in mildly symptomatic patients. The diagnostic ability was especially high in cases with high viral load. The rapid antigen test is intended to be used alongside RT-PCR and not replace it. RADT can be of benefit in reducing the use of PCR.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Abdulkarim Abdulrahman", - "author_inst": "National task force for combating the corona virus (COVID-19), Mohammed bin Khalifa Cardiac Centre, Bahrain" - }, - { - "author_name": "Fathi Mustafa", - "author_inst": "Royal College of Surgeons in Ireland - Medical University of Bahrain , Bahrain" - }, - { - "author_name": "Abdulla Ismael AlAwadhi", - "author_inst": "National task force for combating the corona virus (COVID-19), Bahrain Defense Force Hospital, Bahrain" - }, - { - "author_name": "Qadar Alansari", - "author_inst": "Ministry of Finance and National Economy, Bahrain" - }, - { - "author_name": "Batool AlAlawi", - "author_inst": "Ministry of Health, Bahrain" - }, - { - "author_name": "Manaf AlQahtani", - "author_inst": "National task force for combating the corona virus (COVID-19), Bahrain Defense Force Hospital, Bahrain" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.10.20228528", "rel_title": "Screening of the H69 and V70 deletions in the SARS-CoV-2 spike protein with a RT-PCR diagnosis assay reveals low prevalence in Lyon, France", @@ -1107854,6 +1105772,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.11.20224030", + "rel_title": "Gender- and age-related differences in misuse of face masks in COVID-19 prevention in central European cities", + "rel_date": "2020-11-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.11.20224030", + "rel_abs": "1ObjectiveCorrect use of face masks is required for their efficacy in preventing possible droplet infections with SARS-CoV-2. We tried to provide information about differences in the distribution of gender and age groups wearing face masks incorrectly.\n\nDesignPilot field study\n\nMethodsVisual observation of mask use in public, not age- and gender-related places in central European large cities regarding incorrect mask-wearing (n=523); statistical analysis (nominal scale) in terms of gender and estimated age group using the total numbers, binomial test and chi-square test.\n\nResultsThere is no significant difference (binomial test: p-value = 0.43) in mask misuse between the genders (female: 271 (51.8%), male: 252 (48.2%) and 0 non-binary individuals (0%)). There is a significant difference (chi-square test: p-value < 2.2e-16) in age group distribution (170 young 10-29 years (32.5%), 261 middle-aged 30-59 years (49.9%), 92 older adults [≥] 60 years (17.6%)). In total numbers, the highest counts were observed in middle-aged persons with 261 counts (49.9%).\n\nConclusionOur study shows an uneven age-distribution of people wearing the face mask in public improperly.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Linda Eckl", + "author_inst": "Department of Medicine, University of Regensburg, 93040 Regensburg, Germany" + }, + { + "author_name": "Stefan Hansch", + "author_inst": "Department of Medicine, University of Regensburg, 93040 Regensburg, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.11.20220962", "rel_title": "Short-term forecasts to inform the response to the COVID-19 epidemic in the UK", @@ -1108426,45 +1106367,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.11.08.20227884", - "rel_title": "Host genetic liability for severe COVID-19 overlaps with alcohol drinking behavior and diabetic outcomes and in over 1 million participants", - "rel_date": "2020-11-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.08.20227884", - "rel_abs": "To distinguish correlation from causation, we performed in-silico analyses of three COVID-19 outcomes (N>1,000,000). We show genetic correlation and putative causality with depressive symptoms, metformin use, and alcohol use. COVID-19 risk loci associated with several hematologic biomarkers. Comprehensive findings inform genetic contributions to COVID-19 epidemiology, molecular mechanisms, and risk factors.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Frank R Wendt", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Antonella De Lillo", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Gita A Pathak", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Flavio De Angelis", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "- COVID-19 Host Genetics Initiative", - "author_inst": "" - }, - { - "author_name": "Renato Polimanti", - "author_inst": "Yale School of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "genetic and genomic medicine" - }, { "rel_doi": "10.1101/2020.11.08.20227470", "rel_title": "pyPOCQuant - A tool to automatically quantify Point-Of-Care Tests from images", @@ -1109640,6 +1107542,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.09.20228023", + "rel_title": "Diagnosis and Tracking of Past SARS-CoV-2 Infection in a Large Study of Vo', Italy Through T-Cell Receptor Sequencing", + "rel_date": "2020-11-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.09.20228023", + "rel_abs": "In viral diseases T cells exert a prominent role in orchestrating the adaptive immune response and yet a comprehensive assessment of the T-cell repertoire, compared and contrasted with antibody response, after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is currently lacking. A prior population-scale study of the municipality of Vo', Italy, conducted after the initial SARS-CoV-2 outbreak uncovered a high frequency of asymptomatic infected individuals and their role in transmission in this town. Two months later, we sampled the same population's T-cell receptor repertoire structure in terms of both diversity (breadth) and frequency (depth) to SARS-CoV-2 antigens to identify associations with both humoral response and protection. For this purpose, we analyzed T-cell receptor and antibody signatures from over 2,200 individuals, including 76 PCR-confirmed SARS-CoV-2 cases (25 asymptomatic, 42 symptomatic, 9 hospitalized). We found that 97.4% (74/76) of PCR confirmed cases had elevated levels of T-cell receptors specific for SARS-CoV-2 antigens. The depth and breadth of the T-cell receptor repertoire were both positively associated with neutralizing antibody titers; helper CD4+ T cells directed towards viral antigens from spike protein were a primary factor in this correlation. Higher clonal depth of the T-cell response to the virus was also significantly associated with more severe disease course. A total of 40 additional suspected infections were identified based on T-cell response from the subjects without confirmatory PCR tests, mostly among those reporting symptoms or having household exposure to a PCR-confirmed infection. Taken together, these results establish that T cells are a sensitive, reliable and persistent measure of past SARS-CoV-2 infection that are differentially activated depending on disease morbidity.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Rachel M Gittelman", + "author_inst": "Adaptive Biotechnologies" + }, + { + "author_name": "Enrico Lavezzo", + "author_inst": "University of Padua" + }, + { + "author_name": "Thomas M Snyder", + "author_inst": "Adaptive Biotechnologies" + }, + { + "author_name": "H Jabran Zahid", + "author_inst": "Microsoft Research" + }, + { + "author_name": "Rebecca Elyanow", + "author_inst": "Adaptive Biotechnologies" + }, + { + "author_name": "Sudeb Dalai", + "author_inst": "Adaptive Biotechnologies" + }, + { + "author_name": "Ilan Kirsch", + "author_inst": "Adaptive Biotechnologies" + }, + { + "author_name": "Lance Baldo", + "author_inst": "Adaptive Biotechnologies" + }, + { + "author_name": "Laura Manuto", + "author_inst": "University of Padua" + }, + { + "author_name": "Elisa Franchin", + "author_inst": "University of Padua" + }, + { + "author_name": "Claudia Del Vecchio", + "author_inst": "University of Padua" + }, + { + "author_name": "Monia Pacenti", + "author_inst": "Azienda Ospedale Padova" + }, + { + "author_name": "Caterina Boldrin", + "author_inst": "Azienda Ospedale Padova" + }, + { + "author_name": "Margherita Cattai", + "author_inst": "Azienda Ospedale Padova" + }, + { + "author_name": "Francesca Saluzzo", + "author_inst": "University of Padua" + }, + { + "author_name": "Andrea Padoan", + "author_inst": "University of Padua" + }, + { + "author_name": "Mario Plebani", + "author_inst": "University of Padua" + }, + { + "author_name": "Fabio Simeoni", + "author_inst": "IRCCS Ospedale San Raffaele" + }, + { + "author_name": "Jessica Bordini", + "author_inst": "IRCCS Ospedale San Raffaele" + }, + { + "author_name": "Nicola I Lor\u00e8", + "author_inst": "IRCCS Ospedale San Raffaele" + }, + { + "author_name": "Dejan Lazarevic", + "author_inst": "IRCCS Ospedale San Raffaele" + }, + { + "author_name": "Daniela M Cirillo", + "author_inst": "IRCCS Ospedale San Raffaele" + }, + { + "author_name": "Paolo Ghia", + "author_inst": "IRCCS Ospedale San Raffaele" + }, + { + "author_name": "Stefano Toppo", + "author_inst": "University of Padua" + }, + { + "author_name": "Jonathan M Carlson", + "author_inst": "Microsoft Research" + }, + { + "author_name": "Harlan S Robins", + "author_inst": "Adaptive Biotechnologies" + }, + { + "author_name": "Giovanni Tonon", + "author_inst": "IRCCS Ospedale San Raffaele" + }, + { + "author_name": "Andrea Crisanti", + "author_inst": "University of Padua" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.09.20228015", "rel_title": "A time-resolved proteomic and diagnostic map characterizes COVID-19 disease progression and predicts outcome", @@ -1110312,157 +1108341,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.11.09.20228098", - "rel_title": "Peginterferon-lambda for the treatment of COVID-19 in outpatients", - "rel_date": "2020-11-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.09.20228098", - "rel_abs": "BackgroundThere are currently no effective treatments for outpatients with coronavirus disease 2019 (COVID-19). Interferon-lambda-1 is a Type III interferon involved in the innate antiviral response with activity against respiratory pathogens.\n\nMethodsIn this double-blind, placebo-controlled trial, outpatients with laboratory-confirmed COVID-19 were randomized to a single subcutaneous injection of peginterferon-lambda 180g or placebo within 7 days of symptom onset or first positive swab if asymptomatic. The primary endpoint was proportion negative for SARS-CoV-2 RNA on Day 7 post-injection.\n\nFindingsThere were 30 patients per arm, with median baseline SARS-CoV-2 viral load of 6.71 (IQR 1.3-8.0) log copies/mL. The decline in SARS-CoV-2 RNA was greater in those treated with peginterferon-lambda than placebo (p=0.04). On Day 7, 24 participants (80%) in the peginterferon-lambda group had an undetectable viral load compared to 19 (63%) in the placebo arm (p=0.15). After controlling for baseline viral load, peginterferon lambda treatment resulted in a 4.12-fold (95CI 1.15-16.7, p=0.029) higher likelihood of viral clearance by Day 7. Of those with baseline viral load above 10E6 copies/mL, 15/19 (79%) in the peginterferon-lambda group were undetectable on Day 7 compared to 6/16 (38%) in the placebo group (p=0.012). Adverse events were similar between groups with only mild reversible transaminase elevations more frequently observed in the peginterferon-lambda group.\n\nInterpretationPeginterferon-lambda accelerated viral decline in outpatients with COVID-19 resulting in a greater proportion with viral clearance by Day 7, particularly in those with high baseline viral load. Peginterferon-lambda may have potential to prevent clinical deterioration and shorten duration of viral shedding.\n\n(NCT04354259)\n\nFundingThis study was supported by the Toronto COVID-19 Action Initiative, University of Toronto and the Ontario First COVID-19 Rapid Research Fund. Medication was supplied by Eiger BioPharma.\n\nResearch in ContextTreatment trials for COVID-19 have largely focused on hospitalized patients and no treatments are approved for people with mild to moderate disease in the outpatient setting. A number of studies in ambulatory populations have been registered but no controlled studies in the outpatient setting have been reported to date (Pubmed Search October 20, 2020, COVID-19 treatment; controlled trials). Uncontrolled case series of hydroxychloroquine with or without azithromycin have been reported with mixed results but no clear signal of efficacy and some concerns raised about cardiac toxicity. Treamtent in the outpatient setting has potential to prevent infected individuals from deteriorating and perhaps more importantly, may shorten the duration of viral shedding, reducing the risk of transmission and the duration required for self-isolation, with significant public health and societal impact.\n\nAdded value of this studyThis is the first study to show an antiviral effect in outpatients with COVID-19. After controlling for baseline viral load, those treated with peginterferon-lambda had a 4.12-fold (95%CI 1.15-16.7, p=0.029) higher odds of viral clearance by Day 7 compared to those who received placebo. The viral load decline was faster with pegterferon-lambda and the effect was most pronounced in those with high viral loads. In individuals with a baseline viral load of 10E6 copies/mL or higher, 15/19 (79%) in the peginterferon-lambda arm cleared by Day 7 compared to 6/16 (38%) (p=0.012) in the placebo arm (OR 6.25, 95%CI 1.49-31.1, p=0.012), translating to a median time to viral clearance of 7 days (95%CI 6.2-7.8 days) with peginterferon-lambda compared to 10 days (95%CI 7.8-12.2 days) with placebo (p=0.038). Those with low viral loads (<10E6 copies/mL) cleared quickly in both groups. Peginterferon-lambda was well-tolerated with a similar side effect profile to placebo and no concerning laboratory adverse events.\n\nImplications of all available evidenceThere is no currently approved therapy for outpatients with COVID-19. This study showed that peginterferon-lambda accelerated viral clearance, particularly in those with high baseline viral loads, highlighting the importance of quantitative viral load testing in the evaluation of antiviral agents for COVID-19. Treatment early in the course of disease may prevent clinical deterioration and shorenting of the duration of viral shedding may have important public health impact by limiting transmission and reducing the duration required for self-isolation. Additional trials of peginterferon-lambda and other antiviral strategies in the outpatient setting are required.", - "rel_num_authors": 34, - "rel_authors": [ - { - "author_name": "Jordan J. Feld", - "author_inst": "Toronto Centre for Liver Disease, Toronto General Hospital, University of Toronto" - }, - { - "author_name": "Christopher Kandel", - "author_inst": "University of Toronto" - }, - { - "author_name": "Mia J Biondi", - "author_inst": "Toronto Centre for Liver Disease, University Health Network, University of Toronto" - }, - { - "author_name": "Robert A Kozak", - "author_inst": "Sunnybrook Health Sciences Centre, University of Toronto" - }, - { - "author_name": "Muhammad Atif Zahoor", - "author_inst": "Toronto Centre for Liver Disease, University Health Network, University of Toronto" - }, - { - "author_name": "Camille Lemieux", - "author_inst": "University Health Network, University of Toronto" - }, - { - "author_name": "Sergio M Borgia", - "author_inst": "Division of Infectious Diseases, William Osler Health System and McMaster University, Hamilton" - }, - { - "author_name": "Andrea K Boggild", - "author_inst": "University Health Network, University of Toronto" - }, - { - "author_name": "Jeff Powis", - "author_inst": "Michael Garron Hospital, University of Toronto" - }, - { - "author_name": "Janine McCready", - "author_inst": "Michael Garron Hospital, University of Toronto" - }, - { - "author_name": "Darrell HS Tan", - "author_inst": "St Michaels Hospital, University of Toronto" - }, - { - "author_name": "Tiffany Chan", - "author_inst": "Trillium Health Partners, Toronto" - }, - { - "author_name": "Bryan Coburn", - "author_inst": "University Health Network, University of Toronto" - }, - { - "author_name": "Deepali Kumar", - "author_inst": "University Health Network, University of Toronto" - }, - { - "author_name": "Atul Humar", - "author_inst": "University Health Network, University of Toronto" - }, - { - "author_name": "Adrienne Chan", - "author_inst": "Sunnybrook Health Sciences Centre, University of Toronto" - }, - { - "author_name": "Seham Noureldin", - "author_inst": "Toronto Centre for Liver Disease, University Health Network, University of Toronto" - }, - { - "author_name": "Joshua Booth", - "author_inst": "Toronto Centre for Liver Disease, University Health Network, University of Toronto" - }, - { - "author_name": "Rachel Hong", - "author_inst": "Toronto Centre for Liver Disease, University Health Network, University of Toronto" - }, - { - "author_name": "David Smookler", - "author_inst": "Toronto Centre for Liver Disease, University Health Network, University of Toronto" - }, - { - "author_name": "Wesam Aleyadeh", - "author_inst": "Toronto Centre for Liver Disease, University Health Network, University of Toronto" - }, - { - "author_name": "Anjali Patel", - "author_inst": "Toronto Centre for Liver Disease, University Health Network, University of Toronto" - }, - { - "author_name": "Bethany Barber", - "author_inst": "Toronto Centre for Liver Disease, University Health Network, University of Toronto" - }, - { - "author_name": "Julia Casey", - "author_inst": "Toronto Centre for Liver Disease, University Health Network, University of Toronto" - }, - { - "author_name": "Ryan Hiebert", - "author_inst": "Sunnybrook Health Sciences Centre, University of Toronto" - }, - { - "author_name": "Henna Mistry", - "author_inst": "Sunnybrook Health Sciences Centre, University of Toronto" - }, - { - "author_name": "Ingrid Choong", - "author_inst": "Eiger BioPharmaceuticals, Palo Alto, California" - }, - { - "author_name": "Colin Hislop", - "author_inst": "Eiger BioPharmaceuticals, Palo Alto, California" - }, - { - "author_name": "Deanna Santer", - "author_inst": "The Li Ka Shing Institute of Virology, University of Alberta" - }, - { - "author_name": "D. Lorne Tyrrell", - "author_inst": "The Li Ka Shing Institute of Virology, University of Alberta" - }, - { - "author_name": "Jeffrey S. Glenn", - "author_inst": "Departments of Medicine and Microbiology & Immunology, Stanford University School of Medicine, Palo Alto, Ca" - }, - { - "author_name": "Adam J. Gehring", - "author_inst": "Toronto Centre for Liver Disease, Toronto General Hospital, University Health Network, University of Toronto" - }, - { - "author_name": "Harry LA Janssen", - "author_inst": "Toronto Centre for Liver Disease, Toronto General Hospital, University Health Network, University of Toronto" - }, - { - "author_name": "Bettina Hansen", - "author_inst": "Institute of Health Policy, Management and Evaluation, University of Toronto" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.09.20228601", "rel_title": "Validation and testing of a method for detection of SARS-CoV-2 RNA in healthy human stool", @@ -1111994,6 +1109872,45 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.11.10.377366", + "rel_title": "Unification of the M/ORF3-related proteins points to a diversified role for ion conductance in pathogenesis of coronaviruses and other nidoviruses", + "rel_date": "2020-11-11", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.10.377366", + "rel_abs": "The new coronavirus, SARS-CoV-2, responsible for the COVID-19 pandemic has emphasized the need for a better understanding of the evolution of virus-host conflicts. ORF3a in both SARS-CoV-1 and SARS-CoV-2 are ion channels (viroporins) and involved in virion assembly and membrane budding. Using sensitive profile-based homology detection methods, we unify the SARS-CoV ORF3a family with several families of viral proteins, including ORF5 from MERS-CoVs, proteins from beta-CoVs (ORF3c), alpha-CoVs (ORF3b), most importantly, the Matrix (M) proteins from CoVs, and more distant homologs from other nidoviruses. By sequence analysis and structural modeling, we show that these viral families utilize specific conserved polar residues to constitute an ion-conducting pore in the membrane. We reconstruct the evolutionary history of these families, objectively establish the common origin of the M proteins of CoVs and Toroviruses. We show that the divergent ORF3a/ORF3b/ORF5 families represent a duplication stemming from the M protein in alpha- and beta-CoVs. By phyletic profiling of major structural components of primary nidoviruses, we present a model for their role in virion assembly of CoVs, ToroVs and Arteriviruses. The unification of diverse M/ORF3 ion channel families in a wide range of nidoviruses, especially the typical M protein in CoVs, reveal a conserved, previously under-appreciated role of ion channels in virion assembly, membrane fusion and budding. We show that the M and ORF3 are under differential evolutionary pressures; in contrast to the slow evolution of M as core structural component, the CoV-ORF3 clade is under selection for diversification, which indicates it is likely at the interface with host molecules and/or immune attack.\n\nIMPORTANCECoronaviruses (CoVs) have become a major threat to human welfare as the causative agents of several severe infectious diseases, namely Severe Acute Respiratory Syndrome (SARS), Middle Eastern Respiratory Syndrome (MERS), and the recently emerging human coronavirus disease 2019 (COVID-19). The rapid spread, severity of these diseases, as well as the potential re-emergence of other CoV-associated diseases have imposed a strong need for a thorough understanding of function and evolution of these CoVs. By utilizing robust domain-centric computational strategies, we have established homologous relationships between many divergent families of CoV proteins, including SARS-CoV/SARS-CoV-2 ORF3a, MERS-CoV ORF5, proteins from both beta-CoVs (ORF3c) and alpha-CoVs (ORF3b), the typical CoV Matrix proteins, and many distant homologs from other nidoviruses. We present evidence that they are active ion channel proteins, and the Cov-specific ORF3 clade proteins are under selection for rapid diversification, suggesting they might have been involved in interfering host molecules and/or immune attack.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Yongjun Tan", + "author_inst": "Saint Louis University" + }, + { + "author_name": "Theresa Schneider", + "author_inst": "Saint Louis University" + }, + { + "author_name": "Prakash Shukla", + "author_inst": "University of Utah School of Medicine" + }, + { + "author_name": "Mahesh Chandrasekharan", + "author_inst": "University of Utah School of Medicine" + }, + { + "author_name": "L. Aravind", + "author_inst": "National Center of Biotechnology Information" + }, + { + "author_name": "Dapeng Zhang", + "author_inst": "Saint Louis University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.11.10.377333", "rel_title": "Characterization and structural basis of a lethal mouse-adapted SARS-CoV-2", @@ -1112562,73 +1110479,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.06.20227330", - "rel_title": "The COVID-19 epidemic in the Czech Republic: retrospective analysis of measures (not) implemented during the spring first wave", - "rel_date": "2020-11-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.06.20227330", - "rel_abs": "Running across the globe for more than a year, the COVID-19 pandemic keeps demonstrating its strength. Despite a lot of understanding, uncertainty regarding the efficiency of interventions still persists. We developed an age-structured epidemic model parameterized with sociological data for the Czech Republic and found that (1) delaying the spring 2020 lockdown by four days produced twice as many confirmed cases by the end of the lockdown period, (2) personal protective measures such as face masks appear more effective than just a reduction of social contacts, (3) only sheltering the elderly is by no means effective, and (4) leaving schools open is a risky strategy. Despite the onset of vaccination, an evidence-based choice and timing of non-pharmaceutical interventions still remains the most important weapon against the COVID-19 pandemic.\n\nOne sentence summaryWe address several issues regarding COVID-19 interventions that still elicit controversy and pursue ignorance", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Jan Smycka", - "author_inst": "Center for Theoretical Study, Praha, Czech Republic" - }, - { - "author_name": "Rene Levinsky", - "author_inst": "CERGE-EI, Praha, Czech Republic" - }, - { - "author_name": "Eva Hromadkova", - "author_inst": "CERGE-EI, Praha, Czech Republic" - }, - { - "author_name": "Michal Soltes", - "author_inst": "CERGE-EI, Praha, Czech Republic" - }, - { - "author_name": "Josef Slerka", - "author_inst": "New Media Studies, Faculty of Arts at the Charles University, Czech Republic" - }, - { - "author_name": "Vit Tucek", - "author_inst": "Department of Mathematics, University of Zagreb, Croatia" - }, - { - "author_name": "Jan Trnka", - "author_inst": "Department of Biochemistry, Cell and Molecular Biology, Third Faculty of Medicine, Charles University, Praha, Czech Republic" - }, - { - "author_name": "Martin Smid", - "author_inst": "Czech Academy of Sciences, Institute of Information Theory and Automation, Praha, Czech Republic" - }, - { - "author_name": "Milan Zajicek", - "author_inst": "Czech Academy of Sciences, Institute of Information Theory and Automation, Praha, Czech Republic" - }, - { - "author_name": "Tomas Diviak", - "author_inst": "Department of Criminology, School of Social Sciences, University of Manchester" - }, - { - "author_name": "Roman Neruda", - "author_inst": "Czech Academy of Sciences, Institute of Computer Science, Praha, Czech Republic" - }, - { - "author_name": "Petra Vidnerova", - "author_inst": "Czech Academy of Sciences, Institute of Computer Science, Praha, Czech Republic" - }, - { - "author_name": "Ludek Berec", - "author_inst": "Faculty of Science, University of South Bohemia, Ceske Budejovice, Czech Republic" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.09.20228205", "rel_title": "Symptoms suggestive of COVID-19 in households with and without children: a descriptive survey", @@ -1113628,6 +1111478,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.07.370726", + "rel_title": "In Vitro Efficacy of \"Essential Iodine Drops\" Against Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2)", + "rel_date": "2020-11-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.07.370726", + "rel_abs": "BackgroundAerosolization of respiratory droplets is considered the main route of coronavirus disease 2019 (COVID-19). Therefore, reducing the viral load of Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2) shed via respiratory droplets is potentially an ideal strategy to prevent the spread of the pandemic. The in vitro virucidal activity of intranasal Povidone-Iodine (PVP-I) has been demonstrated recently to reduce SARS-CoV-2 viral titres. This study evaluated the virucidal activity of the aqueous solution of Iodine-V (a clathrate complex formed by elemental iodine and fulvic acid) as in Essential Iodine Drops (EID) with 200 g elemental iodine/ml content against SARS-CoV-2 to ascertain whether it is a better alternative to PVP-I.\n\nMethodsSARS-CoV-2 (USAWA1/2020 strain) virus stock was prepared by infecting Vero 76 cells (ATCC CRL-1587) until cytopathic effect (CPE). The virucidal activity of EID against SARS-CoV-2 was tested in three dilutions (1:1; 2:1 and 3:1) in triplicates by incubating at room temperature (22 {+/-} 2{degrees}C) for either 60 or 90 seconds. The surviving viruses from each sample were quantified by a standard end-point dilution assay.\n\nResultsEID (200 g iodine/ml) after exposure for 60 and 90 seconds was compared to controls. In both cases, the viral titre was reduced by 99% (LRV 2.0). The 1:1 dilution of EID with virus reduced SARS-CoV-2 virus from 31,623 cell culture infectious dose 50% (CCCID50) to 316 CCID50 within 90 seconds.\n\nConclusionSubstantial reductions in LRV by Iodine-V in EID confirmed the activity of EID against SARS-CoV-2 in vitro, demonstrating that Iodine-V in EID is effective at inactivating the virus in vitro and therefore suggesting its potential application intranasally to reduce SARS-CoV-2 transmission from known or suspected COVID-19 patients.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Zoltan Kontos", + "author_inst": "IOI Investment Zrt." + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pharmacology and toxicology" + }, { "rel_doi": "10.1101/2020.11.10.374587", "rel_title": "Susceptibility of well-differentiated airway epithelial cell cultures from domestic and wildlife animals to SARS-CoV-2", @@ -1114192,61 +1112061,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.11.05.20224436", - "rel_title": "Anxiety and depression among people living in quarantine centers during COVID-19 pandemic: A mixed method study from western Nepal", - "rel_date": "2020-11-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.05.20224436", - "rel_abs": "BackgroundIn response to the COVID-19 pandemic, incoming travelers were quarantined at specific centers in Nepal and major checkpoints in Nepal-India border. Nepal adopted a generic public health approaches to control and quarantine returnee migrants, with little attention towards the quality of quarantine facilities and its aftermath, such as the poor mental health of the returnee migrants. The main objective of this study was to explore the status of anxiety and depression, and factors affecting them among returnee migrants living in institutional quarantine centers of western Nepal.\n\nMethodsA mixed method approach was used which included a quantitative survey and in-depth interviews (IDIs). Survey questionnaire utilized Beck Depression Inventory (BDI) and Beck Anxiety Inventory (BAI) tools, which were administered among 441 quarantined returnee migrants and IDIs were conducted among 12 participants which included a mix of quarantined migrants and healthcare workers from the quarantine centres. Descriptive and inferential analyses were conducted on quantitative data; and thematic analysis was utilized for qualitative data.\n\nResultsMild depression (9.1%; 40/441) and anxiety (16.1%, 71/441) was common among respondents followed by moderate depression and anxiety {depression (3.4%; 15/441), anxiety (4.1%, 18/441)} and severe depression and anxiety {depression (1.1%; 5/441), anxiety (0.7%, 3/441)}. Anxiety and depression were independent of their socio-demographic characteristics. Perceived fear of contracting COVID-19, severity and death were prominent among the respondents.\n\nRespondents experienced stigma and discrimination in addition to being at the risk of disease and possible loss of employment and financial responsibilities. In addition, poor (quality and access to) health services, and poor living condition at the quarantine centres adversely affected respondents mental health.\n\nConclusionDepression and anxiety among quarantined population warrants more research. Institutional quarantine centers of Karnali province of Nepal were in poor conditions which adversely impacted mental health of the respondents. Poor resources allocation for health, hygiene and living conditions can be counterproductive to the population quarantined.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Udaya Bahadur BC", - "author_inst": "Public Health Service Office Surkhet, Ministry of Social Development, Karnali Province, Nepal" - }, - { - "author_name": "Sunil Pokharel", - "author_inst": "Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK" - }, - { - "author_name": "Sabika Munikar", - "author_inst": "Post Basic Nursing Science Faculty, Om Health Campus, Purbanchal University, Kathmandu, Nepal" - }, - { - "author_name": "Chetan Nidhi Wagle", - "author_inst": "Public Health Service Office Surkhet, Ministry of Social Development, Karnali Province, Nepal" - }, - { - "author_name": "Pratik Adhikary", - "author_inst": "School of Public Health, UC Berkeley, USA" - }, - { - "author_name": "Brish Bahadur Shahi", - "author_inst": "Health Division, Ministry of Social Development, Karnali Province, Nepal" - }, - { - "author_name": "Chandra Thapa", - "author_inst": "Savitribai Phule Pune University, Pune, Maharashtra, India" - }, - { - "author_name": "Ram Prasad Bhandari", - "author_inst": "Province Hospital, Ministry of Social Development, Karnali Province, Nepal" - }, - { - "author_name": "Bipin Adhikari", - "author_inst": "Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand" - }, - { - "author_name": "Kanchan Thapa", - "author_inst": "Central Department of Population Studies, Tribhuvan University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.09.20228320", "rel_title": "Optimal Allocation of Limited Test Resources for the Quantification of COVID-19 Infections", @@ -1115186,6 +1113000,101 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.11.09.374769", + "rel_title": "Neutrophil extracellular traps induce the epithelial-mesenchymal transition: implications in post-COVID-19 fibrosis", + "rel_date": "2020-11-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.09.374769", + "rel_abs": "The release of neutrophil extracellular traps (NETs), a process termed NETosis, avoids pathogen spread but may cause tissue injury. NETs have been found in severe COVID-19 patients, but their role in disease development is still unknown. The aim of this study is to assess the capacity of NETs to drive epithelial-mesenchymal transition (EMT) of lung epithelial cells and to analyze the involvement of NETs in COVID-19.\n\nNeutrophils activated with PMA (PMA-Neu), a stimulus known to induce NETs formation, induce both EMT and cell death in the lung epithelial cell line, A549. Notably, NETs isolated from PMA-Neu induce EMT without cell damage. Bronchoalveolar lavage fluid of severe COVID-19 patients showed high concentration of NETs. Thus, we tested in an in vitro alveolar model the hypothesis that virus-induced NET may drive EMT. Co-culturing A549 at air-liquid interface with alveolar macrophages, neutrophils and SARS-CoV2, we demonstrated a significant induction of the EMT in A549 together with high concentration of NETs, IL8 and IL1{beta}, best-known inducers of NETosis. Lung tissues of COVID-19 deceased patients showed that epithelial cells are characterized by increased mesenchymal markers. These results show for the first time that NETosis plays a major role in triggering lung fibrosis in COVID-19 patients.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Laura Pandolfi", + "author_inst": "Fondazione IRCCS Policlinico San Matteo" + }, + { + "author_name": "Sara Bozzini", + "author_inst": "IRCCS Policlinico San Matteo Foundation" + }, + { + "author_name": "Frangipane Vanessa", + "author_inst": "IRCCS Policlinico San Matteo Foundation" + }, + { + "author_name": "Elena Percivalle", + "author_inst": "Fondazione IRCCS Policlinico San Matteo" + }, + { + "author_name": "Ada De Luigi", + "author_inst": "Istituto di Ricerche Farmacologiche Mario Negri IRCCS" + }, + { + "author_name": "Martina Bruna Violatto", + "author_inst": "Istituto di Ricerche Farmacologiche Mario Negri IRCCS" + }, + { + "author_name": "Gianluca Lopez", + "author_inst": "ASST Fatebenefratelli Sacco" + }, + { + "author_name": "Elisa Gabanti", + "author_inst": "IRCCS Policlinico S. Matteo Foundation" + }, + { + "author_name": "Luca Carsana", + "author_inst": "ASST Fatebenefratelli Sacco" + }, + { + "author_name": "Monica Morosini", + "author_inst": "IRCCS Policlinico S. Matteo Foundation" + }, + { + "author_name": "Mara De Amici", + "author_inst": "IRCCS Policlinico S. Matteo Foundation" + }, + { + "author_name": "Manuela Nebuloni", + "author_inst": "ASST Fatebenefratelli Sacco" + }, + { + "author_name": "Tommaso Fossali", + "author_inst": "ASST Fatebenefratelli Sacco" + }, + { + "author_name": "Riccardo Colombo", + "author_inst": "ASST Fatebenefratelli Sacco" + }, + { + "author_name": "Veronica Codullo", + "author_inst": "IRCCS Policlinico S. Matteo Foundation" + }, + { + "author_name": "Massimiliano Gnecchi", + "author_inst": "IRCCS Policlinico S. Matteo Foundation" + }, + { + "author_name": "Paolo Bigini", + "author_inst": "Istituto di Ricerche Farmacologiche Mario Negri IRCCS" + }, + { + "author_name": "Fausto Baldanti", + "author_inst": "Molecular Virology Unit, Fondazione IRCCS Policlinico San Matteo" + }, + { + "author_name": "Daniele Lilleri", + "author_inst": "IRCCS Policlinico S. Matteo Foundation" + }, + { + "author_name": "Federica Meloni", + "author_inst": "IRCCS Policlinico S. Matteo Foundation" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.11.09.373449", "rel_title": "Cloning, Expression and Biophysical Characterization of a Yeast-expressed Recombinant SARS-CoV-2 Receptor Binding Domain COVID-19 Vaccine Candidate", @@ -1115845,101 +1113754,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.11.05.20226654", - "rel_title": "Multiplexed, quantitative serological profiling of COVID-19 from a drop of blood by a point-of-care test", - "rel_date": "2020-11-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.05.20226654", - "rel_abs": "Highly sensitive, specific, and point-of-care (POC) serological assays are an essential tool to manage the COVID-19 pandemic. Here, we report on a microfluidic, multiplexed POC test that can profile the antibody response against multiple SARS-CoV-2 antigens--Spike S1 (S1), Nucleocapsid (N), and the receptor binding domain (RBD)--simultaneously from a 60 {micro}L drop of blood, plasma, or serum. We assessed the levels of anti-SARS-CoV-2 antibodies in plasma samples from 19 individuals (at multiple time points) with COVID-19 that required admission to the intensive care unit and from 10 healthy individuals. This POC assay shows good concordance with a live virus microneutralization assay, achieved high sensitivity (100%) and specificity (100%), and successfully tracked the longitudinal evolution of the antibody response in infected individuals. We also demonstrated that we can detect a chemokine, IP-10, on the same chip, which may provide prognostic insight into patient outcomes. Because our test requires minimal user intervention and is read by a handheld detector, it can be globally deployed in the fight against COVID-19 by democratizing access to laboratory quality tests.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Jacob T Heggestad", - "author_inst": "Duke University" - }, - { - "author_name": "David Kinnamon", - "author_inst": "Duke University" - }, - { - "author_name": "Lyra Olson", - "author_inst": "Duke University" - }, - { - "author_name": "Jason Liu", - "author_inst": "Duke University" - }, - { - "author_name": "Garrett Kelly", - "author_inst": "Duke University" - }, - { - "author_name": "Simone Wall", - "author_inst": "Duke University" - }, - { - "author_name": "Cassio Fontes", - "author_inst": "Duke University" - }, - { - "author_name": "Daniel Joh", - "author_inst": "Duke University" - }, - { - "author_name": "Angus Hucknall", - "author_inst": "Duke University" - }, - { - "author_name": "Carl Pieper", - "author_inst": "Duke University" - }, - { - "author_name": "Ibtehaj Naqvi", - "author_inst": "Duke University" - }, - { - "author_name": "Lingye Chen", - "author_inst": "Duke University" - }, - { - "author_name": "Loretta Que", - "author_inst": "Duke University" - }, - { - "author_name": "Thomas Oguin III", - "author_inst": "Duke University" - }, - { - "author_name": "Smita Nair", - "author_inst": "Duke University" - }, - { - "author_name": "Bruce Sullenger", - "author_inst": "Duke University" - }, - { - "author_name": "Christopher Woods", - "author_inst": "Duke University School of Medicine" - }, - { - "author_name": "Gregory Sempowski", - "author_inst": "Duke University" - }, - { - "author_name": "Bryan Kraft", - "author_inst": "Duke University" - }, - { - "author_name": "Asutosh Chilkoti", - "author_inst": "Duke University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.11.05.20226449", "rel_title": "Increasing both specificity and sensitivity of SARS-CoV-2 antibody tests by using an adaptive orthogonal testing approach", @@ -1117319,6 +1115133,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.04.20225904", + "rel_title": "Development and Validation of Early Warning Score Systems for COVID-19 Patients", + "rel_date": "2020-11-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.04.20225904", + "rel_abs": "COVID-19 is a major, urgent, and ongoing threat to global health. Globally more than 24 million have been infected and the disease has claimed more than a million lives as of October 2020. Predicting which patients will need respiratory support is important to guiding individual patient treatment and also to ensuring sufficient resources are available. We evaluated the ability of six common Early Warning Scores (EWS) to identify respiratory deterioration defined as the need for advanced respiratory support (high-flow nasal oxygen, continuous positive airways pressure, non-invasive ventilation, intubation) within a prediction window of 24 hours. We show these scores perform sub-optimally at this specific task. Therefore, we develop an alternative Early Warning Score based on a Gradient Boosting Trees (GBT) algorithm that is able to predict deterioration within the next 24 hours with high AUROC 94% and an accuracy, sensitivity and specificity of 70%, 96%, 70%, respectively. Our GBT model outperformed the best EWS (LDTEWS:NEWS), increasing the AUROC by 14%. Our GBT model makes the prediction based on the current and baseline measures of routinely available vital signs and blood tests.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Alexey Youssef", + "author_inst": "Institute of Biomedical Engineering, Dept. Engineering Science, University of Oxford" + }, + { + "author_name": "Samaneh Kouchaki", + "author_inst": "Centre for Vision, Speech, and Signal Processing, University of Surrey" + }, + { + "author_name": "Farah Shamout", + "author_inst": "New York University Abu Dhabi, Engineering Division" + }, + { + "author_name": "Jacob Armstrong", + "author_inst": "Institute of Biomedical Engineering, Dept. Engineering Science, University of Oxford" + }, + { + "author_name": "Rasheed El-Bouri", + "author_inst": "Institute of Biomedical Engineering, Dept. Engineering Science, University of Oxford" + }, + { + "author_name": "Thomas Taylor", + "author_inst": "Institute of Biomedical Engineering, Dept. Engineering Science, University of Oxford" + }, + { + "author_name": "Drew Birrenkott", + "author_inst": "Stanford School of Medicine, Stanford University" + }, + { + "author_name": "Baptiste Vasey", + "author_inst": "Institute of Biomedical Engineering, Dept. Engineering Science, University of Oxford" + }, + { + "author_name": "Andrew Soltan", + "author_inst": "Institute of Biomedical Engineering, Dept. Engineering Science, University of Oxford" + }, + { + "author_name": "Tingting Zhu", + "author_inst": "Institute of Biomedical Engineering, Dept. Engineering Science, University of Oxford" + }, + { + "author_name": "David A Clifton", + "author_inst": "Institute of Biomedical Engineering, Dept. Engineering Science, University of Oxford" + }, + { + "author_name": "David W Eyre", + "author_inst": "John Radcliffe Hospital, Oxford University Hospitals" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.04.20225961", "rel_title": "Biometric covariates and outcome in COVID-19 patients: Are we looking close enough?", @@ -1117631,73 +1115508,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nursing" }, - { - "rel_doi": "10.1101/2020.11.04.20226118", - "rel_title": "Elevated COVID-19 outcomes among persons living with diagnosed HIV infection in New York State: Results from a population-level match of HIV, COVID-19, and hospitalization databases", - "rel_date": "2020-11-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.04.20226118", - "rel_abs": "BackgroundNew York State (NYS) has been an epicenter for both COVID-19 and HIV/AIDS epidemics. Persons Living with diagnosed HIV (PLWDH) may be more prone to COVID-19 infection and severe outcomes, yet few population-based studies have assessed the extent to which PLWDH are diagnosed, hospitalized, and have died with COVID-19, relative to non-PLWDH.\n\nMethodsNYS HIV surveillance, COVID-19 laboratory confirmed diagnoses, and hospitalization databases were matched. COVID-19 diagnoses, hospitalization, and in-hospital death rates comparing PLWDH to non-PLWDH were computed, with unadjusted rate ratios (RR) and indirect standardized RR (sRR), adjusting for sex, age, and region. Adjusted RR (aRR) for outcomes among PLWDH were assessed by age/CD4-defined HIV disease stage, and viral load suppression, using Poisson regression models.\n\nResultsFrom March 1-June 7, 2020, PLWDH were more frequently diagnosed with COVID-19 than non-PLWDH in unadjusted (RR [95% confidence interval (CI)]: 1.43[1.38-1.48), 2,988 PLWDH], but not in adjusted comparisons (sRR [95% CI]: 0.94[0.91-0.97]). Per-population COVID-19 hospitalization was higher among PLWDH (RR [95% CI]: 2.61[2.45-2.79], sRR [95% CI]: 1.38[1.29-1.47], 896 PLWDH), as was in-hospital death (RR [95% CI]: 2.55[2.22-2.93], sRR [95%CI]: 1.23 [1.07-1.40], 207 PLWDH), albeit not among those hospitalized (sRR [95% CI]: 0.96[0.83-1.09]). Among PLWDH, hospitalization risk increased with disease progression from HIV Stage 1 to Stage 2 (aRR [95% CI]:1.27[1.09-1.47]) and Stage 3 (aRR [95% CI]: 1.54[1.24-1.91]), and for those virally unsuppressed (aRR [95% CI]: 1.54[1.24-1.91]).\n\nConclusionPLWDH experienced poorer COVID-related outcomes relative to non-PLWDH, with 1-in-522 PLWDH dying with COVID-19, seemingly driven by higher rates of severe disease requiring hospitalization.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "James M Tesoriero", - "author_inst": "New York State Department of Health" - }, - { - "author_name": "Carol-Ann E Swain", - "author_inst": "New York State Department of Health" - }, - { - "author_name": "Jennifer L Pierce", - "author_inst": "New York State Department of Health" - }, - { - "author_name": "Lucila Zamboni", - "author_inst": "New York State Department of Health" - }, - { - "author_name": "Meng Wu", - "author_inst": "New York State Department of Health" - }, - { - "author_name": "David R Holtgrave", - "author_inst": "University at Albany School of Public Health" - }, - { - "author_name": "Charles J Gonzalez", - "author_inst": "New York State Department of Health" - }, - { - "author_name": "Tomoko Udo", - "author_inst": "University at Albany School of Public Health" - }, - { - "author_name": "Johanne E Morne", - "author_inst": "New York State Department of Health" - }, - { - "author_name": "Rachel Hart-Malloy", - "author_inst": "New York State Department of Health" - }, - { - "author_name": "Deepa T Rajulu", - "author_inst": "New York State Department of Health" - }, - { - "author_name": "Shu-Yin John Leung", - "author_inst": "New York State Department of Health" - }, - { - "author_name": "Eli S Rosenberg", - "author_inst": "University at Albany School of Pubic Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "hiv aids" - }, { "rel_doi": "10.1101/2020.11.04.20225862", "rel_title": "Clinical and microbiological assessments of COVID-19 in healthcare workers: a prospective longitudinal study", @@ -1119073,6 +1116883,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.11.04.20225557", + "rel_title": "Spatial Profiling of Lung SARS-CoV-2 and Influenza Virus Infection Dissects Virus-Specific Host Responses and Gene Signatures", + "rel_date": "2020-11-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.04.20225557", + "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that emerged in late 2019 has spread globally, causing a pandemic of respiratory illness designated coronavirus disease 2019 (COVID-19). Robust blood biomarkers that reflect tissue damage are urgently needed to better stratify and triage infected patients. Here, we use spatial transcriptomics to generate an in-depth picture of the pulmonary transcriptional landscape of COVID-19 (10 patients), pandemic H1N1 (pH1N1) influenza (5) and uninfected control patients (4). Host transcriptomics showed a significant upregulation of genes associated with inflammation, type I interferon production, coagulation and angiogenesis in the lungs of COVID-19 patients compared to non-infected controls. SARS-CoV-2 was non-uniformly distributed in lungs with few areas of high viral load and these were largely only associated with an increased type I interferon response. A very limited number of genes were differentially expressed between the lungs of influenza and COVID-19 patients. Specific interferon-associated genes (including IFI27) were identified as candidate novel biomarkers for COVID-19 differentiating this COVID-19 from influenza. Collectively, these data demonstrate that spatial transcriptomics is a powerful tool to identify novel gene signatures within tissues, offering new insights into the pathogenesis of SARS-COV-2 to aid in patient triage and treatment.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Arutha Kulasinghe", + "author_inst": "Queensland University" + }, + { + "author_name": "Chin Wee Tan", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research" + }, + { + "author_name": "Anna Flavia Ribeiro dos Santos Miggiolaro", + "author_inst": "Pontificia Universidade Catolica do Parana" + }, + { + "author_name": "James Monkman", + "author_inst": "Queensland University of Technology" + }, + { + "author_name": "Dharmesh Bhuva", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research" + }, + { + "author_name": "Jarbas da Silva Motta Junior", + "author_inst": "Pontifical Catholic University of Parana" + }, + { + "author_name": "Caroline Busatta Vaz de Paula", + "author_inst": "Pontifical Catholic University of Parana" + }, + { + "author_name": "Seigo Nagashima", + "author_inst": "Pontifical Catholic University of Parana" + }, + { + "author_name": "Cristina Pellegrino Baena", + "author_inst": "Pontifical Catholic University of Parana" + }, + { + "author_name": "Paulo Souza-Fonseca Guimaraes", + "author_inst": "Pontifical Catholic University of Parana" + }, + { + "author_name": "Lucia Noronha", + "author_inst": "Pontifical Catholic University of Parana" + }, + { + "author_name": "Timothy McCulloch", + "author_inst": "University of Queensland Diamantina Institute" + }, + { + "author_name": "Gustavo Rodrigues Rossi", + "author_inst": "University of Queensland Diamantina Institute" + }, + { + "author_name": "Caroline Cooper", + "author_inst": "University of Queensland" + }, + { + "author_name": "Benjamin Tang", + "author_inst": "University of Syndey" + }, + { + "author_name": "Kirsty Short", + "author_inst": "University of Queensland" + }, + { + "author_name": "Melissa J Davis", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research" + }, + { + "author_name": "Fernando Souza-Fonseca Guimaraes", + "author_inst": "University of Queensland Diamantina Institute" + }, + { + "author_name": "Gabrielle T Belz", + "author_inst": "University of Queensland Diamantina Institute" + }, + { + "author_name": "Ken O'Byrne", + "author_inst": "Queensland University of Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.06.370916", "rel_title": "Acrylamide Fragment Inhibitors that Induce Unprecedented Conformational Distortions in Enterovirus 71 3C and SARS-CoV-2 Main Protease", @@ -1119637,185 +1117542,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.11.03.367391", - "rel_title": "Evolution of Antibody Immunity to SARS-CoV-2", - "rel_date": "2020-11-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.03.367391", - "rel_abs": "Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has infected 78 million individuals and is responsible for over 1.7 million deaths to date. Infection is associated with development of variable levels of antibodies with neutralizing activity that can protect against infection in animal models. Antibody levels decrease with time, but the nature and quality of the memory B cells that would be called upon to produce antibodies upon re-infection has not been examined. Here we report on the humoral memory response in a cohort of 87 individuals assessed at 1.3 and 6.2 months after infection. We find that IgM, and IgG anti-SARS-CoV-2 spike protein receptor binding domain (RBD) antibody titers decrease significantly with IgA being less affected. Concurrently, neutralizing activity in plasma decreases by five-fold in pseudotype virus assays. In contrast, the number of RBD-specific memory B cells is unchanged. Memory B cells display clonal turnover after 6.2 months, and the antibodies they express have greater somatic hypermutation, increased potency and resistance to RBD mutations, indicative of continued evolution of the humoral response. Analysis of intestinal biopsies obtained from asymptomatic individuals 4 months after coronavirus disease-2019 (COVID-19) onset, using immunofluorescence, or polymerase chain reaction, revealed persistence of SARS-CoV-2 nucleic acids and immunoreactivity in the small bowel of 7 out of 14 volunteers. We conclude that the memory B cell response to SARS-CoV-2 evolves between 1.3 and 6.2 months after infection in a manner that is consistent with antigen persistence.", - "rel_num_authors": 41, - "rel_authors": [ - { - "author_name": "Christian Gaebler", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Zijun Wang", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Julio C. C. Lorenzi", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Frauke Muecksch", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Shlomo Finkin", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Minami Tokuyama", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Alice Cho", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Mila Jankovic", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Dennis Schaefer-Babajew", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Thiago Y. Oliveira", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Melissa Cipolla", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Charlotte Viant", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Christopher O. Barnes", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Arlene Hurley", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Martina Turroja", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Kristie Gordon", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Katrina G. Millard", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Victor Ramos", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Fabian Schmidt", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Yiska Weisblum", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Divya Jha", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Michael Tankelevich", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Jim Yee", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Irina Shimeliovich", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Davide F. Robbiani", - "author_inst": "Institute for Research in Biomedicine" - }, - { - "author_name": "Zhen Zhao", - "author_inst": "Weill Cornell Medicine" - }, - { - "author_name": "Anna Gazumyan", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Theodora Hatziioannou", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Pamela J. Bjorkman", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Saurabh Mehandru", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Paul D. Bieniasz", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Marina Caskey", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Michel C. Nussenzweig", - "author_inst": "The Rockefeller University" - }, - { - "author_name": "Thomas Hagglof", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Robert E. Schwartz", - "author_inst": "Weill Cornell Graduate School of Medical Sciences" - }, - { - "author_name": "Yaron Bram", - "author_inst": "Weill Cornell" - }, - { - "author_name": "Gustavo Martinez-Delgado", - "author_inst": "Mount Sinai" - }, - { - "author_name": "Pilar Mendoza", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Gaelle Breton", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Juan Dizon", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Roshni Patel", - "author_inst": "Rockefeller University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.11.04.367359", "rel_title": "SARS-CoV-2 RBD219-N1C1: A Yeast-Expressed SARS-CoV-2 Recombinant Receptor-Binding Domain Candidate Vaccine Stimulates Virus Neutralizing Antibodies and T-cell Immunity in Mice", @@ -1121078,6 +1118804,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.11.03.20225565", + "rel_title": "COVID-19 surveillance - a descriptive study on data quality issues", + "rel_date": "2020-11-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.03.20225565", + "rel_abs": "BackgroundHigh-quality data is crucial for guiding decision making and practicing evidence-based healthcare, especially if previous knowledge is lacking. Nevertheless, data quality frailties have been exposed worldwide during the current COVID-19 pandemic. Focusing on a major Portuguese surveillance dataset, our study aims to assess data quality issues and suggest possible solutions.\n\nMethodsOn April 27th 2020, the Portuguese Directorate-General of Health (DGS) made available a dataset (DGSApril) for researchers, upon request. On August 4th, an updated dataset (DGSAugust) was also obtained. The quality of data was assessed through analysis of data completeness and consistency between both datasets.\n\nResultsDGSAugust has not followed the data format and variables as DGSApril and a significant number of missing data and inconsistencies were found (e.g. 4,075 cases from the DGSApril were apparently not included in DGSAugust). Several variables also showed a low degree of completeness and/or changed their values from one dataset to another (e.g. the variable underlying conditions had more than half of cases showing different information between datasets). There were also significant inconsistencies between the number of cases and deaths due to COVID-19 shown in DGSAugust and by the DGS reports publicly provided daily.\n\nConclusionsThe low quality of COVID-19 surveillance datasets limits its usability to inform good decisions and perform useful research. Major improvements in surveillance datasets are therefore urgently needed - e.g. simplification of data entry processes, constant monitoring of data, and increased training and awareness of health care providers - as low data quality may lead to a deficient pandemic control.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Cristina Costa-Santos", + "author_inst": "Department of Community Medicine, Information and Health Decision Sciences-MEDCIDS, Faculty of Medicine, University of Porto" + }, + { + "author_name": "Ana Luisa Neves", + "author_inst": "Department of Community Medicine, Information and Health Decision Sciences-MEDCIDS, Faculty of Medicine, University of Porto" + }, + { + "author_name": "Ricardo Correia", + "author_inst": "Department of Community Medicine, Information and Health Decision Sciences-MEDCIDS, Faculty of Medicine, University of Porto" + }, + { + "author_name": "Paulo Santos", + "author_inst": "Department of Community Medicine, Information and Health Decision Sciences-MEDCIDS, Faculty of Medicine, University of Porto" + }, + { + "author_name": "Matilde Monteiro-Soares", + "author_inst": "Department of Community Medicine, Information and Health Decision Sciences-MEDCIDS, Faculty of Medicine, University of Porto" + }, + { + "author_name": "Alberto Freitas", + "author_inst": "Department of Community Medicine, Information and Health Decision Sciences-MEDCIDS, Faculty of Medicine, University of Porto" + }, + { + "author_name": "Ines Ribeiro-Vaz", + "author_inst": "Department of Community Medicine, Information and Health Decision Sciences-MEDCIDS, Faculty of Medicine, University of Porto" + }, + { + "author_name": "Teresa Henriques", + "author_inst": "Department of Community Medicine, Information and Health Decision Sciences-MEDCIDS, Faculty of Medicine, University of Porto" + }, + { + "author_name": "Pedro Pereira Rodrigues", + "author_inst": "Department of Community Medicine, Information and Health Decision Sciences-MEDCIDS, Faculty of Medicine, University of Porto" + }, + { + "author_name": "Altamiro Costa-Pereira", + "author_inst": "Department of Community Medicine, Information and Health Decision Sciences-MEDCIDS, Faculty of Medicine, University of Porto" + }, + { + "author_name": "Ana Margarida Pereira", + "author_inst": "Department of Community Medicine, Information and Health Decision Sciences-MEDCIDS, Faculty of Medicine, University of Porto" + }, + { + "author_name": "Joao Fonseca", + "author_inst": "Department of Community Medicine, Information and Health Decision Sciences-MEDCIDS, Faculty of Medicine, University of Porto" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.03.20225409", "rel_title": "COVID-19 reopening strategies at the county level in the face of uncertainty: Multiple Models for Outbreak Decision Support", @@ -1122190,25 +1119979,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.11.05.368647", - "rel_title": "SLAMF7 engagement super-activates macrophages in acute and chronic inflammation", - "rel_date": "2020-11-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.05.368647", - "rel_abs": "Macrophages regulate protective immune responses to infectious microbes, but aberrant macrophage activation frequently drives pathological inflammation. To identify regulators of vigorous macrophage activation, we analyzed RNA-seq data from synovial macrophages and identified SLAMF7 as a receptor associated with a super-activated macrophage state in rheumatoid arthritis. We implicated IFN-{gamma} as a key regulator of SLAMF7 expression. Engaging this receptor drove an exuberant wave of inflammatory cytokine expression, and induction of TNF- following SLAMF7 engagement amplified inflammation through an autocrine signaling loop. We observed SLAMF7-induced gene programs not only in macrophages from rheumatoid arthritis patients, but in gut macrophages from active Crohns disease patients and lung macrophages from severe COVID-19 patients. This suggests a central role for SLAMF7 in macrophage super-activation with broad implications in pathology.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Accelerating Medicines Partnership (AMP) RA/SLE Network", - "author_inst": "." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.10.30.20223115", "rel_title": "COVID-19 in Hospitalized Ethiopian Children: Characteristics and Outcome Profile", @@ -1123296,6 +1121066,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.11.02.20224584", + "rel_title": "The signature features of COVID-19 pandemic in a hybrid mathematical model - implications for optimal work-school lockdown policy", + "rel_date": "2020-11-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.02.20224584", + "rel_abs": "BackgroundThe coronavirus disease 2019 (COVID-19) first identified in China, spreads rapidly across the globe and is considered the fastest moving pandemic in history. The new disease has challenged policymakers and scientists on key issues such as the magnitude of the first-time problem, the susceptibility of the population, the severity of the disease, and its symptoms. Most countries have adopted \"lockdown\" policies to reduce the spatial spread of COVID-19, but they have damaged the economic and moral fabric of society. Timely action to prevent the spread of the virus is critical, and mathematical modeling in non-pharmaceutical intervention (NPI) policy management has proven to be a major weapon in this fight due to the lack of an effective COVID-19 vaccine.\n\nMethodsWe present a new hybrid model for COVID-19 dynamics using both an age-structured mathematical model and spatio-temporal model in silico, analyzing the data of COVID-19 in Israel. The age-structured mathematical model is based on SIRD two age-class model. The spatial model examines a circle of day and night (with one-hour resolution) and three main locations (work / school or home) for every individual.\n\nResultsWe determine mathematically the basic reproduction number R0 via the next-generation matrix based on Markov chain theory. Then, we analyze the stability of the equilibria and the effects of the significant differences in infection rates between children and adults. Using the hybrid model, we have introduced a method for estimating the reproduction number of an epidemic in real time from the data of daily notification of cases. The results of the proposed model are confirmed by the Israeli Lockdown experience with a mean square error of 0.205 over two weeks. The model was able to predict changes in R0 by opening schools on September 1, 2020, resulting in R0 = 2.2, which entailed a months quarantine of all areas of life. According to the model, by extending the school day to 9 hours, and assuming that children and adults go to school and work every day (except weekends), we get a significant reduction in R0 of 1.45. Finally, model-based analytical-numerical results are obtained and displayed in graphical profiles.\n\nConclusionsThe use of mathematical models promises to reduce the uncertainty in the choice of \"Lockdown\" policies. Our unique use of contact details from 2 classes (children and adults), the interaction of populations depending on the time of day (the cycle of day and night), and several physical locations, allowed a new look at the differential dynamics of the spread and control of infection. Using knowledge about how the length of the work and school day affects the dynamics of the spread of the disease can be useful for improving control programs, mitigation, and policy.\n\nAuthor summaryEverybody in the modern world understands today that the pandemics threat is not less dangerous than the wars. COVID-19 showed us that pandemics effects the economies of all the countries over the world brings to a total lockdown of social life and enormous mortality. There was no effective vaccine/treatment, to stop the spread of COVID-19 and, therefore, policymakers have taken unprecedented measures, including quarantines, public health measures, travel bans, and others, without knowing in advance the effect of these restrictions.\n\nIn this study, we develop a mathematical model of the pandemic spread taking into account the different dynamics of the disease in two age groups of children and adults. Using this model we succeeded to simulate the COVID-19 spread in Israel. The current study accurately predicts the effect of the work/school lockdown on the outbreaks. We have proven that by keeping schools open and increasing the school day to 8-9 hours, infection rates are reduced. Our results also show that if at least half of the adult population is a lockdown, the effect of childrens isolation on the infection rate is small, indicating the importance of multiple age groups of the population in the selection of restrictions.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Teddy Lazebnik", + "author_inst": "Bar Ilan University" + }, + { + "author_name": "Svetlana Bunimovich-Mendrazitsky", + "author_inst": "Ariel University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.11.02.20224659", "rel_title": "The CCR5-delta32 variant might explain part of the association between COVID-19 and the chemokine-receptor gene cluster", @@ -1123704,25 +1121497,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.11.01.20214122", - "rel_title": "Simulation model for productivity, risk and GDP impact forecasting of the COVID-19 portfolio vaccines", - "rel_date": "2020-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.01.20214122", - "rel_abs": "Executive summaryThe paper presents the methodology and modeling results for COVID-19 vaccines portfolio forecasting, including R&D output (rate and likelihood of approvals at a vaccine technology platform level) and manufacturing production output to meet worldwide demand.\n\nIn order to minimize the time and risk of global vaccination, scaling up of Operation Warp Speed (OWS) and other programs could be very beneficial, leading to increased financing for additional vaccine development programs, in both Phase III clinical trials and in manufacturing. It would also lead to a reduction of the global production time for world vaccination, from 75 months for a baseline scenario to 36 months, reducing potential global GDP loss by as much as US$4.2 trillion (US [~] $1 trillion) when compared to the baseline scenario.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Vladimir Shnaydman", - "author_inst": "ORBee Consulting" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.11.02.20224568", "rel_title": "Effectiveness of quarantine and testing to prevent COVID-19 transmission from arriving travelers", @@ -1124750,6 +1122524,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2020.11.03.20225284", + "rel_title": "SARS-CoV-2 transmission during team-sport: Do players develop COVID-19 after participating in rugby league matches with SARS-CoV-2 positive players?", + "rel_date": "2020-11-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.03.20225284", + "rel_abs": "ObjectivesEvaluate the interactions between SARS-CoV-2 positive players and other players during rugby league matches, to determine the risk of in-game SARS-CoV-2 transmission.\n\nDesignObservational.\n\nSettingSuper League rugby league during four matches in which SARS-CoV-2 positive players were retrospectively found to have participated (2nd August and 4th October 2020).\n\nParticipants136 male elite rugby league players: eight SARS-CoV-2 positive participants, 28 identified close contacts and 100 other players who participated in any of the four matches.\n\nMain Outcome measuresClose contacts were defined by analysis of video footage for player interactions and microtechnology (GPS) data for proximity analysis. Close contacts and other players involved in the matches becoming positive for SARS-CoV-2 by RT-PCR within 14 days of the match were reported.\n\nResultsThe eight SARS-CoV-2 positive players were involved in up to 14 tackles with other individual players. SARS-CoV-2 positive players were within a 2 m proximity of other players for up to 316 secs, from 60 interactions. One identified contact returned a positive SARS-CoV-2 result within 14 days of the match (subsequently linked to an outbreak within their club environment, rather than in-match transmission), whereas the other 27 identified contacts returned negative SARS-CoV-2 follow up tests and no one developed COVID-19 symptoms. Ninety-five players returned negative and five players returned positive SARS-CoV-2 RT-PCR routine tests within 14 days of the match. Sources of transmission in the five cases were linked to internal club COVID-19 outbreaks and wider-community transmission.\n\nConclusionDespite a high number of tackle involvements and close proximity interactions between SARS-CoV-2 positive players and players on the same and opposition teams during a rugby league match, these data suggest that in-game SARS-CoV-2 transmission is limited during these types of team sport activities played outdoors.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Ben Jones", + "author_inst": "Leeds Beckett University" + }, + { + "author_name": "Gemma C Phillips", + "author_inst": "Rugby Football League" + }, + { + "author_name": "Simon PT Kemp", + "author_inst": "Rugby Football Union" + }, + { + "author_name": "Brendan Payne", + "author_inst": "Newcastle University" + }, + { + "author_name": "Brian Hart", + "author_inst": "Catapult Sports" + }, + { + "author_name": "Matthew Cross", + "author_inst": "Premiership Rugby" + }, + { + "author_name": "Keith Stokes", + "author_inst": "University of Bath" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.02.20224782", "rel_title": "Prevalence Of COVID-19 In Rural Versus Urban Areas in a Low-Income Country: Findings from a State-Wide Study in Karnataka, India", @@ -1125286,49 +1123103,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2020.11.02.20224709", - "rel_title": "Gender-affirming care, mental health, and economic stability in the time of COVID-19: a global cross-sectional study of transgender and non-binary people", - "rel_date": "2020-11-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.11.02.20224709", - "rel_abs": "BackgroundTransgender and non-binary people are disproportionately burdened by barriers to quality healthcare, mental health challenges, and economic hardship. This study examined the impact of the novel coronavirus disease (COVID-19) pandemic and subsequent control measures on gender-affirming care, mental health, and economic stability among transgender and non-binary people globally.\n\nMethodsWe collected global cross-sectional data from 964 transgender and non-binary adult users of the Hornet and Her apps from April to August 2020 to characterize changes in gender-affirming care, mental health, and economic stability as a result of the COVID-19 pandemic. We conducted Poisson regression models to assess if access to gender-affirming care and ability to live according to ones gender were related to depressive symptoms, anxiety, and changes in suicidal ideation.\n\nResultsIndividuals resided in 76 countries, including Turkey (27.4%,n=264/964) and Thailand (20.6%,n=205). A majority were non-binary (66.8%,n=644) or transfeminine (29.4%,n=283). Due to the COVID-19 pandemic, 55.0% (n=320/582) reported reduced access to gender- affirming resources, and 38.0% (n=327/860) reported reduced time lived according to their gender. About half screened positive for depression (50.4%,442/877) and anxiety (45.8%,n=392/856). One in six (17.0%,n=112/659) expected losses of health insurance, and 77.0% (n=724/940) expected income reductions. The prevalence of depressive symptoms, anxiety, and increased suicidal ideation were 1.63 (95% CI: 1.36-1.97), 1.61 (95% CI: 1.31-1.97), and 1.74 (95% CI: 1.07-2.82) times higher for individuals whose access to gender- affirming resources was reduced versus not.\n\nDiscussionThe COVID-19 pandemic has reduced access to gender-affirming resources and the ability of transgender and non-binary people to live according to their gender worldwide. These reductions may drive the increased depressive symptoms, anxiety, and suicidal ideation reported in this sample. To improve transgender and non-binary health globally, increased access to gender-affirming resources should be achieved through policies (e.g., digital prescriptions), flexible interventions (e.g., telehealth), and support for existing transgender health initiatives.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Brooke Jarrett", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Sarah M Peitzmeier", - "author_inst": "University of Michigan School of Nursing" - }, - { - "author_name": "Arjee Restar", - "author_inst": "JohnsHopkins Bloomberg School of Public Health" - }, - { - "author_name": "Tyler Adamson", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "Sean Howell", - "author_inst": "Hornet" - }, - { - "author_name": "Stefan Baral", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - }, - { - "author_name": "S. Wilson Beckham", - "author_inst": "Johns Hopkins Bloomberg School of Public Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.11.03.20225268", "rel_title": "Test-adjusted results of mortality for Covid-19 in Germany, USA, UK", @@ -1126444,6 +1124218,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.10.28.20221200", + "rel_title": "Effective community screening for asymptomatic and symptomatic COVID-19 with a fast and extremely low cost COVID-Anosmia Checker tool", + "rel_date": "2020-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.28.20221200", + "rel_abs": "BackgroundCOVID-19 curve can be flattened by adopting mass screening protocols with aggressive testing and isolating infected populations. The current approach largely depends on RT-PCR/rapid antigen tests that require expert personnel resulting in higher costs and reduced testing frequency. Loss of smell is reported as a major symptom of COVID-19, however, a precise olfactory testing tool to identify COVID-19 patient is still lacking.\n\nMethodsTo quantitatively check for the loss of smell, we developed an odor strip, \"COVID-Anosmia checker\", spotted with gradients of coffee and lemon grass oil. We validated its efficiency in healthy and COVID-19 positive subjects. A trial screening to identify SARS-CoV-2 infected persons was also carried out to check the sensitivity and specificity of our screening tool.\n\nFindingsIt was observed that COVID positive participants were hyposmic instead of being anosmic when they were subjected to smelling higher odor concentration. Our tool identified 97% of symptomatic and 94% of asymptomatic COVID-19 positive subjects after excluding most confounding factors like concurrent chronic sinusitis. Further, it was possible to reliably predict COVID-19 infection by calculating a loss of smell score with 100% specificity. We coupled this tool with a mobile application, which takes the input response from the user, and can readily categorize the user in the appropriate risk groups.\n\nConclusionLoss of smell can be used as a reliable marker for screening for COVID-19. Our tool can be used for first-line screening to trace out COVID-19 infection effectively. It can be used in difficult to reach geographical locations.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Budhaditya Basu", + "author_inst": "Neuro-Stem Cell Biology Laboratory, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala-695 014, India" + }, + { + "author_name": "Paul Ann Riya", + "author_inst": "Neuro-Stem Cell Biology Laboratory, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala-695 014, India" + }, + { + "author_name": "Joby Issac", + "author_inst": "Cancer Biology Programs-12 (CRP-12), Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala-695 014, India" + }, + { + "author_name": "Surendran Parvathy", + "author_inst": "Neuro-Stem Cell Biology Laboratory, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala-695 014, India" + }, + { + "author_name": "Biju Surendran Nair", + "author_inst": "Neuro-Stem Cell Biology Laboratory, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala-695 014, India" + }, + { + "author_name": "Pradipta Tokdar", + "author_inst": "BioNEST, KINFRA Hi-Tech Park Campus, Rajiv Gandhi Centre for Biotechnology (RGCB), Kalamassery, Cochin, Kerala-683 503, India" + }, + { + "author_name": "Devika Sanal Kumar", + "author_inst": "Department of Biochemistry, Saveetha Medical College Hospital, Thandalam, Kanchipuram District, Tamilnadu-602 105, India" + }, + { + "author_name": "Pranav Ravi Kulkarni", + "author_inst": "Department of General Medicine, Saveetha Medical College Hospital, Thandalam, Kanchipuram District, Tamilnadu-602 105, India" + }, + { + "author_name": "Gowtham Hanumanram", + "author_inst": "Department of General Medicine, Saveetha Medical College Hospital, Thandalam, Kanchipuram District, Tamilnadu-602 105, India" + }, + { + "author_name": "Mohanan Jagadeesan", + "author_inst": "Department of General Medicine, Saveetha Medical College Hospital, Thandalam, Kanchipuram District, Tamilnadu-602 105, India" + }, + { + "author_name": "Prasanna Karthik Suthakaran", + "author_inst": "Department of General Medicine, Saveetha Medical College Hospital, Thandalam, Kanchipuram District, Tamilnadu-602 105, India" + }, + { + "author_name": "Lal Devayani Vasudevan Nair", + "author_inst": "Department of Paediatrics, Saveetha Medical College Hospital, Thandalam, Kanchipuram District, Tamilnadu-602 105, India" + }, + { + "author_name": "Rosy Vennila", + "author_inst": "Department of Microbiology, Saveetha Medical College Hospital, Thandalam, Kanchipuram District, Tamilnadu-602 105, India" + }, + { + "author_name": "Rajendran Kannan", + "author_inst": "Department of General Medicine, Saveetha Medical College Hospital, Thandalam, Kanchipuram District, Tamilnadu-602 105, India" + }, + { + "author_name": "Balarama Kaimal", + "author_inst": "Department of Biochemistry, Saveetha Medical College Hospital, Thandalam, Kanchipuram District, Tamilnadu-602 105, India" + }, + { + "author_name": "Gopa Kumar Anoop", + "author_inst": "Neologix (Wafi Technology), Office No: 4058, 4th Floor, 2xl Building, Bu Daniq, Al Qasimiyah, Post Box: 73500, UAE" + }, + { + "author_name": "Iype Joseph", + "author_inst": "Pathogen Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala-695 014, India" + }, + { + "author_name": "Radhakrishnan Nair", + "author_inst": "Laboratory Medicine and Molecular Diagnostics, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala-695 014, India" + }, + { + "author_name": "Saji George", + "author_inst": "BioNEST, KINFRA Hi-Tech Park Campus, Rajiv Gandhi Centre for Biotechnology (RGCB), Kalamassery, Cochin, Kerala-683 503, India" + }, + { + "author_name": "Jackson James", + "author_inst": "Rajiv Gandhi Center for Biotechnology" + }, + { + "author_name": "Madhavan Radhakrishna Pillai", + "author_inst": "Pathogen Biology, Rajiv Gandhi Centre for Biotechnology (RGCB), Thiruvananthapuram, Kerala-695 014, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.10.28.20221952", "rel_title": "Preventing COVID-19 Fatalities: State versus Federal Policies", @@ -1126824,37 +1124697,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.28.20221408", - "rel_title": "ROLE OF CYTOKINES AND OTHER PROPHETIC VARIABLES IN THE DEVELOPMENT AND PROGRESSION OF DISEASE IN PATIENTS SUFFERING FROM COVID-19", - "rel_date": "2020-11-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.28.20221408", - "rel_abs": "INTRODUCTIONOutbreak of the novel COVID-19 infection identifies both causative agents that threaten global pandemic in 2003 and 2011. It is an enveloped virus with spike (S) protein attached that facilitates its receptor binding on the surface. Although it has brought about the global interest for the researchers and medical practitioner in the identification of potential targets that may be addressed in order to cope up with the situation. In the current study potential role of cytokines and related inflammatory markers have been identified that interplays in the progression of disease in COVID-19 patients.\n\nMATERIALS AND METHODSCurrent study substitutes hundred and fifty (n=150) patients with novel-COVID-19 and hundred (n=100) healthy controls. After getting informed consent serum samples of the participants were collected and analyzed for their significance in the disease progression. Levels of Interleukins i.e., (IL- 1,6,8,10,11) and tumor necrosis factor-alpha (TNF-) were determined with help of their specific spectrophotometric and ELISA methods.\n\nRESULTSFindings of study show significant increase in the levels of interleukins and TNF- that signifies the presence of \"cytokine storm\" in worsening the condition in respect to the exposure of COVID-19. Levels of IL-1 and 6 were significantly higher in patients (98.69{+/-}39.35pg/ml and 71.95{+/-}28.41 pg/ml) as compared to controls (30.06{+/-}14.19pg/ml and 9.46{+/-}3.43pg/ml) where, (p=0.001 and 0.007). It also suggests that IL-6 is most sensitive test with about (98%) sensitivity in comparison with 96%,95%, 95%,93% and 92% in case of IL-10,1,8,11 and TNF- respectively.\n\nCONCLUSIONCurrent study elucidate the effects of cytokines and respective inflammatory markers in the progression of the COVID-19. Findings show that activation of macrophages and neutrophils have significant role in the worsening of the symptoms and progression of the viral infection. Thus, use of certain blockers in initial stages could serve with potent benefits in coping up the infectious condition.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "arif malik", - "author_inst": "Institute of Molecular Biology and Biotechnology, The University of Lahore" - }, - { - "author_name": "Saima Iqbal", - "author_inst": "Institute of Molecular Biology and Biotechnology, The University of Lahore" - }, - { - "author_name": "Sulayman Waquar", - "author_inst": "Institute of Molecular Biology and Biotechnology, The University of Lahore" - }, - { - "author_name": "Muhammad Mansoor Hafeez", - "author_inst": "The University of Lahore" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.29.20218743", "rel_title": "A chest-CT and clinical chemistry based flowchart for rapid COVID-19 triage at emergency departments - a multicenter study", @@ -1127926,6 +1125768,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.30.20222950", + "rel_title": "Differences and similarities in diagnostic methods and treatments for Coronavirus disease 2019 (COVID-19): a scoping review", + "rel_date": "2020-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.30.20222950", + "rel_abs": "AimsWe investigate a range of studies related to COVID-19 with focus on scientific evidence reporting the main diagnosis and treatments of the disease.\n\nMain MethodsScoping review conducted in the databases, MEDLINE, Cochrane, Embase, LILACS, Scopus, and Web of Science, and the gray Google Scholar literature, until May 2020. We follow PRISMA-SCR and the recommendations of the Joanna Briggs Institute. The identified studies were independently selected by peers. The qualitative data extracted were synthesized and organized into categories, and the quantitative data were generated through descriptive and inferential statistics.\n\nKey-findings6060 articles were identified, of which 30 were included in this review. The publications are predominantly from China (n=22, 73.3%), and with a type of cross-sectional study (n=12, 40.0%), followed by a cohort (n=7, 23.0%). Among them, 16 studies addressed the diagnosis, and computed tomography was considered as non-invasive complementary method for detecting and evaluating the progression of COVID-19. Laboratory tests have been used to detect enzymatic or viral activities, and to monitor the inflammation associated with COVID-19. 14 studies included different therapeutic associations, such as Lopinavir/Ritonavir (LPV/r) and Arbidol, Hydroxychloroquine, Azithromycin, Tocilizumab and Remdesivir, and Corticosteroids/Plasminogen.\n\nSignificanceThe evidence related to diagnostic methods are clear, and include tomography and laboratory tests. Medicinal or associated medications for the treatment of COVID-19, although showing a reduction in signs and COVID-19-related symptoms, can cause adverse effects of mild or severe intensity depending on viral load and inflammatory activity. Additional studies should be performed to identify the most reliable treatment for COVID-19.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Alessandro Rolim Scholze Sr.", + "author_inst": "UENP" + }, + { + "author_name": "Emiliana Cristina Melo", + "author_inst": "UENP" + }, + { + "author_name": "Carina Bortolato Major", + "author_inst": "UENP" + }, + { + "author_name": "Carolina Fordellone Cruz", + "author_inst": "UENP" + }, + { + "author_name": "Leia Regina Alcantara", + "author_inst": "UENP" + }, + { + "author_name": "Camila Dalcol", + "author_inst": "UENP" + }, + { + "author_name": "Fabio Rodrigues Ferreira Seiva", + "author_inst": "UENP" + }, + { + "author_name": "Maria de Fatima Mantovani", + "author_inst": "UFPR" + }, + { + "author_name": "Angela Mattei", + "author_inst": "Conselho Regional de Enfermagem do Parana" + }, + { + "author_name": "Henrique Spaulonci Silveira", + "author_inst": "UNESP" + }, + { + "author_name": "Luiz Gustavo de Almeida Chuffa Sr.", + "author_inst": "UNESP" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.30.20217364", "rel_title": "Therapeutic efficacy of Honey and Nigella sativa against COVID-19: A multi-center randomized controlled clinical trial (HNS-COVID-PK)", @@ -1128778,57 +1126679,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.29.20219931", - "rel_title": "A longitudinal comparison of spike and nucleocapsid SARS-CoV-2 antibody responses in a tertiary hospitals laboratory workers with validation of DBS specimen analysis.", - "rel_date": "2020-11-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.29.20219931", - "rel_abs": "There is a requirement for easily accessible, high throughput serological testing as part of the SARS-CoV-2 pandemic response. Whilst of limited diagnostic use in an acute individual setting, its use on a population level is key to informing a coherent public health response. As experience of commercial assays increases, so too does knowledge of their precision and limitations. Here we present our experience of these systems thus far. We perform a spot sero-prevalence study amongst staff in a tertiary hospitals clinical microbiology laboratory, before undertaking validation of DBS serological testing as an alternate specimen for analysis. Finally, we characterise the spike and nucleocapsid antibody response over 160 days post a positive PCR test in nine non-hospitalised staff members.\n\nAmongst a cohort of 195 staff, 17 tested positive for SARS-CoV-2 antibodies (8.7%). Self-reporting of SARS-CoV2 infection (P=<0.0001) and testing of a household contact (P = 0.027) were significant variables amongst the positive and negative sub-groups. Testing of 28 matched serum and DBS samples demonstrated 96% accuracy between the sample types. A differential rate of decline of SARS-CoV-2 antibodies against nucleocapsid or spike protein was observed. At 4 months post a positive PCR test 7/9 (78%) individuals had detectable antibodies against spike protein, but only 2/9 (22%) had detectable antibodies against nucleocapsid protein. This study reveals a broad agreement amongst commercial platforms tested and suggests the use of DBS as an alternate specimen option to enable widespread population testing for SARS-CoV-2 antibodies. These results suggest potential limitations of these platforms in estimating historical infection. By setting this temporal point of reference for this cohort of non-patient facing laboratory staff, future exposure risks and mitigation strategies can be evaluated more fully.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Isa Murrell", - "author_inst": "Public Health Wales" - }, - { - "author_name": "Donall Forde", - "author_inst": "Public Health Wales" - }, - { - "author_name": "Linda Tyson", - "author_inst": "Public Health Wales" - }, - { - "author_name": "Lisa Chichester", - "author_inst": "Public Health Wales" - }, - { - "author_name": "Anna Garratt", - "author_inst": "Public Health Wales" - }, - { - "author_name": "Owen Vineall", - "author_inst": "Public Health Wales" - }, - { - "author_name": "Nicki Palmer", - "author_inst": "Public Health Wales" - }, - { - "author_name": "Rachel Jones", - "author_inst": "Public Health Wales" - }, - { - "author_name": "Catherine Moore", - "author_inst": "Public Health Wales" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.29.20222406", "rel_title": "A minimal model for household-based testing and tracing in epidemics", @@ -1130063,6 +1127913,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.30.20223156", + "rel_title": "COVID-19 Pandemic Among Immigrant Latinx Farmworker and Non-farmworker Families: A Rural-Urban Comparison of Economic, Educational, Healthcare, and Immigration Concerns", + "rel_date": "2020-11-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.30.20223156", + "rel_abs": "COVID-19 has highlighted social and health injustices in the US. Structural inequalities have increased the likelihood of immigrants contracting COVID-19, by being essential workers and through poverty that forces this population to continue working. Rural and urban immigrant families may face different concerns. Using a telephone survey in May 2020 of 105 Latinx families in an existing study, quantitative and qualitative data were gathered on work and household economics, childcare and education, healthcare, and community climate. Analyses show that, although rural and urban groups experienced substantial economic effects, impacts were more acute for urban families. Rural workers reported fewer workplace protective measures for COVID-19. For both groups, fear and worry, particularly about finances and children, dominated reports of their situations with numerous reports of experiencing stress and anxiety. The experience of the pandemic is interpreted as an example of contextual vulnerability of a population already experiencing structural violence through social injustice.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Sara A. Quandt", + "author_inst": "Wake Forest School of Medicine" + }, + { + "author_name": "Natalie J. LaMonto", + "author_inst": "Lawrence University" + }, + { + "author_name": "Dana C. Mora", + "author_inst": "Wake Forest School of Medicine" + }, + { + "author_name": "Jennifer W. Talton", + "author_inst": "Wake Forest School of Medicine" + }, + { + "author_name": "Paul J. Laurienti", + "author_inst": "Wake Forest School of Medicine" + }, + { + "author_name": "Thomas A. Arcury", + "author_inst": "Wake Forest School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.11.02.364729", "rel_title": "Identification of Cross-Reactive CD8+ T Cell Receptors with High Functional Avidity to a SARS-CoV-2 Immunodominant Epitope and Its Natural Mutant Variants", @@ -1130451,53 +1128340,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.11.03.366609", - "rel_title": "Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design", - "rel_date": "2020-11-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.11.03.366609", - "rel_abs": "Having claimed over 1 million lives worldwide to date, the ongoing COVID-19 pandemic has created one of the biggest challenges to develop an effective drug to treat infected patients. Among all the proteins expressed by the virus, RNA helicase is a fundamental protein for viral replication, and it is highly conserved among the coronaviridae family. To date, there is no high-resolution structure of helicase bound with ATP and RNA. We present here structural insights and molecular dynamics (MD) simulation results of the SARS-CoV-2 RNA helicase both in its apo form and in complex with its natural substrates. Our structural information of the catalytically competent helicase complex provides valuable insights for the mechanism and function of this enzyme at the atomic level, a key to develop specific inhibitors for this potential COVID-19 drug target.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "D\u00e9nes Berta", - "author_inst": "University College London" - }, - { - "author_name": "Sam Alexander Martino", - "author_inst": "University College London" - }, - { - "author_name": "Andrei Pisliakov", - "author_inst": "University of Dundee" - }, - { - "author_name": "Nadia Elghobashi-Meinhardt", - "author_inst": "Technische Universit\u00e4t Berlin" - }, - { - "author_name": "Geoffrey Wells", - "author_inst": "University College London" - }, - { - "author_name": "Sarah A Harris", - "author_inst": "University of Leeds" - }, - { - "author_name": "Elisa Frezza", - "author_inst": "Universit\u00e9 de Paris" - }, - { - "author_name": "Edina Rosta", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.11.02.365049", "rel_title": "Computational prediction of SARS-CoV-2 encoded miRNAs and their putative host targets", @@ -1131853,6 +1129695,81 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.10.27.20220897", + "rel_title": "The effect of eviction moratoriums on the transmission of SARS-CoV-2", + "rel_date": "2020-11-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.27.20220897", + "rel_abs": "Massive unemployment during the COVID-19 pandemic could result in an eviction crisis in US cities. Here we model the effect of evictions on SARS-CoV-2 epidemics, simulating viral transmission within and among households in a theoretical metropolitan area. We recreate a range of urban epidemic trajectories and project the course of the epidemic under two counterfactual scenarios, one in which a strict moratorium on evictions is in place and enforced, and another in which evictions are allowed to resume at baseline or increased rates. We find, across scenarios, that evictions lead to significant increases in infections. Applying our model to Philadelphia using locally-specific parameters shows that the increase is especially profound in models that consider realistically heterogenous cities in which both evictions and contacts occur more frequently in poorer neighborhoods. Our results provide a basis to assess municipal eviction moratoria and show that policies to stem evictions are a warranted and important component of COVID-19 control.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Anjalika Nande", + "author_inst": "Program for Evolutionary Dynamics, Harvard University, Cambridge, MA, 02138" + }, + { + "author_name": "Justin Sheen", + "author_inst": "Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA 19104" + }, + { + "author_name": "Emma L Walters", + "author_inst": "Department of Urban and Regional Planning, University of Illinois at Urbana-Champaign, Champaign, IL 61820" + }, + { + "author_name": "Brennan Klein", + "author_inst": "Northeastern University Network Science Institute" + }, + { + "author_name": "Matteo Chinazzi", + "author_inst": "Northeastern University Network Science Institute" + }, + { + "author_name": "Andrei Gheorghe", + "author_inst": "Program for Evolutionary Dynamics, Harvard University, Cambridge, MA, 02138" + }, + { + "author_name": "Ben Adlam", + "author_inst": "Program for Evolutionary Dynamics, Harvard University, Cambridge, MA, 02138" + }, + { + "author_name": "Julianna Shinnick", + "author_inst": "Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA 19104" + }, + { + "author_name": "Maria Florencia Tejeda", + "author_inst": "Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA 19104" + }, + { + "author_name": "Samuel V Scarpino", + "author_inst": "Northeastern University Network Science Institute" + }, + { + "author_name": "Alessandro Vespignani", + "author_inst": "Northeastern University Network Science Institute" + }, + { + "author_name": "Andrew J Greenlee", + "author_inst": "Department of Urban and Regional Planning, University of Illinois at Urbana-Champaign, Champaign, IL 61820" + }, + { + "author_name": "Daniel Schneider", + "author_inst": "Department of Urban and Regional Planning, University of Illinois at Urbana-Champaign, Champaign, IL 61820" + }, + { + "author_name": "Michael Z. Levy", + "author_inst": "Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104" + }, + { + "author_name": "Alison L Hill", + "author_inst": "Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.27.20221028", "rel_title": "Remote fingerstick blood collection for SARS-CoV-2 antibody testing", @@ -1132273,41 +1130190,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.28.20221069", - "rel_title": "Psychological and social impact of COVID-19 in Pakistan: Need for Gender Responsive Policies", - "rel_date": "2020-11-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.28.20221069", - "rel_abs": "BACKGROUNDCOVID-19 has rapidly crossed borders, infecting people throughout the world. Women may be especially vulnerable to depression and anxiety due to the pandemic,\n\nAIMSThis study attempted to assess how gender impacts risk perceptions, anxiety levels behavioral responses to the COVID 19 pandemic in Pakistan in order to recommend gender responsive health policies\n\nMETHODSA cross-sectional online survey was conducted. Participants were asked to complete a sociodemographic data form, the Hospital Anxiety and Depression Scale (HADS), and questions on their risk perceptions, preventive behavior and information exposure. Regression analysis was used to assess effects of factors such as age, gender and household income on anxiety levels.\n\nRESULTSOf the 1390 respondents, 478 were women, and 913 were men. Women considered their chances of survival to be relatively lower than men (59 % women vs 73% men). They were also more anxious (62% women vs 50% men), and more likely to adopt precautionary behavior, such as avoiding going to the hospital (78% women vs. 71% men), not going to work (72% women and 57% men), and using disinfectants (93% women and 86% men). Men were more likely to trust friends, family and social media as reliable sources of COVID-19 information, while women were more likely to trust doctors.\n\nCONCLUSIONWomen experience a disproportion burden of the psychological and social impact of the pandemic compared to men. Involving doctors in healthcare communication targeting women, might prove effective. Social media and radio programs may be effective in disseminating information related to COVID among men.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Dr. Fauziah Rabbani", - "author_inst": "Aga Khan University" - }, - { - "author_name": "Dr. Hyder Ali Khan", - "author_inst": "Aga Khan University" - }, - { - "author_name": "Dr. Suneel Piryani", - "author_inst": "Aga Khan University" - }, - { - "author_name": "Areeba Raza Khan", - "author_inst": "Aga Khan University" - }, - { - "author_name": "Dr. Fahad Abid", - "author_inst": "Specialist Early Intervention in Psychosis Pakistan" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.10.31.363473", "rel_title": "TMPRSS2 and ADAM17 interactions with ACE2 complexed with SARS-CoV-2 and B0AT1 putatively in intestine, cardiomyocytes, and kidney", @@ -1133315,6 +1131197,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.27.20220970", + "rel_title": "A Machine Learning Study of 534,023 Medicare Beneficiaries with COVID-19: Implications for Personalized Risk Prediction", + "rel_date": "2020-10-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.27.20220970", + "rel_abs": "BackgroundGlobal demand for a COVID-19 vaccine will exceed the initial limited supply. Identifying individuals at highest risk of COVID-19 death may help allocation prioritization efforts. Personalized risk prediction that uses a broad range of comorbidities requires a cohort size larger than that reported in prior studies.\n\nMethodsMedicare claims data was used to identify patients age 65 years or older with diagnosis of COVID-19 between April 1, 2020 and August 31, 2020. Demographic characteristics, chronic medical conditions, and other patient risk factors that existed before the advent of COVID-19 were identified. A random forest model was used to empirically explore factors associated with COVID-19 death. The independent impact of factors identified were quantified using multivariate logistic regression with random effects.\n\nResultsWe identified 534,023 COVID-19 patients of whom 38,066 had an inpatient death. Demographic characteristics associated with COVID-19 death included advanced age (85 years or older: aOR: 2.07; 95% CI, 1.99-2.16), male sex (aOR, 1.88; 95% CI, 1.82-1.94), and non-white race (Hispanic: aOR, 1.74; 95% CI, 1.66-1.83). Leading comorbidities associated with COVID-19 mortality included sickle cell disease (aOR, 1.73; 95% CI, 1.21-2.47), chronic kidney disease (aOR, 1.32; 95% CI, 1.29-1.36), leukemias and lymphomas (aOR, 1.22; 95% CI, 1.14-1.30), heart failure (aOR, 1.19; 95% CI, 1.16-1.22), and diabetes (aOR, 1.18; 95% CI, 1.15-1.22).\n\nConclusionsWe created a personalized risk prediction calculator to identify candidates for early vaccine and therapeutics allocation (www.predictcovidrisk.com). These findings may be used to protect those at greatest risk of death from COVID-19.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Chen Dun", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Christi Walsh", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Sunjae Bae", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Amesh Adalja", + "author_inst": "Johns Hopkins University Center for Health Security" + }, + { + "author_name": "Eric Toner", + "author_inst": "Johns Hopkins University Center for Health Security" + }, + { + "author_name": "Timothy A Lash", + "author_inst": "West Health Institute" + }, + { + "author_name": "Farah Hashim", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Joseph Paturzo", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Dorry L Segev", + "author_inst": "Johns Hopkins University School of Medicine" + }, + { + "author_name": "Martin A Makary", + "author_inst": "Johns Hopkins University School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.28.20221333", "rel_title": "Clinical Suspicion of COVID-19 in Nursing Home residents: symptoms and mortality risk factors", @@ -1133947,73 +1131884,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.29.20222372", - "rel_title": "The COVID-19 Healthcare Personnel Study (CHPS): Overview, Methods and Preliminary Report", - "rel_date": "2020-10-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.29.20222372", - "rel_abs": "IntroductionThe COVID-19 Healthcare Personnel Study (CHPS) was designed to assess and mitigate adverse short and long-term physical and mental health impacts of the COVID-19 pandemic on New Yorks health care workforce. Here we report selected baseline results.\n\nMethodsOnline survey of New York State physicians, nurse practitioners and physician assistants registered with the New York State Department of Health. Survey-weighted descriptive results were analyzed using frequencies, proportions, and means, with 95% confidence intervals. Odds ratios were calculated for association using survey-weighted logistic regression.\n\nResultsApproximately 51.5% (95% CI 49.1, 54.0) of the survey-weighted respondents reported having worked directly or in close physical contact with COVID-19 patients. Of those tested for COVID-19, 27.3% (95% CI 22.5, 32.2) were positive. Having symptoms consistent with COVID-19 was associated with reporting a subsequent positive COVID-19 test (OR=14.0, 95% CI 5.7, 34.7). Over half of the respondents, (57.6%) reported a negative impact of the COVID-19 efforts on their mental health. Respondents who indicated that they were redeployed or required to do different functions than usual in response to COVID-19 were more likely to report negative mental health impacts (OR=1.3, 95% CI 1.1, 1.6).\n\nConclusionsAt the height of the COVID-19 pandemic in New York State in Spring 2020, more than half of physicians, nurse practitioners and physician assistants included in this study responded to the crisis, often at a cost to their physical and mental health and disruption to their lives.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "- The COVID-19 Healthcare Personnel Study (CHPS)", - "author_inst": "" - }, - { - "author_name": "Charles DiMaggio", - "author_inst": "NYU Grossman School of Medicine, Department of Surgery" - }, - { - "author_name": "David Abramson", - "author_inst": "NYU Global Institute for Public Health" - }, - { - "author_name": "Ezra Susser", - "author_inst": "Mailman School of Public Health, Columbia University" - }, - { - "author_name": "Christina Hoven", - "author_inst": "New York State Psychiatric Institute, Mailman School of Public Health, Columbia University" - }, - { - "author_name": "Qixuan Chen", - "author_inst": "Mailman School of Public Health, Columbia University" - }, - { - "author_name": "Howard Andrews", - "author_inst": "Columbia University Irving Medical Center, NY State Psychiatric Institute" - }, - { - "author_name": "Daniel Herman", - "author_inst": "Silberman School of Social Work, Hunter College, CUNY" - }, - { - "author_name": "Jonah Kreniske", - "author_inst": "Department of Global Health and Social Medicine, Harvard Medical School" - }, - { - "author_name": "Megan Ryan", - "author_inst": "Global Psychiatric Epidemiology Group, New York State Psychiatric Institute" - }, - { - "author_name": "Ida Susser", - "author_inst": "Hunter College and Graduate Center, City University of New York" - }, - { - "author_name": "Lorna Thorpe", - "author_inst": "Department of Population Health NYU Grossman School of Medicine" - }, - { - "author_name": "Guohua Li", - "author_inst": "Department of Anesthesiology, Columbia University Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.27.20215566", "rel_title": "Trip duration drives shift in travel network structure with implications for the predictability of spatial disease spread", @@ -1135581,6 +1133451,553 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.10.26.356014", + "rel_title": "COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms", + "rel_date": "2020-10-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.26.356014", + "rel_abs": "We describe a large-scale community effort to build an open-access, interoperable, and computable repository of COVID-19 molecular mechanisms - the COVID-19 Disease Map. We discuss the tools, platforms, and guidelines necessary for the distributed development of its contents by a multi-faceted community of biocurators, domain experts, bioinformaticians, and computational biologists. We highlight the role of relevant databases and text mining approaches in enrichment and validation of the curated mechanisms. We describe the contents of the Map and their relevance to the molecular pathophysiology of COVID-19 and the analytical and computational modelling approaches that can be applied for mechanistic data interpretation and predictions. We conclude by demonstrating concrete applications of our work through several use cases and highlight new testable hypotheses.", + "rel_num_authors": 133, + "rel_authors": [ + { + "author_name": "Marek Ostaszewski", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg" + }, + { + "author_name": "Anna Niarakis", + "author_inst": "Department of Biology, Univ. Evry, University of Paris-Saclay, GenHotel, Genopole, 91025, Evry, France" + }, + { + "author_name": "Alexander Mazein", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg" + }, + { + "author_name": "Inna Kuperstein", + "author_inst": "Institut Curie, PSL Research University, Paris, France." + }, + { + "author_name": "Robert Phair", + "author_inst": "Integrative Bioinformatics, Inc., 346 Paul Ave, Mountain View, CA, USA" + }, + { + "author_name": "Aurelio Orta-Resendiz", + "author_inst": "Institut Pasteur, HIV, Inflammation and Persistence Unit, Paris, France" + }, + { + "author_name": "Vidisha Singh", + "author_inst": "Laboratoire Europeen de Recherche pour la Polyarthrite Rhumatoide - Genhotel, Univ Evry, Universite Paris-Saclay, 2, rue Gaston Cremieux, 91057 EVRY-GENOPOLE ce" + }, + { + "author_name": "Sara Sadat Aghamiri", + "author_inst": "Inserm- Institut national de la sante et de la recherche medicale. Saint-Louis Hospital 1 avenue Claude Vellefaux Pavillon Bazin 75475 Paris" + }, + { + "author_name": "Marcio Luis Acencio", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg" + }, + { + "author_name": "Enrico Glaab", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg" + }, + { + "author_name": "Andreas Ruepp", + "author_inst": "Institute of Experimental Genetics (IEG), Helmholtz Zentrum Munchen-German Research Center for Environmental Health (GmbH), Ingolstadter Landstrasse 1, D-85764 " + }, + { + "author_name": "Gisela Fobo", + "author_inst": "Institute of Experimental Genetics (IEG), Helmholtz Zentrum Munchen-German Research Center for Environmental Health (GmbH), Ingolstadter Landstrasse 1, D-85764 " + }, + { + "author_name": "Corinna Montrone", + "author_inst": "Institute of Experimental Genetics (IEG), Helmholtz Zentrum Munchen-German Research Center for Environmental Health (GmbH), Ingolstadter Landstrasse 1, D-85764 " + }, + { + "author_name": "Barbara Brauner", + "author_inst": "Institute of Experimental Genetics (IEG), Helmholtz Zentrum Munchen-German Research Center for Environmental Health (GmbH), Ingolstadter Landstrasse 1, D-85764 " + }, + { + "author_name": "Goar Frishman", + "author_inst": "Institute of Experimental Genetics (IEG), Helmholtz Zentrum Munchen-German Research Center for Environmental Health (GmbH), Ingolstadter Landstrasse 1, D-85764 " + }, + { + "author_name": "Julia Somers", + "author_inst": "Oregong Health & Sciences Univerity; Department of Molecular and Medical Genetics; 3222 SW Research Drive, Portland, Oregon, U.S.A 97239" + }, + { + "author_name": "Matti Hoch", + "author_inst": "Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany" + }, + { + "author_name": "Shailendra Kumar Gupta", + "author_inst": "Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany" + }, + { + "author_name": "Julia Scheel", + "author_inst": "Department of Systems Biology and Bioinformatics, University of Rostock, 18051 Rostock, Germany" + }, + { + "author_name": "Hanna Borlinghaus", + "author_inst": "Department of Computer and Information Science, University of Konstanz, Konstanz, Germany" + }, + { + "author_name": "Tobias Czauderna", + "author_inst": "Monash University, Faculty of Information Technology, Department of Human-Centred Computing, Wellington Rd, Clayton VIC 3800, Australia" + }, + { + "author_name": "Falk Schreiber", + "author_inst": "Department of Computer and Information Science, University of Konstanz, Konstanz, Germany" + }, + { + "author_name": "Arnau Montagud", + "author_inst": "Barcelona Supercomputing Center (BSC), Barcelona, Spain" + }, + { + "author_name": "Miguel Ponce de Leon", + "author_inst": "Barcelona Supercomputing Center (BSC), Barcelona, Spain" + }, + { + "author_name": "Akira Funahashi", + "author_inst": "Keio University, Department of Biosciences and Informatics, 3-14-1 Hiyoshi Kouhoku-ku Yokohama Japan 223-8522" + }, + { + "author_name": "Yusuke Hiki", + "author_inst": "Keio University, Department of Biosciences and Informatics, 3-14-1 Hiyoshi Kouhoku-ku Yokohama Japan 223-8522" + }, + { + "author_name": "Noriko Hiroi", + "author_inst": "Sanyo-Onoda City University, Faculty of Pharmaceutical Sciences, University St.1-1-1, Yamaguchi, Japan 756-0884" + }, + { + "author_name": "Takahiro G Yamada", + "author_inst": "Keio University, Department of Biosciences and Informatics, 3-14-1 Hiyoshi Kouhoku-ku Yokohama Japan 223-8522" + }, + { + "author_name": "Andreas Drager", + "author_inst": "Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tu" + }, + { + "author_name": "Alina Renz", + "author_inst": "Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tu" + }, + { + "author_name": "Muhammad Naveez", + "author_inst": "Riga Technical University, Institute of Applied Computer Systems,1 Kalku Street, LV-1658 Riga, Latvia" + }, + { + "author_name": "Zsolt Bocskei", + "author_inst": "Sanofi R&D Translational Sciences" + }, + { + "author_name": "Daniela Bornigen", + "author_inst": "Bioinformatics Core Facility, Universitaetsklinikum Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany" + }, + { + "author_name": "Liam Fergusson", + "author_inst": "The University of Edinburgh, Royal (Dick) School of Veterinary Medicine, Easter Bush Campus, Midlothian, EH25 9RG" + }, + { + "author_name": "Marta Conti", + "author_inst": "Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany" + }, + { + "author_name": "Marius Rameil", + "author_inst": "University of Bonn, Germany" + }, + { + "author_name": "Vanessa Nakonecnij", + "author_inst": "Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany" + }, + { + "author_name": "Jakob Vanhoefer", + "author_inst": "Faculty of Mathematics and Natural Sciences, University of Bonn, Bonn, Germany" + }, + { + "author_name": "Leonard Schmiester", + "author_inst": "Helmholtz Zentrum Munchen - German Research Center for Environmental Health, Institute of Computational Biology, 85764 Neuherberg, Germany" + }, + { + "author_name": "Muying Wang", + "author_inst": "Department of Chemical Engineering, University of Pittsburgh" + }, + { + "author_name": "Emily E Ackerman", + "author_inst": "University of Pittsburgh, Department of Chemical and Petroleum Engineering" + }, + { + "author_name": "Jason E Shoemaker", + "author_inst": "Dept. of Chemical & Petroleum Engineering, University of Pittsburgh" + }, + { + "author_name": "Jeremy Zucker", + "author_inst": "Pacific Northwest National Laboratory" + }, + { + "author_name": "Kristie L Oxford", + "author_inst": "Pacific Northwest National Laboratory" + }, + { + "author_name": "Jeremy Teuton", + "author_inst": "Pacific Northwest National Laboratory" + }, + { + "author_name": "Ebru Kocakaya", + "author_inst": "Ankara University, Stem Cell Institute, Ceyhun Atif Kansu St. No: 169 06520 Cevizlidere/ANKARA/TURKEY" + }, + { + "author_name": "Gokce Yagmur Summak", + "author_inst": "Ankara University, Stem Cell Institute, Ceyhun Atif Kansu St. No: 169 06520 Cevizlidere/ANKARA/TURKEY" + }, + { + "author_name": "Kristina Hanspers", + "author_inst": "Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158" + }, + { + "author_name": "Martina Kutmon", + "author_inst": "Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands" + }, + { + "author_name": "Susan Coort", + "author_inst": "Maastricht University, NUTRIM, Bioinformatics-BiGCaT, PO Box 616, 6200 MD, Maastricht, the Netherlands" + }, + { + "author_name": "Lars Eijssen", + "author_inst": "Department of Bioninformatics-BiGCaT, NUTRIM, Maastricht University, Universiteitssingel 60, 6229 ER Maastricht, The Netherlands" + }, + { + "author_name": "Friederike Ehrhart", + "author_inst": "Maastricht University, Department of Bioinformatics, NUTRIM, Universiteitssingel 60; 6229 ER Maastricht; The Netherlands" + }, + { + "author_name": "Rex D. A. B.", + "author_inst": "Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore 575018, India" + }, + { + "author_name": "Denise Slenter", + "author_inst": "Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands" + }, + { + "author_name": "Marvin Martens", + "author_inst": "Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, 6229 ER Maastricht, The Netherlands" + }, + { + "author_name": "Nhung Pham", + "author_inst": "Maastricht University, NUTRIM, Bioinformatics-BiGCaT, PO Box 616, 6200 MD, Maastricht, the Netherlands" + }, + { + "author_name": "Robin Haw", + "author_inst": "Adaptive Oncology, Ontario Institute for Cancer Research, MaRS Centre, 661 University Avenue, Suite 510, Toronto, Ontario, Canada M5G 0A3" + }, + { + "author_name": "Bijay Jassal", + "author_inst": "Ontario Institute for Cancer Research (OICR), 661 University Ave Suite 510, Toronto, ON M5G 0A3, Canada" + }, + { + "author_name": "Lisa Matthews", + "author_inst": "NYU Grossman School of Medicine, New York NY 10016 USA" + }, + { + "author_name": "Marija Orlic-Milacic", + "author_inst": "Ontario Institute for Cancer Research, Department of Computational Biology, MaRS Centre, South Tower, 661 University Avenue, Suite 500, Toronto, Ontario, Canada" + }, + { + "author_name": "Andrea Senff-Ribeiro", + "author_inst": "Ontario Institute for Cancer Research (OICR) (Canada)" + }, + { + "author_name": "Karen Rothfels", + "author_inst": "Ontario Institute for Cancer Research, Department of Computational Biology, MaRS Centre, South Tower, 661 University Avenue, Suite 500, Toronto, Ontario, Canada" + }, + { + "author_name": "Veronica Shamovsky", + "author_inst": "NYU Langone Medical Center, New York, USA" + }, + { + "author_name": "Ralf Stephan", + "author_inst": "Ontario Institute for Cancer Research, MaRS Centre, 661 University Ave, Suite 510, Toronto, Ontario, Canada" + }, + { + "author_name": "Cristoffer Sevilla", + "author_inst": "EMBL-EBI, Molecular Systems, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD" + }, + { + "author_name": "Thawfeek Mohamed Varusai", + "author_inst": "Reactome, EMBL-EBI, Cambridge, UK" + }, + { + "author_name": "Jean-Marie Ravel", + "author_inst": "University of Lorraine, INSERM UMR_S 1256, Nutrition, Genetics, and Environmental Risk Exposure (NGERE), Faculty of Medicine of Nancy, F-54000 Nancy, France." + }, + { + "author_name": "Vera Ortseifen", + "author_inst": "Senior Research Group in Genome Research of Industrial Microorganisms, Center for Biotechnology, Bielefeld University, Universitaetsstrasse 27, 33615 Bielefeld," + }, + { + "author_name": "Silvia Marchesi", + "author_inst": "Uppsala University - Sweden" + }, + { + "author_name": "Piotr Gawron", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg" + }, + { + "author_name": "Ewa Smula", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg" + }, + { + "author_name": "Laurent Heirendt", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg" + }, + { + "author_name": "Venkata Satagopam", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg" + }, + { + "author_name": "Guanming Wu", + "author_inst": "Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239-3098, USA" + }, + { + "author_name": "Anders Riutta", + "author_inst": "Gladstone Institutes, Institute for Data Science and Biotechnology, 1650 Owens St., San Francisco, CA 94131, USA" + }, + { + "author_name": "Martin Golebiewski", + "author_inst": "Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg (Germany)" + }, + { + "author_name": "Stuart Owen", + "author_inst": "The University of Manchester, Department of Computer Science, Oxford Road, Manchester, M13 9PL, UK" + }, + { + "author_name": "Carole Goble", + "author_inst": "The University of Manchester, Department of Computer Science, Oxford Road, Manchester, M13 9PL, UK" + }, + { + "author_name": "Xiaoming Hu", + "author_inst": "Heidelberg Institute for Theoretical Studies (HITS), Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg (Germany)" + }, + { + "author_name": "Rupert Overall", + "author_inst": "German Center for Neurodegenerative Diseases (DZNE) Dresden, Tatzberg 41, 01307 Dresden, Germany." + }, + { + "author_name": "Dieter Maier", + "author_inst": "Biomax Informatics AG, Robert-Koch-Str. 2, 82152 Planegg, Germany" + }, + { + "author_name": "Angela Bauch", + "author_inst": "Biomax Informatics AG, Robert-Koch-Str. 2, 82152 Planegg, Germany" + }, + { + "author_name": "Benjamin M Gyori", + "author_inst": "Harvard Medical School, Laboratory of Systems Pharmacology, 200 Longwood Avenue, Boston, MA" + }, + { + "author_name": "John A Bachman", + "author_inst": "Harvard Medical School, Laboratory of Systems Pharmacology, 200 Longwood Avenue, Boston, MA" + }, + { + "author_name": "Carlos Vega", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg" + }, + { + "author_name": "Valentin Groues", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg" + }, + { + "author_name": "Miguel Vazquez", + "author_inst": "Barcelona Supercomputing Center (BSC), Barcelona, Spain" + }, + { + "author_name": "Pablo Porras", + "author_inst": "EMBL-EBI, Molecular Systems, Wellcome Genome Campus, CB10 1SD, Hinxton, UK" + }, + { + "author_name": "Luana Licata", + "author_inst": "University of Rome Tor Vergata, Department of Biology, Via della Ricerca Scientifica 1, 00133 Rome, Italy" + }, + { + "author_name": "Marta Iannuccelli", + "author_inst": "University of Rome Tor Vergata, Department of Biology, Via della Ricerca Scientifica 1, 00133 Rome, Italy" + }, + { + "author_name": "Francesca Sacco", + "author_inst": "University of Rome Tor Vergata, Department of Biology, Via della Ricerca Scientifica 1, 00133 Rome, Italy" + }, + { + "author_name": "Denes Turei", + "author_inst": "Heidelberg Univarsity, Institute for Computational Biomedicine, BQ 0053, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany" + }, + { + "author_name": "Augustin Luna", + "author_inst": "cBio Center, Divisions of Biostatistics and Computational Biology, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, USA." + }, + { + "author_name": "Ozgun Babur", + "author_inst": "University of Massachusetts Boston, Computer Science Department, 100 William T, Morrissey Blvd, Boston, MA 02125" + }, + { + "author_name": "Sylvain Soliman", + "author_inst": "Inria Saclay Ile-de-France" + }, + { + "author_name": "Alberto Valdeolivas", + "author_inst": "Heidelberg University, Faculty of Medicine and Heidelberg University Hospital, Institute of Computational Biomedicine, Bioquant, 69120 Heidelberg, Germany" + }, + { + "author_name": "Marina Esteban-Medina", + "author_inst": "Clinical Bioinformatics Area. Fundacion Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain." + }, + { + "author_name": "Maria Pena-Chilet", + "author_inst": "Clinical Bioinformatics Area. Fundacion Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain." + }, + { + "author_name": "Kinza Rian", + "author_inst": "Clinical Bioinformatics Area. Fundacion Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio, 41013, Sevilla, Spain." + }, + { + "author_name": "Tomas Helikar", + "author_inst": "University of Nebraska-Lincoln, Department of Biochemistry, 1901 Vine St., Lincoln, NE, 68588, USA" + }, + { + "author_name": "Bhanwar Lal Puniya", + "author_inst": "University of Nebraska-Lincoln, Department of Biochemistry, 1901 Vine St., Lincoln, NE, 68588, USA" + }, + { + "author_name": "Anastasia Nesterova", + "author_inst": "Elsevier, Life Science Department" + }, + { + "author_name": "Anton Yuryev", + "author_inst": "Elsevier, Professional Services, 1600 John F Kennedy Blvd #1800, Philadelphia, PA 19103" + }, + { + "author_name": "Anita de Waard", + "author_inst": "Elsevier, Research Collaborations Unit, 71 Hanley Lane, Jericho, VT 05465" + }, + { + "author_name": "Dezso Modos", + "author_inst": "Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom" + }, + { + "author_name": "Agatha Treveil", + "author_inst": "Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom" + }, + { + "author_name": "Marton Laszlo Olbei", + "author_inst": "Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, United Kingdom" + }, + { + "author_name": "Bertrand De Meulder", + "author_inst": "Association EISBM" + }, + { + "author_name": "Aurelien Naldi", + "author_inst": "Inria Saclay - Ile de France, Lifeware group, 91120 Palaiseau, France" + }, + { + "author_name": "Aurelien Dugourd", + "author_inst": "Heidelberg University, Faculty of Medicine, and Heidelberg University Hospital, Institute for Computational Biomedicine, Bioquant, Heidelberg, Germany" + }, + { + "author_name": "Laurence Calzone", + "author_inst": "Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, F-75005, Paris, France." + }, + { + "author_name": "Chris Sander", + "author_inst": "cBio Center, Divisions of Biostatistics and Computational Biology, Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, 02215, USA." + }, + { + "author_name": "Emek Demir", + "author_inst": "Oregon Health and Science University, Department of Molecular and Medical Genetics, 3222 SW Research Drive, Mail Code: L103, Portland, Oregon, U.S.A. 97239" + }, + { + "author_name": "Tamas Korcsmaros", + "author_inst": "Earlham Institute, Norwich Research Park, NR4 7UZ, Norwich, UK" + }, + { + "author_name": "Tom C Freeman", + "author_inst": "The Roslin Institute, University of Edinburgh EH25 9RG" + }, + { + "author_name": "Franck Auge", + "author_inst": "Sanofi R&D, Translational Sciences, 1 av Pierre Brossolette 91395 Chilly-Mazarin France" + }, + { + "author_name": "Jacques S Beckmann", + "author_inst": "University of Lausanne, Lausanne, Switzerland" + }, + { + "author_name": "Jan Hasenauer", + "author_inst": "Interdisciplinary Research Unit Mathematics and Life Sciences, University of Bonn, Germany" + }, + { + "author_name": "Olaf Wolkenhauer", + "author_inst": "University of Rostock, Dept of Systems Biology & Bioinformatics" + }, + { + "author_name": "Egon Willighagen", + "author_inst": "Department of Bioinformatics-BiGCaT, NUTRIM, Maastricht University, Maastricht, The Netherlands" + }, + { + "author_name": "Alexander R Pico", + "author_inst": "Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA" + }, + { + "author_name": "Chris Evelo", + "author_inst": "Dept. Bioinformatics - BiGCaT, Maastricht University, The Netherlands" + }, + { + "author_name": "Lincoln D Stein", + "author_inst": "Ontario Institute for Cancer Research, Adaptive Oncology Theme, 661 University Ave, Toronto, ON M5G 1M1 Canada" + }, + { + "author_name": "Henning Hermjakob", + "author_inst": "European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, UK" + }, + { + "author_name": "Julio Saez-Rodriguez", + "author_inst": "Institute for Computational Biomedicine Heidelberg University, Faculty of Medicine, Im Neuenheimer Feld 267, 69120 Heidelberg" + }, + { + "author_name": "Joaquin Dopazo", + "author_inst": "Clinical Bioinformatics Area. Fundacion Progreso y Salud (FPS). CDCA, Hospital Virgen del Rocio. 41013. Sevilla. Spain." + }, + { + "author_name": "Alfonso Valencia", + "author_inst": "Barcelona Supercomputing Center (BSC), Barcelona, Spain" + }, + { + "author_name": "Hiroaki Kitano", + "author_inst": "Systems Biology Institute, Tokyo Japan" + }, + { + "author_name": "Emmanuel Barillot", + "author_inst": "Institut Curie, PSL Research University, Paris, France." + }, + { + "author_name": "Charles Auffray", + "author_inst": "European Institute for Systems Biology and Medicine (EISBM), Vourles, France" + }, + { + "author_name": "Rudi Balling", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg" + }, + { + "author_name": "Reinhard Schneider", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg" + }, + { + "author_name": "- the COVID-19 Disease Map Community", + "author_inst": "-" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "systems biology" + }, { "rel_doi": "10.1101/2020.10.28.358614", "rel_title": "Induced pulmonary comorbidities render CD-1 mice sensitive to SARS-CoV-2", @@ -1136261,45 +1134678,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.10.28.359257", - "rel_title": "In vitro assessment of the virucidal activity of four mouthwashes containing Cetylpyridinium Chloride, ethanol, zinc and a mix of enzyme and proteins against a human coronavirus", - "rel_date": "2020-10-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.28.359257", - "rel_abs": "Backgroundsaliva is established to contain high counts SARS-CoV-2 virus and contact with saliva droplets, contaminated surfaces or airborne particles are sources of viral transmission. The generation of infective aerosols during clinical procedures is of particular concern. Therefore, a fuller understanding of the potential of mouthwash to reduce viral counts and modulate the risk of transmission in medical professional and public context is an important research topic.\n\nMethodwe determined the virucidal activity of four anti-bacterial mouthwashes against a surrogate for SARS-CoV-2, Human CoV-SARS 229E, using a standard ASTM suspension test, with dilution and contact times applicable to recommended mouthwash use.\n\nResultsthe mouthwash formulated with 0.07% Cetylpyridinium Chloride exhibited virucidal effects providing a [≥]3.0 log reduction HCoV-229E viral count. Mouthwashes containing 15.7% ethanol, 0.2% zinc sulphate heptahydrate and a mix of enzymes and proteins did not demonstrate substantive virucidal activity in this test.\n\nConclusionmouthwash containing 0.07% Cetylpyridinium Chloride warrants further laboratory and clinical assessment to determine their potential benefit in reducing the risk of SARS-CoV-2.\n\nHighlightsSARS-CoV-2 can be transmitted through contact with infective saliva.\n\nStudies are needed to understand if mouthwash can lower SARS-CoV-2 transmission risk.\n\n0.07% Cetylpyridinium Chloride (CPC) mouthwash exhibited virucidal effects against HCoV-SARS 229E.\n\nFurther studies on potential of 0.07% CPC mouthwash against SARS-CoV-2 are warranted.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Alison Green", - "author_inst": "Unilever Research and Development Port Sunlight, Quarry Road East, Bebington, Wirral, UK, CH63 3JW" - }, - { - "author_name": "Glyn Roberts", - "author_inst": "Unilever Research and Development Port Sunlight, Quarry Road East, Bebington, Wirral, UK, CH63 3JW" - }, - { - "author_name": "Timothy Tobery", - "author_inst": "Unilever Research and Development Trumbull, 40 Merritt Boulevard, Trumbull, CT 06611, USA" - }, - { - "author_name": "Carol Vincent", - "author_inst": "Unilever Research and Development Trumbull, 40 Merritt Boulevard, Trumbull, CT 06611, USA" - }, - { - "author_name": "Matteo Barili", - "author_inst": "Unilever Oral Care, Via Lever Gibbs, 3, Casalpusterlengo, 26841, LO, Italy" - }, - { - "author_name": "Carolyn Jones", - "author_inst": "Unilever Oral Care, Via Lever Gibbs, 3, Casalpusterlengo, 26841, LO, Italy" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.10.28.358945", "rel_title": "SARS-CoV-2 replication triggers an MDA-5-dependent interferon production which is unable to efficiently control replication", @@ -1137475,6 +1135853,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.22.20216010", + "rel_title": "Fernando de Noronha: how an island controlled the community transmission of COVID-19 in Brazil", + "rel_date": "2020-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.22.20216010", + "rel_abs": "IntroductionFernando Noronha (FNA) is a small Brazilian archipelago in the Atlantic, part of the state of Pernambuco that COVID-19 has decimated. Anticipating the worst from the pandemic, Island and state authorities implemented a series of public health actions to contain the epidemic. This paper, reporting the results of the first wave of a cohort study, documents the measures and their effects through a cohort study.\n\nMethodsMeasures were documented at the time of implementation. A random sample of 904 residents were selected from the health register, interviewed and tested for COVID-19 (RT-PCR and serology). The survey explored socioeconomic variables and adherence to prevention behaviors.\n\nResultsFlights were reduced from 38 to once a week, FNA was closed to tourism, schools were closed, and testing and tracing contacts was mandated along with social distancing and use of masks. A household lockdown was briefly imposed for residents. A prevalence of 5.1% was found, and a total of 158 cases of COVID-19 was estimated, although only 28 had been reported in routine surveillance. Half of the population reported food insecurity and applied for government COVID-19 benefits. Adherence to control measures was high, except for intrahousehold mask use with family and friends.\n\nConclusionDespite high levels of COVID-19 in Pernambuco, continued exposure through the provision of essential services from the mainland, and lack of direction from national authorities, FNA was able to implement a series of prevention measures unique in Brazil that contained the epidemic on the island.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Mozart Julio Tabosa Sales", + "author_inst": "Instituto de Medicina Integral Professor Fernando Figueira" + }, + { + "author_name": "Ligia S Kerr", + "author_inst": "Universidade Federal do Ceara" + }, + { + "author_name": "Regina Vianna Brizolara", + "author_inst": "Departamento de Doencas de Condicoes Cronicas e Infeccoes Sexualmente Transmissiveis da Secretaria de Vigilancia em Saude do Ministerio da Saude" + }, + { + "author_name": "Ivana Cristina de Holanda Cunha Barreto", + "author_inst": "Fundacao Oswaldo Cruz Ceara" + }, + { + "author_name": "Rosa Livia Freitas Almeida", + "author_inst": "Universidade de Fortaleza" + }, + { + "author_name": "Paulo Goes", + "author_inst": "Universidade de Pernambuco" + }, + { + "author_name": "Luis Odorico Monteiro de Andrade", + "author_inst": "Fundacao Oswaldo Cruz Ceara" + }, + { + "author_name": "Leuridan Torres", + "author_inst": "Instituto de Medicina Integral Prof. Fernando Figueira - IMIP" + }, + { + "author_name": "Flavia Kelly Alvarenga Pinto", + "author_inst": "Ministerio da Saude" + }, + { + "author_name": "Francisco Marto Leal Pinheiro-Junior", + "author_inst": "Universidade Federal do Ceara" + }, + { + "author_name": "Rebeca Valentim Leite", + "author_inst": "Universidade Federal de Pernambuco/Faculdade de Medicina de Olinda" + }, + { + "author_name": "Amanda Carolina Abreu Felix Cavalcanti de Abreu", + "author_inst": "Secretaria Estadual de Saude de Pernambuco" + }, + { + "author_name": "Rebecca Lucena Theophilo", + "author_inst": "Instituto de Medicina Integral Professor Fernando Figueira; Fundacao Oswaldo Cruz Ceara" + }, + { + "author_name": "Fernando Rodrigues Magalhaes", + "author_inst": "Autarquia Territorial Distrito Estadual de Fernando de Noronha, Pernambuco" + }, + { + "author_name": "Susane Lindinalva da Silva", + "author_inst": "Universidade Federal de Pernambuco; Faculdade de Medicina de Olinda" + }, + { + "author_name": "Carl Kendall", + "author_inst": "Universidade Federal do Ceara; Tulane School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.19.20215293", "rel_title": "Adaptive COVID-19 Forecasting via Bayesian Optimization", @@ -1137819,73 +1136276,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.23.20218164", - "rel_title": "SARS-CoV-2 seroprevalence in healthcare workers of dedicated COVID hospitals and non COVID hospitals of District Srinagar, Kashmir", - "rel_date": "2020-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.23.20218164", - "rel_abs": "Background and objectiveSARS-CoV-2 infection poses tremendous challenge to the healthcare system of nations across the globe. Serological testing for SARS-CoV-2 infection in healthcare workers, which form a high-risk group, helps in identifying the burden of hidden infection in an institutional setting.\n\nMethodsWe present the results of a cross-sectional serosurvey in healthcare workers from two different hospital settings based on their role in the management of SARS-CoV-2 patients in District Srinagar, Kashmir. In addition to testing for the presence of SARS-CoV-2 specific IgG, we collected information on influenza-like symptoms in the last four weeks and the status of RT-PCR testing. SARS-CoV-2 specific IgG antibodies were detected in serum samples using a sensitive and specific chemiluminescent microparticle immunoassay technology.\n\nInterpretation and ConclusionOf 2915 healthcare workers who participated in the study, we analysed data from 2905 healthcare workers. The overall prevalence of SARS-CoV-2 specific IgG antibodies was 2.5% (95% CI 2.0-3.1) in the healthcare workers of District Srinagar. Healthcare workers who had ever worked at a dedicated-COVID hospital had a substantially lower seroprevalence of 0.6% (95% CI: 0.2 - 1.9). Among healthcare workers who had tested positive for RT-PCR, seroprevalence was 27.6% (95% CI: 14.0 - 47.2).The seroprevalence of SARS-CoV-2 infection in healthcare workers of District Srinagar is low, reflecting that a high proportion of healthcare workers are still susceptible to the infection. It is crucial to lay thrust on infection prevention and control activities and standard hygiene practices by the healthcare staff to protect them from acquiring infection within the healthcare setting.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Muhammad S Khan", - "author_inst": "government medical college srinagar" - }, - { - "author_name": "Inaamul Haq", - "author_inst": "government medical college srinagar" - }, - { - "author_name": "mariya A qurieshi", - "author_inst": "Department of Community Medicine Government Medical College, Srinagar, India" - }, - { - "author_name": "Sabhiya Majid", - "author_inst": "government medical college" - }, - { - "author_name": "Arif Bhat", - "author_inst": "government medical college" - }, - { - "author_name": "tanzeela Qazi", - "author_inst": "GMC SRINAGAR" - }, - { - "author_name": "iqra chowdry", - "author_inst": "GMC SRINAGAR" - }, - { - "author_name": "muhammad Obaid", - "author_inst": "GMC SRINAGAR" - }, - { - "author_name": "Iram Sabah", - "author_inst": "GMC" - }, - { - "author_name": "Misbah Kawoosa", - "author_inst": "GMC" - }, - { - "author_name": "Abdul Lone", - "author_inst": "GMC" - }, - { - "author_name": "Shahroz Nabi", - "author_inst": "GMC" - }, - { - "author_name": "Ishtiyaq Sumji", - "author_inst": "GMC" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.23.20218073", "rel_title": "Evaluation of filtration efficacy of various types of face-masks using ambient and PAO aerosols following with different sterilization methods", @@ -1138809,6 +1137199,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2020.10.24.20215061", + "rel_title": "MEGA: Machine Learning-Enhanced Graph Analytics for COVID-19 Infodemic Control", + "rel_date": "2020-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.24.20215061", + "rel_abs": "The COVID-19 pandemic brought not only global devastation but also an unprecedented infodemic of false or misleading information that spread rapidly through online social networks. Network analysis plays a crucial role in the science of fact-checking by modeling and learning the risk of infodemics through statistical processes and computation on mega-sized graphs. This paper proposes MEGA, Machine Learning-Enhanced Graph Analytics, a framework that combines feature engineering and graph neural networks to enhance the efficiency of learning performance involving massive graphs. Infodemic risk analysis is a unique application of the MEGA framework, which involves detecting spambots by counting triangle motifs and identifying influential spreaders by computing the distance centrality. The MEGA framework is evaluated using the COVID-19 pandemic Twitter dataset, demonstrating superior computational efficiency and classification accuracy.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Ching Nam Hang", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Pei-Duo Yu", + "author_inst": "Chung Yuan Christian University" + }, + { + "author_name": "Siya Chen", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Chee Wei Tan", + "author_inst": "Nanyang Technological University" + }, + { + "author_name": "Guanrong Chen", + "author_inst": "City University of Hong Kong" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.10.23.20217901", "rel_title": "Rapid Development of a De Novo Convalescent Plasma Program in Response to a Global Pandemic: A Large Southeastern U.S. Blood Center's Experience", @@ -1139397,49 +1137822,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.24.20218974", - "rel_title": "Low serum vitamin D level and COVID-19 infection and outcomes, a multivariate meta-analysis", - "rel_date": "2020-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.24.20218974", - "rel_abs": "ObjectiveThis study aimed to determine whether serum vitamin D is independently associated with COVID-19 infection and outcomes in patients with COVID-19.\n\nMethodsWe identified relevant studies by searching the PubMed, Embase, and medRxiv databases from December 2019 to October 1, 2020. Odds ratios (ORs) were pooled using random-effects models. Only reports with multivariate adjusted results were included to avoid the impact of potential confounding factors.\n\nResultsA total of six studies with 377,265 patients were identified. Overall, in the categorical analysis, a low serum vitamin D level was associated with an increased risk of COVID-19 infection (OR: 1.47, 95% CI: 1.09- 1.97, I2=81%), hospitalization (OR: 1.83, 95% CI: 1.22-2.74, I2=0%), but not in-hospital death (OR: 2.73, 95% CI: 0.27-27.61). Notably, when vitamin D level was analyzed as a continuous variable, each 5 ng/ml increase in vitamin D level was not associated with any increased risk of COVID-19 infection (OR: 1.04, 95% CI: 0.96-1.12, I2=74%) or in-hospital death (OR: 1.02, 95% CI: 0.93-1.12).\n\nConclusionsLow serum vitamin D is associated with an increased risk of COVID-19 infection and hospitalization. In-hospital death showed a tendency to be increased in COVID-19 patients with low vitamin D levels. The ongoing clinical trials for evaluation of vitamin D supplementation will be key to the validation of this adjunctive treatment for COVID-19 patients.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "jie chen", - "author_inst": "the Third Affiliated Hospital of Nanchang University" - }, - { - "author_name": "lixia xie", - "author_inst": "the Second Affiliated Hospital of Nanchang University" - }, - { - "author_name": "ping yuan", - "author_inst": "the Second Affiliated Hospital of Nanchang University" - }, - { - "author_name": "peng yu", - "author_inst": "the Second Affiliated Hospital of Nanchang University" - }, - { - "author_name": "jianyong ma", - "author_inst": "the Second Affiliated Hospital of Nanchang University" - }, - { - "author_name": "chunhua zheng", - "author_inst": "the Third Affiliated Hospital of Nanchang University" - }, - { - "author_name": "xiao liu", - "author_inst": "Second affiliated Hospital of Nanchang University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2020.10.25.20216671", "rel_title": "Estimating the Case Fatality Ratio for COVID-19 using a Time-Shifted Distribution Analysis", @@ -1140455,6 +1138837,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.10.26.20218370", + "rel_title": "Outcomes evaluated in controlled clinical trials on the management of COVID-19: A methodological systematic review", + "rel_date": "2020-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.26.20218370", + "rel_abs": "It is crucial that randomized controlled trials (RCTs) on the management of coronavirus disease 2019 (COVID-19) evaluate the outcomes that are critical to patients and clinicians, to facilitate relevance, interpretability, and comparability.\n\nThis methodological systematic review describes the outcomes evaluated in 415 RCTs on the management of COVID-19, that were registered with ClinicalTrials.gov, by 5/5/2020.\n\nSignificant heterogeneity was observed in the selection of outcomes and the instruments used to measure them. Mortality, adverse events and treatment success or failure are only evaluated in 64.4%, 48.4% and 43% of the included studies, respectively, while other outcomes are selected less often. Studies focusing on more severe presentations (hospitalized patients or requiring intensive care) most frequently evaluate mortality and adverse events, while hospital admission and viral detection/load are most frequently assessed in the community setting. Outcome measurement instruments are poorly reported and heterogeneous. In general, simple instruments that can control for important sources of bias are favoured. Follow-up does not exceed one month in 64.3% of these earlier trials, and long-term COVID-19 burden is rarely assessed.\n\nThe methodological issues identified could delay the introduction of potentially life-saving treatments in clinical practice. Our findings demonstrate the need for consensus in the design of RCTs.\n\nTake home message@ERSpublications: This systematic review describes the heterogeneity in outcomes evaluated in 415 RCTs on COVID-19 management and the instruments used to measure them. Our findings reveal a need for consensus in the design of future RCTs.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Alexander G. Mathioudakis", + "author_inst": "Division of Infection, Immunity and Respiratory Medicine, The University of Manchester & North West Lung Centre, Manchester University NHS Foundation Trust, Man" + }, + { + "author_name": "Markus Fally", + "author_inst": "Department of Internal Medicine, Section for Pulmonary Diseases, Herlev Gentofte Hospital, Hellerup, Denmark." + }, + { + "author_name": "Rola Hashad", + "author_inst": "North West Lung Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust, Southmoor Road, Manchester, UK & Department of Medical Microbiology an" + }, + { + "author_name": "Ahmed Kouta", + "author_inst": "Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester Academic Health Science Centre" + }, + { + "author_name": "Ali Sina Hadi", + "author_inst": "Department of Respiratory Medicine, Salford Royal Infirmary NHS Foundation Trust, Manchester, UK." + }, + { + "author_name": "Sean Blandin Knight", + "author_inst": "Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, The University of Manchester, Manchester Academic Health Science Centre" + }, + { + "author_name": "Nawar Diar Bakerly", + "author_inst": "Department of Respiratory Medicine, Salford Royal Infirmary NHS Foundation Trust, Manchester, UK & Manchester Metropolitan University, Manchester, UK" + }, + { + "author_name": "Dave Singh", + "author_inst": "Division of Infection, Immunity and Respiratory Medicine, The University of Manchester & North West Lung Centre, Manchester University NHS Foundation Trust & Me" + }, + { + "author_name": "Paula R Williamson", + "author_inst": "MRC/NIHR Trials Methodology Research Partnership, Department of Health Data Science, University of Liverpool, Liverpool, UK." + }, + { + "author_name": "Timothy Felton", + "author_inst": "Division of Infection, Immunity and Respiratory Medicine, The University of Manchester & North West Lung Centre, Manchester University NHS Foundation Trust, Man" + }, + { + "author_name": "Jorgen Vestbo", + "author_inst": "Division of Infection, Immunity and Respiratory Medicine, The University of Manchester & North West Lung Centre, Manchester University NHS Foundation Trust, Man" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2020.10.26.20219733", "rel_title": "What does the COVID-19 pandemic mean for the next decade of onchocerciasis control and elimination?", @@ -1140831,37 +1139272,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.22.20184630", - "rel_title": "COVID-19 infections following outdoor mass gatherings in low incidence areas: retrospective cohort study", - "rel_date": "2020-10-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.22.20184630", - "rel_abs": "ObjectiveIndoor mass gatherings in counties with high COVID-19 incidence have been linked to infections. We examined if outdoor mass gatherings in counties with low COVID-19 incidence are also followed by infections.\n\nMethodsWe retrospectively examined COVID-19 incidence in 20 counties that held mass gathering rallies (19 outdoor and 1 indoor) in the United States in August-September 2020. They were compared to the rest of the United States counties. We utilized a 7-day moving average and compared the change on the gathering date and 15 days later, based on the 95% confidence interval. For control counties we used the median of the gathering dates.\n\nSettingThe United States\n\nPopulation8.4 million in the counties holding mass gatherings, and 324 Million in the rest of the counties in the United States.\n\nMain Outcome MeasureChange in COVID-19 incidence rate per 100,000 capita during the two weeks following mass gatherings.\n\nResultsIn the two weeks following the gatherings, the COVID-19 incidence increased significantly in 14 of 20 counties. The county with the highest incidence increase (3.8-fold) had the 2nd lowest incidence before the gathering. The county with the highest decrease (0.4-fold) had the 3rd highest incidence before the gathering. At the gathering date, the average incidence of counties with gatherings was lower than the rest of the United States, and after the gathering, it increased 1.5-fold, while the rest of the United States increased 1.02-fold.\n\nConclusionThese results suggest that even outdoor gatherings in areas with low COVID-19 incidence are followed by increased infections, and that further precautions should be taken at such gatherings.\n\nWhat is already known on the topicMass gatherings have been linked to COVID-19 infections, but it is less clear how much it happens outdoors, and in areas with low incidence.\n\nWhat this study addsCOVID-19 infections increased significantly in 14 of 20 counties that held mass gathering rallies in the United States, 19 of which were outdoors. The county with the highest incidence increase (3.8-fold) was outdoors and had a low incidence before the gathering. The average incidence of all 20 counties with gatherings was lower at the gathering day compared with the rest of the United State, and it increased 1.5-fold following the gatherings. Our findings suggest a need for precautions in mass gatherings, even when outdoors and in areas with a low incidence of COVID-19.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Oren Miron", - "author_inst": "Ben Gurion University" - }, - { - "author_name": "Kun-Hsing Yu", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Rachel Wilf-Miron", - "author_inst": "Tel Aviv University" - }, - { - "author_name": "Nadav Davidovich", - "author_inst": "Ben Gurion University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.26.20219972", "rel_title": "Development of Multiplexed RT-LAMP for Detection of SARS-CoV-2 and Influenza Viral RNA", @@ -1142425,6 +1140835,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "surgery" }, + { + "rel_doi": "10.1101/2020.10.26.20218636", + "rel_title": "Lung transplantation for pulmonary fibrosis secondary to severe COVID-19", + "rel_date": "2020-10-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.26.20218636", + "rel_abs": "Lung transplantation can potentially be a life-saving treatment for patients with non-resolving COVID-19 acute respiratory distress syndrome. Concerns limiting transplant include recurrence of SARS-CoV-2 infection in the allograft, technical challenges imposed by viral-mediated injury to the native lung, and potential risk for allograft infection by pathogens associated with ventilator-induced pneumonia in the native lung. Additionally, the native lung might recover, resulting in long-term outcomes preferable to transplant. Here, we report the results of the first two successful lung transplantation procedures in patients with non-resolving COVID-19 associated acute respiratory distress syndrome in the United States. We performed smFISH to detect both positive and negative strands of SARS-CoV-2 RNA in the explanted lung tissue, extracellular matrix imaging using SHIELD tissue clearance, and single cell RNA-Seq on explant and warm post-mortem lung biopsies from patients who died from severe COVID-19 pneumonia. Lungs from patients with prolonged COVID-19 were free of virus but pathology showed extensive evidence of injury and fibrosis which resembled end-stage pulmonary fibrosis. Single cell RNA-Seq of the explanted native lungs from transplant and paired warm post-mortem autopsies showed similarities between late SARS-CoV-2 acute respiratory distress syndrome and irreversible end-stage pulmonary fibrosis requiring lung transplantation. There was no recurrence of SARS-CoV-2 or pathogens associated with pre-transplant ventilator associated pneumonias following transplantation in either patient. Our findings suggest that some patients with severe COVID-19 develop fibrotic lung disease for which lung transplantation is the only option for survival.\n\nSingle sentence summarySome patients with severe COVID-19 develop end-stage pulmonary fibrosis for which lung transplantation may be the only treatment.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Ankit Bharat", + "author_inst": "Northwestern University" + }, + { + "author_name": "Melissa Querrey", + "author_inst": "Northwestern University" + }, + { + "author_name": "Nikolay S Markov", + "author_inst": "Northwestern University" + }, + { + "author_name": "Samuel S Kim", + "author_inst": "Northwestern University" + }, + { + "author_name": "Chitaru Kurihara", + "author_inst": "Northwestern University" + }, + { + "author_name": "Rafael Garza-Castillon Jr.", + "author_inst": "Northwestern University" + }, + { + "author_name": "Adwaiy Manerikar", + "author_inst": "Northwestern University" + }, + { + "author_name": "Ali Shilatifard", + "author_inst": "Northwestern University" + }, + { + "author_name": "Rade Tomic", + "author_inst": "Northwestern University" + }, + { + "author_name": "Yuliya Politanska", + "author_inst": "Northwestern University" + }, + { + "author_name": "Hiam Abdala-Valencia", + "author_inst": "Northwestern University" + }, + { + "author_name": "Anjana V Yeldandi", + "author_inst": "Northwestern University" + }, + { + "author_name": "Jon W Lomasney", + "author_inst": "Northwestern University" + }, + { + "author_name": "Alexander V Misharin", + "author_inst": "Northwestern University" + }, + { + "author_name": "GR Scott Budinger", + "author_inst": "Northwestern University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "transplantation" + }, { "rel_doi": "10.1101/2020.10.27.20220061", "rel_title": "Decline in mortality among hospitalised covid-19 patients in Sweden: a nationwide observational study", @@ -1142961,49 +1141446,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.10.27.357731", - "rel_title": "SARS-CoV-2 viroporin triggers the NLRP3 inflammatory pathway", - "rel_date": "2020-10-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.27.357731", - "rel_abs": "Cytokine storm resulting from a heightened inflammatory response is a prominent feature of severe COVID-19 disease. This inflammatory response results from assembly/activation of a cell-intrinsic defense platform known as the inflammasome. We report that the SARS-CoV-2 viroporin encoded by ORF3a activates the NLRP3 inflammasome, the most promiscuous of known inflammasomes. ORF3a triggers IL-1{beta} expression via NF{kappa}B, thus priming the inflammasome while also activating it via ASC-dependent and -independent modes. ORF3a-mediated inflammasome activation requires efflux of potassium ions and oligomerization between NEK7 and NLRP3. With the selective NLRP3 inhibitor MCC950 able to block ORF3a-mediated inflammasome activation and key ORF3a residues needed for virus release and inflammasome activation conserved in SARS-CoV-2 isolates across continents, ORF3a and NLRP3 present prime targets for intervention.\n\nSummaryDevelopment of anti-SARS-CoV-2 therapies is aimed predominantly at blocking infection or halting virus replication. Yet, the inflammatory response is a significant contributor towards disease, especially in those severely affected. In a pared-down system, we investigate the influence of ORF3a, an essential SARS-CoV-2 protein, on the inflammatory machinery and find that it activates NLRP3, the most prominent inflammasome by causing potassium loss across the cell membrane. We also define key amino acid residues on ORF3a needed to activate the inflammatory response, and likely to facilitate virus release, and find that they are conserved in virus isolates across continents. These findings reveal ORF3a and NLRP3 to be attractive targets for therapy.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Huanzhou Xu", - "author_inst": "College of Medicine University of Florida" - }, - { - "author_name": "Siddhi A Chitre", - "author_inst": "College of Medicine University of Florida" - }, - { - "author_name": "Ibukun A Akinyemi", - "author_inst": "College of Medicine University of Florida" - }, - { - "author_name": "Julia C Loeb", - "author_inst": "University of Florida" - }, - { - "author_name": "John A Lednicky", - "author_inst": "University of Florida" - }, - { - "author_name": "Michael T McIntosh", - "author_inst": "College of Medicine University of Florida" - }, - { - "author_name": "Sumita Bhaduri-McIntosh", - "author_inst": "College of Medicine University of Florida" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.10.27.357558", "rel_title": "SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility", @@ -1144043,6 +1142485,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pathology" }, + { + "rel_doi": "10.1101/2020.10.26.355784", + "rel_title": "A theoretical analysis of the putative ORF10 protein in SARS-CoV-2", + "rel_date": "2020-10-26", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.26.355784", + "rel_abs": "Upstream of the 3-untranslated region in the SARS-CoV-2 genome is ORF10 which has been proposed to encode for the ORF10 protein. Current research is still unclear on whether this protein is synthesized, but further investigations are still warranted. Herein, this study uses multiple bioinformatic tools to biochemically and functionally characterize the ORF10 protein, along with predicting its tertiary structure. Results indicate a highly ordered, hydrophobic, and thermally stable protein that contains at least one transmembrane region. This protein also possesses high residue protein-binding propensity, primarily in the N-terminal half. An assessment of forty-one missense mutations reveal slight changes in residue flexibility, mainly in the C-terminal half. However, these same mutations do not inflict significant changes on protein stability and other biochemical features. The predicted model suggests the ORF10 protein contains a {beta}--{beta} motif with a {beta}-molecular recognition feature occurring in the first {beta}-strand. Functionally, the ORF10 protein could be a membrane protein. A single pocket was identified in this protein but found to possess low druggability. The ORF10 itself consists of two distinct lineages: the SARS-CoV lineage and the SARS-CoV-2 lineage. Evidence of strong positive selection (dN/dS = 4.01) and purifying selection (dN/dS = 0.713) were found within the SARS-CoV-2 lineage and SARS-CoV lineage, respectively. Collectively, these results continue to assess the biological relevance of ORF10 and its putatively encoded protein, thereby aiding in diagnostic and possibly vaccine development.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Noah Avery Schuster", + "author_inst": "DePauw University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.10.26.355099", "rel_title": "Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome", @@ -1144595,49 +1143056,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.10.23.353219", - "rel_title": "The papain-like protease of coronaviruses cleaves ULK1 to disrupt host autophagy", - "rel_date": "2020-10-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.23.353219", - "rel_abs": "The ongoing pandemic of COVID-19 alongside the outbreaks of SARS in 2003 and MERS in 2012 underscore the significance to understand betacoronaviruses as a global health challenge. SARS-CoV-2, the etiological agent for COVID-19, has infected more than 29 million individuals worldwide with nearly ~1 million fatalities. Understanding how SARS-CoV-2 initiates viral pathogenesis is of the utmost importance for development of antiviral drugs. Autophagy modulators have emerged as potential therapeutic candidates against SARS-CoV-2 but recent clinical setbacks underline the urgent need for better understanding the mechanism of viral subversion of autophagy. Using murine hepatitis virus-A59 (MHV-A59) as a model betacoronavirus, time-course infections revealed a significant loss in the protein level of ULK1, a canonical autophagy regulating serine-threonine kinase, and the concomitant appearance of a possible cleavage fragment. To investigate whether virus-encoded proteases target this protein, we conducted in vitro and cellular cleavage assays and identified ULK1 as a novel bona fide substrate of SARS-CoV-2 papain-like protease (PLpro). Mutagenesis studies discovered that ULK1 is cleaved at a conserved PLpro recognition sequence (LGGG) after G499, separating its N-terminal kinase domain from the C-terminal substrate recognition region. Consistent with this, over-expression of SARS-CoV-2 PLpro is sufficient to impair starvation-induced canonical autophagy and disrupt formation of ULK1-ATG13 complex. Finally, we demonstrated a dual role for ULK1 in MHV-A59 replication, serving a pro-viral functions during early replication that is inactivated at late stages of infection. In conclusion, our study identified a new mechanism by which PLpro of betacoronaviruses induces viral pathogenesis by targeting cellular autophagic pathway (Word count=250)\n\nIMPORTANCEThe recent COVID-19 global pandemic alongside the 2003 SARS and 2012 MERS outbreaks underscore an urgent need to better understand betacoronaviruses as pathogens that pose global challenge to human health. Studying the underlying biology of how betacoronaviruses subvert innate cellular defense pathways such as autophagy will help to guide future efforts to develop anti-viral therapy. (Word count= 55)", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Yasir Mohamud", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Yuan Chao Xue", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Huitao Liu", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Chen Seng Ng", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Amirhossein Bahreyni", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Eric Jan", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Honglin Luo", - "author_inst": "University of British Columbia" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "cell biology" - }, { "rel_doi": "10.1101/2020.10.21.20217117", "rel_title": "Risk Factors Associated with Increased Antibiotic Use in COVID-19 Hospitalized Patients", @@ -1145633,6 +1144051,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.21.20216713", + "rel_title": "COVID-19 adaptive humoral immunity models: non-neutralizing versus antibody-disease enhancement scenarios", + "rel_date": "2020-10-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.21.20216713", + "rel_abs": "The interplay between the virus, infected cells and the immune responses to SARS-CoV-2 is still under debate. Extending the basic model of viral dynamics we propose here a formal approach to describe the neutralizing versus weakly (or non-)neutralizing scenarios and compare with the possible effects of antibody-dependent enhancement (ADE). The theoretical model is consistent with data available from the literature; we show that weakly neutralizing antibodies or ADE can both give rise to either final virus clearance or disease progression, but the immuno-dynamic is different in each case. Given that a significant part of the world population is already naturally immunized or vaccinated, we also discuss the implications on secondary infections infections following vaccination or in presence of immune system dysfunctions.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Antoine Danchin", + "author_inst": "Institut Cochin" + }, + { + "author_name": "Oriane Pagani-Azizi", + "author_inst": "Univerite Paris Dauphine - PSL & ESPCI Paris PSL" + }, + { + "author_name": "Gabriel TURINICI", + "author_inst": "Universite Paris Dauphine - PSL" + }, + { + "author_name": "Ghozlane Yahiaoui", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2020.10.20.20216473", "rel_title": "Mathematical Analysis of COVID-19 Transmission Dynamics. A Case Study with Nigeria", @@ -1145945,85 +1144394,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "hematology" }, - { - "rel_doi": "10.1101/2020.10.21.20216192", - "rel_title": "Broadly-targeted autoreactivity is common in severe SARS-CoV-2 Infection", - "rel_date": "2020-10-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.21.20216192", - "rel_abs": "An emerging feature of COVID-19 is the identification of autoreactivity in patients with severe disease that may contribute to disease pathology, however the origin and resolution of these responses remain unclear. Previously, we identified strong extrafollicular B cell activation as a shared immune response feature between both severe COVID-19 and patients with advanced rheumatic disease. In autoimmune settings, this pathway is associated with relaxed peripheral tolerance in the antibody secreting cell compartment and the generation of de novo autoreactive responses. Investigating these responses in COVID-19, we performed single-cell repertoire analysis on 7 patients with severe disease. In these patients, we identify the expansion of a low-mutation IgG1 fraction of the antibody secreting cell compartment that are not memory derived, display low levels of selective pressure, and are enriched for autoreactivity-prone IGHV4-34 expression. Within this compartment, we identify B cell lineages that display specificity to both SARS-CoV-2 and autoantigens, including pathogenic autoantibodies against glomerular basement membrane, and describe progressive, broad, clinically relevant autoreactivity within these patients correlated with disease severity. Importantly, we identify anti-carbamylated protein responses as a common hallmark and candidate biomarker of broken peripheral tolerance in severe COVID-19. Finally, we identify the contraction of this pathway upon recovery, and re-establishment of tolerance standards coupled with a concomitant loss of acute-derived ASCs irrespective of antigen specificity. In total, this study reveals the origins, breadth, and resolution of acute-phase autoreactivity in severe COVID-19, with significant implications in both early interventions and potential treatment of patients with post-COVID sequelae.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Matthew Woodruff", - "author_inst": "Emory University" - }, - { - "author_name": "Richard P Ramonell", - "author_inst": "Emory University" - }, - { - "author_name": "Ankur Singh Saini", - "author_inst": "Emory University" - }, - { - "author_name": "Natalie S. Haddad", - "author_inst": "Emory University" - }, - { - "author_name": "Fabliha A Anam", - "author_inst": "Emory University" - }, - { - "author_name": "Mark E. Rudolph", - "author_inst": "Exagen, Inc." - }, - { - "author_name": "Regina Bugrovsky", - "author_inst": "Emory University" - }, - { - "author_name": "Jennifer Hom", - "author_inst": "Emory University" - }, - { - "author_name": "Kevin S. Cashman", - "author_inst": "Emory University" - }, - { - "author_name": "Doan C. Nguyen", - "author_inst": "Emory University" - }, - { - "author_name": "Shuya Kyu", - "author_inst": "Emory University" - }, - { - "author_name": "Michael Piazza", - "author_inst": "Nicoya" - }, - { - "author_name": "Christopher M. Tipton", - "author_inst": "Emory University" - }, - { - "author_name": "Scott Jenks", - "author_inst": "Emory University" - }, - { - "author_name": "F. Eun-Hyung Lee", - "author_inst": "Emory University" - }, - { - "author_name": "Ignacio Sanz", - "author_inst": "Emory University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.22.20213207", "rel_title": "Clinical correlations of SARS-CoV-2 antibody responses in patients with COVID-19 infection", @@ -1147231,6 +1145601,109 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.10.23.344085", + "rel_title": "Sterilizing Immunity against SARS-CoV-2 Infection in Mice by a Single-Shot and Modified Imidazoquinoline TLR7/8 Agonist-Adjuvanted Recombinant Spike Protein Vaccine", + "rel_date": "2020-10-23", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.23.344085", + "rel_abs": "The search for vaccines that protect from severe morbidity and mortality as a result of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19) is a race against the clock and the virus. Several vaccine candidates are currently being tested in the clinic. Inactivated virus and recombinant protein vaccines can be safe options but may require adjuvants to induce robust immune responses efficiently. In this work we describe the use of a novel amphiphilic imidazoquinoline (IMDQ-PEG-CHOL) TLR7/8 adjuvant, consisting of an imidazoquinoline conjugated to the chain end of a cholesterol-poly(ethylene glycol) macromolecular amphiphile). This amphiphile is water soluble and exhibits massive translocation to lymph nodes upon local administration, likely through binding to albumin. IMDQ-PEG-CHOL is used to induce a protective immune response against SARS-CoV-2 after single vaccination with trimeric recombinant SARS-CoV-2 spike protein in the BALB/c mouse model. Inclusion of amphiphilic IMDQ-PEG-CHOL in the SARS-CoV-2 spike vaccine formulation resulted in enhanced immune cell recruitment and activation in the draining lymph node. IMDQ-PEG-CHOL has a better safety profile compared to native soluble IMDQ as the former induces a more localized immune response upon local injection, preventing systemic inflammation. Moreover, IMDQ-PEG-CHOL adjuvanted vaccine induced enhanced ELISA and in vitro microneutralization titers, and a more balanced IgG2a/IgG1 response. To correlate vaccine responses with control of virus replication in vivo, vaccinated mice were challenged with SARS-CoV-2 virus after being sensitized by intranasal adenovirus-mediated expression of the human angiotensin converting enzyme 2 (ACE2) gene. Animals vaccinated with trimeric recombinant spike protein vaccine without adjuvant had lung virus titers comparable to non-vaccinated control mice, whereas animals vaccinated with IMDQ-PEG-CHOL-adjuvanted vaccine controlled viral replication and infectious viruses could not be recovered from their lungs at day 4 post infection. In order to test whether IMDQ-PEG-CHOL could also be used to adjuvant vaccines currently licensed for use in humans, proof of concept was also provided by using the same IMDQ-PEG-CHOL to adjuvant human quadrivalent inactivated influenza virus split vaccine, which resulted in enhanced hemagglutination inhibition titers and a more balanced IgG2a/IgG1 antibody response. Enhanced influenza vaccine responses correlated with better virus control when mice were given a lethal influenza virus challenge. Our results underscore the potential use of IMDQ-PEG-CHOL as an adjuvant to achieve protection after single immunization with recombinant protein and inactivated vaccines against respiratory viruses, such as SARS-CoV-2 and influenza viruses.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Sonia Jangra", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Jana De Vrieze", + "author_inst": "Ghent University" + }, + { + "author_name": "Angela Choi", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Raveen Rathnasinghe", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Gabriel Laghlali", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Annemiek Uvyn", + "author_inst": "Ghent University" + }, + { + "author_name": "Simon Van Herck", + "author_inst": "Ghent University" + }, + { + "author_name": "Lutz Nuhn", + "author_inst": "Ghent University" + }, + { + "author_name": "Kim Deswarte", + "author_inst": "Ghent University/VIB Center for Inflammation Research" + }, + { + "author_name": "Zifu Zhong", + "author_inst": "Ghent University" + }, + { + "author_name": "Niek Sanders", + "author_inst": "Ghent University" + }, + { + "author_name": "Stefan Lienenklaus", + "author_inst": "Hannover Medical School" + }, + { + "author_name": "Sunil David", + "author_inst": "Virovax" + }, + { + "author_name": "Shirin Strohmeier", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Fatima Amanat", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Florian Krammer", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Hamida Hammad", + "author_inst": "Ghent University/VIB Center for Inflammation Research" + }, + { + "author_name": "Bart N Lambrecht", + "author_inst": "Ghent University/VIB Center for Inflammation Research/Erasmus Medical Center" + }, + { + "author_name": "Lynda Coughlan", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Adolfo Garcia-Sastre", + "author_inst": "Icahn School of Medicine at Mount Sinai/Global Health and Emerging Pathogens Institute/Tisch Cancer Institute" + }, + { + "author_name": "Bruno G De Geest", + "author_inst": "Ghent University" + }, + { + "author_name": "Michael Schotsaert", + "author_inst": "Icahn School of Medicine at Mount Sinai/Global Health and Emerging Pathogens Institute" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.10.22.343673", "rel_title": "Potential Achilles heels of SARS-CoV-2 displayed by the base order-dependent component of RNA folding energy", @@ -1147651,41 +1146124,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.21.20216945", - "rel_title": "The effect of COVID-19 on critical care research: A prospective longitudinal multinational survey", - "rel_date": "2020-10-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.21.20216945", - "rel_abs": "ImportanceThe COVID-19 pandemic has increased the need for high-quality evidence in critical care, while also increasing the barriers to conducting the research needed to produce such evidence.\n\nObjectiveTo determine the effect of the first wave of the COVID-19 pandemic on critical care clinical research.\n\nDesignMonthly electronic survey (March 2020 - February 2021).\n\nSettingAdult or pediatric intensive care units (ICUs) from any country participating in at least one research study before the COVID-19 pandemic.\n\nParticipantsWe recruited one researcher or research coordinator per center, identified via established research networks.\n\nIntervention(s)None\n\nMain Outcome(s) and Measure(s)Primary: Suspending recruitment in clinical research; Secondary: impact of specific factors on research conduct (5-point scales from no effect to very large effect). We assessed the association between research continuity and month, presence of hospitalized patients with COVID-19, and population (pediatric vs. adult ICU) using mixed-effects logistic regression.\n\nResults127 centers (57% pediatric) from 23 countries participated. 95 (75%) of centers suspended recruitment in at least some studies and 37 (29%) suspended recruitment in all studies on at least one month. The proportion of centers reporting recruitment in all studies increased over time (OR per month 1.3, 95% CI 1.2 to 1.4, p < 0.001), controlling for hospitalized patients with COVID-19 and type of ICU (pediatric vs. other). The five factors most frequently identified as having a large or very large effect on clinical research were: local prioritization of COVID-19 specific research (68, 54%), infection control policies limiting access to patients with COVID-19 (61, 49%), infection control policies limiting access to the ICU (52, 41.6%), increased workload of clinical staff (38, 30%), and safety concerns of research staff (36, 29%).\n\nConclusions and RelevanceDecisions to pause or pursue clinical research varied across centers. Research activity increased over time, despite the presence of hospitalized patients with COVID-19. Guiding principles with local adaptation to safely sustain research during this and future pandemics are urgently needed.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSWhat was the effect of the COVID-19 pandemic on research in 127 adult and pediatric intensive care units (ICUs) between March 2020 and February 2021?\n\nFindings95 (75%) centers suspended recruitment into at least some studies. Active recruitment into studies increased over time (OR per month 1.3, 95% CI 1.2 to 1.4, p < 0.001), controlling for ICU type and the presence of patients with COVID-19.\n\nMeaningResearch activity varied across centers and increased over time, despite the presence of hospitalized patients with COVID-19. Guiding principles to safely sustain research during this and future pandemics are urgently needed.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Mark Duffett", - "author_inst": "McMaster University" - }, - { - "author_name": "Deborah J Cook", - "author_inst": "McMaster University" - }, - { - "author_name": "Geoff Strong", - "author_inst": "McMaster University" - }, - { - "author_name": "Jan Hau Lee", - "author_inst": "KK Women's and Children's Hospital" - }, - { - "author_name": "Michelle E Kho", - "author_inst": "McMaster University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.10.21.20216986", "rel_title": "Simulation and prediction of further spread of COVID-19 in The Republic of Serbia by SEIRDS model of disease transmission", @@ -1148765,6 +1147203,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.20.20214965", + "rel_title": "Innate Immune Response Modulation and Resistance to SARS-CoV-2 infection: A Prospective Comparative Cohort Study in High Risk Healthcare Workers", + "rel_date": "2020-10-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.20.20214965", + "rel_abs": "To evaluate ability of modulated innate immune response to provide resistance to development of symptomatic RT-PCR confirmed COVID-19, 96 inpatient front line health care workers (HCW) were cohorted in 1:2 ratio to receive TLR2 agonist (heat killed Mycobacterium w, Mw; n=32) as innate immune response modulator or observation (n=64). All were followed up for 100 days. The incidence of COVID-19 was 31 (32.3%) for the entire cohort, with only one developing COVID-19 in Mw group (3.1% vs 46.8%. protective efficacy - 93.33%, p=0.0001; 95% CI 53.3-99.1). Self-limiting local injection site reaction was the only side effect and was seen in 14 HCW. Findings from the study suggest the potential for providing resistance against novel pathogen like SARS-CoV-2 by modulating innate immune response.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Dr Sarita Rani Jaiswal", + "author_inst": "Dharamshila Narayana Super-speciality Hospital , New Delhi" + }, + { + "author_name": "Anupama Mehta", + "author_inst": "Dharamshila Narayana Super-speciality Hospital , New Delhi" + }, + { + "author_name": "Dr. Gitali Bhagwati", + "author_inst": "Dharamshila Narayana Super-speciality Hospital , New Delhi" + }, + { + "author_name": "Mr. Rohit Lakhchaura", + "author_inst": "Dharamshila Narayana Super-speciality Hospital , New Delhi" + }, + { + "author_name": "Dr. Hemamalini Aiyer", + "author_inst": "Dharamshila Narayana Super-speciality Hospital , New Delhi" + }, + { + "author_name": "Dr. Bakulesh M Khamar", + "author_inst": "Cadila Pharmaceuticals Limited, Ahmedabad" + }, + { + "author_name": "Dr. Suparno Chakrabarti", + "author_inst": "Manashi Chakrabarti Foundation, New Delhi" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.20.20216127", "rel_title": "Saliva as testing sample for SARS-CoV-2 detection by RT-PCR in low prevalence community setting.", @@ -1149281,45 +1147762,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.20.20212522", - "rel_title": "Analytical solution of equivalent SEIR and agent-based model of COVID-19; showing the bounds of contact tracing", - "rel_date": "2020-10-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.20.20212522", - "rel_abs": "Mathematical models not only forecast the possible future but also is used to find hidden parameters of the COVID-19 pandemic. Numerical estimates can inform us of both goals. Still, the interdependencies of parameters stay obscure. Many numerical solutions have been proposed so far; however, the analytical relationship between the outbreak growth, decay and equilibrium are much less studied. In this study, we have employed both an equivalent agent-based model and a Susceptible-Exposed-Infected-Recovered (SEIR)-like model to prove that the growth rate can be determined analytically in terms of other model parameters, including contact tracing rate. We identify the most sensitive parameters as undocumented transmission rate and documentation ratio. Unfortunately, these are the parameters we have the least knowledge. We derived an identity that predicts the effectiveness of contact tracing in a country from observable parameters. We underline an unavoidable dilemma: that even in the case of high contact tracing, we cannot bring the outbreak to stalemate without applying substantial quarantine; however, some countries are benefiting from contact tracing. Besides, we have shown that the seemingly same parameters of the SEIR models and agent-based models are not equivalent. We propose a correction to bridge both models.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Huseyin Tunc", - "author_inst": "Yildiz Technical University, Department of Mathematics" - }, - { - "author_name": "Fatma Zehra Sari", - "author_inst": "Gebze Technical University, Institute of Biotechnology" - }, - { - "author_name": "Busra Darendeli", - "author_inst": "Yildiz Technical University, Department of Bioengineering" - }, - { - "author_name": "Ramin Nashebi", - "author_inst": "Yildiz Technical University, Department of Mathematics" - }, - { - "author_name": "Murat Sari", - "author_inst": "Yildiz Technical University, Department of Mathematics" - }, - { - "author_name": "Seyfullah Enes Kotil", - "author_inst": "Bahcesehir University Medical School, Department of Medicinal Microbiology" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.20.20215756", "rel_title": "Changes of evening exposure to electronic devices during the COVID-19 lockdown affect the time course of sleep disturbances", @@ -1150502,6 +1148944,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.19.20181057", + "rel_title": "Efficacy of stay-at-home policy and transmission of COVID-19 in Toronto, Canada: a mathematical modeling study", + "rel_date": "2020-10-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.19.20181057", + "rel_abs": "BackgroundIn many parts of the world, restrictive non-pharmaceutical interventions (NPI) that aim to reduce contact rates, including stay-at-home orders, limitations on gatherings, and closure of public places, are being lifted, with the possibility that the epidemic resurges if alternative measures are not strong enough. Here we aim to capture the combination of use of NPIs and reopening measures which will prevent an infection rebound.\n\nMethodsWe employ an SEAIR model with household structure able to capture the stay-at-home policy (SAHP). To reflect the changes in the SAHP over the course of the epidemic, we vary the SAHP compliance rate, assuming that the time to compliance of all the people requested to stay-at-home follows a Gamma distribution. Using confirmed case data for the City of Toronto, we evaluate basic and instantaneous reproduction numbers and simulate how the average household size, the stay-at-home rate, the efficiency and duration of SAHP implementation, affect the outbreak trajectory.\n\nFindingsThe estimated basic reproduction number R_0 was 2.36 (95% CI: 2.28, 2.45) in Toronto. After the implementation of the SAHP, the contact rate outside the household fell by 39%. When people properly respect the SAHP, the outbreak can be quickly controlled, but extending its duration beyond two months (65 days) had little effect. Our findings also suggest that to avoid a large rebound of the epidemic, the average number of contacts per person per day should be kept below nine. This study suggests that fully reopening schools, offices, and other activities, is possible if the use of other NPIs is strictly adhered to.\n\nInterpretationOur model confirmed that the SAHP implemented in Toronto had a great impact in controlling the spread of COVID-19. Given the lifting of restrictive NPIs, we estimated the thresholds values of maximum number of contacts, probability of transmission and testing needed to ensure that the reopening will be safe, i.e. maintaining an Rt < 1.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSA survey on published articles was made through PubMed and Google Scholar searches. The search was conducted from March 1 to August 13, 2020 and all papers published until the end of this research were considered. The following terms were used to screen articles on mathematical models: \"household structure\", \"epidemic model\", \"SARS-CoV-2\", \"COVID-19\", \"household SIR epidemic\", \"household SIS epidemic\", \"household SEIR epidemic\", \"quarantine, isolation model\", \"quarantine model dynamics\", \"structured model isolation\". Any article showing, in the title, application of epidemic models in a specific country/region or infectious diseases rather than SARS-CoV-2 were excluded. Articles in English were considered.\n\nAdded value of this studyWe develop an epidemic model with household structure to study the effects of SAHP on the infection within households and transmission of COVID-19 in Toronto. The complex model provides interesting insights into the effectiveness of SAHP, if the average number of individuals in a household changes. We found that the SAHP might not be adequate if the size of households is relatively large. We also introduce a new quantity called symptomatic diagnosis completion ratio (d_c). This indicator is defined as the ratio of cumulative reported cases and the cumulative cases by episode date at time t, and it is used in the model to inform the implementation of SAHP.\n\nIf cases are diagnosed at the time of symptom onset, isolation will be enforced immediately. A delay in detecting cases will lead to a delay in isolation, with subsequent increase in the transmission of the infection. Comparing different scenarios (before and after reopening phases), we were able to identify thresholds of these factors which mainly affect the spread of the infection: the number of daily tests, average number of contacts per individual, and probability of transmission of the virus. Our results show that if any of the three above mentioned factors is reduced, then the other two need to be adjusted to keep a reproduction number below 1. Lifting restrictive closures will require the average number of contacts a person has each day to be less than pre-COVID-19, and a high rate of case detection and tracing of contacts. The thresholds found will inform public health decisions on reopening.\n\nImplications of all the available evidenceOur findings provide important information for policymakers when planning the full reopening phase. Our results confirm that prompt implementation of SAHP was crucial in reducing the spread of COVID-19. Also, based on our analyses, we propose public health alternatives to consider in view of a full reopening. For example, for different post-reopening scenarios, the average number of contacts per person needs to be reduced if the symptomatic diagnosis completion ratio is low and the probability of transmission increases. Namely, if fewer tests are completed and the usage of NPIs decreases, then the epidemic can be controlled only if individuals can maintain contact with a maximum average number of 4-5 people per person per day. Different recommendations can be provided by relaxing/strengthening one of the above-mentioned factors.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Pei Yuan", + "author_inst": "York University" + }, + { + "author_name": "Juan Li", + "author_inst": "Shanxi University" + }, + { + "author_name": "Elena Aruffo", + "author_inst": "York University" + }, + { + "author_name": "Qi Li", + "author_inst": "Shanghai Normal University" + }, + { + "author_name": "Tingting Zheng", + "author_inst": "Xingjiang University" + }, + { + "author_name": "Nicholas Ogden", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Beate Sander", + "author_inst": "University Health Network" + }, + { + "author_name": "Jane Heffernan", + "author_inst": "York University" + }, + { + "author_name": "Evgenia Gatov", + "author_inst": "Toronto Public Health" + }, + { + "author_name": "Effie Gournis", + "author_inst": "Toronto Public Health" + }, + { + "author_name": "Sarah Collier", + "author_inst": "Toronto Public Health" + }, + { + "author_name": "Yi Tan", + "author_inst": "York University" + }, + { + "author_name": "Jun Li", + "author_inst": "Xidian University" + }, + { + "author_name": "Julien Arino", + "author_inst": "University of Manitoba" + }, + { + "author_name": "Jacques Belair", + "author_inst": "University of Montreal" + }, + { + "author_name": "James Watmough", + "author_inst": "University of New Brunswick Fredericton" + }, + { + "author_name": "Jude Dzevela Kong", + "author_inst": "York University" + }, + { + "author_name": "Iain Moyles", + "author_inst": "York University" + }, + { + "author_name": "Huaiping Zhu", + "author_inst": "York University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.19.20214916", "rel_title": "From multiplex serology to serolomics: A novel approach to the antibody response against the SARS-CoV-2 proteome", @@ -1150834,25 +1149367,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.15.20213223", - "rel_title": "Prediction of Covid-19 Infections Through December 2020 for 10 US States Incorporating Outdoor Temperature and School Re-Opening Effects-September Update", - "rel_date": "2020-10-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.15.20213223", - "rel_abs": "A two-parameter, human behavior Covid-19 infection growth model predicts total infections between-4.2% (overprediction) and 4.5% (underprediction) of actual infections from July 27, 2020 to September 30, 2020 for 10 US States (NY, WA, GA, IL, MN, FL, OH, MI, CA, NC). During that time, total Covid-19 infections for 9 of the 10 modeled US States grew by 60% (MI) to 95% (MN). Only NY limited Covid-19 infection growth with an 11% increase from July 27 to September 30, 2020.\n\nSeptember is a month with contraposing effects of increased social interaction (eg, physical school openings) and outdoor temperatures decreasing to the 50F (10C) to 70F (21C) range in which outdoor activities and building ventilation are beneficially increased. All State infection predictions except GA, FL and CA predictions through September 30 are bounded by four prediction scenarios (no school with outdoor temperature effect, no school with no outdoor temperature effect, school with temperature effect, school with no temperature effect). GA, FL and CA continued along a path slightly below the linear infection growth boundary separating infection growth and decay, resulting in overprediction of infection growth over the two month simulation period(-3.1% for GA, -1.9% for FL, and -4.5% for CA).\n\nThree eastern States (NY, NC, and GA) are most accurately represented by models that assume no significant change in social interactions coupled with minor outdoor temperature effects. Four midwestern States (IL, MI, MN, OH) are most accurately modeled with minor outdoor temperature effects due to a delayed decrease in average outdoor temperatures in the Midwest. The remaining three States (WA, FL, and CA) are also in good agreement with the model but with differing weather condition and social interaction impacts.\n\nOverall, model predictions continue to support the basic premise that human behavior in the US oscillates across a linear infection growth boundary that divides accelerated infection growth and decaying infection transmission.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Ty A Newell", - "author_inst": "University of Illinois" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.14.20212829", "rel_title": "Characteristics and evolution of COVID-19 cases in Brazil: mathematical modeling and simulation", @@ -1152152,6 +1150666,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.10.16.20213769", + "rel_title": "Impact of the COVID-19 pandemic on Suicide and Self Harm among Patients Presenting to the Emergency Department of a Teaching Hospital in Nepal", + "rel_date": "2020-10-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.16.20213769", + "rel_abs": "BackgroundThe COVID-19 pandemic is a global challenge that is not just limited to the physical consequences but also a significant degree of a mental health crisis. Self-harm (SH) and suicide are its extreme effects. The aim of this study was to provide an overview of the impact of the COVID-19 pandemic on the occurrence and clinical profile of suicide and SH in our ED.\n\nMethodsThis is a cross-sectional observational study conducted in the ED of a tertiary care center. Records of all fatal and nonfatal SH patients presenting to the ED during the lockdown period (March 24-June 23, 2020; Period1), matching periods in the previous year (March 24-June 23,2019; Period 2) and 3 months period prior (December 24 2019-March 23, 2020; Period 3) was included by searching the electronic medical record (EMR) system. The prevalence and the clinical profile of the patients were compared between these three periods.\n\nResultsA total of 125 (periods 1=55, 2=38, and 3=32) suicide and SH cases were analyzed. The cases of suicide/SH had increased by 44% and 71.9% during the lockdown period in comparison to the period 2 and 3. Organophosphate poisoning was the most common mode. Females were predominant in all three periods with a mean age of 32 (95%CI: 29.3-34.7). There was a significant delay in arrival of the patients in period 1 (p-value=0.045) with increased hospital admission (p-value =0.009) and in-hospital mortality (18.2% vs 2.6 % and 3.1%) (p-value=.001).\n\nConclusionWe found an increase in patients presenting with suicide and SH in our ED during the pandemic which is likely to reflect an increased prevalence of mental illness in the community. We hope that the result will prime all mental health care stakeholders to initiate mental health screening and intervention for the vulnerable population during this period of crisis.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Roshana Shrestha", + "author_inst": "Kathmandu University School of Medical Sciences" + }, + { + "author_name": "Shisir Siwakoti", + "author_inst": "Kathmandu University School of Medical Sciences" + }, + { + "author_name": "Saumya Singh", + "author_inst": "Kathmandu University School of Medical Sciences" + }, + { + "author_name": "Anmol Purna Shrestha", + "author_inst": "Kathmandu University School of Medical Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2020.10.18.20214767", "rel_title": "Guiding Austria through the COVID-19 Epidemics with a Forecast-Based Early Warning System", @@ -1152576,33 +1151121,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.16.20214049", - "rel_title": "Quantifying Asymptomatic Infection and Transmission of COVID-19 in New York City using Observed Cases, Serology and Testing Capacity", - "rel_date": "2020-10-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.16.20214049", - "rel_abs": "The contributions of asymptomatic infections to herd immunity and community transmission are key to the resurgence and control of COVID-19, but are difficult to estimate using current models that ignore changes in testing capacity. Using a model that incorporates daily testing information fit to the case and serology data from New York City, we show that the proportion of symptomatic cases is low, ranging from 13% to 18%, and that the reproductive number may be larger than often assumed. Asymptomatic infections contribute substantially to herd immunity, and to community transmission together with pre-symptomatic ones. If asymptomatic infections transmit at similar rates than symptomatic ones, the overall reproductive number across all classes is larger than often assumed, with estimates ranging from 3.2 to 4.4. If they transmit poorly, then symptomatic cases have a larger reproductive number ranging from 3.9 to 8.1. Even in this regime, pre-symptomatic and asymptomatic cases together comprise at least 50% of the force of infection at the outbreak peak. We find no regimes in which all infection sub-populations have reproductive numbers lower than 3. These findings elucidate the uncertainty that current case and serology data cannot resolve, despite consideration of different model structures. They also emphasize how temporal data on testing can reduce and better define this uncertainty, as we move forward through longer surveillance and second epidemic waves. Complementary information is required to determine the transmissibility of asymptomatic cases, which we discuss. Regardless, current assumptions about the basic reproductive number of SARS-Cov-2 should be reconsidered.\n\nSignificance StatementAs health officials face another wave of COVID-19, they require estimates of the proportion of infected cases that develop symptoms, and the extent to which symptomatic and asymptomatic cases contribute to community transmission. Recent asymptomatic testing guidelines are ambiguous. Using an epidemiological model that includes testing capacity, we show that most infections are asymptomatic but contribute substantially to community transmission in the aggregate. Their individual transmissibility remains uncertain. If they transmit as well as symptomatic infections, the epidemic may spread at faster rates than current models often assume. If they do not, then each symptomatic case generates on average a higher number of secondary infections than typically assumed. Regardless, controlling transmission requires community-wide interventions informed by extensive, well-documented asymptomatic testing.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Rahul Subramanian", - "author_inst": "University of Chicago" - }, - { - "author_name": "Qixin He", - "author_inst": "University of Chicago" - }, - { - "author_name": "Mercedes Pascual", - "author_inst": "University of Chicago" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.18.20214411", "rel_title": "Monitoring for outbreak associated excess mortality in an African city: Detection limits in Antananarivo, Madagascar", @@ -1153542,6 +1152060,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.10.18.20214601", + "rel_title": "The Response of Pakistani Social Workers amid the COVID-19 Pandemic: A Qualitative Analysis of the Main Challenges", + "rel_date": "2020-10-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.18.20214601", + "rel_abs": "The study aimed to highlight the main challenges faced by the social workers amid the pandemic. A qualitative study was conducted between March 2020 to May 2020 in Karachi, Pakistan. All participants who belonged to a non-profit organization were eligible to participate. Open-ended questions were asked by the participants. The mean age of the participants was 24.8 {+/-} 5.9 years. The main challenges faced by the social workers were: i) resistance from the family and friends, ii) lack of personal protective equipment, iii) mistrust from public, iv) uncooperative government/authorities.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Kiran Abbas", + "author_inst": "Jinnah Postgraduate Medical Centre" + }, + { + "author_name": "Muhammad Inam UlHaq", + "author_inst": "Shifa College of Medicine" + }, + { + "author_name": "Wareesha Afaq Zaidi", + "author_inst": "Shifa College of Medicine" + }, + { + "author_name": "Ahmed Kaleem", + "author_inst": "Shifa College of Medicine" + }, + { + "author_name": "Hamza Sohail", + "author_inst": "Jinnah Sindh Medical University" + }, + { + "author_name": "Moiz Ahmed", + "author_inst": "Jinnah Postgraduate Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.10.20.346262", "rel_title": "Zebrafish studies on the vaccine candidate to COVID-19, the Spike protein: Production of antibody and adverse reaction", @@ -1154194,141 +1152751,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.17.343863", - "rel_title": "Development and pre-clinical characterization of two therapeutic equine formulations towards SARS-CoV-2 proteins for the potential treatment of COVID-19", - "rel_date": "2020-10-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.17.343863", - "rel_abs": "In the current global emergency due to SARS-CoV-2 outbreak, passive immunotherapy emerges as a promising treatment for COVID-19. Among animal-derived products, equine formulations are still the cornerstone therapy for treating envenomations due to animal bites and stings. Therefore, drawing upon decades of experience in manufacturing snake antivenom, we developed and preclinically evaluated two anti-SARS-CoV-2 polyclonal equine formulations as potential alternative therapy for COVID-19. We immunized two groups of horses with either S1 (anti-S1) or a mixture of S1, N, and SEM mosaic (anti-Mix) viral recombinant proteins. Horses reached a maximum anti-viral antibody level at 7 weeks following priming, and showed no major adverse acute or chronic clinical alterations. Two whole-IgG formulations were prepared via hyperimmune plasma precipitation with caprylic acid and then formulated for parenteral use. Both preparations had similar physicochemical and microbiological quality and showed ELISA immunoreactivity towards S1 protein and the receptor binding domain (RBD). The anti-Mix formulation also presented immunoreactivity against N protein. Due to high anti-S1 and anti-RBD antibody content, final products exhibited high in vitro neutralizing capacity of SARS-CoV-2 infection, 80 times higher than a pool of human convalescent plasma. Pre-clinical quality profiles were similar among both products, but clinical efficacy and safety must be tested in clinical trials. The technological strategy we describe here can be adapted by other producers, particularly in low- and middle-income countries.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "Guillermo Le\u00f3n", - "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" - }, - { - "author_name": "Mar\u00eda Herrera", - "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" - }, - { - "author_name": "Mari\u00e1ngela Vargas", - "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" - }, - { - "author_name": "Mauricio Arguedas", - "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" - }, - { - "author_name": "Andr\u00e9s S\u00e1nchez", - "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" - }, - { - "author_name": "\u00c1lvaro Segura", - "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" - }, - { - "author_name": "Aar\u00f3n G\u00f3mez", - "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" - }, - { - "author_name": "Gabriela Solano", - "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" - }, - { - "author_name": "Eugenia Corrales-Aguilar", - "author_inst": "Virology-CIET (Research Center for Tropical Diseases), Facultad de Microbiolog\u00eda, Universidad de Costa Rica" - }, - { - "author_name": "Kenneth Risner", - "author_inst": "National Center for Biodefense and Infectious Diseases, George Mason University" - }, - { - "author_name": "Aarthi Narayanan", - "author_inst": "National Center for Biodefense and Infectious Diseases, George Mason University" - }, - { - "author_name": "Charles Bailey", - "author_inst": "National Center for Biodefense and Infectious Diseases, George Mason University" - }, - { - "author_name": "Mauren Villalta", - "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" - }, - { - "author_name": "Andr\u00e9s Hern\u00e1ndez", - "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" - }, - { - "author_name": "Adriana S\u00e1nchez", - "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" - }, - { - "author_name": "Daniel Cordero", - "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" - }, - { - "author_name": "Daniela Solano", - "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" - }, - { - "author_name": "Gina Dur\u00e1n", - "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" - }, - { - "author_name": "Eduardo Segura", - "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" - }, - { - "author_name": "Maykel Cerdas", - "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" - }, - { - "author_name": "Deibid Uma\u00f1a", - "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" - }, - { - "author_name": "Edwin Moscoso", - "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" - }, - { - "author_name": "Ricardo Estrada", - "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" - }, - { - "author_name": "Jairo Guti\u00e9rrez", - "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" - }, - { - "author_name": "Marcos M\u00e9ndez", - "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" - }, - { - "author_name": "Ana Cecilia Castillo", - "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" - }, - { - "author_name": "Laura S\u00e1nchez", - "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" - }, - { - "author_name": "Jos\u00e9 Mar\u00eda Guti\u00e9rrez", - "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" - }, - { - "author_name": "Cecilia D\u00edaz", - "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" - }, - { - "author_name": "Alberto Alape", - "author_inst": "Instituto Clodomiro Picado, Facultad de Microbiolog\u00eda, Universidad de Costa Rica" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.10.19.344713", "rel_title": "A novel viral protein translation mechanism reveals mitochondria as a target for antiviral drug development", @@ -1155360,6 +1153782,20 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.10.16.20213967", + "rel_title": "National Routine Adult Immunization Programs among World Health Organization Member States: An Assessment of Health Systems to Deploy Future SARS-CoV-2 Vaccines", + "rel_date": "2020-10-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.16.20213967", + "rel_abs": "IntroductionAs the SARS-CoV-2 pandemic disproportionately affects older adults, future pandemic vaccine response will rely on existing adult immunization infrastructures.\n\nMethodsWe evaluated the 2018 WHO/UNICEF Joint Reporting Form on Immunization for country reports on adult immunization programs. We described countries with programs and used multivariable regression to identify independent factors associated with having them.\n\nResultsOf 194 WHO Member States, 120 (62%) reported having any adult vaccination program. The Americas and Europe had the most adult immunization programs, most commonly Hepatitis B and influenza vaccines (>45% and >90% of countries). Africa and South-East Asia had the fewest adult immunization programs, with <11% of countries reporting any adult immunization programs for influenza or hepatitis vaccines, and none for pneumococcal vaccines. In bivariate analyses, high- or upper-middle income, introduction of new or underused vaccines, having achieved pediatric vaccine coverage goals, and meeting National Immunization Technical Advisory Groups basic functional indicators were significantly associated (p<0.001) with having any adult immunization programs. In multivariable analyses, the factor most strongly associated with adult immunization programs was country income, with high- or upper-middle income countries significantly more likely to report having a program (aOR 19.3, 95% CI 6.5, 57.7).\n\nDiscussionThat 38% of countries lack functional platforms for adult immunization has major implications for future SARS-CoV-2 vaccine deployment. Systems for vaccine storage and handling, delivery, and waste management for adult immunization do not exist in much of the world. Developing countries should strengthen immunization programs to reach adults with SARS-CoV-2 vaccines when they become available.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.10.16.20211029", "rel_title": "Three-month outcomes in hospitalized COVID-19 patients", @@ -1155764,157 +1154200,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.10.20207449", - "rel_title": "Recovery of monocyte exhaustion is associated with resolution of lung injury in COVID-19 convalescence.", - "rel_date": "2020-10-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.10.20207449", - "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection resulting in the clinical syndrome COVID-19 is associated with an exaggerated immune response and monocyte infiltrates in the lungs and other peripheral tissues. It is now increasingly recognised that chronic morbidity persists in some patients. We recently demonstrated profound alterations of monocytes in hospitalised COVID-19 patients. It is currently unclear whether these abnormalities resolve or progress following patient discharge. We show here that blood monocytes in convalescent patients at their 12 week follow up, have a greater propensity to produce pro-inflammatory cytokines TNF and IL-6, which was consistently higher in patients with resolution of lung injury as indicated by a normal chest X-ray and no shortness of breath (a key symptom of lung injury). Furthermore, monocytes from convalescent patients also displayed enhanced levels of molecules involved in leucocyte migration, including chemokine receptor CXCR6, adhesion molecule CD31/PECAM and integrins VLA-4 and LFA-1. Expression of migration molecules on monocytes was also consistently higher in convalescent patients with a normal chest X-ray. These data suggest persistent changes in innate immune function following recovery from COVID-19 and indicate that immune modulating therapies targeting monocytes and leucocyte migration may be useful in recovering COVID-19 patients with persistent symptoms.", - "rel_num_authors": 34, - "rel_authors": [ - { - "author_name": "Nicholas A Scott", - "author_inst": "Lydia Becker Institute of Immunology and Inflammation, University of Manchester" - }, - { - "author_name": "Sean Blandin Knight", - "author_inst": "Lydia Becker Institute of Immunology and Inflammation, University of Manchester" - }, - { - "author_name": "Laurence Pearmain", - "author_inst": "North West Lung Centre, Wythenshawe Hospital, Manchester University NHS Foundation Trust" - }, - { - "author_name": "Oliver Brand", - "author_inst": "Lydia Becker Institute of Immunology and Inflammation, University of Manchester" - }, - { - "author_name": "David J Morgan", - "author_inst": "Lydia Becker Institute of Immunology and Inflammation, University of Manchester" - }, - { - "author_name": "Chris Jagger", - "author_inst": "Lydia Becker Institute of Immunology and Inflammation, University of Manchester" - }, - { - "author_name": "Saba Khan", - "author_inst": "Lydia Becker Institute of Immunology and Inflammation, University of Manchester" - }, - { - "author_name": "Pamela Hackney", - "author_inst": "Research Innovation, Manchester University NHS Foundation Trust" - }, - { - "author_name": "Lara Smith", - "author_inst": "Research Innovation, Manchester University NHS Foundation Trust" - }, - { - "author_name": "Madhvi Menon", - "author_inst": "Lydia Becker Institute of Immunology and Inflammation, University of Manchester" - }, - { - "author_name": "Joanne Konkel", - "author_inst": "Lydia Becker Institute of Immunology and Inflammation, University of Manchester" - }, - { - "author_name": "Halima A Shuwa", - "author_inst": "Lydia Becker Institute of Immunology and Inflammation, University of Manchester" - }, - { - "author_name": "Miriam Franklin", - "author_inst": "Lydia Becker Institute of Immunology and Inflammation, University of Manchester" - }, - { - "author_name": "Verena Kaestele", - "author_inst": "Lydia Becker Institute of Immunology and Inflammation, University of Manchester" - }, - { - "author_name": "Sarah Harbach", - "author_inst": "Lydia Becker Institute of Immunology and Inflammation, University of Manchester" - }, - { - "author_name": "Seema Brij", - "author_inst": "Department of Respiratory Medicine, Manchester Royal Infirmary, Manchester University NHS Foundation Trust" - }, - { - "author_name": "Andrew Ustianowski", - "author_inst": "Regional Infectious Diseases Unit, North Manchester General Hospital, Manchester" - }, - { - "author_name": "Alison Uriel", - "author_inst": "Regional Infectious Diseases Unit, North Manchester General Hospital, Manchester" - }, - { - "author_name": "Gabriella Lindergard", - "author_inst": "Regional Infectious Diseases Unit, North Manchester General Hospital, Manchester" - }, - { - "author_name": "Nawar Diar Bakerly", - "author_inst": "Department of Respiratory Medicine, Salford Royal NHS Foundation Trust, Manchester" - }, - { - "author_name": "Paul Dark", - "author_inst": "Division of Infection, Immunity and Respiratory Medicine, NIHR Manchester Biomedical Research Centre, University of Manchester, Education and Research Centre, W" - }, - { - "author_name": "Alexander Mathioudakis", - "author_inst": "Division of Infection, Immunity and Respiratory Medicine, NIHR Manchester Biomedical Research Centre, University of Manchester, Education and Research Centre, W" - }, - { - "author_name": "Kathryn Gray", - "author_inst": "Lydia Becker Institute of Immunology and Inflammation, University of Manchester" - }, - { - "author_name": "Graham Lord", - "author_inst": "Lydia Becker Institute of Immunology and Inflammation, University of Manchester" - }, - { - "author_name": "Timothy Felton", - "author_inst": "Division of Infection, Immunity and Respiratory Medicine, Manchester NIHR BRC, Education and Research Centre, Wythenshawe Hospital, Manchester" - }, - { - "author_name": "Chris Brightling", - "author_inst": "Department of Respiratory Sciences, Leicester NIHR BRC, University of Leicester" - }, - { - "author_name": "Ling-Pei Ho", - "author_inst": "MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford" - }, - { - "author_name": "- NIHR Respiratory TRC", - "author_inst": "-" - }, - { - "author_name": "- CIRCO", - "author_inst": "-" - }, - { - "author_name": "Karen Piper Hanley", - "author_inst": "Division of Diabetes, Endocrinology and Gastroenterology, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science " - }, - { - "author_name": "Angela Simpson", - "author_inst": "Division of Infection, Immunity and Respiratory Medicine, Manchester NIHR BRC, Education and Research Centre, Wythenshawe Hospital, Manchester" - }, - { - "author_name": "John R Grainger", - "author_inst": "Lydia Becker Institute of Immunology and Inflammation, University of Manchester" - }, - { - "author_name": "Tracy Hussell", - "author_inst": "Lydia Becker Institute of Immunology and Inflammation, University of Manchester" - }, - { - "author_name": "Elizabeth R Mann", - "author_inst": "Lydia Becker Institute of Immunology and Inflammation, University of Manchester" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.13.20182949", "rel_title": "sMAdCAM:IL-6 (sMIL Index): A novel signature associated with COVID-19 disease progression and development of anti-SARS-CoV-2 antibodies", @@ -1157194,6 +1155479,45 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.10.16.342428", + "rel_title": "The Theory and Practice of the viral dose in neutralization assay: insights on SARS-CoV-2 \"doublethink\" effect.", + "rel_date": "2020-10-16", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.16.342428", + "rel_abs": "Due to the global spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there is an urgent need for reliable high-throughput serological assays in order to evaluate the immunological responses against SARS-COV-2 virus and to enable population screening, as well as vaccines and drugs efficacy testing. Several serological assays for SARS-CoV-2 are now becoming available in the market. However, it has also become extremely important to have well-established assays with desirable high sensitivity and specificity. To date, the micro-neutralization (MN) assay, is currently considered the gold-standard being capable of evaluating and detecting, functional neutralizing antibodies (nAbs). Several protocols exist for microneutralization assays which vary in several steps of the protocol: cell seeding conditions, number of cells seeded, virus amount used in the infection step, virus-serum-cells incubation period etc. These potential differences account for a high degree of variability and inconsistency of the results and using a harmonized protocol for the micro-neutralization assay could potentially solve this.\n\nGiven this situation, the main aim of our study was to carry out SARS-CoV-2 wild type virus MN assay in order to investigate which optimal tissue culture infective dose 50 (TCID50) infective dose in use is the most adequate choice for implementation in terms of reproducibility, standardization possibilities and comparability of results. Therefore, we assessed the MN by using two different viral infective doses: a standard dose of 100 TCID50/well and a lower dose of 25 TCID50/well. The results obtained, yielded by MN on using the lower infective dose (25 TCID50), were in line with those obtained with the standard infective dose; in some cases, however, we detected a titre that was one or two dilution steps higher, which maintained all negative samples negative. This suggesting that the lower dose can potentially have a positive impact on the detection and estimation of neutralizing antibodies present in a given sample, showing higher sensitivity but similar specificity and therefore, it would require a more accurate assessment and cross-laboratories standardisation especially when MN is employed as serological assay of choice for pre-clinical and clinical studies.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Eleonora Molesti", + "author_inst": "Vismederi Research s.r.l." + }, + { + "author_name": "Alessandro Manenti", + "author_inst": "Vismederi s.r.l. and Vismederi Research s.r.l." + }, + { + "author_name": "Marta Maggetti", + "author_inst": "Vismederi s.r.l." + }, + { + "author_name": "Giulia Lapini", + "author_inst": "Vismederi s.r.l." + }, + { + "author_name": "Alessandro Torelli", + "author_inst": "Vismederi s.r.l." + }, + { + "author_name": "Emanuele Montomoli", + "author_inst": "Vismederi s.r.l. and Universita degli Studi di Siena" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "confirmatory results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.10.16.341883", "rel_title": "The effect of temperature and humidity on the stability of SARS-CoV-2 and other enveloped viruses", @@ -1157610,37 +1155934,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.13.20211284", - "rel_title": "Stay-at-home policy: is it a case of exception fallacy? An internet-based ecological study", - "rel_date": "2020-10-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.13.20211284", - "rel_abs": "BackgroundCountries with strict lockdown had a spike on the number of deaths. A recent mathematical model has suggested that staying at home did not play a dominant role in reducing COVID-19 transmission. Comparison between number of deaths and social mobility is difficult due to the non-stationary nature of the COVID-19 data.\n\nObjectiveTo propose a novel approach to assess the association between staying at home values and the reduction/increase in the number of deaths due to COVID-19 in several regions around the world.\n\nMethodsIn this ecological study, data from www.google.com/covid19/mobility/, ourworldindata.org and covid.saude.gov.br were combined. Countries with >100 deaths and with a Healthcare Access and Quality Index of [≥]67 were included. Data were preprocessed and analyzed using the difference between number of deaths/million between 2 regions and the difference between the percentage of staying at home. Analysis was performed using linear regression and residual analysis\n\nResultsAfter preprocessing the data, 87 regions around the world were included, yielding 3,741 pairwise comparisons for linear regression analysis. Only 63 (1.6%) comparisons were significant.\n\nDiscussionWith our results, we were not able to explain if COVID-19 mortality is reduced by staying as home in [~]98% of the comparisons after epidemiological weeks 9 to 34.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Ricardo F Savaris", - "author_inst": "Universidade Federal do Rio Grande do Sul" - }, - { - "author_name": "Guilherme Pumi", - "author_inst": "Universidade Federal do Rio Grande do Sul" - }, - { - "author_name": "Jovani Dalzochio", - "author_inst": "University of Vale do Rio dos Sinos (UNISINOS)" - }, - { - "author_name": "Rafael Kunst", - "author_inst": "University of Vale do Rio dos Sinos (UNISINOS)" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.14.20210815", "rel_title": "Sociodemographic correlates of access to sanitary pads among college students in Lucknow during COVID 19 lockdown", @@ -1158740,6 +1157033,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.10.11.20210906", + "rel_title": "High Food Insecurity in Latinx Families and Associated COVID-19 Infection in the Greater Bay Area, California", + "rel_date": "2020-10-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.11.20210906", + "rel_abs": "BackgroundFood insecurity impacts nearly one-in-four Latinx households in the United States and has been exacerbated by the novel coronavirus or COVID-19 pandemic.\n\nMethodsWe examined the impact of COVID-19 on household and child food security in three preexisting, longitudinal, Latinx urban cohorts in the San Francisco Bay Area (N=375 households, 1,875 individuals). Households were initially recruited during pregnancy and postpartum at Zuckerberg San Francisco General Hospital (ZSFG) and UCSF Benioff prior to the COVID-19 pandemic. For this COVID sub-study, participants responded to a 15-minute telephonic interview. Participants answered 18 questions from the US Food Security Food Module (US HFSSM), described food consumption, housing and employment status, and history of COVID-19 infection as per community or hospital-based testing. Food security and insecurity levels were compared with prior year metrics.\n\nResultsWe found low levels of household food security in Latinx families (by cohort: 29.2%; 34.2%; 60.0%) and child food security (56.9%; 54.1%; 78.0%) with differences between cohorts explained by self-reported levels of education and employment status. Food security levels were much lower than those reported previously in two cohorts where data had been recorded from prior years. Reported history of COVID-19 infection in households was 4.8% (95% Confidence Interval (CI); 1.5-14.3%); 7.2% (95%CI; 3.6-13.9%) and 3.5% (95%CI; 1.7-7.2%) by cohort and was associated with food insecurity in the two larger cohorts (p=0.03; p=0.01 respectively).\n\nConclusionsLatinx families in the Bay Area with children are experiencing a sharp rise in food insecurity levels during the COVID-19 epidemic. Food insecurity, similar to other indices of poverty, is associated with increased risk for COVID-19 infection. Comprehensive interventions are needed to address food insecurity in Latinx populations and further studies are needed to better assess independent associations between household food insecurity, poor nutritional health and risk of COVID-19 infection.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Milagro Escobar", + "author_inst": "UCSF" + }, + { + "author_name": "Andrea DeCastro Mendez", + "author_inst": "UCSF" + }, + { + "author_name": "Maria Romer Encinas", + "author_inst": "UCSF" + }, + { + "author_name": "Janet Wojcicki", + "author_inst": "UCSF" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "nutrition" + }, { "rel_doi": "10.1101/2020.10.12.20211342", "rel_title": "Network Graph Representation of COVID-19 Scientific Publications to Aid Knowledge Discovery", @@ -1159132,33 +1157456,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.12.20211094", - "rel_title": "Prioritisation of population groups with the most interactions for COVID-19 vaccination can substantially reduce total fatalities", - "rel_date": "2020-10-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.12.20211094", - "rel_abs": "Background: The unprecedented rapid development of vaccines against the SARS-CoV-2 virus creates in itself a new challenge for governments and health authorities: the effective vaccination of large numbers of people in a short time and, possibly, with shortage of vaccine doses. To whom vaccinate first and in what sequence, if any at all, to avoid the most fatalities remains an open question. Methods: A compartmental model considering age-related groups was developed to evaluate and compare vaccine distribution strategies in terms of the total avoidable fatalities. Population groups are established based on relevant differences in mortality (due to e.g. their age) and risk-related traits (such as their behaviour and number of daily person-to-person interactions). Vaccination distribution strategies were evaluated for different vaccine effectiveness levels, population coverage and vaccination rate using data mainly from Spain. Findings: Our results show that, if children could also be included in the vaccination, a rollout by priority to groups with the highest number of daily person-to-person interactions can achieve large reductions in total fatalities. This is due to the importance of the avoided subsequent infections inflicted on the rest of the population by highly interactive individuals. If children are excluded from the vaccination, the differences between priority strategies become smaller and appear highly depending on rollout rate, coverage and the levels of self-protection and awareness exercised by the population. Interpretation: These results are in possible contradiction with several published plans for COVID-19 vaccination and highlight the importance of conducting an open comprehensive and thorough analysis of this problem leaving behind possible preconceptions.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Jorge Rodriguez", - "author_inst": "Khalifa University" - }, - { - "author_name": "Mauricio Paton", - "author_inst": "Khalifa University" - }, - { - "author_name": "Juan M Acuna", - "author_inst": "Khalifa University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.12.20211169", "rel_title": "COVID-19 in Italy: targeted testing as a proxy of limited health care facilities and a key to reducing hospitalization rate and the death toll.", @@ -1160454,6 +1158751,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2020.10.13.20212126", + "rel_title": "Epidemiologial Analysis of Patients Presenting to a West London District General Hospital Requiring Admission with Covid-19", + "rel_date": "2020-10-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.13.20212126", + "rel_abs": "BackgroundCoronavirus has lead to significant morbidity and mortality both within the UK and worldwide. We hypothesise there are local clusters of coronavirus which would therefore be amenable to targeted public health measures.\n\nMethodsThis is a retrospective, observational case series conducted in a West London District General Hospital. All patients admitted to hospital with a radiological or microbiological diagnosis of Covid-19 were included (children under 16 years were excluded). Consecutive sampling was used and baseline characteristics including age, sex, postcode and final patient outcome were collected from the electronic health records. Patient origin postcode was plotted to a map of the local area and an online cloud based mapping analysis system was used to generate heat maps and case density maps which were compared to living base layers. The primary outcome was identification of local clusters of cases of coronavirus. Secondary outcome was identification of population characteristics that may provide evidence for more targetted public health intervention in a second wave.\n\nResultsLocal clusters of infection were identified within the target population. These appeared to correlate with higher indices of deprivation, poorer overall health and high household occupancy suggesting a role for public health measures to target these areas.\n\nConclusionThere is a role for targeted public health measures in tackling the spread of coronavirus, paying particular attention to those who live in more deprived areas.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Eleanor Heald", + "author_inst": "West Middlesex University Hospital" + }, + { + "author_name": "Natalie Ring", + "author_inst": "West Middlesex University Hospital" + }, + { + "author_name": "Dinesh Vatvani", + "author_inst": "None" + }, + { + "author_name": "David Shackleton", + "author_inst": "West Middlesex University Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2020.10.12.20211201", "rel_title": "Mathematical Perspective of Covid-19 Pandemic: Disease Extinction Criteria in Deterministic and Stochastic Models", @@ -1160742,37 +1159070,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.13.20212118", - "rel_title": "Does autism protect against COVID quarantine effects?", - "rel_date": "2020-10-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.13.20212118", - "rel_abs": "IntroductionCOVID-19 outbreak has imposed an eight-week confinement in France. During this period, children and their families were exposed to a full-time home life. The aim of this study was to assess the emotional experience and tolerance of children with autism spectrum disorder (ASD) in this particular context.\n\nMethodA clinical survey was proposed to parents and rated by professionals once a week during the quarantine period in France. 95 autistic children followed by the child and adolescent psychiatry department of Tours university hospital were assessed from the 18th of March to the 8th of May. The following clinical points were investigated: child anxiety, family anxiety, behavior problems, impact on sleep, impact on appetite, impact on school work, family tension, confinement intolerance, difficulties to follow a schedule, isolation behavior.\n\nResultsDespite minor changes in family anxiety and school work, no difference was highlighted between clinical scores collected at the beginning and at the end of this period. ASD children with or without intellectual disability had non-significant clinical changes during quarantine. This evolution was also independent of the accommodation type (house or apartment) and the parental status (relationship, separated or isolated).\n\nConclusionThe sameness dimension in autism and parents adaptation may be involved in this clinical stability during COVID confinement. Moreover, specialized tools and support provided by professionals could have participated to these outcomes and must be regularly promoted in order to help families in this still difficult period.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Marco Guidotti", - "author_inst": "EXcellence Center in Autism and neurodevelopmental disorders - Tours" - }, - { - "author_name": "Adrien Gateau", - "author_inst": "EXcellence Center in Autism and neurodevelopmental disorders - Tours" - }, - { - "author_name": "Joelle Malvy", - "author_inst": "EXcellence Center in Autism and neurodevelopmental disorders - Tours" - }, - { - "author_name": "Frederique Bonnet-Brilhault", - "author_inst": "EXcellence Center in Autism and neurodevelopmental disorders - Tours" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.10.13.20212092", "rel_title": "Circulating Proteins Influencing COVID-19 Susceptibility and Severity: a Mendelian Randomization Study", @@ -1162040,6 +1160337,129 @@ "type": "new results", "category": "physiology" }, + { + "rel_doi": "10.1101/2020.10.14.337535", + "rel_title": "Immunogenicity of novel mRNA COVID-19 vaccine MRT5500 in mice and non-human primates", + "rel_date": "2020-10-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.14.337535", + "rel_abs": "An effective vaccine to address the global pandemic of coronavirus disease 2019 (COVID-19) is an urgent public health priority1. Novel synthetic mRNA and vector-based vaccine technologies offer an expeditious development path alternative to traditional vaccine approaches. Here we describe the efforts to utilize an mRNA platform for rational design and evaluations of mRNA vaccine candidates based on Spike (S) glycoprotein of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the virus causing COVID-19. Several mRNA constructs expressing various structural conformations of S-protein, including wild type (WT), a pre-fusion stabilized mutant (2P), a furin cleavage-site mutant (GSAS) and a double mutant form (2P/GSAS), were tested in a preclinical animal model for their capacity to elicit neutralizing antibodies (nAbs). The lead 2P/GSAS candidate was further assessed in dose-ranging studies in mice and Cynomolgus macaques. The selected 2P/GSAS vaccine formulation, now designated MRT5500, elicited potent nAbs as measured in two types of neutralization assays. In addition, MRT5500 elicited TH1-biased responses in both mouse and non-human primate species, a result that helps to address a hypothetical concern regarding potential vaccine-associated enhanced respiratory diseases associated with TH2-biased responses. These data position MRT5500 as a viable vaccine candidate for clinical development against COVID-19.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Kirill V Kalnin", + "author_inst": "Sanofi Pasteur" + }, + { + "author_name": "Timothy Plitnik", + "author_inst": "Yoh Services LLC" + }, + { + "author_name": "Michael Kishko", + "author_inst": "Sanofi Pasteur" + }, + { + "author_name": "Jinrong Zhang", + "author_inst": "Sanofi Pasteur" + }, + { + "author_name": "Donghui Zhang", + "author_inst": "Sanofi Pasteur" + }, + { + "author_name": "Andrien Beauvais", + "author_inst": "Sanofi Pasteur" + }, + { + "author_name": "Natalie G Anosova", + "author_inst": "Sanofi Pasteur" + }, + { + "author_name": "Timothy Tibbitts", + "author_inst": "Sanofi Pasteur" + }, + { + "author_name": "Joshua M DiNapoli", + "author_inst": "Sanofi Pasteur" + }, + { + "author_name": "Po-Wei D Huang", + "author_inst": "Sanofi Pasteur" + }, + { + "author_name": "James Huleatt", + "author_inst": "Sanofi Pasteur" + }, + { + "author_name": "Deanne Vincent", + "author_inst": "Sanofi Pasteur" + }, + { + "author_name": "Katherine Fries", + "author_inst": "Sanofi Pasteur" + }, + { + "author_name": "Shrirang Karve", + "author_inst": "Translate Bio" + }, + { + "author_name": "Rebecca Goldman", + "author_inst": "Sanofi Pasteur" + }, + { + "author_name": "Hardip Gopani", + "author_inst": "Translate Bio" + }, + { + "author_name": "Anusha Dias", + "author_inst": "Translate Bio" + }, + { + "author_name": "Khang Tran", + "author_inst": "Translate Bio" + }, + { + "author_name": "Minnie Zacharia", + "author_inst": "Translate Bio" + }, + { + "author_name": "Xiaobo Gu", + "author_inst": "Translate Bio" + }, + { + "author_name": "Lianne Boeglin", + "author_inst": "Translate Bio" + }, + { + "author_name": "Sudha Chivukula", + "author_inst": "Sanofi Pasteur" + }, + { + "author_name": "Ron Swearingen", + "author_inst": "Translate Bio" + }, + { + "author_name": "Victoria Landolfi", + "author_inst": "Sanofi Pasteur" + }, + { + "author_name": "Tong-Ming Fu", + "author_inst": "Sanofi Pasteur" + }, + { + "author_name": "Frank DeRosa", + "author_inst": "Translate Bio" + }, + { + "author_name": "Danilo Casimiro", + "author_inst": "Sanofi Pasteur" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.10.14.339515", "rel_title": "The viral protein NSP1 acts as a ribosome gatekeeper for shutting down host translation and fostering SARS-CoV-2 translation", @@ -1162440,61 +1160860,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.10.08.20209544", - "rel_title": "What Specimen Urologists Should Be Most Concerned About ? A Systematic Review and Meta-Analysis", - "rel_date": "2020-10-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.08.20209544", - "rel_abs": "ObjectiveInvestigating the infectivity of body fluid can be useful for preventative measures in the community and ensuring safety in the operating rooms and on the laboratory practices.\n\nMethodsWe performed a literature search of clinical trials, cohorts, and case series using PubMed/MEDLINE, Google Scholar, and Cochrane library, and downloadable database of CDC. We excluded case reports and searched all-language articles for review and repeated until the final drafting. The search protocol was registered in the PROSPERO database.\n\nResultsThirty studies with urinary sampling for viral shedding were included. A total number of 1,271 patients were enrolled initially, among which 569 patients had undergone urinary testing. Nine studies observed urinary viral shedding in urine from 41 patients. The total incidence of urinary SARS-CoV-2 shedding was 8%, compared to 21.3% and 39.5 % for blood and stool, respectively. The summarized risk ratio (RR) estimates for urine positive rates compared to the pharyngeal rate was 0.08. The pertaining RR urine compared to blood and stool positive rates were 0.20 and 0.33 respectively.\n\nConclusionsOur review concludes that not only the SARS-CoV-2 can be excreted in the urine in eight percent of patients but also its incidence may have associations with the severity of the systemic disease, ICU admission, and fatality rates. Moreover, the findings in our review suggest that a larger population size may reveal more positive urinary cases possibly by minimizing biases. However, it is important to notice that it is the naso-pharyngeal specimens, stool, and serum that show more possibilities to became positive, respectively.\n\nTake-home bullet points The urinary shedding incidence was 8%, compared to 21.3% and 39.5 % for blood and stool, respectively.\nUrinary shedding may have associations with the severity of the systemic disease, ICU admission, and fatality rates.\nRepeat urinary testing is warranted throughout the disease phases, especially in clinically suspected cases with an initially negative results.\nTechnical errors in handling samples, as well as different rRT-PCR methods can be responsible for diversity found in results, in part.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "M. Reza Roshandel", - "author_inst": "Icahn School of Medicine, Mount Sinai Hospitals" - }, - { - "author_name": "Masoud Nateqi", - "author_inst": "Texas Tech University" - }, - { - "author_name": "Ramin Lak", - "author_inst": "Pars Advanced and Minimally Invasive Medical Manners Research Center" - }, - { - "author_name": "Pooya Aavani", - "author_inst": "Department of Biology, Emory University, Atlanta, Georgia" - }, - { - "author_name": "Reza Sari Motlagh", - "author_inst": "Urology Department of Medical University of Vienna" - }, - { - "author_name": "Tannaz Aghaei Badr", - "author_inst": "Icahn School of Medicine, Mount Sinai Hospitals" - }, - { - "author_name": "John Sfakianos", - "author_inst": "Urology Department of Icahn School of Medicine, Mount Sinai Hospitals" - }, - { - "author_name": "Steven A Kaplan", - "author_inst": "Urology Department of Icahn School of Medicine, Mount Sinai Hospitals" - }, - { - "author_name": "Shahrokh Shariat", - "author_inst": "Urology Department of Medical University of Vienna, Austria; European Association of Urology, Research Foundation, Arnhem, Netherland" - }, - { - "author_name": "Ashutosh K. Tewari", - "author_inst": "Urology Department of Icahn School of Medicine, Mount Sinai Hospitals" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "urology" - }, { "rel_doi": "10.1101/2020.10.09.20210377", "rel_title": "Antimicrobial Resistance, Evidences on Irrational Anti-microbial Prescribing and Consumption during COVID-19 Pandemic and Possible Mitigation Strategies: A Bangladesh Perspective", @@ -1164101,6 +1162466,49 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.10.13.308676", + "rel_title": "A 3D Structural Interactome to Explore the Impact of Evolutionary Divergence, Population Variation, and Small-molecule Drugs on SARS-CoV-2-Human Protein-Protein Interactions", + "rel_date": "2020-10-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.13.308676", + "rel_abs": "The recent COVID-19 pandemic has sparked a global public health crisis. Vital to the development of informed treatments for this disease is a comprehensive understanding of the molecular interactions involved in disease pathology. One lens through which we can better understand this pathology is through the network of protein-protein interactions between its viral agent, SARS-CoV-2, and its human host. For instance, increased infectivity of SARS-CoV-2 compared to SARS-CoV can be explained by rapid evolution along the interface between the Spike protein and its human receptor (ACE2) leading to increased binding affinity. Sequence divergences that modulate other protein-protein interactions may further explain differences in transmission and virulence in this novel coronavirus. To facilitate these comparisons, we combined homology-based structural modeling with the ECLAIR pipeline for interface prediction at residue resolution, and molecular docking with PyRosetta. This enabled us to compile a novel 3D structural interactome meta-analysis for the published interactome network between SARS-CoV-2 and human. This resource includes docked structures for all interactions with protein structures, enrichment analysis of variation along interfaces, predicted {Delta}{Delta}G between SARS-CoV and SARS-CoV-2 variants for each interaction, predicted impact of natural human population variation on binding affinity, and a further prioritized set of drug repurposing candidates predicted to overlap with protein interfaces{dagger}. All predictions are available online{dagger} for easy access and are continually updated when new interactions are published.\n\n {dagger}Some sections of this pre-print have been redacted to comply with current bioRxiv policy restricting the dissemination of purely in silico results predicting potential therapies for SARS-CoV-2 that have not undergone thorough peer-review. The results section titled \"Prioritization of Candidate Inhibitors of SARS-CoV-2-Human Interactions Through Binding Site Comparison,\" Figure 4, Supplemental Table 9, and all links to our web resource have been removed. Blank headers left in place to preserve structure and item numbering. Our full manuscript will be published in an appropriate journal following peer-review.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Shayne Davis Wierbowski", + "author_inst": "Cornell University" + }, + { + "author_name": "Siqi Liang", + "author_inst": "Cornell University" + }, + { + "author_name": "You Chen", + "author_inst": "Cornell University" + }, + { + "author_name": "Nicole Marie Andre", + "author_inst": "Cornell University" + }, + { + "author_name": "Steven M Lipkin", + "author_inst": "Weill-Cornell Medicine" + }, + { + "author_name": "Gary R Whittaker", + "author_inst": "Cornell University" + }, + { + "author_name": "Haiyuan Yu", + "author_inst": "Cornell University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "systems biology" + }, { "rel_doi": "10.1101/2020.10.13.331306", "rel_title": "Pilot production of SARS-CoV-2 related proteins in plants: a proof of concept for rapid repurposing of indoors farms into biomanufacturing facilities", @@ -1164561,25 +1162969,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.08.20209437", - "rel_title": "Estimating the Burden of COVID-19 Symptoms Among Participants at the 2020 USA Curling Club Nationals Tournament", - "rel_date": "2020-10-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.08.20209437", - "rel_abs": "The COVID-19 pandemic has been a significant cause of global morbidity and mortality, with evidence suggesting that activities involving heavier breathing, such as singing and exercise, can result in increased risk for disease transmission. The USA Curling Club Nationals is a week-long curling tournament to determine the mens and womens club-level champions. The 2020 tournament took place March 7-14 at the Potomac Curling Club in Laurel, MD, and featured teams from across the United States. Preventative measures, such as increased cleaning and disinfection of surfaces, single use and disposable food containers, and canceling traditional event banquets were implemented. Despite these measures, players, coaches, officials, volunteers, and spectators contracted the virus as a result of participation in the event. We surveyed participants to assess total positivity, potential days of transmission, and the burden of symptoms experienced among the participants. We found that 55.6% of all participants reported experiencing symptoms consistent with COVID-19, with nearly all experiencing more than one symptom. Although most participants symptoms resolved quickly, 9.6% of all participants experienced symptoms for at least one month and 12.6% of all participants reported taking at least 30 days before they felt they had returned to normal. As a result of this study, we believe curling tournaments have the potential to be high-risk events for the transmission of COVID-19. Further infection prevention measures that were not yet publicly implemented at the time of this tournament may be an effective method of lowering transmission risk, although further research is required.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Paul M Luethy", - "author_inst": "University of Maryland School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.08.20209163", "rel_title": "Meta-analysis and adjusted estimation of COVID-19 case fatality risk in India and its association with the underlying comorbidities", @@ -1165786,6 +1164175,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.07.20208686", + "rel_title": "An Innovative Non-Pharmaceutical Intervention to Mitigate SARS-CoV02 Spread: Probability Sampling to Identify and Isolate Asymptomatic Cases", + "rel_date": "2020-10-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.07.20208686", + "rel_abs": "Studies estimate that a substantial proportion of SARS-CoV-2 transmission occurs through individuals who do not exhibit symptoms. Mitigation strategies test only those who are moderately to severely symptomatic, excluding the substantial portion of cases that are asymptomatic yet still infectious and likely responsible for a large proportion of the virus spread (1-8). While isolating asymptomatic cases will be necessary to effectively control viral spread, these cases are functionally invisible and there is no current method to identify them for isolation. To address this major omission in COVID-19 control, we develop a strategy, Sampling-Testing-Quarantine (STQ), for identifying and isolating individuals with asymptomatic SARS-CoV-2 in order to mitigate the epidemic. STQ uses probability sampling in the general population, regardless of symptoms, then isolates the individuals who test positive along with their household members who are high probability for asymptomatic infections. To test the potential efficacy of STQ, we use an agent-based model, designed to computationally simulate the epidemic in the Seattle with infection parameters, like R0 and asymptomatic fraction, derived from population data. Our results suggest that STQ can substantially slow and decrease the spread of COVID-19, even in the absence of school and work shutdowns. Results also recommend which sampling techniques, frequency of implementation, and population subject to isolation are most efficient in reducing spread with limited numbers of tests.\n\nSignificance StatementA substantial portion of SARS-CoV-2 infections are spread through asymptomatic carriers. Until a vaccine is developed, research indicates an urgent need to identify these asymptomatic infections to control COVID-19, but there is currently no effective strategy to do so. In this study, we develop such a strategy, a procedure called Sampling-Testing-Quarantine (STQ), that combines techniques from survey methods for sampling from the general population and testing and isolation techniques from epidemiology. With computational simulations, we demonstrate that STQ procedures can dramatically decrease and slow COVID-19 spread, even in the absence of widespread work, school, and community lockdowns. We also find particular implementation strategies (including sampling techniques, frequencies of implementation, and people who are subject to isolation) are most efficient in mitigating spread.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Nathalie E Williams", + "author_inst": "University of Washington" + }, + { + "author_name": "Xiaozheng Yao", + "author_inst": "Virginia Tech" + }, + { + "author_name": "Ankita Pall", + "author_inst": "University of Washington" + }, + { + "author_name": "Xiaolu Qian", + "author_inst": "University of Washington" + }, + { + "author_name": "Mansi Rathod", + "author_inst": "University of Washington" + }, + { + "author_name": "Chang Xu", + "author_inst": "University of Washington" + }, + { + "author_name": "Adrian Dobra", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.07.20208421", "rel_title": "Forecasting COVID-19 cases in the Philippines using various mathematical models", @@ -1166154,33 +1164586,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.07.20208744", - "rel_title": "One size fits all?: Modeling face-mask fit on population-based faces", - "rel_date": "2020-10-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.07.20208744", - "rel_abs": "The use of face masks by the general population during viral outbreaks such as the COVID-19 pandemic, although at times controversial, has been effective in slowing down the spread of the virus. The fit of simple cloth masks on the face as well as the resulting perimeter leakage and face mask efficacy are expected to be highly dependent on the type of mask and facial topology. However, this effect has to date, not been examined and quantified. Here, we study the leakage of a rectangular cloth mask on a large virtual population of subjects with diverse facial features, using computational mechanics modeling. The effect of weight, age, gender, and height on the leakage is studied. The Centers for Disease Control and Prevention (CDC) recommended mask size was used as a basis for comparison and was found not to be the most effective design for all subjects. Thin, feminine, and young faces benefit from mask sizes smaller than that recommended by the CDC. The results show that side-edge tuck-in of the masks could lead to a larger localized gap opening in many face categories, and is therefore not recommended for all. The perimeter leakage from the face mask worn by thin/feminine faces is mostly from the leakage area along the bottom edge of the mask and therefore, a tuck-in of the bottom edge of the mask or a mask smaller than the CDC recommended mask size are proposed as a more effective design. The leakage from the top edge of the mask is determined to be largely unaffected by mask size and tuck-in ratio, meaning that other mechanical alterations such as a nose wire strip are necessary to reduce the leakage at this site.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Tomas Solano", - "author_inst": "Florida State University" - }, - { - "author_name": "Rajat Mittal", - "author_inst": "Johns Hopkins University" - }, - { - "author_name": "Kourosh Shoele", - "author_inst": "Florida State University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.10.07.20208801", "rel_title": "Level of Knowledge in the COVID-19 Pandemic: A Cross-Sectional Survey of Canadian Medical Students", @@ -1167356,6 +1165761,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.07.20208462", + "rel_title": "Assessing the Impact of Area Deprivation Index on COVID-19 Prevalence: A Contrast Between Rural and Urban U.S. Jurisdictions", + "rel_date": "2020-10-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.07.20208462", + "rel_abs": "BackgroundThe COVID-19 pandemic has impacted communities differentially, with poorer and minority populations being more adversely affected. Prior rural health research suggests such disparities may be exacerbated during the pandemic and in remote parts of the U.S.\n\nObjectivesTo understand the spread and impact of COVID-19 across the U.S., county level data for confirmed cases of COVID-19 were examined by Area Deprivation Index (ADI) scores and Metropolitan vs. Nonmetropolitan designations from the National Center for Health Statistics (NCHS). These designations were the basis for making comparisons between Urban and Rural jurisdictions.\n\nMethodsKendalls Tau-B was used to compare effect sizes between jurisdictions on select ADI composites and well researched social determinants of health (SDH). Spearman coefficients and a moderation analysis using Poisson modeling was used to explore the relationship between ADI and COVID-19 prevalence in the context of county designation.\n\nResultsResults show that the relationship between area deprivation and COVID-19 prevalence was positive and higher for rural counties, when compared to urban ones and that family income and poverty had a stronger relationship with prevalence than other ADI component measures.\n\nConclusionsThough most Americans live in Metropolitan Areas, rural communities were found to be associated with a stronger relationship between deprivation and COVID-19 prevalence. Models for predicting COVID-19 prevalence by ADI and county type reinforced this observation but revealed no moderating effect of county type on ADI.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Christopher Kitchen", + "author_inst": "Johns Hopkins, School of Public Health" + }, + { + "author_name": "Elham Hatef", + "author_inst": "Johns Hopkins School of Public Health" + }, + { + "author_name": "Hsien Yen Chang", + "author_inst": "Johns Hopkins School of Public Health" + }, + { + "author_name": "Jonathan Weiner", + "author_inst": "Johns Hopkins School of Public Health" + }, + { + "author_name": "Hadi Kharrazi", + "author_inst": "Johns Hopkins, School of Public Health" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.10.07.20208702", "rel_title": "Long-term COVID-19 symptoms in a large unselected population", @@ -1167896,73 +1166336,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2020.10.07.20208389", - "rel_title": "A Comparative COVID 19 Characterizations and Clinical Course Analysis between ICU and Non ICU Settings", - "rel_date": "2020-10-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.07.20208389", - "rel_abs": "ObjectiveWith COVID-19 pandemic severely affecting India and Ahmedabad city being one accounting for half COVID cases, objective was to determine disease course and severity of in patients at a COVID care hospital.\n\nDesignA Clinical trial registry of India registered observational study (CTRI/2020/05/025247).\n\nSettingCertified COVID hospital located in Ahmedabad, Gujarat, India.\n\nParticipants549 COVID positive patients hospitalized between 15 th May to 10 th August, 2020 and treated in ICU and non ICU settings.\n\nMain Outcome MeasureComparative analysis of demographic, clinical characteristics, investigations, treatment, complications and outcome of COVID patients in ICU and non ICU settings.\n\nResultsOf the 549 hospitalized COVID positive patients, 159 were admitted in ICU during disease course while 390 had ward admissions. Overall median age was 52 (1-86) years. The ICU group was older (>65years), with associated comorbidities like hypertension and diabetes (p<0.001); higher proportion of males (79.25%); with dyspnea as a major clinical characteristic and consolidation in lungs as a major radiological finding as compared to ward patients. C - reactive protein, D-Dimer and Ferritin were higher in ICU patients. Overall 50% females depicted elevated Ferritin levels. Steriods(92.45%)and tocilizumab (69.18%) were more frequently used for ICU patients. Remdesivir was prescribed to both ICU and non ICU patients. Favirapir was also a line of treatment for 25% of ICU patients. Convalescent plasma therapy was given to 7 ICU patients. Complications like acute kidney injury (13.84%), shock (10.69 %), sepsis and encephalopathy were observed in ICU patients. Overall mortality rate was 5.47 % with higher mortality among males in comparison to females (p<0.0001).\n\nConclusionAbout 29% of overall patients required ICU admission that was commonly elderly males. Chances of ICU admission were higher with baselines comorbidities (1.5 times) and dyspnea (3.4 times) respectively. A multi-specialty COVID care team and updated treatment protocols improves outcomes.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Amit Patel", - "author_inst": "Care Institute of Medical Sciences" - }, - { - "author_name": "Parloop Bhatt", - "author_inst": "Care Institute of Medical Sciences" - }, - { - "author_name": "Surabhi Madan", - "author_inst": "Care Institute of Medical Sciences" - }, - { - "author_name": "Nitesh Shah", - "author_inst": "Care Institute of Medical Sciences" - }, - { - "author_name": "Vipul Thakkar", - "author_inst": "Care Institute of Medical Sciences" - }, - { - "author_name": "Bhagyesh Shah", - "author_inst": "Care Institute of Medical Sciences" - }, - { - "author_name": "Rashmi Chovatia", - "author_inst": "Care Institute of Medical Sciences" - }, - { - "author_name": "Hardik Shah", - "author_inst": "Care Institute of Medical Sciences" - }, - { - "author_name": "Minesh Patel", - "author_inst": "Care Institute of Medical Sciences" - }, - { - "author_name": "Pradip Dabhi", - "author_inst": "Care Institute of Medical Sciences" - }, - { - "author_name": "Aditi Nanavati", - "author_inst": "Care Institute of Medical Sciences" - }, - { - "author_name": "Milan Chag", - "author_inst": "Care Institute of Medical Sciences" - }, - { - "author_name": "Keyur Parikh", - "author_inst": "Care Institute of Medical Sciences" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.10.08.20193623", "rel_title": "Clinical characteristics and outcomes of adult patients admitted with COVID-19 in East London: a retrospective cohort analysis", @@ -1169242,6 +1167615,65 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.10.07.20208587", + "rel_title": "Remote home monitoring (virtual wards) during the COVID-19 pandemic: a living systematic review", + "rel_date": "2020-10-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.07.20208587", + "rel_abs": "ObjectivesThe aim of this review was to analyse the implementation and impact of remote home monitoring models (virtual wards) during COVID-19, identifying their main components, processes of implementation, target patient populations, impact on outcomes, costs and lessons learnt.\n\nDesignA rapid systematic review to capture an evolving evidence base. We used the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) statement.\n\nSettingThe review included models led by primary and secondary care across seven countries.\n\nParticipants27 articles were included in the review.\n\nMain outcome measuresImpact of remote home monitoring on virtual length of stay, escalation, emergency department attendance/reattendance, admission/readmission and mortality.\n\nResultsThe aim of the models was to maintain patients safe in the right setting. Most models were led by secondary care and confirmation of COVID-19 was not required (in most cases). Monitoring was carried via online platforms, paper-based systems with telephone calls or (less frequently) through wearable sensors. Models based on phone calls were considered more inclusive. Patient/carer training was identified as a determining factor of success. We could not reach substantive conclusions regarding patient safety and the identification of early deterioration due to lack of standardised reporting and missing data. Economic analysis was not reported for most of the models and did not go beyond reporting resources used and the amount spent per patient monitored.\n\nConclusionsFuture research should focus on staff and patient experiences of care and inequalities in patients access to care. Attention needs to be paid to the cost-effectiveness of the models and their sustainability, evaluation of their impact on patient outcomes by using comparators, and the use of risk-stratification tools.\n\nProtocol registrationThe review protocol was published on PROSPERO (CRD: 42020202888).\n\nRESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSRemote home monitoring models for other conditions have been studied, but their adaptation to monitor COVID-19 patients and the analysis of their implementation constitute gaps in research.\n\nAdded value of this studyThe review covers a wide range of remote home monitoring models (pre-hospital as well as step-down wards) implemented in primary and secondary care sectors in eight countries and focuses on their implementation and impact on outcomes (including costs).\n\nImplications of all the available evidenceThe review provides a rapid overview of an emerging evidence base that can be used to inform changes in policy and practice regarding the home monitoring of patients during COVID-19. Attention needs to be paid to the cost-effectiveness of the models and their sustainability, evaluation of their impact on patient outcomes by using comparators, and the use of risk-stratification tools.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Cecilia Vindrola-Padros", + "author_inst": "University College London" + }, + { + "author_name": "Kelly Singh", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Manbinder S Sidhu", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Theo Georghiou", + "author_inst": "Nuffield Trust" + }, + { + "author_name": "Chris Sherlaw-Johnson", + "author_inst": "Nuffield Trust" + }, + { + "author_name": "Sonila M Tomini", + "author_inst": "University College London" + }, + { + "author_name": "Nathan Cohen", + "author_inst": "University College London" + }, + { + "author_name": "Matthew Inada-Kim", + "author_inst": "Hampshire Hospitals NHS Foundation Trust" + }, + { + "author_name": "Karen Kirkham", + "author_inst": "General Practitioner NHS Dorset" + }, + { + "author_name": "Allison Streetly", + "author_inst": "Kings College London" + }, + { + "author_name": "Naomi J Fulop", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2020.10.07.20187641", "rel_title": "Two-tiered SARS-CoV-2 seroconversion screening in the Netherlands and stability of nucleocapsid, spike protein domain 1 and neutralizing antibodies", @@ -1169726,29 +1168158,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.10.07.20207845", - "rel_title": "Isolation of infected people and their contacts is likely to be effective against many short-term epidemics", - "rel_date": "2020-10-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.07.20207845", - "rel_abs": "BackgroundIsolation of infected people and their contacts may be an effective way to control outbreaks of infectious disease, such as influenza and SARS-CoV-2. Models can provide insights into the efficacy of contact tracing, coupled with isolating or quarantining at risk people.\n\nMethodsWe developed an agent-based model and simulated 15, 000 short term illnesses, with varying characteristics. For each illness we ran ten simulations on the following scenarios: (1) No tracing or isolation (None), (2) isolation of agents who have tested positive (Isolation), (3) scenario 2 coupled with minimal contact tracing and quarantine of contacts (Minimum), (4) scenario 3 with more effective contact tracing (Moderate), and (5) perfect isolation of agents who test positive and perfect tracing and quarantine of all their contacts (Maximum).\n\nResultsThe median total infections of the Isolation, Minimum, Moderate and Maximum scenarios were 80%, 40%, 17% and 4% of the no intervention scenario respectively.\n\nConclusionsIsolation of infected patients and quarantine of their contacts, even if moderately well implemented, is likely to substantially reduce the number of infections in an outbreak. Randomized controlled trials to confirm these results in the real world and to analyse the cost effectiveness of contact tracing and isolation during coronavirus and influenza outbreaks are warranted.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Nathan Geffen", - "author_inst": "University of Cape Town" - }, - { - "author_name": "Marcus O Low", - "author_inst": "University of Cape Town" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.07.20207795", "rel_title": "High seroprevalence of SARS-CoV-2 antibodies among people living in precarious situations in Ile de France", @@ -1170891,6 +1169300,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.06.20207472", + "rel_title": "Clinical, laboratory, and temporal predictors of neutralizing antibodies to SARS-CoV-2 after COVID-19", + "rel_date": "2020-10-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.06.20207472", + "rel_abs": "BackgroundSARS-CoV-2-specific antibodies may protect from reinfection and disease, providing the rationale for administration of plasma containing SARS-CoV-2 neutralizing antibodies (nAb) as a treatment for COVID-19. The clinical factors and laboratory assays to streamline plasma donor selection, and the durability of nAb responses, are incompletely understood.\n\nMethodsAdults with virologically-documented SARS-CoV-2 infection in a convalescent plasma donor screening program were tested for serum IgG to SARS-CoV-2 spike protein S1 domain, nucleoprotein (NP), and for nAb.\n\nResultsAmongst 250 consecutive persons studied a median of 67 days since symptom onset, 243/250 (97%) were seropositive on one or more assays. Sixty percent of donors had nAb titers [≥]1:80. Correlates of higher nAb titer included older age (adjusted OR [AOR] 1.03/year of age, 95% CI 1.00-1.06), male sex (AOR 2.08, 95% CI 1.13-3.82), fever during acute illness (AOR 2.73, 95% CI 1.25-5.97), and disease severity represented by hospitalization (AOR 6.59, 95% CI 1.32-32.96). Receiver operating characteristic (ROC) analyses of anti-S1 and anti-NP antibody results yielded cutoffs that corresponded well with nAb titers, with the anti-S1 assay being slightly more predictive. NAb titers declined in 37 of 41 paired specimens collected a median of 98 days (range, 77-120) apart (P<0.001). Seven individuals (2.8%) were persistently seronegative and lacked T cell responses.\n\nConclusionsNab titers correlated with COVID-19 severity, age, and sex. Standard commercially available SARS-CoV-2 IgG results can serve as useful surrogates for nAb testing. Functional nAb levels were found to decline and a small proportion of COVID-19 survivors lack adaptive immune responses.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Jim Boonyaratanakornkit", + "author_inst": "Fred Hutchinon Cancer Research Center" + }, + { + "author_name": "Chihiro Morishima", + "author_inst": "University of Washington" + }, + { + "author_name": "Stacy Selke", + "author_inst": "University of Washington" + }, + { + "author_name": "Danniel Zamora", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Sarah McGuffin", + "author_inst": "University of Washington" + }, + { + "author_name": "Adrienne E Shapiro", + "author_inst": "University of Washington" + }, + { + "author_name": "Victoria L Campbell", + "author_inst": "University of Washington" + }, + { + "author_name": "Christopher L McClurkan", + "author_inst": "University of Washington" + }, + { + "author_name": "Lichen Jing", + "author_inst": "University of Washington" + }, + { + "author_name": "Robin Gross", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Janie Liang", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Elena Postnikova", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Steven Mazur", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Anu Chaudhary", + "author_inst": "University of Washington" + }, + { + "author_name": "Marie K Das", + "author_inst": "University of Washington" + }, + { + "author_name": "Susan L Fink", + "author_inst": "University of Washington" + }, + { + "author_name": "Andrew Bryan", + "author_inst": "University of Washington" + }, + { + "author_name": "Alex L Greninger", + "author_inst": "University of Washington" + }, + { + "author_name": "Keith R Jerome", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Michael R Holbrook", + "author_inst": "National Institutes of Health" + }, + { + "author_name": "Terry B Gernsheimer", + "author_inst": "University of Washington" + }, + { + "author_name": "Mark H Wener", + "author_inst": "University of Washington" + }, + { + "author_name": "Anna Wald", + "author_inst": "University of Washington" + }, + { + "author_name": "David M Koelle", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.06.20208066", "rel_title": "Real-World Effectiveness of hydroxychloroquine, azithromycin, and ivermectin among hospitalized COVID-19 patients: Results of a target trial emulation using observational data from a nationwide Healthcare System in Peru", @@ -1171195,41 +1169715,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.06.20208009", - "rel_title": "Misinterpretation of viral load in COVID-19.", - "rel_date": "2020-10-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.06.20208009", - "rel_abs": "Knowledge of viral load is essential for formulating strategies for antiviral treatment, vaccination, and epidemiological control of COVID-19. Moreover, patients identification with high viral load could also be useful to understand risk factors such as age, comorbidities, severity of symptoms and hypoxia to decide the need for hospitalization. Several studies are evaluating the importance of analyzing viral load in different types of samples, clinical outcomes and viral transmission pathways. However, in a great number of emerging studies cycle threshold (Ct) values by itself is often used as a viral load indicator, which may be a mistake. In this study, we compared tracheal aspirate with nasopharyngeal samples obtained from critically ill COVID-19 patients and demonstrate how the raw Ct could lead to misinterpretation of results. Further, we analyzed nasopharyngeal swabs positive samples and propose a method to reduce evaluation error that could occur from using raw Ct. Based on these findings, we show the impact that normalization of Ct values has on interpretation of viral load data from different biological samples from patients with COVID-19, transmission and lastly in relations with clinical outcomes.\n\nImportanceIn a pandemic, prevention of disease transmission is key. Reliable data for profiles of viral load are needed and important to guide antiviral treatment, infection control and vaccination. The differential expression of SARS-CoV-2 viral RNA among patient groups is a current topic of interest and viral load has been associated with a diversity of outcomes. However, in a great number of emerging studies cycle threshold (Ct) values by itself is often used as a viral load indicator, which may be a mistake. In this study, we compared tracheal aspirate with nasopharyngeal samples obtained from critically ill COVID-19 patients and demonstrate how the raw Ct could lead to misinterpretation of results. Based on these findings, we show the impact that normalization of Ct values has on interpretation of viral load data from different biological samples from patients with COVID-19, transmission and lastly in relations with clinical outcomes.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Renan Lyra Miranda", - "author_inst": "Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do C\u00e9rebro Paulo Niemeyer" - }, - { - "author_name": "Alexandro Guterres", - "author_inst": "Instituto Estadual do C\u00e9rebro Paulo Niemeyer" - }, - { - "author_name": "Carlos Henrique de Azeredo Lima", - "author_inst": "Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do C\u00e9rebro Paulo Niemeyer" - }, - { - "author_name": "Paulo Niemeyer Filho", - "author_inst": "Instituto Estadual do C\u00e9rebro Paulo Niemeyer" - }, - { - "author_name": "M\u00f4nica Roberto Gadelha", - "author_inst": "Neuropathology and Molecular Genetics Laboratory, Instituto Estadual do C\u00e9rebro Paulo Niemeyer" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.08.330688", "rel_title": "CD8+ T cell responses in convalescent COVID-19 individuals target epitopes from the entireSARS-CoV-2 proteome and show kinetics of early differentiation", @@ -1172445,6 +1170930,105 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.10.07.307546", + "rel_title": "Making the invisible enemy visible", + "rel_date": "2020-10-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.07.307546", + "rel_abs": "During the COVID-19 pandemic, structural biologists rushed to solve the structures of the 28 proteins encoded by the SARS-CoV-2 genome in order to understand the viral life cycle and enable structure-based drug design. In addition to the 204 previously solved structures from SARS-CoV-1, 548 structures covering 16 of the SARS-CoV-2 viral proteins have been released in a span of only 6 months. These structural models serve as the basis for research to understand how the virus hijacks human cells, for structure-based drug design, and to aid in the development of vaccines. However, errors often occur in even the most careful structure determination - and may be even more common among these structures, which were solved quickly and under immense pressure.\n\nThe Coronavirus Structural Task Force has responded to this challenge by rapidly categorizing, evaluating and reviewing all of these experimental protein structures in order to help downstream users and original authors. In addition, the Task Force provided improved models for key structures online, which have been used by Folding@Home, OpenPandemics, the EU JEDI COVID-19 challenge and others.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Tristan Croll", + "author_inst": "CIMR, University of Cambridge, UK" + }, + { + "author_name": "Kay Diederichs", + "author_inst": "University of Konstanz, Germany" + }, + { + "author_name": "Florens Fischer", + "author_inst": "HARBOR, Unversity of Hamburg, Germany" + }, + { + "author_name": "Cameron Fyfe", + "author_inst": "Paris, France" + }, + { + "author_name": "Yunyun Gao", + "author_inst": "HARBOR, Unversity of Hamburg, Germany" + }, + { + "author_name": "Sam Horrell", + "author_inst": "Diamond Lightsource, UK" + }, + { + "author_name": "Agnel Praveen Joseph", + "author_inst": "Science and Technology Facilities Council, UK" + }, + { + "author_name": "Luise Kandler", + "author_inst": "HARBOR, Unversity of Hamburg, Germany" + }, + { + "author_name": "Oliver Kippes", + "author_inst": "HARBOR, Unversity of Hamburg, Germany" + }, + { + "author_name": "Ferdinand Kirsten", + "author_inst": "HARBOR, Unversity of Hamburg, Germany" + }, + { + "author_name": "Konstantin M\u00fcller", + "author_inst": "RVZ, University of W\u00fcrzburg, Germany" + }, + { + "author_name": "Kristopher Nolte", + "author_inst": "HARBOR, Unversity of Hamburg, Germany" + }, + { + "author_name": "Alexander Payne", + "author_inst": "Memorial Sloane Kettering Cancer Center, USA" + }, + { + "author_name": "Matthew G. Reeves", + "author_inst": "RVZ, University of W\u00fcrzburg, Germany" + }, + { + "author_name": "Jane Richardson", + "author_inst": "Duke University, USA" + }, + { + "author_name": "Gianluca Santoni", + "author_inst": "European Synchrotron Radiation Facility, France" + }, + { + "author_name": "Sabrina St\u00e4b", + "author_inst": "RVZ, University of W\u00fcrzburg, Germany" + }, + { + "author_name": "Dale Tronrud", + "author_inst": "University of Oregon, USA" + }, + { + "author_name": "Lea von Soosten", + "author_inst": "HARBOR, Unversity of Hamburg, Germany" + }, + { + "author_name": "Christopher Williams", + "author_inst": "Duke University, USA" + }, + { + "author_name": "Andrea Thorn", + "author_inst": "HARBOR, Unversity of Hamburg, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.10.07.330324", "rel_title": "Mass spectrometric based detection of protein nucleotidylation in the RNA polymerase of SARS-CoV-2", @@ -1172981,29 +1171565,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2020.10.04.20206318", - "rel_title": "The relationship between neighborhood poverty and COVID-19 mortality within racial/ethnic groups (Cook County, Illinois)", - "rel_date": "2020-10-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.04.20206318", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSBackgroundC_ST_ABSPrior research has identified higher rates of COVID-19 mortality among people of color (relative to non-Hispanic whites) and populations in high-poverty neighborhoods (relative to wealthier neighborhoods). It is unclear, however, whether non-Hispanic whites in high-poverty neighborhoods experience elevated mortality, or whether people of color living in wealthy areas are relatively protected. Exploring socioeconomic position in combination with race/ethnicity can lead to a more detailed understanding of the specific processes that result in COVID-19 inequities.\n\nMethods and FindingsWe used census and individual-level mortality data for the non-Hispanic white, non-Hispanic Black, and Hispanic/Latinx populations of Cook County, Illinois, USA. We excluded deaths related to nursing homes and other institutions. We calculated age and gender-adjusted mortality rates by race/ethnicity, census tract poverty quartile, and age group (0-64 and [≥]65 years).\n\nWithin all racial/ethnic groups, COVID-19 mortality rates were greatest in the highest-poverty quartile and lowest in the lowest-poverty quartile. The mortality rate for younger non-Hispanic whites in the highest-poverty quartile was 13.5 times that of younger non-Hispanic whites in the lowest-poverty quartile (95% CI: 8.5, 21.4). For young people in the highest-poverty quartile, the non-Hispanic white and Black mortality rates were similar. Among younger people in the lowest-poverty quartile, non-Hispanic Black and Hispanic/Latinx people had mortality rates nearly three times that of non-Hispanic whites. For the older population, the mortality rate among non-Hispanic whites in the highest-poverty quartile was less than that of lowest-poverty non-Hispanic Black and Hispanic/Latinx populations.\n\nConclusionsOur findings suggest racial/ethnic inequalities in COVID-19 mortality are partly, but not entirely, attributable to the higher average socioeconomic position of non-Hispanic whites relative to the non-Hispanic Black and Hispanic/Latinx populations. Future research on health equity in COVID-19 outcomes should collect and analyze individual-level data on the potential mechanisms driving population distributions of exposure, severe illness, and death.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Justin M Feldman", - "author_inst": "Harvard University" - }, - { - "author_name": "Mary T Bassett", - "author_inst": "Harvard University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.04.20206136", "rel_title": "Strategies for infection control and prevalence of anti-SARS-CoV-2 IgG in 4,554 employees of a university hospital in Munich, Germany", @@ -1173907,6 +1172468,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.03.20204545", + "rel_title": "SARS-CoV-2 Prevalence and Seroprevalence among Healthcare Workers in Belgian Hospitals: Baseline Results of a Prospective Cohort Study", + "rel_date": "2020-10-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.03.20204545", + "rel_abs": "BackgroundGiven the current SARS-CoV-2 pandemic and the occurrence of a second wave, assessing the burden of disease among health care workers (HCWs) is crucial. We aim to document the prevalence of SARS-CoV-2 and the seroprevalence of anti-SARS-CoV-2 IgG among HCWs in Belgian hospitals, and to study potential risk factors for the infection in order to guide infection prevention and control (IPC) measures in healthcare institutions.\n\nMethodsWe performed a cross-sectional analysis of the baseline results (April 22 - April 26) of an ongoing cohort study. All staff who were present in the hospital during the sampling period and whose profession involved contact with patients were eligible. Fourteen hospitals across Belgium and 50 HCW per hospital were randomly selected. RT-qPCR was performed to detect SARS-CoV-2 RNA on nasopharyngeal swabs, and a semi-quantitative IgG ELISA was used to detect anti-SARS-CoV-2 antibodies in sera. Individual characteristics likely to be associated with seropositivity were collected using an online questionnaire.\n\nFindings698 participants completed the questionnaire; 80.8% were women, median age was 39.5, and 58.5% were nurses. Samples were collected on all 699 participants. The weighted anti-SARS-CoV-2 IgG seroprevalence was 7.7% (95%CI, 4.7%-12.2%), while 1.1% (95%CI, 0.4%-3.0%) of PCR results were positive. Unprotected contact with a confirmed case was the only factor associated with seropositivity (PR 2.16, 95% CI, 1.4-3.2).\n\nInterpretationMost Belgian HCW did not show evidence of SARS-CoV-2 infection by late April 2020, and unprotected contact was the most important risk factor. This confirms the importance of widespread availability of protective equipment and use of adequate IPC measures in hospital settings.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Laure Mortgat", + "author_inst": "Sciensano, Brussels; EPIET, Stockholm" + }, + { + "author_name": "Cyril Barbezange", + "author_inst": "Sciensano, Brussels" + }, + { + "author_name": "Natalie Fischer", + "author_inst": "Sciensano, Brussels; EUPHEM, Stockholm" + }, + { + "author_name": "Leo Heyndrickx", + "author_inst": "Institute of Tropical Medicine, Antwerp" + }, + { + "author_name": "Veronik Hutse", + "author_inst": "Sciensano, Brussels" + }, + { + "author_name": "Isabelle Thomas", + "author_inst": "Sciensano, Brussels" + }, + { + "author_name": "Bea Vuylsteke", + "author_inst": "Institute of Tropical Medicine, Antwerp" + }, + { + "author_name": "Kevin Arien", + "author_inst": "Institute of Tropical Medicine, Antwerp; University of Antwerp" + }, + { + "author_name": "Isabelle Desombere", + "author_inst": "Sciensano, Brussels" + }, + { + "author_name": "Els Duysburgh", + "author_inst": "Sciensano, Brussels" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.03.20206284", "rel_title": "The excess insulin requirement in severe COVID-19 compared to non-COVID-19 viral pneumonitis is related to the severity of respiratory failure and pre-existing diabetes.", @@ -1174263,25 +1172879,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.10.03.20206359", - "rel_title": "PREDICTIONS FOR EUROPE FOR THE COVID-19 PANDEMICAFTER LOCKDOWN WAS LIFTED USING AN SIR MODEL", - "rel_date": "2020-10-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.03.20206359", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWI analyze a simplified SIR model developed from a paper written by Gyan Bhanot and Charles de Lisi in May of 2020 to find the successes and limitations of their predictions. In particular, I study the predicted cases and deaths fitted to data from March and its potential application to data in September. The data is observed to fit the model as predicted until around 150 days after December 31, 2019, after which many countries lift their lockdowns and begin to reopen. A plateau in cases followed by an increase approximately 1.5 months after is also observed. In terms of deaths, the data fits the shape of the model, but the model mostly underestimates the death toll after around 160 days. An analysis of the residuals is provided to locate the precise date of the departure of each country from its accepted data estimates and test each data point to its predicted value using a Z-test to determine whether each observation can fit the given model. The observed behavior is matched to policy measures taken in each country to attach an explanation to these observations. I notice that an international reopening results in a sharp increase in cases, and aim to plot this new growth in cases and predict when the pandemic will end for each country.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Jay Patwardhan", - "author_inst": "John P Stevens High School" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.10.03.20206250", "rel_title": "A Data-Informed Approach for Analysis, Validation, and Identification of COVID-19 Models", @@ -1175541,6 +1174138,33 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.10.06.327742", + "rel_title": "Cytoplasmic short linear motifs in ACE2 and integrin beta3 link SARS-CoV-2 host cell receptors to endocytosis and autophagy", + "rel_date": "2020-10-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.06.327742", + "rel_abs": "The spike protein of the SARS-CoV-2 interacts with angiotensin converting enzyme 2 (ACE2) and enters the host cell by receptor-mediated endocytosis. Concomitantly, evidence is pointing to the involvement of additional host cell receptors, such as integrins. The cytoplasmic tails of ACE2 and integrin {beta}3 contain a plethora of predicted binding motifs. Here, we confirm the functionality of some of these motifs through affinity measurements. The class I PDZ binding motif in the ACE2 cytoplasmic tail binds the first PDZ domain of the scaffold protein NHERF3. The clathrin-adaptor subunit AP2 2 interacts with an endocytic motif in the ACE2 with low affinity and the interaction is abolished by phosphorylation of Tyr781. Furthermore, the C-terminal region of integrin b3 contains a LC3-interacting region, and its interaction with ATG8 domains is enhanced by phosphorylation. Together, our data provides possible molecular links between host cell receptors and endocytosis and autophagy.\n\nOne sentence summaryAffinity measurements confirmed binding of short linear motifs in the cytoplasmic tails of ACE2 and integrin {beta}3, thereby linking the receptors to endocytosis and autophagy.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Johanna Kliche", + "author_inst": "Uppsala University" + }, + { + "author_name": "Muhammad Ali", + "author_inst": "Uppsala University" + }, + { + "author_name": "Ylva Ivarsson", + "author_inst": "Uppsala University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.10.06.328369", "rel_title": "SARS-CoV-2 infection damages airway motile cilia and impairs mucociliary clearance", @@ -1175865,81 +1174489,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.10.02.20205880", - "rel_title": "Multi-cohort analysis of host immune response identifies conserved protective and detrimental modules associated with severity irrespective of virus", - "rel_date": "2020-10-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.02.20205880", - "rel_abs": "SARS-CoV-2 pandemic, the fourth pandemic of the decade, has underscored gaps in global pandemic preparedness and the need for generalizable tests to avert overwhelming healthcare systems worldwide, irrespective of a virus. We integrated 4,780 blood transcriptome profiles from patients infected with one of 16 viruses across 34 independent cohorts from 18 countries, and 71 scRNA-seq profiles of 264,224 immune cells across three independent cohorts. We found a myeloid cell-dominated conserved host response associated with severity. It showed increased hematopoiesis, myelopoiesis, and myeloid-derived suppressor cells with increased severity. We identified four gene modules that delineate distinct trajectories associated with mild and severe outcomes, and show the interferon response was decoupled from protective host response during severe viral infection. These modules distinguished non-severe from severe viral infection with clinically useful accuracy. Together, our findings provide insights into immune response dynamics during viral infection, and identify factors that may influence patient outcomes.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Hong Zheng", - "author_inst": "Stanford University" - }, - { - "author_name": "Aditya M Rao", - "author_inst": "Stanford University" - }, - { - "author_name": "Denis Dermadi", - "author_inst": "Stanford University" - }, - { - "author_name": "Jiaying Toh", - "author_inst": "Stanford University" - }, - { - "author_name": "Lara Murphy Jones", - "author_inst": "Stanford University" - }, - { - "author_name": "Michele Donato", - "author_inst": "Stanford University" - }, - { - "author_name": "Yiran Liu", - "author_inst": "Stanford University" - }, - { - "author_name": "Yapeng Su", - "author_inst": "Institute for Systems Biology" - }, - { - "author_name": "Minas Karagiannis", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Theodoros Marantos", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Yehudit Hasin-Brumshtein", - "author_inst": "Inflammatix, Inc" - }, - { - "author_name": "Yudong D He", - "author_inst": "Inflammatix, Inc" - }, - { - "author_name": "Evangelos J Giamarellos-Bourboulis", - "author_inst": "National and Kapodistrian University of Athens" - }, - { - "author_name": "Jim Heath", - "author_inst": "Institute for Systems Biology" - }, - { - "author_name": "Purvesh Khatri", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.10.02.20205609", "rel_title": "Comparing biomarkers for COVID-19 disease with commonly associated preexisting conditions and complications.", @@ -1177131,6 +1175680,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.10.03.20206110", + "rel_title": "COVID-19 Viral Loads, Environment, Ventilation, Masks, Exposure Time, And Severity : A Pragmatic Guide Of Estimates", + "rel_date": "2020-10-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.03.20206110", + "rel_abs": "It can be shown that over 94% of COVID-19 superspreading events occurred in limited ventilation areas suggesting aerosolized transmission is a strong contributor to COVID-19 infections.\n\nThis study helps answer \"How long may a person safely remain within various environments?\" And \"What exposure levels could result in immunity without becoming ill via asymptomatic graduated inoculation?\"\n\nCOVID-19 infection likelihood, symptom severity, and immune response dependencies include viral load exposure amount. A better understanding of these relationships could help determine what Non-Pharmaceutical Interventions (NPI) would help reduce severe case counts and improve at-large epidemiologic responses in specific scenarios.\n\nThis study references peer reviewed and published studies and uses them as data sources for an estimation model that calculates infection likelihood given exposure within several example scenarios. Information from ASHRAE office ventilation standards, typical home ventilation characteristics, and an outdoor air setting are used to establish several specific examples of indoor and outdoor scenarios.\n\nThe model establishes a reference scenario using objectively measured air sample viral load concentration levels found within a carefully documented hospital environment containing 2 sick patients. The model extrapolates the reference scenario into several example scenarios that have varied exposure time duration, ventilation amount, with/without surgical mask use, activity/respiration levels, and infected subject shedding levels. It uses the reference data and scenario extrapolations to calculate an estimate of total viral load exposure dose for each scenario.\n\nThe study then interprets the various scenario total exposure dose estimates using an National Institute of Health human challenge study where volunteers were exposed to multiple specific viral quantities and observed in a clinical environment to objectively determine likelihood of infection, severity level, and immune response given each specific exposure dose. To simplify pragmatic use of the results, each example scenario presents the estimated total exposure dose alongside an intuitive severity category of Not Ill, Minor Illness, Clinical Mild Illness, and Possible Severe Illness which are based on a defined interpretation of the NIH study results. Immune response data related to these categories is also provided along with discussion related to asymptomatic infection, graduated inoculation, and immunity.\n\nWhen appropriately interpreted for individualized applications, the estimates herein could contribute to guidance for those at low-risk for a severe case that have no obvious COVID-19 co-morbidities, with the understanding that those at higher risk should seek to avoid all exposure risk. The estimates herein may help efforts to strike a balance in developing holistic epidemiologic interventions that consider the effects of these interventions on economic, civic, social, and mental health, which have pathologies within their own realms.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "David E. Epperly", + "author_inst": "ReallyCorrect.com" + }, + { + "author_name": "Kristopher R. Rinehart", + "author_inst": "California Mobile Physicians" + }, + { + "author_name": "David N. Caney", + "author_inst": "Tahoe Blue Ltd" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.10.04.325662", "rel_title": "Motif Analysis in k-mer Networks: An Approach towards Understanding SARS-CoV-2 Geographical Shifts", @@ -1177507,37 +1176083,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "transplantation" }, - { - "rel_doi": "10.1101/2020.10.01.20204255", - "rel_title": "COVID-19 Pandemic in University Hospital: Impact on Medical Training of Medical Interns", - "rel_date": "2020-10-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.10.01.20204255", - "rel_abs": "IntroductionCoronavirus 2019 (COVID-19) has strike all nations hard since the end of year 2019, Malaysia unable to escape the fate as well. Healthcare system, financial growth, industrial development and educational programme are stunted. Inevitably, professional training and education are affected which include the medical training of medical interns.\n\nMethodsThis is a cross-sectional, pilot study to determine the impact of the pandemic on University Malaya Medical Centre (UMMC) medical interns. A survey which comprises 37-items was used. Data are analysed by Ordinal Logistic Regression Analysis.\n\nResultsMedical interns feel that they lack clinical skills (p = 0.005) and need more exposure in surgical operations (p =0.029). Some are satisfied with the introduction of triage (p = 0.024), online teaching (p = 0.005) and bedside teaching (p=0.023). Most of them think they are fit and ready to handle the pandemic (p = 0.012 and 0.025 respectively) except first year medical interns (p = 0.029). Some feel like their time are wasted (p <0.05) as they are involved in many non-clinical activities (p = 0.003).\n\nConclusionIn summary, COVID-19 has a great impact on medical training amongst medical interns. Alternative measures should be taken to minimize the interruption in training of our future leaders in medical field.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "WeiHonn Lim", - "author_inst": "University Malaya Medical Centre" - }, - { - "author_name": "Li Ying Teoh", - "author_inst": "University of Malaya Medical Centre" - }, - { - "author_name": "Kanesh Kumaran Seevalingam", - "author_inst": "University of Malaya Medical Centre" - }, - { - "author_name": "Shanggar Kuppusamy", - "author_inst": "University of Malaya Medical Centre" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "medical education" - }, { "rel_doi": "10.1101/2020.10.02.20205070", "rel_title": "Development, evaluation, and validation of machine learning models for COVID-19 detection based on routine blood tests", @@ -1178821,6 +1177366,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.30.20204917", + "rel_title": "Epidemiological and clinical characteristics of COVID-19 in Brazil using digital technology", + "rel_date": "2020-10-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.30.20204917", + "rel_abs": "BackgroundBrazil has the third-highest number of Coronavirus disease 2019 (COVID-19) cases worldwide. Understanding the epidemiology of COVID-19 from reported cases is challenging due to heterogeneous testing rates. We estimated the number of COVID-19 cases in Brazil on a national and regional level using digital technology.\n\nMethodsWe used a web-based application to perform a population-based survey from March 21st to August 29th, 2020 in Brazil. We obtained responses from 243 461 individuals across all federative units, who answered questions on COVID-19-related symptoms, chronic diseases and address of residence. COVID-19 was defined as at least one of the following: fever, cough, dyspnea and nasal flaring, associated with a history of close contact with a suspect or confirmed COVID-19 case in the previous 14 days. A stratified two-stage weighted survey analysis was performed to estimate the population level prevalence of COVID-19 cases.\n\nResultsAfter calibration weighing, we estimated that 10 339 461 cases of COVID-19 occurred, yielding a 2.75 estimated infection per officially reported case. Estimated/reported ratios varied across Brazilian states and were higher in states with lower human development indexes. Areas with lower income levels displayed higher rates of COVID-19 cases (66 vs 38 cases/1000 people in the lowest and highest income strata respectively, p<0.001), but presented lower rates of COVID-19 testing.\n\nConclusionIn this population-based survey using digital technology in Brazil, we estimated that the COVID-19 case rates were 2.75 times higher than officially reported. The estimated per reported case ratios were higher in areas with worse socioeconomic status.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Faissal Nemer Hajar", + "author_inst": "Federal University of Parana" + }, + { + "author_name": "Miguel Morita Fernandes-Silva", + "author_inst": "Federal University of Parana" + }, + { + "author_name": "Gustavo S. Pereira da Cunha", + "author_inst": "Federal University of Parana" + }, + { + "author_name": "Geny Herrera", + "author_inst": "TOTVS labs" + }, + { + "author_name": "Ali Hamud", + "author_inst": "B.Braun Group" + }, + { + "author_name": "Valderilio F Azevedo", + "author_inst": "Universidade Federal do Parana" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.30.20204842", "rel_title": "Oil Immersed Lossless Total Analysis System (OIL-TAS): Integrated RNA Extraction and Detection for SARS-CoV-2 Testing", @@ -1179213,105 +1177797,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.10.02.324145", - "rel_title": "SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs", - "rel_date": "2020-10-02", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.10.02.324145", - "rel_abs": "T cell-mediated immunity may play a critical role in controlling and establishing protective immunity against SARS-CoV-2 infection; yet the repertoire of viral epitopes responsible for T cell response activation remains mostly unknown. Identification of viral peptides presented on class I human leukocyte antigen (HLA-I) can reveal epitopes for recognition by cytotoxic T cells and potential incorporation into vaccines. Here, we report the first HLA-I immunopeptidome of SARS-CoV-2 in two human cell lines at different times post-infection using mass spectrometry. We found HLA-I peptides derived not only from canonical ORFs, but also from internal out-of-frame ORFs in Spike and Nucleoprotein not captured by current vaccines. Proteomics analyses of infected cells revealed that SARS-CoV-2 may interfere with antigen processing and immune signaling pathways. Based on the endogenously processed and presented viral peptides that we identified, we estimate that a pool of 24 peptides would provide one or more peptides for presentation by at least one HLA allele in 99% of the human population. These biological insights and the list of naturally presented SARS-CoV-2 peptides will facilitate data-driven selection of peptides for immune monitoring and vaccine development.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Shira Weingarten-Gabbay", - "author_inst": "Broad Institute" - }, - { - "author_name": "Susan Klaeger", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Siranush Sarkizova", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Leah R Pearlman", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Da-Yuan Chen", - "author_inst": "Department of Biochemistry, Boston University School of Medicine" - }, - { - "author_name": "Matthew R Bauer", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Hannah B Taylor", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Hasahn L Conway", - "author_inst": "Department of Biochemistry, Boston University School of Medicine" - }, - { - "author_name": "Christopher H Tomkins-Tinch", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Yaara Finkel", - "author_inst": "Department of Molecular Genetics, Weizmann Institute of Science" - }, - { - "author_name": "Aharon Nachshon", - "author_inst": "Department of Molecular Genetics, Weizmann Institute of Science" - }, - { - "author_name": "Matteo Gentili", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Keith D Rivera", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Derin B Keskin", - "author_inst": "Translational Immunogenomics Laboratory, Dana-Farber Cancer Institute" - }, - { - "author_name": "Charles M Rice", - "author_inst": "Laboratory of Virology and Infectious Disease, The Rockefeller University" - }, - { - "author_name": "Karl R Clauser", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Nir Hacohen", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Steven A Carr", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Jennifer G Abelin", - "author_inst": "Broad Institute of MIT and Harvard" - }, - { - "author_name": "Mohsan Saeed", - "author_inst": "Department of Biochemistry, Boston University School of Medicine" - }, - { - "author_name": "Pardis C Sabeti", - "author_inst": "Broad Institute of MIT and Harvard" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.10.02.324046", "rel_title": "Safe and effective two-in-one replicon-and-VLP minispike vaccine for COVID-19", @@ -1180683,6 +1179168,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.27.20202671", + "rel_title": "Time-series clustering for home dwell time during COVID-19: what can we learn from it?", + "rel_date": "2020-09-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.27.20202671", + "rel_abs": "In this study, we investigate the potential driving factors that lead to the disparity in the time-series of home dwell time, aiming to provide fundamental knowledge that benefits policy-making for better mitigation strategies of future pandemics. Taking Metro Atlanta as a study case, we perform a trend-driven analysis by conducting Kmeans time-series clustering using fine-grained home dwell time records from SafeGraph, and further assess the statistical significance of sixteen demographic/socioeconomic variables from five major categories. We find that demographic/socioeconomic variables can explain the disparity in home dwell time in response to the stay-at-home order, which potentially leads to disparate exposures to the risk from the COVID-19. The results further suggest that socially disadvantaged groups are less likely to follow the order to stay at home, pointing out the extensive gaps in the effectiveness of social distancing measures exist between socially disadvantaged groups and others. Our study reveals that the long-standing inequity issue in the U.S. stands in the way of the effective implementation of social distancing measures. Policymakers need to carefully evaluate the inevitable trade-off among different groups, making sure the outcomes of their policies reflect interests of the socially disadvantaged groups.\n\nHighlightsO_LIWe perform a trend-driven analysis by conducting Kmeans time-series clustering using fine- grained home dwell time records from SafeGraph.\nC_LIO_LIWe find that demographic/socioeconomic variables can explain the disparity in home dwell time in response to the stay-at-home order.\nC_LIO_LIThe results suggest that socially disadvantaged groups are less likely to follow the order to stay at home, potentially leading to more exposures to the COVID-19.\nC_LIO_LIPolicymakers need to make sure the outcomes of their policies reflect the interests of the disadvantaged groups.\nC_LI", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Xiao Huang", + "author_inst": "University of Arkansas" + }, + { + "author_name": "Zhenlong Li", + "author_inst": "University of South Carolina" + }, + { + "author_name": "Junyu Lu", + "author_inst": "Arizona State University" + }, + { + "author_name": "Sicheng Wang", + "author_inst": "Rutgers University" + }, + { + "author_name": "Hanxue Wei", + "author_inst": "Cornell University" + }, + { + "author_name": "Baixu Chen", + "author_inst": "University of Michigan" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.29.20202598", "rel_title": "Passive Microwave Radiometry (MWR) for diagnostics of COVID-19 lung complications.", @@ -1181043,45 +1179567,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.30.20204644", - "rel_title": "Estimation of novel coronavirus (covid-19) reproduction number and case fatality rate: a systematic review and meta-analysis", - "rel_date": "2020-09-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.30.20204644", - "rel_abs": "Understanding the transmission dynamics and the severity of the novel coronavirus disease 2019 (COVID-19) informs public health interventions, surveillance, and planning. Two important parameters, the basic reproduction number (R0) and case fatality rate (CFR) of COVID-19, help in this understanding process. The objective of this study was to estimate the R0 and CFR of COVID-19 and assess whether the parameters vary in different regions of the world. We carried out a systematic review to retrieve the published estimates of the R0 and the CFR in articles from international databases between 1st January and 31st August 2020. Random-effect models and Forest plots were implemented to evaluate the mean effect size of the R0 and the CFR. Furthermore, the R0 and CFR of the studies were quantified based on geographic location, the tests/thousand population, and the median population age of the countries where studies were conducted. The I2 statistic and the Cochrans Q test were applied to assess statistical heterogeneity among the selected studies. Forty-five studies involving R0 and thirty-four studies involving CFR were included. The pooled estimation of the R0 was 2.69 (95% CI: 2.40, 2.98), and that of the CFR was 2.67 (2.25, 3.13). The CFR in different regions of the world varied significantly, from 2.51 (2.12, 2.95) in Asia to 7.11 (6.38, 7.91) in Africa. We observed higher mean CFR values for the countries with lower tests (3.15 vs. 2.16) and greater median population age (3.13 vs. 2.27). However, the R0 did not vary significantly in different regions of the world. An R0 of 2.69 and CFR of 2.67 indicate the severity of the COVID-19. Although R0 and CFR may vary over time, space, and demographics, we recommend considering these figures in control and prevention measures.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Tanvir Ahammed", - "author_inst": "Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh" - }, - { - "author_name": "Aniqua Anjum", - "author_inst": "Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh" - }, - { - "author_name": "Mohammad Meshbahur Rahman", - "author_inst": "Biomedical Research Foundation, Dhaka-1230, Bangladesh" - }, - { - "author_name": "Najmul Haider", - "author_inst": "Royal Veterinary College" - }, - { - "author_name": "Richard Kock", - "author_inst": "Royal Veterinary College" - }, - { - "author_name": "Md. Jamal Uddin", - "author_inst": "Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.30.20199943", "rel_title": "Propagation of Viral Bioaerosols Indoors", @@ -1182313,6 +1180798,57 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.09.29.318931", + "rel_title": "Computational identification of human biological processes and protein sequence motifs putatively targeted by SARS-CoV-2 proteins using protein-protein interaction networks", + "rel_date": "2020-09-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.29.318931", + "rel_abs": "While the COVID-19 pandemic is causing important loss of life, knowledge of the effects of the causative SARS-CoV-2 virus on human cells is currently limited. Investigating protein-protein interactions (PPIs) between viral and host proteins can provide a better understanding of the mechanisms exploited by the virus and enable the identification of potential drug targets. We therefore performed an in-depth computational analysis of the interactome of SARS-CoV-2 and human proteins in infected HEK293 cells published by Gordon et al. to reveal processes that are potentially affected by the virus and putative protein binding sites. Specifically, we performed a set of network-based functional and sequence motif enrichment analyses on SARS-CoV-2-interacting human proteins and on a PPI network generated by supplementing viral-host PPIs with known interactions. Using a novel implementation of our GoNet algorithm, we identified 329 Gene Ontology terms for which the SARS-CoV-2-interacting human proteins are significantly clustered in the network. Furthermore, we present a novel protein sequence motif discovery approach, LESMoN-Pro, that identified 9 amino acid motifs for which the associated proteins are clustered in the network. Together, these results provide insights into the processes and sequence motifs that are putatively implicated in SARS-CoV-2 infection and could lead to potential therapeutic targets.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Rachel Nadeau", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Soroush Shahryari Fard", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Amit Scheer", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Emily Hashimoto-Roth", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Dallas Nygard", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Iryna Abramchuk", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Yun-En Chung", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Steffany A. L. Bennett", + "author_inst": "University of Ottawa" + }, + { + "author_name": "Mathieu Lavallee-Adam", + "author_inst": "University of Ottawa" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.09.30.320242", "rel_title": "Host range projection of SARS-CoV-2: South Asia perspective", @@ -1182821,49 +1181357,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.27.20199737", - "rel_title": "High-Quality Masks Can Reduce Infections and Deaths in the US", - "rel_date": "2020-09-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.27.20199737", - "rel_abs": "ObjectivesTo evaluate the effectiveness of widespread adoption of masks or face coverings to reduce community transmission of the SARS-CoV-2 virus that causes Covid-19.\n\nMethodsWe employed an agent-based stochastic network simulation model, where Covid-19 progresses across census tracts according to a variant of SEIR. We considered a mask order that was initiated 3.5 months after the first confirmed Covid-19 case. We evaluated scenarios where wearing a mask reduces transmission and susceptibility by 50% or 80%; an individual wears a mask with a probability of 0%, 20%, 40%, 60%, 80%, or 100%.\n\nResultsIf 60% of the population wears masks that are 50% effective, this decreases the cumulative infection attack rate (CAR) by 25%, the peak prevalence by 51%, and the population mortality by 25%. If 100% of people wear masks (or 60% wear masks that are 80% effective), this decreases the CAR by 38%, the peak prevalence by 67%, and the population mortality by 40%.\n\nConclusionsAfter community transmission is present, masks can significantly reduce infections.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Erik Rosenstrom", - "author_inst": "North Carolina State University" - }, - { - "author_name": "Buse Oruc Aglar", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Nathaniel Hupert", - "author_inst": "Cornell University" - }, - { - "author_name": "Julie S. Ivy", - "author_inst": "North Carolina State University" - }, - { - "author_name": "Pinar Keskinocak", - "author_inst": "Georgia Institute of Technology" - }, - { - "author_name": "Maria Mayorga", - "author_inst": "North Carolina State University" - }, - { - "author_name": "Julie L Swann", - "author_inst": "North Carolina State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.28.20203455", "rel_title": "Two Color Single Molecule Sequencing on GenoCare 1600 Platform to Facilitate Clinical Applications", @@ -1184227,6 +1182720,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.28.20203166", + "rel_title": "Comparison of infection control strategies to reduce COVID-19 outbreaks in homeless shelters in the United States: a simulation study", + "rel_date": "2020-09-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.28.20203166", + "rel_abs": "BackgroundCOVID-19 outbreaks have occurred in homeless shelters across the US, highlighting an urgent need to identify the most effective infection control strategy to prevent future outbreaks.\n\nMethodsWe developed a microsimulation model of SARS-CoV-2 transmission in a homeless shelter and calibrated it to data from cross-sectional polymerase-chain-reaction (PCR) surveys conducted during COVID-19 outbreaks in five shelters in three US cities from March 28 to April 10, 2020. We estimated the probability of averting a COVID-19 outbreak when an exposed individual is introduced into a representative homeless shelter of 250 residents and 50 staff over 30 days under different infection control strategies, including daily symptom-based screening, twice-weekly PCR testing and universal mask wearing.\n\nResultsThe proportion of PCR-positive residents and staff at the shelters with observed outbreaks ranged from 2.6% to 51.6%, which translated to basic reproduction number (R0) estimates of 2.9-6.2. The probability of averting an outbreak diminished with higher transmissibility (R0) within the simulated shelter and increasing incidence in the local community. With moderate community incidence (~30 confirmed cases/1,000,000 people/day), the estimated probabilities of averting an outbreak in a low-risk (R0=1.5), moderate-risk (R0=2.9), and high-risk (R0=6.2) shelter were, respectively: 0.35, 0.13 and 0.04 for daily symptom-based screening; 0.53, 0.20, and 0.09 for twice-weekly PCR testing; 0.62, 0.27 and 0.08 for universal masking; and 0.74, 0.42 and 0.19 for these strategies combined.\n\nConclusionsIn high-risk homeless shelter environments and locations with high community incidence of COVID-19, even intensive infection control strategies (incorporating daily symptom-screening, frequent PCR testing and universal mask wearing) are unlikely to prevent outbreaks, suggesting a need for non-congregate housing arrangements for people experiencing homelessness. In lower-risk environments, combined interventions should be employed to reduce outbreak risk.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Lloyd A. C. Chapman", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Margot Kushel", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Sarah N. Cox", + "author_inst": "San Francisco Department of Public Health" + }, + { + "author_name": "Ashley Scarborough", + "author_inst": "San Francisco Department of Public Health" + }, + { + "author_name": "Caroline Cawley", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Trang Nguyen", + "author_inst": "San Francisco Department of Public Health" + }, + { + "author_name": "Isabel Rodriguez-Barraquer", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Bryan Greenhouse", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Elizabeth Imbert", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Nathan C. Lo", + "author_inst": "University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.29.20203745", "rel_title": "Changes to the sebum lipidome upon COVID-19 infection observed via non-invasive and rapid sampling from the skin", @@ -1184635,101 +1183183,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.09.28.317685", - "rel_title": "SARS-CoV-2 D614G Variant Exhibits Enhanced Replication ex vivo and Earlier Transmission in vivo", - "rel_date": "2020-09-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.28.317685", - "rel_abs": "The D614G substitution in the S protein is most prevalent SARS-CoV-2 strain circulating globally, but its effects in viral pathogenesis and transmission remain unclear. We engineered SARS-CoV-2 variants harboring the D614G substitution with or without nanoluciferase. The D614G variant replicates more efficiency in primary human proximal airway epithelial cells and is more fit than wildtype (WT) virus in competition studies. With similar morphology to the WT virion, the D614G virus is also more sensitive to SARS-CoV-2 neutralizing antibodies. Infection of human ACE2 transgenic mice and Syrian hamsters with the WT or D614G viruses produced similar titers in respiratory tissue and pulmonary disease. However, the D614G variant exhibited significantly faster droplet transmission between hamsters than the WT virus, early after infection. Our study demonstrated the SARS-CoV2 D614G substitution enhances infectivity, replication fitness, and early transmission.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Yixuan J Hou", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Shiho Chiba", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Peter Halfmann", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Camille Ehre", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Makoto Kuroda", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Kenneth H Dinnon III", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Sarah R Leist", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Alexandra Sch\u00e4fer", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Noriko Nakajima", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Kenta Takahashi", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Rhianna E Lee", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Teresa M Mascenik", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Caitlin E Edwards", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Longping V Tse", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Richard C Boucher", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Scott H Randell", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Tadaki Suzuki", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Lisa E Gralinski", - "author_inst": "University of North Carolina at Chapel Hill" - }, - { - "author_name": "Yoshihiro Kawaoka", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Ralph S. Baric", - "author_inst": "University of North Carolina at Chapel Hill" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.09.29.20203141", "rel_title": "COVID-19 in Portugal: predictability ofhospitalization, ICU and respiratory-assistance needs", @@ -1185941,6 +1184394,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.09.27.20202754", + "rel_title": "Remdesivir for the treatment of COVID-19: A living systematic review", + "rel_date": "2020-09-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.27.20202754", + "rel_abs": "Objective This living systematic review aims to provide a timely, rigorous and continuously updated summary of the evidence available on the role of remdesivir in the treatment of patients with COVID-19 Methods We adapted an already published common protocol for multiple parallel systematic reviews to the specificities of this question. Eligible studies were randomised trials evaluating the effect of remdesivir versus placebo or no treatment. We conducted searches in the LOVE (Living OVerview of Evidence) platform for COVID-19, a system that maps PICO questions to a repository maintained through regular searches in electronic databases, preprint servers, trial registries and other resources relevant to COVID-19. All the searches covered the period until 25 August 2020. No date or language restrictions were applied. Two reviewers independently evaluated potentially eligible studies according to predefined selection criteria, and extracted data on study characteristics, methods, outcomes, and risk of bias, using a predesigned, standardised form. We performed meta-analyses using random-effect models and assessed overall certainty in evidence using the GRADE approach. A living, web-based version of this review will be openly available during the COVID-19 pandemic. We will resubmit it every time the conclusions change or whenever there are substantial updates. Results Our search strategy yielded 574 references. Finally, we included 3 randomised trials evaluating remdesivir in addition to standard care versus standard care alone. The evidence is very uncertain about the effect of remdesivir on mortality (RR 0.7, 95% CI 0.46 to 1.05; very low certainty evidence) and the need for invasive mechanical ventilation (RR 0.69, 95% CI 0.39 to 1.24; very low certainty evidence). On the other hand, remdesivir likely results in a large reduction in the incidence of adverse effects in patients with COVID-19 (RR 1.29, 95% CI 0.58 to 2.84; moderate certainty evidence). Conclusions The evidence is insufficient for the outcomes critical for making decisions about the role of remdesivir in the treatment of patients with COVID-19, so it is not possible to balance the potential benefits, if any, with the adverse effects and costs. PROSPERO Registration number CRD42020183384 Keywords COVID-19, Coronavirus disease, Severe Acute Respiratory Syndrome Coronavirus 2, Coronavirus Infections, Systematic Review, Remdesivir, Antivirals", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Francisca Verdugo-Paiva", + "author_inst": "Epistemonikos Foundation" + }, + { + "author_name": "Maria Paz Acuna", + "author_inst": "Unidad de Infectologia, Hospital Dr Sotero del Rio, Santiago, Chile" + }, + { + "author_name": "Ivan Sola", + "author_inst": "Biomedical Research Institute Sant Pau, Barcelona, Spain" + }, + { + "author_name": "Gabriel Rada", + "author_inst": "Epistemonikos Foundation" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.27.20202556", "rel_title": "Scrutinizing the Spread of Covid-19 in Madagascar", @@ -1186341,109 +1184825,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.09.27.316174", - "rel_title": "Discovery and Development of Human SARS-CoV-2 Neutralizing Antibodies using an Unbiased Phage Display Library Approach", - "rel_date": "2020-09-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.27.316174", - "rel_abs": "SARS-CoV-2 neutralizing antibodies represent an important component of the ongoing search for effective treatment of and protection against COVID-19. We report here on the use of a naive phage display antibody library to identify a panel of fully human SARS-CoV-2 neutralizing antibodies. Following functional profiling in vitro against an early pandemic isolate as well as a recently emerged isolate bearing the D614G Spike mutation, the clinical candidate antibody, STI-1499, and the affinity-engineered variant, STI-2020, were evaluated for in vivo efficacy in the Syrian golden hamster model of COVID-19. Both antibodies demonstrated potent protection against the pathogenic effects of the disease and a dose-dependent reduction of virus load in the lungs, reaching undetectable levels following a single dose of 500 micrograms of STI-2020. These data support continued development of these antibodies as therapeutics against COVID-19 and future use of this approach to address novel emerging pandemic disease threats.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Xia Cao", - "author_inst": "Sorrento Therapeutics, Inc." - }, - { - "author_name": "Junki Maruyama", - "author_inst": "University of Texas Medical Branch, Department of Pathology, Galveston National Laboratory" - }, - { - "author_name": "Heyue Zhou", - "author_inst": "Sorrento Therapeutics, Inc." - }, - { - "author_name": "Lisa Kerwin", - "author_inst": "Sorrento Therapeutics, Inc." - }, - { - "author_name": "Rachel Sattler", - "author_inst": "University of Texas Medical Branch, Department of Pathology, Galveston National Laboratory" - }, - { - "author_name": "John T Manning", - "author_inst": "University of Texas Medical Branch, Department of Pathology, Galveston National Laboratory" - }, - { - "author_name": "Sachi Johnson", - "author_inst": "Sorrento Therapeutics, Inc." - }, - { - "author_name": "Susan Richards", - "author_inst": "Sorrento Therapeutics, Inc." - }, - { - "author_name": "Yan Li", - "author_inst": "Sorrento Therapeutics, Inc." - }, - { - "author_name": "Weiqun Shen", - "author_inst": "Sorrento Therapeutics, Inc." - }, - { - "author_name": "Benjamin Blair", - "author_inst": "Sorrento Therapeutics, Inc." - }, - { - "author_name": "Na Du", - "author_inst": "Sorrento Therapeutics, Inc." - }, - { - "author_name": "Kyndal Morais", - "author_inst": "Sorrento Therapeutics, Inc." - }, - { - "author_name": "Kate Lawrence", - "author_inst": "Sorrento Therapeutics, Inc." - }, - { - "author_name": "Lucy Lu", - "author_inst": "Sorrento Therapeutics, Inc." - }, - { - "author_name": "Chin-I Pai", - "author_inst": "Sorrento Therapeutics, Inc." - }, - { - "author_name": "Donghui Li", - "author_inst": "Sorrento Therapeutics, Inc." - }, - { - "author_name": "Mark Brunswick", - "author_inst": "Sorrento Therapeutics, Inc." - }, - { - "author_name": "Yanliang Zhang", - "author_inst": "Sorrento Therapeutics, Inc." - }, - { - "author_name": "Henry Ji", - "author_inst": "Sorrento Therapeutics, Inc." - }, - { - "author_name": "Slobodan Paessler", - "author_inst": "University of Texas Medical Branch, Department of Pathology, Galveston National Laboratory" - }, - { - "author_name": "Robert D Allen", - "author_inst": "Sorrento Therapeutics, Inc." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.09.28.316604", "rel_title": "Host transcriptomic profiling of COVID-19 patients with mild, moderate, and severe clinical outcomes", @@ -1187383,6 +1185764,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, + { + "rel_doi": "10.1101/2020.09.25.20197061", + "rel_title": "Hearing the voices of Australian healthcare workers during the COVID-19 pandemic", + "rel_date": "2020-09-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.25.20197061", + "rel_abs": "BackgroundThe statistics of healthcare worker (HCW) COVID-19 infections do not convey the lived experience of HCWs during the pandemic. This study explores the working conditions and issues faced by Australian HCWs.\n\nMethodsQualitative analysis of free-text responses from Australian HCWs from 3 August to 5 August 2020 from an open letter calling for better respiratory protection for HCWs, transparent reporting of HCW COVID-19 infections and diversity in national infection control policy development. The open letter was sent to an email list of 23,000 HCWs from a previous campaign and promoted on social media.\n\nResultsAmong 2,733 HCWs who signed the open letter during the study period, 407 free-text responses were analysed. Doctors and nurses accounted for 58% and 35% of respondents, respectively. Most respondents came from Victoria (48%); New South Wales (18%); Queensland (12%) or Western Australia (12%). Dominant themes included concerns about: work health and safety standards; guidelines on respiratory protection including the omission of fit-testing of P2/N95 respirators; deficiencies in the availability, quality, appropriateness and training of personal protective equipment; a top-down workplace culture that enabled bullying in response to concerns about safety that culminated a loss of trust in leadership, self-reported COVID-19 infections in some respondents and moral injury.\n\nConclusionOccupational moral injury in HCWs is the consequence of lapses in leadership at policy-making and organisational levels that have violated the normative expectations of HCWs. The challenge for healthcare leaders is to address workplace culture, consultation and engagement with HCWs in order to prevent this hidden pandemic from spreading throughout the health system.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Michelle Ananda-Rajah", + "author_inst": "Hospital, Melbourne" + }, + { + "author_name": "Benjamin Veness", + "author_inst": "Hospital, Melbourne" + }, + { + "author_name": "Danielle Berkovic", + "author_inst": "School of Public Health and Preventive Medicine, Monash University, Melbourne" + }, + { + "author_name": "Catriona Parker", + "author_inst": "School of Public Health and Preventive Medicine, Monash University, Melbourne" + }, + { + "author_name": "Greg Kelly", + "author_inst": "Hospital, Sydney" + }, + { + "author_name": "Darshini Ayton", + "author_inst": "School of Public Health and Preventive Medicine, Monash University, Melbourne" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2020.09.25.20201343", "rel_title": "Onset, duration, and persistence of taste and smell changes and other COVID-19 symptoms: longitudinal study in Israeli patients", @@ -1187775,29 +1186195,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.09.23.20200212", - "rel_title": "Impact of Personal Care Habits on Post-Lockdown COVID-19 Contagion: Insights from Agent-based Simulations", - "rel_date": "2020-09-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.23.20200212", - "rel_abs": "After the first wave of spread of the COVID-19 pandemic, countries around the world are struggling to recover their economies by slowly lifting the mobility restrictions and social distance measures enforced during the crisis. Therefore, the post-lockdown containment of the disease will depend strongly not any more on government-imposed interventions but on personal care measures, taken voluntarily by their citizens. In this respect, recent studies have shed some light regarding the effectiveness individual protection habits may have in preventing SARS-Cov-2 transmission, particularly physical contact distancing, facial mask wearing and hand-washing habits. In this paper we describe experiments performed on a simulated COVID-19 epidemic in an artificial population using an agent based model, so as to illustrate to what extent the interplay between such personal care habits contributes to mitigate the spread of the disease, assuming the lack of other population-wide non-pharmaceutical interventions or vaccines. We discuss scenarios where wide adherence to these voluntary care habits alone, can be enough to contain the unfold of the contagion. Our model purpose is illustrative and contributes to ratify the importance of disseminating the message regarding the collective benefits of mass adoption of personal protection and hygiene habits, as an exit strategy for COVID-19 in the new normal state.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Lindsay Alvarez-Pomar", - "author_inst": "Universidad Distrital Francisco Jose de Caldas" - }, - { - "author_name": "Sergio Rojas-Galeano", - "author_inst": "Universidad Distrital Francisco Jose de Caldas" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.09.23.20191726", "rel_title": "SCOAT-Net: A Novel Network for Segmenting COVID-19 Lung Opacification from CT Images", @@ -1189189,6 +1187586,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.09.24.20200873", + "rel_title": "Anti-SARS-CoV-2 IgM and IgG antibodies in health workers in Sergipe, Brazil", + "rel_date": "2020-09-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.24.20200873", + "rel_abs": "BackgroundThe exponential growth of COVID-19 cases in Brazil is overloading health systems with overcrowding of hospitals and overflowing intensive care units. Increasing infection rates in health professionals can lead to the collapse of the health system and further worsen the pandemic. The aim of this study was to evaluate the seroprevalence of IgM and IgG for SARS-CoV-2 in health workers in Sergipe, Brazil.\n\nMethodsThe targeted tests involved health professionals working on the front line to combat COVID-19. The samples were collected in the month of June, in six hospital units in the state of Sergipe.\n\nResults471 health professionals were tested. Of these, 28 workers (5.95%) tested positive for IgM and 64 (13.59%) tested positive for IgG. 9 workers (1.91%) tested positive for IgM and were also positive for IgG.\n\nDiscussionHealth workers must be monitored constantly, because if they are infected, they can spread the virus to colleagues, hospitalized patients and even family members.\n\nConclusionKnowing the prevalence of antibodies to the virus in health workers is an important measure of viral spread control.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "MONICA SANTOS DE MELO Sr.", + "author_inst": "UNIVERSIDADE FEDERAL DE SERGIPE" + }, + { + "author_name": "LYSANDRO PINTO BORGES Sr.", + "author_inst": "UNIVERSIDADE FEDERAL DE SERGIPE" + }, + { + "author_name": "DANIELA RAGUER VALADAO SOUZA Sr.", + "author_inst": "UNIVESIDADE FEDERAL DE SERGIPE" + }, + { + "author_name": "ALINE FAGUNDES MARTINS Sr.", + "author_inst": "UNIVESIDADE FEDERAL DE SERGIPE" + }, + { + "author_name": "JOSE MELQUIADES DE REZENDE NETO Sr.", + "author_inst": "UNIVESIDADE FEDERAL DE SERGIPE" + }, + { + "author_name": "ANDERSON ALVES RIBEIRO Sr.", + "author_inst": "Federal University of the Southern Border" + }, + { + "author_name": "ARYANNE SANTOS Jr.", + "author_inst": "UNIVESIDADE FEDERAL DE SERGIPE" + }, + { + "author_name": "GRAZIELLY BISPO DA INVENCAO Jr.", + "author_inst": "UNIVESIDADE FEDERAL DE SERGIPE" + }, + { + "author_name": "IGOR LEONARDO SANTOS MATOS Jr.", + "author_inst": "UNIVESIDADE FEDERAL DE SERGIPE" + }, + { + "author_name": "KEZIA ALVES DO SANTOS Jr.", + "author_inst": "UNIVESIDADE FEDERAL DE SERGIPE" + }, + { + "author_name": "NICOLAS ALESSANDRO ALVES SOUZA Jr.", + "author_inst": "UNIVESIDADE FEDERAL DE SERGIPE" + }, + { + "author_name": "PAMELA CHAVES BORGES Jr.", + "author_inst": "UNIVESIDADE FEDERAL DE SERGIPE" + }, + { + "author_name": "MAKSON GLEYDSON BRITO DE OLIVEIRA Sr.", + "author_inst": "UNIVERSIDADE FEDERAL DE SERGIPE" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.23.20199877", "rel_title": "A low-cost, rapidly scalable, emergency use ventilator for the COVID-19 crisis", @@ -1189581,53 +1188045,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.24.20200394", - "rel_title": "Hitting the diagnostic sweet spot: Point-of-care SARS-CoV-2 salivary antigen testing with an off-the-shelf glucometer", - "rel_date": "2020-09-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.24.20200394", - "rel_abs": "Significant barriers to the diagnosis of latent and acute SARS-CoV-2 infection continue to hamper population-based screening efforts required to contain the COVID-19 pandemic in the absence of effective antiviral therapeutics or vaccines. We report an aptamer-based SARS-CoV-2 salivary antigen assay employing only low-cost reagents ($3.20/test) and an off-the-shelf glucometer. The test was engineered around a glucometer as it is quantitative, easy to use, and the most prevalent piece of diagnostic equipment globally making the test highly scalable with an infrastructure that is already in place. Furthermore, many glucometers connect to smartphones providing an opportunity to integrate with contract tracing apps, medical providers, and electronic medical records. In clinical testing, the developed assay detected SARS-CoV-2 infection in patient saliva across a range of viral loads - as benchmarked by RT-qPCR - within one hour, with 100% sensitivity (positive percent agreement) and distinguished infected specimens from off-target antigens in uninfected controls with 100% specificity (negative percent agreement). We propose that this approach can provide an inexpensive, rapid, and accurate diagnostic for distributed screening of SARS-CoV-2 infection at scale.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Naveen K Singh", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Partha Ray", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Aaron F Carlin", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Celestine Magallanes", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Sydney Morgan", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Louise C Laurent", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Eliah Aronoff-Spencer", - "author_inst": "UC San Diego" - }, - { - "author_name": "Drew A. Hall", - "author_inst": "University of California, San Diego" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.25.20200956", "rel_title": "An easy, reliable and rapid SARS-CoV2 RT-LAMP based test for Point-of-Care and diagnostic lab", @@ -1190911,6 +1189328,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.23.20150961", + "rel_title": "Prospective comparison of saliva and nasopharyngeal swab sampling for mass screening for COVID-19", + "rel_date": "2020-09-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.23.20150961", + "rel_abs": "Current testing for COVID-19 relies on quantitative reverse-transcriptase polymerase chain reaction from a nasopharyngeal swab specimen. Saliva samples have advantages regarding ease and painlessness of collection, which does not require trained staff and may allow self-sampling. We enrolled 776 persons at various field-testing sites and collected nasopharyngeal and pooled saliva samples. 162 had a positive COVID-19 RT-PCR, 61% were mildly symptomatic and 39% asymptomatic. The sensitivity of RT-PCR on saliva samples versus nasopharygeal swabs varied depending on the patient groups considered or on Ct thresholds. There were 10 (6.2%) patients with a positive saliva sample and a negative nasopharyngeal swab, all of whom had Ct values<25. For symptomatic patients for whom the interval between symptoms onset and sampling was <10 days sensitivity was 77% but when excluding persons with isolated Ngen positivity (54/162), sensitivity was 90%. In asymptomatic patients, the sensitivity was only 24%. When we looked at patients with Cts <30, sensitivity was 83% or 88.9% when considering 2 genes. The relatively good performance for patients with low Cts suggests that Saliva testing could be a useful and acceptable tool to identify infectious persons in mass screening contexts, a strategically important task for contact tracing and isolation in the community.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "- COVISAL Guyane", + "author_inst": "" + }, + { + "author_name": "mathieu nacher", + "author_inst": "Centre Hospitalier Andree Rosemon" + }, + { + "author_name": "magalie demar", + "author_inst": "Centre Hospitalier Andree Rosemon" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.23.20200089", "rel_title": "Epidemiological measures for informing the general public during the SARS-CoV-2-outbreak: simulation study about bias by incomplete case-detection", @@ -1191311,45 +1189755,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.09.24.310490", - "rel_title": "Broad-spectrum, patient-adaptable inhaled niclosamide-lysozyme particles are efficacious against coronaviruses in lethal murine infection models", - "rel_date": "2020-09-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.24.310490", - "rel_abs": "Niclosamide (NIC) has demonstrated promising in vitro antiviral efficacy against SARS-CoV-2, the causative agent of the COVID-19 pandemic. Though NIC is already FDA-approved, the oral formulation produces systemic drug levels that are too low to inhibit SARS-CoV-2. As an alternative, direct delivery of NIC to the respiratory tract as an aerosol could target the primary site of for SARS-CoV-2 acquisition and spread. We have developed a niclosamide powder suitable for delivery via dry powder inhaler, nebulizer, and nasal spray through the incorporation of human lysozyme (hLYS) as a carrier molecule. This novel formulation exhibits potent in vitro and in vivo activity against MERS-CoV and SARS-CoV-2 and may protect against methicillin-resistance staphylococcus aureus pneumonia and inflammatory lung damage occurring secondary to CoV infections. The suitability of the formulation for all stages of the disease and low-cost development approach will ensure wide-spread utilization", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Ashlee D Brunaugh", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "Hyojong Seo", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "Zachary Warnken", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "Li Ding", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "Sang Heui Seo", - "author_inst": "Chungnam National University" - }, - { - "author_name": "Hugh D.C. Smyth", - "author_inst": "University of Texas at Austin" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2020.09.24.311027", "rel_title": "S-Trimer, a COVID-19 subunit vaccine candidate, induces protective immunity in nonhuman primates", @@ -1192693,6 +1191098,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.20.20198515", + "rel_title": "Efficacy and Safety of Guduchi Ghan Vati in the Management of Asymptomatic COVID-19 infection: An Open Label Feasibility Study", + "rel_date": "2020-09-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.20.20198515", + "rel_abs": "BackgroundGuduchi Ghan Vati (aqueous extract of Tinospora cordifolia) is an essential herbal plant in Indian traditional medicine (Ayurveda) that is well documented as an immunomodulator and antimicrobial agent. A recent in silico study found the therapeutic efficacy of Guduchi against SARS-CoV-2. Based on available evidence, we conducted a feasibility study of the safety and efficacy of Guduchi Ghan Vati in asymptomatic patients with covid-19.\n\nPatients and methodsAn open label, feasibility trial was conducted on 46 patients in the hospital setting. A single-arm study with no control group and blinding was executed in Jodhpur, Rajasthan, India. All patients orally received 2 tablets (1000 mg) twice daily for 2 weeks. Clinical parameters were collected at baseline, day 3, day 7 and day 14. Patients were continuously monitored for side effects and adverse reactions during the study period..\n\nResultsOut of 46 asymptomatic patients included in the study, 40 completed the 14-day follow-up period. None developed any Covid-19 symptoms after admission to the hospital. On day 3 post-treatment, viral clearance was reported in 16 (32.5%) patients. By the end of D-7, 38 (95%) patients had viral load disappearance. Follow-up at D-14 showed that all participants tested negative.\n\nConclusionIn adult patients with asymptomatic Covid-19, Gudhuchi Ghan Vati could be effective. Randomized controlled trials with larger sample sizes in patients with Covid-19 are urgently needed to confirm the definite benefit with Ayurveda.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Abhimanyu Kumar", + "author_inst": "Dr Sarvepalli Radhakrishnan Rajasthan Ayurved University, Jodhpur, India" + }, + { + "author_name": "Govind Prasad", + "author_inst": "Dr Sarvepalli Radhakrishnan Rajasthan Ayurved University, Jodhpur, India" + }, + { + "author_name": "Sanjay Srivastav", + "author_inst": "Dr Sarvepalli Radhakrishnan Rajasthan Ayurved University Jodhpur, India" + }, + { + "author_name": "Vinod Kumar Gautam", + "author_inst": "Dr Sarvepalli Radhakrishnan Rajasthan Ayurved University Jodhpur, India" + }, + { + "author_name": "Neha Sharma", + "author_inst": "Aarogyam (UK) CIC, United Kingdom" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.21.20198671", "rel_title": "T cell anergy in COVID-19 reflects virus persistence and poor outcomes", @@ -1193061,49 +1191501,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.20.20198432", - "rel_title": "COVID-19 dynamics across the US: A deep learning study of human mobility and social behavior", - "rel_date": "2020-09-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.20.20198432", - "rel_abs": "This paper presents a deep learning framework for epidemiology system identification from noisy and sparse observations with quantified uncertainty. The proposed approach employs an ensemble of deep neural networks to infer the time-dependent reproduction number of an infectious disease by formulating a tensor-based multi-step loss function that allows us to efficiently calibrate the model on multiple observed trajectories. The method is applied to a mobility and social behavior-based SEIR model of COVID-19 spread. The model is trained on Google and Unacast mobility data spanning a period of 66 days, and is able to yield accurate future forecasts of COVID-19 spread in 203 US counties within a time-window of 15 days. Strikingly, a sensitivity analysis that assesses the importance of different mobility and social behavior parameters reveals that attendance of close places, including workplaces, residential, and retail and recreational locations, has the largest impact on the basic reproduction number. The model enables us to rapidly probe and quantify the effects of government interventions, such as lock-down and re-opening strategies. Taken together, the proposed framework provides a robust workflow for data-driven epidemiology model discovery under uncertainty and produces probabilistic forecasts for the evolution of a pandemic that can judiciously inform policy and decision making. All codes and data accompanying this manuscript are available at https://github.com/PredictiveIntelligenceLab/DeepCOVID19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Mohamed Aziz Bhouri", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Francisco Sahli Costabal", - "author_inst": "Pontificia Universidad Catolica de Chile" - }, - { - "author_name": "Hanwen Wang", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Kevin Linka", - "author_inst": "Stanford University" - }, - { - "author_name": "Mathias Peirlinck", - "author_inst": "Stanford University" - }, - { - "author_name": "Ellen Kuhl", - "author_inst": "Stanford University" - }, - { - "author_name": "Paris Perdikaris", - "author_inst": "University of Pennsylvania" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.21.20198416", "rel_title": "Estimate of the actual number of COVID-19 cases from the analysis of deaths.", @@ -1194555,6 +1192952,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.09.21.20195537", + "rel_title": "Downregulation of Defensin genes in SARS-CoV-2 infection", + "rel_date": "2020-09-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.21.20195537", + "rel_abs": "Defensins, crucial components of the innate immune system, play a vital role against infection as part of frontline immunity. Association of SARS-CoV-2 infection with defensins has not been investigated till date. In this study, we have investigated the expression of defensin genes in the buccal cavity during COVID-19 infection. Nasopharyngeal/Oropharyngeal swab samples collected for screening SARS-CoV-2 infection were analyzed for the expression of major defensin genes by the quantitative real-time reverse transcription polymerase chain reaction, qRT-PCR. 40 SARS-CoV-2 infected positive and 40 negative swab samples were selected for the study. Based on the RT-PCR analysis involving gene specific primer for defensin genes, 10 defensin genes were found to be expressed in the Nasopharyngeal/Oropharyngeal cavity. Six defensin genes were further found to be significantly downregulated in SARS-CoV-2 infected patients as against the control, negative samples based on differential expression analysis. The genes significantly downregulated were defensin beta 4A, 4B, 106B, 107B, 103A and defensin alpha 1B. Downregulation of several defensin genes suggests that innate immunity provided by defensins is or may be compromised in SARS-CoV-2 infection resulting in progression of the disease caused by the virus. Upregulation of defensin gene expression and use of defensin peptides could be attractive therapeutic interventions.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Mohammed M Idris", + "author_inst": "CSIR - Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Sarena Banu", + "author_inst": "CSIR - Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Archana B Siva", + "author_inst": "CSIR - Centre for Cellular and Molecular Biology" + }, + { + "author_name": "Ramakrishnan Nagaraj", + "author_inst": "CSIR-Centre for Cellular and Molecular Biology" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.21.20194019", "rel_title": "Putting (Big) Data in Action: Saving Lives with Countrywide Population Movement Monitoring Using Mobile Devices during the COVID-19 Crisis", @@ -1194891,97 +1193319,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "addiction medicine" }, - { - "rel_doi": "10.1101/2020.09.20.20196907", - "rel_title": "Microfluidic Affinity Profiling reveals a Broad Range of Target Affinities for Anti-SARS-CoV-2 Antibodies in Plasma of Covid Survivors", - "rel_date": "2020-09-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.20.20196907", - "rel_abs": "The clinical outcome of SARS-CoV-2 infections, which can range from asymptomatic to lethal, is crucially shaped by the concentration of antiviral antibodies and by their affinity to their targets. However, the affinity of polyclonal antibody responses in plasma is difficult to measure. Here we used Microfluidic Antibody Affinity Profiling (MAAP) to determine the aggregate affinities and concentrations of anti-SARS-CoV-2 antibodies in plasma samples of 42 seropositive individuals, 19 of which were healthy donors, 20 displayed mild symptoms, and 3 were critically ill. We found that dissociation constants, Kd, of anti-receptor binding domain antibodies spanned 2.5 orders of magnitude from sub-nanomolar to 43 nM. Using MAAP we found that antibodies of seropositive individuals induced the dissociation of pre-formed spike-ACE2 receptor complexes, which indicates that MAAP can be adapted as a complementary receptor competition assay. By comparison with cytopathic-effect based neutralisation assays, we show that MAAP can reliably predict the cellular neutralisation ability of sera, which may be an important consideration when selecting the most effective samples for therapeutic plasmapheresis and tracking the success of vaccinations.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Matthias M. Schneider", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Marc Emmenegger", - "author_inst": "Institute of Neuropathology" - }, - { - "author_name": "Catherine K. Xu", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Itzel Condado Morales", - "author_inst": "Insitute of Neuropathology, University Hospital Zurich" - }, - { - "author_name": "Georg Meisl", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Priscilla Turelli", - "author_inst": "Ecole Polytechnique Federale de Lausanne" - }, - { - "author_name": "Chryssa Zografou", - "author_inst": "University of Zurich" - }, - { - "author_name": "Manuela R. Zimmermann", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Beat M. Frey", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Sebastian Fiedler", - "author_inst": "Fluidic Analytics" - }, - { - "author_name": "Viola Denninger", - "author_inst": "Fluidic Analytics" - }, - { - "author_name": "Raphael P.B. Jacquat", - "author_inst": "Department of Chemistry, University of Cambridge" - }, - { - "author_name": "Lidia Madrigal", - "author_inst": "University Hospital Zurich" - }, - { - "author_name": "Alison Isley", - "author_inst": "Fluidic Analytics, Cambridge" - }, - { - "author_name": "Vasilis Kosmoliaptsis", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Heike Fiegler", - "author_inst": "Fluidic Analytics" - }, - { - "author_name": "Didier Trono", - "author_inst": "Ecole Polytechnique Federale de Lausanne" - }, - { - "author_name": "Tuomas P. J. Knowles", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Adriano AA Aguzzi", - "author_inst": "University of Zurich" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2020.09.23.20197756", "rel_title": "A population-based seroprevalence survey of severe acute respiratory syndrome coronavirus 2 infection in Beijing, China", @@ -1196293,6 +1194630,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.16.20195925", + "rel_title": "OpenABM-Covid19 - an agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing", + "rel_date": "2020-09-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.16.20195925", + "rel_abs": "SARS-CoV-2 has spread across the world, causing high mortality and unprecedented restrictions on social and economic activity. Policymakers are assessing how best to navigate through the ongoing epidemic, with models being used to predict the spread of infection and assess the impact of public health measures. Here, we present OpenABM-Covid19: an agent-based simulation of the epidemic including detailed age-stratification and realistic social networks. By default the model is parameterised to UK demographics and calibrated to the UK epidemic, however, it can easily be re-parameterised for other countries. OpenABM-Covid19 can evaluate non-pharmaceutical interventions, including both manual and digital contact tracing. It can simulate a population of 1 million people in seconds per day allowing parameter sweeps and formal statistical model-based inference. The code is open-source and has been developed by teams both inside and outside academia, with an emphasis on formal testing, documentation, modularity and transparency. A key feature of OpenABM-Covid19 is its Python interface, which has allowed scientists and policymakers to simulate dynamic packages of interventions and help compare options to suppress the COVID-19 epidemic.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Robert Hinch", + "author_inst": "Big Data Institute, University of Oxford" + }, + { + "author_name": "William J M Probert", + "author_inst": "Big Data Institute, University of Oxford" + }, + { + "author_name": "Anel Nurtay", + "author_inst": "Big Data Institute, University of Oxford" + }, + { + "author_name": "Michelle Kendall", + "author_inst": "Big Data Institute, University of Oxford" + }, + { + "author_name": "Chris Wymatt", + "author_inst": "Big Data Institute, University of Oxford" + }, + { + "author_name": "Matthew Hall", + "author_inst": "Big Data Institute, University of Oxford" + }, + { + "author_name": "Katrina Lythgoe", + "author_inst": "Big Data Institute, University of Oxford" + }, + { + "author_name": "Ana Bulas Cruz", + "author_inst": "Big Data Institute, University of Oxford" + }, + { + "author_name": "Lele Zhao", + "author_inst": "Big Data Institute, University of Oxford" + }, + { + "author_name": "Andrea Stewart", + "author_inst": "Big Data Institute, University of Oxford" + }, + { + "author_name": "Luca Ferritti", + "author_inst": "Big Data Institute, University of Oxford" + }, + { + "author_name": "Daniel Montero", + "author_inst": "IBM United Kingdom" + }, + { + "author_name": "James Warren", + "author_inst": "IBM United Kingdom" + }, + { + "author_name": "Nicole Mather", + "author_inst": "IBM United Kingdom" + }, + { + "author_name": "Matthew Abueg", + "author_inst": "Google Research" + }, + { + "author_name": "Neo Wu", + "author_inst": "Google Research" + }, + { + "author_name": "Anthony Finkelstein", + "author_inst": "Department of Computer Science, University College London" + }, + { + "author_name": "David G Bonsall", + "author_inst": "Big Data Institute, University of Oxford" + }, + { + "author_name": "Lucie Abeler-Dorner", + "author_inst": "Big Data Institute, University of Oxford" + }, + { + "author_name": "Christophe Fraser", + "author_inst": "Big Data Institute, University of Oxford" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.17.20192245", "rel_title": "Nasopharyngeal SARS-CoV2 viral loads in young children do not differ significantly from those in older children and adults", @@ -1196617,89 +1195049,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.21.20199133", - "rel_title": "Reorganization of Substance Use Treatment and Harm Reduction Services during the COVID-19 Pandemic: A Global Survey", - "rel_date": "2020-09-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.21.20199133", - "rel_abs": "BackgroundThe COVID-19 pandemic has impacted people with substance use disorders (SUDs) worldwide and healthcare systems have reorganized their services in response to the pandemic.\n\nMethodsOne week after the announcement of the COVID-19 as a pandemic, in a global survey, 177 addiction medicine professionals described COVID-19-related health responses in their own 77 countries in terms of SUD treatment and harm reduction services. The health response is categorized around (1) managerial measures and systems, (2) logistics, (3) service providers and (4) vulnerable groups.\n\nResultsRespondents from over 88% of countries reported that core medical and psychiatric care for SUDs had continued; however, only 56% of countries reported having had any business continuity plan, and, 37.5% of countries reported shortages of methadone or buprenorphine supplies. Participants of 41% of countries reported partial discontinuation of harm-reduction services such as needle and syringe programs and condom distribution. 57% of overdose prevention interventions and 81% of outreach services also having been negatively impacted.\n\nConclusionsParticipants reported that SUD treatment and harm reduction services had been significantly impacted globally early during the COVID-19 pandemic. Based on our findings, we provide a series of recommendations to support countries to be prepared more efficiently for future waves or similar pandemics to 1) help policymakers generate business continuity plans, 2) maintain use of evidence-based interventions for people with SUDs, 3) be prepared for adequate medication supplies, 4) integrate harm reduction programs with other treatment modalities and 5) have specific considerations for vulnerable groups such as immigrants and refugees.\n\nHighlightsO_LICOVID-19 negatively impacted services for PWSUD globally.\nC_LIO_LIAddiction medicine downgraded more than other psychiatry services.\nC_LIO_LIBusiness continuity plan for PWSUD services reported only in about half of the countries.\nC_LIO_LIRefugees & migrants had more negative impact compared to other vulnerable groups.\nC_LIO_LIHarm reduction services discontinued partially or totally during pandemic.\nC_LI", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Seyed Ramin Radfar", - "author_inst": "Integrated Substance Abuse Programs Department, University of California, Los Angeles, USA; Department of Psychiatry, Tehran University of Medical Sciences, Te" - }, - { - "author_name": "Cornelis A J De Jong", - "author_inst": "Radboud University, Netherlands" - }, - { - "author_name": "Ali Farhoudian", - "author_inst": "Department of Psychiatry, Tehran University of Medical Sciences, Tehran, Iran; Substance Abuse and Dependence Research Center, University of Social Welfare and " - }, - { - "author_name": "Mohsen Ebrahimi", - "author_inst": "Iranian National Center for Addiction Studies, Tehran University of Medical Sciences, Iran; Materials and Energy Research Center, Iran" - }, - { - "author_name": "Parnian Rafei", - "author_inst": "Department of Psychology, Faculty of Psychology and Education, University of Tehran, Iran" - }, - { - "author_name": "Mehrnoosh Vahidi", - "author_inst": "Department of Psychiatry, Tehran University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Masud Yunesian", - "author_inst": "School of Public Health, Tehran University of Medical Sciences, Tehran, Iran" - }, - { - "author_name": "Christos Kouimtsidis", - "author_inst": "Surrey and Borders Partnership NHS Foundation Trust, UK" - }, - { - "author_name": "Shalini Arunogiri", - "author_inst": "Turning Point, Eastern Health, Box Hill, Australia" - }, - { - "author_name": "Omid Massah", - "author_inst": "Substance Abuse and Dependence Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran" - }, - { - "author_name": "Abbas Deylamizadeh", - "author_inst": "Rebirth Charity Society NGO, Tehran, Iran" - }, - { - "author_name": "Kathleen T Brady", - "author_inst": "Medical University of South Carolina, USA" - }, - { - "author_name": "Anja Busse", - "author_inst": "Prevention, Treatment and Rehabilitation Section; Drug Prevention and Health Branch, Division for Operations, United Nations Office on Drugs and Crime, Vienna, " - }, - { - "author_name": "- ISAM-PPIG Global Survey Consortium", - "author_inst": "" - }, - { - "author_name": "Marc N Potenza", - "author_inst": "Yale School of Medicine, Connecticut Council on Problem Gambling and Connecticut Mental Health Center, USA" - }, - { - "author_name": "Hamed Ekhtiari", - "author_inst": "Laureate Institute for Brain Research, Tulsa, OK, USA" - }, - { - "author_name": "Alexander Mario Baldacchino", - "author_inst": "University of St Andrews, UK" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "addiction medicine" - }, { "rel_doi": "10.1101/2020.09.22.20199398", "rel_title": "Epidemiological characteristics of COVID-19 cases in non-Italian nationals notified to the Italian surveillance system", @@ -1197926,6 +1196275,109 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.18.20197327", + "rel_title": "Hydroxychloroquine as pre-exposure prophylaxis for COVID-19 in healthcare workers: a randomized trial", + "rel_date": "2020-09-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.18.20197327", + "rel_abs": "Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a rapidly emerging virus causing the ongoing Covid-19 pandemic with no known effective prophylaxis. We investigated whether hydroxychloroquine could prevent SARS CoV-2 in healthcare workers at high-risk of exposure. Methods: We conducted a randomized, double-blind, placebo-controlled clinical trial of healthcare workers with ongoing exposure to persons with Covid-19, including those working in emergency departments, intensive care units, Covid-19 hospital wards, and first responders. Participants across the United States and in the Canadian province of Manitoba were randomized to hydroxychloroquine 400mg once weekly or twice weekly for 12 weeks. The primary endpoint was confirmed or probable Covid-19-compatible illness. We measured hydroxychloroquine whole blood concentrations. Results: We enrolled 1483 healthcare workers, of which 79% reported performing aerosol-generating procedures. The incidence of Covid-19 (laboratory-confirmed or symptomatic compatible illness) was 0.27 events per person-year with once-weekly and 0.28 events per person-year with twice-weekly hydroxychloroquine compared with 0.38 events per person-year with placebo. For once weekly hydroxychloroquine prophylaxis, the hazard ratio was 0.72 (95%CI 0.44 to 1.16; P=0.18) and for twice weekly was 0.74 (95%CI 0.46 to 1.19; P=0.22) as compared with placebo. Median hydroxychloroquine concentrations in whole blood were 98 ng/mL (IQR, 82-120) with once-weekly and 200 ng/mL (IQR, 159-258) with twice-weekly dosing. Hydroxychloroquine concentrations did not differ between participants who developed Covid-19 (154 ng/mL) versus participants without Covid-19 (133 ng/mL; P=0.08). Conclusions: Pre-exposure prophylaxis with hydroxychloroquine once or twice weekly did not significantly reduce laboratory-confirmed Covid-19 or Covid-19-compatible illness among healthcare workers.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Radha Rajasingham", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Ananta S Bangdiwala", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Melanie R Nicol", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Caleb P Skipper", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Katelyn A Pastick", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Margaret L Axelrod", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Matthew F Pullen", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Alanna A Nascene", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Darlisha A Williams", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Nicole W Engen", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Elizabeth C Okafor", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Brian I Rini", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Ingrid A Mayer", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Emily G McDonald", + "author_inst": "McGill University" + }, + { + "author_name": "Todd C Lee", + "author_inst": "McGill University" + }, + { + "author_name": "Peter Li", + "author_inst": "Oregon Health & Science University" + }, + { + "author_name": "Lauren J MacKenzie", + "author_inst": "University of Manitoba" + }, + { + "author_name": "Justin M Balko", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Stephen J Dunlop", + "author_inst": "Hennepin Healthcare" + }, + { + "author_name": "Katherine H Hullsiek", + "author_inst": "University of Minnesota" + }, + { + "author_name": "David R Boulware", + "author_inst": "University of Minnesota" + }, + { + "author_name": "SARAH M LOFGREN", + "author_inst": "UNIVERSITY OF MINNESOTA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.17.20196436", "rel_title": "Comparison of COVID-19 outcomes among shielded and non-shielded populations: A general population cohort study of 1.3 million", @@ -1198406,49 +1196858,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.09.21.306357", - "rel_title": "Cryo-EM structure of S-Trimer, a subunit vaccine candidate for COVID-19", - "rel_date": "2020-09-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.21.306357", - "rel_abs": "Less than a year after its emergence, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected over 22 million people worldwide with a death toll approaching 1 million. Vaccination remains the best hope to ultimately put this pandemic to an end. Here, using Trimer-Tag technology, we produced both wild-type (WT) and furin site mutant (MT) S-Trimers for COVID-19 vaccine studies. Cryo-EM structures of the WT and MT S-Trimers, determined at 3.2 [A] and 2.6 [A] respectively, revealed that both antigens adopt a tightly closed conformation and their structures are essentially identical to that of the previously solved full-length WT S protein in detergent. These results validate Trimer-Tag as a platform technology in production of metastable WT S-Trimer as a candidate for COVID-19 subunit vaccine.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Jiahao Ma", - "author_inst": "Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University; National Institute of Biological Sciences, 102206 Beijing, China" - }, - { - "author_name": "Danmei Su", - "author_inst": "Clover Biopharmaceuticals, Chengdu, China" - }, - { - "author_name": "Xueqin Huang", - "author_inst": "Clover Biopharmaceuticals, Chengdu, China" - }, - { - "author_name": "Ying Liang", - "author_inst": "Clover Biopharmaceuticals, Chengdu, China" - }, - { - "author_name": "Yan Ma", - "author_inst": "National Institute of Biological Sciences, Beijing; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 102206 Beijing, China." - }, - { - "author_name": "Peng Liang", - "author_inst": "Clover Biopharmaceuticals, Chengdu, China" - }, - { - "author_name": "Sanduo Zheng", - "author_inst": "National Institute of Biological Sciences, Beijing; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 102206 Beijing, China." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.09.21.306720", "rel_title": "Investigation of COVID-19 comorbidities reveals genes and pathways coincident with the SARS-CoV-2 viral disease", @@ -1199332,6 +1197741,125 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.15.20188896", + "rel_title": "Pre-existing T cell memory as a risk factor for severe 1 COVID-19 in the elderly", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.15.20188896", + "rel_abs": "Coronavirus disease 2019 (COVID-19) displays high clinical variability but the parameters that determine disease severity are still unclear. Pre-existing T cell memory has been hypothesized as a protective mechanism but conclusive evidence is lacking. Here we demonstrate that all unexposed individuals harbor SARS-CoV-2-specific memory T cells with marginal cross-reactivity to common cold corona and other unrelated viruses. They display low functional avidity and broad protein target specificities and their frequencies correlate with the overall size of the CD4+ memory compartment reflecting the \"immunological age\" of an individual. COVID-19 patients have strongly increased SARS-CoV-2-specific inflammatory T cell responses that are correlated with severity. Strikingly however, patients with severe COVID-19 displayed lower TCR functional avidity and less clonal expansion. Our data suggest that a low avidity pre-existing T cell memory negatively impacts on the T cell response quality against neoantigens such as SARS-CoV-2, which may predispose to develop inappropriate immune reactions especially in the elderly. We propose the immunological age as an independent risk factor to develop severe COVID-19.\n\nKey points- Pre-existing SARS-CoV-2-reactive memory T cells are present in all humans, but have low functional avidity and broad target specificities\n- Pre-existing memory T cells show only marginal cross-reactivity to common cold corona viruses\n- Frequencies of pre-existing memory T cells increase with the size of the CD4+ memory compartment reflecting the \"immunological age\" of the individual\n- Low-avidity and polyclonal, but strongly enhanced SARS-CoV-2 specific T cell responses develop in severe COVID-19, suggesting their origin from pre-existing memory\n- The immunological age may represent a risk factor to develop severe COVID-19", + "rel_num_authors": 26, + "rel_authors": [ + { + "author_name": "Petra Bacher", + "author_inst": "Institute of Immunology, Christian-Albrechts-University of Kiel & UKSH Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Elisa Rosati", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany" + }, + { + "author_name": "Daniela Esser", + "author_inst": "Neuroimmunology, Institute of Clinical Chemistry, University Hospital Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Gabriela Rios Martini", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany" + }, + { + "author_name": "Carina Saggau", + "author_inst": "Institute of Immunology, Christian-Albrechts-University of Kiel & UKSH Schleswig-Holstein, 11 Kiel, Germany" + }, + { + "author_name": "Esther Schiminsky", + "author_inst": "Institute of Immunology, Christian-Albrechts-University of Kiel & UKSH Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Justina Dargvainiene", + "author_inst": "Neuroimmunology, Institute of Clinical Chemistry, University Hospital Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Ina Schr\u00f6der", + "author_inst": "Neuroimmunology, Institute of Clinical Chemistry, University Hospital Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Imke Wieters", + "author_inst": "Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt & Goethe University Frankfurt, Frankfurt am Main, Germany" + }, + { + "author_name": "Fabian Eberhardt", + "author_inst": "Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt & Goethe University Frankfurt, Frankfurt am Main, Germany" + }, + { + "author_name": "Holger Neb", + "author_inst": "Department of Anesthesiology, Intensive Care Medicine and Pain Therapy, University Hospital Frankfurt, Frankfurt am Main, Germany." + }, + { + "author_name": "Yascha Khodamoradi", + "author_inst": "Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt & Goethe University Frankfurt, Frankfurt am Main, Germany" + }, + { + "author_name": "Michael Sonntagbauer", + "author_inst": "Department of Anesthesiology, Intensive Care Medicine and Pain Therapy, University Hospital Frankfurt, Frankfurt am Main, Germany." + }, + { + "author_name": "Maria JGT Vehreschild", + "author_inst": "Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt & Goethe University Frankfurt, Frankfurt am Main, Germany" + }, + { + "author_name": "Claudio Conrad", + "author_inst": "Department of Internal Medicine, Hospital of Preetz, Preetz, Germany" + }, + { + "author_name": "Florian Tran", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany." + }, + { + "author_name": "Philip Rosenstiel", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany." + }, + { + "author_name": "Robert Markewitz", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany." + }, + { + "author_name": "Klaus-Peter Wandinger", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany." + }, + { + "author_name": "Jan Rybniker", + "author_inst": "University of Cologne, Medical Faculty and University Hospital Cologne, Department I of Internal Medicine, 50937 Cologne, Germany" + }, + { + "author_name": "Matthias Kochanek", + "author_inst": "University of Cologne, Medical Faculty and University Hospital Cologne, Department I of Internal Medicine, 50937 Cologne, Germany" + }, + { + "author_name": "Frank Leypoldt", + "author_inst": "Neuroimmunology, Institute of Clinical Chemistry, University Hospital Schleswig-Holstein, Kiel, Germany" + }, + { + "author_name": "Oliver A Cornely", + "author_inst": "University of Cologne, Medical Faculty and University Hospital Cologne, Department I of Internal Medicine, 50937 Cologne, Germany" + }, + { + "author_name": "Philipp Koehler", + "author_inst": "University of Cologne, Medical Faculty and University Hospital Cologne, Department I of Internal Medicine, 50937 Cologne, Germany" + }, + { + "author_name": "Andre Franke", + "author_inst": "Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany" + }, + { + "author_name": "Alexander Scheffold", + "author_inst": "Institute of Immunology, Christian Albrechts University of Kiel, Kiel, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "allergy and immunology" + }, { "rel_doi": "10.1101/2020.09.14.20186494", "rel_title": "Efficacy of commercial mouth-rinses on SARS-CoV-2 viral load in saliva: Randomized Control Trial in Singapore", @@ -1199700,25 +1198228,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.14.20194589", - "rel_title": "Improved estimation of time-varying reproduction numbers at low case incidence and between epidemic waves", - "rel_date": "2020-09-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.14.20194589", - "rel_abs": "We construct a recursive Bayesian smoother, termed EpiFilter, for estimating the effective reproduction number, R, from the incidence of an infectious disease in real time and retrospectively. Our approach borrows from Kalman filtering theory, is quick and easy to compute, generalisable, deterministic and unlike many current methods, requires no change-point or window size assumptions. We model R as a flexible, hidden Markov state process and exactly solve forward-backward algorithms, to derive R estimates that incorporate all available incidence information. This unifies and extends two popular methods, EpiEstim, which considers past incidence, and the Wallinga-Teunis method, which looks forward in time. We find that this combination of maximising information and minimising assumptions significantly reduces the bias and variance of R estimates. Moreover, these properties make EpiFilter more statistically robust in periods of low incidence, where existing methods can become destabilised. As a result, EpiFilter offers improved inference of time-varying transmission patterns that are especially advantageous for assessing the risk of upcoming waves of infection in real time and at various spatial scales.\n\nAuthor SummaryInferring changes in the transmissibility of an infectious disease is crucial for understanding and controlling epidemic spread. The effective reproduction number, R, is widely used to assess transmissibility. R measures the average number of secondary cases caused by a primary case and has provided insight into many diseases including COVID-19. An upsurge in R can forewarn of upcoming infections, while suppression of R can indicate if public health interventions are working. Reliable estimates of temporal changes in R can contribute important evidence to policymaking. Popular R-inference methods, while powerful, can struggle when cases are few because data are noisy. This can limit detection of crucial variations in transmissibility that may occur, for example, when infections are waning or when analysing transmissibility over fine geographic scales. In this paper we improve the general reliability of R-estimates and specifically increase robustness when cases are few. By adapting principles from control engineering, we formulate EpiFilter, a novel method for inferring R in real time and retrospectively. EpiFilter can potentially double the information extracted from epidemic time-series (when compared to popular approaches), significantly filtering the noise within data to minimise both bias and uncertainty of R-estimates and enhance the detection of salient changepoints in transmissibility.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Kris Varun Parag", - "author_inst": "Imperial College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.14.20194308", "rel_title": "Antibodies to SARS-CoV-2 and risk of future sickness", @@ -1201214,6 +1199723,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.16.20195826", + "rel_title": "Modeling the Spread and Control of COVID-19", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.16.20195826", + "rel_abs": "Data-centric models of COVID-19 have been tried, but have certain limitations. In this work, we propose an agent-based model of the epidemic in a confined space of agents representing humans. An extension to the SEIR model allows us to consider the difference between the appearance (black-box view) of the spread of disease, and the real situation (glass-box view). Our model allows for simulations of lockdowns, social distancing, personal hygiene, quarantine, and hospitalization, with further considerations of different parameters such as the extent to which hygiene and social distancing are observed in a population. Our results give qualitative indications of the effects of various policies and parameters; for instance, that lockdowns by themselves are extremely unlikely to bring an end to an epidemic and may indeed make things worse, that social distancing matters more than personal hygiene, and that the growth of infection comes down significantly for moderately high levels of social distancing and hygiene, even in the absence of herd immunity.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Ashutosh Trivedi", + "author_inst": "Spext Co." + }, + { + "author_name": "Nanda Kishore Sreenivas", + "author_inst": "Oracle" + }, + { + "author_name": "Shrisha Rao", + "author_inst": "International Institute of Information Technology - Bangalore" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.16.20188227", "rel_title": "Parents' and guardians' views on the acceptability of a future Covid-19 vaccine: a multi-methods study in England", @@ -1201654,37 +1200190,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2020.09.17.20190595", - "rel_title": "The \"Great Lockdown\": Inactive Workers and Mortality by Covid-19", - "rel_date": "2020-09-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.17.20190595", - "rel_abs": "In response to the Covid-19 outbreak the Italian Government imposed an economic lockdown on March 22, 2020 and ordered the closing of all non-essential economic activities. This paper estimates the causal effects of this measure on mortality by Covid-19 and on mobility patterns. The identification of the causal effects exploits the variation in the active population across municipalities induced by the economic lockdown. The difference-in-differences empirical design compares outcomes in municipalities above and below the median variation in the share of active population before and after the lockdown within a province, also controlling for municipality-specific dynamics, daily-shocks at the provincial level and municipal unobserved characteristics. Our results show that the intensity of the economic lockdown is associated with a statistically significant reduction in mortality by Covid-19 and, in particular, for age groups between 40-64 and older (with larger and more significant effects for individuals above 50). Back of the envelope calculations indicate that 4,793 deaths were avoided, in the 26 days between April 5 to April 30, in the 3,518 municipalities which experienced a more intense lockdown. Several robustness checks corroborate our empirical findings.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Nicola Borri", - "author_inst": "Luiss University" - }, - { - "author_name": "Francesco Drago", - "author_inst": "University of Catania" - }, - { - "author_name": "Chiara Santantonio", - "author_inst": "Luiss University" - }, - { - "author_name": "Francesco Sobbrio", - "author_inst": "University of Rome Tor Vergata" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.09.17.20185090", "rel_title": "Selecting pharmacies for COVID-19 testing to ensure access", @@ -1202800,6 +1201305,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.15.20195487", + "rel_title": "Identification of potential biomarkers and inhibitors for SARS-CoV-2 infection", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.15.20195487", + "rel_abs": "The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has overwhelmed many health systems globally. Here, we aim to identify biological markers and associated biological processes of COVID-19 using a bioinformatics approach to elucidate their potential pathogenesis. The gene expression profile of the GSE152418 dataset was originally produced by using the high-throughput Illumina NovaSeq 6000. Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) and Gene Ontology (GO) enrichment analyses were applied to identify functional categories and biochemical pathways. KEGG and GO results suggested that biological pathways such as \"Cancer pathways\" and \"Insulin pathways\" were mostly affected in the development of COVID-19. Moreover, we identified several genes including EP300, CREBBP, and POLR2A were involved in the virus activities in COVID-19 patients. We further predicted that some inhibitors may have the potential to block the SARS-CoV-2 infection based on the L1000FWD analysis. Therefore, our study provides further insights into the underlying pathogenesis of COVID-19.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Hanming Gu", + "author_inst": "School of Electronic, Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, China; SHU-UTS SILC Business School, Shanghai University," + }, + { + "author_name": "Gongsheng Yuan", + "author_inst": "Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.16.20196170", "rel_title": "Environmental and climatic impact on the infection and mortality of SARS-CoV-2 in Peru", @@ -1203500,49 +1202028,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.09.17.20196832", - "rel_title": "COVID-19 pediatric mortality rates are heterogenous between countries", - "rel_date": "2020-09-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.17.20196832", - "rel_abs": "Introduction: Severe COVID-19 is infrequent in children, with a lethality rate of about 0.08%. This study aims to explore differences in the pediatric mortality rate between countries. Methods: Countries with populations over 5 million that report COVID-19 deaths disaggregated data by quinquennial or decennial age groups were analyzed. Data were extracted from COVID-19 Cases and Deaths by Age Database, national ministries of health, and the World Health Organization. Results: 23 countries were included in the analysis. Pediatric mortality varied from 0 to 12.1 deaths per million people of the corresponding age group, with the highest rate in Peru. In most countries, deaths were more frequent in the 0-4 years old age group, except for Brazil. The pediatric/ general COVID-19 mortality showed a great variation between countries and ranged from 0 (Republic of Korea) to 10.4% (India). Pediatric and Pediatric/general COVID mortality have a strong correlation with 2018 neonatal mortality (r=0.77, p<0.001 and r= 0.88, p<0.001 respectively), while it has a moderate or absent (r=0.47, p=0.02 and r=0.19, p=0.38, respectively) correlation with COVID-19 mortality in the general population. Conclusions: There is an important heterogenicity in pediatric COVI-19 mortality between countries that parallels historical neonatal mortality. Neonatal mortality is a known index of the quality of a country s Health System which points to the importance of social determinants of health in pediatric COVID-19 mortality disparities, an issue which should be further explored.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Nadia Gonzalez-Garcia", - "author_inst": "HOSPITAL INFANTIL DE MEXICO FEDERICO GOMEZ" - }, - { - "author_name": "America Liliana Miranda-Lora", - "author_inst": "HOSPITAL INFANTIL DE MEXICO FEDERICO GOMEZ" - }, - { - "author_name": "Jorge Mendez-Galvan", - "author_inst": "HOSPITAL INFANTIL DE MEXICO FEDERICO GOMEZ" - }, - { - "author_name": "Javier T Granados-Riveron", - "author_inst": "HOSPITAL INFANTIL DE MEXICO FEDERICO GOMEZ" - }, - { - "author_name": "Jaime Nieto-Zermeno", - "author_inst": "HOSPITAL INFANTIL DE MEXICO FEDERICO GOMEZ" - }, - { - "author_name": "Juan Garduno-Espinosa", - "author_inst": "HOSPITAL INFANTIL DE MEXICO FEDERICO GOMEZ" - }, - { - "author_name": "MARIA F CASTILLA-PEON", - "author_inst": "HOSPITAL INFANTIL DE MEXICO FEDERICO GOMEZ" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.09.17.20183392", "rel_title": "Disparities in COVID-19 Related Mortality in U.S. Prisons and the General Population", @@ -1204770,6 +1203255,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.17.20196352", + "rel_title": "The epidemiological characteristics of COVID-19 in Libya during the ongoing-armed conflict.", + "rel_date": "2020-09-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.17.20196352", + "rel_abs": "Abstract Introduction: COVID-19 can have even more dire consequences in countries with ongoing armed conflict. Libya, the second largest African country, has been involved in a major conflict since 2011. This study analyzed the epidemiological situation of the COVID-19 pandemic in Libya, examined the impact of the armed conflict in Libya on the spread of the pandemic, and proposes strategies for dealing with the pandemic during this conflict. Methods: We collected the available information on all COVID-19 cases in the different regions of Libya, covering the period from March 25 to May 25, 2020. The cumulative number of cases and the daily new cases are presented in a way to illustrate the patterns and trends of COVID-19 and the effect of the ongoing armed conflict was assessed regionally. Results: A total of 698 cases of COVID-19 were reported in Libya during a period of three months. The number of cases varied from one region to another and was affected by the fighting. The largest number of cases was reported in the southern part of the country, which has been severely affected by the conflict in comparison to the eastern and western parts of the country. Conclusion: This study describes the epidemiological pattern of COVID-19 in Libya and how it has been affected by the ongoing armed conflict. This conflict seems to have hindered access to populations and thereby masked the true dimensions of the pandemic. Hence, efforts should be combined to combat these consequences.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Mohamed A Daw Sr.", + "author_inst": "University of Tripoli, Faculty of Medicine" + }, + { + "author_name": "Abdallah Hussean El-Bouzedi", + "author_inst": "University of Tripoli, Department of Laboratory Medicine, Faculty of Biotechnology, Tripoli University, CC 82668, Tripoli, Libya" + }, + { + "author_name": "Mohamed Omar Ahmed", + "author_inst": "Department of Microbiology & Parasitology, Faculty of Veterinary Medicine, University of Tripoli, CC 82668 Libya." + }, + { + "author_name": "Ali Ali Alejenef", + "author_inst": "Department of Medicine Faculty of Medicine, Zentan , University of Aljabel Alkarbi, Libya" + } + ], + "version": "1", + "license": "cc0_ng", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.18.20194175", "rel_title": "Metabolic stress and disease-stage specific basigin expression of peripheral blood immune cell subsets in COVID-19 patients", @@ -1205314,49 +1203830,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.09.16.300319", - "rel_title": "A soluble ACE2 microbody protein fused to a single immunoglobulin Fc domain is a potent inhibitor of SARS-CoV-2 infection in cell culture", - "rel_date": "2020-09-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.16.300319", - "rel_abs": "Soluble forms of ACE2 have recently been shown to inhibit SARS-CoV-2 infection. We report on an improved soluble ACE2, termed a \"microbody\" in which the ACE2 ectodomain is fused to Fc domain 3 of the immunoglobulin heavy chain. The protein is smaller than previously described ACE2-Ig Fc fusion proteins and contains an H345A mutation in the ACE2 catalytic active site that inactivates the enzyme without reducing its affinity for the SARS-CoV-2 spike. The disulfide-bonded ACE2 microbody protein inhibited entry of lentiviral SARS-CoV-2 spike protein pseudotyped virus and live SARS-CoV-2 with a potency 10-fold higher than unmodified soluble ACE2 and was active after initial virus binding to the cell. The ACE2 microbody inhibited the entry of ACE2-specific {beta} coronaviruses and viruses with the high infectivity variant D614G spike. The ACE2 microbody may be a valuable therapeutic for COVID-19 that is active against SARS-CoV-2 variants and future coronaviruses that may arise.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Takuya Tada", - "author_inst": "NYU Langone Medical Center" - }, - { - "author_name": "Chen Fan", - "author_inst": "Weill Cornell Medical College" - }, - { - "author_name": "Ramanjit Kaur", - "author_inst": "NYU Langone Medical Center" - }, - { - "author_name": "Kenneth A Stapleford", - "author_inst": "NYU Langone Medical Center" - }, - { - "author_name": "Harry Gristick", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Crina Nimigean", - "author_inst": "Weill Cornell Medical College" - }, - { - "author_name": "Nathaniel R Landau", - "author_inst": "NYU Langone Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.09.17.299933", "rel_title": "Identification of novel antiviral drug combinations in vitro and tracking their development", @@ -1206764,6 +1205237,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.14.20191833", + "rel_title": "Variation across population subgroups of COVID-19 antibody testing performance", + "rel_date": "2020-09-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.14.20191833", + "rel_abs": "Understanding variations in the performance of serological tests for SARS-CoV-2 across varying demographics is relevant to clinical interpretations and public policy derived from their results. Appropriate use of serological assays to detect anti-SARS-CoV-2 antibodies requires estimation of their accuracy over large populations and an understanding of the variance in performance over time and across demographic groups. In this manuscript we focus on anti-SARS-CoV-2 IgG, IgA, and IgM antibody tests approved under emergency use authorizations and determine the recall of the serological tests compared to RT-PCR tests by Logical Observation Identifiers Names and Codes (LOINCs). Variability in test performance was further examined over time and by demographics. The recall of the most common IgG assay (LOINC 94563-4) was 91.2% (95% CI: 90.5%, 91.9%). IgA (LOINC 94562-6) and IgM (94564-2) assays performed significantly worse than IgG assays with estimated recall rates of 20.6% and 27.3%, respectively. A statistically significant difference in recall (p = 0.019) was observed across sex with a higher recall in males than females, 92.1% and 90.4%, respectively. Recall also differed significantly by age group, with higher recall in those over 45 compared to those under 45, 92.9% and 88.0%, respectively (p< 0.001). While race was unavailable for the majority of the individuals, a significant difference was observed between recall in White individuals and Black individuals (p = 0.007) and White individuals and Hispanic individuals (p = 0.001). The estimates of recall were 89.3%, 95.9%, and 94.2% for White, Black, and Hispanic individuals respectively.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Halley L Brantley", + "author_inst": "UnitedHealth Group" + }, + { + "author_name": "Richard M Yoo", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Glen I Jones", + "author_inst": "UnitedHealth Group" + }, + { + "author_name": "Marel A Stock", + "author_inst": "UnitedHealth Group" + }, + { + "author_name": "Peter J Park", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Natalie E Sheils", + "author_inst": "UnitedHealth Group" + }, + { + "author_name": "Isaac S Kohane", + "author_inst": "Harvard Medical School" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.16.299891", "rel_title": "High affinity modified ACE2 receptors prevent SARS-CoV-2 infection", @@ -1207120,125 +1205636,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.03.20187112", - "rel_title": "Treatment with an Anti-CK2 Synthetic Peptide Improves Clinical Response in Covid-19 Patients with Pneumonia. A Randomized and Controlled Clinical Trial", - "rel_date": "2020-09-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.03.20187112", - "rel_abs": "PurposeThe instrumental role of CK2 in the SARS-Cov2 infection has pointed out this protein kinase as a promising therapeutic target in Covid-19. Anti-SARS-Cov2 activity has been reported by CK2 inhibitors in vitro; however, any anti-CK2 clinical approach has been investigated in Covid-19. This exploratory trial aimed to explore safety and putative clinical benefit of CIGB-325, an anti-CK2 peptide previously assessed in cancer.\n\nMethodsA monocentric, parallel group design, therapeutic exploratory trial of intravenous CIGB-325 in adults hospitalized with Covid-19 was performed. Twenty patients were randomly assigned to receive CIGB-325 (2.5 mg/kg/day during 5-consecutive days) plus standard-of-care (10 patients) or standard-of-care (10 patients). Adverse events were classified by the WHO Adverse Reaction Terminology. Parametric and non-parametric statistical analyses were performed according to the type of variable. Considering the small sample size, differences between groups were estimated by Bayesian analysis.\n\nFindingsCIGB-325 induced transient mild and/or moderate adverse events like pruritus, flushing and rash in some patients. Both therapeutic regimens were similar respect to SARS-Cov2 clearance in nasopharynx swabs over the time. However, CIGB-325 significantly reduced the median number of pulmonary lesions (9.5 to 5.5, p = 0.042) at day 7 and proportion of patients with such effect was also higher according to Bayesian analysis (pDif > 0; 0.951). Additionally, CIGB-325 significantly reduced the CPK (p = 0.007) and LDH (p = 0.028) plasma levels at day 7.\n\nImplicationsOur preliminary findings suggest that this anti-CK2 clinical approach could be combined with standard-of-care in Covid-19 thus warranting larger studies.", - "rel_num_authors": 26, - "rel_authors": [ - { - "author_name": "Leticia R. Cruz", - "author_inst": "Luis Diaz Soto Hospital" - }, - { - "author_name": "Idania Baladron", - "author_inst": "Center for Genetic Engineering and Biotechnology" - }, - { - "author_name": "Aliusha Rittoles", - "author_inst": "Luis Diaz Soto Hospital" - }, - { - "author_name": "Pablo A. Diaz", - "author_inst": "Center for Genetic Engineering and Biotechnology" - }, - { - "author_name": "Carmen Valenzuela", - "author_inst": "Center for Molecular Immunology" - }, - { - "author_name": "Raul Santana", - "author_inst": "Luis Diaz Soto Hospital" - }, - { - "author_name": "Maria M. Vazquez", - "author_inst": "Center for Genetic Engineering and Biotechnology" - }, - { - "author_name": "Ariadna Garcia", - "author_inst": "Luis Diaz Soto Hospital" - }, - { - "author_name": "Deyli Chacon", - "author_inst": "Luis Diaz Soto Hospital" - }, - { - "author_name": "Delvin Thompson", - "author_inst": "Luis Diaz Soto Hospital" - }, - { - "author_name": "Gustavo Perera", - "author_inst": "Luis Diaz Soto Hospital" - }, - { - "author_name": "Ariel Gonzalez", - "author_inst": "International Center of Health La Pradera" - }, - { - "author_name": "Rafael Reyes", - "author_inst": "National Institute of Oncology and Radiobiology" - }, - { - "author_name": "Loida Torres", - "author_inst": "International Center of Health La Pradera" - }, - { - "author_name": "Jesus Perez", - "author_inst": "Luis Diaz Soto Hospital" - }, - { - "author_name": "Yania Valido", - "author_inst": "Luis Diaz Soto Hospital" - }, - { - "author_name": "Ralysmay Rodriguez", - "author_inst": "Luis Diaz Soto Hospital" - }, - { - "author_name": "Dania M. Vazquez", - "author_inst": "Center for Genetic Engineering and Biotechnology" - }, - { - "author_name": "Mauro Rosales", - "author_inst": "Faculty of Biology, University of Havana" - }, - { - "author_name": "Ailyn C. Ramon", - "author_inst": "Center for Genetic Engineering and Biotechnology" - }, - { - "author_name": "George V. Perez", - "author_inst": "Center for Genetic Engineering and Biotechnology" - }, - { - "author_name": "Gerardo Guillen", - "author_inst": "Center for Genetic Engineering and Biotechnology" - }, - { - "author_name": "Verena Muzio", - "author_inst": "Center for Genetic Engineering and Biotechnology" - }, - { - "author_name": "Yasser Perera", - "author_inst": "China-Cuba Biotechnology Joint Innovation Center" - }, - { - "author_name": "Silvio E. Perea", - "author_inst": "Center for Genetic Engineering and Biotechnology" - }, - { - "author_name": "- ATENEA-Co-300 Group", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pharmacology and therapeutics" - }, { "rel_doi": "10.1101/2020.09.10.20187427", "rel_title": "Words Matter: Political and gender analysis of speeches made by heads of government during the COVID-19 pandemic", @@ -1208662,6 +1207059,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.12.20193094", + "rel_title": "The Immune-Buffer COVID-19 Exit Strategy that Protects the Elderly", + "rel_date": "2020-09-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.12.20193094", + "rel_abs": "COVID-19 is a viral respiratory illness, caused by the SARS-CoV-2 virus with frequent symptoms of fever and shortness of breath. COVID-19 has a high mortality rate among elders. The virus has spread world-wide, leading to shut-down of many countries around the globe with the aim of stopping the spread of the disease. To date, there are uncertainties regarding the main factors in the disease spread, so sever social distancing measures and broad testing are required in order to protect the population at risk. With the increasing spread of the virus, there is growing fraction of the general population that may be immune to COVID-19, following infection. This immunised cohort can be uncovered via large-scale screening for the SARS-CoV-2 (Corona) virus and/or its antibodies. We propose that this immune cohort be deployed as a buffer between the general population and the population most at risk from the disease. Here we show that under a broad range of realistic scenarios deploying such an immunized buffer between the general population and the population at risk may lead to a dramatic reduction in the number of deaths from the disease. This provides an impetus for: screening for the SARS-CoV-2 virus and/or its antibodies on the largest scale possible, and organizing at the family, community, national and international levels to protect vulnerable populations by deploying immunized buffers between them and the general population wherever possible.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Vered Rom-Kedar", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Omer Yaniv", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Roy Malka", + "author_inst": "Lynx MD" + }, + { + "author_name": "Ehud Shapiro", + "author_inst": "Weizmann Institute of Science" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.12.20193284", "rel_title": "Estimates of outbreak-specific SARS-CoV-2 epidemiological parameters from genomic data", @@ -1209022,53 +1207450,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.12.20193409", - "rel_title": "Clinical characteristics and outcomes of patients with COVID-19 and ARDS admitted to a third level health institution in Mexico City", - "rel_date": "2020-09-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.12.20193409", - "rel_abs": "BackgroundIn December 2019, the first cases of severe pneumonia associated with a new coronavirus were reported in Wuhan, China. Severe respiratory failure requiring intensive care was reported in up to 5% of cases. There is, however, limited information available in Mexico.\n\nObjectivesThe purpose of this study was to describe the clinical manifestations, and outcomes in a COVID-19 cohort attended to from March to May 2020 in our RICU. In addition, we explored the association of clinical variables with mortality.\n\nMethodsThe first consecutive patients admitted to the RICU from March 3, 2020, to Jun 24, 2020, with confirmed COVID-19 were investigated. Clinical and laboratory data were obtained. Odds ratios (ORs) were calculated using a logistic regression model. The survival endpoint was mortality at discharge from the RICU.\n\nResultsData from 68 consecutive patients were analyzed. Thirty-eight patients survived, and 30 died (mortality: 44.1 %). Of the 16 predictive variables analyzed, only 6 remained significant in the multivariate analysis [OR (95% confidence interval)]: no acute kidney injury (AKI)/AKI 1: [.61 (.001;.192)]; delta lymphocyte count: [.061 (.006;.619)]; delta ventilatory ratio: [8.19 (1.40;47.8)]; norepinephrine support at admission: [34.3 (2.1;550)]; body mass index: [1.41 (1.09;1.83)]; and bacterial coinfection: [18.5 (1.4;232)].\n\nConclusionsWe report the characteristics and outcome of patients with ARDS and COVID-19. We found six independent factors associated with the mortality risk: delta lymphocyte count, delta ventilatory ratio, BMI, norepinephrine support, no AKI/AKI 1, and bacterial coinfection.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "GUSTAVO LUGO GOYTIA", - "author_inst": "INSTITUTO NACIONAL DE ENFERMEDADES RESPIRATORIAS ISMAEL COSIO VILLEGAS" - }, - { - "author_name": "Carmen Hernandez-Cardenas,", - "author_inst": "Instituto Nacional de Enfermedades Respiratorias" - }, - { - "author_name": "Carlos Torruco-Sotelo", - "author_inst": "Instituto Nacional de Enfermedades Respiratorias" - }, - { - "author_name": "Felipe Jurado", - "author_inst": "Instituto Nacional de Enfermedades Respiratorias" - }, - { - "author_name": "Hector Serna-secundino", - "author_inst": "Instituto Nacional de Enfermedades Respiratorias" - }, - { - "author_name": "Cristina Aguilar", - "author_inst": "Instituto Nacional de Enfermedades Respiratorias" - }, - { - "author_name": "Jose Garcia-Olanzaran", - "author_inst": "Instituto Nacional de Enfermedades Respiratorias" - }, - { - "author_name": "Diana Hernandez-Garcia", - "author_inst": "Instituto Nacional de Enfermedades Respiratorias" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.09.13.20193532", "rel_title": "Role of Weather Factors in COVID-19 Deaths in Tropical Climate: A Data-Driven Study Focused on Brazil", @@ -1210148,6 +1208529,57 @@ "type": "new results", "category": "neuroscience" }, + { + "rel_doi": "10.1101/2020.09.14.296715", + "rel_title": "Self-assembling nanoparticles presenting receptor binding domain and stabilized spike as next-generation COVID-19 vaccines", + "rel_date": "2020-09-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.14.296715", + "rel_abs": "Vaccination against SARS-CoV-2 provides an effective tool to combat the COIVD-19 pandemic. Here, we combined antigen optimization and nanoparticle display to develop vaccine candidates for SARS-CoV-2. We first displayed the receptor-binding domain (RBD) on three self-assembling protein nanoparticle (SApNP) platforms using the SpyTag/SpyCatcher system. We then identified heptad repeat 2 (HR2) in S2 as the cause of spike metastability, designed an HR2-deleted glycine-capped spike (S2G{Delta}HR2), and displayed S2G{Delta}HR2 on SApNPs. An antibody column specific for the RBD enabled tag-free vaccine purification. In mice, the 24-meric RBD-ferritin SApNP elicited a more potent neutralizing antibody (NAb) response than the RBD alone and the spike with two stabilizing proline mutations in S2 (S2P). S2G{Delta}HR2 elicited two-fold-higher NAb titers than S2P, while S2G{Delta}HR2 SApNPs derived from multilayered E2p and I3-01v9 60-mers elicited up to 10-fold higher NAb titers. The S2G{Delta}HR2-presenting I3-01v9 SApNP also induced critically needed T-cell immunity, thereby providing a promising vaccine candidate.\n\nONE-SENTENCE SUMMARYThe SARS-CoV-2 receptor binding domain and S2G{Delta}HR2 spike elicited potent immune responses when displayed on protein nanoparticles as vaccine candidates.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Linling He", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Xiaohe Lin", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Ying Wang", + "author_inst": "Temple University" + }, + { + "author_name": "Ciril Abraham", + "author_inst": "Temple University" + }, + { + "author_name": "Cindy Sou", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Timothy Ngo", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Yi Zhang", + "author_inst": "Temple University" + }, + { + "author_name": "Ian A. Wilson", + "author_inst": "The Scripps Research Institute" + }, + { + "author_name": "Jiang Zhu", + "author_inst": "The Scripps Research Institute" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.09.14.296814", "rel_title": "Phylogenomic reveals multiple introductions and early spread of SARS-CoV-2 into Peru", @@ -1210588,69 +1209020,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.11.20180521", - "rel_title": "On Machine Learning-Based Short-Term Adjustment of Epidemiological Projections of COVID-19 in US", - "rel_date": "2020-09-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.11.20180521", - "rel_abs": "Epidemiological models have provided valuable information for the outlook of COVID-19 pandemic and relative impact of different mitigation scenarios. However, more accurate forecasts are often needed at near term for planning and staffing. We present our early results from a systemic analysis of short-term adjustment of epidemiological modeling of COVID 19 pandemic in US during March-April 2020. Our analysis includes the importance of various types of features for short term adjustment of the predictions. In addition, we explore the potential of data augmentation to address the data limitation for an emerging pandemic. Following published literature, we employ data augmentation via clustering of regions and evaluate a number of clustering strategies to identify early patterns from the data. From our early analysis, we used CovidActNow as our underlying epidemiological model and found that the most impactful features for the one-day prediction horizon are population density, workers in commuting flow, number of deaths in the day prior to prediction date, and the autoregressive features of new COVID-19 cases from three previous dates of the prediction. Interestingly, we also found that counties clustered with New York County resulted in best preforming model with maximum of R2= 0.90 and minimum of R2= 0.85 for state-based and COVID-based clustering strategy, respectively.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Sarah KEFAYATI", - "author_inst": "IBM Watson Health" - }, - { - "author_name": "Hu Huang", - "author_inst": "IBM Watson Health" - }, - { - "author_name": "Prithwish Chakraborty", - "author_inst": "IBM Research" - }, - { - "author_name": "Fred Roberts", - "author_inst": "IBM Watson Health" - }, - { - "author_name": "Vishrawas Gopalakrishnan", - "author_inst": "IBM Watson Health" - }, - { - "author_name": "Raman Srinivasan", - "author_inst": "IBM Watson Health" - }, - { - "author_name": "Sayali Pethe", - "author_inst": "IBM Watson Health" - }, - { - "author_name": "Piyush Madan", - "author_inst": "IBM Research" - }, - { - "author_name": "Ajay Deshpande", - "author_inst": "IBM Watson Health" - }, - { - "author_name": "Xuan Liu", - "author_inst": "IBM Watson Health" - }, - { - "author_name": "Jianying Hu", - "author_inst": "IBM Research" - }, - { - "author_name": "Gretchen Jackson", - "author_inst": "IBM Watson Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.11.20192971", "rel_title": "Mask-Wearing During the COVID-19 Pandemic", @@ -1211790,6 +1210159,89 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.09.11.294363", + "rel_title": "Ketogenesis restrains aging-induced exacerbation of COVID in a mouse model", + "rel_date": "2020-09-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.11.294363", + "rel_abs": "Increasing age is the strongest predictor of risk of COVID-19 severity. Unregulated cytokine storm together with impaired immunometabolic response leads to highest mortality in elderly infected with SARS-CoV-2. To investigate how aging compromises defense against COVID-19, we developed a model of natural murine beta coronavirus (mCoV) infection with mouse hepatitis virus strain MHV-A59 (mCoV-A59) that recapitulated majority of clinical hallmarks of COVID-19. Aged mCoV-A59-infected mice have increased mortality and higher systemic inflammation in the heart, adipose tissue and hypothalamus, including neutrophilia and loss of {gamma}{delta} T cells in lungs. Ketogenic diet increases beta-hydroxybutyrate, expands tissue protective {gamma}{delta} T cells, deactivates the inflammasome and decreases pathogenic monocytes in lungs of infected aged mice. These data underscore the value of mCoV-A59 model to test mechanism and establishes harnessing of the ketogenic immunometabolic checkpoint as a potential treatment against COVID-19 in the elderly.\n\nHighlights - Natural MHV-A59 mouse coronavirus infection mimics COVID-19 in elderly.\n- Aged infected mice have systemic inflammation and inflammasome activation\n- Murine beta coronavirus (mCoV) infection results in loss of pulmonary {gamma}{delta} T cells.\n- Ketones protect aged mice from infection by reducing inflammation.\n\n\neTOC BlurbElderly have the greatest risk of death from COVID-19. Here, Ryu et al report an aging mouse model of coronavirus infection that recapitulates clinical hallmarks of COVID-19 seen in elderly. The increased severity of infection in aged animals involved increased inflammasome activation and loss of {gamma}{delta} T cells that was corrected by ketogenic diet.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Seungjin Ryu", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Irina Shchukina", + "author_inst": "Washington University in St. Louis" + }, + { + "author_name": "Yun-Hee Youm", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Hua Qing", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Brandon K Hilliard", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Tamara Dlugos", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Xinbo Zhang", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Yuki Yasumoto", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Carmen J. Booth", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Carlos Fernandez-Hernando", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Yajaira Suarez", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Kamal M Khanna", + "author_inst": "New York University School of Medicine" + }, + { + "author_name": "Tamas Horvath", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Marcelo O Dietrich", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Maxim Artyomov", + "author_inst": "Washington University School of Medicine" + }, + { + "author_name": "Andrew Wang", + "author_inst": "Yale University School of Medicine" + }, + { + "author_name": "Vishwa Deep Dixit", + "author_inst": "Yale University School of Medicine" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.09.12.294413", "rel_title": "Inferring MHC interacting SARS-CoV-2 epitopes recognized by TCRs towards designing T cell-based vaccines", @@ -1212262,41 +1210714,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.11.20192450", - "rel_title": "Impacts of the COVID-19 epidemic on the department of stomatology in a tertiary hospital: a case study in the General Hospital of the Central Theater Command, Wuhan, China", - "rel_date": "2020-09-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.11.20192450", - "rel_abs": "ObjectivesThe aim of this study is to depict the impacts of COVID-19 pandemic on the clinical services and academic activities in the department of stomatology of a tertiary hospitals in Wuhan, China.\n\nMethodsWe obtained historical data of the Department of Stomatology from the Health Information System of the General Hospital of Central Theater Command, Wuhan, China between January 2018 and June 2020. Line plots were used to illustrate temporal trend of the variables. Mean {+/-} standard deviation and median with interquartile range were used to summarize the variables. The Kruskal-Wallis equality-of-populations rank test was used to compare the difference between groups.\n\nResultsA significant decrease was noted in the monthly average number of patients seeking the outpatient services for the year 2020. The monthly numbers of patients seeking outpatient services were decreased by two thirds from 2018 to 2020. The number of emergency cases also decreased significantly by 64% in 2020. The monthly number of teaching hours decreased from 3.8 {+/-} 1.5 in 2018 and 4.7 {+/-} 1.4 in 2019 to 1.7 {+/-} 1.9 in 2020. The number of interns also decreased more than 70% in 2020.\n\nConclusionsThe impacts of COVID 19 in the stomatology clinic were significant with notable decreases in clinical services and education offered to the stomatology students. We must find solutions to keep as many as needed dental profession stay on thriving and to remain on the frontline of healthcare.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Qingshan Dong", - "author_inst": "Department of Stomatology, General Hospital of the Central Theater Command, Wuhan Hubei Province, China" - }, - { - "author_name": "Angelica Kuria", - "author_inst": "Department of Health, Nyandarua County, Kenya" - }, - { - "author_name": "Yanming Weng", - "author_inst": "Department of Stomatology, General Hospital of the Central Theater Command, Wuhan Hubei Province, China" - }, - { - "author_name": "Yu Liu", - "author_inst": "Department of Stomatology, General Hospital of the Central Theater Command, Wuhan Hubei Province, China" - }, - { - "author_name": "Yang Cao", - "author_inst": "Orebro University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "dentistry and oral medicine" - }, { "rel_doi": "10.1101/2020.09.09.20191270", "rel_title": "Quantitative particle analysis of particulate matter release during orthodontic procedures: A pilot study.", @@ -1213280,6 +1211697,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.08.20190686", + "rel_title": "Mortality and risk factors among US Black, Hispanic, and White patients with COVID-19", + "rel_date": "2020-09-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.08.20190686", + "rel_abs": "Background: Little is known about risk factors for COVID-19 outcomes, particularly across diverse racial and ethnic populations in the United States. Methods: In this prospective cohort study, we followed 3,086 COVID-19 patients hospitalized on or before April 13, 2020 within an academic health system in New York (The Mount Sinai Health System) until June 2, 2020. Multivariable logistic regression was used to evaluate demographic, clinical, and laboratory factors as independent predictors of in-hospital mortality. The analysis was stratified by self-reported race and ethnicity. Findings: A total of 3,086 COVID-19 patients were hospitalized, of whom 680 were excluded (78 due to missing race or ethnicity data, 144 were Asian, and 458 were of other unspecified race/ethnicity). Of the 2,406 patients included, 892 (37.1%) were Hispanic, 825 (34.3%) were black, and 689 (28.6%) were white. Black and Hispanic patients were younger than White patients (median age 67 and 63 vs. 73, p<0.001 for both), and they had different comorbidity profiles. Older age and baseline hypoxia were associated with increased mortality across all races. There were suggestive but non-significant interactions between Black race and diabetes (p=0.09), and obesity (p=0.10). Among inflammatory markers associated with COVID-19 mortality, there was a significant interaction between Black race and interleukin-1-beta (p=0.04), and a suggestive interactions between Hispanic ethnicity and procalcitonin (p=0.07) and interleukin-8 (p=0.09). Interpretation: In this large, racially and ethnically diverse cohort of COVID-19 patients in New York City, we identified similarities and important differences across racial and ethnic groups in risk factors for in-hospital mortality.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Tomi Jun", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Sharon Nirenberg", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Patricia Kovatch", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Kuan-lin Huang", + "author_inst": "Icahn School of Medicine at Mount Sinai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.10.20186064", "rel_title": "Mitochondrial induced T cell apoptosis and aberrant myeloid metabolic programs define distinct immune cell subsets during acute and recovered SARS-CoV-2 infection", @@ -1213892,41 +1212340,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.09.10.20191932", - "rel_title": "Evaluating the effects of cardiometabolic exposures on circulating proteins which may contribute to SARS-CoV-2 severity", - "rel_date": "2020-09-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.10.20191932", - "rel_abs": "Background: Developing insight into the pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is of critical importance to overcome the global pandemic caused by coronavirus disease 2019 (covid-19). In this study, we have applied Mendelian randomization (MR) to systematically evaluate the effect of 10 cardiometabolic risk factors and genetic liability to lifetime smoking on 97 circulating host proteins postulated to either interact or contribute to the maladaptive host response of SARS-CoV-2. Methods: We applied the inverse variance weighted (IVW) approach and several robust MR methods in a two-sample setting to systemically estimate the genetically predicted effect of each risk factor in turn on levels of each circulating protein. Multivariable MR was conducted to simultaneously evaluate the effects of multiple risk factors on the same protein. We also applied MR using cis-regulatory variants at the genomic location responsible for encoding these proteins to estimate whether their circulating levels may influence SARS-CoV-2 severity. Findings: In total, we identified evidence supporting 105 effects between risk factors and circulating proteins which were robust to multiple testing corrections and sensitivity analyses. For example, body mass index provided evidence of an effect on 23 circulating proteins with a variety of functions, such as inflammatory markers c-reactive protein (IVW Beta=0.34 per standard deviation change, 95% CI=0.26 to 0.41, P=2.19x10-16) and interleukin-1 receptor antagonist (IVW Beta=0.23, 95% CI=0.17 to 0.30, P=9.04x10-12). Further analyses using multivariable MR provided evidence that the effect of BMI on lowering immunoglobulin G, an antibody class involved in protecting the body from infection, is substantially mediated by raised triglycerides levels (IVW Beta=-0.18, 95% CI=-0.25 to -0.12, P=2.32x10-08, proportion mediated=44.1%). The strongest evidence that any of the circulating proteins highlighted by our initial analysis influence SARS-CoV-2 severity was identified for soluble glycoprotein 130 (odds ratio=1.81, 95% CI=1.25 to 2.62, P=0.002), a signal transductor for interleukin-6 type cytokines which are involved in the bodys inflammatory response. However, based on current case samples for severe SARS-CoV-2 we were unable to replicate findings in independent samples. Interpretation: Our findings highlight several key proteins which are influenced by established exposures for disease. Future research to determine whether these circulating proteins mediate environmental effects onto risk of SARS-CoV-2 are warranted to help elucidate therapeutic strategies for covid-19 disease severity.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Tom G Richardson", - "author_inst": "MRC Integrative Epidemiology Unit" - }, - { - "author_name": "Si Fang", - "author_inst": "MRC Integrative Epidemiology Unit" - }, - { - "author_name": "Ruth E Mitchell", - "author_inst": "MRC Integrative Epidemiology Unit" - }, - { - "author_name": "Michael V Holmes", - "author_inst": "MRC Population Health Research Unit" - }, - { - "author_name": "George Davey Smith", - "author_inst": "MRC Integrative Epidemiology Unit" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.09.20191296", "rel_title": "SARS-CoV-2 Antibody Prevalence and Association with Routine Laboratory Values in a Life Insurance Applicant Population", @@ -1215054,6 +1213467,49 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.09.08.20190629", + "rel_title": "Model-informed COVID-19 vaccine prioritization strategies by age and serostatus", + "rel_date": "2020-09-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.08.20190629", + "rel_abs": "When a vaccine for COVID-19 becomes available, limited initial supply will raise the question of how to prioritize the available doses and thus underscores the need for transparent, evidence-based strategies that relate knowledge of, and uncertainty in, disease transmission, risk, vaccine efficacy, and existing population immunity. Here, we employ a model-informed approach to vaccine prioritization that evaluates the impact of prioritization strategies on cumulative incidence and mortality and accounts for population factors such as age, contact structure, and seroprevalence, and vaccine factors including imperfect and age-varying efficacy. This framework can be used to evaluate and compare existing strategies, and it can also be used to derive an optimal prioritization strategy to minimize mortality or incidence. We find that a transmission-blocking vaccine should be prioritized to adults ages 20-49y to minimize cumulative incidence and to adults over 60y to minimize mortality. Direct vaccination of adults over 60y minimizes mortality for vaccines that do not block transmission. We also estimate the potential benefit of using individual-level serological tests to redirect doses to only seronegative individuals, improving the marginal impact of each dose. We argue that this serology-informed vaccination approach may improve the efficiency of vaccination efforts while partially addressing existing inequities in COVID-19 burden and impact.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Kate M Bubar", + "author_inst": "University of Colorado Boulder" + }, + { + "author_name": "Kyle Reinholt", + "author_inst": "University of Colorado Boulder" + }, + { + "author_name": "Stephen M Kissler", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Marc Lipsitch", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Sarah Cobey", + "author_inst": "University of Chicago" + }, + { + "author_name": "Yonatan Grad", + "author_inst": "Harvard T. H. Chan School of Public Health" + }, + { + "author_name": "Daniel B Larremore", + "author_inst": "University of Colorado Boulder" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.09.20190983", "rel_title": "Exploring Patterns and Trends in COVID-19 Exports from China, Italy, and Iran", @@ -1215426,37 +1213882,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2020.09.08.20190884", - "rel_title": "Prison population reductions and COVID-19: A latent profile analysis synthesizing recent evidence from the Texas state prison system", - "rel_date": "2020-09-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.08.20190884", - "rel_abs": "ImportancePeople in prison are particularly vulnerable to infectious disease due to close living conditions and the lack of protective equipment. Public health professionals and prison administrators seek information to guide best practices regarding prison population to capacity rates for the COVID-19 outbreak.\n\nObjectiveUsing latent profile analysis, we sought to characterize Texas prisons on levels of COVID-19 cases and deaths among incarcerated residents, and COVID-19 cases among prison staff.\n\nDesignThis observational study was a secondary data analysis of publicly available data from the Texas Department of Criminal Justice (TBDJ). Data were downloaded and analyzed on July 24, 2020. This project was completed in collaboration with the COVID Prison Project.\n\nSettingOne-hundred and three prisons in the state of Texas.\n\nParticipantsThe unit of analysis is the individual prison units that comprise the TDCJ.\n\nExposuresNone\n\nMain Outcomes and MeasuresLatent profiles on levels of incarcerated resident COVID-19 cases, staff COVID-19 cases, and incarcerated resident COVID-19 deaths.\n\nResultsWe identified relevant profiles from the data: a low outbreak profile, a high outbreak profile, and a high death profile. Additionally, current prison population and level of employee staffing predicted membership in the high outbreak and high death profiles when compared to the low outbreak profile.\n\nConclusions and RelevanceHousing persons at 85% of prison capacity may minimize the risk of infection and death related to COVID-19. Implementing this 85% standard as an absolute minimum should be prioritized at prisons across the US.\n\nKEY POINTSO_ST_ABSQuestionC_ST_ABSIs there a population to capacity ratio for prisons to successfully reduce the number of COVID-19 infections and deaths among its incarcerated populations?\n\nFindingsThe prisons that were most effective in reducing prison outbreaks and deaths operated at 85% of their current capacity.\n\nMeaningPrisons should operate at 85% of capacity or less to successfully minimize the harmful effects of COVID-19 on incarcerated populations.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Noel A. Vest", - "author_inst": "Stanford University" - }, - { - "author_name": "Oshea D. Johnson", - "author_inst": "University of Miami" - }, - { - "author_name": "Kathryn M Nowotny", - "author_inst": "University of Miami" - }, - { - "author_name": "Lauren Brinkley-Rubinstein", - "author_inst": "University of North Carolina" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.09.08.20190751", "rel_title": "Periodic variations in the Covid-19 infection and fatality rates", @@ -1216520,6 +1214945,29 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.09.10.290841", + "rel_title": "CD8 T cell epitope generation toward the continually mutating SARS-CoV-2 spike protein in genetically diverse human population: Implications for disease control and prevention", + "rel_date": "2020-09-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.10.290841", + "rel_abs": "The ongoing pandemic of SARS-CoV-2 has brought tremendous crisis on global health care systems and industrial operations that dramatically affect the economic and social life of numerous individuals worldwide. Understanding anti-SARS-CoV-2 immune responses in population with different genetic backgrounds and tracking the viral evolution are crucial for successful vaccine design. In this study, we reported the generation of CD8 T cell epitopes by a total of 80 alleles of three major class I HLAs using NetMHC 4.0 algorithm for the spike protein of SARS-CoV-2, a key antigen that is targeted by both B cells and T cells. We found diverse capacities of S protein specific epitope presentation by different HLA alleles with very limited number of predicted epitopes for HLA-B*2705, HLA-B*4402 and HLA-B*4403 and as high as 132 epitopes for HLA-A*6601. Our analysis of 1000 S protein sequences from field isolates collected globally over the past few months identified three recurrent point mutations including L5F, D614G and G1124V. Differential effects of these mutations on CD8 T cell epitope generation by corresponding HLA alleles were observed. Finally, our multiple alignment analysis indicated the absence of seasonal CoV induced cross-reactive CD8 T cells to drive these mutations. Our findings provided molecular explanations for the observation that individuals with certain HLA alleles such as B*44 are more prone to SARS-CoV-2 infection. Studying anti-S protein specific CD8 T cell immunity in diverse genetic background is critical for better control and prevention of the SARS-CoV-2 pandemic.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Hailong Guo", + "author_inst": "none" + }, + { + "author_name": "Elisa Guo", + "author_inst": "none" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.09.02.20187096", "rel_title": "On the Role of Artificial Intelligence in Medical Imaging of COVID-19", @@ -1216940,33 +1215388,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.04.20188235", - "rel_title": "Trend prediction of COVID-19 based on ARIMA model in mainland of China", - "rel_date": "2020-09-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.04.20188235", - "rel_abs": "The ongoing pandemic of COVID-19 has aroused widespread concern around the world and poses a severe threat to public health worldwide. In this paper, the autoregressive integrated moving average (ARIMA) model was used to predict the epidemic trend of COVID-19 in mainland of China. We collected the cumulative cases, cumulative deaths, and cumulative recovery in mainland of China from January 20 to June 30, 2020, and divided the data into experimental group and test group. The ARIMA model was fitted with the experimental group data, and the optimal model was selected for prediction analysis. The predicted data were compared with the test group. The average relative errors of actual cumulative cases, deaths, recovery and predicted values in each province are between -22.32%-22.66%, -9.52%-0.08%, -8.84%-1.16, the results of the comprehensive experimental group and test group show The error of fitting and prediction is small, the degree of fitting is good, the model supports and is suitable for the prediction of the epidemic situation, which has practical guiding significance for the prevention and control of the epidemic situation.\n\nHighlightsO_LIWe predicted future COVID-19 occurrences in mainland of China based on ARIMA model.\nC_LIO_LIWe validated the model based on the previous outbreak data with actual data for June, 2020.\nC_LIO_LIThe measures taken by the government have contained spread of the epidemic\nC_LIO_LIThe combination of multiple models may improve the robustness of the model\nC_LI", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Han Chuqiao", - "author_inst": "Xinjiang University" - }, - { - "author_name": "Ju xifeng", - "author_inst": "xinjiang University" - }, - { - "author_name": "zheng jianghua", - "author_inst": "Xinjiang University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.06.20189514", "rel_title": "The impact of work loss on mental and physical health during the COVID-19 pandemic: Findings from a prospective cohort study", @@ -1218242,6 +1216663,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.09.07.20189779", + "rel_title": "Influenza may facilitate the spread of SARS-CoV-2", + "rel_date": "2020-09-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.07.20189779", + "rel_abs": "As in past pandemics, co-circulating pathogens may play a role in the epidemiology of coronavirus disease 2019 (COVID-19), caused by the novel severe acute respiratory syndrome coronavirus 2 (SARSCoV-2). Here we hypothesized that influenza interacted with SARS-CoV-2 during the early 2020 epidemic of COVID-19 in Europe. We developed a population-based model of SARS-CoV-2 transmission, combined with mortality incidence data in four European countries, to test a range of assumptions about the impact of influenza. We found consistent evidence for a 2-2.5-fold population-level increase in SARSCoV-2 transmission associated with influenza during the period of co-circulation. These results suggest the need to increase vaccination against influenza, not only to reduce the burden due to influenza viruses, but also to counteract their facilitatory impact on SARS-CoV-2.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Matthieu Domenech de Celles", + "author_inst": "Max Planck Institute for Infection Biology" + }, + { + "author_name": "Jean-Sebastien Casalegno", + "author_inst": "Virpath, Centre International de Recherche en Infectiologie (CIRI)" + }, + { + "author_name": "Bruno Lina", + "author_inst": "Virpath, Centre International de Recherche en Infectiologie (CIRI)" + }, + { + "author_name": "Lulla Opatowski", + "author_inst": "Institut Pasteur" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.09.08.20190504", "rel_title": "First report on the Latvian SARS-CoV-2 isolate genetic diversity", @@ -1218586,37 +1217038,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.09.08.20190470", - "rel_title": "Modelling the epidemic growth of preprints on COVID-19 and SARS-CoV-2", - "rel_date": "2020-09-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.08.20190470", - "rel_abs": "The response of the scientific community to the global health emergency caused by the COVID-19 pandemic has produced an unprecedented number of manuscripts in a short period of time, the vast majority of which have been shared in the form of preprints posted on online preprint repositories before peer review. This surge in preprint publications has in itself attracted considerable attention, although mostly in the bibliometrics literature. In the present study we apply a mathematical growth model, known as the generalized Richards model, to describe the time evolution of the cumulative number of COVID-19 related preprints. This mathematical approach allows us to infer several important aspects concerning the underlying growth dynamics, such as its current stage and its possible evolution in the near future. We also analyze the rank-frequency distribution of preprints servers, ordered by the number of COVID-19 preprints they host, and find that it follows a power law in the low rank (high frequency) region, with the high rank (low frequency) tail being better described by a q-exponential function. The Zipf-like law in the high frequency regime indicates the presence of a cumulative advantage effect, whereby servers that already have more preprints receive more submissions.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Giovani L. Vasconcelos", - "author_inst": "Universidade Federal do Parana" - }, - { - "author_name": "Luan P. Cordeiro", - "author_inst": "Universidade Federal do Parana" - }, - { - "author_name": "Gerson C. Duarte-Filho", - "author_inst": "Universidade Federal de Sergipe" - }, - { - "author_name": "Arthur A. Brum", - "author_inst": "Universidade Federal de Pernambuco" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.09.08.20190785", "rel_title": "Analysis of internet trends related to medications for COVID-19in ten countries with the highest number of cases", @@ -1220200,6 +1218621,109 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.09.09.285445", + "rel_title": "Evaluation of Safety and Immunogenicity of an Adjuvanted, TH-1 Skewed, Whole Virion Inactivated SARS-CoV-2 Vaccine - BBV152", + "rel_date": "2020-09-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.09.285445", + "rel_abs": "We report the development and evaluation of safety and immunogenicity of a whole virion inactivated SARS-COV-2 vaccine (BBV152), adjuvanted with aluminium hydroxide gel (Algel), or a novel TLR7/8 agonist adsorbed Algel. We used a well-characterized SARS-CoV-2 strain and an established vero cell platform to produce large-scale GMP grade highly purified inactivated antigen, BBV152. Product development and manufacturing were carried out in a BSL-3 facility. Immunogenicity was determined at two antigen concentrations (3g and 6g), with two different adjuvants, in mice, rats, and rabbits. Our results show that BBV152 vaccine formulations generated significantly high antigen-binding and neutralizing antibody titers, at both concentrations, in all three species with excellent safety profiles. The inactivated vaccine formulation containing TLR7/8 agonist adjuvant-induced Th1 biased antibody responses with elevated IgG2a/IgG1 ratio and increased levels of SARS-CoV-2 specific IFN-{gamma}+ CD4 T lymphocyte response. Our results support further development for Phase I/II clinical trials in humans.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Brunda Ganneru", + "author_inst": "Bharat Biotech" + }, + { + "author_name": "Harsh Jogdand", + "author_inst": "Bharat Biotech" + }, + { + "author_name": "Vijaya Kumar Dharam", + "author_inst": "Bharat Biotech" + }, + { + "author_name": "Narasimha Reddy", + "author_inst": "Bharat Biotech" + }, + { + "author_name": "Sai D Prasad", + "author_inst": "Bharat Biotech" + }, + { + "author_name": "Srinivas Vellimudu", + "author_inst": "Bharat Biotech" + }, + { + "author_name": "Krishna M Ella", + "author_inst": "Bharat Biotech" + }, + { + "author_name": "Rajaram Ravikrishnan", + "author_inst": "RCC Labs" + }, + { + "author_name": "Amit Awasthi", + "author_inst": "THSTI" + }, + { + "author_name": "Jomy Jose", + "author_inst": "RCC Labs" + }, + { + "author_name": "Panduranga Rao", + "author_inst": "Bharat Biotech" + }, + { + "author_name": "Deepak Kumar", + "author_inst": "Bharat Biotech" + }, + { + "author_name": "Raches Ella", + "author_inst": "Bharat Biotech International Limited" + }, + { + "author_name": "Priya Abraham", + "author_inst": "National Institute of Virology, Pune" + }, + { + "author_name": "Pragya Yadav", + "author_inst": "ICMR-National Institute of Virology" + }, + { + "author_name": "Gajanan N Sapkal", + "author_inst": "ICMR-National Institute of Virology" + }, + { + "author_name": "Anita Shete", + "author_inst": "National Institute of Virology-Indian Council of Medical Research" + }, + { + "author_name": "Gururaj Rao Desphande", + "author_inst": "National Institute of Virology-Indian Council of Medical Research" + }, + { + "author_name": "Sreelekshmy Mohandas", + "author_inst": "National Institute of Virology-Indian Council of Medical Research" + }, + { + "author_name": "Atanu Basu", + "author_inst": "National Institute of Virology-Indian Council of Medical Research" + }, + { + "author_name": "Nievedita Gupta", + "author_inst": "Indian Council of Medical Research, India" + }, + { + "author_name": "Krishna Vadrevu Mohan", + "author_inst": "Bharat Biotech" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.09.09.289074", "rel_title": "Structural Genetics of circulating variants affecting the SARS CoV-2 Spike / human ACE2 complex", @@ -1220496,69 +1219020,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.05.20188821", - "rel_title": "Ethnicity and clinical outcomes in COVID-19A Systematic Review and Meta-analysis", - "rel_date": "2020-09-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.05.20188821", - "rel_abs": "ImportanceThe association of ethnicity with outcomes in patients with COVID-19 is unclear.\n\nObjectiveTo determine whether the risk of SARS-CoV-2 infection, COVID-19 intensive care unit (ICU) admission and mortality are associated with ethnicity.\n\nData SourcesWe searched all English language articles published 1st December 2019 - 30th June 2020 within MEDLINE, EMBASE, PROSPERO and the Cochrane library using indexing terms for COVID-19 and ethnicity, as well as manuscripts awaiting peer review on MedRxiv during the same period.\n\nStudy SelectionIncluded studies reported original clinical data, disaggregated by ethnicity, on patients with confirmed or suspected COVID-19. We excluded correspondence, area level, modelling and basic science articles. Two independent reviewers screened articles for inclusion. Of 926 identified articles, 35 were included in the meta-analyses.\n\nData Extraction and SynthesisThe review was conducted according to PRISMA guidelines. Reviewers independently extracted data using a piloted form on: (1) rates of infection, ICU admission and mortality by ethnicity; and (2) unadjusted and adjusted data comparing ethnic minority and White groups. Data were pooled using random effects models.\n\nMain Outcomes and MeasuresOutcomes were: (1) infection with SARS-CoV-2 confirmed on molecular testing; (2) ICU admission; and (3) mortality in COVID-19 confirmed and suspected cases.\n\nResults13,535,562 patients from 35 studies were included in the meta-analyses. Black, Asian and Hispanic individuals had a greater risk of infection compared to White individuals (Black: pooled adjusted RR: 2.06, 95% CI: 1.59-2.67; Asian: 1.35, 95%CI: 1.15-1.59; Hispanic: 1.77, 95% CI: 1.39-2.25). Black individuals were significantly more likely to be admitted to ICU than White individuals (pooled adjusted RR: 1.61, 95% CI: 1.02-2.55). Risk of mortality was similar across ethnicities among hospitalised patients, but increased among Asian and Mixed ethnic groups in the general population.\n\nConclusionsBlack, Asian and Hispanic ethnic groups are at increased risk of SARS-CoV-2 infection. Black individuals may be more likely to require ICU admission for COVID-19. There may also be disparities in risk of death from COVID-19 at a population level. Our findings are of critical public health importance and should inform policy on minimising SARS-CoV-2 exposure in ethnic minority groups.\n\nKEY POINTSO_ST_ABSQuestionC_ST_ABSIs ethnicity associated with vulnerability to, and outcomes from, coronavirus disease 2019 (COVID-19)?\n\nFindingsIn this systematic review and meta-analysis, rates of infection and outcomes from COVID-19 were compared between ethnic groups. Individuals from Black, Asian and Hispanic ethnicity were significantly more vulnerable to SARS-CoV-2 infection than those of White ethnicity. Black individuals were more likely to need intensive care unit (ICU) admission for COVID-19 than White individuals. Risk of mortality was similar across ethnicities among hospitalised patients, but increased among Asian and Mixed ethnic groups in the general population.\n\nMeaningThere is strong evidence for an increased risk of SARS-CoV-2 infection amongst ethnic minorities, and targeted public health policies are required to reduce this risk.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Shirley Sze", - "author_inst": "University of Leicester" - }, - { - "author_name": "Daniel Pan", - "author_inst": "University of Leicester" - }, - { - "author_name": "Laura J Gray", - "author_inst": "University of Leicester" - }, - { - "author_name": "Clareece R Nevill", - "author_inst": "University of Leicester" - }, - { - "author_name": "Christopher A Martin", - "author_inst": "University of Leicester" - }, - { - "author_name": "Joshua Nazareth", - "author_inst": "University of Leicester" - }, - { - "author_name": "Jatinder S Minhas", - "author_inst": "University of Leicester" - }, - { - "author_name": "Pip Divall", - "author_inst": "University Hospitals of Leicester NHS Trust" - }, - { - "author_name": "Kamlesh Khunti", - "author_inst": "University of Leicester" - }, - { - "author_name": "Keith Abrams", - "author_inst": "University of Leicester" - }, - { - "author_name": "Laura B Nellums", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Manish Pareek", - "author_inst": "University of Leicester" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.06.20189159", "rel_title": "Kynurenic acid underlies sex-specific immune responses to COVID-19", @@ -1222902,6 +1221363,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.04.20188094", + "rel_title": "Regression Models for Predictions of COVID-19 New Cases and New Deaths Based on May/June Data in Ethiopia", + "rel_date": "2020-09-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.04.20188094", + "rel_abs": "As the 15 of June 2020, we have 7,984,067 total COVID-19 cases, globally and 435,181 total deaths. Ethiopia was ranked 2nd and 15th in the table by 176 new cases and by 3,521 total new cases from African countries. Then, this study aimed to predict COVID-19 new cases and new deaths based on May/June data in Ethiopia using regression model. In this study, I used Pearsons correlation analysis and the linear regression model to predict COVID-19 new cases and new deaths based on the available data from 12th May to 10th June 2020 in Ethiopia. There was a significant positive correlation between COVID-19 new cases and new deaths with different related variables. In the regression models, the simple linear regression model was a better fit the data of COVID-19 new cases and new deaths than as compared with quadratic and cubic regression models. In the multiple linear regression model, variables such as the number of days, the number of new laboratory tests, and the number of new cases from AA city significantly predicted the COVID-19 new cases. In this model, the number of days and new recoveries significantly predicted new deaths of COVID-19. The number of days, daily laboratory tests, and new cases from Addis Ababa city significantly predicted new COVID-19 cases, and the number of days and new recoveries significantly predicted new deaths from COVID-19. According to this analysis, if strong preventions and action are not taken in the country, the predicted values of COVID-19 new cases and new deaths will be 590 and 12 after two months (after 9th of August) from now, respectively. The researcher recommended that the Ethiopia government, Ministry of Health and Addis Ababa city administrative should give more awareness and protections for societies, and they should also open more COVID-19 laboratory testing centers. Generally, the obtained results of this study may help Ethiopian decision-makers put short-term future plans to face this epidemic.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Alemayehu Siffir Argawu Sr.", + "author_inst": "Ambo University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.04.20188102", "rel_title": "Modeling COVID-19 Transmission in Africa: Country-wise Projections of Total and Severe Infections Under Different Lockdown Scenarios", @@ -1223398,197 +1221878,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.09.04.20184523", - "rel_title": "MOLECULAR EPIDEMIOLOGY TO UNDERSTAND THE SARS-CoV-2 EMERGENCE IN THE BRAZILIAN AMAZON REGION", - "rel_date": "2020-09-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.04.20184523", - "rel_abs": "The COVID-19 pandemic in Brazil has demonstrated an important public health impact, as has been observed in the world. In Brazil, the Amazon Region contributed with a large number of cases of COVID-19, especially in the beginning of the circulation of SARS-CoV-2 in the country. Thus, we describe the epidemiological profile of COVID-19 and the genetic diversity of SARS-CoV-2 strains circulating in the Amazon Region. We observe an extensive spread of virus in this Brazilian site. The data on sex, age and symptoms presented by the investigated individuals were similar to what has been observed worldwide. The genomic analysis of the viruses revealed important amino acid changes, including the D614G and the I33T in Spike and ORF6 proteins, respectively. The latter found in strains originating in Brazil. The phylogenetic analyzes demonstrated the circulation of the lineages B.1 and B.1.1, whose circulation in Brazil has already been previous reported. Our data reveals molecular epidemiology of SARS-CoV-2 in the Amazon Region. These findings also reinforce the importance of continuous genomic surveillance this virus with the aim of providing accurate and updated data to understand and map the transmission network of this agent in order to subsidize operational decisions in public health.", - "rel_num_authors": 44, - "rel_authors": [ - { - "author_name": "Mirleide C dos Santos", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Edivaldo Costa Sousa Jr.", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Jessylene A Ferreira", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Sandro P Silva", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Michel PC Souza", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Jedson F Cardoso", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Amanda M Silva", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Luana S Barbagelata", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Wanderley D Chagas Jr.", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "James L Ferreira", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Edna MA Souza", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Patricia LA Vilaca", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Jainara CS Alves", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Michelle C Abreu", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Patricia S Lobo", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Fabiolla S Santos", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Alessandra AP Lima", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Camila M Bragagnolo", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Luana S Soares", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Patricia SM Almeida", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Darleise S Oliveira", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Carolina KN Amorim", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Iran B Costa", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Dielle M Teixeira", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Edvaldo T Penha Jr.", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Delana AM Bezerra", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Jones AM Siqueira", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Fernando N Tavares", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Felipe B Freitas", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Janete TN Rodrigues", - "author_inst": "Laboratorio Central de Saude Publica do Acre" - }, - { - "author_name": "Janaina Mazaro", - "author_inst": "Laboratorio Central de Saude Publica do Acre" - }, - { - "author_name": "Andreia S Costa", - "author_inst": "Laboratorio Central de Saude Publica do Amapa" - }, - { - "author_name": "Marcia SP Cavalcante", - "author_inst": "Laboratorio Central de Saude Publica do Amapa" - }, - { - "author_name": "Marineide Souza Silva", - "author_inst": "Laboratorio Central de Saude Publica do Amazonas" - }, - { - "author_name": "Ilvanete A Silva", - "author_inst": "Laboratorio Central de Saude Publica do Para" - }, - { - "author_name": "Gleissy AL Borges", - "author_inst": "Laboratorio Central de Saude Publica do Para" - }, - { - "author_name": "Lidio G Lima", - "author_inst": "Laboratorio Central de Saude Publica do Maranhao" - }, - { - "author_name": "Hivylla LS Ferreira", - "author_inst": "Laboratorio Central de Saude Publica do Maranhao" - }, - { - "author_name": "Miriam TFP Livorati", - "author_inst": "Secretaria de Vigilancia em Saude" - }, - { - "author_name": "Andre L Abreu", - "author_inst": "Secretaria de Vigilancia em Saude" - }, - { - "author_name": "Arnaldo C Medeiros", - "author_inst": "Secretaria de Vigilancia em Saude" - }, - { - "author_name": "Hugo R Resque", - "author_inst": "Instituto Evandro Chagas" - }, - { - "author_name": "Rita CM Sousa", - "author_inst": "Programa de Pos Graduacao em Virologia - Instituto Evandro Chagas" - }, - { - "author_name": "Giselle MR Viana", - "author_inst": "Instituto Evandro Chagas" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.04.20184721", "rel_title": "Emergence of the D614A mutation in the spike protein of SARS-CoV-2: Imported cases to the South Korea", @@ -1224644,6 +1222933,73 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.09.06.284992", + "rel_title": "Computationally validated SARS-CoV-2 CTL and HTL Multi-Patch Vaccines designed by reverse epitomics approach, shows potential to cover large ethnically distributed human population worldwide", + "rel_date": "2020-09-06", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.06.284992", + "rel_abs": "BackgroundThe SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) is a positive-sense single-stranded RNA coronavirus responsible for the ongoing 2019-2020 COVID-19 outbreak. The highly contagious COVID-19 disease has spread to 216 countries in less than six months. Though several vaccine candidates are being claimed, an effective vaccine is yet to come. In present study we have designed and theoretically validated novel Multi-Patch Vaccines against SARS-CoV-2.\n\nMethodologyA novel reverse epitomics approach, \"overlapping-epitope-clusters-to-patches\" method is utilized to identify multiple antigenic regions from the SARS-CoV-2 proteome. These antigenic regions are here termed as \"Ag-Patch or Ag-Patches\", for Antigenic Patch or Patches. The identification of Ag-Patches is based on clusters of overlapping epitopes rising from a particular region of SARS-CoV-2 protein. Further, we have utilized the identified Ag-Patches to design Multi-Patch Vaccines (MPVs), proposing a novel methodology for vaccine design and development. The designed MPVs were analyzed for immunologically crucial parameters, physiochemical properties and cDNA constructs.\n\nResultsWe identified 73 CTL (Cytotoxic T-Lymphocyte), 49 HTL (Helper T-Lymphocyte) novel Ag-Patches from the proteome of SARS-CoV-2. The identified Ag-Patches utilized to design MPVs cover 768 (518 CTL and 250 HTL) overlapping epitopes targeting different HLA alleles. Such large number of epitope coverage is not possible for multi-epitope vaccines. The large number of epitopes covered implies large number of HLA alleles targeted, and hence large ethnically distributed human population coverage. The MPVs:Toll-Like Receptor ectodomain complex shows stable nature with numerous hydrogen bond formation and acceptable root mean square deviation and fluctuation. Further, the cDNA analysis favors high expression of the MPVs constructs in human cell line.\n\nConclusionHighly immunogenic novel Ag-Patches are identified from the entire proteome of SARS CoV-2 by a novel reverse epitomics approach. We conclude that the novel Multi-Patch Vaccines could be a highly potential novel approach to combat SARS-CoV-2, with greater effectiveness, high specificity and large human population coverage worldwide.\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=187 HEIGHT=200 SRC=\"FIGDIR/small/284992v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (84K):\norg.highwire.dtl.DTLVardef@176f27org.highwire.dtl.DTLVardef@82a4fcorg.highwire.dtl.DTLVardef@11db43forg.highwire.dtl.DTLVardef@12495b2_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOABSTRACT FIGURE:C_FLOATNO A Multi-Patch Vaccine design to combat SARS-CoV-2 and a method to prepare thereof.\n\nMulti-Patch Vaccine designing to combat SARS-CoV-2 infection by reverse epitomics approach, \"Overlapping-epitope-clusters-to-patches\" method.\n\nC_FIG", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Sukrit Srivastava", + "author_inst": "Indian Foundation for Fundamental Research, India" + }, + { + "author_name": "Sonia Verma", + "author_inst": "ICMR-National Institute of Malaria Research, India" + }, + { + "author_name": "Mohit Kamthania", + "author_inst": "Indian Foundation for Fundamental Research, India" + }, + { + "author_name": "Deepa Agarwal", + "author_inst": "Indian Foundation for Fundamental Research, India" + }, + { + "author_name": "Ajay Kumar Saxena", + "author_inst": "Jawaharlal Nehru University, India" + }, + { + "author_name": "Michael Kolbe", + "author_inst": "Helmholzt-Center for Infection Research, Germany" + }, + { + "author_name": "Sarman Singh", + "author_inst": "All India Institute of Medical Sciences, Bhopal, India" + }, + { + "author_name": "Ashwin Kotnis", + "author_inst": "All India Institute of Medical Sciences, Bhopal, India" + }, + { + "author_name": "Brijesh Rathi", + "author_inst": "Hansraj College, University of Delhi, India" + }, + { + "author_name": "Seema A Nayar", + "author_inst": "Government Medical College, Trivandrum, India" + }, + { + "author_name": "Ho-Joon Shin", + "author_inst": "School of Medicine, Ajou University, South Korea" + }, + { + "author_name": "Kapil Vashisht", + "author_inst": "ICMR-National Institute of Malaria Research, India" + }, + { + "author_name": "Kailash C Pandey", + "author_inst": "ICMR-National Institute of Malaria Research, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.09.06.284695", "rel_title": "Long-term survival of salmon-attached SARS-CoV-2 at 4 degree as a potential source of transmission in seafood markets", @@ -1225088,61 +1223444,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.03.20187062", - "rel_title": "College campuses and COVID-19 mitigation: clinical and economic value", - "rel_date": "2020-09-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.03.20187062", - "rel_abs": "BackgroundDecisions around US college and university operations will affect millions of students and faculty amidst the COVID-19 pandemic. We examined the clinical and economic value of different COVID-19 mitigation strategies on college campuses.\n\nMethodsWe used the Clinical and Economic Analysis of COVID-19 interventions (CEACOV) model, a dynamic microsimulation that tracks infections accrued by students and faculty, accounting for community transmissions. Outcomes include infections, $/infection-prevented, and $/quality-adjusted-life-year ($/QALY). Strategies included extensive social distancing (ESD), masks, and routine laboratory tests (RLT). We report results per 5,000 students (1,000 faculty) over one semester (105 days).\n\nResultsMitigation strategies reduced COVID-19 cases among students (faculty) from 3,746 (164) with no mitigation to 493 (28) with ESD and masks, and further to 151 (25) adding RLTq3 among asymptomatic students and faculty. ESD with masks cost $168/infection-prevented ($49,200/QALY) compared to masks alone. Adding RLTq3 ($10/test) cost $8,300/infection-prevented ($2,804,600/QALY). If tests cost $1, RLTq3 led to a favorable cost of $275/infection-prevented ($52,200/QALY). No strategies without masks were cost-effective.\n\nConclusionExtensive social distancing with mandatory mask-wearing could prevent 87% of COVID-19 cases on college campuses and be very cost-effective. Routine laboratory testing would prevent 96% of infections and require low cost tests to be economically attractive.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Elena Losina", - "author_inst": "BWH" - }, - { - "author_name": "Valia Leifer", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Lucia Millham", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Christopher Panella", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Emily P. Hyle", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Amir M. Mohareb", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Anne M. Neilan", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Andrea L. Ciaranello", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Pooyan Kazemian", - "author_inst": "Case Western Reserve University" - }, - { - "author_name": "Kenneth A. Freedberg", - "author_inst": "Massachusetts General Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.09.01.20186155", "rel_title": "SARS-CoV-2 phylogeny during the early outbreak in the Basel area, Switzerland: import and spread dominated by a single B.1 lineage variant (C15324T)", @@ -1226078,6 +1224379,89 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.09.04.283077", + "rel_title": "Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore", + "rel_date": "2020-09-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.04.283077", + "rel_abs": "Genome sequencing has been widely deployed to study the evolution of SARS-CoV-2 with more than 90,000 genome sequences uploaded to the GISAID database. We published a method for SARS-CoV-2 genome sequencing (https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w) online on January 22, 2020. This approach has rapidly become the most popular method for sequencing SARS-CoV-2 due to its simplicity and cost-effectiveness. Here we present improvements to the original protocol: i) an updated primer scheme with 22 additional primers to improve genome coverage, ii) a streamlined library preparation workflow which improves demultiplexing rate for up to 96 samples and reduces hands-on time by several hours and iii) cost savings which bring the reagent cost down to {pound}10 per sample making it practical for individual labs to sequence thousands of SARS-CoV-2 genomes to support national and international genomic epidemiology efforts.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "John R Tyson", + "author_inst": "Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada." + }, + { + "author_name": "Phillip James", + "author_inst": "Oxford Nanopore Technologies Ltd., Oxford, UK." + }, + { + "author_name": "David Stoddart", + "author_inst": "Oxford Nanopore Technologies Ltd., Oxford, UK." + }, + { + "author_name": "Natalie Sparks", + "author_inst": "Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK." + }, + { + "author_name": "Arthur Wickenhagen", + "author_inst": "MRC-University of Glasgow Centre for Virus Research, Glasgow, UK." + }, + { + "author_name": "Grant Hall", + "author_inst": "Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK." + }, + { + "author_name": "Ji Hyun Choi", + "author_inst": "Division of AIDS, Faculty of Medicine, University of British Columbia, Vancouver, Canada." + }, + { + "author_name": "Hope Lapointe", + "author_inst": "Division of AIDS, Faculty of Medicine, University of British Columbia, Vancouver, Canada." + }, + { + "author_name": "Kimia Kamelian", + "author_inst": "British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada." + }, + { + "author_name": "Andrew D Smith", + "author_inst": "Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK." + }, + { + "author_name": "Natalie Prystajecky", + "author_inst": "British Columbia Centre for Disease Control Public Health Laboratory, Vancouver, Canada." + }, + { + "author_name": "Ian Goodfellow", + "author_inst": "Division of Virology, Department of Pathology, University of Cambridge, Cambridge, UK." + }, + { + "author_name": "Sam J Wilson", + "author_inst": "MRC-University of Glasgow Centre for Virus Research, Glasgow, UK." + }, + { + "author_name": "Richard Harrigan", + "author_inst": "Division of AIDS, Faculty of Medicine, University of British Columbia, Vancouver, Canada." + }, + { + "author_name": "Terrance P Snutch", + "author_inst": "Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada." + }, + { + "author_name": "Nicholas J Loman", + "author_inst": "Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK." + }, + { + "author_name": "Joshua Quick", + "author_inst": "Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK." + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.09.04.282780", "rel_title": "SARS-CoV-2 infection paralyzes cytotoxic and metabolic functions of immune cells", @@ -1226662,37 +1225046,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, - { - "rel_doi": "10.1101/2020.08.29.20184325", - "rel_title": "Face-masking, an acceptable protective measure against COVID-19: Findings of Ugandan high-risk groups", - "rel_date": "2020-09-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.29.20184325", - "rel_abs": "Face-masking could reduce the risk of COVID-19 transmission. We assessed: knowledge, attitudes, perceptions, and practices towards COVID-19 and face-mask use among 644 high risk-individuals in Kampala, Uganda. In data analysis, descriptive, bivariate and multivariate logistic regression analyses, with a 95% confidence interval were considered. Adjusted-odds ratios were used to determine the magnitude of associations. P-values < 0.05 were considered statistically-significant. Majority: 99.7% and 87.3% of the participants respectively had heard and believed that face-masks were protective against COVID-19, while 67.9% reported having received information on face-mask use. Males, food market vendors, those with no formal education, and those aged 24-33, 44-53 and 54-63 years were 0.58, 0.47, 0.25, 1.9, 2.12, and 3.39 times less likely to have received information about face-mask use respectively. Majority, 67.8% owned locally-made, non-medical face-masks, while 77.0% of face-mask owners believed that they knew the right procedure of wearing them. Those who had received information on face-mask use were 2.85 and 1.83 times more likely to own face-masks and to perceive them as protective. Food market vendors were 3.92 times more likely to re-use their face-masks. Our findings suggest that Ugandan high-risk groups have good knowledge, optimistic attitudes and perceptions, and relatively appropriate practices towards COVID-19.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Dickson Aruhomukama", - "author_inst": "Makerere University" - }, - { - "author_name": "Gerald Mboowa", - "author_inst": "Makerere University" - }, - { - "author_name": "David Musoke", - "author_inst": "Makerere University" - }, - { - "author_name": "Douglas Bulafu", - "author_inst": "Makerere University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.09.01.20184333", "rel_title": "Biologic agents for rheumatic diseases in the break of COVID-19: friend or foe?", @@ -1227720,6 +1226073,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.09.02.20187179", + "rel_title": "Pleotropic association between risk and prognosis of COVID-19 and gene expression in blood and lung: A Mendelian randomization analysis", + "rel_date": "2020-09-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.02.20187179", + "rel_abs": "ObjectivesCOVID-19 has caused a large global pandemic. Patients with COVID-19 exhibited considerable variation in disease behavior. Pervious genome-wide association studies have identified potential genetic variants involved in the risk and prognosis of COVID-19, but the underlying biological interpretation remains largely unclear.\n\nMethodsWe applied the summary data-based Mendelian randomization (SMR) method to identify genes that were pleiotropically associated with the risk and various outcomes of COVID-19, including severe respiratory confirmed COVID-19 and hospitalized COVID-19.\n\nResultsIn blood, we identified 2 probes, ILMN_1765146 and ILMN_1791057 tagging IFNAR2, that showed pleiotropic association with hospitalized COVID-19 ({beta} [SE] = 0.42 [0.09], P = 4.75x10-06 and {beta} [SE] = -0.48 [0.11], P = 6.76x10-06, respectively). Although no other probes were significant after correction for multiple testing in both blood and lung, multiple genes as tagged by the top 5 probes were involved in inflammation or antiviral immunity, and several other tagged genes, such as PON2 and HPS5, were involved in blood coagulation.\n\nConclusionsWe identified IFNAR2 and other potential genes that could be involved in the susceptibility or prognosis of COVID-19. These findings provide important leads to a better understanding of the mechanisms of cytokine storm and venous thromboembolism in COVID-19 and potential therapeutic targets for the effective treatment of COVID-19.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Di Liu", + "author_inst": "Capital Medical University" + }, + { + "author_name": "Jingyun Yang", + "author_inst": "Rush University Medical Center" + }, + { + "author_name": "Bowen Feng", + "author_inst": "University of Windsor" + }, + { + "author_name": "Wenjin Lu", + "author_inst": "University College London" + }, + { + "author_name": "Chuntao Zhao", + "author_inst": "Cincinnati Children Hospital Medical Center" + }, + { + "author_name": "Lizhuo Li", + "author_inst": "Capital Medical University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.09.02.20180984", "rel_title": "Post-Anticoagulant D-dimer as a Highly Prognostic Biomarker of COVID-19 Mortality", @@ -1228080,29 +1226472,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.09.02.20186734", - "rel_title": "Could seasonal influenza vaccination influence COVID-19 risk?", - "rel_date": "2020-09-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.02.20186734", - "rel_abs": "BackgroundWith possible resurgence of the SARS-CoV-2 and low seasonal influenza virus circulation next winter, reviewing evidence on a possible interaction between influenza vaccination and COVID-19 risk is important.\n\nObjectiveTo review studies on the effect of influenza vaccines on non-influenza respiratory disease (NIRD).\n\nMethodsUsing different search strategies, 18 relevant studies were identified and their strength, limitations and significance were assessed.\n\nResultsAnalysis of 4 RCT datasets did not suggest increased NIRD risk in recipients of live-attenuated vaccines (LAIV) and results of a cohort study suggested short-term protection consistent with the hypothesis of trained immunity. One RCT, four cohort studies and one test-negative case-control suggested increased NIRD risk in recipients of inactivated influenza vaccines (IIV), whereas five test-negative case-control studies did not show an increased risk associated with a specific viral pathogen. Cross-protection against COVID-19 was suggested in one cross-sectional study on IIV but major biases could not be excluded. Results of four recent ecological studies on COVID-19 were challenging to interpret.\n\nConclusionsAvailable data on LAIV are reassuring but not all those on IIV. A drastic reorientation of 2020-2021 influenza campaigns is probably not warranted but studies aiming to test COVID-19 risk modification among recipients of seasonal influenza vaccines should be planned and funded.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Philippe De wals", - "author_inst": "Laval University" - }, - { - "author_name": "Maziar Divangahi", - "author_inst": "McGill University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.02.20186551", "rel_title": "An epidemic model for economical impact predicting and spatiotemporal spreading of COVID-19", @@ -1229306,6 +1227675,25 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2020.09.03.280727", + "rel_title": "The discovery of gene mutations making SARS-CoV-2 well adapted for humans: host-genome similarity analysis of 2594 genomes from China, the USA and Europe", + "rel_date": "2020-09-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.09.03.280727", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a positive-sense single-stranded virus approximately 30 kb in length, causes the ongoing novel coronavirus disease-2019 (COVID-19). Studies confirmed significant genome differences between SARS-CoV-2 and SARS-CoV, suggesting that the distinctions in pathogenicity might be related to genomic diversity. However, the relationship between genomic differences and SARS-CoV-2 fitness has not been fully explained, especially for open reading frame (ORF)-encoded accessory proteins. RNA viruses have a high mutation rate, but how SARS-CoV-2 mutations accelerate adaptation is not clear. This study shows that the host-genome similarity (HGS) of SARS-CoV-2 is significantly higher than that of SARS-CoV, especially in the ORF6 and ORF8 genes encoding proteins antagonizing innate immunity in vivo. A power law relationship was discovered between the HGS of ORF3b, ORF6, and N and the expression of interferon (IFN)-sensitive response element (ISRE)-containing promoters. This finding implies that high HGS of SARS-CoV-2 genome may further inhibit IFN I synthesis and cause delayed host innate immunity. An ORF1ab mutation, 10818G>T, which occurred in virus populations with high HGS but rarely in low-HGS populations, was identified in 2594 genomes with geolocations of China, the USA and Europe. The 10818G>T caused the amino acid mutation M37F in the transmembrane protein nsp6. The results suggest that the ORF6 and ORF8 genes and the mutation M37F may play important roles in causing COVID-19. The findings demonstrate that HGS analysis is a promising way to identify important genes and mutations in adaptive strains, which may help in searching potential targets for pharmaceutical agents.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Weitao Sun", + "author_inst": "Tsinghua University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.09.03.280719", "rel_title": "A Mental Health Paradox: Mental health was both a motivator and barrier to physical activity during the COVID-19 pandemic", @@ -1229758,53 +1228146,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.09.02.20186742", - "rel_title": "The role of masks in reducing the risk of new waves of COVID-19 in low transmission settings: a modeling study", - "rel_date": "2020-09-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.02.20186742", - "rel_abs": "ObjectivesTo evaluate the risk of a new wave of coronavirus disease 2019 (COVID-19) in a setting with ongoing low transmission, high mobility, and an effective test-and-trace system, under different assumptions about mask uptake.\n\nDesignWe used a stochastic agent-based microsimulation model to create multiple simulations of possible epidemic trajectories that could eventuate over a five-week period following prolonged low levels of community transmission.\n\nSettingWe calibrated the model to the epidemiological and policy environment in New South Wales, Australia, at the end of August 2020.\n\nParticipantsNone\n\nInterventionFrom September 1, 2020, we ran the stochastic model with the same initial conditions(i.e., those prevailing at August 31, 2020), and analyzed the outputs of the model to determine the probability of exceeding a given number of new diagnoses and active cases within five weeks, under three assumptions about future mask usage: a baseline scenario of 30% uptake, a scenario assuming no mask usage, and a scenario assuming mandatory mask usage with near-universal uptake (95%).\n\nMain outcome measureProbability of exceeding a given number of new diagnoses and active cases within five weeks.\n\nResultsThe policy environment at the end of August is sufficient to slow the rate of epidemic growth, but may not stop the epidemic from growing: we estimate a 20% chance that NSW will be diagnosing at least 50 new cases per day within five weeks from the date of this analysis. Mandatory mask usage would reduce this to 6-9%.\n\nConclusionsMandating the use of masks in community settings would significantly reduce the risk of epidemic resurgence.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Robyn M Stuart", - "author_inst": "University of Copenhagen" - }, - { - "author_name": "Romesh G Abeysuriya", - "author_inst": "Burnet Institute" - }, - { - "author_name": "Cliff C Kerr", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Dina Mistry", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Daniel J Klein", - "author_inst": "Institute for Disease Modeling" - }, - { - "author_name": "Richard Gray", - "author_inst": "The Kirby Institute, UNSW Sydney" - }, - { - "author_name": "Margaret Hellard", - "author_inst": "Burnet Institute" - }, - { - "author_name": "Nick Scott", - "author_inst": "Burnet Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.09.01.20182469", "rel_title": "Insights into the practical effectiveness of RT-PCR testing for SARS-CoV-2 from serologic data, a cohort study", @@ -1230780,6 +1229121,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.26.20181719", + "rel_title": "Sample Pooling is a Viable Strategy for SARS-CoV-2 Detection in Low-Prevalence Settings", + "rel_date": "2020-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.26.20181719", + "rel_abs": "BACKGROUNDThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has significantly increased demand on laboratory throughput and reagents for nucleic acid extraction and polymerase chain reaction (PCR). Reagent shortages may limit the expansion of testing required to scale back isolation measures.\n\nAIMTo investigate the viability of sample pooling as a strategy for increasing test throughput and conserving PCR reagents; to report our early experience with pooling of clinical samples.\n\nMETHODSA pre-implementation study was performed to assess the sensitivity and theoretical efficiency of two, four, and eight-sample pools in a real-time reverse transcription PCR-based workflow. A standard operating procedure was developed and implemented in two laboratories during periods of peak demand, inclusive of over 29,000 clinical samples processed in our laboratory.\n\nRESULTSSensitivity decreased (mean absolute increase in cycle threshold value of 0.6, 2.3, and 3.0 for pools of two, four, and eight samples respectively) and efficiency increased as pool size increased. Gains from pooling diminished at high disease prevalence. Our standard operating procedure was successfully implemented across two laboratories. Increased workflow complexity imparts a higher risk of errors, and requires risk mitigation strategies. Turnaround time for individual samples increased, hence urgent samples should not be pooled.\n\nCONCLUSIONSPooling is a viable strategy for high-throughput testing of SARS-CoV-2 in low-prevalence settings.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Brian SW Chong", + "author_inst": "Victorian Infectious Diseases Reference Laboratory" + }, + { + "author_name": "Thomas Tran", + "author_inst": "Victorian Infectious Diseases Reference Laboratory" + }, + { + "author_name": "Julian Druce", + "author_inst": "Victorian Infectious Diseases Reference Laboratory" + }, + { + "author_name": "Susan A Ballard", + "author_inst": "The University of Melbourne at the Peter Doherty Institute for Infection and Immunity" + }, + { + "author_name": "Julie A Simpson", + "author_inst": "Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourne" + }, + { + "author_name": "Mike Catton", + "author_inst": "Victorian Infectious Diseases Reference Laboratory" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.30.20184754", "rel_title": "Impact of temperature on Covid 19 in India", @@ -1231464,61 +1229844,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.30.20184804", - "rel_title": "To isolate or not to isolate: The impact of changing behavior on COVID-19 transmission", - "rel_date": "2020-09-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.30.20184804", - "rel_abs": "The COVID-19 pandemic has caused more than 25 million cases and 800 thousand deaths worldwide to date. Neither vaccines nor therapeutic drugs are currently available for this novel coronavirus. All measures to prevent the spread of COVID-19 are thus based on reducing contact between infected and susceptible individuals. Most of these measures such as quarantine and self-isolation require voluntary compliance by the population. However, humans may act in their (perceived) self-interest only. We construct a mathematical model of COVID-19 transmission with quarantine and hospitalization coupled with a dynamic game model of adaptive human behavior. Susceptible and infected individuals adopt various behavioral strategies based on perceived prevalence and burden of the disease and sensitivity to isolation measures, and they evolve their strategies using a social learning algorithm (imitation dynamics). This results in complex interplay between the epidemiological model, which affects success of different strategies, and the game-theoretic behavioral model, which in turn affects the spread of the disease. We found that the second wave of the pandemic, which has been observed in the US, can be attributed to rational behavior of susceptible individuals, and that multiple waves of the pandemic are possible if the rate of social learning of infected individuals is sufficiently high. To reduce the burden of the disease on the society, it is necessary to incentivize such altruistic behavior by infected individuals as voluntary self-isolation.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Folashade B. Agusto", - "author_inst": "University of Kansas, Lawrence, KS 66045 USA" - }, - { - "author_name": "Igor V. Erovenko", - "author_inst": "University of North Carolina at Greensboro, Greensboro, NC 27412 USA" - }, - { - "author_name": "Alexander Fulk", - "author_inst": "University of Kansas, Lawrence, KS 66045 USA" - }, - { - "author_name": "Qays Abu-Saymeh", - "author_inst": "University of Kansas, Lawrence, KS 66045 USA" - }, - { - "author_name": "Daniel Daniel Romero-Alvarez", - "author_inst": "University of Kansas, Lawrence, KS 66045 USA" - }, - { - "author_name": "Joan Ponce", - "author_inst": "Purdue University, West Lafayette, IN 47907 USA" - }, - { - "author_name": "Suzanne Sindi", - "author_inst": "University of California Merced, Merced, CA 95343 USA" - }, - { - "author_name": "Omayra Ortega", - "author_inst": "Sonoma State University, Rohnert Park, CA 94928" - }, - { - "author_name": "Jarron M. Saint Onge", - "author_inst": "University of Kansas, Lawrence, KS 66045 USA and University of Kansas Medical Center, Kansas City, KS 66160 USA" - }, - { - "author_name": "A. Townsend Peterson", - "author_inst": "University of Kansas, Lawrence, KS 66045 USA" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.31.20183095", "rel_title": "Seroprevalence of SARS-CoV-2 antibodies in children - A prospective multicentre cohort study.", @@ -1232786,6 +1231111,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.31.20184036", + "rel_title": "Assessing the Impact of the Covid-19 Pandemic on US Mortality: A County-Level Analysis", + "rel_date": "2020-09-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.31.20184036", + "rel_abs": "BackgroundCovid-19 excess deaths refer to increases in mortality over what would normally have been expected in the absence of the Covid-19 pandemic. Several prior studies have calculated excess deaths in the United States but were limited to the national or state level, precluding an examination of area-level variation in excess mortality and excess deaths not assigned to Covid-19. In this study, we take advantage of county-level variation in Covid-19 mortality to estimate excess deaths associated with the pandemic and examine how the extent of excess mortality not assigned to Covid-19 varies across subsets of counties defined by sociodemographic and health characteristics.\n\nMethods and FindingsIn this ecological, cross-sectional study, we made use of provisional National Center for Health Statistics (NCHS) data on direct Covid-19 and all-cause mortality occurring in U.S. counties from January 1 to December 31, 2020 and reported before March 12, 2021. We used data with a ten week time lag between the final day that deaths occurred and the last day that deaths could be reported to improve the completeness of data. Our sample included 2,096 counties with 20 or more Covid-19 deaths. The total number of residents living in these counties was 319.1 million. On average, the counties were 18.7% Hispanic, 12.7% non-Hispanic Black and 59.6% non-Hispanic White. 15.9% of the population was older than 65 years. We first modeled the relationship between 2020 all-cause mortality and Covid-19 mortality across all counties and then produced fully stratified models to explore differences in this relationship among strata of sociodemographic and health factors. Overall, we found that for every 100 deaths assigned to Covid-19, 120 all-cause deaths occurred (95% CI, 116 to 124), implying that 17% (95% CI, 14% to 19%) of excess deaths were ascribed to causes of death other than Covid-19 itself. Our stratified models revealed that the percentage of excess deaths not assigned to Covid-19 was substantially higher among counties with lower median household incomes and less formal education, counties with poorer health and more diabetes, and counties in the South and West. Counties with more non-Hispanic Black residents, who were already at high risk of Covid-19 death based on direct counts, also reported higher percentages of excess deaths not assigned to Covid-19. Study limitations include the use of provisional data that may be incomplete and the lack of disaggregated data on county-level mortality by age, sex, race/ethnicity, and sociodemographic and health characteristics.\n\nConclusionsIn this study, we found that direct Covid-19 death counts in the United States in 2020 substantially underestimated total excess mortality attributable to Covid-19. Racial and socioeconomic inequities in Covid-19 mortality also increased when excess deaths not assigned to Covid-19 were considered. Our results highlight the importance of considering health equity in the policy response to the pandemic.\n\nAuthors SummaryO_ST_ABSWhy Was This Study Done?C_ST_ABSO_LIThe Covid-19 pandemic has resulted in excess mortality that would not have occurred in the absence of the pandemic.\nC_LIO_LIExcess deaths include deaths assigned to Covid-19 in official statistics as well as deaths that are not assigned to Covid-19 but are attributable directly or indirectly to Covid-19.\nC_LIO_LIWhile prior studies have identified significant racial and socioeconomic inequities in directly assigned Covid-19 deaths, few studies have documented how excess mortality in 2020 has differed across sociodemographic or health factors in the United States.\nC_LI\n\nWhat Did the Researchers Do and Find?O_LILeveraging data from 2,096 counties on Covid-19 and all-cause mortality, we assessed what percentage of excess deaths were not assigned to Covid-19 and examined variation in excess deaths by county characteristics.\nC_LIO_LIIn these counties, we found that for every 100 deaths directly assigned to Covid-19 in official statistics, an additional 20 deaths occurred that were not counted as direct Covid-19 deaths.\nC_LIO_LIThe proportion of excess deaths not counted as direct Covid-19 deaths was even higher in counties with lower average socioeconomic status, counties with more comorbidities, and counties in the South and West. Counties with more non-Hispanic Black residents who were already at high risk of Covid-19 death based on direct counts, also reported a higher proportion of excess deaths not assigned to Covid-19.\nC_LI\n\nWhat Do These Findings Mean?O_LIDirect Covid-19 death counts significantly underestimate excess mortality in 2020.\nC_LIO_LIMonitoring excess mortality will be critical to gain a full picture of socioeconomic and racial inequities in mortality attributable to the Covid-19 pandemic.\nC_LIO_LITo prevent inequities in mortality from growing even larger, health equity must be prioritized in the policy response to the Covid-19 pandemic.\nC_LI", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Andrew C Stokes", + "author_inst": "Boston University School of Public Health" + }, + { + "author_name": "Dielle J Lundberg", + "author_inst": "Boston University School of Public Health" + }, + { + "author_name": "Irma T Elo", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Katherine Hempstead", + "author_inst": "Robert Wood Johnson Foundation" + }, + { + "author_name": "Jacob Bor", + "author_inst": "Boston University School of Public Health" + }, + { + "author_name": "Samuel H Preston", + "author_inst": "University of Pennsylvania" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.31.20185165", "rel_title": "Estimation of a state of Corona 19 epidemic in August 2020 by multistage logistic model: a case of EU, USA, and World", @@ -1233282,53 +1231646,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, - { - "rel_doi": "10.1101/2020.09.01.20183145", - "rel_title": "Impact of COVID-19 pandemic on cancer care delivery : A Real World Experience", - "rel_date": "2020-09-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.09.01.20183145", - "rel_abs": "BackgroundThere is lack of information on impact of Corona Virus Disease (COVID-19) pandemic on routine cancer care delivery.\n\nAims and ObjectivesTo evaluate the change in Day Care Chemotherapy (DCC) and Out Patient Department (OPD) patient numbers before and after COVID-19 national lockdown.\n\nMaterial and MethodsDemographic data, diagnosis, type and frequency of chemotherapy delivered in Day Care between 1st February 2020 to 31st July 2020 were retrieved. Out Patient Department daily patient numbers were collected. Descriptive statistics, Odds ratio, Chi-square and Student T test were used to measure change in pattern of DDC and OPD patient numbers before and after 24th March 2020 (day of Lockdown). Pearson correlation coefficient was used to measure the strength of correlation between rise in COVID-19 cases and patient numbers.\n\nResults3192 DCC and 8209 OPD visits were recorded in 126 working days. Median age was 47 years(SD + 19.06). Breast (17%) and Gall bladder(15%) were the most common cancers receiving chemotherapy. There was a significant decrease in number of DCC delivered in post COVID lockdown [mean 21.97 (+ 9.7)] compared to pre COVID lockdown [mean 33.30 (+11.4)], t=4.11, p = 0.001.There was a significant decrease in number of OPD visits in post COVID lockdown [mean 47.13 (+ 18.8)] compared to pre COVID lockdown [mean 89.91 (+30.0)], t=7.09, p = 0.001. The odds of receiving weekly chemotherapy over non weekly regimes significantly decreased post COVID lockdown with Odds ratio of 0.52 (95% CI, 0.36-0.75) with Chi square of 12.57, p =0.001. Daily COVID cases in State and OPD patient number were found to be moderately positively correlated on Pearson correlation coefficient, r = 0.35,p =0.001.\n\nConclusionThere was a significant fall in patient visit and chemotherapy cycles immediately after lockdown. The numbers increased later despite rise in COVID-19 cases.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Avinash Pandey", - "author_inst": "Indira Gandhi Institute of Medical Sciences, Patna" - }, - { - "author_name": "Mala Rani", - "author_inst": "Indira Gandhi Institue of Medical Sciences, Patna" - }, - { - "author_name": "Neelam Chandra", - "author_inst": "Indira Gandhi Institue of Medical Sciences, Patna" - }, - { - "author_name": "Mridula Pandey", - "author_inst": "Indira Gandhi Institue of Medical Sciences, Patna" - }, - { - "author_name": "Ravindra Singh", - "author_inst": "Indira Gandhi Institue of Medical Sciences, Patna" - }, - { - "author_name": "Kanchan Monalisa", - "author_inst": "Indira Gandhi Institue of Medical Sciences, Patna" - }, - { - "author_name": "Vikash Yadav", - "author_inst": "Indira Gandhi Institue of Medical Sciences, Patna" - }, - { - "author_name": "Shivkant Singh", - "author_inst": "Indira Gandhi Institue of Medical Sciences, Patna" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "oncology" - }, { "rel_doi": "10.1101/2020.08.31.20185371", "rel_title": "Governor partisanship explains the adoption of statewide mandates to wear face coverings", @@ -1234588,6 +1232905,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.27.20182493", + "rel_title": "A longitudinal study of SARS-CoV-2 infected patients shows high correlation between neutralizing antibodies and COVID-19 severity", + "rel_date": "2020-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.27.20182493", + "rel_abs": "Understanding the immune responses elicited by SARS-CoV-2 infection is critical in terms of protection from re-infection and, thus, for public health policy and for vaccine development against the COVID-19. Here, using either live SARS-CoV-2 particles or retroviruses pseudotyped with the SARS-CoV-2 S viral surface protein (Spike), we studied the neutralizing antibody (nAb) response in serum specimens from a cohort of 140 SARS-CoV-2 qPCR-confirmed patients, including patient with mild symptoms but also more severe form including those that require intensive care. We show that nAb titers were strongly correlated with disease severity and with anti-Spike IgG levels. Indeed, patients from intensive care units exhibited high nAb titers, whereas patients with milder disease symptoms displayed heterogenous nAb titers and asymptomatic or exclusive outpatient care patients had no or poor nAb levels. We found that the nAb activity in SARS-CoV-2-infected patients displayed a relatively rapid decline after recovery, as compared to individuals infected with alternative coronaviruses. We show the absence of cross-neutralization between endemic coronaviruses and SARS-CoV-2, indicating that previous infection by human coronaviruses may not generate protective nAb against SARS-CoV-2 infection. Finally, we found that the D614G mutation in the Spike protein, which has recently been identified as the major variant now found in Europe, does not allow neutralization escape. Altogether, our results contribute to the understanding of the immune correlate of SARS-CoV-2 induced disease and claim for a rapid evaluation of the role of the humoral response in the pathogenesis of SARS-CoV-2.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Vincent Legros", + "author_inst": "Centre International de Recherche en Infectiologie and VetAgro Sup" + }, + { + "author_name": "Sol\u00e8ne Denolly", + "author_inst": "Centre International de Recherche en Infectiologie" + }, + { + "author_name": "Manon Vogrig", + "author_inst": "University-Hospital of Saint-Etienne" + }, + { + "author_name": "Bertrand Boson", + "author_inst": "Centre International de Recherche en Infectiologie" + }, + { + "author_name": "Josselin Rigaill", + "author_inst": "University-Hospital of Saint-Etienne" + }, + { + "author_name": "Sylvie Pillet", + "author_inst": "Centre International de Recherche en Infectiologie and University-Hospital of Saint-Etienne" + }, + { + "author_name": "Florence Grattard", + "author_inst": "Centre International de Recherche en Infectiologie and University-Hospital of Saint-Etienne" + }, + { + "author_name": "Sylvie Gonzalo", + "author_inst": "University-Hospital of Saint-Etienne" + }, + { + "author_name": "Paul Verhoeven", + "author_inst": "Centre International de Recherche en Infectiologie and University-Hospital of Saint-Etienne" + }, + { + "author_name": "Omran Allatif", + "author_inst": "Centre International de Recherche en Infectiologie" + }, + { + "author_name": "Philippe Berthelot", + "author_inst": "Centre International de Recherche en Infectiologie and University-Hospital of Saint-Etienne" + }, + { + "author_name": "Carole P\u00e9lissier", + "author_inst": "University-Hospital of Saint-Etienne" + }, + { + "author_name": "Guillaume Thierry", + "author_inst": "University-Hospital of Saint-Etienne" + }, + { + "author_name": "Elisabeth Botelho-Nevers", + "author_inst": "Centre International de Recherche en Infectiologie and University-Hospital of Saint-Etienne" + }, + { + "author_name": "St\u00e9phane Paul", + "author_inst": "Centre International de Recherche en Infectiologie and University-Hospital of Saint-Etienne" + }, + { + "author_name": "Thierry Walzer", + "author_inst": "Centre International de Recherche en Infectiologie" + }, + { + "author_name": "Fran\u00e7ois-Lo\u00efc Cosset", + "author_inst": "Centre International de Recherche en Infectiologie" + }, + { + "author_name": "Thomas Bourlet", + "author_inst": "Centre International de Recherche en Infectiologie and University-Hospital of Saint-Etienne" + }, + { + "author_name": "Bruno Pozzetto", + "author_inst": "Centre International de Recherche en Infectiologie and University-Hospital of Saint-Etienne" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.26.20182766", "rel_title": "Modeling Dynamic Network Strategies for SARS-CoV-2 Control on a Cruise Ship", @@ -1235128,49 +1233536,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.26.20182675", - "rel_title": "Epidemiological and socio-economic characteristics of the COVID-19 spring outbreak in Quebec, Canada: A population-based study", - "rel_date": "2020-09-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.26.20182675", - "rel_abs": "BackgroundBy mid-July 2020, more than 108,000 COVID-19 cases had been diagnosed in Canada with more than half in the province of Quebec. To be prepared for a potential second wave of COVID-19 in the fall, it seems of utmost importance to analyze the epidemiological and socio-economic characteristics of the spring outbreak in the population.\n\nMethodWe conducted an online survey of the participants of the CARTaGENE population-based cohort, composed of middle-aged and older adults. We collected information on socio-demographic, lifestyle, health condition, COVID-related symptoms and COVID-19 testing. We studied the association between these factors and two outcomes: the status of having been tested for SARS-CoV-2 and the status of having received a positive test when having been tested. These associations were evaluated with univariate and multivariate analyzes using a hybrid tree-based regression model.\n\nResultsAmong the 8,129 respondents from the CARTaGENE cohort, 649 were tested for COVID-19 and 41 were positive. Medical workers and individuals having a contact with a COVID-19 patient had the highest probabilities of being tested (32% and 42.4%, respectively) and of being positive (17.2% and 13.0%, respectively) among those tested. 7.6% of the participants declared that they have experienced at least one of the four COVID-related symptoms chosen by the Public Health authorities (fever, cough, dyspnea, anosmia) but were not tested. Results from the tree-based model analyzes adjusted on exposure factors show that the combination of dyspnea, dry cough and fever was highly associated with being tested whereas anosmia, fever, and headache were the most discriminant factors for having a positive test among those tested. During the spring outbreak, more than one third of the participants have experienced a decrease in access to health services. There were sex and age differences in the socio-economic and emotional impacts of the pandemic.\n\nConclusionWe have shown some discrepancies between the symptoms associated with being tested and being positive. In particular, the anosmia is a major discriminant symptom for positivity whereas ear-nose-throat symptoms seem not to be COVID-related. The results also emphasize the need of increasing the accessibility of testing for the general population.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Rodolphe Jantzen", - "author_inst": "CARTaGENE, CHU Ste-Justine Research Center, 3175 Chemin de la Cote-Sainte-Catherine, H3T1C5, Montreal, Canada" - }, - { - "author_name": "Nolwenn Noisel", - "author_inst": "CARTaGENE, CHU Ste-Justine Research Center, 3175 Chemin de la Cote-Sainte-Catherine, H3T1C5, Montreal, Canada" - }, - { - "author_name": "Sophie Camilleri-Broet", - "author_inst": "McGill University" - }, - { - "author_name": "Catherine Labbe", - "author_inst": "CARTaGENE, CHU Ste-Justine Research Center, 3175 Chemin de la Cote-Sainte-Catherine, H3T1C5, Montreal, Canada" - }, - { - "author_name": "Thibault de Malliard", - "author_inst": "CARTaGENE, CHU Ste-Justine Research Center, 3175 Chemin de la Cote-Sainte-Catherine, H3T1C5, Montreal, Canada" - }, - { - "author_name": "Yves Payette", - "author_inst": "CARTaGENE, CHU Ste-Justine Research Center, 3175 Chemin de la Cote-Sainte-Catherine, H3T1C5, Montreal, Canada" - }, - { - "author_name": "Philippe Broet", - "author_inst": "CARTaGENE, CHU Ste-Justine Research Center, 3175 Chemin de la Cote-Sainte-Catherine, H3T1C5, Montreal, Canada" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.26.20180950", "rel_title": "What is the recovery rate and risk of long-term consequences following a diagnosis of COVID-19? - A harmonised, global longitudinal observational study", @@ -1236378,6 +1234743,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.27.20183624", + "rel_title": "Inflammatory biomarkers in pregnant women with COVID-19: a retrospective cohort study", + "rel_date": "2020-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.27.20183624", + "rel_abs": "Coronavirns disease 2019 is a pandemic viral disease affecting also obstetric patients and uncertainties exist about the prognostic role of inflammatory biomarkers and hemocytometry values in patients with this infection. To clarify that, we assessed the values of several inflammatory biomarkers and hemocytometry variables in a cohort of obstetric patients hospitalized with coronavirus disease 2019 and we correlated the values at admission with the need of oxygen supplementation during the hospitalization. Overall, among 27 (61%) pregnant women and 17 (39%) post-partum women, 6 (14%) patients received oxygen supplementation and 2 (4%) required admission to intensive care unit but none died. During hospitalization neutrophils (p=0.002), neutrophils to lymphocytes ratio (p=0.037) and C reactive protein (p<0.001) decreased significantly, whereas lymphocytes (p<0.001) and platelets (p<0.001) increased. Leukocytes and lymphocytes values at admission were correlated with oxygen need, with respectively a 1% and 5% higher risk of oxygen supplementation for each 1,000 cells decrease. Overall, in obstetric patients hospitalized with coronavirus disease 2019, C reactive protein is the inflammatory biomarker that better mirrors the course of the disease whereas D-dimer or ferritin are not reliable predictors of poor outcome. Care to the need of oxygen supplementation should be reserved to patients with reduced leukocytes or lymphocytes values at admission.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "ANDREA LOMBARDI", + "author_inst": "IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation" + }, + { + "author_name": "Silvia Duiella", + "author_inst": "IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation" + }, + { + "author_name": "Letizia Li Piani", + "author_inst": "IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation" + }, + { + "author_name": "Ferruccio Ceriotti", + "author_inst": "IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation" + }, + { + "author_name": "Massimo Oggioni", + "author_inst": "IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation" + }, + { + "author_name": "Antonio Muscatello", + "author_inst": "IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation" + }, + { + "author_name": "Alessandra Bandera", + "author_inst": "IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation" + }, + { + "author_name": "Andrea Gori", + "author_inst": "IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation" + }, + { + "author_name": "Enrico Ferrazzi", + "author_inst": "IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.27.20182956", "rel_title": "Assessment of the Publication Trends of COVID-19 Systematic Reviews and Randomized Controlled Trials", @@ -1236706,41 +1235122,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.26.20181990", - "rel_title": "Empowering the crowd: Feasible strategies to minimize the spread of COVID-19 in high-density informal settlements", - "rel_date": "2020-09-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.26.20181990", - "rel_abs": "More than 1 billion people live in informal settlements worldwide, where precarious living conditions pose unique challenges to managing a COVID-19 outbreak. Taking Northwest Syria as a case-study, we simulated an outbreak in high-density informal Internally Displaced Persons (IDP) camps using a stochastic Susceptible-Exposed-Infectious-Recovered model. Expanding on previous studies, taking social conditions and population health/structure into account, we modeled several interventions feasible in these settings: moderate self-distancing, self-isolation of symptomatic cases, and protection of the most vulnerable in \"safety zones\". We considered complementary measures to these interventions that can be implemented autonomously by these communities, such as buffer zones, health-checks, and carers for isolated individuals, quantifying their impact on the micro-dynamics of disease transmission. All interventions significantly reduce outbreak probability and some of them reduce mortality when an outbreak does occur. Self-distancing reduces mortality by up to 35% if contacts are reduced by 50%. A reduction in mortality by up to 18% can be achieved by providing 1 self-isolation tent per 8 people. Protecting the most vulnerable in a safety zone reduces the outbreak probability in the vulnerable population and has synergistic effects with the other interventions. Our model predicts that a combination of all simulated interventions may reduce mortality by more than 90% and delay an outbreaks peak by almost two months. Our results highlight the potential for non-medical interventions to mitigate the effects of the pandemic. Similar measures may be applicable to controlling COVID-19 in other informal settlements, particularly IDP camps in conflict regions, around the world.\n\nKey questionsO_ST_ABSWhat is already known?C_ST_ABSO_LISince the onset of the COVID-19 pandemic, many studies have provided evidence for the effectiveness of strategies such as social distancing, testing, contact tracing, case isolation, use of personal protective equipment/facemasks and improved hygiene to reduce the spread of the disease. These studies underlie the recommendations of the World Health Organisation, but their implementation is contingent on local conditions and resources.\nC_LIO_LIMathematical modelling is the basis of many epidemiological studies and has helped inform policymakers considering COVID-19 responses around the world. Nevertheless, only a limited number of studies have applied these models to informal settlements.\nC_LI\n\nWhat are the new findings?O_LIWe developed a mathematical model to study the dynamics of COVID-19 in Syrian IDP camps, elaborating on previous efforts done in similar settings by explicitly parameterizing the camps demographics, living conditions and micro-dynamics of interpersonal contacts in our modelization.\nC_LIO_LIWe designed interventions such as self-distancing, self-isolation and the creation of safety zones to protect the most vulnerable members of the population, among others, through conversations with camp managers with on-the-ground knowledge of what interventions would be feasible and have community buy-in.\nC_LIO_LIOur results show how low-cost, feasible, community-led non-medical interventions can significantly mitigate the impact of COVID-19 in Northwest Syrian IDP camps.\nC_LI\n\nWhat do the new findings imply?O_LIOur model represents a step forward in the much-needed search for epidemiological models that are sufficiently flexible to consider specific social questions. The model can also help inform similar interventions in refugee camps in conflict-torn regions, and potentially be adapted to other informal settlements and vulnerable communities around the world.\nC_LI", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Alberto Pascual-Garc\u00eda", - "author_inst": "ETH-Zurich" - }, - { - "author_name": "Jordan Klein", - "author_inst": "Princeton University" - }, - { - "author_name": "Jennifer Villers", - "author_inst": "Princeton University" - }, - { - "author_name": "Eduard Campillo-Funollet", - "author_inst": "University of Sussex" - }, - { - "author_name": "Chamsy Sarkis", - "author_inst": "Pax Syriana Foundation" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.27.20183129", "rel_title": "The impact of the COVID-19 pandemic on wellbeing and cognitive functioning of older adults", @@ -1237936,6 +1236317,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.08.30.20182451", + "rel_title": "Positive association of Angiotensin II Receptor Blockers, not Angiotensin-Converting Enzyme Inhibitors, with an increased vulnerability to SARS-CoV-2 infection in patients hospitalized for suspected COVID-19 pneumonia", + "rel_date": "2020-09-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.30.20182451", + "rel_abs": "BackgroundAngiotensin converting enzyme (ACE) type 2 is the receptor of SARS-CoV-2 for entry into lungs cells. Because ACE-2 may be modulated by ACE inhibitors (ACEIs) and angiotensin II receptor blockers (ARBs), there is concern that patients treated with ACEIs and ARBs are at higher risk for COVID-19 infection.\n\nAimThis study sought to analyze the association of COVID-19 with previous treatment with ACEI and ARB.\n\nMethodsWe retrospectively reviewed 684 consecutive patients hospitalized for suspected COVID-19 pneumonia and tested by PCR. Patients were split into 2 groups, whether (group 1, n=484) or not (group 2, n=250) COVID-19 was confirmed. Multivariate adjusted comparisons included a propensity score analysis.\n\nResultsAge was 63.6{+/-}18.7 years, and 302(44%) were female. Hypertension was present in 42.6% and 38.4% patients of group 1 and 2, respectively (P=0.28). A treatment with ARBs (20.7% versus 12.0%, respectively, OR 1.92, 95% confidence interval [1.23-2.98], p=0.004) was more frequent in patients of group 1 than in group 2. No difference was found for treatment with ACEIs (12.7% vs 15.7%, respectively, OR 0.81 [0.52-1.26], p=0.35). Propensity score matched multivariate logistic regression confirmed a significant association between COVID-19 and a previous treatment with ARBs (adjusted OR 2.18 [1.29-3.67], p=0.004). Significant interaction between ARBs and ACEIs for the risk of COVID-19 was observed in patients aged>60, women, and hypertensive patients.\n\nConclusionThis study suggests that ACEIs and ARBs are not similarly associated with the COVID-19. In this retrospective series, patients with COVID-19 pneumonia received more frequently a previous treatment with ARBs, than patients without COVID-19.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Jean-Louis GEORGES", + "author_inst": "Cardiology department, Centre Hospitalier de Versailles, Le Chesnay, France" + }, + { + "author_name": "Floriane Floriane Gilles", + "author_inst": "Cardiology department, Centre Hospitalier de Versailles, Le Chesnay, France" + }, + { + "author_name": "Helene Cochet", + "author_inst": "Cardiology department, Centre Hospitalier de Versailles, Le Chesnay, France" + }, + { + "author_name": "Alisson Bertrand", + "author_inst": "Cardiology department, Centre Hospitalier de Versailles, Le Chesnay, France" + }, + { + "author_name": "Marie De Tournemire", + "author_inst": "Cardiology department, Centre Hospitalier de Versailles, Le Chesnay, France" + }, + { + "author_name": "Victorien Monguillon", + "author_inst": "Cardiology department, Centre Hospitalier de Versailles, Le Chesnay, France" + }, + { + "author_name": "Maeva Pasqualini", + "author_inst": "Cardiology department, Centre Hospitalier de Versailles, Le Chesnay, France" + }, + { + "author_name": "Alix Prevot", + "author_inst": "Cardiology department, Centre Hospitalier de Versailles, Le Chesnay, France" + }, + { + "author_name": "Guillaume Roger", + "author_inst": "Cardiology department, Centre Hospitalier de Versailles, Le Chesnay, France" + }, + { + "author_name": "Joseph Saba", + "author_inst": "Cardiology department, Centre Hospitalier de Versailles, Le Chesnay, France" + }, + { + "author_name": "Josephine Soltani", + "author_inst": "Cardiology department, Centre Hospitalier de Versailles, Le Chesnay, France" + }, + { + "author_name": "Mehrsa Koukabi-Fradelizi", + "author_inst": "Emergency department, Centre Hospitalier de Versailles, Le Chesnay, France" + }, + { + "author_name": "Jean Paul Beressi", + "author_inst": "Department of endocrinology and diabetology, Centre Hospitalier de Versailles, Le Chesnay, France" + }, + { + "author_name": "Cecile Laureana", + "author_inst": "Department of medical information and public health, Centre Hospitalier de Versailles, Le Chesnay, France" + }, + { + "author_name": "Jean Fran\u00e7ois Prost", + "author_inst": "Cardiology department, Centre Hospitalier de Versailles, Le Chesnay, France" + }, + { + "author_name": "Livarek Bernard", + "author_inst": "Cardiology department, Centre Hospitalier de Versailles, Le Chesnay, France" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2020.08.27.20179853", "rel_title": "Predicting and interpreting COVID-19 transmission rates from the ensemble of government policies", @@ -1238384,29 +1236844,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.27.20183616", - "rel_title": "A Comparison of Covid-19 Patient Characteristics Before versus After Partial Lockdown in Vietnam", - "rel_date": "2020-09-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.27.20183616", - "rel_abs": "BackgroundGiven the Covid-19 sudden rapid spread in the community since 25 July 2020, an updated analysis of Covid-19 cases was conducted to examine the differences of characteristics of Covid-19 patients before versus after partial lockdown end in Vietnam.\n\nMethodsData of 569 Covid-19 patients confirmed SARS-CoV-2 infection from 23 January to 31 July was collected from available official databases. We divided Covid-19 situation timeline into two main periods, before lockdown end (23 January - 22 April) and after lockdown end (23 April - 31 July).\n\nResultsWe found significant variations in the distribution of Covid-19 patients among different provinces between two periods. Covid-19 confirmed patients were older in the time after lockdown end compared to in the period before lockdown end by a median of 5 years. All discharged Covid-19 patients and no Covid-19 death were in the phase before lockdown, while post lockdown period had still remained significant patients being under treatment, especially reported first fatalities. The number of Covid-19 patients who returned from other countries (excluding China) slightly increased through two stages (p >0.05), partially showing that the continuous volume of people returning Vietnam from abroad during the Covid-19 epidemic.\n\nConclusionsOur analysis indicated demographic and epidemiological disparity of Covid-19 patients before versus after loosening the national partial lockdown in Vietnam. It is important to suggest that, proactive efforts in Covid-19 control after partial lockdown end will be effective when the measures to closely control and monitor repatriation and immigration via the borders of Vietnam are strictly enforced.\n\nWhat is already known on this topicO_LIMost of Covid-19 confirmed patients in Vietnam were acquired overseas.\nC_LIO_LIIn Vietnam, Covid-19 epidemic had the low estimated reproduction ratio (R0) and SARS-CoV-2 spread was on the downward trend before July 25.\nC_LI\n\nWhat this study addsO_LICovid-19 confirmed patients were older in the time after lockdown end compared to in the period before lockdown end by a median of 5 years.\nC_LIO_LIAll discharged Covid-19 patients and no Covid-19 death were in the phase before lockdown, while post lockdown period had still remained significant patients being under treatment, especially reported first fatalities.\nC_LIO_LIContinuous volume of people returning Vietnam from abroad through two stages during the Covid-19 epidemic.\nC_LIO_LIOur analysis might be considered as a prompt reference source for further in-depth surveys to understand the adaptive models of Covid-19 patients among different provinces.\nC_LI", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Hoang-Long Vo", - "author_inst": "Institute for Preventive Medicine and Public Health, Hanoi Medical University, Hanoi 100000, Vietnam" - }, - { - "author_name": "Kim-Duy Vu", - "author_inst": "Institute for Preventive Medicine and Public Health, Hanoi Medical University, Hanoi 100000, Vietnam" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.28.20174946", "rel_title": "Implementation and validation of a pooling strategy for a sustainable screening campaign for the presence of SARS-CoV-2.", @@ -1239646,6 +1238083,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.08.25.20181404", + "rel_title": "Perturbations in the mononuclear phagocyte landscape associated with COVID-19 disease severity", + "rel_date": "2020-08-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.25.20181404", + "rel_abs": "Monocytes and dendritic cells are crucial mediators of innate and adaptive immune responses during viral infection, but misdirected responses by these cells might contribute to immunopathology. A comprehensive map of the mononuclear phagocyte (MNP) landscape during SARS-CoV-2 infection and concomitant COVID-19 disease is lacking. We performed 25-color flow cytometry-analysis focusing on MNP lineages in SARS-CoV-2 infected patients with moderate and severe COVID-19. While redistribution of monocytes towards intermediate subset and decrease in circulating DCs occurred in response to infection, severe disease associated with appearance of Mo-MDSC-like cells and a higher frequency of pre-DC2. Furthermore, phenotypic alterations in MNPs, and their late precursors, were cell-lineage specific and in select cases associated with severe disease. Finally, unsupervised analysis revealed that the MNP profile, alone, could identify a cluster of COVID-19 non-survivors. This study provides a reference for the MNP response to clinical SARS-CoV-2 infection and unravel myeloid dysregulation associated with severe COVID-19.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Egle Kvedaraite", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Laura Hertwig", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Indranil Sinha", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Andrea Ponzetta", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Ida Hed Myrberg", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Magdalini Lourda", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Majda Dzidic", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Mira Akber", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Jonas Klingstrom", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Elin Folkesson", + "author_inst": "Karolinska University Hospital" + }, + { + "author_name": "Rao Muvva", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Puran Chen", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Susanna Brighenti", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Anna Norrby-Teglund", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Lars I. Eriksson", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Olav Rooyackers", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Soo Aleman", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Kristoffer Stralin", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Hans-Gustaf Ljunggren", + "author_inst": "Karolinska Insitutet" + }, + { + "author_name": "Florent Ginhoux", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Niklas Bjorkstrom", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Jan-Inge Henter", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Mattias Svensson", + "author_inst": "Karolinska Institutet" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.25.20181388", "rel_title": "Trying to Find the Answer for Two Questions in Patients with COVID-19:1. Are pulmonary infiltrates of COVID-19 infective or inflammatory in nature (Pneumonia of Pneumonitis)?2. Is Hydroxychloroquine plus Azithromycin or Favipiravir plus Dexamethasone more effective in the COVID-19 treatment?", @@ -1240178,285 +1238722,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.25.20154252", - "rel_title": "SARS-CoV-2-RNA viremia is associated to hypercytokinemia and critical illness in COVID-19", - "rel_date": "2020-08-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.25.20154252", - "rel_abs": "BackgroundSevere COVID-19 is characterized by clinical and biological manifestations typically observed in sepsis. SARS-CoV-2 RNA is commonly detected in nasopharyngeal swabs, however viral RNA can be found also in peripheral blood and other tissues.\n\nWhether systemic spreading of the virus or viral components plays a role in the pathogenesis of the sepsis-like disease observed in severe COVID-19 is currently unknown.\n\nMethodsWe determined the association of plasma SARS-CoV-2 RNA with the biological responses and the clinical severity of patients with COVID-19. 250 patients with confirmed COVID-19 infection were recruited (50 outpatients, 100 hospitalised ward patients, and 100 critically ill). The association between plasma SARS-CoV-2 RNA and laboratory parameters was evaluated using multivariate GLM with a gamma distribution. The association between plasma SARS-CoV-2 RNA and severity was evaluated using multivariate ordinal logistic regression analysis and Generalized Linear Model (GLM) analysis with a binomial distribution.\n\nResultsThe presence of SARS-CoV-2-RNA viremia was independently associated with a number of features consistently identified in sepsis: 1) high levels of cytokines (including CXCL10, CCL-2, IL-10, IL-1ra, IL-15, and G-CSF); 2) higher levels of ferritin and LDH; 3) low lymphocyte and monocyte counts 4) and low platelet counts. In hospitalised patients, the presence of SARS-CoV-2-RNA viremia was independently associated with critical illness: (adjusted OR= 8.30 [CI95%=4.21 - 16.34], p < 0.001). CXCL10 was the most accurate identifier of SARS-CoV-2-RNA viremia in plasma (area under the curve (AUC), [CI95%], p) = 0.85 [0.80 - 0.89), <0.001]), suggesting its potential role as a surrogate biomarker of viremia. The cytokine IL-15 most accurately differentiated clinical ward patients from ICU patients (AUC: 0.82 [0.76 - 0.88], <0.001).\n\nConclusionssystemic dissemination of genomic material of SARS-CoV-2 is associated with a sepsis-like biological response and critical illness in patients with COVID-19. RNA viremia could represent an important link between SARS-CoV-2 infection, host response dysfunction and the transition from moderate illness to severe, sepsis-like COVID-19 disease.", - "rel_num_authors": 66, - "rel_authors": [ - { - "author_name": "Jesus F Bermejo-Martin", - "author_inst": "Group for Biomedical Research in Sepsis (BioSepsis). Instituto de Investigacion Biomedica de Salamanca, (IBSAL) Salamanca / Hospital Universitario Rio Hortega, " - }, - { - "author_name": "Milagros Gonzalez-Rivera", - "author_inst": "Biochemistry Service, Hospital General Universitario Gregorio Maranon, Madrid, Spain." - }, - { - "author_name": "Raquel Almansa", - "author_inst": "Group for Biomedical Research in Sepsis (BioSepsis). Instituto de Investigacion Biomedica de Salamanca, (IBSAL) Salamanca / Hospital Universitario Rio Hortega, " - }, - { - "author_name": "Dariela Micheloud", - "author_inst": "Emergency Department, Hospital General Universitario Gregorio Maranon, Madrid, Spain" - }, - { - "author_name": "Ana P. Tedim", - "author_inst": "IBSAL" - }, - { - "author_name": "Marta Dominguez-Gil", - "author_inst": "Microbiology Service, Hospital Universitario Rio Hortega, Valladolid, Spain." - }, - { - "author_name": "Salvador Resino", - "author_inst": "Unidad de Infeccion Viral e Inmunidad, Centro Nacional de Microbiologia, Instituto de Salud Carlos III, Majadahonda, Spain." - }, - { - "author_name": "Marta Martin-Fernandez", - "author_inst": "Group for Biomedical Research in Sepsis (BioSepsis). Instituto de Investigacion Biomedica de Salamanca, (IBSAL), Salamanca / Hospital Universitario Rio Hortega," - }, - { - "author_name": "Pablo Ryan Murua", - "author_inst": "Internal Medicine, Hospital Universitario Infanta Leonor, Madrid, Spain" - }, - { - "author_name": "Felipe Perez-Garcia", - "author_inst": "Servicio de Microbiologia Clinica, Hospital Universitario Principe de Asturias, Alcala de Henares, Madrid,Spain" - }, - { - "author_name": "Luis Tamayo", - "author_inst": "Intensive Care Unit, Hospital Universitario Rio Hortega, Valladolid, Spain" - }, - { - "author_name": "Raul Lopez-Izquierdo", - "author_inst": "Emergency Department, Hospital Universitario Rio Hortega, Valladolid, Spain." - }, - { - "author_name": "Elena Bustamante", - "author_inst": "Intensive Care Unit, Hospital Clinico Universitario de Valladolid. Spain." - }, - { - "author_name": "Cesar Aldecoa", - "author_inst": "Department of Anesthesiology, Facultad de Medicina de Valladolid, Hospital Universitario Rio Hortega, Valladolid, Spain" - }, - { - "author_name": "Jose Manuel Gomez", - "author_inst": "Intensive Care Unit. Hospital General Universitario Gregorio Maranon. Madrid. Spain." - }, - { - "author_name": "Jesus Rico-Feijoo", - "author_inst": "Anesthesiology and Reanimation Service, Hospital Universitario Rio Hortega, Valladolid, Spain" - }, - { - "author_name": "Antonio Orduna", - "author_inst": "Microbiology Service, Hospital Clinico Universitario de Valladolid, Spain." - }, - { - "author_name": "Raul Mendez", - "author_inst": "Pulmonology Service, University and Polytechnic Hospital La Fe, Valencia, Spain." - }, - { - "author_name": "Isabel Fernandez Natal", - "author_inst": "Clinical Analysis Service. Hospital de Leon, Spain." - }, - { - "author_name": "Gregoria Megias", - "author_inst": "Microbiology Service, Hospital Universitario de Burgos, Spain." - }, - { - "author_name": "Montserrat Gonzalez-Estecha", - "author_inst": "Biochemistry Service, Hospital General Universitario Gregorio Maranon, Madrid, Spain." - }, - { - "author_name": "Demetrio Carriedo", - "author_inst": "Intensive Care Unit. Hospital de Leon, Spain." - }, - { - "author_name": "Cristina Doncel", - "author_inst": "Group for Biomedical Research in Sepsis (BioSepsis) Hospital Universitario Rio Hortega, Valladolid / Centro de Investigacion Biomedica en Red en Enfermedades Re" - }, - { - "author_name": "Noelia Jorge", - "author_inst": "Group for Biomedical Research in Sepsis (BioSepsis) Hospital Universitario Rio Hortega, Valladolid / Centro de Investigacion Biomedica en Red en Enfermedades Re" - }, - { - "author_name": "Alicia Ortega", - "author_inst": "IBSAL" - }, - { - "author_name": "Amanda de la Fuente", - "author_inst": "IBSAL" - }, - { - "author_name": "Felix del Campo", - "author_inst": "Pneumology Service , Rio Hortega University Hospital / Biomedical Engineering Group , University of Valladolid , Valladolid , Spain." - }, - { - "author_name": "Jose Antonio Fernandez-Ratero", - "author_inst": "Intensive Care Unit. Hospital Universitario de Burgos, Spain." - }, - { - "author_name": "Wysali Trapiello", - "author_inst": "Clinical Analysis Service. Hospital Clinico Universitario de Valladolid, Spain." - }, - { - "author_name": "Paula Gonzalez-Jimenez", - "author_inst": "Pulmonology Service, University and Polytechnic Hospital La Fe, Valencia, Spain." - }, - { - "author_name": "Guadalupe Ruiz", - "author_inst": "Clinical Analysis Service. Hospital Clinico Universitario de Valladolid, Spain." - }, - { - "author_name": "Alyson A. Kelvin", - "author_inst": "Dalhousie University, Halifax, Nova Scotia, Canada" - }, - { - "author_name": "Ali Toloue Ostadgavahi", - "author_inst": "Dalhousie University, Halifax, Nova Scotia, Canada" - }, - { - "author_name": "Ruth Oneizat", - "author_inst": "Microbiology Service, Hospital Universitarios Rio Hortega, Valladolid, Spain." - }, - { - "author_name": "Luz Maria Ruiz", - "author_inst": "Microbiology Service, Hospital Universitarios Rio Hortega, Valladolid, Spain." - }, - { - "author_name": "Iria Miguens", - "author_inst": "Emergency Department, Hospital General Universitario Gregorio Maranon, Madrid, Spain" - }, - { - "author_name": "Esther Gargallo", - "author_inst": "Emergency Department, Hospital General Universitario Gregorio Maranon, Madrid, Spain" - }, - { - "author_name": "Iona Munoz", - "author_inst": "Emergency Department, Hospital General Universitario Gregorio Maranon, Madrid, Spain" - }, - { - "author_name": "Sara Pelegrin", - "author_inst": "Anesthesiology and Reanimation Service, Hospital Universitario Rio Hortega, Valladolid, Spain" - }, - { - "author_name": "Silvia Martin", - "author_inst": "Anesthesiology and Reanimation Service, Hospital Universitario Rio Hortega, Valladolid, Spain" - }, - { - "author_name": "Pablo Garcia-Olivares", - "author_inst": "Intensive Care Unit. Hospital General Universitario Gregorio Maranon. Madrid. Spain." - }, - { - "author_name": "Jamil Antonio Cedeno", - "author_inst": "Intensive Care Unit. Hospital General Universitario Gregorio Maranon. Madrid. Spain." - }, - { - "author_name": "Tomas Ruiz-Albi", - "author_inst": "Pneumology Service , Rio Hortega University Hospital, Valladolid, Spain." - }, - { - "author_name": "Carolina Puertas", - "author_inst": "Biochemistry Service, Hospital General Universitario Gregorio Maranon, Madrid, Spain." - }, - { - "author_name": "Jose Angel Berezo", - "author_inst": "Intensive Care Unit, Hospital Universitario Rio Hortega, Valladolid, Spain" - }, - { - "author_name": "Gloria Renedo", - "author_inst": "Intensive Care Unit, Hospital Clinico Universitario de Valladolid. Spain" - }, - { - "author_name": "Ruben Herran", - "author_inst": "Intensive Care Unit, Hospital Universitario Rio Hortega, Valladolid, Spain" - }, - { - "author_name": "Juan Bustamante-Munguira", - "author_inst": "Department of Cardiovascular Surgery, Hospital Clinico Universitario de Valladolid. Spain." - }, - { - "author_name": "Pedro Enriquez", - "author_inst": "Intensive Care Unit. Hospital Universitario Rio Hortega. Valladolid, Spain." - }, - { - "author_name": "Ramon Cicuendez", - "author_inst": "Intensive Care Unit, Hospital Clinico Universitario de Valladolid. Spain." - }, - { - "author_name": "Jesus Blanco", - "author_inst": "Intensive Care Unit, Hospital Universitario Rio Hortega, Valladolid, Spain" - }, - { - "author_name": "Jessica Abadia", - "author_inst": "Infectious diseases clinic, Internal Medicine Department, Rio Hortega University Hospital, Valladolid, Spain" - }, - { - "author_name": "Julia Gomez-Barquero", - "author_inst": "Infectious diseases clinic, Internal Medicine Department, Rio Hortega University Hospital, Valladolid, Spain;" - }, - { - "author_name": "Nuria Mamolar", - "author_inst": "Intensive Care Unit, Hospital Clinico Universitario de Valladolid. Spain." - }, - { - "author_name": "Natalia Blanca-Lopez", - "author_inst": "Internal Medicine, Hospital Universitario Infanta Leonor, Madrid, Spain" - }, - { - "author_name": "Luis Jorge Valdivia", - "author_inst": "Intensive Care Unit. Hospital de Leon, Spain." - }, - { - "author_name": "Belen Fernandez Caso", - "author_inst": "Clinical Analysis Service. Hospital de Leon, Spain." - }, - { - "author_name": "Maria Angeles Mantecon", - "author_inst": "Microbiology Service, Hospital Universitario de Burgos, Spain" - }, - { - "author_name": "Anna Motos", - "author_inst": "Department of Pulmonology, Hospital Clinic de Barcelona, Universidad de Barcelona, Institut D investigacions August Pi I Sunyer (IDIBAPS), Carrer del Rossello, " - }, - { - "author_name": "Laia Fernandez-Barat", - "author_inst": "Department of Pulmonology, Hospital Clinic de Barcelona, Universidad de Barcelona, Institut D investigacions August Pi I Sunyer (IDIBAPS), Carrer del Rossello, " - }, - { - "author_name": "Ricard Ferrer", - "author_inst": "Intensive Care Department, Vall d Hebron Hospital Universitari. SODIR Research Group, Vall d Hebron Institut de Recerca, Passeig de la Vall d Hebron, 119, 08035" - }, - { - "author_name": "Ferran Barbe", - "author_inst": "Respiratory Department, Institut Ricerca Biomedica de Lleida, Hospital Universitari Arnau de Vilanova, Lleida / Centro de Investigacion Biomedica en Red en Enfe" - }, - { - "author_name": "Antoni Torres", - "author_inst": "Department of Pulmonology, Hospital Clinic of Barcelona, University of Barcelona, Institut Dinvestigacions August Pi I Sunyer (IDIBAPS), Ciber de Enfermedades R" - }, - { - "author_name": "Rosario Menendez", - "author_inst": "Pulmonology Service, University and Polytechnic Hospital La Fe, Valencia / Centro de Investigacion Biomedica en Red en Enfermedades Respiratorias, Spain" - }, - { - "author_name": "Jose Maria Eiros", - "author_inst": "Microbiology Service, Hospital Universitarios Rio Hortega, Valladolid, Spain." - }, - { - "author_name": "David J Kelvin", - "author_inst": "Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University,Halifax, Nova Scotia, Canada / International Institute of Infection and Imm" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.25.20181800", "rel_title": "Exposure and risk factors for COVID-19 and the impact of staying home on Michigan residents", @@ -1241928,6 +1240193,65 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.08.30.274464", + "rel_title": "SARS-CoV-2 infects human pluripotent stem cell-derived cardiomyocytes, impairing electrical and mechanical function", + "rel_date": "2020-08-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.30.274464", + "rel_abs": "Global health has been threatened by the COVID-19 pandemic, caused by the novel severe acute respiratory syndrome coronavirus (SARS-CoV-2)1. Although considered primarily a respiratory infection, many COVID-19 patients also suffer severe cardiovascular disease2-4. Improving patient care critically relies on understanding if cardiovascular pathology is caused directly by viral infection of cardiac cells or indirectly via systemic inflammation and/or coagulation abnormalities3,5-9. Here we examine the cardiac tropism of SARS-CoV-2 using human pluripotent stem cell-derived cardiomyocytes (hPSC-CMs) and three-dimensional engineered heart tissues (3D-EHTs). We observe that hPSC-CMs express the viral receptor ACE2 and other viral processing factors, and that SARS-CoV-2 readily infects and replicates within hPSC-CMs, resulting in rapid cell death. Moreover, infected hPSC-CMs show a progressive impairment in both electrophysiological and contractile properties. Thus, COVID-19-related cardiac symptoms likely result from a direct cardiotoxic effect of SARS-CoV-2. Long-term cardiac complications might be possible sequelae in patients who recover from this illness.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Silvia Marchiano", + "author_inst": "University of Washington" + }, + { + "author_name": "Tien-Ying Hsiang", + "author_inst": "University of Washington" + }, + { + "author_name": "Ty Higashi", + "author_inst": "University of Washington" + }, + { + "author_name": "Akshita Kanna", + "author_inst": "University of Washington" + }, + { + "author_name": "Hans Reinecke", + "author_inst": "University of Washington" + }, + { + "author_name": "Xiulan Yang", + "author_inst": "University of Washington" + }, + { + "author_name": "Lil Pabon", + "author_inst": "University of Washington" + }, + { + "author_name": "Nathan J Sniadecki", + "author_inst": "University of Washington" + }, + { + "author_name": "Alessandro Bertero", + "author_inst": "University of Washington" + }, + { + "author_name": "Michael Gale Jr.", + "author_inst": "University of Washington" + }, + { + "author_name": "Charles E Murry", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.08.30.274241", "rel_title": "Stability of SARS-CoV-2 on surfaces", @@ -1242328,49 +1240652,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.08.29.257360", - "rel_title": "The SARS-CoV-2 ORF10 is not essential in vitro or in vivo in humans.", - "rel_date": "2020-08-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.29.257360", - "rel_abs": "SARS-CoV-2 genome annotation revealed the presence of 10 open reading frames (ORFs), of which the last one (ORF10) is positioned downstream the N gene. It is a hypothetical gene, which was speculated to encode a 38 aa protein. This hypothetical protein does not share sequence similarity with any other known protein and cannot be associated with a function. While the role of this ORF10 was proposed, there is a growing evidence showing that the ORF10 is not a coding region.\n\nHere, we identified SARS-CoV-2 variants in which the ORF10 gene was prematurely terminated. The disease was not attenuated, and the transmissibility between humans was not hampered. Also in vitro, the strains replicated similarly, as the related viruses with the intact ORF10. Altogether, based on clinical observation and laboratory analyses, it appears that the ORF10 protein is not essential in humans. This observation further proves that the ORF10 should not be treated as the protein-coding gene, and the genome annotations should be amended.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Katarzyna Pancer", - "author_inst": "Department of Virology, National Institute of Public Health-National Institute of Hygiene, Chocimska 24, 00-791 Warsaw, Poland." - }, - { - "author_name": "Aleksandra Milewska", - "author_inst": "Malopolska Centre of Biotechnology; Jagiellonian University; ul. Gronostajowa 7A; 30-387 Krakow, Poland, Europe" - }, - { - "author_name": "Katarzyna Owczarek", - "author_inst": "Malopolska Centre of Biotechnology; Jagiellonian University; ul. Gronostajowa 7A; 30-387 Krakow, Poland, Europe" - }, - { - "author_name": "Agnieszka Dabrowska", - "author_inst": "Malopolska Centre of Biotechnology; Jagiellonian University; ul. Gronostajowa 7A; 30-387 Krakow, Poland, Europe" - }, - { - "author_name": "Wojciech Branicki", - "author_inst": "Malopolska Centre of Biotechnology; Jagiellonian University; ul. Gronostajowa 7A; 30-387 Krakow, Poland, Europe" - }, - { - "author_name": "Marek Sanak", - "author_inst": "Department of Internal Medicine, Faculty of Medicine, Jagiellonian University Medical College, ul. Skawinska 8, 31-066 Krakow, Poland, Europe" - }, - { - "author_name": "Krzysztof Pyrc", - "author_inst": "Malopolska Centre of Biotechnology; Jagiellonian University; ul. Gronostajowa 7A; 30-387 Krakow, Poland, Europe" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.08.29.273425", "rel_title": "Single-cell analysis of human trophoblast stem cell specification reveals activation of fetal cytotrophoblast expression programs including coronavirus associated host factors and human endogenous retroviruses", @@ -1243658,6 +1241939,20 @@ "type": "confirmatory results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.08.28.255463", + "rel_title": "Resolvin D1 and D2 reduce SARS-Cov-2-induced inflammation in cystic fibrosis macrophages", + "rel_date": "2020-08-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.28.255463", + "rel_abs": "Resolvins (Rv) are endogenous lipid autacoids that mediate resolution of inflammation and bacterial infections. Their roles in SARS-CoV-2 and COVID-19 are of considerable interest in the context of cystic fibrosis (CF) given the paucity of data regarding the effect of this virus on immune cells from individuals with CF. Here, we provide evidence for Rv biosynthesis and regulatory actions on CF macrophage inflammatory responses.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.08.26.269183", "rel_title": "Serum Amyloid P inhibits single stranded RNA-induced lung inflammation, lung damage, and cytokine storm in mice", @@ -1244102,57 +1242397,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.08.26.267781", - "rel_title": "Compositional Variability and Mutation Spectra of Monophyletic SARS-CoV-2 Clades", - "rel_date": "2020-08-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.26.267781", - "rel_abs": "COVID-19 and its causative pathogen SARS-CoV-2 have rushed the world into a staggering pandemic in a few months and a global fight against both is still going on. Here, we describe an analysis procedure where genome composition and its variables are related, through the genetic code, to molecular mechanisms based on understanding of RNA replication and its feedback loop from mutation to viral proteome sequence fraternity including effective sites on replicase-transcriptase complex. Our analysis starts with primary sequence information and identity-based phylogeny based on 22,051 SARS-CoV-2 genome sequences and evaluation of sequence variation patterns as mutation spectrum and its 12 permutations among organized clades tailored to two key mechanisms: strand-biased and function-associated mutations. Our findings include: (1) The most dominant mutation is C-to-U permutation whose abundant second-codon-position counts alter amino acid composition toward higher molecular weight and lower hydrophobicity albeit assumed most slightly deleterious. (2) The second abundance group includes: three negative-strand mutations U-to-C, A-to-G, G-to-A and a positive-strand mutation G-to-U generated through an identical mechanism as C-to-U. (3) A clade-associated and biased mutation trend is found attributable to elevated level of the negative-sense strand synthesis. (4) Within-clade permutation variation is very informative for associating non-synonymous mutations and viral proteome changes. These findings demand a bioinformatics platform where emerging mutations are mapped on to mostly subtle but fast-adjusting viral proteomes and transcriptomes to provide biological and clinical information after logical convergence for effective pharmaceutical and diagnostic applications. Such thoughts and actions are in desperate need, especially in the middle of the War against COVID-19.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Xufei Teng", - "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences" - }, - { - "author_name": "Qianpeng Li", - "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences" - }, - { - "author_name": "Zhao Li", - "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences" - }, - { - "author_name": "Yuansheng Zhang", - "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences" - }, - { - "author_name": "Guangyi Niu", - "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences" - }, - { - "author_name": "Jingfa Xiao", - "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences" - }, - { - "author_name": "Jun Yu", - "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences" - }, - { - "author_name": "Zhang Zhang", - "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences" - }, - { - "author_name": "Shuhui Song", - "author_inst": "Beijing Institute of Genomics, Chinese Academy of Sciences" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.08.27.269738", "rel_title": "SARS-CoV-2 lineage B.6 is the major contributor to transmission in Malaysia", @@ -1245116,6 +1243360,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.24.20180802", + "rel_title": "Tracheal aspirate with closed suction device: a modified technique developed during COVID-19 outbreak.", + "rel_date": "2020-08-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.24.20180802", + "rel_abs": "BackgroundBacterial superinfection as well as ventilation associated pneumonia (VAP) are both frequent events in critical care. During COVID-19 pandemic, usual diagnostic practices such as bronchoalveolar lavage and tracheal aspirate are limited due to their associated high risk of exposure for the operator. In order to set primary focus on the protection of health care personnel, a modified tracheal aspiration (M-TA) technique is developed and used for acquiring a lower respiratory tract of microbiological samples with a closed suction device.\n\nMethodsRetrospective observational study to evaluate effectiveness of M-TA is conducted.\n\nResultsA total of 33 M-TA samples were analyzed. In 66,6% of the cases, results led to a change in medical decision making. A 100% accuracy was achieved regarding COVID-19 diagnosis and a 56% bacterial growth-rate in cultives where VAP was suspected. No health care personnel have developed symptoms nor tested positive for COVID-19 during or after sample collection.\n\nConclusionM-TA technique presented could be considered as a safe and effective procedure with low percentage of complications.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Sofia Schverdfinger", + "author_inst": "Intensive Care Unit, Hospital Italiano de Buenos Aires" + }, + { + "author_name": "Indalecio Carboni Bisso", + "author_inst": "Intensive Care Unit, Hospital Italiano de Buenos Aires" + }, + { + "author_name": "Romina Famiglietti", + "author_inst": "Rehabilitation and Respiratory Care Division - Physiotherapy Service, Hospital Italiano de Buenos Aires" + }, + { + "author_name": "Marcelo Di Grazia", + "author_inst": "Rehabilitation and Respiratory Care Division - Physiotherapy Service, Hospital Italiano de Buenos Aires" + }, + { + "author_name": "Sabrina Di Stefano", + "author_inst": "Intensive Care Unit, Hospital Italiano de Buenos Aires" + }, + { + "author_name": "Marcos Las Heras", + "author_inst": "Intensive Care Unit, Hospital Italiano de Buenos Aires" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.08.25.267625", "rel_title": "MMGB/SA Consensus Estimate of the Binding Free Energy Between the Novel Coronavirus Spike Protein to the Human ACE2 Receptor", @@ -1245764,101 +1244047,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.08.25.267328", - "rel_title": "A unique view of SARS-CoV-2 through the lens of ORF8 protein", - "rel_date": "2020-08-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.25.267328", - "rel_abs": "Immune evasion is one of the unique characteristics of COVID-19 attributed to the ORF8 protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This protein is involved in modulating the host adaptive immunity through downregulating MHC (Major Histocompatibility Complex) molecules and innate immune responses by surpassing the interferon mediated antiviral response of the host. To understand the immune perspective of the host with respect to the ORF8 protein, a comprehensive study of the ORF8 protein as well as mutations possessed by it, is performed. Chemical and structural properties of ORF8 proteins from different hosts, that is human, bat and pangolin, suggests that the ORF8 of SARS-CoV-2 and Bat RaTG13-CoV are very much closer related than that of Pangolin-CoV. Eighty-seven mutations across unique variants of ORF8 (SARS-CoV-2) are grouped into four classes based on their predicted effects. Based on geolocations and timescale of collection, a possible flow of mutations was built. Furthermore, conclusive flows of amalgamation of mutations were endorsed upon sequence similarity and amino acid conservation phylogenies. Therefore, this study seeks to highlight the uniqueness of rapid evolving SARS-CoV-2 through the ORF8.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Sk. Sarif Hassan", - "author_inst": "Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram 721140, India" - }, - { - "author_name": "Shinjini Ghosh", - "author_inst": "Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata 700009, West Bengal, India" - }, - { - "author_name": "Diksha Attrish", - "author_inst": "Dr. B. R. Ambedkar Centre For Biomedical Research (ACBR), University of Delhi (North Campus), Delhi 110007, India" - }, - { - "author_name": "Pabirtra Pal Choudhury", - "author_inst": "Applied Statistics Unit, Indian Statistical Institute, Kolkata 700108, West Bengal, India" - }, - { - "author_name": "Murat Seyran", - "author_inst": "Doctoral studies in natural and technical sciences (SPL 44), University of Vienna" - }, - { - "author_name": "Damiano Pizzol", - "author_inst": "Italian Agency for Development Cooperation - Khartoum, Sudan Street 33, Al Amarat, Sudan" - }, - { - "author_name": "Parise Adadi", - "author_inst": "Department of Food Science, University of Otago, Dunedin 9054, New Zealand" - }, - { - "author_name": "Tarek Muhammed Abd El Aziz", - "author_inst": "Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229-3900, USA" - }, - { - "author_name": "Antonio Soares", - "author_inst": "Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229-3900, USA" - }, - { - "author_name": "Ramesh Kandimalla", - "author_inst": "CSIR-Indian Institute of Chemical Technology Uppal Road, Tarnaka, Hyderabad-500007, Telangana State, India" - }, - { - "author_name": "Kenneth Lundstrom", - "author_inst": "PanTherapeutics, Rte de Lavaux 49, CH1095 Lutry, Switzerland" - }, - { - "author_name": "Murtaza Tambuwala", - "author_inst": "School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK" - }, - { - "author_name": "Alaa AA Aljabali", - "author_inst": "Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University-Faculty of Pharmacy, Irbid 566, Jordan" - }, - { - "author_name": "Amos Lal", - "author_inst": "Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota, USA" - }, - { - "author_name": "Gajendra Kumar Azad", - "author_inst": "Department of Zoology, Patna University, Patna-800005, Bihar, India" - }, - { - "author_name": "Vladimir N Uversky", - "author_inst": "Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA" - }, - { - "author_name": "Samendra P Sherchan", - "author_inst": "Department of Environmental Health Sciences, Tulane University, New Orleans, LA, 70112, USA" - }, - { - "author_name": "Wagner Baetas-da-Cruz", - "author_inst": "ranslational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janei" - }, - { - "author_name": "Bruce Uhal", - "author_inst": "Department of Physiology, Michigan State University, East Lansing, MI 48824, USA" - }, - { - "author_name": "Adam Brufsky", - "author_inst": "UPMC Hillman Cancer Center, 300 Halket Street, Suite 4628, University of Pittsburgh, Pittsburgh, PA, USA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.08.25.265074", "rel_title": "Identification of a polymorphism in the N gene of SARS-CoV-2 that adversely impacts detection by a widely-used RT-PCR assay", @@ -1247394,6 +1245582,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.23.20180273", + "rel_title": "Impact of nonpharmaceutical governmental strategies for prevention and control of COVID-19 in Sao Paulo State, Brazil.", + "rel_date": "2020-08-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.23.20180273", + "rel_abs": "Interrupted time series analyses (ITSA) were performed to measure the impact of social distancing policies (instituted 22/03/2020) and subsequent mandatory masking in the community (instituted 04/05/2020) on the incidence and effective reproductive number (Rt) of COVID-19 in Sao Paulo State, Brazil. Overall, the impact of social distancing both on incidence and Rt was greater than the incremental effect of mandatory masking. Those findings may reflect either a small impact of face masking or the loosening of social distancing after mandatory use of masks.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Cristiane Ravagnani Fortaleza", + "author_inst": "Department of Infectious Diseases, Botucatu School of Medicine, S\u00e3o Paulo State University (UNESP). City of Botucatu, Brazil." + }, + { + "author_name": "Thomas Nogueira Vilches", + "author_inst": "Department of Biostatistics, Botucatu Institute of Biosciences, S\u00e3o Paulo State University (UNESP). City of Botucatu, Brazil." + }, + { + "author_name": "Gabriel Berg de Almeida", + "author_inst": "Department of Infectious Diseases, Botucatu School of Medicine, S\u00e3o Paulo State University (UNESP). City of Botucatu, Brazil." + }, + { + "author_name": "Claudia Pio Ferreira", + "author_inst": "Department of Biostatistics, Botucatu Institute of Biosciences, S\u00e3o Paulo State University (UNESP). City of Botucatu, Brazil." + }, + { + "author_name": "Rejane Maria Tommasini Grotto", + "author_inst": "Faculty of Agronomical Sciences, S\u00e3o Paulo State University (UNESP). City of Botucatu, Brazil." + }, + { + "author_name": "Raul Borges Guimar\u00e3es", + "author_inst": "Department of Geography, Faculty of Science and Technology, S\u00e3o Paulo State University (UNESP). City of Presidente Prudente, Brazil." + }, + { + "author_name": "Lenice do Ros\u00e1rio de Souza", + "author_inst": "Department of Infectious Diseases, Botucatu School of Medicine, S\u00e3o Paulo State University (UNESP). City of Botucatu, Brazil." + }, + { + "author_name": "Carlos Magno Castelo Branco Fortaleza", + "author_inst": "Department of Infectious Diseases, Botucatu School of Medicine, S\u00e3o Paulo State University (UNESP). City of Botucatu, Brazil." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.23.20180356", "rel_title": "COVID-19: Estimation of the Actual Onset of Local Epidemic Cycles, Determination of Total Number of Infective, and Duration of the Incubation Period", @@ -1247710,41 +1245945,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.08.23.20180513", - "rel_title": "3D Printed N95 Equivalent for PPE Shortages: The Kansas City Mask", - "rel_date": "2020-08-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.23.20180513", - "rel_abs": "IntroductionDuring the COVID-19 pandemic, the shortage of personal protective equipment (PPE) was well-reported and discussed, not only in the healthcare sector but across all of society as the demands for PPE skyrocketed. As hospitalizations for COVID-19-related illness continue to increase, many recent reports indicate the supply of PPE is persistently and significantly less than the demand. These PPE shortages encouraged communities of 3D printing experts and hobbyists to design and distribute homemade, 3D-printed PPE, including N95 mask substitutes. The mask presented, the Kansas City Mask (KC Mask), is one such product which was created from the maker community in partnership with local physicians and hospitals. This report discusses the design, manufacturing, and validation of the KC Mask design and its usage in the COVID-19 pandemic as well as future use as stopgap PPE.\n\nMethodsThe KC Mask was adapted from a similar design called the Montana Mask. Mask components were 3D printed and assembled then fit tested by qualitative fit testing (QLFT) at Truman Medical Center in Kansas City, MO as a proof of concept.\n\nResultsThe QLFT was successful and the KC Mask was approved for use by pandemic response administration staff at the hospital. Fortunately, the KC Mask has not required wide utilization, however, because supply chains for Kansas City area hospitals have, at the time of this publication, not yet been exhausted by the pandemic.\n\nConclusionThe results of Truman Medical Centers approval of the KC Mask are promising for this N95 stop-gap substitute. Although further analysis and study is needed for this design, persistently increasing caseloads and PPE shortages necessitate an urgent dissemination of these preliminary results. The authors do not advocate for the KC Mask as a replacement of traditional N95 masks or other PPE but do endorse the KC Mask as a stopgap measure, proven to be effective in situations of dire PPE shortage based on CDC guidelines.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Shiv Dalla", - "author_inst": "University of Kansas School of Medicine" - }, - { - "author_name": "Brandon Bacon", - "author_inst": "University of Missouri - Kansas City, Truman Medical Center" - }, - { - "author_name": "Jack M Ayres", - "author_inst": "University of Kansas School of Medicine" - }, - { - "author_name": "Stephen Holmstead", - "author_inst": "Unaffiliated" - }, - { - "author_name": "Alan J Ahlberg Elliot", - "author_inst": "Unaffiliated" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.08.22.20179994", "rel_title": "Teamwork in the manufacturing workplace may hinder social distance", @@ -1248919,6 +1247119,93 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.08.25.266775", + "rel_title": "The S1/S2 boundary of SARS-CoV-2 spike protein modulates cell entry pathways and transmission", + "rel_date": "2020-08-25", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.25.266775", + "rel_abs": "The global spread of SARS-CoV-2 is posing major public health challenges. One unique feature of SARS-CoV-2 spike protein is the insertion of multi-basic residues at the S1/S2 subunit cleavage site, the function of which remains uncertain. We found that the virus with intact spike (Sfull) preferentially enters cells via fusion at the plasma membrane, whereas a clone (Sdel) with deletion disrupting the multi-basic S1/S2 site instead utilizes a less efficient endosomal entry pathway. This idea was supported by the identification of a suite of endosomal entry factors specific to Sdel virus by a genome-wide CRISPR-Cas9 screen. A panel of host factors regulating the surface expression of ACE2 was identified for both viruses. Using a hamster model, animal-to-animal transmission with the Sdel virus was almost completely abrogated, unlike with Sfull. These findings highlight the critical role of the S1/S2 boundary of the SARS-CoV-2 spike protein in modulating virus entry and transmission.", + "rel_num_authors": 18, + "rel_authors": [ + { + "author_name": "Yunkai Zhu", + "author_inst": "Fudan University Shanghai Medical College" + }, + { + "author_name": "Fei Feng", + "author_inst": "Fudan University Shanghai Medical College" + }, + { + "author_name": "Gaowei Hu", + "author_inst": "Fudan University Shanghai Medical College" + }, + { + "author_name": "Yuyan Wang", + "author_inst": "Fudan University Shanghai Medical College" + }, + { + "author_name": "Yin Yu", + "author_inst": "Fudan University Shanghai Medical College" + }, + { + "author_name": "Yuanfei Zhu", + "author_inst": "Fudan University Shanghai Medical College" + }, + { + "author_name": "Wei Xu", + "author_inst": "Fudan University Shanghai Medical College" + }, + { + "author_name": "Xia Cai", + "author_inst": "Fudan University Shanghai Medical College" + }, + { + "author_name": "Zhiping Sun", + "author_inst": "Fudan University Shanghai Medical College" + }, + { + "author_name": "Wendong Han", + "author_inst": "Fudan University Shanghai Medical College" + }, + { + "author_name": "Rong Ye", + "author_inst": "Fudan University Shanghai Medical College" + }, + { + "author_name": "Hongjun Chen", + "author_inst": "Shanghai Veterinary Research Institute" + }, + { + "author_name": "Qiang Ding", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Qiliang Cai", + "author_inst": "Fudan University Shanghai Medical College" + }, + { + "author_name": "Di Qu", + "author_inst": "Fudan University Shanghai Medical College" + }, + { + "author_name": "Youhua Xie", + "author_inst": "Fudan University Shanghai Medical College" + }, + { + "author_name": "Zhenghong Yuan", + "author_inst": "Fudan University Shanghai Medical College" + }, + { + "author_name": "Rong Zhang", + "author_inst": "Fudan University Shanghai Medical College" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.25.265223", "rel_title": "In Vitro Inactivation of Human Coronavirus by Titania Nanoparticle Coatings and UVC Radiation: Throwing Light on SARS-CoV-2", @@ -1249435,105 +1247722,6 @@ "type": "new results", "category": "pharmacology and toxicology" }, - { - "rel_doi": "10.1101/2020.08.24.264630", - "rel_title": "SARS-CoV-2 neutralizing human antibodies protect against lower respiratory tract disease in a hamster model", - "rel_date": "2020-08-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.24.264630", - "rel_abs": "Effective clinical intervention strategies for COVID-19 are urgently needed. Although several clinical trials have evaluated the use of convalescent plasma containing virus-neutralizing antibodies, the effectiveness has not been proven. We show that hamsters treated with a high dose of human convalescent plasma or a monoclonal antibody were protected against weight loss showing reduced pneumonia and pulmonary virus replication compared to control animals. However, a ten-fold lower dose of convalescent plasma showed no protective effect. Thus, variable and relatively low levels of virus neutralizing antibodies in convalescent plasma may limit their use for effective antiviral therapy, favouring concentrated, purified (monoclonal) antibodies.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Bart L Haagmans", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Danny Noack", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Nisreen M.A. Okba", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Wentao LI", - "author_inst": "Utrecht University" - }, - { - "author_name": "Chunyan Wang", - "author_inst": "Utrecht University" - }, - { - "author_name": "Theo Bestebroer", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Rory de Vries", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Sander Herfst", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Dennis de Meulder", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Peter van Run", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Mart M Lamers", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Bart Rijnders", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Casper Rokx", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Frank J.M. van Kuppeveld", - "author_inst": "Utrecht University" - }, - { - "author_name": "Frank Grosveld", - "author_inst": "Erasmus Medical Center Rotterdam" - }, - { - "author_name": "Dubravka Drabek", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Corine GeurtsvanKessel", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Marion Koopmans", - "author_inst": "Erasmus Medical Center" - }, - { - "author_name": "Berend Jan Bosch", - "author_inst": "Utrecht University" - }, - { - "author_name": "Thijs Kuiken", - "author_inst": "Erasmus MC" - }, - { - "author_name": "Barry Rockx", - "author_inst": "Erasmus University Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.08.22.258459", "rel_title": "The inhaled steroid ciclesonide blocks SARS-CoV-2 RNA replication by targeting viral replication-transcription complex in culture cells", @@ -1250633,6 +1248821,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.21.20179473", + "rel_title": "The unintended consequences of inconsistent pandemic control policies", + "rel_date": "2020-08-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.21.20179473", + "rel_abs": "Controlling the spread of COVID-19 - even after a licensed vaccine is available - requires the effective use of non-pharmaceutical interventions, e.g., physical distancing, limits on group sizes, mask wearing, etc.. To date, such interventions have neither been uniformly nor systematically implemented in most countries. For example, even when under strict stay-at-home orders, numerous jurisdictions granted exceptions and/or were in close proximity to locations with entirely different regulations in place. Here, we investigate the impact of such geographic inconsistencies in epidemic control policies by coupling search and mobility data to a simple mathematical model of SARS-COV2 transmission. Our results show that while stay-at-home orders decrease contacts in most areas of the United States of America (US), some specific activities and venues often see an increase in attendance. Indeed, over the month of March 2020, between 10 and 30% of churches in the US saw increases in attendance; even as the total number of visits to churches declined nationally. This heterogeneity, where certain venues see substantial increases in attendance while others close, suggests that closure can cause individuals to find an open venue, even if that requires longer-distance travel. And, indeed, the average distance travelled to churches in the US rose by 13% over the same period. Strikingly, our mathematical model reveals that, across a broad range of model parameters, partial measures can often be worse than no measures at all. In the most severe cases, individuals not complying with policies by traveling to neighboring jurisdictions can create epidemics when the outbreak would otherwise have been controlled. Taken together, our data analysis and modelling results highlight the potential unintended consequences of inconsistent epidemic control policies and stress the importance of balancing the societal needs of a population with the risk of an outbreak growing into a large epidemic.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Benjamin Muir Althouse", + "author_inst": "Institute for Disease Modeling" + }, + { + "author_name": "Brendan Wallace", + "author_inst": "University of Washington" + }, + { + "author_name": "Brendan Case", + "author_inst": "University of Vermont" + }, + { + "author_name": "Samuel V Scarpino", + "author_inst": "Northeastern University" + }, + { + "author_name": "Antoine Allard", + "author_inst": "Universite Laval" + }, + { + "author_name": "Andrew Berdhal", + "author_inst": "University of Washington" + }, + { + "author_name": "Easton R White", + "author_inst": "University of Vermont" + }, + { + "author_name": "Laurent Hebert-Dufresne", + "author_inst": "University of Vermont" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.22.20179770", "rel_title": "The impact of COVID-19 on acute Trauma and Orthopaedic referrals and surgery in the UK: the \"golden peak weeks\" of the first national multi-centre observational study. The COVid-Emergency Related Trauma and orthopaedics (COVERT) Collaborative", @@ -1251017,49 +1249252,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.08.20.20178723", - "rel_title": "Automatic analysis system of COVID-19 radiographic lung images (XrayCoviDetector)", - "rel_date": "2020-08-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.20.20178723", - "rel_abs": "COVID-19 is a pandemic infectious disease caused by the SARS-CoV-2 virus, having reached more than 210 countries and territories. It produces symptoms such as fever, dry cough, dyspnea, fatigue, pneumonia, and radiological manifestations.\n\nThe most common reported RX and CT findings include lung consolidation and ground-glass opacities.\n\nIn this paper, we describe a machine learning-based system (XrayCoviDetector; until the image has a size www.covidetector.net), that detects automatically, the probability that a thorax radiological image includes COVID-19 lung patterns.\n\nXrayCoviDetector has an accuracy of 0.93, a sensitivity of 0.96, and a specificity of 0.90.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Juan Nicolas Schlotterbeck", - "author_inst": "Health Innovation Center, Clinica las Condes, Santiago, Chile" - }, - { - "author_name": "Carlos E Montoya", - "author_inst": "Health Innovation Center, Clinica las Condes, Santiago, Chile" - }, - { - "author_name": "Patricia Bitar", - "author_inst": "Department of Radiology, Clinica las Condes, Santiago, Chile" - }, - { - "author_name": "Jorge A Fuentes", - "author_inst": "Health Innovation Center, Clinica las Condes, Santiago, Chile" - }, - { - "author_name": "Victor Dinamarca", - "author_inst": "Department of Radiology, Clinica las Condes, Santiago, Chile" - }, - { - "author_name": "Gonzalo M Rojas", - "author_inst": "Health Innovation Center, Clinica las Condes, Santiago, Chile" - }, - { - "author_name": "Marcelo Galvez", - "author_inst": "Academic Direction, Clinica Las Condes, Santiago, Chile" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.08.20.20178780", "rel_title": "Forecasting PPE Consumption during a Pandemic: The Case of Covid-19", @@ -1252259,6 +1250451,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.19.20177477", + "rel_title": "Machine learning based clinical decision supportsystem for early COVID-19 mortality prediction", + "rel_date": "2020-08-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.19.20177477", + "rel_abs": "The coronavirus disease 2019 (COVID-19) is an acute respiratory disease that has been classified as a pandemic by World Health Organization (WHO). The sudden spike in the number of infections and high mortality rates have put immense pressure on the public medical systems. Hence, its crucial to identify the key factors of mortality that yield high accuracy and consistency to optimize patient treatment strategy. This study uses machine learning methods to identify a powerful combination of five features that help predict mortality with 96% accuracy: neutrophils, lymphocytes, lactate dehydrogenase (LDH), high-sensitivity C-reactive protein (hs-CRP) and age. Various machine learning algorithms have been compared to achieve a consistent high accuracy across the days that span the disease. Robust testing with three cases confirm the strong predictive performance of the proposed model. The model predicts with an accuracy of 90% as early as 16 days before the outcome. This study would help accelerate the decision making process in healthcare systems for focused medical treatments early and accurately.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Akshaya Karthikeyan", + "author_inst": "Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad" + }, + { + "author_name": "Akshit Garg", + "author_inst": "Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad" + }, + { + "author_name": "P K Vinod", + "author_inst": "Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad" + }, + { + "author_name": "U. Deva Priyakumar", + "author_inst": "Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.08.19.20178095", "rel_title": "Seroprevalence of Coronavirus Disease 2019 (COVID-19) Among Health Care Workers from Three Pandemic Hospitals of Turkey", @@ -1252699,61 +1250922,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.19.20177956", - "rel_title": "Disparities in COVID-19 Hospitalizations and Mortality among Black and Hispanic Patients: Cross-Sectional Analysis from the Greater Houston Metropolitan Area", - "rel_date": "2020-08-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.19.20177956", - "rel_abs": "BackgroundDisparate racial and ethnic burdens of the Coronavirus Disease 2019 (COVID-19) pandemic may be attributable to higher susceptibility to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) or to factors such as differences in hospitalization and care provision.\n\nMethodsIn our cross-sectional analysis of lab-confirmed COVID-19 cases from a tertiary, eight-hospital healthcare system (Houston Methodist) across greater Houston, multivariable logistic regression models were fitted to evaluate the odds of hospitalization and mortality for non-Hispanic Blacks (NHBs) vs. non-Hispanic Whites (NHWs) and Hispanics vs. non-Hispanics.\n\nFindingsBetween March 3rd and July 18th, 2020, 70,496 individuals were tested for SARS-CoV-2; 12,084 (17{middle dot}1%) tested positive, of whom 3,536 (29{middle dot}3%) were hospitalized. Among positive cases, NHBs and Hispanics were significantly younger than NHWs and Hispanics, respectively (mean age NHBs vs. NHWs: 46.0 vs. 51.7 year and Hispanic vs. non-Hispanic: 44.0 vs. 48.7 years). Despite younger age, NHBs (vs. NHWs) had a higher prevalence of diabetes (25.2%), hypertension (47.7%), and chronic kidney disease (5.0%). Both minority groups resided in lower median income and higher population density areas. In fully adjusted models, NHBs and Hispanics had higher likelihoods of hospitalization, aOR (CI): 1{middle dot}42 (1{middle dot}24-1{middle dot}63) and 1{middle dot}61 (1{middle dot}46-1{middle dot}78), respectively. No differences were observed in intensive care unit (ICU) utilization or treatment parameters. Models adjusted for demographics, vital signs, laboratory parameters, hospital complications, and ICU admission demonstrated non-significantly lower likelihoods of in-hospital mortality among NHBs and Hispanics, aOR (CI): 0{middle dot}65 (0{middle dot}40-1{middle dot}03) and 0{middle dot}89 (0{middle dot}59-1{middle dot}31), respectively.\n\nInterpretationOur data did not demonstrate racial and ethnic differences in care provision and hospital outcomes. Higher susceptibility of racial and ethnic minorities to SARS-CoV-2 and subsequent hospitalization may be driven primarily by social determinants.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Alan Pan", - "author_inst": "Houston Methodist" - }, - { - "author_name": "Osman Khan", - "author_inst": "Houston Methodist" - }, - { - "author_name": "Jennifer Meeks", - "author_inst": "Houston Methodist" - }, - { - "author_name": "Marc Boom", - "author_inst": "Houston Methodist" - }, - { - "author_name": "Faisal Masud", - "author_inst": "Houston Methodist" - }, - { - "author_name": "Julia Andrieni", - "author_inst": "Houston Methodist" - }, - { - "author_name": "Robert Phillips", - "author_inst": "Houston Methodist" - }, - { - "author_name": "Yordanos Tiruneh", - "author_inst": "University of Texas Health Science Center at Tyler" - }, - { - "author_name": "Bita Kash", - "author_inst": "Houston Methodist" - }, - { - "author_name": "Farhaan Vahidy", - "author_inst": "Houston Methodist Research Institute" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.18.20177709", "rel_title": "A delayed SEIQR epidemic model of COVID-19 in Tokyo", @@ -1253713,6 +1251881,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.20.20178541", + "rel_title": "COVID-19 Pandemic Preparedness in a United Kingdom Tertiary and Quaternary Children`s Hospital: Tales of the Unexpected", + "rel_date": "2020-08-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.20.20178541", + "rel_abs": "BackgroundThe paucity of data describing SARS-CoV-2 in the paediatric population necessitated a broad-arching approach to pandemic planning, with preparations put in place to manage a heterogeneous cohort. We describe a diverse group of SARS-CoV-2 positive paediatric patients treated at a large tertiary/quaternary childrens hospital in the United Kingdom and the adaptive coping strategies required.\n\nMethodsAll paediatric patients with positive RT-PCR on a respiratory sample and/or serology for SARS-CoV-2 up to 19th May 2020 were included.\n\nResults57 children met the inclusion criteria. 70% were of non-Caucasian ethnicity with a median age of 9.3 years (IQR 5.16-13.48). Four distinct groups were identified: paediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 (PIMS-TS) (54%), primary respiratory (18%), incidental (7%), and non-specific febrile illnesses with or without extra-pulmonary organ dysfunction (21%). These groups presented in distinct chronological blocks as the pandemic unfolded.\n\nDiscussionThe diverse range of presentations of SARS-CoV-2 infection in this population exemplified the importance of preparedness for the unknown in the midst of a novel infectious pandemic. Descriptions of paediatric patients during the initial phase of the pandemic from other parts of the globe and extrapolation from adult data did not serve as an accurate representation of paediatric COVID-19 in our centre. An adaptive, multidisciplinary approach was paramount. Expanded laboratory testing and incorporation of technology platforms to facilitate remote collaboration in response to strict infection control precautions were both indispensable. Lessons learned during the preparation process will be essential in planning for a potential second wave of SARS-CoV-2.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Nele Alders", + "author_inst": "Great Ormond Street Hospital" + }, + { + "author_name": "Justin Penner", + "author_inst": "Justin.Penner@nhs.net" + }, + { + "author_name": "Karlie Grant", + "author_inst": "Department of Infectious Diseases, Great Ormond Street Hospital for Children, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK" + }, + { + "author_name": "Charlotte Patterson", + "author_inst": "Department of Microbiology, Great Ormond Street Hospital for Children, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK" + }, + { + "author_name": "Jane Hassell", + "author_inst": "Department of Neurology, Great Ormond Street Hospital for Children, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK" + }, + { + "author_name": "Nathalie MacDermott", + "author_inst": "Department of Infectious Diseases, Great Ormond Street Hospital for Children, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK" + }, + { + "author_name": "Sian Pincott", + "author_inst": "Department of General Paediatrics, Great Ormond Street Hospital for Children, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK" + }, + { + "author_name": "Alasdair Bamford", + "author_inst": "Department of Infectious Diseases, Great Ormond Street Hospital for Children, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK" + }, + { + "author_name": "Pascale du Pre", + "author_inst": "Department of Intensive Care, Great Ormond Street Hospital for Children, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK" + }, + { + "author_name": "Mae Johnson", + "author_inst": "Department of Intensive Care, Great Ormond Street Hospital for Children, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK" + }, + { + "author_name": "Karyn Moshal", + "author_inst": "Department of Infectious Diseases, Great Ormond Street Hospital for Children, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.20.20178566", "rel_title": "Development of antibodies to pan-coronavirus spike peptides in convalescent COVID-19 patients", @@ -1254197,61 +1252424,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.08.17.20175117", - "rel_title": "Real-time spatial health surveillance: mapping the UK COVID-19 epidemic", - "rel_date": "2020-08-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.17.20175117", - "rel_abs": "The COVID-19 pandemic has highlighted the need for robust data linkage systems and methods for identifying outbreaks of disease in near real-time. Using self-reported app data and the Secure Anonymised Information Linkage (SAIL) Databank, we demonstrate the use of sophisticated spatial modelling for near-real-time prediction of COVID-19 prevalence at small-area resolution to inform strategic government policy areas. A pre-requisite to an effective control strategy is that predictions need to be accompanied by estimates of their precision, to guard against over-reaction to potentially spurious features of best guess predictions. In the UK, important emerging risk-factors such as social deprivation or ethnicity vary over small distances, hence risk needs to be modelled at fine spatial resolution to avoid aggregation bias. We demonstrate that existing geospatial statistical methods originally developed for global health applications are well-suited to this task and can be used in an anonymised databank environment, thus preserving the privacy of the individuals who contribute their data.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Richard Fry", - "author_inst": "Swansea University" - }, - { - "author_name": "Joe Hollinghurst", - "author_inst": "Swansea University" - }, - { - "author_name": "Helen R Stagg", - "author_inst": "Edinburgh University" - }, - { - "author_name": "Daniel A Thompson", - "author_inst": "Swansea University" - }, - { - "author_name": "Claudio Fronterre", - "author_inst": "Lancaster University" - }, - { - "author_name": "Chris Orton", - "author_inst": "Swansea University" - }, - { - "author_name": "Ronan A Lyons", - "author_inst": "Swansea University" - }, - { - "author_name": "David V Ford", - "author_inst": "Swansea University" - }, - { - "author_name": "Aziz Sheikh", - "author_inst": "Edinburgh University" - }, - { - "author_name": "Peter J Diggle", - "author_inst": "Lancaster University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.08.16.20169979", "rel_title": "Pediatric surgical services in Bangladesh during the COVID 19 pandemic: How they are affected and how to overcome the backlog, keeping healthcare professionals safe.", @@ -1255519,6 +1253691,45 @@ "type": "new results", "category": "neuroscience" }, + { + "rel_doi": "10.1101/2020.08.19.257022", + "rel_title": "Targeting pentose phosphate pathway for SARS-CoV-2 therapy", + "rel_date": "2020-08-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.19.257022", + "rel_abs": "It becomes more and more obvious that deregulation of host metabolism play an important role in SARS-CoV-2 pathogenesis with implication for increased risk of severe course of COVID-19. Furthermore, it is expected that COVID-19 patients recovered from severe disease may experience long-term metabolic disorders. Thereby understanding the consequences of SARS-CoV-2 infection on host metabolism can facilitate efforts for effective treatment option. We have previously shown that SARS-CoV-2-infected cells undergo a shift towards glycolysis and that 2-deoxy-D-glucose (2DG) inhibits SARS-CoV-2 replication. Here, we show that also pentose phosphate pathway (PPP) is remarkably deregulated. Since PPP supplies ribonucleotides for SARS-CoV-2 replication, this could represent an attractive target for an intervention. On that account, we employed the transketolase inhibitor benfooxythiamine and showed dose-dependent inhibition of SARS-CoV-2 in non-toxic concentrations. Importantly, the antiviral efficacy of benfooxythiamine was further increased in combination with 2DG.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Denisa Bojkova", + "author_inst": "Institute of Medical Virology" + }, + { + "author_name": "Rui Costa", + "author_inst": "Department of Infectious Diseases" + }, + { + "author_name": "Marco Bechtel", + "author_inst": "Institute of Medical Virology" + }, + { + "author_name": "Sandra Ciesek", + "author_inst": "Goethe Universtiy Frankfurt" + }, + { + "author_name": "Martin Michaelis", + "author_inst": "University of Kent" + }, + { + "author_name": "Jindrich Cinatl Jr.", + "author_inst": "Klinikum der Goethe-Universitaet" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.08.20.259721", "rel_title": "Temporal landscape of mutation accumulation in SARS-CoV-2 genomes from Bangladesh: possible implications from the ongoing outbreak in Bangladesh", @@ -1255839,33 +1254050,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.08.21.261289", - "rel_title": "Ubiquitous Forbidden Order in R-group classified protein sequence of SARS-CoV-2 and other viruses", - "rel_date": "2020-08-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.21.261289", - "rel_abs": "Each amino acid in a polypeptide chain has a distinctive R-group associated with it. We report here a novel method of species characterization based upon the order of these R-group classified amino acids in the linear sequence of the side chains associated with the codon triplets. In an otherwise pseudo-random sequence, we search for forbidden combinations of kth order. We applied this method to analyze the available protein sequences of various viruses including SARS-CoV-2. We found that these ubiquitous forbidden orders (UFO) are unique to each of the viruses we analyzed. This unique structure of the viruses may provide an insight into viruses chemical behavior and the folding patterns of the proteins. This finding may have a broad significance for the analysis of coding sequences of species in general.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Pratibha Pratibha", - "author_inst": "Indian Institute of Technology Roorkee India" - }, - { - "author_name": "Cyril Shaju", - "author_inst": "Indian Institute of Technology Roorkee India" - }, - { - "author_name": "Kamal Kamal", - "author_inst": "INDIAN INSTITUTE OF TECHNOLOGY ROORKEE INDIA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.08.18.20177261", "rel_title": "Comparisons of COVID-19 dynamics in the different countries of the World using Time-Series clustering", @@ -1257149,6 +1255333,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.18.20177345", + "rel_title": "Time-use and mental health during the COVID-19 pandemic: a panel analysis of 55,204 adults followed across 11 weeks of lockdown in the UK", + "rel_date": "2020-08-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.18.20177345", + "rel_abs": "There is currently major concern about the impact of the global COVID-19 outbreak on mental health. But it remains unclear how individual behaviors could exacerbate or protect against adverse changes in mental health. This study aimed to examine the associations between specific activities (or time-use) and mental health and wellbeing amongst people during the Covid-19 pandemic. Data were from the UCL COVID-19 Social Study; a panel study collecting data weekly during the COVID-19 pandemic. The analytical sample consisted of 55,204 adults living in the UK who were followed up for the strict 11-week lockdown period from 21st March to 31st May 2020. Data were analyzed using fixed-effects and Arellano-Bond models. We found that changes in time spent on a range of activities were associated with changes in mental health and wellbeing. After controlling for bidirectionality, behaviors involving outdoor activities including gardening and exercising predicted subsequent improvements in mental health and wellbeing, while increased time spent on following news about COVID-19 predicted declines in mental health and wellbeing. These results are relevant to the formulation of guidance for people obliged to spend extended periods in isolation during health emergencies, and may help the public to maintain wellbeing during future pandemics.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Feifei Bu", + "author_inst": "University College London" + }, + { + "author_name": "Andrew Steptoe", + "author_inst": "University College London" + }, + { + "author_name": "Hei Wan Mak", + "author_inst": "University College London" + }, + { + "author_name": "Daisy Fancourt", + "author_inst": "University College London" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.19.225854", "rel_title": "Iota carrageenan and xylitol inhibit SARS-CoV-2 in Vero cell culture", @@ -1257573,41 +1255788,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "occupational and environmental health" }, - { - "rel_doi": "10.1101/2020.08.19.257493", - "rel_title": "Exploring G and C-quadruplex structures as potential targets against the severe acute respiratory syndrome coronavirus 2", - "rel_date": "2020-08-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.19.257493", - "rel_abs": "In this paper we report the analysis of the 2019-nCoV genome and related viruses using an upgraded version of the open-source algorithm G4-iM Grinder. This version improves the functionality of the software, including an easy way to determine the potential biological features affected by the candidates found. The quadruplex definitions of the algorithm were optimized for 2019-nCoV. Using a lax quadruplex definition ruleset, which accepts amongst other parameters two residue G- and C-tracks, hundreds of potential quadruplex candidates were discovered. These sequences were evaluated by their in vitro formation probability, their position in the viral RNA, their uniqueness and their conservation rates (calculated in over three thousand different COVID-19 clinical cases and sequenced at different times and locations during the ongoing pandemic). These results were compared sequentially to other Coronaviridae members, other Group IV (+)ssRNA viruses and the entire realm. Sequences found in common with other species were further analyzed and characterized. Sequences with high scores unique to the 2019-nCoV were studied to investigate the variations amongst similar species. Quadruplex formation of the best candidates was then confirmed experimentally. Using NMR and CD spectroscopy, we found several highly stable RNA quadruplexes that may be suitable theranostic targets against the 2019-nCoV.\n\nGRAPHICAL ABSTRACT\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC=\"FIGDIR/small/257493v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (50K):\norg.highwire.dtl.DTLVardef@1ab4843org.highwire.dtl.DTLVardef@152ebeorg.highwire.dtl.DTLVardef@afd7aforg.highwire.dtl.DTLVardef@793707_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Efres Belmonte Reche", - "author_inst": "Advanced (magnetic) Theranostic Nanostructures Lab, INL-International Iberian Nanotechnology Laboratory, Av. Mestre Jose Veiga, 4715-330 Braga, Portugal." - }, - { - "author_name": "Israel Serrano-Chacon", - "author_inst": "Instituto de Quimica Fisica Rocasolano, CSIC, 28006 Madrid, Spain." - }, - { - "author_name": "Carlos Gonzalez", - "author_inst": "Instituto de Quimica Fisica Rocasolano, CSIC, 28006 Madrid, Spain." - }, - { - "author_name": "Juan Gallo", - "author_inst": "Advanced (magnetic) Theranostic Nanostructures Lab, INL-International Iberian Nanotechnology Laboratory, Av. Mestre Jose Veiga, 4715-330 Braga, Portugal." - }, - { - "author_name": "Manuel Banobre-Lopez", - "author_inst": "Advanced (magnetic) Theranostic Nanostructures Lab, INL-International Iberian Nanotechnology Laboratory, Av. Mestre Jose Veiga, 4715-330 Braga, Portugal." - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.08.19.255901", "rel_title": "Mapping the SARS-CoV-2 spike glycoprotein-derived peptidome presented by HLA class II on dendritic cells", @@ -1259171,6 +1257351,29 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.08.18.256735", + "rel_title": "Identification of potential key genes for SARS-CoV-2 infected human bronchial organoids based on bioinformatics analysis", + "rel_date": "2020-08-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.18.256735", + "rel_abs": "There is an urgent need to understand the pathogenesis of the severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2) that leads to COVID-19 and respiratory failure. Our study is to discover differentially expressed genes (DEGs) and biological signaling pathways by using a bioinformatics approach to elucidate their potential pathogenesis. The gene expression profiles of the GSE150819 datasets were originally produced using an Illumina NextSeq 500 (Homo sapiens). KEGG (Kyoto Encyclopedia of Genes and Genomes) and GO (Gene Ontology) were utilized to identify functional categories and significant pathways. KEGG and GO results suggested that the Cytokine-cytokine receptor interaction, P53 signaling pathway, and Apoptosis are the main signaling pathways in SARS-CoV-2 infected human bronchial organoids (hBOs). Furthermore, NFKBIA, C3, and CCL20 may be key genes in SARS-CoV-2 infected hBOs. Therefore, our study provides further insights into the therapy of COVID-19.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Hanming Gu", + "author_inst": "SHU-UTS SILC Business School, Shanghai University, Shanghai, China; School of Electronic, Information and Electrical E" + }, + { + "author_name": "Gongsheng Yuan", + "author_inst": "Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.08.17.20176586", "rel_title": "Risk factors associated with morbidity and mortality outcomes of COVID-19 patients on the 14th and 28th day of the disease course: a retrospective cohort study in Bangladesh", @@ -1259535,117 +1257738,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.08.17.20176552", - "rel_title": "SARS-CoV-2 antibody responses in children with MIS-C and mild and severe COVID-19", - "rel_date": "2020-08-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.17.20176552", - "rel_abs": "SARS-CoV-2 antibody responses in children remain poorly characterized. Here, we show that pediatric patients with multisystem inflammatory syndrome in children (MIS-C) possess higher SARS-CoV-2 spike IgG titers compared to those with severe coronavirus disease 2019 (COVID-19), likely reflecting a longer time since onset of infection in MIS-C patients.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Elizabeth M. Anderson", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Caroline Diorio", - "author_inst": "CHOP" - }, - { - "author_name": "Eileen C. Goodwin", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Kevin O. McNerney", - "author_inst": "CHOP" - }, - { - "author_name": "Madison E. Weirick", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Sigrid Gouma", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Marcus J. Bolton", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Claudia P. Arevalo", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Julie Chase", - "author_inst": "CHOP" - }, - { - "author_name": "Philip Hicks", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Tomaz B. Manzoni", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Amy E. Baxter", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Kurt P. Andrea", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Chakkapong Burudpakdee", - "author_inst": "CHOP" - }, - { - "author_name": "Jessica H. Lee", - "author_inst": "CHOP" - }, - { - "author_name": "Laura A. Vella", - "author_inst": "CHOP" - }, - { - "author_name": "Sarah E. Henrickson", - "author_inst": "CHOP" - }, - { - "author_name": "Rebecca M. Harris", - "author_inst": "CHOP" - }, - { - "author_name": "E. John Wherry", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Paul Bates", - "author_inst": "University of Pennsylvania" - }, - { - "author_name": "Hamid Bassiri", - "author_inst": "CHOP" - }, - { - "author_name": "Edward M Behrens", - "author_inst": "CHOP" - }, - { - "author_name": "David T. Teachey", - "author_inst": "CHOP" - }, - { - "author_name": "Scott Hensley", - "author_inst": "University of Pennsylvania" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.17.20176636", "rel_title": "Evolving Virulence? Decreasing COVID-19 Complications among Massachusetts Healthcare Workers: A Cohort Study", @@ -1261041,6 +1259133,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.08.17.253484", + "rel_title": "Generalized linear models provide a measure of virulence for specific mutations in SARS-CoV-2 strains", + "rel_date": "2020-08-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.17.253484", + "rel_abs": "This study aims to highlight SARS-COV-2 mutations which are associated with increased or decreased viral virulence. We utilize, genetic data from all strains available from GISAID and countries regional information such as deaths and cases per million as well as covid-19-related public health austerity measure response times. Initial indications of selective advantage of specific mutations can be obtained from calculating their frequencies across viral strains. By applying modelling approaches, we provide additional information that is not evident from standard statistics or mutation frequencies alone. We therefore, propose a more precise way of selecting informative mutations. We highlight two interesting mutations found in genes N (P13L) and ORF3a (Q57H). The former appears to be significantly associated with decreased deaths and cases per million according to our models, while the latter shows an opposing association with decreased deaths and increased cases per million. Moreover, protein structure prediction tools show that the mutations infer conformational changes to the protein that significantly alter its structure when compared to the reference protein.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Anastasis Oulas", + "author_inst": "The Cyprus Institute of Neurology and Genetics" + }, + { + "author_name": "Maria Zanti", + "author_inst": "The Cyprus Institute of Neurology and Genetics" + }, + { + "author_name": "Marios Tomazou", + "author_inst": "The Cyprus Institute of Neurology and Genetics" + }, + { + "author_name": "Margarita Zachariou", + "author_inst": "The Cyprus Institute of Neurology and Genetics" + }, + { + "author_name": "George Minadakis", + "author_inst": "The Cyprus Institute of Neurology and Genetics" + }, + { + "author_name": "Marilena M Bourdakou", + "author_inst": "The Cyprus Institute of Neurology and Genetics" + }, + { + "author_name": "Pavlos Pavlidis", + "author_inst": "Foundation for Research and Technology, Hellas" + }, + { + "author_name": "George M Spyrou", + "author_inst": "The Cyprus Institute of Neurology and Genetics" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.08.18.255570", "rel_title": "Spike protein mutational landscape in India: Could Mullers ratchet be a future game-changer for COVID-19?", @@ -1261393,105 +1259532,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.08.15.20175786", - "rel_title": "Universal PCR and antibody testing demonstrate little to no transmission of SARS-CoV-2 in a rural community", - "rel_date": "2020-08-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.15.20175786", - "rel_abs": "BackgroundThe absence of systematic surveillance for SARS-CoV-2 has curtailed accurate appraisal of transmission intensity. Our objective was to perform case detection of an entire rural community to quantify SARS-CoV-2 transmission using PCR and antibody testing.\n\nMethodsWe conducted a cross-sectional survey of the prevalence and cumulative incidence of SARSCoV-2 infection in the rural town of Bolinas, California (population 1,620), four weeks following shelter-in-place orders. Residents and county essential workers were tested between April 20th - 24th, 2020. Prevalence by PCR and seroprevalence combining data from two forms of antibody testing were performed in parallel (Abbott ARCHITECT IgG to nucleocapsid protein and in-house IgG ELISA to the receptor binding domain).\n\nResultsOf 1,891 participants, 1,312 were confirmed Bolinas residents (>80% community ascertainment). Zero participants were PCR positive. Assuming 80% sensitivity, it would have been unlikely to observe these results (p< 0.05) if there were > 3 active infections in the community. Based on antibody results, estimated prevalence of prior infection was 0.16% (95% CrI: 0.02%, 0.46%). Seroprevalence estimates using only one of the two tests would have been higher, with greater uncertainty. The positive predictive value (PPV) of a positive result on both tests was 99.11% (95% CrI: 95.75%, 99.94%), compared to PPV 44.19%-63.32% (95% CrI range 3.25%-98.64%) if only one test was utilized.\n\nConclusionsFour weeks following shelter-in-place, active and prior SARS-CoV-2 infection in a rural Northern California community was extremely rare. In this low prevalence setting, use of two antibody tests increased the PPV and precision of seroprevalence estimates.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Ayesha Appa", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Saki Takahashi", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Isabel Rodriguez-Barraquer", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Gabriel Chamie", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Aenor Sawyer", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "- CLIAHUB Consortium", - "author_inst": "" - }, - { - "author_name": "Elias Duarte", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Jill Hakim", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Keirstinne Turcios", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Joanna Vinden", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Owen Janson", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Aashish Manglik", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Michael J. Peluso", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Steven G Deeks", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Timothy J. Henrich", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Leonel Torres", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Mary Rodgers", - "author_inst": "Abbott Laboratories" - }, - { - "author_name": "John Hackett", - "author_inst": "Abbott Laboratories" - }, - { - "author_name": "Charles Y Chiu", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Diane Havlir", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Bryan Greenhouse", - "author_inst": "University of California, San Francisco" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.15.20175794", "rel_title": "SARS-CoV-2 Antibody Responses Correlate with Resolution of RNAemia But Are Short-Lived in Patients with Mild Illness", @@ -1262631,6 +1260671,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.14.20175299", + "rel_title": "Newborn dried blood spots for serological surveys of COVID-19", + "rel_date": "2020-08-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.14.20175299", + "rel_abs": "As COVID-19 continues to spread across the globe, the need for inexpensive, large-scale prevalence surveillance testing increases. We present a method for testing newborn dried blood spots (DBS) for anti-SARS-COV-2 IgG antibodies, and demonstrate its applicability as an easily accessible proxy for measuring maternal seroprevalence.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Feimei Liu", + "author_inst": "Department of Immunobiology, Yale School of Medicine, New Haven, CT" + }, + { + "author_name": "Mytien Nguyen", + "author_inst": "Department of Immunobiology, Yale School of Medicine, New Haven, CT" + }, + { + "author_name": "Pavithra Vijayakumar", + "author_inst": "Yale School of Medicine" + }, + { + "author_name": "Alanna Kaplan", + "author_inst": "Department of Immunobiology, Yale School of Medicine, New Haven, CT" + }, + { + "author_name": "Amit Meir", + "author_inst": "Boyer Center for Molecular Medicine, Department of Microbial Pathogenesis, Yale University" + }, + { + "author_name": "Yile Dai", + "author_inst": "Department of Immunobiology, Yale School of Medicine, New Haven, CT" + }, + { + "author_name": "Eric Wang", + "author_inst": "Department of Immunobiology, Yale School of Medicine, New Haven, CT" + }, + { + "author_name": "Hannah Walsh", + "author_inst": "Department of Internal Medicine (Infectious Diseases), Yale School of Medicine" + }, + { + "author_name": "Aaron M. Ring", + "author_inst": "Department of Immunobiology, Yale School of Medicine, New Haven, CT" + }, + { + "author_name": "Saad B. Omer", + "author_inst": "Department of Internal Medicine (Infectious Diseases), Yale School of Medicine" + }, + { + "author_name": "Shelli Farhadian", + "author_inst": "Department of Internal Medicine (Infectious Diseases), Yale School of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.14.20174490", "rel_title": "Detection, prevalence, and duration of humoral responses to SARS-CoV-2 under conditions of limited population exposure.", @@ -1263051,37 +1261150,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.14.20175190", - "rel_title": "Bidirectional associations between COVID-19 and psychiatric disorder: a study of 62,354 COVID-19 cases", - "rel_date": "2020-08-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.14.20175190", - "rel_abs": "BackgroundAdverse mental health consequences of COVID-19, including anxiety and depression, have been widely predicted but not yet accurately measured. There are a range of physical health risk factors for COVID-19, but it is not known if there are also psychiatric risk factors.\n\nMethodsWe addressed both questions using cohort studies derived from an electronic health records (EHR) network of 69 million patients including over 62,000 cases of COVID-19. Propensity score matching was used to control for confounding by risk factors for COVID-19 and for more severe illness.\n\nFindingsIn patients with no prior psychiatric history, COVID-19 was associated with an increased incidence of psychiatric diagnoses in the three months after infection compared to 6 other health events (hazard ratio [95% CI] 2.1 [1.8-2.5] compared to influenza; 1.7 [1.5-1.9] compared to other respiratory tract infections; 1.6 [1.4-1.9] compared to skin infection; 1.6 [1.3-1.9] compared to cholelithiasis; 2.2 [1.9-2.6] compared to urolithiasis, and 2.1 [1.9-2.5] compared to fracture of a large bone; all p< 0.0001). The increase was greatest for anxiety disorders but also present for depression, insomnia, and dementia. The results were robust to several sensitivity analyses. There was a [~]30% reduction in psychiatric diagnoses in the total EHR population over the same period. A psychiatric diagnosis in the previous year was associated with a 65% higher incidence of COVID-19 (relative risk 1.65, 95% CI: 1.59-1.71, p< 0.0001). This was independent of known physical health risk factors for COVID-19.\n\nInterpretationCOVID-19 infection has both psychiatric sequelae and psychiatric antecedents. Survivors have an increased rate of new onset psychiatric disorders, and prior psychiatric disorders are associated with a higher risk of COVID-19. The findings have implications for research into aetiology and highlight the need for clinical services to provide multidisciplinary follow-up, and prompt detection and treatment.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Maxime Taquet", - "author_inst": "University of Oxford" - }, - { - "author_name": "Sierra Luciano", - "author_inst": "TriNetX Inc, Cambridge, MA" - }, - { - "author_name": "John R Geddes", - "author_inst": "University of Oxford" - }, - { - "author_name": "Paul J Harrison", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.08.14.20158535", "rel_title": "Impact of contact tracing on COVID-19 mortality: An impact evaluation using surveillance data from Colombia.", @@ -1264589,6 +1262657,141 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.13.20174193", + "rel_title": "CovidNudge: diagnostic accuracy of a novel lab-free point-of-care diagnostic for SARS-CoV-2", + "rel_date": "2020-08-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.13.20174193", + "rel_abs": "3.BackgroundAccess to rapid diagnosis is key to the control and management of SARS-CoV-2. Reverse Transcriptase-Polymerase Chain Reaction (RT-PCR) testing usually requires a centralised laboratory and significant infrastructure. We describe the development and diagnostic accuracy assessment of a novel, rapid point-of-care RT-PCR test, the DnaNudge(R) platform CovidNudge test, which requires no laboratory handling or sample pre-processing.\n\nMethodsNasopharyngeal swabs are inserted directly into a cartridge which contains all reagents and components required for RT-PCR reactions, including multiple technical replicates of seven SARS-CoV-2 gene targets (rdrp1, rdrp2, e-gene, n-gene, n1, n2 and n3) and human ribonuclease P (RNaseP) as positive control. Between April and May 2020, swab samples were tested in parallel using the CovidNudge direct-to-cartridge platform and standard laboratory RT-PCR using swabs in viral transport medium. Samples were collected from three groups: self-referred healthcare workers with suspected COVID-19 (Group 1, n=280/386; 73%); patients attending the emergency department with suspected COVID-19 (Group 2, n=15/386; 4%) and hospital inpatient admissions with or without suspected COVID-19 (Group 3, n=91/386; 23%).\n\nResultsOf 386 paired samples tested across all groups, 67 tested positive on the CovidNudge platform and 71 with standard laboratory RT-PCR. The sensitivity of the test varied by group (Group 1 93% [84-98%], Group 2 100% [48-100%] and Group 3 100% [29-100%], giving an average sensitivity of 94.4% (95% confidence interval 86-98%) and an overall specificity of 100% (95%CI 99-100%; Group 1 100% [98-100%]; Group 2 100% [69-100%] and Group 3 100% [96-100%]). Point of care testing performance was comparable during a period of high (25%) and low (3%) background prevalence. Amplification of the viral nucleocapsid (n1, n2, n3) targets were most sensitive for detection of SARS-CoV2, with the assay able to detect 1x104 viral particles in a single swab.\n\nConclusionsThe CovidNudge platform offers a sensitive, specific and rapid point of care test for the presence of SARS-CoV-2 without laboratory handling or sample pre-processing. The implementation of such a device could be used to enable rapid decisions for clinical care and testing programs.\n\n4. RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSThe WHO has highlighted the development of rapid, point-of-care diagnostics for detection of SARS-CoV-2 as a key priority to tackle COVID-19. The Foundation for Innovative Diagnostics (FIND) has identified over 90 point-of-care, near patient or mobile tests for viral detection of SARS-CoV-2. However, the most widely available rapid tests to date require some sample handling which limits their use at point-of-care. In addition, pressure on supply chains is restricting access to current diagnostics and alternatives are needed urgently.\n\nAdded value of this studyWe describe the development and clinical validation of COVID nudge, a novel point-of-care RT-PCR diagnostic, evaluated during the first wave of the SARS-CoV-2 epidemic. The platform is able to achieve high analytic sensitivity and specificity from dry swabs within a self-contained cartridge. The lack of downstream sample handling makes it suitable for use in a range of clinical settings, without need for a laboratory or specialized operator. Multiplexed assays within the cartridge allow inclusion of a positive human control, which reduces the false negative testing rate due to insufficient sampling.\n\nImplication of the available evidencePoint-of-care testing can relieve pressure on centralized laboratories and increase overall testing capacity, complementing existing approaches. These findings support a role for COVID Nudge as part of strategies to improve access to rapid diagnostics to SARS-CoV-2. Since May 2020, the system has been implemented in UK hospitals and is being rolled out nationwide.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Malick M Gibani", + "author_inst": "Imperial College London" + }, + { + "author_name": "Christofer Toumazou", + "author_inst": "DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London" + }, + { + "author_name": "Mohammadreza Sohbati", + "author_inst": "DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London" + }, + { + "author_name": "Rashmita Sahoo", + "author_inst": "DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London" + }, + { + "author_name": "Maria Karvela", + "author_inst": "DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London" + }, + { + "author_name": "Tsz-Kin Hon", + "author_inst": "DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London" + }, + { + "author_name": "Sara De Mateo", + "author_inst": "DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London" + }, + { + "author_name": "Alison Burdett", + "author_inst": "DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London" + }, + { + "author_name": "K Y Felice Leung", + "author_inst": "DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London" + }, + { + "author_name": "Jake Barnett", + "author_inst": "DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London" + }, + { + "author_name": "Arman Orbeladze", + "author_inst": "DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London" + }, + { + "author_name": "Song Luan", + "author_inst": "DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London" + }, + { + "author_name": "Stavros Pournias", + "author_inst": "DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London" + }, + { + "author_name": "Jiayang Sun", + "author_inst": "DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London" + }, + { + "author_name": "Barnaby Flower", + "author_inst": "Department of Infectious Disease, Imperial College London, United Kingdom" + }, + { + "author_name": "Judith Bedzo-Nutakor", + "author_inst": "DnaNudge Ltd, Translation and Innovation Hub, Imperial College White City Campus, London" + }, + { + "author_name": "Maisarah Amran", + "author_inst": "Imperial College Healthcare NHS Trust, United Kingdom." + }, + { + "author_name": "Rachael Quinlan", + "author_inst": "Department of Infectious Disease, Imperial College London, United Kingdom" + }, + { + "author_name": "Keira Skolimowska", + "author_inst": "Imperial College Healthcare NHS Trust, United Kingdom" + }, + { + "author_name": "Robert Klaber", + "author_inst": "Imperial College Healthcare NHS Trust, United Kingdom" + }, + { + "author_name": "Gary Davies", + "author_inst": "Chelsea & Westminster NHS Foundation Trust, London" + }, + { + "author_name": "David Muir", + "author_inst": "Imperial College Healthcare NHS Trust, United Kingdom" + }, + { + "author_name": "Paul Randell", + "author_inst": "Imperial College Healthcare NHS Trust, United Kingdom" + }, + { + "author_name": "Derrick W M Crook", + "author_inst": "NIHR Oxford Biomedical Research Centre" + }, + { + "author_name": "Graham P Taylor", + "author_inst": "Department of Infectious Disease, Imperial College London, United Kingdom" + }, + { + "author_name": "Wendy Barclay", + "author_inst": "Department of Infectious Disease, Imperial College London, United Kingdom" + }, + { + "author_name": "Nabeela Mughal", + "author_inst": "Chelsea & Westminster NHS Foundation Trust, London" + }, + { + "author_name": "Luke S P Moore", + "author_inst": "Chelsea & Westminster NHS Foundation Trust, London" + }, + { + "author_name": "Katie Jeffery", + "author_inst": "Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom" + }, + { + "author_name": "Graham S Cooke", + "author_inst": "Department of Infectious Disease, Imperial College London, United Kingdom" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.13.20174466", "rel_title": "Assessment of Infection Prevention and Control Protocols, Procedures, and Implementation in Response to the COVID-19 Pandemic in Twenty-three Long-term Care Facilities in Fulton County, Georgia", @@ -1265017,25 +1263220,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.08.13.20174508", - "rel_title": "Data Mining Approach to Analyze Covid19 Dataset of Brazilian Patients", - "rel_date": "2020-08-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.13.20174508", - "rel_abs": "The pandemic originated by coronavirus(covid19), name coined by World Health Organization during the first month in 2020. Actually, almost all the countries presented covid19 positive cases and governments are choosing different health policies to stop the infection and many research groups are working on patients data to understand the virus, at the same time scientists are looking for a vacuum to enhance imnulogy system to tack covid19 virus. One of top countries with more infections is Brazil, until August 11 had a total of 3,112,393 cases. Research Foundation of Sao Paulo State(Fapesp) released a dataset, it was an innovative in collaboration with hospitals(Einstein, Sirio-Libanes), laboratory(Fleury) and Sao Paulo University to foster reseach on this trend topic. The present paper presents an exploratory analysis of the datasets, using a Data Mining Approach, and some inconsistencies are found, i.e. NaN values, null references values for analytes, outliers on results of analytes, encoding issues. The results were cleaned datasets for future studies, but at least a 20% of data were discarded because of non numerical, null values and numbers out of reference range.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Josimar E. Chire Saire", - "author_inst": "University of Sao Paulo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.13.20174615", "rel_title": "Sixty-day mortality among 520 Italian hospitalized COVID-19 patients according to the adopted ventilatory strategy in the context of an integrated multidisciplinary clinical organization: a population-based cohort study", @@ -1266127,6 +1264311,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.11.20171975", + "rel_title": "Clinical and Epidemiological Characteristics of the First Month of the Covid-19 Pandemic in Chile", + "rel_date": "2020-08-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.11.20171975", + "rel_abs": "IntroductionUnderstanding the clinical course and outcomes of patients with Covid-19 in underrepresented populations like Latin America is paramount. In this study, we report the clinical characteristics of Covid-19 in Chile, with a focus on subjects requiring hospitalization during the initial phases of the SARS-CoV-2 pandemic.\n\nMethodsThis is a single center study including all consecutive patients diagnosed with Covid-19 during the first month of the pandemic. Demographics, clinical characteristics and laboratory data were collected within 24 hours of admission. The primary outcome was a composite of ICU admission or all-cause, in-hospital mortality.\n\nResultsDuring the first month of the pandemic, 381 patients were confirmed as positive for SARS-CoV-2 by molecular testing; 88 (23.1%) of them eventually required hospitalization. Median age of the cohort was 39 years (IQR 31-49). Overall mortality was 0.7% and 18 (3.7%) out of the 88 subjects who required hospitalization either died and/or required ICU. Increased body mass index (BMI), C-reactive protein levels (CRP) and the SaTO2/FiO2 index on admission were independently associated with a higher risk of ICU care or death.\n\nDiscussionThe lower mortality observed in our prospective cohort during the first month of SARS-Cov-2 pandemic was lower than previously reported. This finding could be due to a lower threshold for admission, a healthcare system not yet overburdened and a younger population, among other factors. BMI, CRP on admission were strong predictors for ICU care or all-cause, in-hospital mortality. Our data provide important information regarding the clinical course of Covid-19 in Latin America.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Macarena R Vial", + "author_inst": "Facultad de Medicina Clinica Alemana Universidad del Desarrollo" + }, + { + "author_name": "Anne Peters", + "author_inst": "Instituto de Ciencias e Innovacion en Medicina, Facultad de Medicina Clinica Alemana, Universidad del Desarrollo" + }, + { + "author_name": "Inia Perez", + "author_inst": "Facultad de Medicina Clinica Alemana Universidad del Desarrollo" + }, + { + "author_name": "Maria Spencer", + "author_inst": "Instituto de Ciencias e Innovacion en Medicina, Facultad de Medicina Clinica Alemana, Universidad del Desarrollo" + }, + { + "author_name": "Mario Barbe", + "author_inst": "Clinica Alemana de Santiago" + }, + { + "author_name": "Mabel Aylwin", + "author_inst": "Facultad de Medicina Clinica Alemana, Universidad del Desarrollo" + }, + { + "author_name": "Lorena Porte", + "author_inst": "Facultad de Medicina Clinica Alemana, Universidad del Desarrollo" + }, + { + "author_name": "Thomas Weitzel", + "author_inst": "Instituto de Ciencias e Innovacion en Medicina, Facultad de Medicina Clinica Alemana, Universidad del Desarrollo" + }, + { + "author_name": "Pablo Vial", + "author_inst": "Instituto de Ciencias e Innovacion en Medicina, Facultad de Medicina Clinica Alemana, Universidad del Desarrollo" + }, + { + "author_name": "Rafael Araos", + "author_inst": "Instituto de Ciencias e Innovacion en Medicina, Facultad de Medicina Clinica Alemana, Universidad del Desarrollo; Millennium Initiative for Collaborative Resear" + }, + { + "author_name": "Jose M. Munita", + "author_inst": "Instituto de Ciencias e Innovacion en Medicina, Facultad de Medicina Clinica Alemana, Universidad del Desarrollo; Millennium Initiative for Collaborative Resear" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.11.20172692", "rel_title": "Clinical, Laboratory, and Imaging Features of 148 Patients with COVID-19 in Bushehr: A Report from the South of Iran", @@ -1266515,85 +1264758,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.08.11.20173062", - "rel_title": "Quantitative analysis of SARS-CoV-2 RNA from wastewater solids in communities with low COVID-19 incidence and prevalence", - "rel_date": "2020-08-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.11.20173062", - "rel_abs": "In the absence of an effective vaccine to prevent COVID-19 it is important to be able to track community infections to inform public health interventions aimed at reducing the spread and therefore reduce pressures on health-care units, improve health outcomes and reduce economic uncertainty. Wastewater surveillance has rapidly emerged as a potential tool to effectively monitor community infections for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), through measuring trends of viral RNA signal in wastewater systems. In this study SARS-CoV-2 viral RNA N1 and N2 genes are quantified in solids collected from influent post grit solids (PGS) and primary clarified sludge (PCS) in two water resource recovery facilities (WRRF) serving Canadas national capital region, i.e., the City of Ottawa, ON (pop. {approx} 1.1M) and the City of Gatineau, QC (pop. {approx} 280K). PCS samples show signal inhibition using RT-ddPCR compared to RT-qPCR, with PGS samples showing similar quantifiable concentrations of RNA using both assays. RT-qPCR shows higher frequency of detection of N1 and N2 genes in PCS (92.7, 90.6%) as compared to PGS samples (79.2, 82.3%). Sampling of PCS may therefore be an effective approach for SARS-CoV-2 viral quantification, especially during periods of declining and low COVID-19 incidence in the community. The pepper mild mottle virus (PMMV) is determined to have a less variable RNA signal in PCS over a three month period for two WRRFs, regardless of environmental conditions, compared to Bacteroides 16S rRNA or human eukaryotic 18S rRNA, making PMMV a potentially useful biomarker for normalization of SARS-CoV-2 signal. PMMV-normalized PCS RNA signal from WRRFs of two cities correlated with the regional public health epidemiological metrics, identifying PCS normalized to a fecal indicator (PMMV) as a potentially effective tool for monitoring trends during decreasing and low-incidence of infection of SARS-Cov-2 in communities.", - "rel_num_authors": 16, - "rel_authors": [ - { - "author_name": "Patrick M. D'Aoust", - "author_inst": "University of Ottawa - Civil Engineering" - }, - { - "author_name": "Elisabeth Mercier", - "author_inst": "University of Ottawa - Chemical and Biological Engineering" - }, - { - "author_name": "Danika Montpetit", - "author_inst": "University of Ottawa - Chemical and Biological Engineering" - }, - { - "author_name": "Jian-Jun Jia", - "author_inst": "Children's Hospital of Eastern Ontario - Research Institute" - }, - { - "author_name": "Ilya Alexandrov", - "author_inst": "ActivSignal LLC." - }, - { - "author_name": "Nafisa Neault", - "author_inst": "Children's Hospital of Eastern Ontario - Research Institute" - }, - { - "author_name": "Aiman Tariq Baig", - "author_inst": "Children's Hospital of Eastern Ontario - Research Institute" - }, - { - "author_name": "Janice Mayne", - "author_inst": "University of Ottawa - Biochemistry, Microbiology and Immunology" - }, - { - "author_name": "Xu Zhang", - "author_inst": "University of Ottawa - Biochemistry, Microbiology and Immunology" - }, - { - "author_name": "Tommy Alain", - "author_inst": "Children's Hospital of Eastern Ontario - Research Institute" - }, - { - "author_name": "Mark R. Servos", - "author_inst": "University of Waterloo - Department of Biology" - }, - { - "author_name": "Malcolm MacKenzie", - "author_inst": "ActivSignal LLC." - }, - { - "author_name": "Daniel Figeys", - "author_inst": "University of Ottawa - Biochemistry, Microbiology and Immunology" - }, - { - "author_name": "Alex E. MacKenzie", - "author_inst": "Children's Hospital of Eastern Ontario - Research Institute" - }, - { - "author_name": "Tyson E. Graber", - "author_inst": "Children's Hospital of Eastern Ontario - Research Institute" - }, - { - "author_name": "Robert Delatolla", - "author_inst": "University of Ottawa - Civil Engineering" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.08.12.20173302", "rel_title": "Place and underlying cause of death during the COVID19 pandemic: retrospective cohort study of 3.5 million deaths in England and Wales, 2014 to 2020", @@ -1267845,6 +1266009,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.12.20170852", + "rel_title": "knowledge, attitudes and practices (KAP) towards Covid-19 among Palestinians during the Covid-19 outbreak: a cross sectional survey", + "rel_date": "2020-08-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.12.20170852", + "rel_abs": "Coronavirus disease 2019 (COVID-19) is a highly contagious illness that spreads rapidly through human-to-human transmission. On March 5, the government of Palestine declared a state of emergency in order to curb the spread of the virus, a declaration that it extended for a fifth time on July 5th. The degree to which a population complies with corresponding safety measures is surely affected by the peoples knowledge, attitudes and practices (KAP) towards the disease. To explore this hypothesis, we gathered data from 1,731 Palestinians between April 19thand May 1st, 2020 through a KAP questionnaire. The participant pool represented a stratified sample of Palestinians living across a number of governorates in the Gaza Strip and the West Bank, with 36.5% from Gaza and (63.5%) from the West Bank. Gender was almost equally distributed within the sample with (51%) male respondents and (49%) female respondent. The questionnaire included 17 questions about participants knowledge and awareness of COVID- 19, 17 questions regarding the safety measures they had taken in the wake of the outbreak and 3 questions asking them to assess the efficacy of the governments response to the pandemic. The overall correct mean of the knowledge was 79.26+-0.35. Most participants expressed confidence that Covid-19 would be successfully controlled and that Palestine could win the battle against Covid-19, though 62% believed that stricter measurements must be applied. Based on the results of this study, we conclude that health education programs aimed at improving the publics understanding of COVID-19 are important in helping the population maintain appropriate practices, and that findings such as those discussed in this report may provide valuable feedback to lawmakers working to stop the spread of the virus.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Nouar Qutob", + "author_inst": "Arab American University" + }, + { + "author_name": "Faisal Awartani", + "author_inst": "Arab American Universiry" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.08.11.20173120", "rel_title": "Network reinforcement driven drug repurposing for COVID-19 by exploiting disease-gene-drug associations", @@ -1268293,65 +1266480,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.12.20173104", - "rel_title": "First report of tocilizumab use in a cohort of Latin American patients hospitalized for severe COVID-19 pneumonia", - "rel_date": "2020-08-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.12.20173104", - "rel_abs": "Introduction/objectivesAn interleukin-6 inhibition strategy could be effective in selected COVID-19 patients. The objective is to present our experience of tocilizumab use in patients with severe COVID-19.\n\nMethodsObservational retrospective cohort study. Hospitalized patients were evaluated by our multidisciplinary team for eventual use of tocilizumab. Patients with progressive ventilatory impairment and evidence of a hyperinflammatory state despite usual treatment received tocilizumab 8 mg/kg intravenous (maximum dose 800 mg), in addition to standard treatment. The use and time of use of mechanical ventilation (MV), the change of the Alveolar-arterial (A-a) gradient, of the ratio of arterial oxygen partial pressure to fractional inspired oxygen (PaO2/FiO2) and of inflammation laboratory parameters after 72 hours of tocilizumab use was evaluated.\n\nResults29 patients received tocilizumab. 93.1% were men, 37.9% were obese, and 34.5% had hypertension. Of the 20 patients who were not on MV when receiving tocilizumab, 11 required non-invasive MV, for an average of five days, and one of them required intubation. A-a gradient, PaO2/FiO2, and inflammation parameters improved significantly. A better lymphocyte count, which improved significantly after tocilizumab use, was significantly associated with less use of MV. Five patients presented positive culture samples after tocilizumab, three being of clinical significance. A lower lymphocyte count was associated with having a positive culture. No other significant adverse events were seen.\n\nConclusionOur study suggests the utility and shows the safety of tocilizumab use in COVID-19 patients who have respiratory failure and evidence of hyperinflammation. Lymphocyte improvement was a predictor of good response.\n\nKey-pointsO_LIThe use of tocilizumab in patients with severe COVID-19 was safe.\nC_LIO_LIMost of the patients presented a good response in terms of ventilatory and inflammatory parameters.\nC_LIO_LILymphocyte improvement after using tocilizumab was the main predictor of a good outcome.\nC_LI", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Omar Valenzuela", - "author_inst": "Clinica Alemana de Santiago" - }, - { - "author_name": "Sebastian E Ibanez", - "author_inst": "Clinica Alemana de Santiago" - }, - { - "author_name": "Maria Poli", - "author_inst": "Clinica Alemana de Santiago" - }, - { - "author_name": "Patricia Roessler", - "author_inst": "Clinica Alemana de Santiago" - }, - { - "author_name": "Mabel Aylwin", - "author_inst": "Clinica Alemana de Santiago" - }, - { - "author_name": "Gigia Roizen", - "author_inst": "Clinica Alemana de Santiago" - }, - { - "author_name": "Mirentxu Iruretagoyena", - "author_inst": "Clinica Alemana de Santiago" - }, - { - "author_name": "Vivianne Agar", - "author_inst": "Clinica Alemana de Santiago" - }, - { - "author_name": "Javiera Donoso", - "author_inst": "Clinica Alemana de Santiago" - }, - { - "author_name": "Margarita Fierro", - "author_inst": "Clinica Alemana de Santiago" - }, - { - "author_name": "Jose Montes", - "author_inst": "Clinica Alemana de Santiago" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.13.20173914", "rel_title": "Sero-prevalence findings from metropoles in Pakistan: implications for assessing COVID-19 prevalence and case-fatality within a dense, urban working population", @@ -1269259,6 +1267387,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.13.20174227", + "rel_title": "Long-Term Exposure to Outdoor Air Pollution and COVID-19 Mortality: an ecological analysis in England", + "rel_date": "2020-08-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.13.20174227", + "rel_abs": "There is an urgent need to examine what individual and environmental risk factors are associated with COVID-19 mortality. This objective of this study is to investigate the association between long term exposure to air pollution and COVID-19 mortality. We conducted a nationwide, ecological study using zero-inflated negative binomial models to estimate the association between long term (2014-2018) small area level exposure to NOx, PM2.5, PM10 and SO2 and COVID-19 mortality rates in England adjusting for socioeconomic factors and infection exposure. We found that all four pollutant concentrations were positively associated with COVID-19 mortality. The increase in mortality risk ratio per inter quarter range increase was for PM2.5:11%, 95%CIs 6%-17%), PM10 (5%; 95%CIs 1%-11%), NOx (11%, 95%CIs 6%-15%) and SO2 (7%, 95%CIs 3%-11%) were respectively in adjusted models. Public health intervention may need to protect people who are in highly polluted areas from COVID-19 infections.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Zhiqiang Feng", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Mark Cherrie", + "author_inst": "University of Edinburgh" + }, + { + "author_name": "Chris DIBBEN", + "author_inst": "University of Edinburgh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2020.08.13.20174052", "rel_title": "Knowledge, attitude and practice among Ophthalmic Health Care Personnel (HCP) towards COVID-19 pandemic in Nepal: A web-based cross-sectional study", @@ -1269671,49 +1267826,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.13.20170068", - "rel_title": "A novel approach for evaluating contact patterns and risk mitigation strategies for COVID-19 in English Primary Schools with application of Structured Expert Judgement", - "rel_date": "2020-08-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.13.20170068", - "rel_abs": "BackgroundContact patterns are the drivers of close-contacts infections, such as COVID-19. In an effort to control COVID-19 transmission in the UK, schools were closed on 23 March 2020. With social distancing in place, Primary Schools were partially re-opened on 1 June 2020, with plans to fully re-open in September 2020. The impact of social distancing and risk mitigation measures on childrens contact patterns is not known.\n\nMethodsWe conducted a structured expert elicitation of a sample of Primary Headteachers to quantify contact patterns within schools in pre-COVID-19 times and how these patterns were expected to change upon re-opening. Point estimates with uncertainty were determined by a formal performance-based algorithm. Additionally, we surveyed school Headteachers about risk mitigation strategies and their anticipated effectiveness.\n\nResultsExpert elicitation provides estimates of contact patterns that are consistent with contact surveys. We report mean number of contacts per day for four cohorts within schools along with a range at 90% confidence for the variations of contacts among individuals. Prior to lockdown, we estimate that, mean numbers per day, younger children (Reception and Year 1) made 15 contacts [range 8..35] within school, older children (Year 6) 18 contacts [range 5.. 55], teaching staff 25 contacts [range 4.. 55) and non-classroom staff 11 contacts [range 2.. 27]. Compared to pre-COVID times, after schools re-opened the mean number of contacts were reduced by about 53% for young children, about 62% for older children, about 60% for classroom staff and about 64% for other staff. Contacts between teaching and non-teaching staff reduced by 80%, which is consistent with other independent estimates. The distributions of contacts per person are asymmetric indicating a heavy tail of individuals with high contact numbers.\n\nConclusionsWe interpret the reduction in childrens contacts as a consequence of efforts to reduce mixing with interventions such as forming groups of children (bubbles) who are organized to learn together to limit contacts. Distributions of contacts for children and adults can be used to inform COVID-19 transmission modelling. Our findings suggest that while official DfE guidelines form the basis for risk mitigation in schools, individual schools have adopted their own bespoke strategies, often going beyond the guidelines.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Stephen RJ Sparks", - "author_inst": "University of Bristol" - }, - { - "author_name": "William P Aspinall", - "author_inst": "University of Bristol" - }, - { - "author_name": "Ellen Brooks-Pollock", - "author_inst": "University of Bristol" - }, - { - "author_name": "Leon Danon", - "author_inst": "University of Exeter" - }, - { - "author_name": "Roger Cooke", - "author_inst": "Delft University of Technology" - }, - { - "author_name": "Jenni Barclay", - "author_inst": "University of East Anglia" - }, - { - "author_name": "Jane Scarrow", - "author_inst": "University of Grenada" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.12.20173047", "rel_title": "Examining face-mask usage as an effective strategy to control COVID-19 spread", @@ -1270965,6 +1269077,129 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.09.20170910", + "rel_title": "Acute Lung injury evolution in Covid-19", + "rel_date": "2020-08-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.09.20170910", + "rel_abs": "BackgroundPathogenesis of Coronavirus disease 2019 (Covid-19) is poorly understood. Most histologic studies come from post-mortem analysis, with existing data indicating that histologic features of acute respiratory distress syndrome are typically present in fatal cases. However, this observation may be misleading, due to confounding factors in pre-terminal disease, including injury resulting from prolonged mechanical ventilation. Ante-mortem lung biopsy may provide major pathogenetic insights, potentially providing a basis for novel treatment approaches.\n\nAimThis comparative, multicenter, prospective, observational study was planned to identify ante-mortem histological profile and immunohistochemical features of lung tissue in patients with Covid-19 in early and late phases of the disease, including markers of inflammatory cells and major pathways involved in the cytokine storm triggering.\n\nMethodsEnrolled patients underwent lung biopsy, according to the study protocol approved by local Ethical Committee, either within 15 days of the first symptoms appearing (early phase) or after >15 days (more advanced disease). Key exclusion criteria were excessive or uncorrectable bleeding risk and cardiovascular disease with heart failure. Lung samples were obtained by conventional transbronchial biopsy, trans-bronchial lung cryobiopsy or surgical lung biopsy.\n\nResults23 patients were enrolled: 12 patients underwent lung biopsy within 15 days and 11 patients more than 15 days after the onset of symptoms. Early biopsies were characterized by spots of patchy acute lung injury (ALI) with alveolar type II cells hyperplasia and significant vascular abnormalities (disordered angiogenesis with alveolar capillary hyperplasia, luminal enlargement and thickened walls of pulmonary venules, perivascular CD4-T-cell infiltration), with no hyaline membranes. In the later stages, the alveolar architecture appeared disrupted, with areas of organizing ALI, venular congestion and capillary thromboembolic microangiopathy. Striking phenotypic features were demonstrated in hyperplastic pneumocytes and endothelial cells, including the expression of phospho-STAT3 and molecules involved in immunoinhibitory signals (PD-L1 and IDO-1). Alveolar macrophages exhibited macrophage-related markers (CD68, CD11c, CD14) together with unusual markers, such as DC-Lamp/CD208, CD206, CD123/IL3AR.\n\nConclusionA morphologically distinct \"Covid pattern\" was identified in the earlier stages of the disease, with prominent epithelial and endothelial cell abnormalities, that may be potentially reversible, differing strikingly from findings in classical diffuse alveolar damage. These observations may have major therapeutic implications, justifying studies of early interventions aimed at mitigating inflammatory organ injury.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Claudio Doglioni", + "author_inst": "Department of Pathology, University Vita-Salute, Milan and San Raffaele Scientific Institute. Milan, Italy" + }, + { + "author_name": "Claudia Ravaglia", + "author_inst": "Pulmonology Unit, Thoracic Diseases Department. G.B. Morgagni Hospital, Forli, Italy" + }, + { + "author_name": "Giulio Rossi", + "author_inst": "Department of Pathology, S. Maria delle Croci Hospital. Ravenna, Italy" + }, + { + "author_name": "Alessandra Dubini", + "author_inst": "Department of Pathology, G.B. Morgagni Hospital. Forli, Italy" + }, + { + "author_name": "Federica Pedica", + "author_inst": "Department of Pathology, San Raffaele Scientific Institute. Milan, Italy" + }, + { + "author_name": "Sara Piciucchi", + "author_inst": "Department of Radiology, G.B. Morgagni Hospital. Forli, Italy" + }, + { + "author_name": "Antonio Vizzuso", + "author_inst": "Department of Radiology, G.B. Morgagni Hospital. Forli, Italy" + }, + { + "author_name": "Lorenza Pecciarini", + "author_inst": "Department of Pathology, San Raffaele Scientific Institute. Milan, Italy" + }, + { + "author_name": "Franco Stella", + "author_inst": "Alma Mater Studiorum Universita' di Bologna. Thoracic Surgery Unit, G.B. Morgagni Hospital. Forli, Italy" + }, + { + "author_name": "Stefano Maitan", + "author_inst": "Intensive Care Unit, G.B. Morgagni Hospital. Forli, Italy" + }, + { + "author_name": "Vanni Agnoletti", + "author_inst": "Intensive Care Unit, M. Bufalini Hospital. Cesena, Italy" + }, + { + "author_name": "Emiliano Gamberini", + "author_inst": "Intensive Care Unit, M. Bufalini Hospital. Cesena, Italy" + }, + { + "author_name": "Emanuele Russo", + "author_inst": "Intensive Care Unit, M. Bufalini Hospital. Cesena, Italy" + }, + { + "author_name": "Silvia Puglisi", + "author_inst": "Pulmonology Unit, Thoracic Diseases Department. G.B. Morgagni Hospital, Forli, Italy" + }, + { + "author_name": "Antonella Arcadu", + "author_inst": "Pulmonology Unit, Thoracic Diseases Department. G.B. Morgagni Hospital, Forli, Italy" + }, + { + "author_name": "Luca Donati", + "author_inst": "Pulmonology Unit, Thoracic Diseases Department. G.B. Morgagni Hospital, Forli, Italy" + }, + { + "author_name": "Simona Di Cesare", + "author_inst": "Internal Medicine Department, G.B. Morgagni Hospital. Forli, Italy" + }, + { + "author_name": "Carmela Grosso", + "author_inst": "Infectious Diseases Unit, GB Morgagni Hospital. Forli, Italy" + }, + { + "author_name": "Giovanni Poletti", + "author_inst": "Clinical Pathology Unit, The Great Romagna Area Hub Laboratory, Pievesestina, Cesena, Italy" + }, + { + "author_name": "Vittorio Sambri", + "author_inst": "1) Unit of Microbiology, The Great Romagna Area Hub Laboratory, Pievesestina, Cesena, Italy. 2) DIMES, University of Bologna, Bologna, Italy" + }, + { + "author_name": "Elisabetta Fabbri", + "author_inst": "Department of Research and Innovation, AUSL Romagna. Rimini, Italy." + }, + { + "author_name": "Giovanni Pizzolo", + "author_inst": "Verona University, Verona, Italy" + }, + { + "author_name": "Stefano Ugel", + "author_inst": "Immunology Section, Department of Medicine, Verona University Hospital, Verona, Italy" + }, + { + "author_name": "Vincenzo Bronte", + "author_inst": "Immunology Section, Department of Medicine, Verona University Hospital, Verona, Italy" + }, + { + "author_name": "Athol U Wells", + "author_inst": "Lung Disease Unit, Royal Brompton Hospital, London, UK." + }, + { + "author_name": "Marco Chilosi", + "author_inst": "Department of Pathology, Pederzoli Hospital, Peschiera del Garda, Verona, Italy" + }, + { + "author_name": "Venerino Poletti", + "author_inst": "1) Pulmonology Unit, Thoracic Diseases Department. G.B. Morgagni Hospital, Forli, Italy. 2) Department of Respiratory Diseases and Allergy, Aarhus University Ho" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "respiratory medicine" + }, { "rel_doi": "10.1101/2020.08.09.20170985", "rel_title": "COVID-19 in rheumatic diseases: A random cross-sectional telephonic survey", @@ -1271441,29 +1269676,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.26.20162008", - "rel_title": "COVID-19 mild cases determination from correlating COVID-line calls to reported cases", - "rel_date": "2020-08-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.26.20162008", - "rel_abs": "One of the most challenging keys to understand COVID-19 evolution is to have a measure on those mild cases which are never tested because their few symptoms are soft and/or fade away soon. The problem is not only that they are difficult to identify and test, but also that it is believed that they may constitute the bulk of the cases and could be crucial in the pandemic equation. We present a novel and simple algorithm to extract the number of these mild cases by correlating a COVID-line phone calls to reported cases in given districts. The key assumption is to realize that, being a highly contagious disease, the number of calls by mild cases should be proportional to the number of reported cases. Whereas a background of calls not related to infected people should be proportional to the district population. We present the plain mathematics of the method and as a working example we apply it to Buenos Aires Province (Argentina), where it is being currently used. The implementation of this algorithm by other regions would be straightforward and would provide compelling information to the corresponding Health Care Administration.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ezequiel Alvarez", - "author_inst": "University of San Martin" - }, - { - "author_name": "Franco Marsico", - "author_inst": "Ministerio de Salud de la Provincia de Buenos Aires, Argentina" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.09.20171132", "rel_title": "Transmission heterogeneities, kinetics, and controllability of SARS-CoV-2", @@ -1272399,6 +1270611,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.10.20171413", + "rel_title": "High prevalence of SARS-CoV-2 antibodies in care homes affected by COVID-19; a prospective cohort study in England", + "rel_date": "2020-08-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.10.20171413", + "rel_abs": "BackgroundWe investigated six London care homes experiencing a COVID-19 outbreak and found very high rates of SARS-CoV-2 infection among residents and staff. Here we report follow-up serological analysis in these care homes five weeks later.\n\nMethodsResidents and staff had a convalescent blood sample for SARS-CoV-2 antibody levels and neutralising antibodies by SARS-COV-2 RT-PCR five weeks after the primary COVID-19 outbreak investigation.\n\nResultsOf the 518 residents and staff in the initial investigation, 208/241 (86.3%) surviving residents and 186/254 (73.2%) staff underwent serological testing. Almost all SARS-CoV-2 RT-PCR positive residents and staff were antibody positive five weeks later, whether symptomatic (residents 35/35, 100%; staff, 22/22, 100%) or asymptomatic (residents 32/33, 97.0%; staff 21/22, 95.1%). Symptomatic but SARS-CoV-2 RT-PCR negative residents and staff also had high seropositivity rates (residents 23/27, 85.2%; staff 18/21, 85.7%), as did asymptomatic RT-PCR negative individuals (residents 62/92, 67.3%; staff 95/143, 66.4%). Neutralising antibody was present in 118/132 (89.4%) seropositive individuals and was not associated with age or symptoms. Ten residents (10/108, 9.3%) remained RT-PCR positive, but with lower RT-PCR cycle threshold values; all 7 tested were seropositive. New infections were detected in three residents and one staff member.\n\nConclusionsRT-PCR testing for SARS-CoV-2 significantly underestimates the true extent of an outbreak in institutional settings. Elderly frail residents and younger healthier staff were equally able to mount robust and neutralizing antibody responses to SARS-CoV-2. More than two-thirds of residents and staff members had detectable antibodies against SARS-CoV-2 irrespective of their nasal swab RT-PCR positivity or symptoms status.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Shamez N Ladhani", + "author_inst": "Public Health England" + }, + { + "author_name": "Anna J Jeffery-Smith", + "author_inst": "Public Health England" + }, + { + "author_name": "Monika Patel", + "author_inst": "Public Health England" + }, + { + "author_name": "Roshni Janarthanan", + "author_inst": "Public Health England" + }, + { + "author_name": "Jonathan Fok", + "author_inst": "Public Health England" + }, + { + "author_name": "Emma Crawley-Boevey", + "author_inst": "Public Health England" + }, + { + "author_name": "Amoolya Vusirikala", + "author_inst": "Public Health England" + }, + { + "author_name": "Elena Fernandez", + "author_inst": "Public Health England" + }, + { + "author_name": "Marina Sanchez-Perez", + "author_inst": "Public Health England" + }, + { + "author_name": "Suzanne Tang", + "author_inst": "Public Health England" + }, + { + "author_name": "Kate Dun-Campbell", + "author_inst": "Public Health England" + }, + { + "author_name": "Edward Wynne-Evans", + "author_inst": "Public Health England" + }, + { + "author_name": "Anita Bell", + "author_inst": "Public Health England" + }, + { + "author_name": "Bharat Patel", + "author_inst": "Public Health England" + }, + { + "author_name": "Zahin Amin-Chowdhury", + "author_inst": "Public Health England" + }, + { + "author_name": "Felicity Aiano", + "author_inst": "Public Health England" + }, + { + "author_name": "Karthik Paranthaman", + "author_inst": "Public Health England" + }, + { + "author_name": "Thomas Ma", + "author_inst": "Public Health England" + }, + { + "author_name": "Maria Saavedra-Campos", + "author_inst": "Public Health England" + }, + { + "author_name": "Joanna Ellis", + "author_inst": "Public Health England" + }, + { + "author_name": "Meera Chand", + "author_inst": "Public Health England" + }, + { + "author_name": "Kevin Brown", + "author_inst": "Public Health England" + }, + { + "author_name": "Mary E Ramsay", + "author_inst": "Public Health England" + }, + { + "author_name": "Susan Hopkins", + "author_inst": "Public Health England" + }, + { + "author_name": "Nandini Shetty", + "author_inst": "Public Health England" + }, + { + "author_name": "J Yimmy Chow", + "author_inst": "Public Health England" + }, + { + "author_name": "Robin Gopal", + "author_inst": "Public Health England" + }, + { + "author_name": "Maria Zambon", + "author_inst": "Public Health England" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.10.244350", "rel_title": "Human Embryonic Stem Cell-derived Lung Organoids: a Model for SARS-CoV-2 Infection and Drug Test", @@ -1272911,33 +1271250,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2020.08.10.20171439", - "rel_title": "Extended SEIQR type model for COVID-19 epidemic and data analysis", - "rel_date": "2020-08-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.10.20171439", - "rel_abs": "An extended SEIQR type model is considered in order to model the COVID-19 epidemic. It contains the classes of susceptible individuals, exposed, infected symptomatic and asymptomatic, quarantined, hospitalized and recovered. The basic reproduction number and the final size of epidemic are determined. The model is used to fit available data for some European countries. A more detailed model with two different subclasses of susceptible individuals is introduced in order to study the influence of social interaction on the disease progression. The coefficient of social interaction K characterizes the level of social contacts in comparison with complete lockdown (K = 0) and the absence of lockdown (K = 1). The fitting of data shows that the actual level of this coefficient in some European countries is about 0.1, characterizing a slow disease progression. A slight increase of this value in the autumn can lead to a strong epidemic burst.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Swarnali Sharma", - "author_inst": "Vijaygarh Jyotish Ray College, Kolkata, INDIA" - }, - { - "author_name": "Vitaly Volpert", - "author_inst": "Institut Camille Jordan, UMR 5208 CNRS, University Lyon 1, 69622 Villeurbanne, France" - }, - { - "author_name": "Malay Banerjee", - "author_inst": "IIT Kanpur" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.10.20171454", "rel_title": "Stochastic extinction of epidemics: how long does would it take for Sars-Cov-2 to die out?", @@ -1274181,6 +1272493,145 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.06.20169573", + "rel_title": "Beneficial effects of colchicine for moderate to severe COVID-19: an interim analysis of a randomized, double-blinded, placebo controlled clinical trial", + "rel_date": "2020-08-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.06.20169573", + "rel_abs": "IntroductionNeutrophilia and high levels of proinflammatory cytokines and other mediators of inflammation are common finds in patients with severe acute respiratory syndrome due to COVID-19. By its action on leukocytes, we propose colchicine as an intervention worthy of being tested.\n\nObjectiveTo evaluate whether the addition of colchicine to standard treatment for COVID-19 results in better outcomes.\n\nMethodsWe present the interim analysis of a single-center randomized, double-blinded, placebo controlled clinical trial of colchicine for the treatment of moderate to severe COVID-19, with 38 patients allocated 1:1 from April 11 to July 06, 2020. Colchicine regimen was 0.5 mg thrice daily for 5 days, then 0.5 mg twice daily for 5 days. The first dose was 1.0 mg whether body weight was [≥] 80 kg.\n\nEndpointsThe primary endpoints were the need for supplemental oxygen; time of hospitalization; need for admission and length of stay in intensive care units; and death rate and causes of mortality. As secondary endpoints, we assessed: serum C-reactive protein, serum Lactate dehydrogenase and relation neutrophil to lymphocyte of peripheral blood samples from day zero to day 7; the number, type, and severity of adverse events; frequency of interruption of the study protocol due to adverse events; and frequency of QT interval above 450 ms.\n\nResultsThirty-five patients (18 for Placebo and 17 for Colchicine) completed the study. Both groups were comparable in terms of demographic, clinical and laboratory data at baseline. Median (and interquartile range) time of need for supplemental oxygen was 3.0 (1.5-6.5) days for the Colchicine group and 7.0 (3.0-8.5) days for Placebo group (p = 0.02). Median (IQR) time of hospitalization was 6.0 (4.0-8.5) days for the Colchicine group and 8.5 (5.5-11.0) days for Placebo group (p = 0.03). At day 2, 53% vs 83% of patients maintained the need for supplemental oxygen, while at day 7 the values were 6% vs 39%, in the Colchicine and Placebo groups, respectively (log rank; p = 0.01). Hospitalization was maintained for 53% vs 78% of patients at day 5 and 6% vs 17% at day 10, for the Colchicine and Placebo groups, respectively (log rank; p = 0.01). One patient per group needed admission to ICU. No recruited patient died. At day 4, patients of Colchicine group presented significant reduction of serum C-reactive protein compared to baseline (p < 0.001). The majority of adverse events were mild and did not lead to patient withdrawal. Diarrhea was more frequent in the Colchicine group (p = 0.17). Cardiac adverse events were absent.\n\nDiscussionThe use of colchicine reduced the length of supplemental oxygen therapy and the length of hospitalization. Clinical improvement was in parallel with a reduction on serum levels of C-reactive protein. The drug was safe and well tolerated. Colchicine may be considered a beneficial and not expensive option for COVID-19 treatment. Clinical trials with larger numbers of patients should be conducted to further evaluate the efficacy and safety of colchicine as an adjunctive therapy for hospitalized patients with moderate to severe COVID-19.", + "rel_num_authors": 31, + "rel_authors": [ + { + "author_name": "Maria Isabel F Lopes", + "author_inst": "Faculdade de Medicina de Ribeirao Preto - Universidade de Sao Paulo" + }, + { + "author_name": "Leticia P Bonjorno", + "author_inst": "Faculdade de Medicina de Ribeirao Preto - Universidade de Sao Paulo" + }, + { + "author_name": "Marcela C Giannini", + "author_inst": "Faculdade de Medicina de Ribeirao Preto - Universidade de Sao Paulo" + }, + { + "author_name": "Natalia B Amaral", + "author_inst": "Faculdade de Medicina de Ribeirao Preto - Universidade de Sao Paulo" + }, + { + "author_name": "Maira N Benatti", + "author_inst": "Faculdade de Medicina de Ribeirao Preto - Universidade de Sao Paulo" + }, + { + "author_name": "Uebe C Rezek", + "author_inst": "Faculdade de Medicina de Ribeirao Preto - Universidade de Sao Paulo" + }, + { + "author_name": "Laerte L Emrich-Filho", + "author_inst": "Faculdade de Medicina de Ribeirao Preto - Universidade de Sao Paulo" + }, + { + "author_name": "Betania AA Sousa", + "author_inst": "Faculdade de Medicina de Ribeirao Preto - Universidade de Sao Paulo" + }, + { + "author_name": "Sergio CL Almeida", + "author_inst": "Faculdade de Medicina de Ribeirao Preto - Universidade de Sao Paulo" + }, + { + "author_name": "Rodrigo Luppino-Assad", + "author_inst": "Faculdade de Medicina de Ribeirao Preto - Universidade de Sao Paulo" + }, + { + "author_name": "Flavio P Veras", + "author_inst": "Faculdade de Medicina de Ribeirao Preto - Universidade de Sao Paulo" + }, + { + "author_name": "Ayda Schneider", + "author_inst": "Faculdade de Medicina de Ribeirao Preto - Universidade de Sao Paulo" + }, + { + "author_name": "Tamara S Rodrigues", + "author_inst": "Faculdade de Medicina de Ribeirao Preto - Universidade de Sao Paulo" + }, + { + "author_name": "Luiz OS Leiria", + "author_inst": "Faculdade de Medicina de Ribeirao Preto - Universidade de Sao Paulo" + }, + { + "author_name": "Larissa D Cunha", + "author_inst": "Faculdade de Medicina de Ribeirao Preto - Universidade de Sao Paulo" + }, + { + "author_name": "Jose C Alves-Filho", + "author_inst": "Faculdade de Medicina de Ribeirao Preto - Universidade de Sao Paulo" + }, + { + "author_name": "Thiago M Cunha", + "author_inst": "Faculdade de Medicina de Ribeirao Preto - Universidade de Sao Paulo" + }, + { + "author_name": "Eurico Arruda Neto", + "author_inst": "Faculdade de Medicina de Ribeirao Preto - Universidade de Sao Paulo" + }, + { + "author_name": "Carlos H Miranda", + "author_inst": "Sao Paulo University" + }, + { + "author_name": "Antonio Pazin-Filho", + "author_inst": "Faculdade de Medicina de Ribeirao Preto - Universidade de Sao Paulo" + }, + { + "author_name": "Maria A Martins", + "author_inst": "Faculdade de Medicina de Ribeirao Preto - Universidade de Sao Paulo" + }, + { + "author_name": "Marcos C Borges", + "author_inst": "Faculdade de Medicina de Ribeirao Preto - Universidade de Sao Paulo" + }, + { + "author_name": "Benedito AL Fonseca", + "author_inst": "Faculdade de Medicina de Ribeirao Preto - Universidade de Sao Paulo" + }, + { + "author_name": "Valdes R Bollela", + "author_inst": "Faculdade de Medicina de Ribeirao Preto - Universidade de Sao Paulo" + }, + { + "author_name": "Cristina M Del-Ben", + "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" + }, + { + "author_name": "Fernando Q Cunha Sr.", + "author_inst": "Ribeirao Preto Medical School, University of Sao Paulo" + }, + { + "author_name": "Dario S Zamboni", + "author_inst": "Universidade de Sao Paulo, School of Medicine Ribeirao Preto" + }, + { + "author_name": "Rodrigo C Santana", + "author_inst": "Faculdade de Medicina de Ribeirao Preto - Universidade de Sao Paulo" + }, + { + "author_name": "Fernando C Vilar", + "author_inst": "Faculdade de Medicina de Ribeirao Preto - Universidade de Sao Paulo" + }, + { + "author_name": "Paulo Louzada-Junior", + "author_inst": "Faculdade de Medicina de Ribeirao Preto - Universidade de Sao Paulo" + }, + { + "author_name": "Rene D R Oliveira", + "author_inst": "Hospital das Clinicas de Ribeirao Preto" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.07.20170035", "rel_title": "Quantifying threat from COVID-19 infection hazard in Primary Schools in England", @@ -1274637,37 +1273088,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.07.20170407", - "rel_title": "Model-based projections for COVID-19 outbreak size and student-days lost to closure in Ontario childcare centres and primary schools", - "rel_date": "2020-08-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.07.20170407", - "rel_abs": "There is a pressing need for evidence-based scrutiny of plans to re-open childcare during the COVID-19 pandemic. Here we developed an agent-based model of SARS-CoV-2 transmission within a childcare center and households. Scenarios varied the student-to-educator ratio (15:2, 8:2, 7:3), and family clustering (siblings together vs. random assignment). We also evaluated a primary school setting (30:1, 15:1 and 8:1) including cohorts that alternate weekly. In the childcare scenarios, grouping siblings significantly reduced outbreak size and student-days lost. We identify an intensification cascade specific to classroom outbreaks of respiratory viruses with presymptomatic infection. In both childcare and primary school settings, each doubling of class size from 8 to 15 to 30 more than doubled the outbreak size and student-days lost, by factors of 2-5, respectively 2.5-4.5, depending on the scenario. Proposals for childcare and primary school reopening could be enhanced for safety by switching to lower ratios and sibling groupings.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Brendon Phillips", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Dillon Browne", - "author_inst": "University of Waterloo" - }, - { - "author_name": "Madhur Anand", - "author_inst": "University of Guelph" - }, - { - "author_name": "Chris Bauch", - "author_inst": "University of Waterloo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.07.20170357", "rel_title": "An Observational Study of COVID-19 from A Large Healthcare System in Northern New Jersey: Diagnosis, Clinical Characteristics, and Outcomes", @@ -1275891,6 +1274311,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.08.11.20172502", + "rel_title": "The COVID-19 Early Detection in Doctors and Healthcare Workers (CEDiD) Study: study protocol for a prospective observational trial", + "rel_date": "2020-08-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.11.20172502", + "rel_abs": "BackgroundThe global COVID-19 pandemic has caused worldwide disruption with its exponential spread mandating national and international lockdown measures. Hospital-associated transmission has been identified as a major factor in the perpetuation of COVID-19, with healthcare workers at high-risk of becoming infected with SARS-CoV-2 and representing important vectors for spread, but not routinely having their clinical observations monitored or being tested for COVID-19.\n\nMethodsA single-center, prospective observational study of 60 healthcare workers will explore how many healthcare workers in high-risk areas develop COVID-19 infection over a thirty day period. High-risk areas are defined as COVID positive wards, the intensive care unit or the accident and emergency department. Healthcare workers (HCWs) will be recruited and have daily self-administered nasopharyngeal SARS-CoV-2 PCR tests. They will also be provided with a wearable medical device to measure their clinical observations during non-working hours, and be asked to complete a daily self-reported symptom questionnaire over the study period. Statistical analysis will assess the proportion of healthcare workers who develop COVID-19 infection as a primary objective, with secondary objectives exploring what symptoms are developed, time-to-event, and deviations in clinical observations.\n\nDiscussionAt present clinical observations, symptoms and COVID-19 PCR swabs are not routinely undertaken for healthcare workers. If the CEDiD (COVID-19 Early Detection in Doctors and Healthcare Workers) study is successful, it will provide useful information for workforce decisions in reducing hospital-associated transmission of COVID-19. The data will help in determining whether there are early warning signs for development of COVID-19 infections amongst healthcare workers and may contribute to the evidence base advocating for more regular testing of healthcare workers observations, symptoms and COVID-19 status.\n\nTrial registrationClinicalTrials.gov, NCT04363489. Registered on 27th July 2020", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Alexander Zargaran", + "author_inst": "Guy's and St Thomas' NHS Foundation Trust" + }, + { + "author_name": "Dina Radenkovic", + "author_inst": "Guy's and St Thomas' NHS Foundation Trust" + }, + { + "author_name": "Iakovos Theodoulou", + "author_inst": "Guy's and St Thomas' NHS Foundation Trust" + }, + { + "author_name": "Andrea Paraboschi", + "author_inst": "Empatica" + }, + { + "author_name": "Chelsea Trengrove", + "author_inst": "Empatica" + }, + { + "author_name": "Gary Colville", + "author_inst": "Guy's and St Thomas' NHS Foundation Trust" + }, + { + "author_name": "Gill Arbane", + "author_inst": "Guy's and St Thomas' NHS Foundation Trust" + }, + { + "author_name": "Kariem El-Boghdadly", + "author_inst": "Guy's and St Thomas' NHS Foundation Trust" + }, + { + "author_name": "Gaia Nebbia", + "author_inst": "Guy's and St Thomas' NHS Foundation Trust" + }, + { + "author_name": "Rocio Teresa Martinez-Nunez", + "author_inst": "King's College London" + }, + { + "author_name": "Anne Greenough", + "author_inst": "King's College London" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.08.11.20172478", "rel_title": "Clustering of age standardised COVID-19 infection fatality ratios and death trajectories", @@ -1276383,49 +1274862,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.10.20172189", - "rel_title": "Janus Kinase-Inhibitor and Type I Interferon Ability to Produce Favorable Clinical Outcomes in COVID-19 Patients: A Systematic Review and Meta-Analysis", - "rel_date": "2020-08-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.10.20172189", - "rel_abs": "BackgroundNovel coronavirus (SARS-CoV-2) has infected over 17 million. Novel therapies are urgently needed. Janus-kinase (JAK) inhibitors and Type I interferons have emerged as potential antiviral candidates for COVID-19 patients for their proven efficacy against diseases with excessive cytokine release and by their ability to promote viral clearance in past coronaviruses, respectively. We conducted a systemic review and meta-analysis to evaluate role of these therapies in COVID-19 patients.\n\nMethodsMEDLINE and MedRxiv were searched until July 30th, 2020, including studies that compared treatment outcomes of humans treated with JAK-inhibitor or Type I interferon against controls. Inclusion necessitated data with clear risk estimates or those that permitted back-calculation.\n\nResultsWe searched 733 studies, ultimately including four randomized and eleven non-randomized clinical trials. JAK-inhibitor recipients had significantly reduced odds of mortality (OR, 0.12; 95%CI, 0.03-0.39, p=0.0005) and ICU admission (OR, 0.05; 95%CI, 0.01-0.26, p=0.0005), and had significantly increased odds of hospital discharge (OR, 22.76; 95%CI, 10.68-48.54, p<0.00001), when compared to standard treatment group. Type I interferon recipients had significantly reduced odds of mortality (OR, 0.19; 95%CI, 0.04-0.85, p=0.03), and increased odds of discharge bordering significance (OR, 1.89; 95%CI, 1.00-3.59, p=0.05).\n\nConclusionsJAK-inhibitor treatment is significantly associated with positive clinical outcomes regarding mortality, ICU admission, and discharge. Type I interferon treatment is associated with positive clinical outcomes regarding mortality and discharge. While these data show promise, additional randomized clinical trials are needed to further elucidate the efficacy of JAK-inhibitors and Type I interferons and clinical outcomes in COVID-19.\n\nKEY MESSAGESO_ST_ABSKey QuestionC_ST_ABSCan treatment of hospitalized COVID-19 patients with JAK-inhibitor or Type I interferon confer favorable clinical outcomes?\n\nBottom LineMeta-analysis demonstrates that JAK-inhibitor treatment was significantly associated with favorable clinical outcomes in terms of mortality, requiring mechanical ventilation, and hospital discharge, while treatment with Type I interferon was significantly associated with decreased mortality.\n\nWhy Read On?This study conducted a systematic review of human trials that treated patients with JAK-inhibitors or Type I interferon, and it elaborates on the potential benefits of administering these therapies at different moments of the disease course despite apparently opposite mechanism of action of these two interventions.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Lucas Walz", - "author_inst": "Yale School of Public Health; Yale School of Medicine" - }, - { - "author_name": "Avi J. Cohen", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Andre P. Rebaza", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "James Vanchieri", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Martin D. Slade", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Charles S. Dela Cruz", - "author_inst": "Yale School of Medicine" - }, - { - "author_name": "Lokesh Sharma", - "author_inst": "Yale School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.11.20172031", "rel_title": "Coordinated support for local action: A modeling study of strategies to facilitate behavior adoption in urban poor communities of Liberia for sustained COVID-19 suppression", @@ -1277833,6 +1276269,57 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.08.07.242271", + "rel_title": "SARS-CoV-2 neutralization and serology testing of COVID-19 convalescent plasma from donors with non-severe disease", + "rel_date": "2020-08-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.07.242271", + "rel_abs": "We determined the antigen binding activity of convalescent plasma units from 47 individuals with a history of non-severe COVID-19 using three clinical diagnostic serology assays (Beckman, DiaSorin, and Roche) with different SARS-CoV-2 targets. We compared these results with functional neutralization activity using a fluorescent reporter strain of SARS-CoV-2 in a microwell assay. This revealed positive correlations of varying strength (Spearman r = 0.37-0.52) between binding and neutralization. Donors age 48-75 had the highest neutralization activity. Units in the highest tertile of binding activity for each assay were enriched (75-82%) for those with the highest levels of neutralization.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Thomas J. Gniadek", + "author_inst": "NorthShore University HealthSystem" + }, + { + "author_name": "Joshua M. Thiede", + "author_inst": "University of Minnesota" + }, + { + "author_name": "William E. Matchett", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Abigail R. Gress", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Kathryn A. Pape", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Marc K. Jenkins", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Vineet D Menachery", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Ryan A. Langlois", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Tyler D. Bold", + "author_inst": "University of Minnesota" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.08.09.243451", "rel_title": "Nonstructural protein 1 of SARS-CoV-2 is a potent pathogenicity factor redirecting host protein synthesis machinery toward viral RNA.", @@ -1278553,37 +1277040,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2020.08.04.20168054", - "rel_title": "SARS-CoV-2 and the Role of Orofecal Transmission: Systematic Review", - "rel_date": "2020-08-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.04.20168054", - "rel_abs": "BackgroundHow SARS-CoV-2 is transmitted is of key public health importance. SARS-CoV-2 has been detected in the feces of some Covid-19 patients which suggests the possibility that the virus could additionally be transmitted via the orofecal route.\n\nMethodsThis review is part of an Open Evidence Review on Transmission Dynamics of Covid-19. We conduct ongoing searches using LitCovid, medRxiv, Google Scholar and Google for Covid-19; assess study quality based on five criteria and report important findings on an ongoing basis. Where necessary authors are contacted for further details or clarification on the content of their articles.\n\nResultsWe found 59 studies: nine reviews and 51 primary studies or reports (one cohort study also included a review) examining the potential role of orofecal transmission of SARS-CoV-2. Half (n=29) were done in China. Thirty seven studies reported positive fecal samples for SARS-CoV-2 based on RT-PCR results (n=1,034 patients). Six studies reported isolating the virus from fecal samples of nine patients, one study isolated the virus from rectal tissue and one laboratory study found that SARS-CoV-2 productively infected human small intestinal organoids. Eleven studies report on fecal samples found in sewage, and two sampled bathrooms and toilets.\n\nConclusionsVarious observational and mechanistic evidence support the hypothesis that SARS-CoV-2 can infect and be shed from the human gastrointestinal tract. Policy should emphasize the importance of strict personal hygiene measures, and chlorine-based disinfection of surfaces in locations where there is presumed or known SARS-CoV-2 activity.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Carl Heneghan", - "author_inst": "University of Oxford" - }, - { - "author_name": "Elizabeth Spencer", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jon Brassey", - "author_inst": "Trip Database" - }, - { - "author_name": "Tom Jefferson", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.10.241414", "rel_title": "SARS-CoV-2 Quasispecies Mediate Rapid Virus Evolution and Adaptation", @@ -1279883,6 +1278339,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.08.06.20164848", + "rel_title": "Single-cell RNA-seq reveals profound monocyte changes in Paediatric Inflammatory Multisystem Syndrome Temporally associated with SARS-CoV-2 infection (PIMS-TS)", + "rel_date": "2020-08-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.06.20164848", + "rel_abs": "Multisystem inflammatory syndrome in children (MIS-C) is a life-threatening disease occurring several weeks after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. MIS-C has overlapping clinical features with Kawasaki Disease (KD), a rare childhood vasculitis. MIS-C therapy is largely based on KD treatment protocols but whether these diseases share underpinning immunological perturbations is unknown. We performed deep immune profiling on blood samples from healthy children and patients with MIS-C or KD. Acute MIS-C patients had highly activated neutrophils, classical monocytes and memory CD8+ T-cells; increased frequencies of B-cell plasmablasts and CD27-IgD-double-negative B-cells; and increased levels of pro-inflammatory (IL6, IL18, IP10, MCP1) but also anti-inflammatory (IL-10, IL1-RA, sTNFR1, sTNFR2) cytokines. Increased neutrophil count correlated with inflammation,cardiac dysfunction and disease severity. Two days after intravenous immunoglobulin (IVIG) treatment, MIS-C patients had increased CD163 expression on monocytes, expansion of a novel population of immature neutrophils, and decreased levels of pro- and anti-inflammatory cytokines in the blood accompanied by a transient increase in arginase in some patients. Our data show MIS-C and KD share substantial immunopathology and identify potential new mechanisms of action for IVIG, a widely used anti-inflammatory drug used to treat MIS-C, KD and other inflammatory diseases.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Eleni Syrimi", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Eanna Fennell", + "author_inst": "University of Limerick" + }, + { + "author_name": "Alex Richter", + "author_inst": "University of Birmingham" + }, + { + "author_name": "Pavle Vrljicak", + "author_inst": "University of Warwick" + }, + { + "author_name": "Richard Stark", + "author_inst": "University of Warwick" + }, + { + "author_name": "Sascha Ott", + "author_inst": "University of Warwick" + }, + { + "author_name": "Paul G Murray", + "author_inst": "University of Birmingham and University of Limerick" + }, + { + "author_name": "Eslam Al-abadi", + "author_inst": "Birmingham Womens and Childrens NHS Foundation Trust" + }, + { + "author_name": "Ashish Chikermane", + "author_inst": "Birmingham Womens and Childrens NHS foundation trust" + }, + { + "author_name": "Pamela Dawson", + "author_inst": "Birmingham Womens and Childrens NHS foundation trust" + }, + { + "author_name": "Scott Hackett", + "author_inst": "University Hospitals Birmingham NHS foundation trust" + }, + { + "author_name": "Deepthi Jyothish", + "author_inst": "Birmingham Womens and Childrens NHS foundation trust" + }, + { + "author_name": "Hari Krishnan Kanthimathinathan", + "author_inst": "Birmingham Womens and Childrens NHS foundation trust" + }, + { + "author_name": "Sean Monaghan", + "author_inst": "Birmingham Womens and Childrens hospital NHS foundation trust" + }, + { + "author_name": "Prasad Nagakumar", + "author_inst": "Birmingham Womens and Childrens NHS foundation trust and University of Birmingham" + }, + { + "author_name": "Naeem Khan", + "author_inst": "Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham," + }, + { + "author_name": "Sian Faustini", + "author_inst": "Clinical Immunology Service, Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham," + }, + { + "author_name": "Barnaby R Scholefield", + "author_inst": "Birmingham Womens and Childrens NHS foundation trust and University of Birmingham" + }, + { + "author_name": "Steven Welch", + "author_inst": "University Hospitals Birmingham NHS Foundation Trust" + }, + { + "author_name": "Pamela Kearns", + "author_inst": "NIHR Birmingham Biomedical Research Centre and Institute of Cancer and Genomic Sciences, University of Birmingham" + }, + { + "author_name": "Graham Taylor", + "author_inst": "University of Birmingham" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "pediatrics" + }, { "rel_doi": "10.1101/2020.08.06.20164129", "rel_title": "Associations between personal protective equipment and nursing staff stress during the COVID-19 pandemic", @@ -1280323,61 +1278878,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.05.20168476", - "rel_title": "Specificity and Performance of Nucleocapsid and Spike-based SARS-CoV-2 Serologic Assays", - "rel_date": "2020-08-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.05.20168476", - "rel_abs": "There is an urgent need for an accurate antibody test for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this paper, we have developed 3 ELISA methods, trimer spike IgA, trimer spike IgG, and nucleocapsid IgG, for detecting anti-SARS-CoV-2 antibodies. We evaluated their performance in comparison with four commercial ELISAs, EDI Novel Coronavirus COVID-19 ELISA IgG and IgM, Euroimmun Anti-SARS-CoV-2 ELISA IgG and IgA, and one lateral flow assay, DPP(R) COVID-19 IgM/IgG System (Chembio). Both sensitivity and specificity were evaluated and the causes of false-positive reactions were determined.\n\nThe assays were compared using 300 pre-epidemic samples and 100 PCR-confirmed COVID-19 samples. The sensitivities and specificities of the assays were as follows: 90%/100% (in-house trimer spike IgA), 90%/99.3% (in-house trimer spike IgG), 89%/98.3% (in-house nucleocapsid IgG), 73.7%/100% (EDI nucleocapsid IgM), 84.5%/95.1% (EDI nucleocapsid IgG), 95%/93.7% (Euroimmun S1 IgA), 82.8%/99.7% (Euroimmun S1 IgG), 82.0%/91.7% (Chembio nucleocapsid IgM), 92%/93.3% (Chembio nucleocapsid IgG).\n\nThe presumed causes of positive signals from pre-epidemic samples in commercial and in-house assays were mixed. In some cases, positivity varied with assay repetition. In other cases, reactivity was abrogated by competitive inhibition (spiking the sample with analyte prior to performing the assay). In other cases, reactivity was consistently detected but not abrogated by analyte spiking.\n\nOverall, there was wide variability in assay performance using our samples, with in-house tests exhibiting the highest combined sensitivity and specificity. The causes of \"false positivity\" in pre-epidemic samples may be due to plasma antibodies apparently reacting with the analyte, or spurious reactivity may be directed against non-specific components in the assay system. Identification of these targets will be essential to improving assay performance.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Zahra Rikhtegaran Tehrani", - "author_inst": "University of Maryland, School of Madicine" - }, - { - "author_name": "Saman Saadat", - "author_inst": "University of Maryland, School of Medicine" - }, - { - "author_name": "Ebtehal Saleh", - "author_inst": "University of Maryland, School of Madicine" - }, - { - "author_name": "Xin Ouyang", - "author_inst": "University of Maryland, School of Madicine" - }, - { - "author_name": "Niel Constantine", - "author_inst": "University of Maryland, School of Madicine" - }, - { - "author_name": "Anthony L. DeVico", - "author_inst": "University of Maryland, School of Madicine" - }, - { - "author_name": "Anthony D. Harris", - "author_inst": "University of Maryland, School of Madicine" - }, - { - "author_name": "George K. Lewis", - "author_inst": "University of Maryland, School of Madicin" - }, - { - "author_name": "Shyam Kottilil", - "author_inst": "University of Maryland, School of Madicine" - }, - { - "author_name": "Mohammad M. Sajadi", - "author_inst": "University of Maryland, School of Madicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.07.20169490", "rel_title": "HIV infection and COVID-19 death: population-based cohort analysis of UK primary care data and linked national death registrations within the OpenSAFELY platform", @@ -1281841,6 +1280341,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "urology" }, + { + "rel_doi": "10.1101/2020.08.04.20167650", + "rel_title": "Measurement lessons of a repeated cross-sectional household food insecurity survey during the COVID-19 pandemic in Mexico", + "rel_date": "2020-08-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.04.20167650", + "rel_abs": "ObjectiveTo validate the telephone modality of the Latin American and Caribbean Food Security Scale (ELCSA) included in three waves of a phone survey to estimate the monthly household food insecurity (HFI) prevalence during the COVID-19 pandemic in Mexico.\n\nDesignWe examined the reliability and internal validity of the ELCSA scale in three repeated waves of a cross-sectional surveys with Rasch models. We estimated the monthly prevalence of food insecurity in the general population and in households with and without children, and compared them with a national 2018 survey. We tested concurrent validity by testing associations of HFI with socioeconomic status and anxiety.\n\nSettingENCOVID-19 is a monthly telephone cross-sectional survey collecting information on the well-being of Mexican households during the pandemic lockdown. Surveys used probabilistic samples and we used data from April (n=833), May (n=850), and June 2020 (n=1,674).\n\nParticipantsMexicans 18 years or older who had a mobile telephone.\n\nResultsELCSA had adequate model fit and HFI was associated, within each wave, with more poverty and anxiety. The COVID-19 lockdown was associated with an important reduction in food security; decreasing stepwise from 38.9% in 2018 to 24.9% in June 2020 in households with children.\n\nConclusionsTelephone surveys are a feasible strategy to monitor food insecurity with ELCSA", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Pablo Gaitan-Rossi", + "author_inst": "Universidad Iberoamericana" + }, + { + "author_name": "Mireya Vilar-Compte", + "author_inst": "Universidad Iberoamericana" + }, + { + "author_name": "Graciela Teruel", + "author_inst": "Universidad Iberoamericana" + }, + { + "author_name": "Rafael Perez-Escamilla", + "author_inst": "Yale" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "nutrition" + }, { "rel_doi": "10.1101/2020.08.04.20168237", "rel_title": "Short-term change in air pollution following the COVID-19 state of emergency: A national analysis for the United States", @@ -1282053,77 +1280584,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.08.04.20168518", - "rel_title": "Phylodynamics reveals the role of human travel and contact tracing in controlling COVID-19 in four island nations", - "rel_date": "2020-08-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.04.20168518", - "rel_abs": "BackgroundNew Zealand, Australia, Iceland, and Taiwan all saw success at controlling the first wave of the COVID-19 pandemic. As islands, they make excellent case studies for exploring the effects of international travel and human movement on the spread of COVID-19.\n\nMethodsWe employed a range of robust phylodynamic methods and genome subsampling strategies to infer the epidemiological history of SARS-CoV-2 in these four countries. We compared these results to transmission clusters identified by the New Zealand Ministry of Health by contract tracing strategies.\n\nFindingsWe estimated the effective reproduction number of COVID-19 as 1-1.4 during early stages of the pandemic, and show that it declined below 1 as human movement was restricted. We also showed that this disease was introduced many times into each country, and that introductions slowed down markedly following the reduction of international travel in mid March 2020. Finally, we confirmed that New Zealand transmission clusters identified via standard health surveillance strategies largely agree with those defined by genomic data.\n\nInterpretationWe have demonstrated how the use of genomic data and computational biology methods can assist health officials in characterising the epidemiology of viral epidemics, and for contact tracing.\n\nFundingThis research was funded by the Health Research Council of New Zealand, the Ministry of Business, Innovation, and Employment, the Royal Society of New Zealand, and the New Zealand Ministry of Health.\n\nResearch in ContextO_ST_ABSEvidence before this studyC_ST_ABSOur study looks at the early months of the COVID-19 pandemic, a period in which the first wave was controlled in four \"island\" nations - New Zealand, Australia, Taiwan, and Iceland. All prior data used in this study was collected from late 2019 until the end of April 2020. This includes over 3000 SARS-CoV-2 genomic sequences which were collected in this period (and subsequently deposited into GISAID), as well as arrival and departure information (provided by official statistics from each country), human mobility data collected from mobile phones (by Apple), and COVID-19 case data (released by the World Health Organisation). Even early on during the COVID-19 pandemic, the properties of SARS-CoV-2 - including the reproduction number and mutation rate - were well characterised, and a range of these estimates have been covered in our article. Our Bayesian phylodynamic models, including their prior distributions, are informed by all of the above sources of information. Finally, we have incorporated all of the available information on COVID-19 transmission clusters identified by the New Zealand Ministry of Health during this period.\n\nAdded value of this studyWe quantified the decline in the reproduction number of SARS-CoV-2, following the decline in human mobility, in four \"island\" countries. We also demonstrated how importation events of SARS-CoV-2 into each considered country declined markedly following the reduction of international travel. Our results shed a different light on these patterns because of (i) our locations of choice - the four countries had success in dealing with the first pandemic wave, with their geographic isolation contributing to cleaner signals of human mobility, and (ii) our novel and empirically driven phylodynamic model, which we built from explicitly modelling mobile phone data in the four islands. Furthermore, by crossing epidemiological against ge3nomic data, our paper quantitatively assesses the ability of contact tracing, as implemented by the New Zealand Ministry of Health (NZMH), in identifying COVID-19 transmission clusters. We find evidence for a high efficacy of the specific measures taken - and when they were taken - by the NZMH in identifying transmission clusters, considered worldwide to have been successful in its response to the pandemic. Our analyses also illustrate the power of viral genomic data in assisting contact tracing.\n\nImplications of all the available evidenceThe conclusions drawn from this research inform effective policy for locations pursuing an elimination strategy. We confirm the accuracy of standard contact tracing methods at identifying clusters and show how these methods are improved using genomic data. We demonstrate how the overseas introduction rates and domestic transmission rates of an infectious viral agent can be surveilled using genomic data, and the important role each plays in overall transmission. Specifically, we have quantified these processes for four countries and have shown that they did decline significantly following declines in human travel and mobility. The phylodynamic methods used in this work is shown to be robust and applicable to a range of scenarios where appropriate subsampling is used.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Jordan Douglas", - "author_inst": "University of Auckland" - }, - { - "author_name": "Fabio K Mendes", - "author_inst": "Centre for Computational Evolution, The University of Auckland, Auckland, New Zealand" - }, - { - "author_name": "Remco Bouckaert", - "author_inst": "Centre for Computational Evolution, The University of Auckland, Auckland, New Zealand" - }, - { - "author_name": "Dong Xie", - "author_inst": "Centre for Computational Evolution, The University of Auckland, Auckland, New Zealand" - }, - { - "author_name": "Cinthy L Jimenez-Silva", - "author_inst": "Centre for Computational Evolution, The University of Auckland, Auckland, New Zealand" - }, - { - "author_name": "Christiaan Swanepoel", - "author_inst": "Centre for Computational Evolution, The University of Auckland, Auckland, New Zealand" - }, - { - "author_name": "Joep de Ligt", - "author_inst": "Institute of Environmental Science and Research, Wellington, New Zealand" - }, - { - "author_name": "Xiaoyun Ren", - "author_inst": "Institute of Environmental Science and Research, Wellington, New Zealand" - }, - { - "author_name": "Matt Storey", - "author_inst": "Institute of Environmental Science and Research, Wellington, New Zealand" - }, - { - "author_name": "James Hadfield", - "author_inst": "Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA" - }, - { - "author_name": "Colin R Simpson", - "author_inst": "School of Health, Victoria University of Wellington, Wellington, New Zealand" - }, - { - "author_name": "Jemma L Geoghegan", - "author_inst": "Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand" - }, - { - "author_name": "Alexei J Drummond", - "author_inst": "Centre for Computational Evolution, The University of Auckland, Auckland, New Zealand" - }, - { - "author_name": "David Welch", - "author_inst": "Centre for Computational Evolution, The University of Auckland, Auckland, New Zealand" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.04.20168203", "rel_title": "Seroprevalence of SARS-CoV-2-Specific IgG Antibodies Among Adults Living in Connecticut Between March 1 and June 1, 2020: Post-Infection Prevalence (PIP) Study", @@ -1283487,6 +1281947,137 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.05.20168435", + "rel_title": "First-in-Human Trial of a SARS CoV 2 Recombinant Spike Protein Nanoparticle Vaccine", + "rel_date": "2020-08-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.05.20168435", + "rel_abs": "BackgroundNVX-CoV2373 is a recombinant nanoparticle vaccine composed of trimeric full-length SARS-CoV-2 spike glycoproteins. We present the Day 35 primary analysis of our trial of NVX-CoV2373 with or without the saponin-based Matrix-M1 adjuvant in healthy adults.\n\nMethodsThis is a randomized, observer-blinded, placebo-controlled, phase 1 trial in 131 healthy adults. Trial vaccination comprised two intramuscular injections, 21 days apart. Primary outcomes were reactogenicity, safety labs, and immunoglobulin G (IgG) anti-spike protein response. Secondary outcomes included adverse events, wild-type virus neutralizing antibody, and T-cell responses.\n\nResultsParticipants received NVX-CoV2373 with or without Matrix-M1 (n=106) or placebo (n=25). There were no serious adverse events. Reactogenicity was mainly mild in severity and of short duration (mean [≤]2 days), with second vaccinations inducing greater local and systemic reactogenicity. The adjuvant significantly enhanced immune responses and was antigen dose-sparing, and the two-dose 5g NVX-CoV2373/Matrix-M1 vaccine induced mean anti-spike IgG and neutralizing antibody responses that exceeded the mean responses in convalescent sera from COVID-19 patients with clinically significant illnesses. The vaccine also induced antigen-specific T cells with a largely T helper 1 (Th1) phenotype.\n\nConclusionsNVX-CoV2373/Matrix-M1 was well tolerated and elicited robust immune responses (IgG and neutralization) four-fold higher than the mean observed in COVID-19 convalescent serum from participants with clinical symptoms requiring medical care and induced CD4+ T-cell responses biased toward a Th1 phenotype. These findings suggest that the vaccine may confer protection and support transition to efficacy evaluations to test this hypothesis. (Funded by the Coalition for Epidemic Preparedness Innovations; ClinicalTrials.gov number, NCT04368988).", + "rel_num_authors": 29, + "rel_authors": [ + { + "author_name": "Cheryl Keech", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Gary Albert", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Patricia Reed", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Susan Neal", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Joyce S. Plested", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Mingzhu Zhu", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Shane Cloney-Clark", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Haixia Zhou", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Nita Patel", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Matthew B. Frieman", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Robert E. Haupt", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "James Logue", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Marisa McGrath", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Stuart Weston", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "Pedro A. Piedra", + "author_inst": "Baylor University College of Medicine" + }, + { + "author_name": "Iksung Cho", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Andreana Robertson", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Chinar Desai", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Kathleen Callahan", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Maggie Lewis", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Patricia Price-Abbott", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Neil Formica", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Vivek Shinde", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Louis Fries", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Jason D. Linkliter", + "author_inst": "Nucleus Network Pty Ltd" + }, + { + "author_name": "Paul Griffin", + "author_inst": "Q-Pharm" + }, + { + "author_name": "Bethanie Wilkinson", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Gale Smith", + "author_inst": "Novavax, Inc." + }, + { + "author_name": "Gregory M. Glenn", + "author_inst": "Novavax, Inc." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.05.20168872", "rel_title": "Inflammasome activation in COVID-19 patients", @@ -1283971,29 +1282562,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.08.06.240333", - "rel_title": "Computational Hot-Spot Analysis of the SARS-CoV-2 Receptor Binding Domain / ACE2 Complex", - "rel_date": "2020-08-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.06.240333", - "rel_abs": "Infection and replication of SARS CoV-2 (the virus that causes COVID-19) requires entry to the interior of host cells. In humans, a Protein-Protein Interaction (PPI) between the SARS CoV-2 Receptor-Binding Domain (RBD) and the extracellular peptidase domain of ACE2, on the surface of cells in the lower respiratory tract, is an initial step in the entry pathway. Inhibition of the SARS CoV-2 RBD / ACE2 PPI is currently being evaluated as a target for therapeutic and/or prophylactic intervention. However, relatively little is known about the molecular underpinnings of this complex. Employing multiple computational platforms, we predicted hot-spot residues in a positive control PPI (PMI / MDM2) and the CoV-2 RBD/ACE2 complex. Computational alanine scanning mutagenesis was performed to predict changes in Gibbs free energy that are associated with mutating residues at the positive control (PMI/MDM2) or SARS RBD/ACE2 binding interface to alanine. Additionally, we used the Adaptive Poisson-Boltzmann Solver to calculate macromolecular electrostatic surfaces at the interface of the positive control PPI and SARS CoV-2 / ACE2 PPI. Collectively, this study illuminates predicted hot-spot residues, and clusters, at the SARS CoV-2 RBD / ACE2 binding interface, potentially guiding the development of reagents capable of disrupting this complex and halting COVID-19.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Pedro A. Rosario", - "author_inst": "Delaware State University" - }, - { - "author_name": "Brian R McNaughton", - "author_inst": "Delaware State University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.08.06.238915", "rel_title": "Peptide Antidotes to SARS-CoV-2 (COVID-19)", @@ -1285433,6 +1284001,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.26.20156380", + "rel_title": "The Impact of COVID-19 on Medical Practice: A Nationwide Survey of Dermatologists and Healthcare Providers", + "rel_date": "2020-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.26.20156380", + "rel_abs": "BackgroundThe COVID-19 pandemic has dramatically changed medical practice worldwide. It posed a significant impact on different health services, including dermatology.\n\nMethodsA Cross-sectional observational study of 200 healthcare providers and 100 dermatologists (survey 1 and 2, respectively) were conducted.\n\nObjectivesTo determine the prevalence of occupational skin diseases among healthcare providers working amid the pandemic, and to demonstrate the outbreaks impact on dermatology practice.\n\nResultsMost healthcare providers (83%) reported hygiene-related hand dermatitis. The rates of PPE-related dermatoses were estimated to be 73%, including pressure injuries (51.9%), acne (33.1%), non-gloves contact dermatitis (29.9%), nonspecific rash (17.5%), urticaria (9.1%) and skin infections (3.2%). The emerging COVID-19-related cutaneous manifestations were recognized by 20% of surveyed dermatologists, including maculopapular rash (41.67%), urticaria (37.50%), chilblain (25%) and vasculitis (16.67). Telemedicine was provided by 73% of the dermatologists, and 89% reported minimal use of immunosuppressive drugs amid the pandemic.\n\nConclusionsThis article highlights the emergence of hygiene-related hand dermatitis and PPE-related dermatoses among healthcare providers working in the COVID-19 era. It also provides an appreciation of the major impact of COVID-19 on different aspects of dermatology practice in Iraq, and how the dermatologists adapt to these unfamiliar circumstances to meet the challenges.\n\nHighlightsO_LICOVID-19 is associated with an ongoing emergence of occupational skin disease among healthcare providers\nC_LIO_LICOVID-19 posed a significant impact on medical practice, including the epidemiology of diseases, the use of telemedicine, and modification of management plans\nC_LIO_LIDermatologists play a crucial role in recognizing the cutaneous manifestations associated with COVID-19 infection.\nC_LI", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Mohammed Shanshal", + "author_inst": "Baghdad Teaching Hospital" + }, + { + "author_name": "Hayder Saad Ahmed", + "author_inst": "University of Tikrit, College of Medicine, Department of Dermatology and Venereology" + }, + { + "author_name": "Hayder Asfoor", + "author_inst": "University of Kerbala, College of Medicine, Department of Medicine" + }, + { + "author_name": "Raad Ibrahim Salih", + "author_inst": "University of Tikrit, College of Medicine, Department of Dermatology and Venereology" + }, + { + "author_name": "Shehab Ahmed Ali", + "author_inst": "Al- iskandria Hospital, Department of Dermatology and Venereology" + }, + { + "author_name": "Yusif k. Aldabouni", + "author_inst": "Baghdad Teaching Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "dermatology" + }, { "rel_doi": "10.1101/2020.07.31.20165696", "rel_title": "Paradoxical Case Fatality Rate dichotomy of Covid-19 among rich and poor nations points to the hygiene hypothesis.", @@ -1286025,69 +1284632,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.31.20165738", - "rel_title": "Early clinical characteristics of Covid-19: scoping review", - "rel_date": "2020-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.31.20165738", - "rel_abs": "BackgroundThe Coronavirus disease 2019 (covid-19) pandemic has spread rapidly across the globe. Accurate clinical characterisation studies conducted early in the pandemic are essential to informing research, diagnosis and clinical management efforts. In this scoping review we identify the clinical characteristics of patients admitted to hospital in the early months of the pandemic, focusing on symptoms, laboratory and imaging findings, and clinical outcomes.\n\nMethodsA scoping review. MEDLINE, EMBASE and Global Health databases were searched for studies published from January 1st 2020 to April 28th 2020. Studies which reported on at least 100 hospitalised patients with covid-19 of any age were included.\n\nResultsOf 1,249 studies identified through the search 78 studies were eligible for inclusion; one randomized control trial and 77 observational studies presenting data on 77,443 patients admitted with covid-19. Most studies were conducted in China (82%), 9% in the US and 10% in Europe and two studies were set in more than one country. No studies included patients from low and middle income countries. Coagulopathy was underrecognised as a complication in the early months of the pandemic. Use of corticosteroids varied widely, and the use of anticoagulants was reported in only one study. Fever, cough and dyspnoea are less common in older adults; gastrointestinal symptoms, as the only presenting feature was underrecognised. The most common laboratory finding was lymphocytopenia. Inflammatory biomarkers were commonly elevated, including C-reactive protein and interleukin-6. Typical computed tomography findings include bilateral infiltrates however imaging may be normal in early disease. Data on clinical characteristics in children and vulnerable populations were limited.\n\nConclusionsClinical characterisation studies from early in the pandemic indicated that covid-19 is a multisystem disease, with biomarkers indicating inflammation and coagulopathy. However, early data collection on symptoms and clinical outcomes did not consistently reflect this wide spectrum. Corticosteroid use varied widely, and anticoagulants were rarely used. Clinicians should remain vigilant to the possibility of covid-19 in patients presenting without fever, cough and dyspnoea, particularly in older adults. Further characterisation studies in different at-risk populations is needed.\n\nReview registrationAvailable at https://osf.io/r2ch9", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Lakshmi Manoharan", - "author_inst": "University of Oxford" - }, - { - "author_name": "Jonathan W S Cattrall", - "author_inst": "Liverpool University Hospitals NHS Foundation Trust, University of Liverpool" - }, - { - "author_name": "Carlyn Harris", - "author_inst": "Emory University School of Medicine" - }, - { - "author_name": "Katherine Newell", - "author_inst": "University of Oxford" - }, - { - "author_name": "Blake Thomson", - "author_inst": "University of Oxford" - }, - { - "author_name": "Mark G Pritchard", - "author_inst": "University of Oxford" - }, - { - "author_name": "Peter G Bannister", - "author_inst": "Brighton and Sussex Medical School" - }, - { - "author_name": "Louise Sigfrid", - "author_inst": "University of Oxford" - }, - { - "author_name": "Tom Solomon", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Peter W Horby", - "author_inst": "University of Oxford" - }, - { - "author_name": "Gail Carson", - "author_inst": "University of Oxford" - }, - { - "author_name": "Piero L Olliaro", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.31.20154070", "rel_title": "False-Negative Mitigation in Group Testing for COVID-19 Screening", @@ -1287423,6 +1285967,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.31.20166298", + "rel_title": "Estimating the reproductive number R0 of SARS-CoV-2 in the United States and eight European countries and implications for vaccination", + "rel_date": "2020-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.31.20166298", + "rel_abs": "SARS-CoV-2 rapidly spread from a regional outbreak to a global pandemic in just a few months. Global research efforts have focused on developing effective vaccines against SARS-CoV-2 and the disease it causes, COVID-19. However, some of the basic epidemiological parameters, such as the exponential epidemic growth rate and the basic reproductive number, R0, across geographic areas are still not well quantified. Here, we developed and fit a mathematical model to case and death count data collected from the United States and eight European countries during the early epidemic period before broad control measures were implemented. Results show that the early epidemic grew exponentially at rates between 0.19-0.29/day (epidemic doubling times between 2.4-3.6 days). We discuss the current estimates of the mean serial interval, and argue that existing evidence suggests that the interval is between 6-8 days in the absence of active isolation efforts. Using parameters consistent with this range, we estimated the median R0 value to be 5.8 (confidence interval: 4.7-7.3) in the United States and between 3.6 and 6.1 in the eight European countries. This translates to herd immunity thresholds needed to stop transmission to be between 73% and 84%. We further analyze how vaccination schedules depends on R0, the duration of vaccine-induced immunity to SARS-CoV-2, and show that individual-level heterogeneity in vaccine induced immunity can significantly affect vaccination schedules.\n\nSignificanceWith the global efforts to develop vaccines for COVID-19, it is important to understand the contagiousness of the virus to design regional vaccination policy. To that end, we fit a mathematical model to data collected from the early epidemic period in the United States and eight European countries, estimating that the early epidemic doubles between 2.4-3.6 days. This suggests that SARS-CoV-2 is highly transmissible in the absence of strong control measures irrespective of heterogeneity in geographic and social settings. We estimated the median basic reproduction number, R0 to be 5.8 (confidence interval: 4.7-7.3) in the United States and between 3.6 and 6.1 in the eight European countries. The herd immunity needed to stop transmission is high (between 73% and 84%).", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Ruian Ke", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Ethan Obie Romero-Severson", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Steven Sanche", + "author_inst": "Los Alamos National Laboratory" + }, + { + "author_name": "Nick Hengartner", + "author_inst": "Los Alamos National Laboratory" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.31.20166348", "rel_title": "Containing the Spread of Infectious Disease on College Campuses", @@ -1287759,65 +1286334,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.02.20166256", - "rel_title": "Clinical characteristics and antibody response to SARS-CoV-2 spike 1 protein using the VITROS Anti-SARS-CoV-2 antibody tests in COVID-19 patients in Japan", - "rel_date": "2020-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.02.20166256", - "rel_abs": "BackgroundWe evaluated clinical characteristics and the clinical utility of VITROS SARS-CoV-2 antibody tests according to COVID-19 severity in patients in Japan.\n\nMethodsWe analyzed 255 serum specimens from 130 COVID-19 patients and examined clinical records and laboratory data. Presence of total (IgA, IgM, and IgG) and specific IgG antibody for the spike 1 antigen of SARS-CoV2 was determined using VITROS Anti-SARS-CoV-2 antibody tests.\n\nFindingsOverall, 98 (75.4%) and 32 (24.6%) patients had mild and severe COVID-19, respectively. On admission, 76 (58.5%) and 45 (34.6%) patients were positive for total and IgG antibody assays. Among 91 patients at discharge, 90 (98.9%) and 81 (89.0%) patients were positive for total and IgG antibody, respectively. Clinical background and laboratory findings on admission, but not the prevalence or concentration of total or IgG antibody, were associated with disease prognosis. Total and IgG antibody intensity were significantly higher in severe cases than in mild cases in serum collected after 11 days from onset, but not within 10 days.\n\nConclusionVITROS Anti-SARS-CoV-2 Total and IgG assays will be useful as supporting diagnostic and surveillance tools and for evaluation of humoral immune response to COVID-19. Clinical background and laboratory findings are preferable predictors of disease prognosis.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Mayu Nagura-Ikeda", - "author_inst": "Self-Defense Forces Central Hospital" - }, - { - "author_name": "Kazuo Imai", - "author_inst": "Saitama Medical University" - }, - { - "author_name": "Katsumi Kubota", - "author_inst": "Saitama Medical University Hospital" - }, - { - "author_name": "Sakiko Noguchi", - "author_inst": "Saitama Medical University Hospital" - }, - { - "author_name": "Yutaro Kitagawa", - "author_inst": "Saitama Medical University Hospital" - }, - { - "author_name": "Masaru Matsuoka", - "author_inst": "Saitama Medical University Hospital" - }, - { - "author_name": "Sakiko Tabata", - "author_inst": "Self-Defense Forces Central Hospital" - }, - { - "author_name": "Kazuyasu Miyoshi", - "author_inst": "Self-Defense Forces Central Hospital" - }, - { - "author_name": "Toshimitsu Ito", - "author_inst": "Self-Defense Forces Central Hospital" - }, - { - "author_name": "Kaku Tamura", - "author_inst": "Self-Defense Forces Central Hospital" - }, - { - "author_name": "Takuya Maeda", - "author_inst": "Saitama Medical University Hospital" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.03.20167056", "rel_title": "The impact of relaxing interventions on human contact patterns and SARS-CoV-2 transmission in China", @@ -1288733,6 +1287249,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, + { + "rel_doi": "10.1101/2020.08.01.20163733", + "rel_title": "Characteristics of 24,516 Patients Diagnosed with COVID-19 Illness in a National Clinical Research Network: Results from PCORnet", + "rel_date": "2020-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.01.20163733", + "rel_abs": "BackgroundNational data from diverse institutions across the United States are critical for guiding policymakers as well as clinical and public health leaders. This study characterized a large national cohort of patients diagnosed with COVID-19 in the U.S., compared to patients diagnosed with viral pneumonia and influenza.\n\nMethods and FindingsWe captured cross-sectional information from 36 large healthcare systems in 29 U.S. states, participating in PCORnet(R), the National Patient-Centered Clinical Research Network. Patients included were those diagnosed with COVID-19, viral pneumonia and influenza in any care setting, starting from January 1, 2020. Using distributed queries executed at each participating institution, we acquired information for patients on care setting (any, ambulatory, inpatient or emergency department, mechanical ventilator), age, sex, race, state, comorbidities (assessed with diagnostic codes), and medications used for treatment of COVID-19 (hydroxychloroquine with or without azithromycin; corticosteroids, anti-interleukin-6 agents).\n\nDuring this time period, 24,516 patients were diagnosed with COVID-19, with 42% in an emergency department or inpatient hospital setting; 79,639 were diagnosed with viral pneumonia (53% inpatient/ED) and 163,984 with influenza (41% inpatient/ED). Among COVID-19 patients, 68% were 20 to <65 years of age, with more of the hospitalized/ED patients in older age ranges (23% 65+ years vs. 12% for COVID-19 patients in the ambulatory setting). Patients with viral pneumonia were of a similar age, and patients with influenza were much younger. Comorbidities were common, especially for patients with COVID-19 and viral pneumonia, with hypertension (32% for COVID-19 and 46% for viral pneumonia), arrhythmias (20% and 35%), and pulmonary disease (19% and 40%) the most common. Hydroxychloroquine was used in treatment for 33% and tocilizumab for 11% of COVID-19 patients on mechanical ventilators (25% received azithromycin as well).\n\nConclusion and RelevancePCORnet leverages existing data to capture information on one of the largest U.S. cohorts to date of patients diagnosed with COVID-19 compared to patients diagnosed with viral pneumonia and influenza.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Jason P Block", + "author_inst": "Harvard Pilgrim Health Care Institute/Harvard Medical School" + }, + { + "author_name": "Keith A. Marsolo", + "author_inst": "Duke University" + }, + { + "author_name": "Kshema Nagavedu", + "author_inst": "Harvard Pilgrim Health Care Institute" + }, + { + "author_name": "L Charles Bailey", + "author_inst": "Childrens Hospital of Philadelphia" + }, + { + "author_name": "Henry Cruz", + "author_inst": "PCORnet" + }, + { + "author_name": "Christopher B. Forrest", + "author_inst": "Childrens Hospital of Philadelphia" + }, + { + "author_name": "Kevin Haynes", + "author_inst": "HealthCore" + }, + { + "author_name": "Adrian F. Hernandez", + "author_inst": "Duke Clinical Research Institute" + }, + { + "author_name": "Rainu Kaushal", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Abel Kho", + "author_inst": "Northwestern University" + }, + { + "author_name": "Kathleen M. McTigue", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Vinit P. Nair", + "author_inst": "PRACnet" + }, + { + "author_name": "Richard Platt", + "author_inst": "Harvard Pilgrim Health Care Institute/Harvard Medical School" + }, + { + "author_name": "Jon Puro", + "author_inst": "OCHIN, Inc" + }, + { + "author_name": "Russell L. Rothman", + "author_inst": "Vanderbilt University Medical Center" + }, + { + "author_name": "Elizabeth Shenkman", + "author_inst": "College of Medicine, University of Florida" + }, + { + "author_name": "Lemuel Russell Waitman", + "author_inst": "University of Kansas Medical Center" + }, + { + "author_name": "Mark G. Weiner", + "author_inst": "Weill Cornell Medicine" + }, + { + "author_name": "Neely Williams", + "author_inst": "Community Partners Network Inc" + }, + { + "author_name": "Thomas W. Carton", + "author_inst": "Louisiana Public Health Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.02.20166876", "rel_title": "SARS-CoV-2 Seroprevalence in Relation to Timing of Symptoms", @@ -1289341,25 +1287952,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.08.03.20167304", - "rel_title": "Correlation between daily infections and fatality rate due to Covid-19 in Germany", - "rel_date": "2020-08-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.03.20167304", - "rel_abs": "The officially reported daily Covid-19 fatality rate is modelled with a trend line based on a nominal day-to-day reproduction rate and a cosine to take account of weekly fluctuations. Although the time trajectories of officially reported infections and fatalities are pronouncedly different, the reproduction rates obtained therefrom are similar. The long-term effective reproduction rate is around 0.835 and the administrative measures to contain the pandemic seem not to have an immediate reducing effect but well the ease of restrictions an increasing one. The fatality trajectory represented by its trend line can be projected from the number of daily infections by assuming a time lapse between symptom onset and death between 17 and 19 days and a time-dependent nominal lethality. The time trajectory of this lethality increases from 2.5% at March 16 when public life was restricted to 6% within 20 days indicating relatively more infections of vulnerable people. After stipulating face mask wearing at April 27, the nominal lethality decreases down to 1% later in summer. A detailed analysis shows that mask wearing really reduces the number of fatal infections and the officially reported daily infections in May and June are less lethal than before.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Dieter Mergel", - "author_inst": "University of Duisburg-Essen, Faculty of Physics" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.08.03.20164137", "rel_title": "A Comprehensive Analysis of COVID-19 Transmission and Fatality Rates at the County level in the United States considering Socio-Demographics, Health Indicators, Mobility Trends and Health Care Infrastructure Attributes", @@ -1290447,6 +1289039,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.08.04.20163782", + "rel_title": "Fitting models to the COVID-19 outbreak and estimating R", + "rel_date": "2020-08-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.08.04.20163782", + "rel_abs": "The COVID-19 pandemic has brought to the fore the need for policy makers to receive timely and ongoing scientific guidance in response to this recently emerged human infectious disease. Fitting mathematical models of infectious disease transmission to the available epidemiological data provides a key statistical tool for understanding the many quantities of interest that are not explicit in the underlying epidemiological data streams. Of these, the effective reproduction number, R, has taken on special significance in terms of the general understanding of whether the epidemic is under control (R < 1). Unfortunately, none of the epidemiological data streams are designed for modelling, hence assimilating information from multiple (often changing) sources of data is a major challenge that is particularly stark in novel disease outbreaks.\n\nHere, focusing on the dynamics of the first-wave (March-June 2020), we present in some detail the inference scheme employed for calibrating the Warwick COVID-19 model to the available public health data streams, which span hospitalisations, critical care occupancy, mortality and serological testing. We then perform computational simulations, making use of the acquired parameter posterior distributions, to assess how the accuracy of short-term predictions varied over the timecourse of the outbreak. To conclude, we compare how refinements to data streams and model structure impact estimates of epidemiological measures, including the estimated growth rate and daily incidence.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Matt J Keeling", + "author_inst": "University of Warwick" + }, + { + "author_name": "Louise Dyson", + "author_inst": "University of Warwick" + }, + { + "author_name": "Glen Guyver-Fletcher", + "author_inst": "University of Warwick" + }, + { + "author_name": "Alex Holmes", + "author_inst": "University of Warwick" + }, + { + "author_name": "Malcolm G Semple", + "author_inst": "University of Liverpool" + }, + { + "author_name": "- ISARIC4C Investigators", + "author_inst": "" + }, + { + "author_name": "Michael J Tildesley", + "author_inst": "University of Warwick" + }, + { + "author_name": "Edward M Hill", + "author_inst": "University of Warwick" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.08.03.20167791", "rel_title": "SalivaDirect: Simple and sensitive molecular diagnostic test for SARS-CoV-2 surveillance", @@ -1291150,41 +1289789,6 @@ "type": "confirmatory results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.08.04.236653", - "rel_title": "Pathogenetic Perspective of Missense Mutations of ORF3a Protein of SARS-CoV2", - "rel_date": "2020-08-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.08.04.236653", - "rel_abs": "One of the most important proteins for COVID-19 pathogenesis in SARS-CoV2 is the ORF3a protein which is the largest accessory protein among others accessory proteins coded by coronavirus genome. The major roles of the protein include virulence, infectivity, ion channel activity, morphogenesis and virus release. The coronavirus, SARS-CoV2 is continuously evolving naturally and thereby the encoded proteins are also mutating rapidly. Therefore, critical study of mutations in ORF3a is certainty important from the pathogenetic perspective. Here, a sum of 175 various non-synonymous mutations in the ORF3a protein of SARS-CoV2 are identified and their corresponding effects in structural stability and functions of the protein ORF3a are studied. Broadly three different classes of mutations, such as neutral, disease and mixed (neutral and disease) type mutations were observed. Consecutive mutations in some ORF3a proteins are established based on timeline of detection of mutations. Considering the amino acid compositions over the ORF3a primary protein sequences, twenty clusters are detected based on K-means clustering method. Our findings on 175 novel mutations of ORF3a proteins will extend our knowledge of ORF3a, a vital accessory protein in SARS-CoV2, which would assist to enlighten on the pathogenicity of this life-threatening COVID-19.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Sk. Sarif Hassan", - "author_inst": "Pingla Thana Mahavidyalaya" - }, - { - "author_name": "Diksha Attrish", - "author_inst": "Dr. B. R. Ambedkar Centre For Biomedical Research (ACBR), University of Delhi (North Campus), Delhi 110007, India" - }, - { - "author_name": "Shinjini Ghosh", - "author_inst": "Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, Kolkata 700009, West Bengal, India" - }, - { - "author_name": "Pabitra Pal Choudhury", - "author_inst": "Applied Statistics Unit, Indian Statistical Institute, Kolkata 700108, India" - }, - { - "author_name": "Bidyut Roy", - "author_inst": "Human Genetics Unit, Indian Statistical Institute, Kolkata 700108, West Bengal, India" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.08.02.20159418", "rel_title": "Overcoming Reporting Delays Is Critical to Timely Epidemic Monitoring: The Case of COVID-19 in New York City", @@ -1292672,6 +1291276,45 @@ "type": "new results", "category": "genetics" }, + { + "rel_doi": "10.1101/2020.07.30.20158790", + "rel_title": "Real-Time Monitoring of COVID-19 in Scotland", + "rel_date": "2020-08-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.30.20158790", + "rel_abs": "To manage the public health risk posed by COVID-19 and assess the impact of interventions, policy makers must be able to closely monitor the epidemics trajectory. Here we present a simple methodology based on basic surveillance metrics for monitoring the spread of COVID-19 and its burden on health services in Scotland. We illustrate how this has been used throughout the epidemic in Scotland and explore the underlying biases that have affected its interpretation.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Giles David Calder-Gerver", + "author_inst": "The Usher Institute, College of Medicine and Veterinary Medicine, The University of Edinburgh" + }, + { + "author_name": "Stella Mazeri", + "author_inst": "The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh" + }, + { + "author_name": "Samuel Haynes", + "author_inst": "The Institute for Cell Biology, School of Biological Sciences, The University of Edinburgh" + }, + { + "author_name": "Camille Anna Simonet", + "author_inst": "The Institute of Evolutionary Biology, School of Biological Sciences, The University of Edinburgh" + }, + { + "author_name": "Mark EJ Woolhouse", + "author_inst": "The Usher Institute, College of Medicine and Veterinary Medicine, The University of Edinburgh" + }, + { + "author_name": "Helen K Brown", + "author_inst": "The Roslin Institute, Royal (Dick) School of Veterinary Studies, The University of Edinburgh" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.30.20165399", "rel_title": "Covid-19 mortality rates in Northamptonshire UK: initial sub-regional comparisons and provisional SEIR model of disease spread", @@ -1293380,37 +1292023,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.30.20114959", - "rel_title": "Impact of tocilizumab administration on mortality in severe COVID-19", - "rel_date": "2020-08-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.30.20114959", - "rel_abs": "PurposeThe novel coronavirus disease 2019 (COVID-19) worldwide pandemic has placed a significant burden on hospitals and healthcare providers. The immune response to this disease is thought to lead to a cytokine storm, which contributes to the severity of illness. There is an urgent need to confirm whether the use of tocilizumab provides a benefit in individuals with COVID-19.\n\nMethodsA single-center propensity-score matched cohort study, including all consecutive COVID-19 patients, admitted to the medical center who were either discharged from the medical center or expired between March 1, 2020, and May 5, 2020, was performed. Patients were stratified according to the receipt of tocilizumab for cytokine storm and matched to controls using propensity scores. The primary outcome was in-hospital mortality.\n\nResultsA total of 132 patients were included in the matched dataset (tocilizumab=66; no tocilizumab=66). Approximately 73% of the patients were male. Hypertension (55%), diabetes mellitus (31%), and chronic pulmonary disease (15%) were the most common comorbidities present. There were 18 deaths (27.3%) in the tocilizumab group and 18 deaths (27.3%) in the no tocilizumab group (odds ratio, 1.0; 95% confidence interval, 0.465 - 2.151; p=1.00). Advanced age, history of myocardial infarction, dementia, chronic pulmonary disease, heart failure, and malignancy were significantly more common in patients who died.\n\nConclusionThe current analysis does not support the use of tocilizumab for the management of cytokine storm in patients with COVID-19. Use of this therapeutic agent should be limited to the context of a clinical trial until more evidence is available.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Andrew Tsai", - "author_inst": "Robert Wood Johnson University Hospital Somerset" - }, - { - "author_name": "Oumou Diawara", - "author_inst": "Robert Wood Johnson University Hospital Somerset" - }, - { - "author_name": "Ronald G Nahass", - "author_inst": "ID Care" - }, - { - "author_name": "Luigi Brunetti", - "author_inst": "Ernest Mario School of Pharmacy" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.08.01.232199", "rel_title": "Rapid Inactivation of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by Tungsten Trioxide-Based (WO3) Photocatalysis", @@ -1294626,6 +1293238,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.29.20164814", + "rel_title": "Whether the Weather Will Help Us Weather the COVID-19 Pandemic: Using Machine Learning to Measure Twitter Users' Perceptions", + "rel_date": "2020-08-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.29.20164814", + "rel_abs": "ObjectiveThe potential ability for weather to affect SARS-CoV-2 transmission has been an area of controversial discussion during the COVID-19 pandemic. Individuals perceptions of the impact of weather can inform their adherence to public health guidelines; however, there is no measure of their perceptions. We quantified Twitter users perceptions of the effect of weather and analyzed how they evolved with respect to real-world events and time.\n\nMaterials and MethodsWe collected 166,005 tweets posted between January 23 and June 22, 2020 and employed machine learning/natural language processing techniques to filter for relevant tweets, classify them by the type of effect they claimed, and identify topics of discussion.\n\nResultsWe identified 28,555 relevant tweets and estimate that 40.4% indicate uncertainty about weathers impact, 33.5% indicate no effect, and 26.1% indicate some effect. We tracked changes in these proportions over time. Topic modeling revealed major latent areas of discussion.\n\nDiscussionThere is no consensus among the public for weathers potential impact. Earlier months were characterized by tweets that were uncertain of weathers effect or claimed no effect; later, the portion of tweets claiming some effect of weather increased. Tweets claiming no effect of weather comprised the largest class by June. Major topics of discussion included comparisons to influenzas seasonality, President Trumps comments on weathers effect, and social distancing.\n\nConclusionThere is a major gap between scientific evidence and public opinion of weathers impacts on COVID-19. We provide evidence of publics misconceptions and topics of discussion, which can inform public health communications.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Marichi Gupta", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Adity Bansal", + "author_inst": "Indian Institute of Technology Delhi" + }, + { + "author_name": "Bhav Jain", + "author_inst": "MIT" + }, + { + "author_name": "Jillian Rochelle", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Atharv Oak", + "author_inst": "MIT" + }, + { + "author_name": "Mohammad S. Jalali", + "author_inst": "Harvard Medical School" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.30.20164855", "rel_title": "SABCoM: A Spatial Agent-Based Covid-19 Model", @@ -1295110,53 +1293761,6 @@ "type": "new results", "category": "bioengineering" }, - { - "rel_doi": "10.1101/2020.07.31.190454", - "rel_title": "Unsupervised machine learning reveals key immune cell subsets in COVID-19, rhinovirus infection, and cancer therapy", - "rel_date": "2020-08-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.31.190454", - "rel_abs": "For an emerging disease like COVID-19, systems immunology tools may quickly identify and quantitatively characterize cells associated with disease progression or clinical response. With repeated sampling, immune monitoring creates a real-time portrait of the cells reacting to a novel virus before disease specific knowledge and tools are established. However, single cell analysis tools can struggle to reveal rare cells that are under 0.1% of the population. Here, the machine learning workflow Tracking Responders Expanding (T-REX) was created to identify changes in both very rare and common cells in diverse human immune monitoring settings. T-REX identified cells that were highly similar in phenotype and localized to hotspots of significant change during rhinovirus and SARS-CoV-2 infections. Specialized reagents used to detect the rhinovirus-specific CD4+ cells, MHCII tetramers, were not used during unsupervised analysis and instead left out to serve as a test of whether T-REX identified biologically significant cells. In the rhinovirus challenge study, T-REX identified virus-specific CD4+ T cells based on these cells being a distinct phenotype that expanded by [≥]95% following infection. T-REX successfully identified hotspots containing virus-specific T cells using pairs of samples comparing Day 7 of infection to samples taken either prior to infection (Day 0) or after clearing the infection (Day 28). Mapping pairwise comparisons in samples according to both the direction and degree of change provided a framework to compare systems level immune changes during infectious disease or therapy response. This revealed that the magnitude and direction of systemic immune change in some COVID-19 patients was comparable to that of blast crisis acute myeloid leukemia patients undergoing induction chemotherapy and characterized the identity of the immune cells that changed the most. Other COVID-19 patients instead matched an immune trajectory like that of individuals with rhinovirus infection or melanoma patients receiving checkpoint inhibitor therapy. T-REX analysis of paired blood samples provides an approach to rapidly identify and characterize mechanistically significant cells and to place emerging diseases into a systems immunology context.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Sierra M. Barone", - "author_inst": "Vanderbilt University" - }, - { - "author_name": "Alberta G.A. Paul", - "author_inst": "University of Virginia School of Medicine" - }, - { - "author_name": "Lyndsey M. Muehling", - "author_inst": "University of Virginia School of Medicine" - }, - { - "author_name": "Joanne A. Lannigan", - "author_inst": "University of Virginia School of Medicine" - }, - { - "author_name": "William W. Kwok", - "author_inst": "Benaroya Research Institute at Virginia Mason" - }, - { - "author_name": "Ronald B. Turner", - "author_inst": "University of Virginia School of Medicine" - }, - { - "author_name": "Judith A. Woodfolk", - "author_inst": "University of Virginia School of Medicine" - }, - { - "author_name": "Jonathan M. Irish", - "author_inst": "Vanderbilt University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "systems biology" - }, { "rel_doi": "10.1101/2020.07.30.230102", "rel_title": "Hybrid capture-based sequencing enables unbiased recovery of SAR-CoV-2 genomes from fecal samples and characterization of the dynamics of intra-host variants", @@ -1296328,6 +1294932,89 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.07.30.228460", + "rel_title": "Phylogenomic analysis of SARS-CoV-2 genomes from western India reveals unique linked mutations", + "rel_date": "2020-07-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.30.228460", + "rel_abs": "India has become the third worst-hit nation by the COVID-19 pandemic caused by the SARS-CoV-2 virus. Here, we investigated the molecular, phylogenomic, and evolutionary dynamics of SARS-CoV-2 in western India, the most affected region of the country. A total of 90 genomes were sequenced. Four nucleotide variants, namely C241T, C3037T, C14408T (Pro4715Leu), and A23403G (Asp614Gly), located at 5UTR, Orf1a, Orf1b, and Spike protein regions of the genome, respectively, were predominant and ubiquitous (90%). Phylogenetic analysis of the genomes revealed four distinct clusters, formed owing to different variants. The major cluster (cluster 4) is distinguished by mutations C313T, C5700A, G28881A are unique patterns and observed in 45% of samples. We thus report a newly emerging pattern of linked mutations. The predominance of these linked mutations suggests that they are likely a part of the viral fitness landscape. A novel and distinct pattern of mutations in the viral strains of each of the districts was observed. The Satara district viral strains showed mutations primarily at the 3' end of the genome, while Nashik district viral strains displayed mutations at the 5' end of the genome. Characterization of Pune strains showed that a novel variant has overtaken the other strains. Examination of the frequency of three mutations i.e., C313T, C5700A, G28881A in symptomatic versus asymptomatic patients indicated an increased occurrence in symptomatic cases, which is more prominent in females. The age-wise specific pattern of mutation is observed. Mutations C18877T, G20326A, G24794T, G25563T, G26152T, and C26735T are found in more than 30% study samples in the age group of 10-25. Intriguingly, these mutations are not detected in the higher age range 61-80. These findings portray the prevalence of unique linked mutations in SARS-CoV-2 in western India and their prevalence in symptomatic patients.\n\nImportanceElucidation of the SARS-CoV-2 mutational landscape within a specific geographical location, and its relationship with age and symptoms, is essential to understand its local transmission dynamics and control. Here we present the first comprehensive study on genome and mutation pattern analysis of SARS-CoV-2 from the western part of India, the worst affected region by the pandemic. Our analysis revealed three unique linked mutations, which are prevalent in most of the sequences studied. These may serve as a molecular marker to track the spread of this viral variant to different places.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Dhiraj Paul", + "author_inst": "National Centre for Cell Science Pune" + }, + { + "author_name": "Kunal Jani", + "author_inst": "National Centre for Cell Science Pune" + }, + { + "author_name": "Janesh Kumar", + "author_inst": "National Centre for Cell Science Pune" + }, + { + "author_name": "Radha Chauhan", + "author_inst": "National Centre for Cell Science Pune" + }, + { + "author_name": "Vasudevan Seshadri", + "author_inst": "National Centre for Cell Science Pune" + }, + { + "author_name": "Girdhari Lal", + "author_inst": "National Centre for Cell Science Pune" + }, + { + "author_name": "Rajesh Karyakarte", + "author_inst": "B. J. Government Medical College, Pune" + }, + { + "author_name": "Suvarna Joshi", + "author_inst": "B. J. Government Medical College, Pune" + }, + { + "author_name": "Murlidhar Tambe", + "author_inst": "B. J. Government Medical College, Pune" + }, + { + "author_name": "Sourav Sen", + "author_inst": "Armed Forces Medical College Pune" + }, + { + "author_name": "Santosh Karade", + "author_inst": "Armed Forces Medical College Pune" + }, + { + "author_name": "Kavita Bala Anand", + "author_inst": "Armed Forces Medical College Pune" + }, + { + "author_name": "Shelinder Pal Singh Shergill", + "author_inst": "Armed Forces Medical College Pune" + }, + { + "author_name": "Rajiv Mohan Gupta", + "author_inst": "Armed Forces Medical College Pune" + }, + { + "author_name": "Manoj Kumar Bhat", + "author_inst": "National Centre for Cell Science Pune" + }, + { + "author_name": "Arvind Sahu", + "author_inst": "National Centre for Cell Science Pune" + }, + { + "author_name": "Yogesh S Shouche", + "author_inst": "National Centre for Cell Science Pune" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.07.30.229120", "rel_title": "A Newcastle disease virus (NDV) expressing membrane-anchored spike as a cost-effective inactivated SARS-CoV-2 vaccine", @@ -1296752,53 +1295439,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.07.31.230730", - "rel_title": "Biomechanical Characterization of SARS-CoV-2 Spike RBD and Human ACE2 Protein-Protein Interaction", - "rel_date": "2020-07-31", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.31.230730", - "rel_abs": "The current COVID-19 pandemic has led to a devastating impact across the world. SARS-CoV-2 (the virus causing COVID-19) is known to use receptor-binding domain (RBD) at viral surface spike (S) protein to interact with the angiotensin-converting enzyme 2 (ACE2) receptor expressed on many human cell types. The RBD-ACE2 interaction is a crucial step to mediate the host cell entry of SARS-CoV-2. Recent studies indicate that the ACE2 interaction with the SARS-CoV-2 S protein has higher affinity than its binding with the structurally identical S protein of SARS-CoV-1, the virus causing the 2002-2004 SARS outbreak. However, the biophysical mechanism behind such binding affinity difference is unclear. This study utilizes a combined single-molecule force spectroscopy and steered molecular dynamics (SMD) simulation approach to quantify the specific interactions between CoV-2 or CoV-1 RBD and ACE2. Depending on the loading rates, the unbinding forces between CoV-2 RBD and ACE2 range from 70 to 110 pN, and are 30-50% higher than those of CoV-1 RBD and ACE2 under similar loading rates. SMD results indicate that CoV-2 RBD interacts with the N-linked glycan on Asn90 of ACE2. This interaction is mostly absent in the CoV-1 RBD-ACE2 complex. During the SMD simulations, the extra RBD-N-glycan interaction contributes to a greater force and prolonged interaction lifetime. The observation is confirmed by our experimental force spectroscopy study. After the removal of N-linked glycans on ACE2, its mechanical binding strength with CoV-2 RBD decreases to a similar level of the CoV-1 RBD-ACE2 interaction. Together, the study uncovers the mechanism behind the difference in ACE2 binding between SARS-CoV-2 and SARS-CoV-1, and could aid in the development of new strategies to block SARS-CoV-2 entry.\n\nSTATEMENT OF SIGNIFICANCEThis study utilizes a combined single-molecule force spectroscopy and steered molecular dynamics simulation approach to quantify the specific interactions between SARS-CoV-2 or SARS-CoV-1 receptor-binding domain and human ACE2. The study reveals the mechanism behind the difference in ACE2 binding between SARS-CoV-2 and SARS-CoV-1, and could aid in the development of new strategies to block SARS-CoV-2 entry.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Wenpeng Cao", - "author_inst": "Lehigh University" - }, - { - "author_name": "Chuqiao Dong", - "author_inst": "Lehigh University" - }, - { - "author_name": "Seonghan Kim", - "author_inst": "Lehigh University" - }, - { - "author_name": "Decheng Hou", - "author_inst": "Lehigh University" - }, - { - "author_name": "Wanbo Tai", - "author_inst": "New York Blood Center" - }, - { - "author_name": "Lanying Du", - "author_inst": "New York Blood Center" - }, - { - "author_name": "Wonpil Im", - "author_inst": "Lehigh University" - }, - { - "author_name": "X. Frank Zhang", - "author_inst": "Lehigh University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.07.31.230870", "rel_title": "A novel isoform of ACE2 is expressed in human nasal and bronchial respiratory epithelia and is upregulated in response to RNA respiratory virus infection", @@ -1297954,6 +1296594,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.28.20154153", + "rel_title": "Quality controlled SARS-CoV-2 duplex procedure to reduce time and scarce molecular biology diagnosis reagents", + "rel_date": "2020-07-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.28.20154153", + "rel_abs": "The aim of this study was to provide validated procedures allowing to detect the SARS-CoV-2 and an internal control in a unique one-step duplex RT-qPCR. Two internal controls were tested, targeting either the Schmallenberg virus RNA provided by the NARILIS laboratory (University of Namur) with a HEX-labelled probe or a Diagenode Diagnostics internal control with a Cy5-labelled probe. Our results showed that Ct values of the RT-qPCR duplex assay were even smaller in the optimized working conditions, allowing to use the optimized qPCR conditions in routine diagnosis.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Anaelle Collin", + "author_inst": "IFAC VIVALIA" + }, + { + "author_name": "Carole Chaboteaux", + "author_inst": "IFAC VIVALIA" + }, + { + "author_name": "Veronique Fontaine", + "author_inst": "ULB" + }, + { + "author_name": "Philippe Lefevre", + "author_inst": "IFAC VIVALIA" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.20.20156018", "rel_title": "Transmission of SARS-CoV-2 following exposure in school settings: experience from two Helsinki area exposure incidents.", @@ -1298426,45 +1297097,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.28.20163980", - "rel_title": "Stochastic modelling of the effects of human-mobility restriction and viral infection characteristics on the spread of COVID-19", - "rel_date": "2020-07-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.28.20163980", - "rel_abs": "After several weeks of \"lockdown\" as the sole answer to the COVID-19 pandemic, many countries are restarting their economic and social activities. However, balancing the re-opening of society against the implementation of non-pharmaceutical measures needed for minimizing interpersonal contacts requires a careful assessment of the risks of infection as a function of the confinement relaxation strategies. Here, we present a stochastic coarse grained model that examines this problem. In our model, people are allowed to move between discrete positions on a one-dimensional grid with viral infection possible when two people are collocated at the same site. Our model features three sets of adjustable parameters, which characterize (i) viral transmission, (ii) viral detection, and (iii) degree of personal mobility, and as such, it is able to provide a qualitative assessment of the potential for second-wave infection outbreaks based on the timing, extent, and pattern of the lockdown relaxation strategy. In line with general expectations, our model predicts that a full lockdown yields the best results, namely, the lowest number of total infections. A less anticipated result was that when personal mobility is increased beyond a critical level, the risk of infection rapidly reaches a constant value, which depends solely on the population density. Furthermore, according to our model, confinement alone is not effective if it is not accompanied by a detection capacity (coupled with quarantine) that surpasses 40% of the patients during their symptomatic phase. The results of our simulation also showed that keeping the virus transmission probability to less than 0.4, which can be achieved in real life by respecting social distancing or wearing masks, is as effective as imposing a mild lockdown. Finally, we note that detection and quarantine of pre-symptomatic patients, even with a probability as low as 0.2, would reduce the final numbers of infections by a factor of ten or more.\n\nAvailabilityhttp://domserv.lab.tuat.ac.jp/COVID19.html (under preparation)", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Shiho Ando", - "author_inst": "Tokyo University of Agriculture and Technology" - }, - { - "author_name": "Yuki Matsuzawa", - "author_inst": "Tokyo University of Agriculture and Technology" - }, - { - "author_name": "Hiromichi Tsurui", - "author_inst": "Juntendo University" - }, - { - "author_name": "Tetsuya Mizutani", - "author_inst": "Tokyo Noko Daigaku" - }, - { - "author_name": "Damien Hall", - "author_inst": "Nagoya Institute of Technology" - }, - { - "author_name": "Yutaka Kuroda", - "author_inst": "Tokyo University of Agriculture and Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.29.20164392", "rel_title": "Estimating missing deaths in Delhi's COVID-19 data", @@ -1299668,6 +1298300,53 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.07.30.228221", + "rel_title": "Immuno-informatics Design of a Multimeric Epitope Peptide Based Vaccine Targeting SARS-CoV-2 Spike Glycoprotein", + "rel_date": "2020-07-30", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.30.228221", + "rel_abs": "Developing an efficacious vaccine to SARS-CoV-2 infection is critical to stem COVID-19 fatalities and providing the global community with immune protection. We have used a bioinformatic approach to aid in the design of an epitope peptide-based vaccine against the spike protein of the virus. Five antigenic B cell epitopes with viable antigenicity and a total of 27 discontinuous B cell epitopes were mapped out structurally in the spike protein for antibody recognition. We identified eight CD8+ T cell 9-mers along with 12 CD4+ T cell 14-15-mer as promising candidate epitopes putatively restricted by a large number of MHC-I and II alleles respectively. We used this information to construct an in silico chimeric peptide vaccine whose translational rate was highly expressed when cloned in pET28a (+) vector. The vaccine construct was predicted to elicit high antigenicity and cell-mediated immunity when given as a homologous prime-boost, with triggering of toll-like receptor 5 by the adjuvant linker. The vaccine was characterized by an increase in IgM and IgG and an array of Th1 and Th2 cytokines. Upon in silico challenge with SARS-CoV-2, there was a decrease in antigen levels using our immune simulations. We therefore propose that potential vaccine designs consider this approach.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Onyeka S. Chukwudozie", + "author_inst": "University of Lagos" + }, + { + "author_name": "Clive M. Gray", + "author_inst": "University of Capetown" + }, + { + "author_name": "Tawakalt A. Fagbayi", + "author_inst": "University of Lagos" + }, + { + "author_name": "Rebecca C. Chukwuanukwu", + "author_inst": "Nnamdi Azikiwe University, Nnewi Campus, Nigeria" + }, + { + "author_name": "Victor O. Oyebanji", + "author_inst": "University of Ibadan" + }, + { + "author_name": "Taiwo T. Bankole", + "author_inst": "University of Lagos" + }, + { + "author_name": "Richard A Adewole", + "author_inst": "University of Lagos" + }, + { + "author_name": "Daniel M Eze", + "author_inst": "University of Ibadan" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.07.30.228478", "rel_title": "Substrate specificity of SARS-CoV-2 nsp10-nsp16 methyltransferase", @@ -1300148,29 +1298827,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2020.07.23.20160887", - "rel_title": "Divide in Vaccine Belief in COVID-19 Conversations: Implications for Immunization Plans", - "rel_date": "2020-07-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.23.20160887", - "rel_abs": "The development of a viable COVID-19 vaccine is a work in progress, but the success of the immunization campaign will depend upon public acceptance. In this paper, we classify Twitter users in COVID-19 discussion into vaccine refusers (anti-vaxxers) and vaccine adherers (vaxxers) communities. We study the divide between anti-vaxxers and vaxxers in the context of whom they follow. More specifically, we look at followership of 1) the U.S. Congress members, 2) four major religions (Christianity, Hinduism, Judaism and Islam), 3) accounts related to the healthcare community, and 4) news media accounts. Our results indicate that there is a partisan divide between vaxxers and anti-vaxxers. We find a religious community with a higher than expected fraction of anti-vaxxers. Further, we find that the variance of vaccine belief within the news media accounts operated by Russian and Iranian governments is higher compared to news media accounts operated by other governments. Finally, we provide messaging and policy implications to inform the COVID-19 vaccine and future vaccination plans.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Aman Tyagi", - "author_inst": "Carnegie Mellon University" - }, - { - "author_name": "Kathleen M. Carley", - "author_inst": "Carnegie Mellon University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.07.23.20160796", "rel_title": "PLEXIT - Therapeutic plasma exchange (TPE) for Covid-19 cytokine release storm (CRS), a retrospective propensity matched control study", @@ -1301322,6 +1299978,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.07.27.20162677", + "rel_title": "An Analysis of Territorial Patterns in COVID-19 Mortality in France, Spain, Italy and the UK", + "rel_date": "2020-07-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.27.20162677", + "rel_abs": "This paper provides an overview of territorial patterns of COVID-19 deaths in four European countries severely affected by the pandemic, Spain, France, Italy, and the United Kingdom. The analysis focuses on cumulated COVID-19 mortality at the sub-regional level, following the territorial subdivision of countries adopted by the European Union. The paper builds upon a dataset with highly granular information on COVID- 19 deaths assembled from various sources. The analysis shows remarkable differences in territorial patterns of COVID-19 mortality, both within and across the four countries reviewed. Results somewhat differ depending on the aspect considered (concentration of deaths or mortality rates) but, in general, Italy, France and Spain display significant territorial disparities, with selected sub-regions being disproportionately affected by the pandemic. Instead, the picture is more uniform in the UK, with comparatively lower differences across the various sub- regions. These findings suggest that analyses of COVID-19 mortality at the national level (and, sometimes, even at the regional level) may conceal major differences and therefore be of limited use, both analytically and from an operational viewpoint.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Roberto Zavatta", + "author_inst": "Economisti Associati" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.07.27.20161430", "rel_title": "Transport effect of COVID-19 pandemic in France", @@ -1301738,49 +1300413,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2020.07.27.20162057", - "rel_title": "Predicting PPE use, post-traumatic stress, and physical symptoms during the early weeks of COVID-19 lockdowns in the USA", - "rel_date": "2020-07-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.27.20162057", - "rel_abs": "The COVID-19 pandemic combined with inconsistent governmental and public health recommendations, media communications emphasizing threat, and widespread lockdowns created a complex psychological environment for Americans. In this study, 450 MTurk workers completed measures of (a) risk for COVID-19, (b) perceived vulnerability to disease, (c) intolerance of uncertainty, (d) mindfulness, (e) COVID-19 preventive health behaviors, (f) post-Trauma symptoms, and (g) stress related physical symptoms. The surveys were completed between April 9, 2020 and April 18, 2020 which is a period that corresponded to the first 2-3 weeks of lockdown for most participants.\n\nA substantial number of participants reported a reduction employment status and 69% were in self-isolation. The participants reported a high degree of perceived vulnerability with 68% indicating they felt there was a 50/50 chance or greater they would contract COVID-19. Mask wearing was variable: 16% \"not at all,\" 20% \"some of the time,\" 42% \"a good part of the time,\" and 26% \"most of the time.\" Using clinical cutoff on the post-trauma scale, 70% of the sample would be considered to have symptoms consistent with PTSD. The mean level of physical symptoms was significantly (p < .001) and substantially higher (d = 1.46) than norms.\n\nPPE use was positively associated with level of education and mindfulness nonreactivity and negatively associated with age, having a current medical condition, and mindfulness nonjudgment. Post trauma and physical health symptoms were strongly predicted by susceptibility variables and intolerance of uncertainty.\n\nHighlightsO_LICOVID-19 created a complex psychological environment for Americans due to threat exposure combined with contradictory communications from government and media.\nC_LIO_LIIn a survey of 450 Americans, 68% reported that there was a 50/50 chance of greater they would contract COVID-19 and 70% of participants reported symptoms that met criteria for PTSD.\nC_LIO_LIMask wearing was variable with only 26% reporting use \"most of the time.\"\nC_LIO_LIParticipants who reported: older age, having one or mode medical conditions, less educational attainment, and less judgmental attitudes about their own thinking reported lower PPE use.\nC_LIO_LIIntolerance of uncertainty and perceived susceptibility were associated with higher PTSD symptoms.\nC_LIO_LIMindfulness awareness and being judgmental attitudes about thinking were associated with lower PTSD symptoms.\nC_LI", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "William H OBrien", - "author_inst": "Bowling Green State University" - }, - { - "author_name": "Shan Wang", - "author_inst": "Duke Kunshan University" - }, - { - "author_name": "Aniko Viktoria Varga", - "author_inst": "Bowling Green State University" - }, - { - "author_name": "Huanzhen Xu", - "author_inst": "Bowling Green State University" - }, - { - "author_name": "Tracy E Sims", - "author_inst": "Bowling Green State University" - }, - { - "author_name": "Kristin A Horan", - "author_inst": "University of Central Florida" - }, - { - "author_name": "Chung Xiann Lim", - "author_inst": "Bowling Green State University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.07.27.20156836", "rel_title": "Modeling the initial phase of SARS-CoV-2 deposition in the respiratory tract mimicked by the 11C radionuclide", @@ -1303004,6 +1301636,157 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.07.28.20163022", + "rel_title": "Eleven Routine Clinical Features Predict COVID-19 Severity", + "rel_date": "2020-07-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.28.20163022", + "rel_abs": "Severity prediction of COVID-19 remains one of the major clinical challenges for the ongoing pandemic. Here, we have recruited a 144 COVID-19 patient cohort consisting of training, validation, and internal test sets, longitudinally recorded 124 routine clinical and laboratory parameters, and built a machine learning model to predict the disease progression based on measurements from the first 12 days since the disease onset when no patient became severe. A panel of 11 routine clinical factors, including oxygenation index, basophil counts, aspartate aminotransferase, gender, magnesium, gamma glutamyl transpeptidase, platelet counts, activated partial thromboplastin time, oxygen saturation, body temperature and days after symptom onset, constructed a classifier for COVID-19 severity prediction, achieving accuracy of over 94%. Validation of the model in an independent cohort containing 25 patients achieved accuracy of 80%. The overall sensitivity, specificity, PPV and NPV were 0.70, 0.99, 0.93 and 0.93, respectively. Our model captured predictive dynamics of LDH and CK while their levels were in the normal range. This study presents a practical model for timely severity prediction and surveillance for COVID-19, which is freely available at webserver https://guomics.shinyapps.io/covidAI/.", + "rel_num_authors": 34, + "rel_authors": [ + { + "author_name": "Kai Zhou", + "author_inst": "Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, China" + }, + { + "author_name": "Yaoting Sun", + "author_inst": "Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China; Institute of Basic Medical Sciences, W" + }, + { + "author_name": "Lu Li", + "author_inst": "Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China; Institute of Basic Medical Sciences, W" + }, + { + "author_name": "Zelin Zang", + "author_inst": "School of Engineering, Westlake University, Hangzhou, China" + }, + { + "author_name": "Jing Wang", + "author_inst": "Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, China" + }, + { + "author_name": "Jun Li", + "author_inst": "Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, China" + }, + { + "author_name": "Junbo Liang", + "author_inst": "Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, China" + }, + { + "author_name": "Fangfei Zhang", + "author_inst": "Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China; Institute of Basic Medical Sciences, W" + }, + { + "author_name": "Qiushi Zhang", + "author_inst": "Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China; Institute of Basic Medical Sciences, W" + }, + { + "author_name": "Weigang Ge", + "author_inst": "Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China; Institute of Basic Medical Sciences, W" + }, + { + "author_name": "Hao Chen", + "author_inst": "Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China; Institute of Basic Medical Sciences, W" + }, + { + "author_name": "Xindong Sun", + "author_inst": "Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China; Institute of Basic Medical Sciences, W" + }, + { + "author_name": "Liang Yue", + "author_inst": "Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China; Institute of Basic Medical Sciences, W" + }, + { + "author_name": "Xiaomai Wu", + "author_inst": "Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, China" + }, + { + "author_name": "Bo Shen", + "author_inst": "Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, China" + }, + { + "author_name": "Jiaqin Xu", + "author_inst": "Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, China" + }, + { + "author_name": "Hongguo Zhu", + "author_inst": "Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, China" + }, + { + "author_name": "Shiyong Chen", + "author_inst": "Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, China" + }, + { + "author_name": "Hai Yang", + "author_inst": "Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, China" + }, + { + "author_name": "Shigao Huang", + "author_inst": "Institute of Translational Medicine, Faculty of Health Sciences, University of Macau 999078, Macau SAR, China." + }, + { + "author_name": "Minfei Peng", + "author_inst": "Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, China" + }, + { + "author_name": "Dongqing Lv", + "author_inst": "Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, China" + }, + { + "author_name": "Chao Zhang", + "author_inst": "Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, China" + }, + { + "author_name": "Haihong Zhao", + "author_inst": "Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, China" + }, + { + "author_name": "Luxiao Hong", + "author_inst": "Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, China" + }, + { + "author_name": "Zhehan Zhou", + "author_inst": "Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, China" + }, + { + "author_name": "Haixiao Chen", + "author_inst": "Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, China" + }, + { + "author_name": "Xuejun Dong", + "author_inst": "Shaoxing People's Hospital (Shaoxing Hospital, Zhejiang University School of Medicine), Shaoxing, Zhejiang, 312000" + }, + { + "author_name": "Chunyu Tu", + "author_inst": "Shaoxing People's Hospital (Shaoxing Hospital, Zhejiang University School of Medicine), Shaoxing, Zhejiang, 312000" + }, + { + "author_name": "Minghui Li", + "author_inst": "Shaoxing People's Hospital (Shaoxing Hospital, Zhejiang University School of Medicine), Shaoxing, Zhejiang, 312000" + }, + { + "author_name": "Yi Zhu", + "author_inst": "Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China; Institute of Basic Medical Sciences, W" + }, + { + "author_name": "Baofu Chen", + "author_inst": "Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, China" + }, + { + "author_name": "Stan Z. Li", + "author_inst": "School of Engineer, Westlake University, Hangzhou, China" + }, + { + "author_name": "Tiannan Guo", + "author_inst": "Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China; Institute of Basic Medical Sciences, W" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.28.20162735", "rel_title": "Age-severity matched cytokine profiling reveals specific signatures in Covid-19 patients", @@ -1303696,33 +1302479,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.07.29.227389", - "rel_title": "On the molecular mechanism of SARS-CoV-2 retention in the upper respiratory tract", - "rel_date": "2020-07-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.29.227389", - "rel_abs": "Cell surface receptor engagement is a critical aspect of viral infection. At low pH, binding of SARS-CoV and its ACE2 receptor has a tight interaction that catalyzes the fusion of the spike and endosomal membranes followed by genome release. Largely overlooked has been the role of neutral pH in the respiratory tract, where we find that SARS-CoV stabilizes a transition state that enhances the off-rate from its receptor. An alternative pH-switch is found in CoV-2-like coronaviruses of tropical pangolins, but with a reversed phenotype where the tight interaction with ACE2 is at neutral pH. We show that a single point mutation in pangolin-CoV, unique to CoV-2, that deletes the last His residue in their receptor binding domain perpetuates this tight interaction independent of pH. This tight bond, not present in previous respiratory syndromes, implies that CoV-2 stays bound to the highly expressed ACE2 receptors in the nasal cavity about 100 times longer than CoV. This finding supports the unfamiliar pathology of CoV-2, observed virus retention in upper respiratory tract1, longer incubation times and extended periods of shedding. Implications to combat pandemics that, like SARS-CoV-2, export evolutionarily successful strains via higher transmission rates due to retention in nasal epithelium and their evolutionary origin are discussed.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Kristina A Paris", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Ulises Santiago", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Carlos J. Camacho", - "author_inst": "University of Pittsburgh" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.07.29.226217", "rel_title": "Impact Analysis of SARS-CoV2 on Signaling Pathways during COVID19 Pathogenesis using Codon Usage Assisted Host-Viral Protein Interactions", @@ -1304662,6 +1303418,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, + { + "rel_doi": "10.1101/2020.07.27.224089", + "rel_title": "Antibodies that potently inhibit or enhance SARS-CoV-2 spike protein-ACE2 interaction isolated from synthetic single-chain antibody libraries", + "rel_date": "2020-07-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.27.224089", + "rel_abs": "Antibodies with high affinity against the receptor binding domain (RBD) of the SARS-CoV-2 S1 ectodomain were identified from screens using the Retained Display (ReD) platform employing a 1 x 1011 clone single-chain antibody (scFv) library. Numerous unique scFv clones capable of inhibiting binding of the viral S1 ectodomain to the ACE2 receptor in vitro were characterized. To maximize avidity, selected clones were reformatted as bivalent diabodies and monoclonal antibodies (mAb). The highest affinity mAb completely neutralized live SARS-CoV-2 virus in cell culture for four days at a concentration of 6.7 nM, suggesting potential therapeutic and/or prophylactic use. Furthermore, scFvs were identified that greatly increased the interaction of the viral S1 trimer with the ACE2 receptor, with potential implications for vaccine development.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Matthew D Beasley", + "author_inst": "Affinity Biosciences" + }, + { + "author_name": "Sanja Aracic", + "author_inst": "Affinity Biosciences Pty. Ltd." + }, + { + "author_name": "Fiona M Gracey", + "author_inst": "Affinity Biosciences Pty. Ltd" + }, + { + "author_name": "Ruban Kannan", + "author_inst": "Affinity Biosciences Pty. Ltd." + }, + { + "author_name": "Avisa Masarati", + "author_inst": "Affinity Biosciences Pty. Ltd." + }, + { + "author_name": "S. R. Premaratne", + "author_inst": "Affinity Biosciences Pty. Ltd." + }, + { + "author_name": "Madhara Udawela", + "author_inst": "Affinity Biosciences Pty. Ltd." + }, + { + "author_name": "Rebecca E Wood", + "author_inst": "Affinity Biosciences Pty. Ltd." + }, + { + "author_name": "Shereen Jabar", + "author_inst": "Affinity Biosciences Pty. Ltd." + }, + { + "author_name": "Nicole Church", + "author_inst": "Affinity Biosciences Pty. Ltd." + }, + { + "author_name": "Thien-Kim Le", + "author_inst": "Affinity Biosciences Pty. Ltd." + }, + { + "author_name": "Dahna Makris", + "author_inst": "Affinity Biosciences Pty. Ltd." + }, + { + "author_name": "Bradley K McColl", + "author_inst": "Affinity Biosciences Pty. Ltd." + }, + { + "author_name": "Ben R Kiefel", + "author_inst": "Affinity Biosciences Pty. Ltd." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.07.28.225102", "rel_title": "Pyronaridine and artesunate are potential antiviral drugs against COVID-19 and influenza", @@ -1305230,49 +1304057,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.07.22.20154542", - "rel_title": "Prophylaxis with tetracyclines in ARDS: Potential therapy for COVID-19-induced ARDS?", - "rel_date": "2020-07-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20154542", - "rel_abs": "There is an immediate need for therapies related to coronavirus disease 2019 (COVID-19), especially candidate drugs that possess anti-inflammatory and immunomodulatory effects with low toxicity profiles. We hypothesized the application of pleiotropic tetracyclines as potential therapeutic candidates. Here, we present a retrospective multi-institutional cohort study evaluating ventilatory status in patients who had taken a tetracycline antibiotic within a year prior to diagnosis of acute respiratory distress syndrome (ARDS). The primary outcomes were the need for mechanical ventilation and duration of mechanical ventilation. The secondary outcome was the duration of intensive care unit (ICU) stay. Data was evaluated using logistic regression and treatment effects regression models. Minocycline or doxycycline treatment within a year prior to ARDS diagnosis was associated with a 75% reduced likelihood for mechanical ventilation during hospital stay. Furthermore, tetracycline antibiotic therapy corresponded to significant reductions in duration of mechanical ventilation and ICU stay in ARDS patients. These data suggest tetracyclines may provide prophylactic benefit in reducing ventilatory support for ARDS patients and support further evaluation in a randomized prospective trial.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "James D Byrne", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Rameen Shakur", - "author_inst": "Massachusetts Institute of Technology" - }, - { - "author_name": "Joy Collins", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Sarah L Becker", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Cameron C Young", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Hannah Boyce", - "author_inst": "Brigham and Women's Hospital" - }, - { - "author_name": "Carlo Traverso", - "author_inst": "Massachusetts Institute of Technology" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.07.28.225078", "rel_title": "Serial co-expression analysis of host factors from SARS-CoV viruses highly converges with former high-throughput screenings and proposes key regulators and co-option of cellular pathways", @@ -1306384,6 +1305168,141 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.24.20161828", + "rel_title": "Covid-19 automated diagnosis and risk assessment through Metabolomics and Machine-Learning", + "rel_date": "2020-07-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.24.20161828", + "rel_abs": "COVID-19 is still placing a heavy health and financial burden worldwide. Impairments in patient screening and risk management play a fundamental role on how governments and authorities are directing resources, planning reopening, as well as sanitary countermeasures, especially in regions where poverty is a major component in the equation. An efficient diagnostic method must be highly accurate, while having a cost-effective profile.\n\nWe combined a machine learning-based algorithm with instrumental analysis using mass spectrometry to create an expeditious platform that discriminate COVID-19 in plasma samples within minutes, while also providing tools for risk assessment, to assist healthcare professionals in patient management and decision-making. A cross-sectional study with 728 patients (369 confirmed COVID-19 and 359 controls) was enrolled from three Brazilian epicentres (Sao Paulo capital, Sao Paulo countryside and Manaus) in the months of April, May, June and July 2020.\n\nWe were able to elect and identify 21 molecules that are related to the diseases pathophysiology and 26 features to patients health-related outcomes. With specificity >97% and sensitivity >83% from blinded data, this screening approach is understood as a tool with great potential for real-world application.", + "rel_num_authors": 30, + "rel_authors": [ + { + "author_name": "Jeany Delafiori", + "author_inst": "Innovare Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas, Brazil" + }, + { + "author_name": "Luiz Claudio Navarro", + "author_inst": "RECOD Laboratory, Computing Institute, University of Campinas, Campinas, Brazil" + }, + { + "author_name": "Rinaldo Focaccia Siciliano", + "author_inst": "Instituto do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Gisely Cardoso de Melo", + "author_inst": "Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Brazil and Amazonas State University, Manaus, Brazil" + }, + { + "author_name": "Estela Natacha Brandt Busanello", + "author_inst": "Innovare Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas, Brazil" + }, + { + "author_name": "Jos\u00e9 Carlos Nicolau", + "author_inst": "Instituto do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Geovana Manzan Sales", + "author_inst": "Innovare Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas, Brazil" + }, + { + "author_name": "Arthur Noin de Oliveira", + "author_inst": "Innovare Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas, Brazil" + }, + { + "author_name": "Fernando Fonseca Almeida Val", + "author_inst": "Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Brazil and Amazonas State University, Manaus, Brazil" + }, + { + "author_name": "Diogo Noin de Oliveira", + "author_inst": "Innovare Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas, Brazil" + }, + { + "author_name": "Adriana Eguti", + "author_inst": "Sumar\u00e9 State Hospital, Sumar\u00e9, Brazil" + }, + { + "author_name": "Luiz Augusto dos Santos", + "author_inst": "Paul\u00ednia Municipal Hospital, Paul\u00ednia, Brazil" + }, + { + "author_name": "Talia Falc\u00e3o Dal\u00e7\u00f3quio", + "author_inst": "Instituto do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Adriadne Justi Bertolin", + "author_inst": "Instituto do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Jo\u00e3o Carlos Cardoso Alonso", + "author_inst": "Paul\u00ednia Municipal Hospital, Paul\u00ednia, Brazil and Laboratory of Urogenital Carcinogenesis and Immunotherapy, University of Campinas, Campinas, Brazil" + }, + { + "author_name": "Rebeca Linhares Abreu-Netto", + "author_inst": "Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Brazil and Amazonas State University, Manaus, Brazil" + }, + { + "author_name": "Rocio Salsoso", + "author_inst": "Instituto do Coracao (InCor), Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Djane Ba\u00eda-da-Silva", + "author_inst": "Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Brazil and Amazonas State University, Manaus, Brazil" + }, + { + "author_name": "Vanderson Souza Sampaio", + "author_inst": "Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Brazil and Health Surveillance Foundation of Amazonas State, Manaus, Brazil" + }, + { + "author_name": "Carla Cristina Judice", + "author_inst": "Laboratory of Tropical Diseases, Institute of Biology, University of Campinas, Campinas, Brazil" + }, + { + "author_name": "Fabio Maranh\u00e3o Trindade Costa", + "author_inst": "Laboratory of Tropical Diseases, Institute of Biology, University of Campinas, Campinas, Brazil" + }, + { + "author_name": "Nelson Dur\u00e1n", + "author_inst": "Laboratory of Urogenital Carcinogenesis and Immunotherapy, University of Campinas, Campinas, Brazil" + }, + { + "author_name": "Maur\u00edcio Wesley Perroud", + "author_inst": "Sumar\u00e9 State Hospital, Sumar\u00e9, Brazil" + }, + { + "author_name": "Ester Cerdeira Sabino", + "author_inst": "Institute of Tropical Medicine, University of S\u00e3o Paulo, S\u00e3o Paulo, Brazil" + }, + { + "author_name": "Marcus Vinicius Guimar\u00e3es Lacerda", + "author_inst": "Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Brazil and Le\u00f4nidas and Maria Deane Institute, FIOCRUZ, Manaus, Brazil" + }, + { + "author_name": "Leonardo Oliveira Reis", + "author_inst": "UroScience Laboratory, University of Campinas, Campinas, Brazil" + }, + { + "author_name": "Wagner Jos\u00e9 F\u00e1varo", + "author_inst": "Laboratory of Urogenital Carcinogenesis and Immunotherapy, University of Campinas, Campinas, Brazil" + }, + { + "author_name": "Wuelton Marcelo Monteiro", + "author_inst": "Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Brazil and Amazonas State University, Manaus, Brazil" + }, + { + "author_name": "Anderson Rezende Rocha", + "author_inst": "RECOD Laboratory, Computing Institute, University of Campinas, Campinas, Brazil" + }, + { + "author_name": "Rodrigo Ramos Catharino", + "author_inst": "Innovare Biomarkers Laboratory, School of Pharmaceutical Sciences, University of Campinas, Campinas, Brazil" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.25.20161885", "rel_title": "Mathematical modelling based study and prediction of COVID-19 epidemic dissemination under the impact of lockdown in India", @@ -1306992,53 +1305911,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.27.222836", - "rel_title": "Targeting the endolysosomal host-SARS-CoV-2 interface by the clinically licensed antidepressant fluoxetine", - "rel_date": "2020-07-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.27.222836", - "rel_abs": "The Corona Virus Disease 2019 (COVID-19) pandemic caused by the Severe Acute Respiratory Syndrome Related Coronavirus 2 (SARS-CoV-2) is a global health emergency. As only very limited therapeutic options are clinically available, there is an urgent need for the rapid development of safe, effective, and globally available pharmaceuticals that inhibit SARS-CoV-2 entry and ameliorate COVID-19. In this study, we explored the use of small compounds acting on the homeostasis of the endolysosomal host-pathogen interface, to fight SARS-CoV-2 infection. We find that fluoxetine, a widely used antidepressant and a functional inhibitor of acid sphingomyelinase (FIASMA), efficiently inhibited the entry and propagation of SARS-CoV-2 in the cell culture model without cytotoxic effects and also exerted potent antiviral activity against two currently circulating influenza A virus subtypes, an effect which was also observed upon treatment with the FIASMAs amiodarone and imipramine. Mechanistically, fluoxetine induced both impaired endolysosomal acidification and the accumulation of cholesterol within the endosomes. As the FIASMA group consists of a large number of small compounds that are well-tolerated and widely used for a broad range of clinical applications, exploring these licensed pharmaceuticals may offer a variety of promising antivirals for host-directed therapy to counteract enveloped viruses, including SARS-CoV-2 and COVID 19.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Sebastian Schloer", - "author_inst": "University of Muenster, Center for Molecular Biology of Inflammation" - }, - { - "author_name": "Linda Brunotte", - "author_inst": "Universtity of Muenster, Center for Molecular Biology of Inflammation" - }, - { - "author_name": "Jonas Goretzko", - "author_inst": "University of Muenster, Center for Molecular Biology of Inflammation" - }, - { - "author_name": "Angeles Mecate-Zambrano", - "author_inst": "University of Muenster, Center for Molecular Biology of Inflammation" - }, - { - "author_name": "Nadja Korthals", - "author_inst": "University of Muenster, Center for Molecular Biology of Inflammation" - }, - { - "author_name": "Volker Gerke", - "author_inst": "University of Muenster, Center for Molecular Biology of Inflammation" - }, - { - "author_name": "Stephan Ludwig", - "author_inst": "University of Muenster, Center for Molecular Biology of Inflammation" - }, - { - "author_name": "Ursula Rescher", - "author_inst": "University of Muenster Centre for Molecular Biology of Inflammation" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.07.27.220954", "rel_title": "Molecular mechanisms of Cardiac Injury associated with myocardial SARS-CoV-2 infection", @@ -1308362,6 +1307234,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.20.20157818", + "rel_title": "Optimal Testing Strategy for the Identification of COVID-19 Infections", + "rel_date": "2020-07-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.20.20157818", + "rel_abs": "The systematic identification of infectious, yet unreported, individuals is critical for the containment of the COVID-19 pandemic. We present a strategy for identifying the location, timing and extent of testing that maximizes information gain for such infections. The optimal testing strategy relies on Bayesian experimental design and forecasting epidemic models that account for time dependent interventions. It is applicable at the onset and spreading of the epidemic and can forewarn for a possible recurrence of the disease after relaxation of interventions. We examine its application in Switzerland and show that it can provide timely and systematic guidance for the effective identification of infectious individuals with finite testing resources. The methodology and the open source code are readily adaptable to countries around the world.\n\nWe present a strategy for the optimal allocation of testing resources in order to detect COVID-19 infections in a countrys population.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Michail Chatzimanolakis", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Pascal Weber", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Georgios Arampatzis", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Daniel W\u00e4lchli", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Petr Karnakov", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Ivica Ki\u010di\u0107", + "author_inst": "ETH Zurich" + }, + { + "author_name": "Costas Papadimitriou", + "author_inst": "University of Thessaly" + }, + { + "author_name": "Petros Koumoutsakos", + "author_inst": "ETH Zurich" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.20.20157826", "rel_title": "A logistic model of CoV-2 propagation", @@ -1308742,53 +1307661,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2020.07.20.20157149", - "rel_title": "Association of contact to small children with mild course of COVID-19", - "rel_date": "2020-07-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.20.20157149", - "rel_abs": "It is known that severe COVID-19 cases in small children are rare. If a childhood-related infection would be protective against severe course of COVID-19, it would be expected that adults with intensive and regular contact to small children also may have a mild course of COVID-19 more frequently. To test this hypothesis, a survey among 4,010 recovered COVID-19 patients was conducted in Germany. 1,186 complete answers were collected. 6.9% of these patients reported frequent and regular job-related contact to children below 10 years of age and 23.2% had own small children, which is higher than expected. In the relatively small subgroup with intensive care treatment (n=19), patients without contact to small children were overrepresented. These findings are not well explained by age, gender or BMI distribution of those patients and should be validated in other settings.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Martin Dugas", - "author_inst": "University of Muenster, Germany" - }, - { - "author_name": "Inga Marie Schrempf", - "author_inst": "University Hospital Muenster, Germany" - }, - { - "author_name": "Kevin Ochs", - "author_inst": "University Hospital Muenster, Germany" - }, - { - "author_name": "Christopher Froemmel", - "author_inst": "University Hospital Muenster, Germany" - }, - { - "author_name": "Leonard Greulich", - "author_inst": "University of Muenster, Germany" - }, - { - "author_name": "Philipp Neuhaus", - "author_inst": "University of Muenster, Germany" - }, - { - "author_name": "Phil-Robin Tepasse", - "author_inst": "University Hospital Muenster, Germany" - }, - { - "author_name": "Hartmut HJ Schmidt", - "author_inst": "University Hospital Muenster, Germany" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.20.20156398", "rel_title": "Clinical and laboratory evaluation of patients with SARS-CoV-2 pneumonia treated with high-titer convalescent plasma: a prospective study", @@ -1310664,6 +1309536,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.22.20159798", + "rel_title": "The Epidemiology Workbench: a Tool for Communities to Strategize in Response to COVID-19 and other Infectious Diseases", + "rel_date": "2020-07-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20159798", + "rel_abs": "COVID-19 poses a dramatic challenge to health, community life, and the economy of communities across the world. While the properties of the virus are similar from place to place, the impact has been dramatically different from place to place, due to such factors as population density, mobility, age distribution, etc. Thus, optimum testing and social distancing strategies may also be different from place to place. The Epidemiology Workbench provides access to an agent-based model in which a communitys demographic, geographic, and public health information together with a social distancing and testing strategy may be input, and a range of possible outcomes computed, to inform local authorities on coping strategies. The model is adaptable to other infectious diseases, and to other strains of coronavirus. The tool is illustrated by scenarios for the cities of Urbana and Champaign, Illinois, the home of the University of Illinois at Urbana-Champaign. Our calculations suggest that massive testing is the most effective strategy to combat the likely increase in local cases due to mass ingress of a student population carrying a higher viral load than that currently present in the community.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Santiago N\u00fa\u00f1ez-Corrales", + "author_inst": "University of Illinois at Urbana-Champaign" + }, + { + "author_name": "Eric Jakobsson", + "author_inst": "University of Illinois at Urbana-Champaign" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.24.20159947", "rel_title": "Effect of manual and digital contact tracing on COVID-19 outbreaks: a study on empirical contact data", @@ -1310972,33 +1309867,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, - { - "rel_doi": "10.1101/2020.07.23.20158980", - "rel_title": "Prevalence of mask wearing in northern Vermont in response to SARS-CoV-2", - "rel_date": "2020-07-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.23.20158980", - "rel_abs": "ObjectivesInformation on prevalence of face mask usage in response to SARS-CoV-2 is required to both model disease spread and to improve compliance with mask usage. We sought to (1) estimate the prevalence of mask usage in northern Vermont and to (2) assess the effect of age and sex on mask usage.\n\nMethodsWe monitored the entrances to businesses and visually assessed individuals age, sex, and mask usage from a distance. We collected 1004 observations from 16 May through 30 May 2020 as businesses began to reopen following an extended state-wide lockdown. We analyzed these data using Bayesian random effects logistic regression.\n\nResults75.5% of individuals used a mask with significant effects of age and sex on mask usage. Females were more likely than males to wear masks (83.8%, n=488 vs. 67.6%, n=516); the odds of mask usage in males were 53% of those for females. Elders were most likely to wear a mask (91.4%, n=209) followed by young adults (74.8%, n=246), middle-aged adults (70.7%, n=519) and children (53.3%, n=30). The odds of an elder wearing a mask were 16.7 times that of a child, while the odds for young adults and middle-aged adults were [~]3 times greater than for a child. Highest mask usage was in elder females (96.3%, n=109) and lowest mask usage was in male children (43.8%, n=16).\n\nConclusionsWe found high prevalence of mask usage overall, but also large differences in mask usage with age and sex. Females and elders had the highest use of face masks.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Brian Beckage", - "author_inst": "University of Vermont" - }, - { - "author_name": "Thomas E Buckley", - "author_inst": "Colchester High School" - }, - { - "author_name": "Maegan E Beckage", - "author_inst": "Essex High School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.21.20159038", "rel_title": "Stringent thresholds for SARS-CoV-2 IgG assays result in under-detection of cases reporting loss of taste/smell", @@ -1312234,6 +1311102,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.20.20157933", + "rel_title": "A data-driven metapopulation model for the Belgian COVID-19 epidemic: assessing the impact of lockdown and exit strategies", + "rel_date": "2020-07-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.20.20157933", + "rel_abs": "BackgroundIn response to the ongoing COVID-19 pandemic, several countries adopted measures of social distancing to a different degree. For many countries, after successfully curbing the initial wave, lockdown measures were gradually lifted. In Belgium, such relief started on May 4th with phase 1, followed by several subsequent phases over the next few weeks.\n\nMethodsWe analysed the expected impact of relaxing stringent lockdown measures taken according to the phased Belgian exit strategy. We developed a stochastic, data-informed, meta-population model that accounts for mixing and mobility of the age-structured population of Belgium. The model is calibrated to daily hospitalization data and serological data and is able to reproduce the outbreak at the national level. We consider different scenarios for relieving the lockdown, quantified in terms of relative reductions in pre-pandemic social mixing and mobility. We validate our assumptions by making comparisons with social contact data collected during and after the lockdown.\n\nResultsOur model is able to successfully describe the initial wave of COVID-19 in Belgium and identifies interactions during leisure/other activities as pivotal in the exit strategy. Indeed, we find a smaller impact of school re-openings as compared to restarting leisure activities and re-openings of work places. We also assess the impact of case isolation of new (suspected) infections, and find that it allows re-establishing relatively more social interactions while still ensuring epidemic control. Scenarios predicting a second wave of hospitalizations were not observed, suggesting that the per-contact probability of infection has changed with respect to the pre-lockdown period.\n\nConclusionsCommunity contacts are found to be most influential, followed by professional contacts and school contacts, respectively, for an impending second wave of COVID-19. Regular re-assessment is crucial to adjust to evolving behavioral changes that can affect epidemic diffusion. In addition to social distancing, sufficient capacity for extensive testing and contact tracing is essential for successful mitigation.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Pietro Coletti", + "author_inst": "Data Science Institute, I-BioStat, UHasselt" + }, + { + "author_name": "Pieter Libin", + "author_inst": "Data Science Institute, I-BioStat, UHasselt" + }, + { + "author_name": "Oana Petrof", + "author_inst": "Data Science Institute, I-BioStat, UHasselt" + }, + { + "author_name": "Lander Willem", + "author_inst": "Antwerp University" + }, + { + "author_name": "Abrams Steven", + "author_inst": "Data Science Institute, I-BioStat, UHasselt" + }, + { + "author_name": "Sereina A. Herzog", + "author_inst": "Antwerp University" + }, + { + "author_name": "Christel Faes", + "author_inst": "Data Science Institute, I-BioStat, UHasselt" + }, + { + "author_name": "James Wambua", + "author_inst": "Data Science Institute, I-BioStat, UHasselt" + }, + { + "author_name": "Elise J. Kuylen", + "author_inst": "Universiteit Antwerpen" + }, + { + "author_name": "Philippe Beutels", + "author_inst": "University of Antwerp" + }, + { + "author_name": "Niel Hens", + "author_inst": "Hasselt University and University of Antwerp" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.24.20157982", "rel_title": "Dynamics of SARS-CoV-2 with Waning Immunity in the UK Population", @@ -1312590,137 +1311517,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.25.217158", - "rel_title": "High neutralizing potency of swine glyco-humanized polyclonal antibodies against SARS-CoV-2", - "rel_date": "2020-07-25", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.25.217158", - "rel_abs": "Perfusion of convalescent plasma (CP) has demonstrated a potential to improve the pneumonia induced by SARS-CoV-2, but procurement and standardization of CP are barriers to its wide usage. Many monoclonal antibodies (mAbs) have been developed but appear insufficient to neutralize SARS-CoV-2 unless two or three of them are being combined. Therefore, heterologous polyclonal antibodies of animal origin, that have been used for decades to fight against infectious agents might represent a highly efficient alternative to the use of CP or mAbs in COVID-19 by targeting multiple antigen epitopes. However, conventional heterologous polyclonal antibodies trigger human natural xenogeneic antibody responses particularly directed against animal-type carbohydrate epitopes, mainly the N-glycolyl form of the neuraminic acid (Neu5Gc) and the Gal 1,3-galactose (Gal), ultimately forming immune complexes and potentially leading to serum sickness or allergy. To circumvent these drawbacks, we engineered animals lacking the genes coding for the cytidine monophosphate-N-acetylneuraminic acid hydroxylase (CMAH) and 1,3-galactosyl-transferase (GGTA1) enzymes to produce glyco-humanized polyclonal antibodies (GH-pAb) lacking Neu5Gc and -Gal epitopes. We found that pig IgG Fc domains fail to interact with human Fc receptors and thereby should confer the safety advantage to avoiding macrophage dependent exacerbated inflammatory responses, a drawback possibly associated with antibody responses against SARS-CoV-2 or to avoiding a possible antibody-dependent enhancement (ADE). Therefore, we immunized CMAH/GGTA1 double knockout (DKO) pigs with the SARS-CoV-2 spike receptor-binding domain (RBD) to elicit neutralizing antibodies. Animals rapidly developed a hyperimmune response with anti-SARS-CoV-2 end-titers binding dilutions over one to a million and end-titers neutralizing dilutions of 1:10,000. The IgG fraction purified and formulated following clinical Good Manufacturing Practices, named XAV-19, neutralized Spike/angiotensin converting enzyme-2 (ACE-2) interaction at a concentration < 1g/mL and inhibited infection of human cells by SARS-CoV-2 in cytopathic assays. These data and the accumulating safety advantages of using glyco-humanized swine antibodies in humans warranted clinical assessment of XAV-19 to fight against COVID-19.", - "rel_num_authors": 29, - "rel_authors": [ - { - "author_name": "Bernard Vanhove", - "author_inst": "Xenothera" - }, - { - "author_name": "Odile Duvaux", - "author_inst": "Xenothera" - }, - { - "author_name": "Juliette Rousse", - "author_inst": "Xenothera" - }, - { - "author_name": "Pierre-Joseph Royer", - "author_inst": "Xenothera" - }, - { - "author_name": "Gwenaelle Evanno", - "author_inst": "Xenothera" - }, - { - "author_name": "Carine Ciron", - "author_inst": "Xenothera" - }, - { - "author_name": "Elsa Lheriteau", - "author_inst": "Xenothera" - }, - { - "author_name": "Laurent Vacher", - "author_inst": "Xenothera" - }, - { - "author_name": "Nadine Gervois", - "author_inst": "University of Nantes" - }, - { - "author_name": "Romain Oger", - "author_inst": "University of Nantes" - }, - { - "author_name": "Yannick Jacques", - "author_inst": "University of Nantes" - }, - { - "author_name": "Sophie Conchon", - "author_inst": "University of Nantes" - }, - { - "author_name": "Apolline Salama", - "author_inst": "University of Nantes" - }, - { - "author_name": "Roberto Duchi", - "author_inst": "Avantea" - }, - { - "author_name": "Irina Lagutina", - "author_inst": "Avantea" - }, - { - "author_name": "Andrea Perota", - "author_inst": "University of Nantes" - }, - { - "author_name": "Philippe Delahaut", - "author_inst": "CER Groupe" - }, - { - "author_name": "Matthieu Ledure", - "author_inst": "CER Groupe" - }, - { - "author_name": "Melody Paulus", - "author_inst": "CER Groupe" - }, - { - "author_name": "Ray So", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Chris Ka Pun Mok", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Roberto Bruzzone", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Marc Bouillet", - "author_inst": "Xenothera" - }, - { - "author_name": "Sophie Brouard", - "author_inst": "University of Nantes" - }, - { - "author_name": "Emanuele Cozzi", - "author_inst": "Padua University Hospital" - }, - { - "author_name": "Cesare Galli", - "author_inst": "Avantea" - }, - { - "author_name": "Dominique Blanchard", - "author_inst": "Xenothera" - }, - { - "author_name": "Jean-Marie Bach", - "author_inst": "Oniris" - }, - { - "author_name": "Jean-Paul Soulillou", - "author_inst": "University of Nantes" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.07.24.205583", "rel_title": "Rapid generation of circulating and mucosal decoy ACE2 using mRNA nanotherapeutics for the potential treatment of SARS-CoV-2", @@ -1313836,6 +1312632,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.23.217083", + "rel_title": "An in-silico study on SARS-CoV-2: Its compatibility with human tRNA pool, and the polymorphism arising in a single lineage over a month", + "rel_date": "2020-07-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.23.217083", + "rel_abs": "SARS-CoV-2 has caused a global pandemic that has costed enormous human lives in the recent past. The present study is an investigation of the viral codon adaptation, ORFs stability and tRNA co-adaptation with humans. We observed that for the codon usage bias in viral ssRNA, ORFs have near values of folding free energies and codon adaptation index with mRNAs of the human housekeeping CDS. However, the correlation between the stability of the ORFs in ssRNA and CAI is stronger than the mRNA stability and CAI of HKG, suggesting a greater expression capacity of SARS-CoV-2. Mutational analysis reflects polymorphism in the virus for ORF1ab, surface glycoprotein and nucleocapsid phosphoprotein ORFs. Non-synonymous mutations have shown non-polar substitutions. Out of the twelve mutations nine are for a higher t-RNA copy number. Viruses in general have high mutation rates. To understand the chances of survival for the mutated SARS-CoV-2 we did simulation for synonymous mutations. It resulted in 50% ORFs with higher stability than their native equivalents. Thus, considering only the synonymous mutations the virus can exhibit a lot of polymorphism. Collectively our data provides new insights for SARS-CoV-2 mutations and the human t-RNA compatibility.\n\nSignificanceSurvivability of SARS-CoV-2 in humans is essential for its spread. It has overlapping genes exhibiting a high codon optimization with humans even after a higher codon usage bias. They seem to possess cognizance for high copy number t-RNA (cognate or near-cognate) in humans, while mutating. Even though, it has been well established that native transcripts posses the highest stability, our in-silico studies show that SARS-CoV-2 under mutations give rise to ORFs with higher stability. These results significantly present the viruss ability and the credibility of survival for the mutants. Despite its focus on a geographical location it explains the ongoing behavior of SARS-CoV-2 for a steady existence in humans as all the different lineages have a common origin. Wuhan, China.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Manish Victor", + "author_inst": "Bose Institute" + }, + { + "author_name": "Rohit Das", + "author_inst": "Bose Institute" + }, + { + "author_name": "Tapash Ghosh", + "author_inst": "Bose Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.07.19.20157362", "rel_title": "On the effect of age on the transmission of SARS-CoV-2 in households, schools and the community", @@ -1314220,49 +1313043,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.07.24.219139", - "rel_title": "Tissue-specific and interferon-inducible expression of non-functional ACE2 through endogenous retrovirus co-option", - "rel_date": "2020-07-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.24.219139", - "rel_abs": "Angiotensin-converting enzyme 2 (ACE2) is an entry receptor for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), as well as a regulator of several physiological processes. ACE2 has recently been proposed to be interferon-inducible, suggesting that SARS-CoV-2 may exploit this phenomenon to enhance viral spread and questioning the efficacy of interferon treatment in Coronavirus disease 2019 (COVID-19). Using a recent de novo transcript assembly that captured previously unannotated transcripts, we describe a novel isoform of ACE2, generated by co-option of an intronic long terminal repeat (LTR) retroelement promoter. The novel transcript, termed LTR16A1-ACE2, exhibits specific expression patterns across the aerodigestive and gastrointestinal tracts and, importantly, is highly responsive to interferon stimulation. In stark contrast, expression of canonical ACE2 is completely unresponsive to interferon stimulation. Moreover, the LTR16A1-ACE2 translation product is a truncated, unstable ACE2 form, lacking domains required for SARS-CoV-2 binding and therefore unlikely to contribute to or enhance viral infection.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Kevin Ng", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "Jan Attig", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "William Bolland", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "George Young", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Jack Major", - "author_inst": "The Francis Crick Institute" - }, - { - "author_name": "Andreas Wack", - "author_inst": "Francis Crick Institute" - }, - { - "author_name": "George Kassiotis", - "author_inst": "The Francis Crick Institute" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.07.24.219857", "rel_title": "High Affinity Nanobodies Block SARS-CoV-2 Spike Receptor Binding Domain Interaction with Human Angiotensin Converting Enzyme", @@ -1315270,6 +1314050,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.23.20160820", + "rel_title": "Clinical Impact, Costs, and Cost-Effectiveness of Expanded SARS-CoV-2 Testing in Massachusetts", + "rel_date": "2020-07-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.23.20160820", + "rel_abs": "BackgroundWe projected the clinical and economic impact of alternative testing strategies on COVID-19 incidence and mortality in Massachusetts using a microsimulation model.\n\nMethodsWe compared five testing strategies: 1) PCR-severe-only: PCR testing only patients with severe/critical symptoms; 2) Self-screen: PCR-severe-only plus self-assessment of COVID-19-consistent symptoms with self-isolation if positive; 3) PCR-any-symptom: PCR for any COVID-19-consistent symptoms with self-isolation if positive; 4) PCR-all: PCR-any-symptom and one-time PCR for the entire population; and, 5) PCR-all-repeat: PCR-all with monthly re-testing. We examined effective reproduction numbers (Re, 0.9-2.0) at which policy conclusions would change. We used published data on disease progression and mortality, transmission, PCR sensitivity/specificity (70/100%) and costs. Model-projected outcomes included infections, deaths, tests performed, hospital-days, and costs over 180-days, as well as incremental cost-effectiveness ratios (ICERs, $/quality-adjusted life-year [QALY]).\n\nResultsIn all scenarios, PCR-all-repeat would lead to the best clinical outcomes and PCR-severe-only would lead to the worst; at Re 0.9, PCR-all-repeat vs. PCR-severe-only resulted in a 63% reduction in infections and a 44% reduction in deaths, but required >65-fold more tests/day with 4-fold higher costs. PCR-all-repeat had an ICER <$100,000/QALY only when Re [≥]1.8. At all Re values, PCR-any-symptom was cost-saving compared to other strategies.\n\nConclusionsTesting people with any COVID-19-consistent symptoms would be cost-saving compared to restricting testing to only those with symptoms severe enough to warrant hospital care. Expanding PCR testing to asymptomatic people would decrease infections, deaths, and hospitalizations. Universal screening would be cost-effective when paired with monthly retesting in settings where the COVID-19 pandemic is surging.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Anne M Neilan", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Elena Losina", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Audrey C. Bangs", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Clare Flanagan", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Christopher Panella", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "G. Ege Eskibozkurt", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Amir M. Mohareb", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Emily P. Hyle", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Justine A. Scott", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Milton C. Weinstein", + "author_inst": "Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Mark J. Siedner", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Krishna P Reddy", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Guy Harling", + "author_inst": "University College London" + }, + { + "author_name": "Kenneth A. Freedberg", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Fatma M. Shebl", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Pooyan Kazemian", + "author_inst": "Massachusetts General Hospital" + }, + { + "author_name": "Andrea L. Ciaranello", + "author_inst": "Massachusetts General Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.23.20160895", "rel_title": "ASSESSING THE AGE SPECIFICITY OF INFECTION FATALITY RATES FOR COVID-19: META-ANALYSIS & PUBLIC POLICY IMPLICATIONS", @@ -1315550,45 +1314413,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "palliative medicine" }, - { - "rel_doi": "10.1101/2020.07.22.20160333", - "rel_title": "The COVID-19 Pandemic Impact on Primary Health Care services: An Experience from Qatar", - "rel_date": "2020-07-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20160333", - "rel_abs": "IntroductionIn March 2020, Qatar started reporting increased numbers of COVID-19 positive cases. The Ministry of Public Health in Qatar has developed an emergency action plan to respond to the outbreak with the Primary Health Care Corporation (PHCC) as a main component of that response.\n\nAimThe aim of this review is to understand and document the Impact of COVID 19 on PHCC in Qatar in terms of response, modifications of services and introduction of new alternatives\n\nMethodologyA retrospective data analysis was conducted for all the COVID-19 swabbing activities and for all the utilization services volume across the PHCC health centers between January 2018 and May 2020.\n\nResultsPHCC allocated testing sites for COVID-19 resulted in conducting 54824 swabs with 11455 positive cases and positivity rate of 20.8% between 14th of March and 15th of June 2020. The overall PHCC services utilization declined with overall reduction of 50% in April 2020. Alternative virtual and remote services were provided, telemedicine was introduced, and it made up 50% of the consultation volumes for April 2020. Home refill delivery medications managed to provide a total of 20920 delivered prescriptions by end of May 2020.\n\nConclusion and recommendationsTo decrease the risk of infection to the patients and health care workers, PHCC in Qatar cancelled the appointments for some high-risk population. However, PHCC introduced virtual remote services that managed to make up for the in-person utilization volume and reflected acceptance in patients behaviours. PHCC continued in detecting positive COVID-19 cases among its targeted communities.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Mohamed Al Kuwari", - "author_inst": "Primary Health Care Corporation" - }, - { - "author_name": "Mariam Abdulmalik", - "author_inst": "Primary Health Care Corporation" - }, - { - "author_name": "Samya Al Abdulla", - "author_inst": "Primary Health Care Corporation" - }, - { - "author_name": "Ahmad Haj Bakri", - "author_inst": "Primary Health Care Corporation" - }, - { - "author_name": "John Gibb", - "author_inst": "Primary Health Care Corporation" - }, - { - "author_name": "Mujeeb Kandy", - "author_inst": "Primary Health Care Corporation" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "primary care research" - }, { "rel_doi": "10.1101/2020.07.24.20161315", "rel_title": "Anxiety and perceived risk during COVID-19 outbreak", @@ -1316536,6 +1315360,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.22.20160028", + "rel_title": "Evidence for immunity to SARS-CoV-2 from epidemiological data series", + "rel_date": "2020-07-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.22.20160028", + "rel_abs": "The duration of immunity to SARS-CoV-2 is uncertain. Delineating immune memory typically requires longitudinal serological studies that track antibody prevalence in the same cohort for an extended time. However, this information is needed in faster timescales. Notably, the dynamics of an epidemic where recovered patients become immune for any period should differ significantly from those of one where the recovered promptly become susceptible. Here, we exploit this difference to provide a reliable protocol that can estimate immunity early in an epidemic. We verify this protocol with synthetic data, discuss its limitations, and then apply it to evaluate human immunity to SARS-CoV-2 in mortality data series from New York City. Our results indicate that New Yorks mortality figures are incompatible with immunity lasting anything below 105 or above 211 days (90% CI.), and set an example on how to assess immune memory in emerging pandemics before serological studies can be deployed.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Pablo Yubero", + "author_inst": "Spanish National Biotechnology Center (CNB-CSIC)" + }, + { + "author_name": "Alvar A. Lavin", + "author_inst": "Spanish National Biotechnology Center (CNB-CSIC)" + }, + { + "author_name": "Juan F Poyatos", + "author_inst": "Spanish National Biotechnology Center (CNB-CSIC)" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.22.20159855", "rel_title": "Renin-Angiotensin-Aldosterone-System inhibitor use in patients with COVID-19 infection and prevention of serious events: a cohort study in commercially insured patients in the US", @@ -1316832,129 +1315683,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.16.20155531", - "rel_title": "Safety of Hydroxychloroquine among Outpatient Clinical Trial Participants for COVID-19", - "rel_date": "2020-07-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.16.20155531", - "rel_abs": "IntroductionUse of hydroxychloroquine in hospitalized patients with COVID-19, especially in combination with azithromycin, has raised safety concerns. Here, we report safety data from three outpatient randomized clinical trials.\n\nMethodsWe conducted three randomized, double-blind, placebo-controlled trials investigating hydroxychloroquine as pre-exposure prophylaxis, post-exposure prophylaxis and early treatment for COVID-19. We excluded individuals with contraindications to hydroxychloroquine. We collected side effects and serious adverse events. We report descriptive analyses of our findings.\n\nResultsWe enrolled 2,795 participants. The median age of research participants was 40 (IQR 34-49) years, and 59% (1633/2767) reported no chronic medical conditions. Overall 2,324 (84%) participants reported side effect data, and 638 (27%) reported at least one medication side effect. Side effects were reported in 29% with daily, 36% with twice weekly, 31% with once weekly hydroxychloroquine compared to 19% with placebo. The most common side effects were upset stomach or nausea (25% with daily, 18% with twice weekly, 16% with weekly, vs. 10% for placebo), followed by diarrhea, vomiting, or abdominal pain (23% for daily, 16% twice weekly, 12% weekly, vs. 6% for placebo). Two individuals were hospitalized for atrial arrhythmias, one on placebo and one on twice weekly hydroxychloroquine. No sudden deaths occurred.\n\nConclusionData from three outpatient COVID-19 trials demonstrated that gastrointestinal side effects were common but mild with the use of hydroxychloroquine, while serious side effects were rare. No deaths occurred related to hydroxychloroquine. Randomized clinical trials can safely investigate whether hydroxychloroquine is efficacious for COVID-19.\n\nShort SummaryData from three randomized clinical trials using hydroxychloroquine for the prevention and treatment of COVID-19 did not suggest significant safety concerns. Gastrointestinal side effects were common but arrhythmias were rare. There were no sudden deaths in any trial.", - "rel_num_authors": 27, - "rel_authors": [ - { - "author_name": "SARAH M LOFGREN", - "author_inst": "UNIVERSITY OF MINNESOTA" - }, - { - "author_name": "Melanie R Nicol", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Ananta S Bangdiwala", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Katelyn A Pastick", - "author_inst": "University of Minnesota School of Medicine" - }, - { - "author_name": "Elizabeth C Okafor", - "author_inst": "University of Minnesota School of Medicine" - }, - { - "author_name": "Caleb P Skipper", - "author_inst": "Department of Medicine, University of Minnesota" - }, - { - "author_name": "Matthew F Pullen", - "author_inst": "Department of Medicine, University of Minnesota" - }, - { - "author_name": "Nicole W Engen", - "author_inst": "Department of Medicine, University of Minnesota" - }, - { - "author_name": "Mahsa Abassi", - "author_inst": "Department of Medicine, University of Minnesota" - }, - { - "author_name": "Darlisha A Williams", - "author_inst": "Department of Medicine, University of Minnesota" - }, - { - "author_name": "Alanna A Nascene", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Margaret L Axelrod", - "author_inst": "Vanderbilt University" - }, - { - "author_name": "Sylvian A Lother", - "author_inst": "University of Manitoba" - }, - { - "author_name": "Lauren J MacKenzie", - "author_inst": "University of Manitoba" - }, - { - "author_name": "Glen Drobot", - "author_inst": "University of Manitoba" - }, - { - "author_name": "Nicole Marten", - "author_inst": "George & Fay Yee Centre for Healthcare Innovation, Winnipeg, Manitoba" - }, - { - "author_name": "Matthew P Cheng", - "author_inst": "McGill University" - }, - { - "author_name": "Ryan Zarychanshi", - "author_inst": "University of Manitoba" - }, - { - "author_name": "Ilan S Schwartz", - "author_inst": "University of Alberta" - }, - { - "author_name": "Michael Silverman", - "author_inst": "Lawson Research Institute, London, Ontario" - }, - { - "author_name": "Zain Chagla", - "author_inst": "McMaster University" - }, - { - "author_name": "Lauren E Kelly", - "author_inst": "George & Fay Yee Centre for Healthcare Innovation, Winnipeg, Manitoba" - }, - { - "author_name": "Emily G McDonald", - "author_inst": "McGill University" - }, - { - "author_name": "Todd C Lee", - "author_inst": "McGill University" - }, - { - "author_name": "Katherine Huppler Hullsiek", - "author_inst": "University of Minnesota" - }, - { - "author_name": "David R Boulware", - "author_inst": "Department of Medicine, University of Minnesota" - }, - { - "author_name": "Radha Rajasingham", - "author_inst": "Department of Medicine, University of Minnesota" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.16.20152868", "rel_title": "SECOND WEEK METHYL-PREDNISOLONE PULSES IMPROVE PROGNOSIS IN PATIENTS WITH SEVERE CORONAVIRUS DISEASE 2019 PNEUMONIA: AN OBSERVATIONAL COMPARATIVE STUDY USING ROUTINE CARE DATA.", @@ -1318222,6 +1316950,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.07.21.20158972", + "rel_title": "Invasive pulmonary aspergillosis in critically ill patients with severe COVID-19 pneumonia: results from the prospective AspCOVID-19 study", + "rel_date": "2020-07-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.21.20158972", + "rel_abs": "BackgroundSuperinfections, including invasive pulmonary aspergillosis (IPA), are well-known complications of critically ill patients with severe viral pneumonia. Aim of this study was to evaluate the incidence, risk factors and outcome of IPA in critically ill patients with severe COVID-19 pneumonia.\n\nMethodsWe prospectively screened 32 critically ill patients with severe COVID-19 pneumonia for a time period of 28 days using a standardized study protocol for oberservation of developement of COVID-19 associated invasive pulmonary aspergillosis (CAPA). We collected laboratory, microbiological, virological and clinical parameters at defined timepoints in combination with galactomannan-antigen-detection from bronchial aspirates. We used logistic regression analyses to assess if COVID-19 was independently associated with IPA and compared it with matched controls.\n\nFindingsCAPA was diagnosed at a median of 4 days after ICU admission in 11/32 (34%) of critically ill patients with severe COVID-19 pneumonia as compared to 8% in the control cohort.\n\nIn the COVID-19 cohort, mean age, APACHE II score and ICU mortality were higher in patients with CAPA than in patients without CAPA (36% versus 9.5%; p<0.001). ICU stay (21 versus 17 days; p=0.340) and days of mechanical ventilation (20 versus 15 days; p=0.570) were not different between both groups. In regression analysis COVID-19 and APACHE II score were independently associated with IPA.\n\nInterpretationCAPA is highly prevalent and associated with a high mortality rate. COVID-19 is independently associated with invasive pulmonary aspergillosis. A standardized screening and diagnostic approach as presented in our study can help to identify affected patients at an early stage.\n\nFundingNone", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Tobias Lahmer", + "author_inst": "Klinikum rechts der Isar, TU Muenchen" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.07.20.20158576", "rel_title": "Assessing the relative contributions of healthcare protocols for epidemic control: an example with network transmission model for COVID-19", @@ -1318814,117 +1317561,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.21.214759", - "rel_title": "Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants", - "rel_date": "2020-07-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.21.214759", - "rel_abs": "Neutralizing antibodies elicited by prior infection or vaccination are likely to be key for future protection of individuals and populations against SARS-CoV-2. Moreover, passively administered antibodies are among the most promising therapeutic and prophylactic anti-SARS-CoV-2 agents. However, the degree to which SARS-CoV-2 will adapt to evade neutralizing antibodies is unclear. Using a recombinant chimeric VSV/SARS-CoV-2 reporter virus, we show that functional SARS-CoV-2 S protein variants with mutations in the receptor binding domain (RBD) and N-terminal domain that confer resistance to monoclonal antibodies or convalescent plasma can be readily selected. Notably, SARS-CoV-2 S variants that resist commonly elicited neutralizing antibodies are now present at low frequencies in circulating SARS-CoV-2 populations. Finally, the emergence of antibody-resistant SARS-CoV-2 variants that might limit the therapeutic usefulness of monoclonal antibodies can be mitigated by the use of antibody combinations that target distinct neutralizing epitopes.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Yiska Weisblum", - "author_inst": "Rockefeller" - }, - { - "author_name": "Fabian Schmidt", - "author_inst": "Rockefeller" - }, - { - "author_name": "Fengwen Zhang", - "author_inst": "Rockefeller" - }, - { - "author_name": "Justin DaSilva", - "author_inst": "Rockefeller" - }, - { - "author_name": "Daniel Poston", - "author_inst": "Rockefeller" - }, - { - "author_name": "Julio C C Lorenzi", - "author_inst": "Rockefeller" - }, - { - "author_name": "Frauke Muecksch", - "author_inst": "Rockefeller" - }, - { - "author_name": "Magdalena Rutkowska", - "author_inst": "Rockefeller" - }, - { - "author_name": "Hans-Heinrich Hoffmann", - "author_inst": "Rockefeller" - }, - { - "author_name": "Eleftherios Michailidis", - "author_inst": "Rockefeller" - }, - { - "author_name": "Christian Gaebler", - "author_inst": "Rockefeller" - }, - { - "author_name": "Marianna Agudelo", - "author_inst": "Rockefeller" - }, - { - "author_name": "Alice Cho", - "author_inst": "Rockefeller" - }, - { - "author_name": "Zijun Wang", - "author_inst": "Rockefeller" - }, - { - "author_name": "Anna Gazumyan", - "author_inst": "Rockefeller" - }, - { - "author_name": "Melissa Cipolla", - "author_inst": "Rockefeller" - }, - { - "author_name": "Larry Luchsinger", - "author_inst": "New York Blood Center" - }, - { - "author_name": "Christopher D Hillyer", - "author_inst": "New York Blood Center" - }, - { - "author_name": "Marina Caskey", - "author_inst": "Rockefeller" - }, - { - "author_name": "Davide F Robbiani", - "author_inst": "Rockefeller" - }, - { - "author_name": "Charles Rice", - "author_inst": "Rockefeller" - }, - { - "author_name": "Michel C Nussenzweig", - "author_inst": "Rockefeller" - }, - { - "author_name": "Theodora Hatziioannou", - "author_inst": "Rockefeller" - }, - { - "author_name": "Paul D Bieniasz", - "author_inst": "The Rockefeller University" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.07.21.214932", "rel_title": "The D614G mutation in the SARS-CoV2 Spike protein increases infectivity in an ACE2 receptor dependent manner", @@ -1319912,6 +1318548,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.18.20156893", + "rel_title": "Do low TB prevalence or lack of BCG VaccinationContribute to Emergence Multisystem Inflammatory Syndrome?", + "rel_date": "2020-07-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.18.20156893", + "rel_abs": "BackgroundEmergence of new multisystem inflammatory syndrome in children (MIS-C) is thought to be associated with COVID-19 pandemic. Covid-19 morbidity and mortality variances among countries have been suggested by previous works to be influenced by BCG and previous latent TB infection (which is reflected by TB prevalence) possibly through inducing heterogeneous immunity against SARS-CoV-2.\n\nAimTo examine influence of BCG status and TB prevalence on variances among countries which report new multisystem inflammatory syndrome in children (MIS-C).\n\nMethodsWe choose all countries which report MIS-C till 23/6/2020, number of cases for each 10 million inhabitants was examined among 3 categories of countries classified according to BCG program status. TB prevalence, MIS-C no. / 10 million (M) population and Covid-19 deaths/M are taken as markers. Receiver operation characteristic - (ROC) curve, with some relative indicators such as (sensitivity and specificity rates), estimation area of trade - off between sensitivity and specificity, and cutoff points are used with different studied markers for discriminating different three pairs of countries (which have different BCG practices).\n\nResultsBCG vaccinations and high TB prevalence are found to be associated with decrease MIS-C no. and COVID-19 deaths\n\nConclusionsFindings might explain variances in MIS-C incidence and in COVID-19 mortality among countries worldwide. Further studies to confirm this relation and to confirm possible similar relations in Kawasaki disease(KD) in previous epidemics is recommended.\n\nWhat is Known- Although the etiology for KD remains unknown, available evidence supports the hypothesis that the pathogenesis is closely associated with dysregulation of immune responses to an infectious agent.\n- BCG and / or Latent TB have heterogeneous beneficial effects.\n\n\nWhat is NewOur study shows that TB prevalence and implementing BCG vaccination have negative statistical association with MIS-C cases and COVID-19 mortality.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Tareef F Raham", + "author_inst": "MOH IRAQ" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.19.20157453", "rel_title": "Recurrent SARS-CoV-2 RNA positivity after COVID-19: A systematic review and meta analysis", @@ -1320364,25 +1319019,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.18.20156695", - "rel_title": "A preliminary model to describe the transmission dynamics of Covid-19 between two neighboring cities or countries", - "rel_date": "2020-07-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.18.20156695", - "rel_abs": "We present a mathematical model that would allow one to describe the transmission dynamics of Covid-19 between two neighboring cities or countries. This model is analyzed both analytical and numerically. It is a preliminary model because it assumes that the migration rate and the mortality rate are constant over time. Despite these simplifications, only two of the four equilibrium conditions were deduced from the system of equations proposed in this paper. Finally, we show an example the transmission dynamics between Portugal and Spain according to the cases registered before June 3, 2020.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Raul Isea", - "author_inst": "IDEA" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.19.20157255", "rel_title": "Sleepless in Lockdown: unpacking differences in sleep loss during the coronavirus pandemicin the UK", @@ -1321590,6 +1320226,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2020.07.19.211110", + "rel_title": "The short and long-range RNA-RNA Interactome of SARS-CoV-2", + "rel_date": "2020-07-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.19.211110", + "rel_abs": "The Coronaviridae is a family of positive-strand RNA viruses that includes SARS-CoV-2, the etiologic agent of the COVID-19 pandemic. Bearing the largest single-stranded RNA genomes in nature, coronaviruses are critically dependent on long-distance RNA-RNA interactions to regulate the viral transcription and replication pathways. Here we experimentally mapped the in vivo RNA-RNA interactome of the full-length SARS-CoV-2 genome and subgenomic mRNAs. We uncovered a network of RNA-RNA interactions spanning tens of thousands of nucleotides. These interactions reveal that the viral genome and subgenomes adopt alternative topologies inside cells, and engage in different interactions with host RNAs. Notably, we discovered a long-range RNA-RNA interaction - the FSE-arch - that encircles the programmed ribosomal frameshifting element. The FSE-arch is conserved in the related MERS-CoV and is under purifying selection. Our findings illuminate RNA structure based mechanisms governing replication, discontinuous transcription, and translation of coronaviruses, and will aid future efforts to develop antiviral strategies.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Omer Ziv", + "author_inst": "Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK" + }, + { + "author_name": "Jonathan Price", + "author_inst": "Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK" + }, + { + "author_name": "Lyudmila Shalamova", + "author_inst": "Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Giessen 35392, Germany" + }, + { + "author_name": "Tsveta Kamenova", + "author_inst": "Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK" + }, + { + "author_name": "Friedemann Weber", + "author_inst": "Institute for Virology, FB10-Veterinary Medicine, Justus-Liebig University, Giessen 35392, Germany" + }, + { + "author_name": "Eric A. Miska", + "author_inst": "Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, CB2 1QN, UK" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "molecular biology" + }, { "rel_doi": "10.1101/2020.07.19.210955", "rel_title": "Interferons and viruses induce a novel primate-specific isoform dACE2 and not the SARS-CoV-2 receptor ACE2", @@ -1322090,33 +1320765,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.18.20152256", - "rel_title": "Providing breastfeeding support during the COVID-19 pandemic: Concerns of mothers who contacted the Australian Breastfeeding Association", - "rel_date": "2020-07-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.18.20152256", - "rel_abs": "Concerns of mothers seeking breastfeeding support during the COVID-19 pandemic, and the experiences of Australian Breastfeeding Association (ABA) volunteers who assisted them, were explored via an online survey. Surveys were completed 16th March to 18th of May 2020 and described the COVID-19 related concerns of 340 individuals. One hundred and thirty six mothers (64%) sought support to protect their infants by continuing breastfeeding, increasing milk supply, or restarting breastfeeding. Mothers were commonly stressed, isolated and needing reassurance. Thirty four (10%) raised concerns about COVID-19 and breastfeeding safety. One hundred and twenty nine (61%) informed volunteers they were unable to access face-to-face health services because of fear or unavailability. Most common breastfeeding concerns were related to insufficient milk or weight gain, painful breasts, relactation, and reducing supplemental milk. Volunteers reported mothers were worried stress had reduced milk supply, that milk supply concerns were exacerbated by the inability to weigh infants, and that seeking medical treatment was being delayed. ABA volunteers stated they felt supported and confident assisting mothers while also expressing distress at mothers situation. ABAs role in emergency response should be recognised and national planning for infant and young child feeding in emergencies, must be urgently developed, funded, and implemented.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Naomi Hull", - "author_inst": "Australian Breastfeeding Association" - }, - { - "author_name": "Renee L Kam", - "author_inst": "Australian Breastfeeding Association" - }, - { - "author_name": "Karleen D Gribble", - "author_inst": "Western Sydney University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2020.07.16.20152033", "rel_title": "An Optimization Framework to Study the Balance Between Expected Fatalities due to COVID-19 and the Reopening of U.S. Communities", @@ -1323264,6 +1321912,33 @@ "type": "new results", "category": "evolutionary biology" }, + { + "rel_doi": "10.1101/2020.07.20.212563", + "rel_title": "In silico comparative genomics of SARS-CoV-2 to determine the source and diversity of the pathogen in Bangladesh", + "rel_date": "2020-07-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.20.212563", + "rel_abs": "The COVID19 pandemic caused by SARS-CoV-2 virus has severely affected most countries of the world including Bangladesh. We conducted comparative analysis of publicly available whole-genome sequences of 64 SARS-CoV-2 isolates in Bangladesh and 371 isolates from another 27 countries to predict possible transmission routes of COVID19 to Bangladesh and genomic variations among the viruses. Phylogenetic analysis indicated that the pathogen was imported in Bangladesh from multiple countries. The viruses found in the southern district of Chattogram were closely related to strains from Saudi Arabia whereas those in Dhaka were similar to that of United Kingdom and France. The 64 SARS-CoV-2 sequences from Bangladesh belonged to three clusters. Compared to the ancestral SARS-CoV-2 sequence reported from China, the isolates in Bangladesh had a total of 180 mutations in the coding region of the genome, and 110 of these were missense. Among these, 99 missense mutations (90%) were predicted to destabilize protein structures. Remarkably, a mutation that leads to an I300F change in the nsp2 protein and a mutation leading to D614G change in the spike protein were prevalent in SARS-CoV-2 genomic sequences, and might have influenced the epidemiological properties of the virus in Bangladesh.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Tushar A Shishir", + "author_inst": "Brac University, Bangladesh" + }, + { + "author_name": "Iftekhar Bin Naser", + "author_inst": "Brac University, Bangladesh" + }, + { + "author_name": "Shah M Faruque", + "author_inst": "Independent University, Bangladesh" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.07.20.212068", "rel_title": "Computational optimization of the SARS-CoV-2 receptor-binding-motif affinity for human ACE2", @@ -1323700,73 +1322375,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.17.20156539", - "rel_title": "Quantifying SARS-CoV-2 infection risk within the Apple/Google exposure notification framework to inform quarantine recommendations", - "rel_date": "2020-07-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.17.20156539", - "rel_abs": "Most Bluetooth-based exposure notification apps use three binary classifications to recommend quarantine following SARS-CoV-2 exposure: a window of infectiousness in the transmitter, [≥]15 minutes duration, and Bluetooth attenuation below a threshold. However, Bluetooth attenuation is not a reliable measure of distance, and infection risk is not a binary function of distance, nor duration, nor timing. We model uncertainty in the shape and orientation of an exhaled virus-containing plume and in inhalation parameters, and measure uncertainty in distance as a function of Bluetooth attenuation. We calculate expected dose by combining this with estimated infectiousness based on timing relative to symptom onset. We calibrate an exponential dose-response curve based on infection probabilities of household contacts. The probability of current or future infectiousness, conditioned on how long post-exposure an exposed individual has been symptom-free, decreases during quarantine, with shape determined by incubation periods, proportion of asymptomatic cases, and asymptomatic shedding durations. It can be adjusted for negative test results using Bayes Theorem. We capture a 10-fold range of risk using 6 infectiousness values, 11-fold range using 3 Bluetooth attenuation bins, [~]6-fold range from exposure duration given the 30 minute duration cap imposed by the Google/Apple v1.1, and [~]11-fold between the beginning and end of 14 day quarantine. Public health authorities can either set a threshold on initial infection risk to determine 14-day quarantine onset, or on the conditional probability of current and future infectiousness conditions to determine both quarantine and duration.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Amanda M Wilson", - "author_inst": "University of Arizona" - }, - { - "author_name": "Nathan Aviles", - "author_inst": "University of Arizona" - }, - { - "author_name": "James I Petrie", - "author_inst": "Covid Watch" - }, - { - "author_name": "Paloma I Beamer", - "author_inst": "University of Arizona" - }, - { - "author_name": "Zsombor Szabo", - "author_inst": "Covid-Watch" - }, - { - "author_name": "Michelle Xie", - "author_inst": "Covid Watch" - }, - { - "author_name": "Janet McIllece", - "author_inst": "World Wide Technology" - }, - { - "author_name": "Yijie Chen", - "author_inst": "University of Arizona" - }, - { - "author_name": "Young-Jun Son", - "author_inst": "University of Arizona" - }, - { - "author_name": "Sameer Halai", - "author_inst": "Covid Watch" - }, - { - "author_name": "Tina White", - "author_inst": "Covid Watch" - }, - { - "author_name": "Kacey C Ernst", - "author_inst": "University of Arizona" - }, - { - "author_name": "Joanna Masel", - "author_inst": "University of Arizona" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.15.20154989", "rel_title": "Bibliometric analysis of COVID-19 literature", @@ -1325058,6 +1323666,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.16.20155812", + "rel_title": "A Contact-Explicit Covid-19 Epidemic and Response Assessment Model", + "rel_date": "2020-07-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.16.20155812", + "rel_abs": "We formulate a refined SEIR epidemic model that explicitly includes a contact class C that either thwarts pathogen invasion and returns to the susceptible class S or progresses successively through latent, asymptomatic, and symptomatic classes L, A, and I. Individuals in both A and I may go directly to an immune class V, and in I to a dead class D. We extend this SCLAIV formulation by including a set of drivers that can be used to develop policy to manage current Covid-19 and similar type disease outbreaks. These drivers include surveillance, social distancing (rate and efficacy), social relaxation, quarantining (linked to contact tracing), patient treatment/isolation and vaccination processes, each of which can be represented by a non-negative constant or an s-shaped switching flow. The latter are defined in terms of onset and switching times, initial and final values, and abruptness of switching. We built a Covid-19NMB-DASA web app to generate both deterministic and stochastic solutions to our SCLAIV and drivers model and use incidence and mortality data to provide both maximum-likelihood estimation (MLE) and Bayesian MCMC fitting of parameters. In the context of South African and English Covid-19 incidence data we demonstrate how to both identify and evaluate the role of drivers in ongoing outbreaks. In particular, we show that early social distancing in South Africa likely averted around 80,000 observed cases (actual number is double if only half the cases are observed) during the months of June and July. We also demonstrated that incidence rates in South Africa will increase to between a conservative estimate of 15 and 30 thousand observed cases per day (at a 50% surveillance level) by the end of August if stronger social distancing measures are not effected during July and August, 2020. On different a note, we show that comparably good local MLE fits of the English data using surveillance, social distancing and social relaxation drivers can represent very different kinds of outbreaks--one with close to 90% and another with under 8% immune individuals. This latter result provides a cautionary tale of why fitting SEIR-like models to incidence or prevalence data can be extremely problematic when not anchored by other critical measures, such as levels of immunity in the population. Our presentation illustrates how our SCLAIV formulation can be used to carry out forensic and scenario analyses of disease outbreaks such as Covid-19 in well defined regions.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Wayne M Getz", + "author_inst": "University of California, Berkeley, Dept ESPM" + }, + { + "author_name": "Ludovica Luisa-Vissat", + "author_inst": "University of California, Berkeley, Dept ESPM" + }, + { + "author_name": "Richard Salter", + "author_inst": "Oberlin College, Dept Computer Science" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.16.20155358", "rel_title": "The risk of severe COVID-19: hospital and ICU admission rates in Norway", @@ -1325402,49 +1324037,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.07.16.20155572", - "rel_title": "Probability of aerosol transmission of SARS-CoV-2", - "rel_date": "2020-07-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.16.20155572", - "rel_abs": "Transmission of SARS-CoV-2 leading to COVID-19 occurs through exhaled respiratory droplets from infected humans. Currently, however, there is much controversy over whether respiratory aerosol microdroplets play an important role as a route of transmission. By measuring and modeling the dynamics of exhaled respiratory droplets we can assess the relative contribution of aerosols in the spreading of SARS-CoV-2. We measure size distribution, total numbers and volumes of respiratory droplets, including aerosols, by speaking and coughing from healthy subjects. Dynamic modelling of exhaled respiratory droplets allows to account for aerosol persistence times in confined public spaces. The probability of infection by inhalation of aerosols when breathing in the same space can then be estimated using current estimates of viral load and infectivity of SARS-CoV-2. In line with the current known reproduction numbers, our study of transmission of SARS-CoV-2 suggests that aerosol transmission is an inefficient route, in particular from non or mildly symptomatic individuals.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Daniel Bonn", - "author_inst": "University of Amsterdam" - }, - { - "author_name": "Scott Howard Smith", - "author_inst": "University of Amsterdam" - }, - { - "author_name": "Aernout Somsen", - "author_inst": "Cardiology Centers of the Netherlands" - }, - { - "author_name": "Cees van Rijn", - "author_inst": "University of Amsterdam" - }, - { - "author_name": "Stefan Kooij", - "author_inst": "University of Amsterdam" - }, - { - "author_name": "Lia van der Hoek", - "author_inst": "University of Amsterdam - AMC" - }, - { - "author_name": "Reinout A Bem", - "author_inst": "Amsterdam University Medical Centers" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.07.16.20155481", "rel_title": "The properties of hot household hygroscopic materials and their potential use for non-medical facemask decontamination", @@ -1327096,6 +1325688,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "rheumatology" }, + { + "rel_doi": "10.1101/2020.07.15.20126730", + "rel_title": "Acute Demyelinating Encephalomyelitis (ADEM) in COVID-19 infection: A Case Series.", + "rel_date": "2020-07-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20126730", + "rel_abs": "ObjectiveTo report three patients infected with COVID-19 with severe respiratory syndrome requiring intubation, who developed acute demyelinating encephalomyelitis (ADEM).\n\nMethodPatient data were obtained from medical records from the North Memorial Health Hospital, Robbinsdale, MN, USA\n\nResultsThree patients (two men and one woman, aged 38 - 63) presented with fatigue, cough and fever leading to development of acute respiratory distress syndrome secondary to COVID-19 infection requiring intubation and ventilatory support. Two patients were unresponsive, one with strong eye deviation to the left and the third patient had severe diffuse weakness. MRI in all patients showed findings consistent with ADEM. CSF showed elevated protein in all patients with normal cell count and no evidence of infection, including negative COVID-19 PCR. All three of the patients received Convalescent plasma therapy for COVID-19. All patients were treated with intravenous corticosteroids and improved, although two responded minimally. Two patients treated with IVIG showed no further improvement.\n\nConclusionNeurological complications from COVID-19 are being rapidly recognized. Our three cases highlight the occurrence of ADEM as a postinfectious/immune mediated complication of COVID-19 infection, which may be responsive to corticosteroid treatment. Early recognition of this complication and treatment is important to avoid long term complications.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Michaela McCuddy", + "author_inst": "Department of Family Medicine, University of Minnesota" + }, + { + "author_name": "Praful Kelkar", + "author_inst": "Minneapolis Clinic of Neurology" + }, + { + "author_name": "Yu Zhao", + "author_inst": "Minneapolis Clinic of Neurology" + }, + { + "author_name": "David Wicklund", + "author_inst": "Minneapolis Radiology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "neurology" + }, { "rel_doi": "10.1101/2020.07.14.20153429", "rel_title": "COVID-19 Pandemic among Latinx Farmworker and Non-farmworker Families in North Carolina: Knowledge, Risk Perceptions, and Preventive Behaviors", @@ -1327716,37 +1326339,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.15.20147041", - "rel_title": "A systematic review uncovers a wide-gap between COVID-19 in humans and animal models", - "rel_date": "2020-07-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20147041", - "rel_abs": "BackgroundAnimal models of COVID-19 have been rapidly reported after the start of the pandemic. We aimed to assess whether the newly created models reproduce the full spectrum of humans COVID-19.\n\nMethodsWe searched the Medline, as well as BioRxiv and MedRxiv preprint servers for original research published in English from January 1, to May 20, 2020. We used the search terms \"COVID-19\" OR \"SARS-CoV-2\" AND, \"animal models\", \"hamsters\", \"nonhuman primates\", \"macaques\", \"rodent\", \"mice\", \"rats\", \"ferrets\", \"rabbits\", \"cats\", and \"dogs\". Inclusion criteria were the establishment of animal models of COVID-19 as an endpoint. Other inclusion criteria were assessment of prophylaxis, therapies, or vaccines, using animal models of COVID-19.\n\nFindings13 peer-reviewed studies and 14 preprints met inclusion criteria. The animals used were nonhuman primates (n=13), mice (n=7), ferrets (n=4), hamsters (n=4), and cats (n=1). All animals supported high viral replication in the upper and lower respiratory tract associated with mild clinical manifestations, lung pathology and full recovery. Older animals displayed relatively more severe illness than the younger ones. No animal models developed hypoxemic respiratory failure, multiple organ dysfunction, culminating in death. All species elicited a specific IgG antibodies response to the spike proteins, which were protective against a second exposure. Transient systemic inflammation was observed occasionally in Rhesus macaques, hamsters, and mice. Notably, none of the animals unveiled cytokine storm or coagulopathy.\n\nConclusionsMost of the animal models of COVID-19 recapitulated mild pattern of human COVID-19 with full recovery phenotype. No severe illness associated with mortality was observed, suggesting a wide gap between COVID-19 in humans and animal models.\n\nFundingThere was no funding source for this study.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Salleh N Ehaideb", - "author_inst": "Experimental Medicine Department, King Abdullah International Medical Research Center/King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Med" - }, - { - "author_name": "Mashan L Abdullah", - "author_inst": "Experimental Medicine Department, King Abdullah International Medical Research Center/King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Med" - }, - { - "author_name": "Bisher Abuyassin", - "author_inst": "Experimental Medicine Department, King Abdullah International Medical Research Center/King Saud bin Abdulaziz University for Health Sciences, King Abdulaziz Med" - }, - { - "author_name": "Abderrezak Bouchama", - "author_inst": "King Abdullah International Medical Research Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.16.20150250", "rel_title": "A community-deployable SARS-CoV-2 screening test using raw saliva with 45 minutes sample-to-results turnaround", @@ -1329014,6 +1327606,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.17.20155226", + "rel_title": "Impact of climatic, demographic and disease control factors on the transmission dynamics of COVID-19 in large cities worldwide", + "rel_date": "2020-07-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.17.20155226", + "rel_abs": "We are now over seven months into a pandemic of COVID-19 caused by the SARS-CoV-2 virus and global incidence continues to rise. In some regions such as the temperate northern hemisphere there are fears of \"second waves\" of infections over the coming months, while in other, vulnerable regions such as Africa and South America, concerns remain that cases may still rise, further impacting local economies and livelihoods. Despite substantial research efforts to date, it remains unresolved as to whether COVID-19 transmission has the same sensitivity to climate and seasonality observed for other common respiratory viruses such as seasonal influenza. Here we investigate any empirical evidence of seasonality using a robust estimation framework. For 304 large cities across the world, we estimated the basic reproduction number (R0) using logistic growth curves fitted to cumulative case data. We then assessed evidence for association with climatic variables through mixed-effects and ordinary least squares (OLS) regression while adjusting for city-level variation in demographic and disease control factors. We find evidence of association between temperature and R0 during the early phase of the epidemic in China only. During subsequent pandemic spread outside China, we instead find evidence of seasonal change in R0, with greater R0 within cities experiencing shorter daylight hours (direct effect coefficient = -0.247, p = 0.006), after separating out effects of calendar day. The effect of daylight hours may be driven by levels of UV radiation, which is known to have detrimental effects on coronaviruses, including SARS-CoV-2. In the global analysis excluding China, climatic variables had weaker explanatory power compared to demographic or disease control factors. Overall, we find a weak but detectable signal of climate variables on the transmission of COVID-19. As seasonal changes occur later in 2020, it is feasible that the transmission dynamics of COVID-19 may shift in a detectable manner. However, rates of transmission and health burden of the pandemic in the coming months will be ultimately determined by population factors and disease control policies.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Soeren Metelmann", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Karan Pattni", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Liam Brierley", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Lisa Cavalerie", + "author_inst": "University of Liverpool / International Livestock Research Institute" + }, + { + "author_name": "Cyril Caminade", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Marcus SC Blagrove", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Joanne Turner", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Kieran J Sharkey", + "author_inst": "University of Liverpool" + }, + { + "author_name": "Matthew Baylis", + "author_inst": "University of Liverpool" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.08.20148692", "rel_title": "Confirmed central olfactory system lesions on brain MRI in COVID-19 patients with anosmia: a case-series", @@ -1329590,97 +1328233,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.17.20156158", - "rel_title": "Multisectoral collaboration for pandemic response and operational support of critical care and emergency departments", - "rel_date": "2020-07-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.17.20156158", - "rel_abs": "BackgroundIn March 2020, an influx of admissions in COVID-19 positive patients threatened to overwhelm healthcare facilities in East Baton Rouge Parish, Louisiana. Exacerbating this problem was a shortage of diagnostic testing capability, resulting in a delay in time-to-result return. An improvement in diagnostic testing availability and timeliness was necessary to improve the allocation of resources and ultimate throughput of patients. The management of a COVID-19 positive patient or patient under investigation requires infection control measures that can quickly consume personal protective equipment (PPE) stores and personnel available to treat these patients. Critical shortages of both PPE and personnel also negatively impact care in patients admitted with non-COVID-19 illnesses.\n\nMethodsA multisectoral partnership of healthcare providers, facilities and academicians created a molecular diagnostic lab within an academic research facility dedicated to testing inpatients and healthcare personnel for SARS-CoV-2. The purpose of the laboratory was to provide a temporary solution to the East Baton Rouge Parish healthcare community until individual facilities were self-sustaining in testing capabilities. We describe the partnership and the impacts of this endeavor by developing a model derived from a combination of data sources, including electronic health records, hospital operations, and state and local resources.\n\nFindingsOur model demonstrates two important principles: the impact of reduced turnaround times (TAT) on potential differences in inpatient population numbers for COVID-19 and savings in PPE attributed to the more rapid TAT.\n\nInterpretationOverall, we provide rationale for and demonstration of the utility of multisectoral partnerships when responding to public health emergencies.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Rebecca C Christofferson", - "author_inst": "Louisiana State University" - }, - { - "author_name": "Hollis R O'Neal", - "author_inst": "Louisiana State University Health Sciences Center, Baton Rouge" - }, - { - "author_name": "Tonya Jagneaux", - "author_inst": "Louisiana State University Health Sciences Center, Baton Rouge" - }, - { - "author_name": "Catherine S O'Neal", - "author_inst": "Louisiana State University Health Sciences Center, Baton Rouge" - }, - { - "author_name": "Christine S Walsh", - "author_inst": "Louisiana State University" - }, - { - "author_name": "E. Handly Mayton", - "author_inst": "Louisiana State University" - }, - { - "author_name": "Luan V Dinh", - "author_inst": "Pennington Biomedical Research Center" - }, - { - "author_name": "Abigail I Fish", - "author_inst": "Louisiana State University" - }, - { - "author_name": "Anh Phan", - "author_inst": "Pennington Biomedical Research Center" - }, - { - "author_name": "Thaya E Stoufflet", - "author_inst": "Louisiana State University" - }, - { - "author_name": "Jonathan R Schroeder", - "author_inst": "Our Lady of the Lake Regional Medical Center" - }, - { - "author_name": "Morgan K Walker", - "author_inst": "Louisiana State University Health Sciences Center, Baton Rouge" - }, - { - "author_name": "Erik A Turner", - "author_inst": "Louisiana State University" - }, - { - "author_name": "Christi G Pierce", - "author_inst": "Our Lady of the Lake Regional Medical Center" - }, - { - "author_name": "K. Scott Wester", - "author_inst": "Our Lady of the Lake Regional Medical Center" - }, - { - "author_name": "Connie DeLeo", - "author_inst": "Baton Rouge General Hospital" - }, - { - "author_name": "Edgardo Tenreiro", - "author_inst": "Baton Rouge General Hospital" - }, - { - "author_name": "Beverly W Ogden", - "author_inst": "Woman's Hospital" - }, - { - "author_name": "Stephania A Cormier", - "author_inst": "Louisiana State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.07.17.20156034", "rel_title": "A deterministic, age-stratified, extended SEIRD model for investigating the effect of non-pharmaceutical interventions on SARS-CoV-2 spread in Belgium", @@ -1330984,6 +1329536,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.07.15.20154997", + "rel_title": "Associations between Demographic Characteristics, Perceived Threat, Perceived Stress, Coping Responses and Adherence to COVID-19 Prevention Measures among Healthcare Students in China: A Cross-Sectional Survey with Implications for the Control of COVID-19", + "rel_date": "2020-07-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20154997", + "rel_abs": "ObjectivesTo investigate the associations between demographic characteristics, perceived threat, perceived stress, coping responses and adherence to COVID-19 prevention measures in Chinese Healthcare students.\n\nDesignA cross-sectional survey collecting data in Hong Kong and Fujian Province of China. Self-administered questionnaires were collected via online platform in April 2020.\n\nParticipantsA convenience and snowball sample of 2706 students aged 18 years or older and studying a healthcare programme in Hong Kong or Fujian.\n\nSettingStudents were recruited in tertiary education institutions/universities in Hong Kong and Putian (a prefecture-level city in eastern Fujian province). The institutions offered various healthcare programmes in degree or sub-degree levels.\n\nMain outcome measuresCompliances to social distancing and personal hygiene measures were assessed by 10-item Social Distancing Scale and 5-item Personal Hygiene Scale respectively. Path analysis was performed to identify factors associated with the compliance outcomes.\n\nResultsThe participants reported high compliances to both social distancing and personal hygiene measures. Confidence to manage the current situation, wishful thinking and empathetic responding directly predicted compliance to social distancing ({beta}=-0.31, p<0.001; {beta}=0.35, p=0.015; {beta}=0.33, p<0.001 respectively) and personal hygiene measures ({beta}==-0.16, p<0.001; {beta}=0.21, p<0.001; {beta}=0.16, p<0.001 respectively). Gender, geographical location, and clinical experience were the only three demographic variables having direct and/or indirect effects on social distancing and personal hygiene measures. The final model constructed demonstrated a very good fit to the data (Chi-square X2=27.27, df=17, P=0.044; X2/df=1.61; GFI=0.998, CFI=0.997, TLI=0.992, RMSEA=0.015).\n\nConclusionsThe predictive model constructed in this study is the first one to explore factors associating with the compliance to infection control measures in healthcare students amid the COVID-19 outbreak. The findings suggest that students who are male, habituate in Hong Kong, have more clinical experience and weak confidence to manage the threat tend to have lower compliance to social distancing and personal hygiene measures. Wishful thinking, contrasting to previous studies, was first found to positively associate with adherence to COVID-19 control measures.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Anson Chui Yan Tang", + "author_inst": "Tung Wah College" + }, + { + "author_name": "Enid Wai Yung Kwong", + "author_inst": "Putian College" + }, + { + "author_name": "Liangying Chen", + "author_inst": "Putian College" + }, + { + "author_name": "Winnie Lai Sheung Cheng", + "author_inst": "Tung Wah College" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.07.16.20155036", "rel_title": "Are the upper bounds for new SARS-CoV-2 infections in Germany useful?", @@ -1331496,37 +1330079,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.15.20154971", - "rel_title": "Time-dependent dynamic transmission potential and instantaneous reproduction number of COVID-19 pandemic in India.", - "rel_date": "2020-07-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20154971", - "rel_abs": "IntroductionDynamic tools and methods to assess the ongoing transmission potential of COVID-19 in India are required. We aim to estimate time-dependent transmissibility of COVID-19 for India using a reproducible framework.\n\nMethodsDaily COVID-19 case incidence time series for India and its states was obtained from https://api.covid19india.org/ and pre-processed. Bayesian approach was adopted to quantify transmissibility at a given location and time, as indicated by the instantaneous reproduction number (Reff). Analysis was carried out in R version 4.0.2 using \"EpiEstim_2.2-3\" package. Serial interval distribution was estimated using \"uncertain_si\" algorithm with inputs of mean, standard deviation, minimum and maximum of mean serial interval as 5.1, 1.2, 3.9 and 7.5 days respectively; and mean, standard deviation, minimum, and maximum of standard deviations of serial interval as 3.7, 0.9, 2.3, and 4.7 respectively with 100 simulations and moving average of seven days.\n\nResultsA total of 9,07,544 cumulative incident cases till July 13th, 2020 were analysed. Daily COVID-19 incidence in the country was seen on the rise; however, transmissibility showed a decline from the initial phases of COVID-19 pandemic in India. The maximum Reff reached at the national level during the study period was 2.57 (sliding week ending April 4th, 2020). Reff on July 13th, 2020 for India was 1.16 with a range from 0.59 to 2.98 across various states/UTs.\n\nConclusionReff provides critical feedback for assessment of transmissibility of COVID-19 and thus is a potential dynamic decision support tool for on-ground public health decision making.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Gurpreet Singh", - "author_inst": "Sree Chitra Tirunal Institute for Medical Sciences & Technology, Trivandrum" - }, - { - "author_name": "Seema Patrikar", - "author_inst": "Armed Forces Medical College, Pune." - }, - { - "author_name": "PS Sarma", - "author_inst": "Sree Chitra Tirunal Institute for Medical Sciences & Technology, Trivandrum." - }, - { - "author_name": "Biju Soman", - "author_inst": "Sree Chitra Tirunal Institute for Medical Sciences & Technology, Trivandrum." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.15.20154419", "rel_title": "Utrametric diffusion model for spread of covid-19 in socially clustered population: Can herd immunity be approached in Sweden?", @@ -1332514,6 +1331066,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.15.20154047", + "rel_title": "Early Improvement of Acute Respiratory Distress Syndrome in Patients with COVID-19: Insights from the Data of ICU Patients in Chongqing, China", + "rel_date": "2020-07-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.15.20154047", + "rel_abs": "Acute respiratory distress syndrome (ARDS) may be the main cause of death in patients with coronavirus disease 2019 (COVID-19). Herein, we retrospect clinical features, outcomes and ARDS characteristics of 75 intensive care unit (ICU) patients with COVID-19 in Chongqing, China. We found a 5.3% case fatality rate of the ICU patients in Chongqing. 93% patients developed ARDS during the intensive care, and more than half were moderate. However, most of the patients (55%) supported with high flow nasal cannula (HFNC) oxygen therapy, but not mechanical ventilation. Nearly one third of patients with ARDS got an early improvement (eiARDS), and the rate is much higher than the other causes of ARDS in a previous study. Patients with eiARDS had a higher survival rate and lower length of ICU stay. The age (< 55 years) is an independent predictor for the eiARDS, and stratification of COVID-19 patients by age is recommended.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Zhu Zhan", + "author_inst": "The Second Affiliated Hospital of Chongqing Medical University" + }, + { + "author_name": "Xin Yang", + "author_inst": "The First Affiliated Hospital of Chongqing Medical University" + }, + { + "author_name": "Hu Du", + "author_inst": "The Second Affiliated Hospital of Chongqing Medical University" + }, + { + "author_name": "Chuanlai Zhang", + "author_inst": "The Second Affiliated Hospital of Chongqing Medical University" + }, + { + "author_name": "Yuyan Song", + "author_inst": "Chongqing public health medical center" + }, + { + "author_name": "Xiaoyun Ran", + "author_inst": "The Second Affiliated Hospital of Chongqing Medical University" + }, + { + "author_name": "An Zhang", + "author_inst": "The Second Affiliated Hospital of Chongqing Medical University" + }, + { + "author_name": "Mei Yang", + "author_inst": "Chongqing Sixth People's Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.07.14.20153734", "rel_title": "Place and causes of acute cardiovascular mortality during the COVID19 pandemic: retrospective cohort study of 580,972 deaths in England and Wales, 2014 to 2020", @@ -1332926,73 +1331525,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.07.13.20153130", - "rel_title": "Asthma in COVID-19: An extra chain fitting around the neck?", - "rel_date": "2020-07-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20153130", - "rel_abs": "IntroductionThe novel coronavirus disease 2019 (COVID-19) has rapidly spread across the globe, overwhelming healthcare systems and depleting resources. The infection has a wide spectrum of presentations, and pre-existing comorbidities have been found to have a dramatic effect on the disease course and prognosis. We sought to analyze the effect of asthma on the disease progression and outcomes of COVID-19 patients.\n\nMethodsWe conducted a multi-center retrospective study of positively confirmed COVID-19 patients from multiple hospitals in Louisiana. Demographics, medical history, comorbidities, clinical presentation, daily laboratory values, complications, and outcomes data were collected and analyzed. The primary outcome of interest was in-hospital mortality. Secondary outcomes were Intensive Care Unit (ICU) admission, risk of intubation, duration of mechanical ventilation, and length of hospital stay.\n\nResultsA total of 502 COVID-19 patients (72 asthma and 430 non-asthma cohorts) were included in the study. The frequency of asthma in hospitalized cohorts was 14.3%, higher than the national prevalence of asthma (7.7%). Univariate analysis revealed that asthma patients were more likely to be obese (75% vs 54.2%, p=0.001), with higher frequency of intubation (40.3% vs 27.8%, p = 0.036), and required longer duration of hospitalization (15.1{+/-}12.5 vs 11.5{+/-}10.6, p=0.015). After adjustment, multivariable analysis showed that asthmatic patients were not associated with higher risk of ICU admission (OR=1.81, 95%CI=0.98-3.09, p=0.06), endotracheal intubation (OR=1.77, 95%CI=0.99-3.04, p=0.06) or complications (OR=1.37, 95%CI=0.82-2.31, p=0.23). Asthmatic patients were not associated with higher odds of prolonged hospital length of stay (OR=1.48, 95%CI=0.82-2.66, p=0.20) or with the duration of ICU stay (OR=0.76, 95%CI=0.28-2.02, p=0.58). Kaplan-Meier curve showed no significant difference in overall survival of the two groups (p=0.65).\n\nConclusionDespite the increased prevalence of hospitalization in asthmatic COVID-19 patients compared to the general population, after adjustment for other variables, it was neither associated with increased severity nor worse outcomes.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Mohammad Hosny Hussein", - "author_inst": "Division of Endocrine and Oncologic Surgery, Department of Surgery, Tulane University, School of Medicine, New Orleans, Louisiana, 70112, USA" - }, - { - "author_name": "Eman Ali Toraih", - "author_inst": "Division of Endocrine and Oncologic Surgery, Department of Surgery, Tulane University, School of Medicine, New Orleans, Louisiana, 70112, USA" - }, - { - "author_name": "Abdallah S Attia", - "author_inst": "Division of Endocrine and Oncologic Surgery, Department of Surgery, Tulane University, School of Medicine, New Orleans, Louisiana, 70112, USA" - }, - { - "author_name": "Mohanad Youssef", - "author_inst": "Division of Endocrine and Oncologic Surgery, Department of Surgery, Tulane University, School of Medicine, New Orleans, Louisiana, 70112, USA" - }, - { - "author_name": "Mahmoud Omar", - "author_inst": "Division of Endocrine and Oncologic Surgery, Department of Surgery, Tulane University, School of Medicine, New Orleans, Louisiana, 70112, USA" - }, - { - "author_name": "Nicholas Burley", - "author_inst": "Tulane University, School of Medicine, New Orleans, Louisiana, 70112, USA" - }, - { - "author_name": "Allen D Zhang", - "author_inst": "Tulane University, School of Medicine, New Orleans, Louisiana, 70112, USA" - }, - { - "author_name": "Jackson Roos", - "author_inst": "Tulane University, School of Medicine, New Orleans, Louisiana, 70112, USA" - }, - { - "author_name": "August Houghton", - "author_inst": "Tulane University, School of Medicine, New Orleans, Louisiana, 70112, USA" - }, - { - "author_name": "Nedum Aniemeka", - "author_inst": "Tulane University, School of Medicine, New Orleans, Louisiana, 70112, USA" - }, - { - "author_name": "Mohamed Ahmed Shama", - "author_inst": "Tulane University, School of Medicine, New Orleans, Louisiana, 70112, USA" - }, - { - "author_name": "Juan Duchesne", - "author_inst": "Trauma/Acute Care and Critical Care, Department of Surgery, Tulane, Tulane School of Medicine, New Orleans, LA, 70112, USA" - }, - { - "author_name": "Emad Kandil", - "author_inst": "Division of Endocrine and Oncologic Surgery, Department of Surgery, Tulane University, School of Medicine, New Orleans, Louisiana, 70112, USA" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "allergy and immunology" - }, { "rel_doi": "10.1101/2020.07.13.20152439", "rel_title": "RT-PCR testing to detect a COVID-19 outbreak in Austria: rapid, accurate and early diagnosis in primary care (The REAP study)", @@ -1334080,6 +1332612,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.13.20153171", + "rel_title": "Connecting in COVID 19: Neurology tele-follow-up experience", + "rel_date": "2020-07-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20153171", + "rel_abs": "IntroductionThe lockdown due to COVID-19 pandemic led to temporary closure of routine hospital services. This prompted the initiation of teleconsult follow-up in our department. The study outlines the experience of tele-follow-up at a tertiary care teaching hospital in India, and the perspective of neurologists about this novel approach.\n\nMethodsThe tele-follow-up was started from 26th March 2020. Data of follow up appointments was provided by the medical record section. The faculty and senior residents conducted the tele-follow-up. Communication was made via voice calls. The data for initial ten days was analyzed to find the utility and experience of the new service.\n\nResultsIn the initial ten working days, data of 968 patients was provided for tele-follow-up. A successful communication was made in 50.3% patients (contact with patients: 27.7% and family members 22.6%). The phone numbers which were not contactable/invalid/not available constituted 36.8% of the data. A total of 35 faculty and residents conducted the tele-follow-up. The utility of tele-follow-up was perceived as good by 71.4% of neurologists. Majority of neurologists (71.4%) observed that >90% of patients were continuing medications. Patients outside the city constituted 50-75% of the list. The survey revealed that all neurologists felt the need to continue tele-follow-up for far off stable patients post lock down and resumption of regular outpatient services.\n\nConclusionThe survey established the feasibility and utility of teleconsult for follow up of patients with neurological diseases who were attending the regular outpatient services before the lock down.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Deepti Vibha", + "author_inst": "All India Institute of Medical Sciences, New Delhi, India" + }, + { + "author_name": "MV Padma Srivastava", + "author_inst": "All India Institute of Medical Sciences, New Delhi, India" + }, + { + "author_name": "Kameshwar Prasad", + "author_inst": "All India Institute of Medical Sciences, New Delhi, India" + }, + { + "author_name": "Manjari Tripathi", + "author_inst": "All India Institute of Medical Sciences, New Delhi, India" + }, + { + "author_name": "Achal Kumar Srivastava", + "author_inst": "All India Institute of Medical Sciences, New Delhi, India" + }, + { + "author_name": "Rohit Bhatia", + "author_inst": "All India Institute of Medical Sciences, New Delhi, India" + }, + { + "author_name": "Mamta Bhushan Singh", + "author_inst": "All India Institute of Medical Sciences, New Delhi, India" + }, + { + "author_name": "Vishnu VY", + "author_inst": "All India Institute of Medical Sciences, New Delhi, India" + }, + { + "author_name": "Roopa Rajan", + "author_inst": "All India Institute of Medical Sciences, New Delhi, India" + }, + { + "author_name": "Rajesh Kumar Singh", + "author_inst": "All India Institute of Medical Sciences, New Delhi, India" + }, + { + "author_name": "Anu Gupta", + "author_inst": "All India Institute of Medical Sciences, New Delhi, India" + }, + { + "author_name": "Animesh Das", + "author_inst": "All India Institute of Medical Sciences, New Delhi, India" + }, + { + "author_name": "Elavarsi A", + "author_inst": "All India Institute of Medical Sciences, New Delhi, India" + }, + { + "author_name": "Divya MR", + "author_inst": "All India Institute of Medical Sciences, New Delhi, India" + }, + { + "author_name": "Bhargavi Ramanujam", + "author_inst": "All India Institute of Medical Sciences, New Delhi, India" + }, + { + "author_name": "Ahmadullah Shariff", + "author_inst": "All India Institute of Medical Sciences, New Delhi, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.13.20152959", "rel_title": "Dissemination and co-circulation of SARS-CoV2 subclades exhibiting enhanced transmission associated with increased mortality in Western Europe and the United States", @@ -1334456,49 +1333067,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.07.14.203463", - "rel_title": "Comprehensive analysis of genomic diversity of SARS-CoV-2 in different geographic regions of India: An endeavour to classify Indian SARS-CoV-2 strains on the basis of co-existing mutations", - "rel_date": "2020-07-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.14.203463", - "rel_abs": "Accumulation of mutations within the genome is the primary driving force for viral evolution within an endemic setting. This inherent feature often leads to altered virulence, infectivity and transmissibility as well as antigenic shift to escape host immunity, which might compromise the efficacy of vaccines and antiviral drugs. Therefore, we aimed at genome-wide analyses of circulating SARS-CoV-2 viruses for the emergence of novel co-existing mutations and trace their spatial distribution within India. Comprehensive analysis of whole genome sequences of 441 Indian SARS-CoV-2 strains revealed the occurrence of 33 different mutations, 21 being distinctive to India. Emergence of novel mutations were observed in S glycoprotein (7/33), NSP3 (6/33), RdRp/NSP12 (4/33), NSP2 (2/33) and N (2/33). Non-synonymous mutations were found to be 3.4 times more prevalent than synonymous mutations. We classified the Indian isolates into 22 groups based on the co-existing mutations. Phylogenetic analyses revealed that representative strain of each group divided themselves into various sub-clades within their respective clades, based on the presence of unique co-existing mutations. India was dominated by A2a clade (55.60%) followed by A3 (37.38%) and B (7%), but exhibited heterogeneous distribution among various geographical regions. The A2a clade mostly predominated in East India, Western India and Central India, whereas A3 clade prevailed in South and North India. In conclusion, this study highlights the divergent evolution of SARS-CoV-2 strains and co-circulation of multiple clades in India. Monitoring of the emerging mutations would pave ways for vaccine formulation and designing of antiviral drugs.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Rakesh Sarkar", - "author_inst": "ICMR-National Institute of Cholera and Enteric Diseases" - }, - { - "author_name": "Suvrotoa Mitra", - "author_inst": "ICMR-National Institute of Cholera and Enteric Diseases" - }, - { - "author_name": "Pritam Chandra", - "author_inst": "ICMR-National Institute of Cholera and Enteric Diseases" - }, - { - "author_name": "Priyanka Saha", - "author_inst": "ICMR-National Institute of Cholera and Enteric Diseases" - }, - { - "author_name": "Anindita Banerjee", - "author_inst": "ICMR-National Institute of Cholera and Enteric Diseases" - }, - { - "author_name": "Shanta Dutta", - "author_inst": "ICMR-National Institute of Cholera and Enteric Diseases" - }, - { - "author_name": "Mamta Chawla-Sarkar", - "author_inst": "ICMR-National Institute of Cholera and Enteric Diseases" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.07.14.203414", "rel_title": "Bivalent binding of a fully human IgG to the SARS-CoV-2 spike proteins reveals mechanisms of potent neutralization", @@ -1335734,6 +1334302,129 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.13.20153106", + "rel_title": "The prevalence of antibodies to SARS-CoV-2 among blood donors in China", + "rel_date": "2020-07-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20153106", + "rel_abs": "ObjectivesThe prevalence of antibodies to SARS-CoV-2 among blood donors in China remains unknown. To reveal the missing information, we investigated the seroprevalence of SARS-CoV-2 antibodies among blood donors in the cities of Wuhan, Shenzhen, and Shijiazhuang of China.\n\nDesignCross-sectional study\n\nSettingThree blood centers, located in the central, south and north China, respectively, recruiting from January to April 2020.\n\nParticipants38,144 healthy blood donors donated in Wuhan, Shenzhen and Shijiazhuang were enrolled, who were all met the criteria for blood donation during the COVID-19 pandemic in China.\n\nMain outcome measuresSpecific antibodies against SARS-CoV-2 including total antibody (TAb), IgG antibody against receptor-binding domain of spike protein (IgG-RBD) and nucleoprotein (IgG-N), and IgM. Pseudotype lentivirus-based neutralization test was performed on all TAb-positive samples. In addition, anonymous personal demographic information, including gender, age, ethnicity, occupation and educational level, and blood type were collected.\n\nResultsA total of 519 samples from 410 donors were confirmed by neutralization tests. The SARS-CoV-2 seroprevalence among blood donors was 2.29% (407/17,794, 95%CI: 2.08% to 2.52%) in Wuhan, 0.029% (2/6,810, 95%CI: 0.0081% to 0.11%) in Shenzhen, and 0.0074% (1/13,540, 95%CI: 0.0013% to 0.042%) in Shijiazhuang, respectively. The earliest emergence of SARS-CoV-2 seropositivity in blood donors was identified on January 20, 2020 in Wuhan. The weekly prevalence of SARS-CoV-2 antibodies in Wuhans blood donors changed dynamically and were 0.08% (95%CI: 0.02% to 0.28%) during January 15 to 22 (before city lockdown), 3.08% (95%CI: 2.67% to 3.55%) during January 23 to April 7 (city quarantine period) and 2.33% (95%CI: 2.06% to 2.63%) during April 8 to 30 (after lockdown easing). Female and older-age were identified to be independent risk factors for SARS-CoV-2 seropositivity among donors in Wuhan.\n\nConclusionsThe prevalence of antibodies to SARS-CoV-2 among blood donors in China was low, even in Wuhan city. According to our data, the earliest emergence of SARS-CoV-2 in Wuhans donors should not earlier than January, 2020. As most of the population of China remained uninfected during the early wave of COVID-19 pandemic, effective public health measures are still certainly required to block viral spread before a vaccine is widely available.", + "rel_num_authors": 27, + "rel_authors": [ + { + "author_name": "Le Chang", + "author_inst": "National Center for Clinical Laboratories, Beijing Hospital" + }, + { + "author_name": "Wanghen Hou", + "author_inst": "School of Public Health, Xiamen University" + }, + { + "author_name": "Lei Zhao", + "author_inst": "Department of Laboratory, Wuhan Blood Center" + }, + { + "author_name": "Yali Zhang", + "author_inst": "School of Public Health, Xiamen University" + }, + { + "author_name": "Yanbin Wang", + "author_inst": "Blood Screenning Laboratory, Hebei Province Blood Center" + }, + { + "author_name": "Linfeng Wu", + "author_inst": "Shenzhen Blood Center" + }, + { + "author_name": "Tingting Xu", + "author_inst": "Department of Laboratory, Wuhan Blood Center" + }, + { + "author_name": "Lilin Wang", + "author_inst": "Shenzhen Blood Center" + }, + { + "author_name": "Juan Wang", + "author_inst": "School of Public Health, Xiamen University" + }, + { + "author_name": "Jian Ma", + "author_inst": "School of Public Health, Xiamen University" + }, + { + "author_name": "Lan Wang", + "author_inst": "Wuhan Blood Center" + }, + { + "author_name": "Junpeng Zhao", + "author_inst": "Shenzhen Blood Center" + }, + { + "author_name": "Jing Xu", + "author_inst": "Wuhan Blood Center" + }, + { + "author_name": "Juan Dong", + "author_inst": "Department of Laboratory, Wuhan Blood Center" + }, + { + "author_name": "Ying Yan", + "author_inst": "National Center for Clinical Laboratories, Beijing Hospital" + }, + { + "author_name": "Ru Yang", + "author_inst": "Department of Transfusion Research, Wuhan Blood Center" + }, + { + "author_name": "Yu Li", + "author_inst": "Department of Laboratory, Wuhan Blood Center" + }, + { + "author_name": "Fei Guo", + "author_inst": "National Center for Clinical Laboratories, Beijing Hospital" + }, + { + "author_name": "Wenjuan Cheng", + "author_inst": "Department of Laboratory, Wuhan Blood Center" + }, + { + "author_name": "Yingying Su", + "author_inst": "School of Public Health, Xiamen University" + }, + { + "author_name": "Jinfeng Zeng", + "author_inst": "Shenzhen Blood Center" + }, + { + "author_name": "Wei Han", + "author_inst": "Blood Screenning Laboratory, Hebei Province Blood Center" + }, + { + "author_name": "Tong Cheng", + "author_inst": "School of Public Health, Xiamen University" + }, + { + "author_name": "Jun Zhang", + "author_inst": "School of Public Health, Xiamen University" + }, + { + "author_name": "Quan Yuan", + "author_inst": "School of Public Health, Xiamen University" + }, + { + "author_name": "Xia Ningshao", + "author_inst": "School of Public Health, Xiamen University" + }, + { + "author_name": "Lunan Wang", + "author_inst": "National Center for Clinical Laboratories, Beijing Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.13.20152447", "rel_title": "O Group is a protective factor for COVID19 in Basque population", @@ -1336202,101 +1334893,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2020.07.13.20152793", - "rel_title": "At what times during infection is SARS-CoV-2 detectable and no longer detectable using RT-PCR based tests?: A systematic review of individual participant data", - "rel_date": "2020-07-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.13.20152793", - "rel_abs": "STRUCTURED SUMMARYO_ST_ABSBackgroundC_ST_ABSTests for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral ribonucleic acid (RNA), using reverse transcription polymerase chain reaction (RT-PCR) are pivotal to detecting current coronavirus disease (COVID-19) and duration of detectable virus indicating potential for infectivity.\n\nMethodsWe conducted an individual participant data (IPD) systematic review of longitudinal studies of RT-PCR test results in symptomatic SARS-CoV-2. We searched PubMed, LitCOVID, medRxiv and COVID-19 Living Evidence databases. We assessed risk of bias using a QUADAS- 2 adaptation. Outcomes were the percentage of positive test results by time and the duration of detectable virus, by anatomical sampling sites.\n\nFindingsOf 5078 studies screened, we included 32 studies with 1023 SARS-CoV-2 infected participants and 1619 test results, from -6 to 66 days post-symptom onset and hospitalisation. The highest percentage virus detection was from nasopharyngeal sampling between 0 to 4 days post-symptom onset at 89% (95% confidence interval (CI) 83 to 93) dropping to 54% (95% CI 47 to 61) after 10 to 14 days. On average, duration of detectable virus was longer with lower respiratory tract (LRT) sampling than upper respiratory tract (URT). Duration of faecal and respiratory tract virus detection varied greatly within individual participants. In some participants, virus was still detectable at 46 days post- symptom onset.\n\nInterpretationRT-PCR misses detection of people with SARS-CoV-2 infection; early sampling minimises false negative diagnoses. Beyond ten days post-symptom onset, lower RT or faecal testing may be preferred sampling sites. The included studies are open to substantial risk of bias so the positivity rates are probably overestimated.\n\nPANEL: RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSThere are numerous reports of negative severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) reverse transcription polymerase chain reaction (RT-PCR) test results in participants with known SARS-CoV-2 infection, and increasing awareness that the ability of RT-PCR tests to detect virus depends on the timing of sample retrieval and anatomical sampling site.\n\nIndividual studies suggest that positive test results from RT-PCR with nasopharyngeal sampling declines within a week of symptoms and that a positive test later in the disease course is more likely from sputum, bronchoalveolar lavage (BAL) or stool, but data are inconsistent.\n\nAdded value of this studyWe searched 5078 titles and abstracts for longitudinal studies reporting individual participant data (IPD) for RT-PCR for participants with COVID-19 linked to either time since symptom onset or time since hospitalisation. Search included SARS-CoV-2 and RT-PCR keywords and MeSH terms. Each included study was subject to careful assessment of risk of bias. This IPD systematic review (SR) addresses RT-PCR test detection rates at different times since symptom onset and hospitalisation for different sampling sites, and summarises the duration of detectable virus. To our knowledge, this is the first rapid SR addressing this topic. We identified 32 studies available as published articles or pre-prints between January 1st and April 24th 2020, including participants sampled at 11 different sampling sites and some participants sampled at more than one site. At earlier time points, nasopharyngeal sampling had the highest virus detection, but the duration of shedding was shorter compared to lower respiratory tract sampling. At 10 to 14 days post-symptom onset, the percentage of positive nasopharyngeal test results was 54% compared to 89% at day 0 to 4. Presence and duration of faecal detection varied by participant, and in nearly half duration was shorter than respiratory sample detection. Virus detection varies for participants and can continue to be detected up to 46 days post-symptom onset or hospitalisation. The included studies were open to substantial risk of bias, so the detection rates are probably overestimates. There was also poor reporting of sampling methods and sparse data on sampling methods that are becoming more widely implemented, such as self-sampling and short nasal swab sampling (anterior nares/mid turbinate).\n\nImplications of all the available evidenceResults from this IPD SR of SARS-CoV-2 testing at different time points and using different anatomical sample sites are important to inform strategies of testing. For prevention of ongoing transmission of SARS-CoV-2, samples for RT-PCR testing need to be taken as soon as possible post-symptom onset, as we confirm that RT-PCR misses more people with infection if sampling is delayed. The percentage of positive RT-PCR tests is also highly dependent on the anatomical site sampled in infected people. Sampling at more than one anatomical site may be advisable as there is variation between individuals in the sites that are infected, as well as the timing of SARS-CoV-2 virus detection at an anatomical site. Testing ten days after symptom onset will lead to a higher frequency of negative tests, particularly if using only upper respiratory tract sampling. However, our estimates may considerably understate the frequency of negative RT-PCR results in people with SARS-CoV- 2 infection. Further investment in this IPD approach is recommended as the amount data available was small given the scale of the pandemic and the importance of the question. More studies, learning from our observations about risk of bias and strengths of example studies (Box 1, Box 2) are urgently needed to inform the optimal sampling strategy by including self-collected samples such as saliva and short nasal swabs. Better reporting of anatomical sampling sites with a detailed methodology on sample collection is also urgently needed.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Sue Mallett", - "author_inst": "University College London, UK" - }, - { - "author_name": "Joy Allen", - "author_inst": "Newcastle University, UK" - }, - { - "author_name": "Sara Graziadio", - "author_inst": "Newcastle upon Tyne Hospitals NHS Foundation Trust, UK" - }, - { - "author_name": "Stuart A Taylor", - "author_inst": "University College London, UK" - }, - { - "author_name": "Naomi S Sakai", - "author_inst": "University College London, UK" - }, - { - "author_name": "Kile Green", - "author_inst": "Newcastle University, UK" - }, - { - "author_name": "Jana Suklan", - "author_inst": "Newcastle University, UK" - }, - { - "author_name": "Chris Hyde", - "author_inst": "University of Exeter, UK" - }, - { - "author_name": "Bethany Shinkins", - "author_inst": "University of Leeds, UK" - }, - { - "author_name": "Zhivko Zhelev", - "author_inst": "University of Exeter, UK" - }, - { - "author_name": "Jaime Peters", - "author_inst": "University of Exeter, UK" - }, - { - "author_name": "Philip Turner", - "author_inst": "University of Oxford, UK" - }, - { - "author_name": "Nia W Roberts", - "author_inst": "University of Oxford, UK" - }, - { - "author_name": "Lavinia Ferrante di Ruffano", - "author_inst": "University of Birmingham, UK" - }, - { - "author_name": "Robert Wolff", - "author_inst": "Kleijnen Systematic Reviews Ltd, UK" - }, - { - "author_name": "Penny Whiting", - "author_inst": "University of Bristol, UK" - }, - { - "author_name": "Amanda Winter", - "author_inst": "Newcastle University, UK" - }, - { - "author_name": "Gauraang Bhatnagar", - "author_inst": "Frimley Health NHS Foundation Trust, UK" - }, - { - "author_name": "Brian D Nicholson", - "author_inst": "University of Oxford, UK" - }, - { - "author_name": "Steve Halligan", - "author_inst": "University College London, UK" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.13.20152876", "rel_title": "Staff testing for COVID-19 via an online pre-registration form", @@ -1337340,6 +1335936,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.11.20151217", + "rel_title": "Impact of COVID-19 Second Wave on Healthcare Networks in the United States", + "rel_date": "2020-07-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.11.20151217", + "rel_abs": "The risk of overwhelming healthcare systems from a second wave of COVID-19 is yet to be quantified. Here, we investigate the impact of different reopening scenarios of states around the U.S. on COVID-19 hospitalized cases and the risk of overwhelming the healthcare system while considering resources at the county level. We show that the second wave might involve an unprecedented impact on the healthcare system if an increasing number of the population becomes susceptible and/or if the various protective measures are discontinued. Furthermore, we explore the ability of different mitigation strategies in providing considerable relief to the healthcare system. The results can aid healthcare planners, policymakers, and state officials in making decisions on additional resources required and on when to return to normalcy.\n\nOne Sentence SummaryA second wave of COVID-19 will have an unprecedented impact on the healthcare system.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Emad M. Hassan", + "author_inst": "Colorado State University" + }, + { + "author_name": "Hussam Mahmoud", + "author_inst": "Colorado State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.11.20151464", "rel_title": "Multidisciplinary approach to COVID-19 risk communication: A framework and tool for individual and regional risk assessment", @@ -1337984,37 +1336603,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.07.12.20152157", - "rel_title": "Quantifying Respiratory Airborne Particle Dispersion Control Through Improvised Reusable Masks", - "rel_date": "2020-07-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.12.20152157", - "rel_abs": "BackgroundFor much of the SARS-CoV-2 (COVID-19) pandemic, many countries have struggled to offer definitive guidance on the wearing of masks or face coverings to reduce the highly infectious disease transmission resulting from a lack of compelling evidence on the effectiveness of communities wearing masks, and slow acceptance that aerosols are a primary SARS-CoV-2 disease transmission mechanism. Recent studies have shown that masks have been effective in several countries and populations, leaving only a lack of quantitative data on the control of airborne dispersion from human exhalation. This current study specifically has the objective to quantify the effectiveness of non-medical grade washable masks or face coverings in controlling airborne dispersion from exhalation (both droplet and aerosol) by measuring changes in direction, particle cloud velocities, and concentration.\n\nDesignThis randomized effectiveness study used a 10% NaCl nebulized polydisperse particle solution (0.3 m up to 10 m in size) delivered by an exhalation simulator to conduct 94 experiment runs with combinations of 8 different fabrics, 5 mask designs, and airflows for both talking and coughing. Multiple particle sensors were instrumented to measure reduction in aerosol dispersion.\n\nResultsThree-way multivariate analysis of variance establishes that fabric, mask design, and exhalation breath level have a statistically significant effect on changing direction, reducing velocity, or concentrations of airborne particles (Fabric: P = < .001, Wilks {Lambda} = .000; Mask design: P = < .001, Wilks' {Lambda} = .000; Breath level: P = < .001, Wilks' {Lambda} = .004). There were also statistically significant interaction effects between combinations of all primary factors.\n\nConclusions and RelevanceThe application of facial coverings or masks can significantly reduce the airborne dispersion of aerosolized particles from exhalation by diffusing the particle cloud direction and slow down its travel speed. Consequently, the results indicate that wearing masks when coupled with social distance can decrease the potentially inhaled dose of SARS-CoV-2 aerosols or droplets especially where infectious contaminants may exist in shared air spaces. The conclusion is well aligned with the concept of \"time-distance-shielding\" from hazardous materials emergency response. However, the effectiveness varies greatly between the specific fabrics and mask designs used.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Nathan J Edwards", - "author_inst": "The MITRE Corporation" - }, - { - "author_name": "Rebecca Widrick", - "author_inst": "The MITRE Corporation" - }, - { - "author_name": "Richard Potember", - "author_inst": "The MITRE Corporation" - }, - { - "author_name": "Mike Gerschefske", - "author_inst": "The MITRE Corporation" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.07.11.20149344", "rel_title": "Placental SARS-CoV-2 in a patient with mild COVID-19 disease", @@ -1339094,6 +1337682,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.07.13.198630", + "rel_title": "Tobacco, but not nicotine and flavor-less electronic cigarettes, induces ACE2 and immune dysregulation", + "rel_date": "2020-07-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.13.198630", + "rel_abs": "COVID-19, caused by the virus SARS-CoV-2, has infected millions worldwide. This pandemic overlaps with the ongoing epidemics of cigarette smoking and electronic cigarette (e-cig) vaping, with over 1 billion smokers and vapers worldwide. However, there is scarce data relating COVID-19 risks and outcome with cigarette or e-cig use. In this study, we mined 3 independent RNA expression datasets from smokers and vapers to understand the potential relationship between vaping/smoking and the dysregulation of key genes and pathways related to COVID-19. We found that smoking, but not vaping, upregulates ACE2, the cellular receptor that SARS-CoV-2 requires for infection. Both smoking and use of nicotine and flavor-containing e-cig led to upregulations of pro-inflammatory cytokine production and expression of genes related to inflammasomes. Vaping flavor-less and nicotine-less e-cig, however, did not lead to significant cytokine dysregulation and inflammasome activation. Release of inflammasome products, such as IL-1B, and cytokine storms are hallmarks of COVID-19 infection, especially in severe cases. Therefore, our findings demonstrated that smoking or vaping, specifically use of flavored or nicotine-containing e-cigs, may critically exacerbate COVID-19-related inflammation or increase susceptibility to the disease. Further scientific and public health investigations should be undertaken to address these concerning links between COVID-19 and e-cig/smoking.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Abby C. Lee", + "author_inst": "UC San Diego; VA San Diego Healthcare System" + }, + { + "author_name": "Jaideep Chakladar", + "author_inst": "UC San Diego; VA San Diego Healthcare System" + }, + { + "author_name": "Wei Tse Li", + "author_inst": "UC San Diego; VA San Diego Healthcare System" + }, + { + "author_name": "Chengyu Chen", + "author_inst": "UC San Diego; VA San Diego Healthcare System" + }, + { + "author_name": "Eric Y. Chang", + "author_inst": "UC San Diego; VA San Diego Healthcare System" + }, + { + "author_name": "Jessica Wang-Rodriguez", + "author_inst": "UC San Diego; VA San Diego Healthcare System" + }, + { + "author_name": "Weg M. Ongkeko", + "author_inst": "UC San Diego; VA San Diego Healthcare System" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.07.12.199505", "rel_title": "PT150 is a modulator of glucocorticoid and androgen receptors with antiviral activity against SARS-CoV-2.", @@ -1339414,97 +1338045,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.07.10.20150045", - "rel_title": "Genomic epidemiology reveals multiple introductions and spread of SARS-CoV-2 in the Indian state of Karnataka", - "rel_date": "2020-07-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.10.20150045", - "rel_abs": "An earlier version of this manuscript was removed owing to inclusion of confidential information relating to an individual", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Chitra Pattabiraman", - "author_inst": "Department of Neurovirology, National Institute of Mental Health and Neurosciences (NIMHANS)" - }, - { - "author_name": "Farhat Habib", - "author_inst": "TruFactor-InMobi Group, Bangalore" - }, - { - "author_name": "Harsha PK", - "author_inst": "Department of Neurovirology, National Institute of Mental Health and Neurosciences (NIMHANS)" - }, - { - "author_name": "Risha Rasheed", - "author_inst": "Department of Neurovirology, National Institute of Mental Health and Neurosciences (NIMHANS)" - }, - { - "author_name": "Vijayalakshmi Reddy", - "author_inst": "Department of Neurovirology, National Institute of Mental Health and Neurosciences (NIMHANS)" - }, - { - "author_name": "Prameela Dinesh", - "author_inst": "Directorate of Health and Family Welfare Services, Government of Karnataka, Bangalore- 560012" - }, - { - "author_name": "Tina Damodar", - "author_inst": "Department of Neurovirology, National Institute of Mental Health and Neurosciences (NIMHANS)" - }, - { - "author_name": "Nakka Vijay Kiran Reddy", - "author_inst": "Department of Neurovirology, National Institute of Mental Health and Neurosciences (NIMHANS)" - }, - { - "author_name": "Kiran Hosallimath", - "author_inst": "Department of Neurovirology, National Institute of Mental Health and Neurosciences (NIMHANS)" - }, - { - "author_name": "Anson K George", - "author_inst": "Department of Neurovirology, National Institute of Mental Health and Neurosciences (NIMHANS)" - }, - { - "author_name": "Banerjee John", - "author_inst": "Department of Neurovirology, National Institute of Mental Health and Neurosciences (NIMHANS)" - }, - { - "author_name": "Amrita Pattanaik", - "author_inst": "Department of Neurovirology, National Institute of Mental Health and Neurosciences (NIMHANS)" - }, - { - "author_name": "Narendra Kumar", - "author_inst": "Department of Neurovirology, National Institute of Mental Health and Neurosciences (NIMHANS)" - }, - { - "author_name": "Reeta S Mani", - "author_inst": "Department of Neurovirology, National Institute of Mental Health and Neurosciences (NIMHANS)" - }, - { - "author_name": "Manjunatha M Venkataswamy", - "author_inst": "Department of Neurovirology, National Institute of Mental Health and Neurosciences (NIMHANS)" - }, - { - "author_name": "Shafeeq K Shahul Hameed", - "author_inst": "Department of Neurovirology, National Institute of Mental Health and Neurosciences (NIMHANS)" - }, - { - "author_name": "Prakash Kumar B.G.", - "author_inst": "Directorate of Health and Family Welfare Services, Government of Karnataka, Bangalore, - 560012" - }, - { - "author_name": "Anita Desai", - "author_inst": "Department of Neurovirology, National Institute of Mental Health and Neurosciences (NIMHANS)" - }, - { - "author_name": "Ravi Vasanthapuram", - "author_inst": "Department of Neurovirology, National Institute of Mental Health and Neurosciences (NIMHANS)" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.07.09.20150086", "rel_title": "Transmission dynamics and control measures of COVID-19 outbreak in China: a modelling study", @@ -1340472,6 +1339012,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.10.20150813", + "rel_title": "Societal heterogeneity contributes to complex dynamic patterns of the COVID-19 pandemics: insights from a novel Stochastic Heterogeneous Epidemic Model (SHEM)", + "rel_date": "2020-07-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.10.20150813", + "rel_abs": "As of August 2020, it has become evident that regional infection curves of COVID-19 exhibit complex patterns which often differ from curves predicted by forecasting models. We hypothesized that this may be due to social heterogeneity not accounted for by regional models. Here we present a new Stochastic Heterogeneous Epidemic Model (SHEM) to investigate the role of heterogenous societal structure. SHEM is intended to be a general tool with which to explore scenarios and determine the expected consequences of various interventions. We represent a society by an arbitrary network of sub-populations that could represent social as well as geographical strata. We created several scenarios with large clusters of people with R0 of COVID-19 interacting with multiple smaller local clusters that have larger internal R0. We find that isolation or embedding of these vulnerable sub-clusters generate complex infection patterns which includes multiple peaks and growth periods, an extended plateau, a prolonged tail, or a delayed second wave of infection, which may or may not form due to stochasticity. We also show that local clusters can either be driving or driven forces in infection progression. Embedded vulnerable groups become hotspots that drive infection despite efforts of the main population to socially distance, while isolated areas suffer delayed but intense infection. Social heterogeneity is a key factor in the formation of complex infection curves. Vulnerable subgroups that cannot implement mitigation strategies can spread infection to socially distanced populations, defeating mitigations. This implies that mitigation of vulnerable groups is essential to control the epidemic.\n\nSignificance StatementWe developed a new multiscale Stochastic Heterogeneous Epidemic Model (SHEM) and demonstrated major roles for social heterogeneity and stochasticity in pandemic development. We simulated viral infection in a theoretical society where small communities that cannot socially distance link to large clusters representing urban populations. Depending on the model parameters, our simulations of COVID-19 infection generated a large variety of dynamic patterns, including multimodal growth periods observed now in the US and worldwide. Infection of small, vulnerable clusters of people defeated mitigation efforts by the main population. The importance of protecting vulnerable subgroups suggests policy implications. Our abstract model could be applied at multiple scales of human societal organization.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Alexander V Maltsev", + "author_inst": "National Institute on Aging, NIH" + }, + { + "author_name": "Michael D Stern", + "author_inst": "National Institute on Aging, NIH" + } + ], + "version": "1", + "license": "cc0", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.10.20151001", "rel_title": "Estimating the Effect of Social Distancing Interventions on COVID-19 in the United States", @@ -1340996,37 +1339559,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.10.20150904", - "rel_title": "Serological Tests for SARS-CoV-2 Coronavirus by Commercially Available Point-of-Care and Laboratory Diagnostics in Pre-COVID-19 Samples in Japan", - "rel_date": "2020-07-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.10.20150904", - "rel_abs": "Serological tests for SARS-CoV-2 coronavirus in pre-COVID-19 samples in Japan showed 1.5%-1.75% positives, and previous surveys might overestimate COVID-19 seroprevalence in several population of Japan. These false negatives could be excluded by combination of different diagnostics to 0.25%.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Mariko Harada Sassa", - "author_inst": "Kyoto University" - }, - { - "author_name": "Zhaoqing Lyu", - "author_inst": "Kyoto University" - }, - { - "author_name": "Tomoko Fujitani", - "author_inst": "Kyoto University" - }, - { - "author_name": "Kouji H. Harada", - "author_inst": "Kyoto University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.10.20150771", "rel_title": "In-house modification and improvement of the CDC real-time PCR diagnostic assay for SARS-CoV-2 detection.", @@ -1342150,6 +1340682,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.10.20147777", + "rel_title": "COVID-19 severity is predicted by earlier evidence of accelerated aging", + "rel_date": "2020-07-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.10.20147777", + "rel_abs": "With no known treatments or vaccine, COVID-19 presents a major threat, particularly to older adults, who account for the majority of severe illness and deaths. The age-related susceptibility is partly explained by increased comorbidities including dementia and type II diabetes [1]. While it is unclear why these diseases predispose risk, we hypothesize that increased biological age, rather than chronological age, may be driving disease-related trends in COVID-19 severity with age. To test this hypothesis, we applied our previously validated biological age measure (PhenoAge) [2] composed of chronological age and nine clinical chemistry biomarkers to data of 347,751 participants from a large community cohort in the United Kingdom (UK Biobank), recruited between 2006 and 2010. Other data included disease diagnoses (to 2017), mortality data (to 2020), and the UK national COVID-19 test results (to May 31, 2020) [3]. Accelerated aging 10-14 years prior to the start of the COVID-19 pandemic was associated with test positivity (OR=1.15 per 5-year acceleration, 95% CI: 1.08 to 1.21, p=3.2x10-6) and all-cause mortality with test-confirmed COVID-19 (OR=1.25, per 5-year acceleration, 95% CI: 1.09 to 1.44, p=0.002) after adjustment for demographics including current chronological age and pre-existing diseases or conditions. The corresponding areas under the curves were 0.669 and 0.803, respectively. Biological aging, as captured by PhenoAge, is a better predictor of COVID-19 severity than chronological age, and may inform risk stratification initiatives, while also elucidating possible underlying mechanisms, particularly those related to inflammaging.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Chia-Ling Kuo", + "author_inst": "University of Connecticu Health" + }, + { + "author_name": "Luke C Pilling", + "author_inst": "University of Exeter" + }, + { + "author_name": "Janice C Atkins", + "author_inst": "University of Exeter" + }, + { + "author_name": "Jane Masoli", + "author_inst": "University of Exeter" + }, + { + "author_name": "Joao Delgado", + "author_inst": "University of Exeter" + }, + { + "author_name": "Christopher Tignanelli", + "author_inst": "University of Minnesota" + }, + { + "author_name": "George Kuchel", + "author_inst": "University of Connecticut" + }, + { + "author_name": "David Melzer", + "author_inst": "University of Exeter" + }, + { + "author_name": "Kenneth B Beckman", + "author_inst": "University of Minnesota" + }, + { + "author_name": "Morgan Levine", + "author_inst": "Yale University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.07.20146332", "rel_title": "Clinical and epidemiological characteristics of children with SARS-CoV-2 infection: case series in Sinaloa", @@ -1342626,69 +1341213,6 @@ "type": "new results", "category": "neuroscience" }, - { - "rel_doi": "10.1101/2020.07.06.20147827", - "rel_title": "Clinical Features of Hemodialysis (HD) patients confirmed with Coronavirus Disease 2019 (COVID-19): a Retrospective Case-Control Study", - "rel_date": "2020-07-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.06.20147827", - "rel_abs": "BackgroundSince December 2019, Coronavirus Disease 2019(COVID-19) occurred in wuhan, China, and outbreaked rapidly into a global pandemic. This current poses great challenges to hemodialysis (HD) patients.\n\nObjectiveTo make a comprehensive evaluation and comparison between HD patients confirmed with COVID-19 and the general HD patients.\n\nMethodsHD patients confirmed with COVID-19 in Wuhan No.5 Hospital were admitted as confirmed group from Jan 10 to Mar 15, 2020. And HD patients not infected in our dialysis center were chosen as control group. General characteristics, laboratory indicators were retrospectively collected, analyzed and compared.\n\nResultsA total of 142 cases were admitted, including 43 cases in confirmed group and 99 in control group. Body mass index (BMI) was slightly lower in confirmed group than that in control group (P=0.011). The proportion of one or less underlying disease in confirmed group(51.16%) was higher than that in control group(14.14%)(P< 0.001), and the proportion of three or more underlying diseases in confirmed group(11.63%) was lower than that in control group(52.53%)(P< 0.001). Patients in confirmed group exhibited significantly lower hemoglobin, lymphocyte count, and lymphocyte percentage, but higher neutrophil percentage, neutrophil-to-lymphocyte ratio (NLR), C-reactive protein, aspartate transaminase, and alkaline phosphatase. There was no significant difference in age, gender, dialysis age, primary disease, the using of ACEI/ARB, platelet-to-lymphocyte ratio (PLR), and other indicators between the two groups.\n\nConclusionsFaced with Severe Acute Respiratory Syndrome-CoV-2 (SARS-CoV-2), HD patients with lower BMI and hemoglobin were more susceptible to be infected, which might be related to malnutrition. Once confirmed with COVID-19, HD patients expressed obviously dis-regulated of inflammation and immune.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Xiaohui Wang", - "author_inst": "Department of Nephrology, Wuhan No.5 Hospital, Wuhan, Hubei Province, 430050, China" - }, - { - "author_name": "Huan Zhou", - "author_inst": "Department of Nephrology, Wuhan No.5 Hospital, Wuhan, Hubei Province, 430050, China" - }, - { - "author_name": "Xiaofen Xiao", - "author_inst": "Department of Nutrition, Wuhan No.5 Hospital, Wuhan, Hubei Province, 430050, China" - }, - { - "author_name": "Xianhua Tan", - "author_inst": "Department of Radiology, Wuhan No.5 Hospital, Wuhan, Hubei Province, 430050, China" - }, - { - "author_name": "Xin Zhang", - "author_inst": "Department of Nephrology, Wuhan No.5 Hospital, Wuhan, Hubei Province, 430050, China" - }, - { - "author_name": "Yong He", - "author_inst": "Department of Nephrology, Wuhan No.5 Hospital, Wuhan, Hubei Province, 430050, China" - }, - { - "author_name": "Jing Li", - "author_inst": "Department of Nephrology, Wuhan No.5 Hospital, Wuhan, Hubei Province, 430050, China" - }, - { - "author_name": "Guosheng Yang", - "author_inst": "Department of Nephrology, Wuhan No.5 Hospital, Wuhan, Hubei Province, 430050, China" - }, - { - "author_name": "Mingmei Li", - "author_inst": "Department of Nephrology, Wuhan No.5 Hospital, Wuhan, Hubei Province, 430050, China" - }, - { - "author_name": "Duan Liu", - "author_inst": "Department of Nephrology, Wuhan No.5 Hospital, Wuhan, Hubei Province, 430050, China" - }, - { - "author_name": "Shanshan Han", - "author_inst": "Department of Nephrology, Wuhan No.5 Hospital, Wuhan, Hubei Province, 430050, China" - }, - { - "author_name": "Haibo Kuang", - "author_inst": "Department of Nutrition, Wuhan No.5 Hospital, Wuhan, Hubei Province, 430050, China" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "nephrology" - }, { "rel_doi": "10.1101/2020.07.08.20149161", "rel_title": "COVIDPEN: A Novel COVID-19 Detection Model using Chest X-Rays and CT Scans", @@ -1343964,6 +1342488,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "obstetrics and gynecology" }, + { + "rel_doi": "10.1101/2020.07.09.20149856", + "rel_title": "SARS-CoV-2 spread across the Colombian-Venezuelan border", + "rel_date": "2020-07-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.09.20149856", + "rel_abs": "IntroductionVenezuela and Colombia both adopted measures of containment early in response to the COVID-19 pandemic. However, Venezuelas ongoing humanitarian crisis has decimated its health care system, and forced millions of Venezuelans to flee through its porous border with Colombia. The extensive shared border, and illegal cross-border transit through improvised trails between the two countries are major challenges for public health authorities. We report the first SARS-CoV-2 genomes from Venezuela, and present a snapshot of the SARS-CoV-2 epidemiologic landscape in the Colombian-Venezuelan border region.\n\nMethodsWe sequenced and assembled viral genomes from total RNA extracted from nasopharyngeal (NP) clinical specimens using a custom reference-based analysis pipeline. Three assemblies obtained were subjected to typing using the Phylogenetic Assignment of Named Global Outbreak LINeages Pangolin tool. A total of 376 publicly available SARS-CoV-2 genomes from South America were obtained from the GISAID database to perform comparative genomic analyses. Additionally, the Wuhan-1 strain was used as reference.\n\nResultsWe found that two of the SARS-CoV-2 genomes from Venezuela belonged to the B1 lineage, and the third to the B.1.13 lineage. We observed a point mutation in the Spike protein gene (D614G substitution), previously reported to be associated with increased infectivity, in all three Venezuelan genomes. An additional three mutations (R203K/G204R substitution) were present in the nucleocapsid (N) gene of one Venezuelan genome.\n\nConclusionsGenomic sequencing demonstrates similarity between SARS-CoV-2 lineages from Venezuela and viruses collected from patients in bordering areas in Colombia and from Brazil, consistent with cross-border transit despite administrative measures including lockdowns. The presence of mutations associated with increased infectivity in the 3 Venezuelan genomes we report and Colombian SARS-CoV-2 genomes from neighboring borders areas may pose additional challenges for control of SARS-CoV-2 spread in the complex epidemiological landscape in Latin American countries. Public health authorities should carefully follow the progress of the pandemic and its impact on displaced populations within the region.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Alberto Paniz-Mondolfi", + "author_inst": "Icahn School of medicina at Mount Sinai" + }, + { + "author_name": "Marina Munoz", + "author_inst": "Universidad del Rosario" + }, + { + "author_name": "Carolina Florez", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Sergio Gomez", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Angelica Rico", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Lisseth Pardo", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Esther C Barros", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Carolina Hernandez", + "author_inst": "Universidad del Rosario" + }, + { + "author_name": "Lourdes Delgado", + "author_inst": "Universidad del Rosario" + }, + { + "author_name": "Jesus Jaimes", + "author_inst": "Universidad del Rosario" + }, + { + "author_name": "Luis Perez", + "author_inst": "Universidad del Rosario" + }, + { + "author_name": "Anibal Teheran", + "author_inst": "Fundacion Universitaria Juan N Corpas" + }, + { + "author_name": "Hala Alshammary", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Ajay Obla", + "author_inst": "Ichan School of Medicine at Mount Sinai" + }, + { + "author_name": "Zenab Khan", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Ana Gonzalez-Reiche", + "author_inst": "Icahn School of Medicina at Mount Sinai" + }, + { + "author_name": "Matthew Hernandez", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Emilia Sordillo", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Viviana Simon", + "author_inst": "Icahn School of Medicine" + }, + { + "author_name": "Harm van Bakel", + "author_inst": "Icahn School of Medicine at Mount Sinai" + }, + { + "author_name": "Juan David Ramirez", + "author_inst": "Universidad del Rosario" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "genetic and genomic medicine" + }, { "rel_doi": "10.1101/2020.07.09.20149955", "rel_title": "A Poorly Understood Disease? The Unequal Distribution of Excess Mortality Due to COVID-19 Across French Municipalities", @@ -1344480,33 +1343103,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.08.20148742", - "rel_title": "Disproportionate incidence of COVID-19 in African Americans correlates with dynamic segregation", - "rel_date": "2020-07-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.08.20148742", - "rel_abs": "Socio-economic disparities quite often have a central role in the unfolding of large-scale catastrophic events. One of the most concerning aspects of the ongoing COVID-19 pandemics [1] is that it disproportionately affects people from Black and African American backgrounds [2-6], creating an unexpected infection gap. Interestingly, the abnormal impact on these ethnic groups seem to be almost uncorrelated with other risk factors, including co-morbidity, poverty, level of education, access to healthcare, residential segregation, and response to cures [7-11]. A proposed explanation for the observed incidence gap is that people from African American backgrounds are more often employed in low-income service jobs, and are thus more exposed to infection through face-to-face contacts [12], but the lack of direct data has not allowed to draw strong conclusions in this sense so far. Here we introduce the concept of dynamic segregation, that is the extent to which a given group of people is internally clustered or exposed to other groups, as a result of mobility and commuting habits. By analysing census and mobility data on more than 120 major US cities, we found that the dynamic segregation of African American communities is significantly associated with the weekly excess COVID-19 incidence and mortality in those communities. The results confirm that knowing where people commute to, rather than where they live, is much more relevant for disease modelling.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Aleix Bassolas", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Sandro Sousa", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Vincenzo Nicosia", - "author_inst": "Queen mary University of London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.07.08.20148965", "rel_title": "A case-control and cohort study to determine the relationship between ethnic background and severe COVID-19", @@ -1345754,6 +1344350,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.07.07.20148551", + "rel_title": "Assessment of N95 and K95 respirator decontamination: fiber integrity, filtration efficiency, and dipole charge density.", + "rel_date": "2020-07-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.07.20148551", + "rel_abs": "Personal protective equipment (PPE) including N95 respirators are critical for persons exposed to SARS-CoV-2. KN95 respirators and N95 decontamination protocols have been described as solutions to a lack of such PPE. However, there are a few materials science studies that characterize the charge distribution and physical changes accompanying disinfection treatments particularly heating. Here, we report the filtration efficiency, dipole charge density, and fiber integrity of pristine N95 and KN95 respirators before and after various decontamination methods. We found that the filter layer of N95 is 8-fold thicker than that of KN95, which explains its 10% higher filtration efficiency (97.03 %) versus KN95 (87.76 %) under pristines condition. After 60 minutes of 70 {degrees}C treatment, the filtration efficiency and dipole charge density of N95 became 97.16% and 12.48 C/m2, while those of KN95 were 83.64% and 1.48 C/m2; moreover, fit factor of N95 was 55 and that of KN95 was 2.7. In conclusion, the KN95 respirator is an inferior alternative of N95 respirator. In both systems, a loss of electrostatic charge does not directly correlate to a decrease in performance.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Wonjun Yim", + "author_inst": "University of California Sandiego" + }, + { + "author_name": "Diyi Cheng", + "author_inst": "University of California Sandiego" + }, + { + "author_name": "Shiv Patel", + "author_inst": "University of California Sandiego" + }, + { + "author_name": "Rui Kui", + "author_inst": "University of California Sandiego" + }, + { + "author_name": "Ying Shirley Meng", + "author_inst": "University of California Sandiego" + }, + { + "author_name": "Jesse V. Jokerst", + "author_inst": "University of California Sandiego" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.08.20141218", "rel_title": "Diagnostic and prognostic value of hematological and immunological markers in COVID-19 infection: A meta-analysis of 6320 patients", @@ -1346674,109 +1345309,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.07.08.194456", - "rel_title": "Human B cell clonal expansion and convergent antibody responses to SARS-CoV-2", - "rel_date": "2020-07-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.08.194456", - "rel_abs": "During virus infection B cells are critical for the production of antibodies and protective immunity. Here we show that the human B cell compartment in patients with diagnostically confirmed SARS-CoV-2 and clinical COVID-19 is rapidly altered with the early recruitment of B cells expressing a limited subset of IGHV genes, progressing to a highly polyclonal response of B cells with broader IGHV gene usage and extensive class switching to IgG and IgA subclasses with limited somatic hypermutation in the initial weeks of infection. We identify extensive convergence of antibody sequences across SARS-CoV-2 patients, highlighting stereotyped naive responses to this virus. Notably, sequence-based detection in COVID-19 patients of convergent B cell clonotypes previously reported in SARS-CoV infection predicts the presence of SARS-CoV/SARS-CoV-2 cross-reactive antibody titers specific for the receptor-binding domain. These findings offer molecular insights into shared features of human B cell responses to SARS-CoV-2 and other zoonotic spillover coronaviruses.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Sandra Cathrine Abel Nielsen", - "author_inst": "Stanford University" - }, - { - "author_name": "Fan Yang", - "author_inst": "Stanford University" - }, - { - "author_name": "Katherine JL Jackson", - "author_inst": "Garvan Institute of Medical Research" - }, - { - "author_name": "Ramona A. Hoh", - "author_inst": "Stanford University" - }, - { - "author_name": "Katharina R\u00f6ltgen", - "author_inst": "Stanford University" - }, - { - "author_name": "Bryan Stevens", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Ji-Yeun Lee", - "author_inst": "Stanford University" - }, - { - "author_name": "Arjun Rustagi", - "author_inst": "Stanford University" - }, - { - "author_name": "Angela J. Rogers", - "author_inst": "Stanford University" - }, - { - "author_name": "Abigail E. Powell", - "author_inst": "Stanford University" - }, - { - "author_name": "Javaria Najeeb", - "author_inst": "Stanford University" - }, - { - "author_name": "Ana Rita Otrelo-Cardoso", - "author_inst": "Stanford University" - }, - { - "author_name": "Kathryn E Yost", - "author_inst": "Stanford University" - }, - { - "author_name": "Bence Daniel", - "author_inst": "Stanford University" - }, - { - "author_name": "Howard Y Chang", - "author_inst": "Stanford University" - }, - { - "author_name": "Ansuman T Satpathy", - "author_inst": "Stanford University" - }, - { - "author_name": "Theodore S. Jardetzky", - "author_inst": "Stanford University" - }, - { - "author_name": "Peter S. Kim", - "author_inst": "Stanford University" - }, - { - "author_name": "Taia T. Wang", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Benjamin A. Pinsky", - "author_inst": "Stanford University School of Medicine" - }, - { - "author_name": "Catherine A Blish", - "author_inst": "Stanford University" - }, - { - "author_name": "Scott D Boyd", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.07.08.194209", "rel_title": "Assessment of SARS-CoV-2 Specific CD4(+) and CD8 (+) T Cell Responses Using MHC Class I and II Tetramers", @@ -1348051,6 +1346583,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.07.05.20145805", + "rel_title": "Optimally Pooled Viral Testing", + "rel_date": "2020-07-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.05.20145805", + "rel_abs": "It has long been known that pooling samples may be used to minimize the total number of tests required in order to identify each infected individual in a population. Pooling is most advantageous in populations with low infection (positivity) rates, but is expected to remain better than non-pooled testing in populations with infection rates up to 30%. For populations with infection rates lower than 10%, additional testing efficiency may be realized by performing a second round of pooling to test all the samples in the positive first-round pools. The present predictions are validated by recent COVID-19 (SARS-CoV-2) pooled testing and detection sensitivity measurements performed using non-optimal pool sizes, and quantify the additional improvement in testing efficiency that could have been obtained using optimal pooling. Although large pools are most advantageous for testing populations with very low infection rates, they are predicted to become highly non-optimal with increasing infection rate, while pool sizes smaller than 10 remain near-optimal over a broader range of infection rates.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Dor Ben-Amotz", + "author_inst": "Purdue University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.07.20147413", "rel_title": "A national cross-sectional survey of public perceptions, knowledge, and behaviors during the COVID-19 pandemic", @@ -1348667,41 +1347218,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.07.20148213", - "rel_title": "No evidence of viral polymorphisms associated with Paediatric Inflammatory Multisystem Syndrome Temporally Associated With SARS-CoV-2 (PIMS-TS).", - "rel_date": "2020-07-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.07.20148213", - "rel_abs": "Generally, children and teenagers do not become seriously ill with COVID-19. However, in countries with high rates of coronavirus disease, children with the syndrome COVID-19 associated inflammation syndrome referred to as PIMS-TS have been reported. Similarities noted between SARS-CoV-2 Spike protein sequences and those of other super antigens has prompted the suggestion that this might be the mechanism by SARS-CoV-ST triggers PIMS-TS. It has also been suggested that the D614G variant found more commonly in the US and across European countries may explain why PIMS-TS appears to be common in these countries. Here we analysed viral sequences from 13 paediatric COVID-19 patients of whom five were diagnosed with PIMS-TS. This is the first characterisation of viruses from PIMS-TS patients. In contrast to what has been hypothesised, we found no evidence of unique sequences associated with the viruses from PIMS-TS patients.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Juanita Pang", - "author_inst": "University College London" - }, - { - "author_name": "Florencia A.T. Boshier", - "author_inst": "University College London" - }, - { - "author_name": "Nele Alders", - "author_inst": "Great Ormond Street Hospital for Children NHS Foundation Trust" - }, - { - "author_name": "Garth Dixon", - "author_inst": "Great Ormond Street Hospital for Children NHS Foundation Trust" - }, - { - "author_name": "Judith Breuer", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.07.20145979", "rel_title": "Effectiveness of Ivermectin as add-on Therapy in COVID-19 Management (Pilot Trial)", @@ -1349945,6 +1348461,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.06.20147256", + "rel_title": "Early Diagnosis and Clinical Significance of Acute Cardiac Injury - Under the Iceberg: A Retrospective Cohort Study of 619 Non-critically Ill Hospitalized COVID-19 Pneumonia Patients", + "rel_date": "2020-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.06.20147256", + "rel_abs": "RationaleCoronavirus disease 2019 (COVID-19) can cause a viral pneumonia together with other extrapulmonary complications. Acute cardiac related injury (ACRI) is common in hospitalized COVID-19 patients.\n\nObjectiveTo explain the pathological mechanism of ACRI and improve the treatment strategy by retrospectively observing the factors associated with ACRI and factors affecting the prognosis of ACRI with COVID-19 at an early stage.\n\nMethods619 COVID-19 patients were from Tongji Hospital, Wuhan. Students t test was used for continuous variables while Pearson {chi}2 test for categorical factors. Univariable and multivariable logistic regression models were applied to estimate odds ratio (OR) with 95% confidence interval (CI).\n\nResultsAmong the 619 OOS Level-I hospitalized COVID-19 patients, 102 (16.5%) were defined as ACRI (stage-1: 59 cases, stage-2: 43 cases). 50% of ACRI patients developed into severe cases and 25 patients died(CFR=24.5%), 42 times that of non-ACRI patients. Elderly (OR=2.83, P<0.001), HTN (OR=2.09, P=0.005), {gamma}-globulin (OR=2.08, P=0.004), TCM (OR=0.55, P=0.017), PLT (OR=2.94, P<0.001) and NLR (OR=2.20, P=0.004) were independently correlated with ACRI. SBP [>=] 140, dyspnea, DM, smoking history were correlated with ACRI-stage2 only. In the prognostic subgroup analysis of ACRI patients, {gamma}-globulin treatment could prolong LOS (29.0 {+/-} 7.2 days Vs 23.5 {+/-} 8.1 days, P=0.004). TCM (OR=0.26, P=0.006), SBP [>=] 160 (OR= 22.70, P=0.005), male (OR=2.66, P=0.044) were associated with severe illness while corticosteroids treatment (OR=3.34, P=0.033) and male (OR=4.303, P=0.008) with death. Surprisingly, we found the mortality of non-elderly patients is higher than elderly (32.4% VS 20.0%, P=0.164), and both IKF and RASI treatment were not correlated with any prognostic indicators including severe, death and LOS.\n\nConclusionThis study observed that several non-traditional issues were associated with early cardiac injury in COVID-19 while many traditional cardiovascular risk factors were not. Besides elderly and male, hypertension was confirmed to be the most important risk factor.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Yang Xie", + "author_inst": "Department of Cardiovascular Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Sichun Chen", + "author_inst": "Medical Research Institute, Wuhan University Renmin Hospital, Wuhan University, Wuhan, China" + }, + { + "author_name": "Xueli Wang", + "author_inst": "Institute of Central China Development, Wuhan University" + }, + { + "author_name": "Baige Li", + "author_inst": "Medical Research Institute, Wuhan University Renmin Hospital, Wuhan University, Wuhan, China" + }, + { + "author_name": "Tianlu Zhang", + "author_inst": "zhangtianlu99@163.com" + }, + { + "author_name": "Xingwei He", + "author_inst": "Department of Cardiovascular Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "NingLing Sun", + "author_inst": "Department of Hypertension at Heart Center, People's Hospital, Peking University" + }, + { + "author_name": "Luyan Wang", + "author_inst": "Heart Center, Peking University Peoples Hospital" + }, + { + "author_name": "Hesong Zeng", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Yin Shen", + "author_inst": "Eye Center, Wuhan University Renmin Hospital, Wuhan University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2020.07.06.20147124", "rel_title": "Does sub-Saharan Africa truly defy the forecasts of the COVID-19 pandemic? Response from population data", @@ -1350293,49 +1348864,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2020.07.07.192005", - "rel_title": "A Fluorescence-based High Throughput-Screening assay for the SARS-CoV RNA synthesis complex", - "rel_date": "2020-07-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.07.192005", - "rel_abs": "The Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) emergence in 2003 introduced the first serious human coronavirus pathogen to an unprepared world. To control emerging viruses, existing successful anti(retro)viral therapies can inspire antiviral strategies, as conserved viral enzymes (eg., viral proteases and RNA-dependent RNA polymerases) represent targets of choice. Since 2003, much effort has been expended in the characterization of the SARS-CoV replication/transcription machinery. Until recently, a pure and highly active preparation of SARS-CoV recombinant RNA synthesis machinery was not available, impeding target-based high throughput screening of drug candidates against this viral family. The current Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic revealed a new pathogen whose RNA synthesis machinery is highly (>96% aa identity) homologous to SARS-CoV. This phylogenetic relatedness highlights the potential use of conserved replication enzymes to discover inhibitors against this significant pathogen, which in turn, contributes to scientific preparedness against emerging viruses. Here, we report the use of a purified and highly active SARS-CoV replication/transcription complex (RTC) to set-up a high-throughput screening of Coronavirus RNA synthesis inhibitors. The screening of a small (1,520 compounds) chemical library of FDA-approved drugs demonstrates the robustness of our assay and will allow to speed-up drug repositioning or novel drug discovery against the SARS-CoV-2.\n\nPrinciple of SARS-CoV RNA synthesis detection by a fluorescence-based high throughput screening assay\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC=\"FIGDIR/small/192005v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (20K):\norg.highwire.dtl.DTLVardef@e8122dorg.highwire.dtl.DTLVardef@18557org.highwire.dtl.DTLVardef@1d95362org.highwire.dtl.DTLVardef@f15222_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights- A new SARS-CoV non radioactive RNA polymerase assay is described\n- The robotized assay is suitable to identify RdRp inhibitors based on HTS", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Cecilia Eydoux", - "author_inst": "AMU" - }, - { - "author_name": "Veronique Fattorini", - "author_inst": "CNRS-AMU" - }, - { - "author_name": "Ashleigh Shannon", - "author_inst": "CNRS-AMU" - }, - { - "author_name": "Thi-Tuyet-Nhung Le", - "author_inst": "CNRS-AMU" - }, - { - "author_name": "Bruno Didier", - "author_inst": "Univ. Strasbourg" - }, - { - "author_name": "Bruno Canard", - "author_inst": "CNRS" - }, - { - "author_name": "Jean-Claude Guillemot", - "author_inst": "AMU" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "biochemistry" - }, { "rel_doi": "10.1101/2020.07.07.190546", "rel_title": "The evolutionary history of ACE2 usage within the coronavirus subgenus Sarbecovirus", @@ -1351311,6 +1349839,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.07.06.20147223", + "rel_title": "Predicting the second wave of COVID-19 in Washtenaw County, MI", + "rel_date": "2020-07-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.06.20147223", + "rel_abs": "The COVID-19 pandemic has highlighted the patchwork nature of disease epidemics, with infection spread dynamics varying wildly across countries and across states within the US. These heterogeneous patterns are also observed within individual states, with patches of concentrated outbreaks. Data is being generated daily at all of these spatial scales, and answers to questions regarded reopening strategies are desperately needed. Mathematical modeling is useful in exactly these cases, and using modeling at a county scale may be valuable to further predict disease dynamics for the purposes of public health interventions. To explore this issue, we study and predict the spread of COVID-19 in Washtenaw County, MI, the home to University of Michigan, Eastern Michigan University, and Google, as well as serving as a sister city to Detroit, MI where there has been a serious outbreak. Here, we apply a discrete and stochastic network-based modeling framework allowing us to track every individual in the county. In this framework, we construct contact networks based on synthetic population datasets specific for Washtenaw County that are derived from US Census datasets. We assign individuals to households, workplaces, schools, and group quarters (such as prisons). In addition, we assign casual contacts to each individual at random. Using this framework, we explicitly simulate Michigan-specific government-mandated workplace and school closures as well as social distancing measures. We also perform sensitivity analyses to identify key model parameters and mechanisms contributing to the observed disease burden in the three months following the first observed cases on COVID-19 in Michigan. We then consider several scenarios for relaxing restrictions and reopening workplaces to predict what actions would be most prudent. In particular, we consider the effects of 1) different timings for reopening, and 2) different levels of workplace vs. casual contact re-engagement. Through simulations and sensitivity analyses, we explore mechanisms driving magnitude and timing of a second wave of infections upon re-opening. This model can be adapted to other US counties using synthetic population databases and data specific to those regions.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Marissa Renardy", + "author_inst": "University of Michigan Medical School" + }, + { + "author_name": "Denise E. Kirschner", + "author_inst": "University of Michigan Medical School" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.05.20146969", "rel_title": "Partial Prediction of the Virus COVID-19 Spread in Russia Based on SIR and SEIR Models", @@ -1351543,33 +1350094,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.06.20147702", - "rel_title": "COVID-19 screening strategies that permit the safe re-opening of college campuses", - "rel_date": "2020-07-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.06.20147702", - "rel_abs": "ImportanceThe COVID-19 pandemic poses an existential threat to many US residential colleges: either they open their doors to students in September or they risk serious financial consequences.\n\nObjectiveTo define SARS-CoV-2 screening performance standards that would permit the safe return of students to campus for the Fall 2020 semester.\n\nDesignDecision and cost-effectiveness analysis linked to a compartmental epidemic model to evaluate campus screening using tests of varying frequency (daily-weekly), sensitivity (70%-99%), specificity (98%-99.7%), and cost ($10-$50/test). Reproductive numbers Rt = {1.5, 2.5, 3.5} defined three epidemic scenarios, with additional infections imported via exogenous shocks. We generally adhered to US government guidance for parameterization data.\n\nParticipantsA hypothetical cohort of 5000 college-age, uninfected students.\n\nMain Outcome(s) and Measure(s)Cumulative tests, infections, and costs; daily isolation dormitory census; incremental cost-effectiveness; and budget impact. All measured over an 80-day, abbreviated semester.\n\nResultsWith Rt = 2.5, daily screening with a 70% sensitive, 98% specific test produces 85 cumulative student infections and isolation dormitory daily census averaging 108 (88% false positives). Screening every 2 (7) days nets 135 (3662) cumulative infections and daily isolation census 66 (252) with 73% (4%) false positives. Across all scenarios, test frequency exerts more influence on outcomes than test sensitivity. Cost-effectiveness analysis selects screening every {2, 1, 7} days with a 70% sensitive test as the preferred strategy for Rt = {2.5, 3.5, 1.5}, implying a screening cost of {$470, $920, $120} per student per semester.\n\nConclusions & RelevanceRapid, inexpensive and frequently conducted screening - even if only 70% sensitive - would be cost-effective and produce a modest number of COVID-19 infections. While the optimal screening frequency hinges on the success of behavioral interventions to reduce the base severity of transmission (Rt), this could permit the safe return of student to campus.\n\nKEY POINTSO_ST_ABSQuestionC_ST_ABSWhat SARS-CoV-2 screening and isolation program will keep U.S. residential college students safe and permit the reopening of campuses?\n\nFindingsFrequent screening (every 2 or 3 days) of all students with a low-sensitivity, high-specificity test will control outbreaks with manageable isolation dormitory utilization at a justifiable cost.\n\nMeaningCampuses can safely reopen in the Fall 2020 but success hinges on frequent screening and uncompromising, continuous attention to basic prevention and behavioral interventions to reduce the baseline severity of transmission.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "A David Paltiel", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Amy Zheng", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Rochelle P Walensky", - "author_inst": "Medical Practice Evaluation Center, Division of Infectious Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, MA" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.29.20133363", "rel_title": "Triplex Real Time RT-PCR for N1, N2 and RP probes from CDC EUA SARS-CoV-2 diagnosis kit.", @@ -1352565,6 +1351089,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.07.01.20136317", + "rel_title": "Who is dying from Covid-19 in the United Kingdom? A review of cremation authorisations from a single South Wales' crematorium.", + "rel_date": "2020-07-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.01.20136317", + "rel_abs": "BackgroundCovid 19 is pandemic in the UK. To date only studies in the UK on hospital deaths have been published in the peer reviewed literature. Legal requirements for cremation in England and Wales require the collection of information that can be used to improve understanding of Covid 19 deaths in both hospital and community settings.\n\nAimTo document demographic and clinical characteristics, including likely place of infection, of individuals dying of Covid 19 to inform public health policy\n\nDesignA comprehensive case series of deaths from Covid 19 between 6 April and 30 May.\n\nSettingA crematorium in South Wales\n\nParticipantsIndividuals for whom an application was made for cremation.\n\nMain outcome measuresAge, sex, date and place of death, occupation, comorbidities, where infection acquired.\n\nResultsOf 752 cremations, 215(28.6%) were Covid-19 of which 115 (53.5%) were male and 100 (46.5%) female. The median age was 82 years, with the youngest patient being 47 years and the oldest 103 years. Over half the deaths (121/215: 56.3%) were over 80 years. Males odds of dying in hospital, rather than the community were 1.96 times that of females (95% Confidence Intervals (CI) 1.03 -3.74, p=0.054) despite being of similar age and having a similar number of comorbidities. Only 21(9.8%) of 215 patients had no comorbidities recorded. Patients dying in nursing homes were significantly older than those dying in hospital(median 88y (IQ range 82-93y) v 80y (IQ range 71-87y): p<0.0001). Patients dying in hospital had significantly more comorbidities than those dying in nursing homes (median 2: IQ range 1-3 v. 1: IQ range 1-2: p <0.001).\n\nConclusionsIn a representative series, comprising both hospital and community deaths, persons over 80 with an average 2 comorbidities predominated. Although men and women were represented in similar proportions, men were more likely to die in hospital. Over half the infections were acquired in either hospitals or nursing and residential homes with implications for the management of the pandemic, historically and in the future.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Roland L. Salmon", + "author_inst": "Retired" + }, + { + "author_name": "Stephen P. Monaghan", + "author_inst": "Public Health Wales" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.07.02.20145219", "rel_title": "Computational fluid dynamic (CFD), air flow-droplet dispersion, and indoor CO2 analysis for healthy public space configuration to complywith COVID 19 protocol", @@ -1352985,45 +1351532,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.29.20131367", - "rel_title": "Evaluation of Viasure SARS-CoV-2 RT-qPCR kit (CerTest Biotec) using CDC FDA EUA RT-qPCR kit as a gold standard.", - "rel_date": "2020-07-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.29.20131367", - "rel_abs": "BackgroundSeveral RT-qPCR kits are available for SARS-CoV-2 diagnosis, some of them with Emergency Use Authorization (EUA) by FDA, but most of them lacking of proper evaluation studies due to covid19 emergency.\n\nObjectiveWe evaluated Viasure RT-qPCR kit (CerTest Biotec, Spain) for SARS-CoV-2 diagnosis using CDC FDA EUA kit as gold standard.\n\nResultsAlthough we found the lack of RNA quality control probe as the main limitation for Viasure kit, the sensitivity was up to 97.5% and specificity was 100%.\n\nConclusionsViasure RT-qPCR kit is a reliable tool for SARS-CoV-2 diagnosis but improvement of an alternative RT-qPCR reaction for RNA extraction quality control as RNaseP is recommended.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Byron Freire-Paspuel", - "author_inst": "Universidad de las Americas" - }, - { - "author_name": "Patricio Alejandro Vega-Marino", - "author_inst": "Agencia de Regulacion y Control de la Bioseguridad y Cuarentena para Galapagos" - }, - { - "author_name": "Alberto Velez", - "author_inst": "Agencia de Regulacion y Control de la Bioseguridad y Cuarentena para Galapagos" - }, - { - "author_name": "Marilyn Cruz", - "author_inst": "Agencia de Regulacion y Control de la Bioseguridad y Cuarentena para Galapagos" - }, - { - "author_name": "Franklin Perez", - "author_inst": "One Lab. Santa Elena. Ecuador" - }, - { - "author_name": "Miguel Angel Garcia Bereguiain", - "author_inst": "Universidad de Las Americas" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.04.20146340", "rel_title": "The UK Covid-19 lockdown weakened in April and May 2020: implications for the size of the epidemic and for outcomes had lockdown been earlier", @@ -1353951,6 +1352459,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.29.20143180", + "rel_title": "Safe contact tracing for COVID-19: A method without privacy breach using functional encryption techniques based-on spatio-temporal trajectory data", + "rel_date": "2020-07-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.29.20143180", + "rel_abs": "The COVID-19 pandemic has spread all over the globe. In the absence of a vaccine, a small number of countries have managed to control the diffusion of viruses by early detection and early quarantine. South Korea, one of the countries which have kept the epidemics well-controlled, has opened the infected patients trajectory to the public. Such a reaction has been regarded as an effective method, however, serious privacy breach cases have been issued in South Korea. Furthermore, some suspected contacts have refused to take infection tests because they are afraid of being exposed. To solve this problem, we propose a privacy-preserving contact tracing method based on spatio-temporal trajectory which can be practically used in many quarantine systems. In addition, we develop a system to visualize the contact tracing workflow.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Wooil Kim", + "author_inst": "Korea University" + }, + { + "author_name": "Hyubjin Lee", + "author_inst": "Korea University" + }, + { + "author_name": "Yon Dohn Chung", + "author_inst": "Korea University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.07.02.20144840", "rel_title": "The reproduction number R for COVID-19 in England: Why hasn't ''lockdown'' been more effective?", @@ -1354311,37 +1352846,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.02.20145052", - "rel_title": "Modeling COVID-19 for lifting non-pharmaceutical interventions", - "rel_date": "2020-07-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.02.20145052", - "rel_abs": "As a result of the COVID-19 worldwide pandemic, the United States instituted various non-pharmaceutical interventions (NPIs) in an effort to the slow the spread of the disease. Although necessary for public safety, these NPIs can also have deleterious effects on the economy of a nation. State and federal leaders need tools that provide insight into which combination of NPIs will have the greatest impact on slowing the disease and at what point in time it is reasonably safe to start lifting these restrictions to everyday life. In the present work, we outline a modeling process that incorporates the parameters of the disease, the effects of NPIs, and the characteristics of individual communities to offer insight into when and to what degree certain NPIs should be instituted or lifted based on the progression of a given outbreak of COVID-19.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Matt Koehler", - "author_inst": "The MITRE Corporation" - }, - { - "author_name": "David M Slater", - "author_inst": "The MITRE Corporation" - }, - { - "author_name": "Garry Jacyna", - "author_inst": "The MITRE Corporation" - }, - { - "author_name": "James R Thompson", - "author_inst": "The MITRE Corporation" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.04.187435", "rel_title": "Snapshot of the evolution and mutation patterns of SARS-CoV-2", @@ -1355401,6 +1353905,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.07.03.20145722", + "rel_title": "Kinetics and performance of the Abbott Architect SARS-CoV-2 IgG antibody assay", + "rel_date": "2020-07-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.03.20145722", + "rel_abs": "ObjectivesTo assess the performance (sensitivity and specificity) of the Abbott Architect SARS-CoV-2 IgG antibody assay across three clinical settings.\n\nMethodsAntibody testing was performed on three clinical cohorts of COVID-19 disease: hospitalised patients with PCR confirmation, hospitalized patients with a clinical diagnosis but negative PCR, and symptomatic healthcare workers (HCWs). Pre-pandemic respiratory infection sera were tested as negative controls. The sensitivity of the assay was calculated at different time points (<5 days, 5-9 days, 10-14 days, 15-19 days, >20 days, >42 days), and compared between cohorts.\n\nResultsPerformance of the Abbot Architect SARS-CoV-2 assay varied significantly between cohorts. For PCR confirmed hospitalised patients (n = 114), early sensitivity was low: <5 days: 44.4% (95%CI: 18.9%-73.3%), 5-9 days: 32.6% (95%CI, 20.5%-47.5%), 10-14 days: 65.2% (95% CI 44.9%-81.2%), 15-20 days: 66.7% (95% CI: 39.1%-86.2%) but by day 20, sensitivity was 100% (95%CI, 86.2-100%).\n\nIn contrast, 17 out of 114 symptomatic healthcare workers tested at >20 days had negative results, generating a sensitivity of 85.1% (95%CI, 77.4% - 90.5%). All pre-pandemic sera were negative, a specificity of 100%. Seroconversion rates were similar for PCR positive and PCR negative hospitalised cases.\n\nConclusionsThe sensitivity of the Abbot Architect SARS-CoV-2 IgG assay increases over time, with sensitivity not peaking until 20 days post symptoms. Performance varied markedly by setting, with sensitivity significantly worse in symptomatic healthcare workers than in the hospitalised cohort. Clinicians, policymakers, and patients should be aware of the reduced sensitivity in this setting.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Fergus Hamilton", + "author_inst": "University of Bristol" + }, + { + "author_name": "Peter Muir", + "author_inst": "Public Health England" + }, + { + "author_name": "Marie Attwood", + "author_inst": "North Bristol NHS Trust" + }, + { + "author_name": "Alan Noel", + "author_inst": "North Bristol NHS Trust" + }, + { + "author_name": "Barry Vipond", + "author_inst": "Public Heath England" + }, + { + "author_name": "Richard Hopes", + "author_inst": "Public Health England" + }, + { + "author_name": "Ed Moran", + "author_inst": "North Bristol NHS Trust" + }, + { + "author_name": "Nick Maskell", + "author_inst": "University of Bristol" + }, + { + "author_name": "Deborah Warwick", + "author_inst": "North Bristol NHS Trust" + }, + { + "author_name": "Mahableshwar Albur", + "author_inst": "North Bristol NHS Trust" + }, + { + "author_name": "Jonathan Turner", + "author_inst": "Public Health England" + }, + { + "author_name": "Alasdair P MacGowan", + "author_inst": "North Bristol NHS Trust" + }, + { + "author_name": "David T Arnold", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.07.02.20145565", "rel_title": "Efficacy of Corticosteroids in Non-Intensive Care Unit Patients with COVID-19 Pneumonia from the New York Metropolitan region", @@ -1355685,49 +1354256,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.07.03.20146167", - "rel_title": "Serial interval, basic reproduction number and prediction of COVID-19 epidemic size in Jodhpur, India", - "rel_date": "2020-07-04", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.03.20146167", - "rel_abs": "BackgroundUnderstanding the epidemiology of COVID-19 is important for design of effective control measures at local level. We aimed to estimate the serial interval and basic reproduction number for Jodhpur, India and to use it for prediction of epidemic size for next one month.\n\nMethodsContact tracing of SARS-CoV-2 infected individuals was done to obtain the serial intervals. Aggregate and instantaneous R0 values were derived and epidemic projection was done using R software v4.0.0.\n\nResultsFrom among 79 infector-infectee pairs, the estimated median and 95 percentile values of serial interval were 5.98 days (95% CI 5.39 - 6.65) and 13.17 days (95% CI 11.27 - 15.57), respectively. The overall R0 value in the first 30 days of outbreak was 1.64 (95% CI 1.12 - 2.25) which subsequently decreased to 1.07 (95% CI 1.06 - 1.09). The instantaneous R0 value over 14 days window ranged from a peak of 3.71 (95% CI 1.85 -2.08) to 0.88 (95% CI 0.81 - 0.96) as on 24 June 2020. The projected COVID-19 case-load over next one month was 1881 individuals. Reduction of R0 from 1.17 to 1.085 could result in 23% reduction in projected epidemic size over the next one month.\n\nConclusionAggressive testing, contact-tracing and isolation of infected individuals in Jodhpur district resulted in reduction of R0. Further strengthening of control measures could lead to substantial reduction of COVID-19 epidemic size. A data-driven strategy was found useful in surge capacity planning and guiding the public health strategy at local level.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Suman Saurabh", - "author_inst": "All India Institute of Medical Sciences (AIIMS), Jodhpur" - }, - { - "author_name": "Mahendra Kumar Verma", - "author_inst": "All India Institute of Medical Sciences (AIIMS), Jodhpur, India" - }, - { - "author_name": "Vaishali Gautam", - "author_inst": "All India Institute of Medical Sciences (AIIMS), Jodhpur, India" - }, - { - "author_name": "Akhil Goel", - "author_inst": "All India Institute of Medical Sciences (AIIMS), Jodhpur, India" - }, - { - "author_name": "Manoj Kumar Gupta", - "author_inst": "All India Institute of Medical Sciences, Jodhpur, India" - }, - { - "author_name": "Pankaj Bhardwaj", - "author_inst": "All India Institute of Medical Sciences (AIIMS), Jodhpur, India" - }, - { - "author_name": "Sanjeev Misra", - "author_inst": "All India Institute of Medical Sciences (AIIMS), Jodhpur, India" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.07.03.20145060", "rel_title": "Health literacy in the general population in the context of epidemic or pandemic coronavirus outbreak situations: rapid scoping review", @@ -1356807,6 +1355335,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.30.20135343", + "rel_title": "Non-Adherence Tree Analysis (NATA) - an adherence improvement framework: a COVID-19 case study", + "rel_date": "2020-07-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.30.20135343", + "rel_abs": "Poor adherence to medication is a global phenomenon that has received a significant amount of research attention yet remains largely unsolved. Medication non-adherence can blur drug efficacy results in clinical trials, lead to substantial financial losses, increase the risk of relapse and hospitalisation, or lead to death. The most common methods measuring adherence are post-treatment measures; that is, adherence is usually measured after the treatment has begun. What the authors are proposing in this multidisciplinary study is a technique for analysing the factors that can cause non-adherence before or during medication treatment.\n\nFault Tree Analysis (FTA), allows system analysts to determine how combinations of simple faults of a system can propagate to cause a total system failure. Monte Carlo simulation is a mathematical algorithm that depends heavily on repeated random sampling to predict the behaviour of a system. In this study, the authors propose the use of Non-Adherence Tree Analysis (NATA), based on the FTA and Monte Carlo simulation techniques, to improve adherence. Firstly, the non-adherence factors of a medication treatment lifecycle are translated into what is referred to as a Non-Adherence Tree (NAT). Secondly, the NAT is coded into a format that is translated into the GoldSim software for performing dynamic system modelling and analysis using Monte Carlo. Finally, the GoldSim model is simulated and analysed to predict the behaviour of the NAT.\n\nThis study produces a framework for improving adherence by analysing social and non-social adherence barriers. The results reveal that the biggest factor that could contribute to non-adherence to a COVID-19 treatment is a therapy-related factor (the side effects of the medication). This is closely followed by a condition-related factor (asymptomatic nature of the disease) then patient-related factors (forgetfulness and other causes). With this information, clinicians can implement relevant measures and allocate resources appropriately to minimise non-adherence.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Ernest E Edifor", + "author_inst": "Manchester Metropolitan University" + }, + { + "author_name": "Regina Brown", + "author_inst": "University of Massachusetts Medical School" + }, + { + "author_name": "Paul Smith", + "author_inst": "Manchester Metropolitan University" + }, + { + "author_name": "Rick Kossik", + "author_inst": "GoldSim Technology Group" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.07.01.20144683", "rel_title": "Bronchoscopy in critically ill COVID-19 Patients: microbiological profile and factors related to nosocomial respiratory infection", @@ -1357263,25 +1355822,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.01.20144667", - "rel_title": "Numerical Analysis of Disastrous Effect of Reopening Too Soon in Georgia, USA", - "rel_date": "2020-07-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.01.20144667", - "rel_abs": "Social distancing restrictions were lifted in Georgia, USA before the daily new Covid-19 cases were significantly reduced below the peak. In this paper we show through numerical analysis the disastrous consequence of this action resulting in a second peak of daily cases which caused additional fatalities.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Santanu Basu", - "author_inst": "Sparkle Optics Corporation" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.01.20144253", "rel_title": "Modeling the Stability of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) on Skin, Currency, and Clothing", @@ -1358297,6 +1356837,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.07.01.20144386", + "rel_title": "Clinical characterization of respiratory droplet production during common airway procedures using high-speed imaging", + "rel_date": "2020-07-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.01.20144386", + "rel_abs": "BackgroundDuring the COVID-19 pandemic, a significant number of healthcare workers have been infected with SARS-CoV-2. However, there remains little knowledge regarding droplet dissemination during airway management procedures in real life settings.\n\nMethods12 different airway management procedures were investigated during routine clinical care. A high-speed video camera (1000 frames/second) was for imaging. Quantitative droplet characteristics as size, distance traveled, and velocity were computed.\n\nResultsDroplets were detected in 8/12 procedures. The droplet trajectories could be divided into two distinctive patterns (type 1/2). Type 1 represented a ballistic trajectory with higher speed droplets whereas type 2 represented a random trajectory of slower particles that persisted longer in air. Speaking and coughing lead to a larger amount of droplets than non-invasive ventilation therapy. The use of tracheal cannula filters reduced the amount of droplets.\n\nConclusionsRespiratory droplet patterns generated during airway management procedures follow two distinctive trajectories based on the influence of aerodynamic forces. Speaking and coughing produce more droplets than non-invasive ventilation therapy confirming these behaviors as exposure risks. Even large droplets may exhibit patterns resembling the fluid dynamics smaller airborne aerosols that follow the airflow convectively and may place the healthcare provider at risk.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Sarina K Mueller", + "author_inst": "Friedrich-Alexander-Universitat Erlangen-Nurnberg Medizinische Fakultat (FAU)" + }, + { + "author_name": "Reinhard Veltrup", + "author_inst": "Friedrich-Alexander-Universitat Erlangen-Nurnberg Medizinische Fakultat (FAU)" + }, + { + "author_name": "Bernhard Jakubass", + "author_inst": "Friedrich-Alexander-Universitat Erlangen-Nurnberg Medizinische Fakultat (FAU)" + }, + { + "author_name": "Stefan Kniesburges", + "author_inst": "Friedrich-Alexander-Universitat Erlangen-Nurnberg Medizinische Fakultat (FAU)" + }, + { + "author_name": "Judith Kempfle", + "author_inst": "Massachusetts Eye Ear, Harvard Medical School" + }, + { + "author_name": "Matthias J. Huebner", + "author_inst": "Friedrich-Alexander-Universitat Erlangen-Nurnberg Medizinische Fakultat (FAU)" + }, + { + "author_name": "Heinrich Iro", + "author_inst": "Friedrich-Alexander-Universitat Erlangen-Nurnberg Medizinische Fakultat (FAU)" + }, + { + "author_name": "Michael Doellinger", + "author_inst": "Friedrich-Alexander-Universitat Erlangen-Nurnberg Medizinische Fakultat (FAU)" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.06.30.20143727", "rel_title": "Twitter and Census Data Analytics to Explore Socioeconomic Factors for Post-COVID-19 Reopening Sentiment", @@ -1358825,89 +1357412,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.07.01.20144030", - "rel_title": "Broad phenotypic alterations and potential dysfunctions of lymphocytes in COVID-19 recovered individuals", - "rel_date": "2020-07-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.07.01.20144030", - "rel_abs": "BackgroundLymphopenia is a typical symptom in the COVID-19 patients. While millions of patients are clinical recovered, little is known about the immune status of lymphocytes in these individuals.\n\nMethodsA clinical recovered cohort (CR) of 55 COVID-19 individuals (discharged from hospital 4 to 11 weeks), and 55 age and sex matched healthy donors cohort (HD) were recruited. Detailed analysis on phenotype of the lymphocytes in peripheral blood mononuclear cells (PBMCs) was performed by flow cytometry.\n\nFindingsCompared with cohort HD, the CD8+ T cells in cohort CR had higher Teff and Tem, but lower Tc1 (IFN-{gamma}+), Tc2 (IL-4+) and Tc17 (IL-17A+) frequencies. The CD4+ T cells of CR had decreased frequency, especially on the Tcm subset. Moreover, CD4+ T cells of CR expressed lower PD-1 and had lower frequencies of Th1 (IFN-{gamma}+), Th2 (IL-4+), Th17 (IL-17A+) as well as circulating Tfh (CXCR5+PD-1+). Accordingly, isotype-switched memory B cell (IgM-CD20hi) in CR had significantly lower proportion in B cells, though level of activation marker CD71 elevated. For CD3-HLA-DRlo lymphocytes of CR, besides levels of IFN-{gamma}, Granzyme B and T-bet were lower, the correlation between T-bet and IFN-{gamma} became irrelevant. In addition, taken into account of discharged days, all the lowered function associated phenotypes showed no recovery tendency within whole observation period.\n\nInterpretationThe CR COVID-19 individuals still showed remarkable phenotypic alterations in lymphocytes after clinical recovery 4 to 11 weeks. This suggests SARS-CoV-2 infection imprints profoundly on lymphocytes and results in long-lasting potential dysfunctions.\n\nFundingKunming Science and Technology Department (2020-1-N-037)", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Jingyi Yang", - "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences (CAS)" - }, - { - "author_name": "Maohua Zhong", - "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences (CAS)," - }, - { - "author_name": "Ejuan Zhang", - "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences (CAS)" - }, - { - "author_name": "Ke Hong", - "author_inst": "Wuhan Jinyintan Hospital" - }, - { - "author_name": "Qingyu Yang", - "author_inst": "Wuhan Jinyintan Hospital" - }, - { - "author_name": "Dihan Zhou", - "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences (CAS)" - }, - { - "author_name": "Jianbo Xia", - "author_inst": "Maternal and Child Health Hospital of Hubei Province" - }, - { - "author_name": "Yao-Qing Chen", - "author_inst": "School of Public Health (Shenzhen), Sun Yat-sen University" - }, - { - "author_name": "Mingbo Sun", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences & Peking Union Medical College" - }, - { - "author_name": "Bali Zhao", - "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences (CAS)" - }, - { - "author_name": "Jie Xiang", - "author_inst": "Wuhan Jinyintan Hospital" - }, - { - "author_name": "Ying Liu", - "author_inst": "Wuhan Jinyintan Hospital" - }, - { - "author_name": "Yang Han", - "author_inst": "Wuhan Jinyintan Hospital" - }, - { - "author_name": "Xi Zhou", - "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences (CAS)" - }, - { - "author_name": "Chaolin Huang", - "author_inst": "Wuhan Jinyintan Hospital" - }, - { - "author_name": "You Shang", - "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Huimin Yan", - "author_inst": "Wuhan Institute of Virology, Chinese Academy of Sciences (CAS)" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.07.01.20143958", "rel_title": "A genome epidemiological study of SARS-CoV-2 introduction into Japan", @@ -1359827,6 +1358331,37 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.07.01.182964", + "rel_title": "Using iCn3D and the World Wide Web for structure-based collaborative research: Analyzing molecular interactions at the root of COVID-19", + "rel_date": "2020-07-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.01.182964", + "rel_abs": "ABSTRACTThe COVID-19 pandemic took us ill-prepared and tackling the many challenges it poses in a timely manner requires world-wide collaboration. Our ability to study the SARS-COV-2 virus and its interactions with its human host in molecular terms efficiently and collaboratively becomes indispensable and mission-critical in the race to develop vaccines, drugs, and neutralizing antibodies. There is already a significant corpus of 3D structures related to SARS and MERS coronaviruses, and the rapid generation of new structures demands the use of efficient tools to expedite the sharing of structural analyses and molecular designs and convey them in their native 3D context in sync with sequence data and annotations. We developed iCn3D (pronounced \u201cI see in 3D\u201d) 1 to take full advantage of web technologies and allow scientists of different backgrounds to perform and share sequence-structure analyses over the Internet and engage in collaborations through a simple mechanism of exchanging \u201clifelong\u201d web links (URLs). This approach solves the very old problem of \u201csharing of molecular scenes\u201d in a reliable and convenient manner. iCn3D links are sharable over the Internet and make data and entire analyses findable, accessible, and reproducible, with various levels of interoperability. Links and underlying data are FAIR 2 and can be embedded in preprints and papers, bringing a 3D live and interactive dimension to a world of text and static images used in current publications, eliminating at the same time the need for arcane supplemental materials. This paper exemplifies iCn3D capabilities in visualization, analysis, and sharing of COVID-19 related structures, sequence variability, and molecular interactions.Competing Interest StatementThe authors have declared no competing interest.View Full Text", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Philippe Youkharibache", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Raul Edouardo Cachau", + "author_inst": "Frederick National Laboratory for Cancer Research: Frederick, MD, US" + }, + { + "author_name": "Thomas Madej", + "author_inst": "National Institute of Health" + }, + { + "author_name": "Jiyao Wang", + "author_inst": "National Institutes of Health" + } + ], + "version": "1", + "license": "cc0", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.07.01.182220", "rel_title": "Association between neutralizing antibodies to SARS-CoV-2 and commercial serological assays", @@ -1360379,29 +1358914,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.24.20138644", - "rel_title": "Strong Correlation Between Prevalence of Severe Vitamin D Deficiency and Population Mortality Rate from COVID-19 in Europe", - "rel_date": "2020-07-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20138644", - "rel_abs": "BackgroundSARS-CoV-2 virus causes a very wide range of COVID-19 disease severity in humans: from completely asymptomatic to fatal, and the reasons behind it are often not understood. There is some data that Vitamin D may have protective effect, so authors decided to analyze European country-wide data to determine if Vitamin D levels are associated with COVID-19 population death rate.\n\nMethodsTo retrieve the Vitamin D levels data, authors analyzed the Vitamin D European population data compiled by 2019 ECTS Statement on Vitamin D Status published in the European Journal of Endocrinology. For the data set to used for analysis, only recently published data, that included general adult population of both genders ages 40-65 or wider, and must have included the prevalence of Vitamin D deficiency.\n\nResultsThere were 10 countries data sets that fit the criteria and were analyzed. Severe Vitamin D deficiency was defined as 25(OH)D less than 25 nmol/L (10 ng/dL). Pearson correlation analysis between death rate per million from COVID-19 and prevalence of severe Vitamin D deficiency shows a strong correlation with r = 0.76, p = 0.01, indicating significant correlation. Correlation remained significant, even after adjusting for age structure of the population. Additionally, over time, correlation strengthened, and r coefficient asymptoticaly increased.\n\nConclusionsAuthors recommend universal screening for Vitamin D deficiency, and further investigation of Vitamin D supplementation in randomized control studies, which may lead to possible treatment or prevention of COVID-19.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Isaac Z Pugach", - "author_inst": "Complete Med Care" - }, - { - "author_name": "Sofya Pugach", - "author_inst": "Complete Med Care" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.29.20143156", "rel_title": "Implications of the COVID-19 San Francisco Bay Area Shelter-in-Place Announcement: A Cross-Sectional Social Media Survey", @@ -1361705,6 +1360217,153 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.07.01.181867", + "rel_title": "periscope: sub-genomic RNA identification in SARS-CoV-2 ARTIC Network Nanopore Sequencing Data", + "rel_date": "2020-07-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.07.01.181867", + "rel_abs": "We have developed periscope, a tool for the detection and quantification of sub-genomic RNA (sgRNA) in SARS-CoV-2 genomic sequence data. The translation of the SARS-CoV-2 RNA genome for most open reading frames (ORFs) occurs via RNA intermediates termed \"sub-genomic RNAs\". sgRNAs are produced through discontinuous transcription which relies on homology between transcription regulatory sequences (TRS-B) upstream of the ORF start codons and that of the TRS-L which is located in the 5 UTR. TRS-L is immediately preceded by a leader sequence. This leader sequence is therefore found at the 5 end of all sgRNA. We applied periscope to 1,155 SARS-CoV-2 genomes from Sheffield, UK and validated our findings using orthogonal datasets and in vitro cell systems. Using a simple local alignment to detect reads which contain the leader sequence we were able to identify and quantify reads arising from canonical and non-canonical sgRNA. We were able to detect all canonical sgRNAs at expected abundances, with the exception of ORF10. A number of recurrent non-canonical sgRNAs are detected. We show that the results are reproducible using technical replicates and determine the optimum number of reads for sgRNA analysis. In VeroE6 ACE2+/- cell lines, periscope can detect the changes in the kinetics of sgRNA in orthogonal sequencing datasets. Finally, variants found in genomic RNA are transmitted to sgRNAs with high fidelity in most cases. This tool can be applied to all sequenced COVID-19 samples worldwide to provide comprehensive analysis of SARS-CoV-2 sgRNA.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Matthew Daniel Parker", + "author_inst": "Sheffield Bioinformatics Core, Neuroscience Institute, The University of Sheffield, Sheffield, UK" + }, + { + "author_name": "Benjamin B Lindsey", + "author_inst": "The Florey Institute, Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield. Sheffield Teaching Hospitals NHS Fo" + }, + { + "author_name": "Shay Leary", + "author_inst": "Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Western Australia, Australia" + }, + { + "author_name": "Silvana Gaudieri", + "author_inst": "School of Human Sciences, University of Western Australia, Crawley, Western Australia, Australia" + }, + { + "author_name": "Abha Chopra", + "author_inst": "Institute for Immunology & Infectious Diseases Discovery Way, Murdoch University, Murdoch, Western Australia" + }, + { + "author_name": "Matthew Wyles", + "author_inst": "Sheffield Institute of Translational Neuroscience, Neuroscience Institute, The University of Sheffield, Sheffield, UK" + }, + { + "author_name": "Adrienn Angyal", + "author_inst": "The Florey Institute, Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK." + }, + { + "author_name": "Luke R Green", + "author_inst": "The Florey Institute, Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK" + }, + { + "author_name": "Paul Parsons", + "author_inst": "Department of Animal and Plant Sciences, Alfred Denny Building, The University of Sheffield, S10 2TN" + }, + { + "author_name": "Rachel M Tucker", + "author_inst": "Department of Animal and Plant Sciences, Alfred Denny Building, The University of Sheffield, S10 2TN" + }, + { + "author_name": "Rebecca Brown", + "author_inst": "The Florey Institute, Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK." + }, + { + "author_name": "Danielle Groves", + "author_inst": "The Florey Institute, Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK." + }, + { + "author_name": "Katie Johnson", + "author_inst": "Sheffield Teaching Hospitals NHS Foundation Trust, Department of Virology/Microbiology, Sheffield, UK." + }, + { + "author_name": "Laura Carrilero", + "author_inst": "Department of Animal and Plant Sciences, Alfred Denny Building, The University of Sheffield, S10 2TN" + }, + { + "author_name": "Joe Heffer", + "author_inst": "IT Services, The University of Sheffield, Sheffield, UK" + }, + { + "author_name": "David Partridge", + "author_inst": "Sheffield Teaching Hospitals NHS Foundation Trust, Department of Virology/Microbiology, The Florey Institute, Department of Infection, Immunity and Cardiovascul" + }, + { + "author_name": "Cariad Evans", + "author_inst": "Sheffield Teaching Hospitals NHS Foundation Trust, Department of Virology/Microbiology, Sheffield, UK." + }, + { + "author_name": "Mohammad Razza", + "author_inst": "Sheffield Teaching Hospitals NHS Foundation Trust, Department of Virology/Microbiology, Sheffield, UK." + }, + { + "author_name": "Alexanda J Keeley", + "author_inst": "Sheffield Teaching Hospitals NHS Foundation Trust, Department of Virology/Microbiology, The Florey Institute, Department of Infection, Immunity and Cardiovascul" + }, + { + "author_name": "Nikki Smith", + "author_inst": "The Florey Institute, Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK." + }, + { + "author_name": "Ana Da Silva Filipe", + "author_inst": "Centre for Virus Research, The University of Glasgow, Glasgow, UK" + }, + { + "author_name": "James G Shepherd", + "author_inst": "Centre for Virus Research, The University of Glasgow, Glasgow, UK" + }, + { + "author_name": "Chris Davis", + "author_inst": "Centre for Virus Research, The University of Glasgow, Glasgow, UK" + }, + { + "author_name": "Sahan Bennett", + "author_inst": "Centre for Virus Research, The University of Glasgow, Glasgow, UK" + }, + { + "author_name": "Alain Kohl", + "author_inst": "Centre for Virus Research, The University of Glasgow, Glasgow, UK" + }, + { + "author_name": "Elihu Aranday-Cortes", + "author_inst": "Centre for Virus Research, The University of Glasgow, Glasgow, UK" + }, + { + "author_name": "Lily Tong", + "author_inst": "Centre for Virus Research, The University of Glasgow, Glasgow, UK" + }, + { + "author_name": "Jenna Nichols", + "author_inst": "Centre for Virus Research, The University of Glasgow, Glasgow, UK" + }, + { + "author_name": "Emma C Thomson", + "author_inst": "Centre for Virus Research, The University of Glasgow, Glasgow, UK" + }, + { + "author_name": "- The COVID-19 Genomics UK (COG-UK) consortium", + "author_inst": "-" + }, + { + "author_name": "Dennis Wang", + "author_inst": "Sheffield Bioinformatics Core, Department of Computer Science, The University of Sheffield, Sheffield, UK." + }, + { + "author_name": "Simon Mallal", + "author_inst": "Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA" + }, + { + "author_name": "Thushan I de Silva", + "author_inst": "The Florey Institute, Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield Teaching Hospitals NHS Fo" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.07.01.182659", "rel_title": "High affinity binding of SARS-CoV-2 spike protein enhances ACE2 carboxypeptidase activity", @@ -1362089,105 +1360748,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2020.06.24.20134288", - "rel_title": "A retrospective study evaluating efficacy and safety of compassionate use of tocilizumab in 13 patients with severe-to-critically ill COVID-19: analysis of well-responding cases and rapidly-worsening cases after tocilizumab administration", - "rel_date": "2020-06-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20134288", - "rel_abs": "We administered tocilizumab into 13 severe-to-critically ill patients with coronavirus disease 2019 (COVID-19) for compassionate use in combination with potential anti-viral agents in those who required an oxygen supply and showed increased laboratory inflammatory markers such as C-reactive protein (CRP) and ferritin. One injection of tocilizumab led to rapid improvements in clinical features, inflammatory findings, and oxygen supply in seven patients with severe COVID-19 and substantial amelioration in two patients who were critically ill, whereas four patients, who exhibited rapidly worsened respiratory function, required artificial ventilatory support even after tocilizumab treatment. Three of these four patients ultimately recovered from deterioration after methylprednisolone treatment. Administration of tocilizumab did not affect viral elimination nor IgG production specific for the virus. Compared with well-responding patients, rapidly-worsened patients showed a significantly higher ratio of ferritin vs. CRP. These findings suggest that tocilizumab has beneficial effects in severe-to-critically ill patients with COVID-19; however, in some cases, addition of methylprednisolone is required for disease rescue.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Shoji Hashimoto", - "author_inst": "Osaka Habikino Medical Center" - }, - { - "author_name": "Heita Kitajima", - "author_inst": "Osaka Habikino Medical Center" - }, - { - "author_name": "Tsuyoshi Arai", - "author_inst": "Osaka Habikino Medical Center" - }, - { - "author_name": "Yoshitaka Tamura", - "author_inst": "Osaka Habikino Medical Center" - }, - { - "author_name": "Takayuki Nagai", - "author_inst": "Osaka Habikino Medical Center" - }, - { - "author_name": "Hiroshi Morishita", - "author_inst": "Osaka Habikino Medical Center" - }, - { - "author_name": "Hiroto Matsuoka", - "author_inst": "Osaka Habikino Medical Center" - }, - { - "author_name": "Yuki Han", - "author_inst": "Osaka Habikino Medical Center" - }, - { - "author_name": "Seijiro Minamoto", - "author_inst": "Osaka Habikino Medical Center" - }, - { - "author_name": "Tomonori Hirashima", - "author_inst": "Osaka Habikino Medical Center" - }, - { - "author_name": "Tomoki Yamada", - "author_inst": "Osaka Habikino Medical Center" - }, - { - "author_name": "Yozo Kashiwa", - "author_inst": "Osaka Habikino Medical Center" - }, - { - "author_name": "Makoto Kameda", - "author_inst": "Osaka Habikino Medical Center" - }, - { - "author_name": "Seiji Yamaguchi", - "author_inst": "Osaka Habikino Medical Center" - }, - { - "author_name": "Kazuko Uno", - "author_inst": "Louis Pasteur Center for Medical Research" - }, - { - "author_name": "Emi Nakayama", - "author_inst": "Research Institute for Microbial Diseases, Osaka University" - }, - { - "author_name": "Tatsuo Shioda", - "author_inst": "Research Institute for Microbial Diseases, Osaka University" - }, - { - "author_name": "Kazuyuki Yoshizaki", - "author_inst": "Institute of Scientific and Industry Research, Osaka University" - }, - { - "author_name": "Sujin Kang", - "author_inst": "Immunology Frontier Research Center, Osaka University" - }, - { - "author_name": "Tadamistu Kishimoto", - "author_inst": "Immunology Frontier Research Center, Osaka University" - }, - { - "author_name": "Toshio Tanaka", - "author_inst": "Osaka Habikino Medical Center" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.22.165936", "rel_title": "Unsupervised cluster analysis of SARS-CoV-2 genomes indicates that recent (June 2020) cases in Beijing are from a genetic subgroup that consists of mostly European and South(east) Asian samples, of which the latter are the most recent", @@ -1363663,6 +1362223,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.29.20142513", + "rel_title": "Epidemic Trend Analysis of SARS-CoV-2 in SAARC Countries Using Modified SIR (M-SIR) Predictive Model", + "rel_date": "2020-06-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.29.20142513", + "rel_abs": "A novel coronavirus causing the severe and fatal respiratory syndrome was identified in China, is now producing outbreaks in more than two hundred countries around the world, and became pandemic by the time. In this article, a modified version of the well known mathematical epidemic model Susceptible (S)- Infected (I)- Recovered (R) is used to analyze the epidemics course of COVID-19 in eight different countries of the South Asian Association for Regional Cooperation (SAARC). To achieve this goal, the parameters of the SIR model are identified by using publicly available data for the corresponding countries: Afghanistan, Bangladesh, Bhutan, India, the Maldives, Nepal, Pakistan and Sri Lanka. Based on the prediction model we estimated the epidemic trend of COVID-19 outbreak in SAARC countries for 20 days, 90 days, and 180 days respectively. An SML (short-mid-long) term prediction model has been designed to understand the early dynamics of COVID-19 Epidemic in the south-east Asian region. The maximum and minimum basic reproduction number (R0 = 1.33 and 1.07) for SAARC countries are predicted to be in Pakistan and Bhutan. We equate simulation results with real data in the SAARC countries on the COVID-19 outbreak, and model potential countermeasure implementation scenarios. Our results should provide policymakers with a method for evaluating the impacts of possible interventions, including lockdown and social distancing, as well as testing and contact tracking.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Samrat Kumar Dey", + "author_inst": "Dhaka International University (DIU)" + }, + { + "author_name": "Md. Mahbubur Rahman", + "author_inst": "Military Institute of Science and Technology (MIST)" + }, + { + "author_name": "Kabid Hassan Shibly", + "author_inst": "Dhaka International University (DIU)" + }, + { + "author_name": "Umme Raihan Siddiqi", + "author_inst": "Shaheed Suhrawardy Medical College (ShSMC)" + }, + { + "author_name": "Arpita Howlader", + "author_inst": "Patuakhali Science and Technology University (PSTU)" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.29.20142463", "rel_title": "Epidemiological investigation of the first 135 COVID-19 cases in Brunei: Implications for surveillance, control, and travel restrictions", @@ -1364147,89 +1362742,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.28.20141838", - "rel_title": "SARS-CoV-2 serological testing using electrochemiluminescence reveals arapid onset of seroconversion in severe COVID-19 patients", - "rel_date": "2020-06-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.28.20141838", - "rel_abs": "Despite ongoing efforts to characterize the host response toward SARS-CoV-2, a major gap in our knowledge still exists regarding the magnitude and duration of the humoral response. We report the development of a rapid, highly specific and sensitive electrochemiluminescent assay for detecting IgM, IgA, and IgG antibodies toward two distinct SARS-CoV-2 antigens namely, the receptor binding domain (RBD) and the nuclear protein (NP). Whereas IgM antibodies toward RBD were detected at early stages of the disease, IgM antibodies against NP did not develop. Analysis of the antibody response in mild versus moderate/severe patients revealed a rapid onset of IgG and IgA antibodies, specifically in moderate/severe patients. Finally, we observed a marked reduction in IgM/IgA antibodies and to lesser extent, IgG, over time. We provide a comprehensive analysis of the human antibody response, and has major implications on our understanding and monitoring of SARS-CoV-2 infections, as well as finding effective vaccines.\n\nOne Sentence SummaryUsing a newly developed assay to detect anti-SARS-Cov-2 IgM, IgG and IgA antibodies we reveal a rapid onset of IgG and IgA antibodies towards distinct viral antigens, specifically in moderate/severe COVID-19 patients,", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Ariel Munitz", - "author_inst": "Department of Clinical Microbiology and Immunology, The Sackler School of Medicine, Tel-Aviv University, Ramat Aviv 69978, Israel." - }, - { - "author_name": "Liat Edry-Botzer", - "author_inst": "Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, 6997801 Israel" - }, - { - "author_name": "Michal Itan", - "author_inst": "Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, 6997801 Israel" - }, - { - "author_name": "Ran Tur-Kaspa", - "author_inst": "Department of Medicine D and the Liver Institute, Rabin Medical Center, Beilinson Hospital, Molecular Hepatology Research Laboratory, Felsenstein Medical Resear" - }, - { - "author_name": "Dror Dicker", - "author_inst": "Internal Medicine D, Hasharon Hospital-Rabin Medical Center, Petach Tikva, Israel. Sackler School of Medicine, Tel Aviv University, 6997801 Israel" - }, - { - "author_name": "Dana Markovitch", - "author_inst": "Internal Medicine D, Hasharon Hospital-Rabin Medical Center, Petach Tikva, Israel. Sackler School of Medicine, Tel Aviv University, 6997801 Israel" - }, - { - "author_name": "Moran Goren", - "author_inst": "Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, 6997801 Israel" - }, - { - "author_name": "Michael Mor", - "author_inst": "Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, 6997801 Israel" - }, - { - "author_name": "Shuval Lev", - "author_inst": "Intensive care unit, Hasharon Hospital-Rabin Medical Center, Petach Tikva, Israel. Sackler School of Medicine, Tel Aviv University, 6997801 Israel" - }, - { - "author_name": "Tamar Gottesman", - "author_inst": "Infectious diseases and infection control, Hasharon Hospital-Rabin Medical Center, Petach Tikva, Israel. Sackler School of Medicine, Tel Aviv University, 699780" - }, - { - "author_name": "Khitam Muhsen", - "author_inst": "Department of Epidemiology and Preventive Medicine, School of Public Health, Tel Aviv University, 6997801 Israel" - }, - { - "author_name": "Daniel Cohen", - "author_inst": "Department of Epidemiology and Preventive Medicine, School of Public Health, Tel Aviv University, 6997801 Israel" - }, - { - "author_name": "Miguel Stein", - "author_inst": "Allergy and Immunology Unit, Wolfson Medical Center, 6997801 Israel" - }, - { - "author_name": "Udi Qimron", - "author_inst": "Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, 6997801 Israel" - }, - { - "author_name": "Natalia Freund", - "author_inst": "Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, 6997801 Israel" - }, - { - "author_name": "Yariv Wine", - "author_inst": "School of Molecular Cell Biology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 6997801 Israel" - }, - { - "author_name": "Motti Gerlic", - "author_inst": "Department of Clinical Microbiology and Immunology, The Sackler School of Medicine, Tel-Aviv University, Ramat Aviv 69978, Israel." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.28.20132498", "rel_title": "EVALUATION OF THE ABBOTT SARS-COV-2 IG-G ASSAY.", @@ -1365569,6 +1364081,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.26.20135715", + "rel_title": "Genomic epidemiology of SARS-CoV-2 in Colombia", + "rel_date": "2020-06-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.26.20135715", + "rel_abs": "Coronavirus disease 2019 (COVID-19) was first diagnosed in Colombia from a traveler arriving from Italy on February 26, 2020. To date, available data on the origins and number or introductions of SARS-CoV-2 into the country are limited. Here, we sequenced SARS-CoV-2 from 43 clinical samples and--together with other 73 genomes sequences available from the country--we investigated the emergence and the routes of importation of COVID-19 into Colombia using epidemiological, historical air travel and phylogenetic observations. Our study provided evidence of multiple introductions, mostly from Europe, with at least 12 lineages being documented. Phylogenetic findings validated the lineage diversity, supported multiple importation events and the evolutionary relationship of epidemiologically-linked transmission chains. Our results reconstruct the early evolutionary history of SARS-CoV-2 in Colombia and highlight the advantages of genome sequencing to complement COVID-19 outbreak investigation.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Katherine Laiton-Donato", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Christian Julian Villabona Arenas", + "author_inst": "London School of Hygiene & Tropical Medicine" + }, + { + "author_name": "Jose A Usme Ciro", + "author_inst": "Universidad Cooperativa de Colombia" + }, + { + "author_name": "Carlos Franco Munoz", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Diego Alejandro Alvarez-Diaz", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Liz S Villabona-Arenas", + "author_inst": "Universidad Industrial de Santander" + }, + { + "author_name": "Susy Echeverria-Londono", + "author_inst": "Imperial College-London" + }, + { + "author_name": "Nicolas D Franco-Sierra", + "author_inst": "Instituto de Investigacion de Recursos Biologicos Alexander von Humboldt" + }, + { + "author_name": "Zulma M Cucunuba", + "author_inst": "Imperial College London" + }, + { + "author_name": "Astrid Carolina Florez-Sanchez", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Carolina Ferro", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Nadim J Ajami", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Diana M Walteros", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Franklin E Prieto-Alvarado", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Carlos A Duran-Camacho", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Martha L Ospina-Martinez", + "author_inst": "Instituto Nacional de Salud" + }, + { + "author_name": "Marcela M Mercado-Reyes", + "author_inst": "Instiuto Nacional de Salud" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.26.20140806", "rel_title": "Combination of Antibody based rapid diagnostic tests used in an algorithm may improve their performance in SARS CoV-2 diagnosis.", @@ -1366105,37 +1364700,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.26.20131144", - "rel_title": "The scale and dynamics of COVID-19 epidemics across Europe", - "rel_date": "2020-06-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.26.20131144", - "rel_abs": "The number of COVID-19 deaths reported from European countries has varied more than 100-fold. In terms of coronavirus transmission, the relatively low death rates in some countries could be due to low intrinsic (e.g. low population density) or imposed contact rates (e.g. non-pharmaceutical interventions) among individuals, or because fewer people were exposed or susceptible to infection (e.g. smaller populations). Here we develop a flexible empirical model (skew-logistic) to distinguish among these possibilities. We find that countries reporting fewer deaths did not generally have intrinsically lower rates of transmission and epidemic growth, and flatter epidemic curves. Rather, countries with fewer deaths locked down earlier, had shorter epidemics that peaked sooner, and smaller populations. Consequently, as lockdowns are eased we expect, and are starting to see, a resurgence of COVID-19 across Europe.\n\nOne Sentence SummaryA flexible empirical model shows that European countries reporting fewer COVID-19 deaths locked down earlier, had shorter epidemics that peaked sooner, and smaller populations.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Christopher Dye", - "author_inst": "Oxford University" - }, - { - "author_name": "Russell C.H. Cheng", - "author_inst": "University of Southampton" - }, - { - "author_name": "John S. Dagpunar", - "author_inst": "University of Southampton" - }, - { - "author_name": "Brian G. Williams", - "author_inst": "Stellenbosch University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.27.20141747", "rel_title": "Evaluation of national responses to COVID-19 pandemic based on Pareto optimality", @@ -1367183,6 +1365747,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, + { + "rel_doi": "10.1101/2020.06.27.20141770", + "rel_title": "Readability of selected governmental and popular health organization websites on Covid-19 public health information: A descriptive analysis", + "rel_date": "2020-06-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.27.20141770", + "rel_abs": "BackgroundThe U.S. Department of Health & Human Services (USDHHS) recommends that health material be written at or below a sixth-grade reading level to ensure readability. The aim of this study was to examine the readability of international and national health organizations on Covid-19 information in their websites employing a previously validated tool.\n\nMethodsA purposive sample of publicly accessible governmental and popular international health organization websites was selected. The readability of the websites Covid-19 public health information was estimated using the previously validated SMOG readability formula, which determined reading level by correlating the number of polysyllabic words.\n\nResultsOf the 10 websites included in the analysis, none had Covid-19 public health information at the USDHHSs recommended reading level. The material ranged in reading level at undergraduate level or above.\n\nDiscussionThe findings indicate that the online Covid-19 materials need to be modified in order to reach recommended reading levels. This study can be of practical use to policy makers and public health government officials when designing, modifying, and evaluating Covid-19 materials. We recommend using simple, non-polysyllable words to ensure that Covid-19 public health information materials are written at the recommended reading levels.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Patricia Moyinoluwa Ojo", + "author_inst": "University College Cork" + }, + { + "author_name": "Tolulope Omowonuola Okeowo", + "author_inst": "University College Cork" + }, + { + "author_name": "Ann Mary Thampy", + "author_inst": "University College Cork" + }, + { + "author_name": "Zubair Kabir", + "author_inst": "University College Cork" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.06.29.20142307", "rel_title": "Temperature and Humidity Do Not Influence Global COVID-19 Incidence as Inferred from Causal Models", @@ -1367591,25 +1366186,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "toxicology" }, - { - "rel_doi": "10.1101/2020.06.28.20141960", - "rel_title": "Data presented by the UK government as lockdown was eased shows the transmission of COVID-19 had already increased.", - "rel_date": "2020-06-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.28.20141960", - "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19) is an international emergency that has been addressed in many countries by changes in and restrictions on behaviour. These are often collectively labelled social distancing and lockdown. On the 23rd June 2020, Boris Johnson, the Prime Minister of the United Kingdom announced substantial easings of restrictions. This paper examines some of the data he presented.\n\nMethodsGeneralised additive models, with negative binomial errors and cyclic term representing day-of-week effects, were fitted to data on the daily numbers of new confirmed cases of COVID-19. Exponential rates for the epidemic were estimated for different periods, and then used to calculate R, the reproduction number, for the disease in different periods.\n\nResultsAfter an initial stabilisation, the lockdown reduced R to around 0.81 (95% CI: 0.79, 0.82). This value increased to around 0.94 (95% CI 0.89, 0.996) for the fortnight from the 9th June 2020.\n\nConclusionsOfficial UK data, presented as the easing of the lockdown was announced, shows that R was already more than half way back to 1 at that point. That suggests there was little scope for the announced changes to be implemented without restarting the spread of the disease.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Mike Lonergan", - "author_inst": "University of Dundee" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.06.28.20142174", "rel_title": "COVID-19: Saving lives and livelihoods using population density driven testing", @@ -1368677,6 +1367253,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2020.06.26.20140905", + "rel_title": "Forecasting COVID-19 Dynamics and Endpoint in Bangladesh: A Data-driven Approach", + "rel_date": "2020-06-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.26.20140905", + "rel_abs": "On December 31, 2019, the World Health Organization (WHO) was informed that atypical pneumonia-like cases have emerged in Wuhan City, Hubei province, China. WHO identified it as a novel coronavirus and declared a global pandemic on March 11th, 2020. At the time of writing this, the COVID-19 claimed more than 440 thousand lives worldwide and led to the global economy and social life into an abyss edge in the living memory. As of now, the confirmed cases in Bangladesh have surpassed 100 thousand and more than 1343 deaths putting startling concern on the policymakers and health professionals; thus, prediction models are necessary to forecast a possible number of cases in the future. To shed light on it, in this paper, we presented data-driven estimation methods, the Long Short-Term Memory (LSTM) networks, and Logistic Curve methods to predict the possible number of COVID-19 cases in Bangladesh for the upcoming months. The results using Logistic Curve suggests that Bangladesh has passed the inflection point on around 28-30 May 2020, a plausible end date to be on the 2nd of January 2021 and it is expected that the total number of infected people to be between 187 thousand to 193 thousand with the assumption that stringent policies are in place. The logistic curve also suggested that Bangladesh would reach peak COVID-19 cases at the end of August with more than 185 thousand total confirmed cases, and around 6000 thousand daily new cases may observe. Our findings recommend that the containment strategies should immediately implement to reduce transmission and epidemic rate of COVID-19 in upcoming days.\n\nHighlightsO_LIAccording to the Logistic curve fitting analysis, the inflection point of the COVID-19 pandemic has recently passed, which was approximately between May 28, 2020, to May 30, 2020.\nC_LIO_LIIt is estimated that the total number of confirmed cases will be around 187-193 thousand at the end of the epidemic. We expect that the actual number will most likely to in between these two values, under the assumption that the current transmission is stable and improved stringent policies will be in place to contain the spread of COVID-19.\nC_LIO_LIThe estimated total death toll will be around 3600-4000 at the end of the epidemic.\nC_LIO_LIThe epidemic of COVID-19 in Bangladesh will be mostly under control by the 2nd of January 2021 if stringent measures are taken immediately.\nC_LI", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Al-Ekram Elahee Hridoy", + "author_inst": "Department of Geography and Environmental Studies, University of Chittagong, Chittagong 4331, Bangladesh" + }, + { + "author_name": "Mohammad Naim", + "author_inst": "Department of Electrical and Computer Engineering, North South University, Dhaka 1229, Bangladesh" + }, + { + "author_name": "Nazim Uddin Emon", + "author_inst": "3Department of Pharmacy, Faculty of Science and Engineering, International Islamic University Chittagong, Chittagong 4318, Bangladesh" + }, + { + "author_name": "Imrul Hasan Tipo", + "author_inst": "Department of Biochemistry and Molecular Biology, University of Chittagong, Chittagong 4331, Bangladesh" + }, + { + "author_name": "Safayet Alam", + "author_inst": "Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Dhaka, Dhaka 1000, Bangladesh" + }, + { + "author_name": "Abdullah Al Mamun", + "author_inst": "Department of Computer Science and Engineering, Chittagong University of Engineering and Technology, Chittagong 4349, Bangladesh" + }, + { + "author_name": "Mohammad Safiqul Islam", + "author_inst": "Department of Pharmacy, Faculty of Science, Noakhali Science and Technology University, Noakhali 3814, Bangladesh" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.06.26.20141077", "rel_title": "Analyses and Forecast for COVID-19 epidemic in India", @@ -1368997,49 +1367616,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "psychiatry and clinical psychology" }, - { - "rel_doi": "10.1101/2020.06.25.20139907", - "rel_title": "Teach, and teach and teach: does the average citizen use masks correctly during daily activities? Results from an observational study with more than 12,000 participants", - "rel_date": "2020-06-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.25.20139907", - "rel_abs": "COVID-19 is a new disease with no treatment and no vaccine so far. The pandemic is still growing in many areas. Among the core measures to prevent disease spread is the use of face masks. We observed 12,588 people in five Brazilian cities within the Baixada Santista metropolitan area. Even though this is densely populated region and heavily impacted by COVID-19 with a high risk population, only 45.1% of the observed population wore in face masks in a correct way, and another 15.5% simply did not use masks at all. The remainder used masks incorrectly, which is evidence of the worst scenario of people believing that they are protected when they are not. This is among the first studies, to the best of our knowledge, that measures real life compliance with face masks during this COVID-19 pandemic. It is our conclusion that it is paramount to first control the virus before allowing people back in the streets. We should not assume that people will wear masks properly. Equally important is to instruct and sensitize people on how to use face masks and why it is important.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Evaldo Stanislau Affonso de Ara\u00fajo", - "author_inst": "1. Sao Judas Tadeu University, Medical School, 2. Hospital das Clinicas, University of Sao Paulo Medical School" - }, - { - "author_name": "Fatima Maria Bernardes Henriques Amaral", - "author_inst": "Sao Judas Tadeu University, Medical School" - }, - { - "author_name": "Dongmin Park", - "author_inst": "Sao Judas Tadeu University, Medical School" - }, - { - "author_name": "Ana Paola Ceraldi Cameira", - "author_inst": "Sao Judas Tadeu University, Medical School" - }, - { - "author_name": "Murilo Augustinho Muniz da Cunha", - "author_inst": "Sao Judas Tadeu University, Medical School" - }, - { - "author_name": "Evelyn Gutierrez Karl", - "author_inst": "Sao Judas Tadeu University, Medical School" - }, - { - "author_name": "Sheila J Henderson", - "author_inst": "Alliant International University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.06.26.20140764", "rel_title": "Predicting the disease outcome in COVID-19 positive patients through Machine Learning: a retrospective cohort study with Brazilian data", @@ -1370135,6 +1368711,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.24.20139188", + "rel_title": "COVID-19 Antibody in Thai Community Hospitals", + "rel_date": "2020-06-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20139188", + "rel_abs": "BackgroundCOVID-19 seroprevalence data has been scarce, especially in less developed countries with a relatively low infection rate.\n\nMethodsA locally developed rapid IgM/IgG test kit was used for screening hospital staff and patients who required procedural treatment or surgery in 52 hospitals in Thailand from April 8 to June 26, 2020. A total of 857 participants were tested--675 were hospital staff and 182 were pre-procedural patients. (Thai Clinical Trials Registry: TCTR20200426002)\n\nResultsOverall, 5.5% of the participants (47 of 857) had positive immunoglobulin M (IgM), 0.2% (2 of 857) had positive immunoglobulin G (IgG) and IgM. Hospitals located in the Central part of Thailand had the highest IgM seroprevalence (11.9%). Preprocedural patients had a higher rate of positive IgM than the hospital staff (12.1% vs. 3.7%). Participants with present upper respiratory tract symptoms had a higher rate of positive IgM than those without (9.6% vs. 4.5%). Three quarters (80.5%, 690 of 857) of the participants were asymptomatic, of which, 31 had positive IgM (4.5%) which consisted of 20 of 566 healthcare workers (3.5%) and 11 of 124 preprocedural patients (8.9%).\n\nConclusionsCOVID-19 antibody test could detect a substantial number of potential silent spreaders in Thai community hospitals. Antibody testing should be encouraged for mass screening, especially in asymptomatic individuals.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Tanawin Nopsopon", + "author_inst": "Chulalongkorn University Faculty of Medicine" + }, + { + "author_name": "Krit Pongpirul", + "author_inst": "Chulalongkorn University Faculty of Medicine" + }, + { + "author_name": "Korn Chotirosniramit", + "author_inst": "Chulalongkorn University Faculty of Medicine" + }, + { + "author_name": "Narin Hiransuthikul", + "author_inst": "Chulalongkorn University Faculty of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.24.20135673", "rel_title": "Seroprevalence of SARS-CoV-2 IgG Specific Antibodies among Healthcare Workers in the Northern Metropolitan Area of Barcelona, Spain, after the first pandemic wave", @@ -1370615,25 +1369222,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.22.20134130", - "rel_title": "Impact of public health interventions on the COVID-19 epidemic: a stochastic model based on data from an African island", - "rel_date": "2020-06-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.22.20134130", - "rel_abs": "A stochastic model was created to simulate the impact of various healthcare measures on the COVID-19 epidemic. Travel restrictions and point of entry or exit screening help to delay the onset of the outbreak by a few weeks. Population surveillance is critical to detect the start of community transmission early and to avoid a surge in cases. Contact reduction and contact tracing are key interventions that can help to control the outbreak. To promptly curb the number of new cases, countries should diagnose patients using a highly sensitive test.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Dooshanveer Nuckchady", - "author_inst": "Dr. A. G. Jeetoo Hospital" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.24.20129817", "rel_title": "Influenza Vaccination and COVID19 Mortality in the USA", @@ -1371605,6 +1370193,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.25.20140434", + "rel_title": "Effects of social distancing on the spreading of COVID-19 inferred from mobile phone data", + "rel_date": "2020-06-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.25.20140434", + "rel_abs": "A better understanding of how the COVID-19 epidemic responds to social distancing efforts is required for the control of future outbreaks and to calibrate partial lock-downs. We present quantitative relationships between key parameters characterizing the COVID-19 epidemiology and social distancing efforts of nine selected European countries. Epidemiological parameters were extracted from the number of daily deaths data, while mitigation efforts are estimated from mobile phone tracking data. The decrease of the basic reproductive number (R0) as well as the duration of the initial exponential expansion phase of the epidemic strongly correlates with the magnitude of mobility reduction. Utilizing these relationships we decipher the relative impact of the timing and the extent of social distancing on the total death burden of the epidemic.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Hamid Khataee", + "author_inst": "The University of Queensland" + }, + { + "author_name": "Istvan Scheuring", + "author_inst": "Hungarian Academy of Sciences" + }, + { + "author_name": "Andras Czirok", + "author_inst": "University of Kansas Medical Center" + }, + { + "author_name": "Zoltan Neufeld", + "author_inst": "University of Queensland" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.24.20139444", "rel_title": "Modelling lockdown-induced 2nd COVID waves in France", @@ -1371905,117 +1370524,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.25.20140384", - "rel_title": "Seroprevalence of Antibodies to SARS-CoV-2 in Six Sites in the United States, March 23-May 3, 2020", - "rel_date": "2020-06-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.25.20140384", - "rel_abs": "ImportanceReported cases of SARS-CoV-2 infection likely underestimate the prevalence of infection in affected communities. Large-scale seroprevalence studies provide better estimates of the proportion of the population previously infected.\n\nObjectiveTo estimate prevalence of SARS-CoV-2 antibodies in convenience samples from several geographic sites in the United States.\n\nDesignSerologic testing of convenience samples using residual sera obtained for routine clinical testing by two commercial laboratory companies.\n\nSettingConnecticut (CT), south Florida (FL), Missouri (MO), New York City metro region (NYC), Utah (UT), and Washington States (WA) Puget Sound region.\n\nParticipantsPersons of all ages with serum collected during intervals from March 23 through May 3, 2020.\n\nExposureSARS-CoV-2 virus infection.\n\nMain outcomes and measuresWe estimated the presence of antibodies to SARS-CoV-2 spike protein using an ELISA assay. We standardized estimates to the site populations by age and sex. Estimates were adjusted for test performance characteristics (96.0% sensitivity and 99.3% specificity). We estimated the number of infections in each site by extrapolating seroprevalence to site populations. We compared estimated infections to number of reported COVID-19 cases as of last specimen collection date.\n\nResultsWe tested sera from 11,933 persons. Adjusted estimates of the proportion of persons seroreactive to the SARS-CoV-2 spike protein ranged from 1.13% (95% confidence interval [CI] 0.70-1.94) in WA to 6.93% (95% CI 5.02-8.92) in NYC (collected March 23-April 1). For sites with later collection dates, estimates ranged from 1.85% (95% CI 1.00-3.23, collected April 6-10) for FL to 4.94% (95% CI 3.61-6.52) for CT (April 26-May 3). The estimated number of infections ranged from 6 to 24 times the number of reported cases in each site.\n\nConclusions and relevanceOur seroprevalence estimates suggest that for five of six U.S. sites, from late March to early May 2020, >10 times more SARS-CoV-2 infections occurred than the number of reported cases. Seroprevalence and under-ascertainment varied by site and specimen collection period. Most specimens from each site had no evidence of antibody to SARS-CoV-2. Tracking population seroprevalence serially, in a variety of specific geographic sites, will inform models of transmission dynamics and guide future community-wide public health measures.\n\nKey findingsO_ST_ABSQuestionC_ST_ABSWhat proportion of persons in six U.S. sites had detectable antibodies to SARS-CoV-2, March 23-May 3, 2020?\n\nFindingsWe tested 11,933 residual clinical specimens. We estimate that from 1.1% of persons in the Puget Sound to 6.9% in New York City (collected March 23-April 1) had detectable antibodies. Estimates ranged from 1.9% in south Florida to 4.9% in Connecticut with specimens collected during intervals from April 6-May 3. Six to 24 times more infections were estimated per site with seroprevalence than with case report data.\n\nMeaningFor most sites, evidence suggests >10 times more SARS-CoV-2 infections occurred than reported cases. Most persons in each site likely had no detectable SARS-CoV-2 antibodies.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Fiona P. Havers", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Carrie Reed", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Travis W. Lim", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Joel M. Montgomery", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "John D. Klena", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Aron J. Hall", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Alicia M. Fry", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Deborah L. Cannon", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Cheng-Feng Chiang", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Aridth Gibbons", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Inna Krapiunaya,", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Maria Morales-Betoulle", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Katherine Roguski", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Mohammed Rasheed", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Brandi Freeman", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Sandra Lester", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Lisa Mills", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Darin S. Carroll", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "S. Michelle Owen", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Jeffrey A. Johnson", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Vera A. Semenova", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "- State Collaborator Group", - "author_inst": "-" - }, - { - "author_name": "Jarad Schiffer", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Natalie P. Thornburg", - "author_inst": "Centers for Disease Control and Prevention" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.24.20138735", "rel_title": "Elevated levels of PM2.5 in crowded Subways of Cities with High COVID-19 related Mortality", @@ -1373199,6 +1371707,25 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.06.25.20139956", + "rel_title": "COVID-19 Confirmed Cases and Fatalities in 883 U.S. Counties with a Population of 50,000 or More: Predictions Based on Social, Economic, Demographic Factors and Shutdown Days", + "rel_date": "2020-06-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.25.20139956", + "rel_abs": "The spread of the COVID-19 virus is highly variable among U.S. counties. Seventeen factors known or thought to be related to spread of the COVID-19 virus were studied by Poisson regression analysis of confirmed cases and deaths in 883 U.S. counties with a population of 50,000 or more as of May 31, 2020. With little exception, each factor was predictive of incidence and mortality. The regression equation can be used to identify priority locations for preventive efforts and preparation for medical care caseloads when prevention is unsuccessful. Based on the correlation of cases and deaths to days since stay-at-home orders were issued, the orders reduced the cases about 48 percent and deaths about 50 percent. Focusing preventive efforts on the more vulnerable counties may be more effective and less economically damaging than statewide shutdowns.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Leon S. Robertson", + "author_inst": "Yale University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.26.173146", "rel_title": "Air and surface measurements of SARS-CoV-2 inside a bus during normal operation", @@ -1373599,29 +1372126,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.24.20139196", - "rel_title": "How Many Lives Has Lockdown Saved in the UK?", - "rel_date": "2020-06-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20139196", - "rel_abs": "We compare the trajectory of deaths (both in hospitals and care homes) on a daily basis in Sweden and England and Wales (which constitute 90 per cent of the UK population) from 11 March to 7 August 2020, the latest date at which the relevant data is available for England and Wales.\n\nDeaths in both Sweden and England and Wales peaked on 8 April. The build up to the peak was very similar in both. Given the time lag between infection and death, the lockdown would have had little effect on the peak number of deaths.\n\nBy the first week of August, the deaths are very similar in both. However, from early May the decline in England and Wales has been much sharper.\n\nWe estimate that to 7 August, lockdown saved 17,700 lives in England and Wales, or just under 20,000 extrapolating to a UK level.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Rickard Bengt Emanuel Nyman", - "author_inst": "University College London" - }, - { - "author_name": "Paul Ormerod", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.24.20139014", "rel_title": "Strategies for Controlling the Spread of COVID-19", @@ -1374628,6 +1373132,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2020.06.24.20138859", + "rel_title": "Using Machine Learning of Clinical Data to Diagnose COVID-19", + "rel_date": "2020-06-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.24.20138859", + "rel_abs": "The recent pandemic of Coronavirus Disease 2019 (COVID-19) has placed severe stress on healthcare systems worldwide, which is amplified by the critical shortage of COVID-19 tests. In this study, we propose to generate a more accurate diagnosis model of COVID-19 based on patient symptoms and routine test results by applying machine learning to reanalyzing COVID-19 data from 151 published studies. We aimed to investigate correlations between clinical variables, cluster COVID-19 patients into subtypes, and generate a computational classification model for discriminating between COVID -19 patients and influenza patients based on clinical variables alone. We discovered several novel associations between clinical variables, including correlations between being male and having higher levels of serum lymphocytes and neutrophils. We found that COVID-19 patients could be clustered into subtypes based on serum levels of immune cells, gender, and reported symptoms. Finally, we trained an XGBoost model to achieve a sensitivity of 92.5% and a specificity of 97.9% in discriminating COVID-19 patients from influenza patients. We demonstrated that computational methods trained on large clinical datasets could yield ever more accurate COVID-19 diagnostic models to mitigate the impact of lack of testing. We also presented previously unknown COVID-19 clinical variable correlations and clinical subgroups.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Wei Tse Li", + "author_inst": "UC San Diego" + }, + { + "author_name": "Jiayan Ma", + "author_inst": "UC San Diego" + }, + { + "author_name": "Neil Shende", + "author_inst": "UC San Diego" + }, + { + "author_name": "Grant Castaneda", + "author_inst": "UC San Diego" + }, + { + "author_name": "Jaideep Chakladar", + "author_inst": "UC San Diego" + }, + { + "author_name": "Joseph C. Tsai", + "author_inst": "UC San Diego" + }, + { + "author_name": "Lauren Apostol", + "author_inst": "UC San Diego" + }, + { + "author_name": "Christine O. Honda", + "author_inst": "UC San Diego" + }, + { + "author_name": "Jingyue Xu", + "author_inst": "UC San Diego" + }, + { + "author_name": "Lindsay M. Wong", + "author_inst": "UC San Diego" + }, + { + "author_name": "Tianyi Zhang", + "author_inst": "UC San Diego" + }, + { + "author_name": "Abby Lee", + "author_inst": "UC San Diego" + }, + { + "author_name": "Aditi Gnanasekar", + "author_inst": "UC San Diego" + }, + { + "author_name": "Thomas K. Honda", + "author_inst": "UC San Diego" + }, + { + "author_name": "Selena Z. Kuo", + "author_inst": "Columbia University Medical Center" + }, + { + "author_name": "Michael Andrew Yu", + "author_inst": "Emory University School of Medicine" + }, + { + "author_name": "Eric Y. Chang", + "author_inst": "VA San Diego" + }, + { + "author_name": "Mahadevan R. Rajasekaran", + "author_inst": "VA San Diego" + }, + { + "author_name": "Weg M. Ongkeko", + "author_inst": "UC San Diego" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.24.167049", "rel_title": "SARS-CoV-2 infection and replication in human fetal and pediatric gastric organoids", @@ -1375180,29 +1373775,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.06.23.167791", - "rel_title": "N-glycosylation network construction and analysis to modify glycans on the spike S glycoprotein of SARS-CoV-2.", - "rel_date": "2020-06-24", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.23.167791", - "rel_abs": "Background The spike S-protein of SARS-CoV-2 is N-glycosylated. The N-glycan structure and composition of this glycoprotein influence how the virus interacts with host cells.Objective To identify a putative N-glycan biosynthesis pathway of SARS-CoV-2 (HEK293 cell recombinant) from previously published mass spectrometric studies, and to identify what effect blocking some enzymes has on the overall glycoprotein profile. Finally, our goal was to provide the biosynthesis network, and glycans in easy-to-use format for further glycoinformatics work.Methods We reconstructed the glycosylation network based on previously published empirical data using GNAT, a glycosylation network analysis tool. Our compilation of the network tool had 23 glycosyltransferase and glucosidase enzymes, and could infer the pathway of glycosylation machinery based on glycans identified in the virus spike protein. Once the glycan biosynthesis pathway was generated, we simulated the effect of blocking specific enzymes - Mannosidase-II and alpha-1,6-fucosyltransferase to see how they would affect the biosynthesis network.Results Of the 23 enzymes, a total of 12 were involved in glycosylation of SARS-CoV-2 - Man-Ia, MGAT1, MGAT2, MGAT4, MGAT5, B4GalT, B4GalT, Man II, SiaT, ST3GalI, ST3GalVI and FucT8. Blocking enzymes resulted in a substantially modified glycan profile of the protein.Conclusions A network analysis of N-glycan biosynthesis of SARS-CoV-2 spike protein shows an elaborate enzymatic pathway with several intermediate glycans, along with the ones identified by mass spectrometric studies. Variations in the final N-glycan profile of the virus, given its site-specific microheterogeneity, could be a factor in the host response to the infection and response to antibodies. Here we provide all the resources generated - the glycans derived from mass spectrometry and intermediate glycans in glycoCT xml format, and the biosynthesis network for future drug and vaccine development work.Competing Interest StatementThe authors have declared no competing interest.View Full Text", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Sridevi Krishnan", - "author_inst": "University of California Davis" - }, - { - "author_name": "Giri P Krishnan", - "author_inst": "University of California San Diego" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "physiology" - }, { "rel_doi": "10.1101/2020.06.24.169383", "rel_title": "Intestinal receptor of SARS-CoV-2 in inflamed IBD tissue is downregulated by HNF4A in ileum and upregulated by interferon regulating factors in colon", @@ -1376113,6 +1374685,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.23.20137455", + "rel_title": "Sensitivity of different RT-qPCR solutions for SARS-CoV-2 detection", + "rel_date": "2020-06-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.23.20137455", + "rel_abs": "ObjectiveThe ongoing COVID-19 pandemic continues imposing a demand for diagnostic screening. In anticipation that the recurrence of outbreaks and the measures for lifting the lockdown worldwide may cause supply chain issues over the coming months, we assessed the sensitivity of a number of one-step retrotranscription and quantitative PCR (RT-qPCR) solutions to detect SARS-CoV-2.\n\nMethodsWe evaluated six different RT-qPCR alternatives for SARS-CoV-2/COVID-19 diagnosis based on standard RNA extractions. That of best sensitivity was also assessed with direct nasopharyngeal swab viral transmission medium (VTM) heating, overcoming the RNA extraction step.\n\nResultsWe found a wide variability in the sensitivity of RT-qPCR solutions that associated with a range of false negatives from as low as 2% (0.3-7.9%) to as much as 39.8% (30.2-50.2). Direct preheating of VTM combined with the best solution provided a sensitivity of 72.5% (62.5-81.0), in the range of some of the solutions based on standard RNA extractions.\n\nConclusionsWe evidenced sensitivity limitations of currently used RT-qPCR solutions. Our results will help to calibrate the impact of false negative diagnoses of COVID-19, and to detect and control new SARS-CoV-2 outbreaks and community transmissions.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Julia Alcoba-Florez", + "author_inst": "Servicio de Microbiologia, Hospital Universitario N. S. de Candelaria" + }, + { + "author_name": "Helena Gil-Campesino", + "author_inst": "Servicio de Microbiologia, Hospital Universitario N. S. de Candelaria" + }, + { + "author_name": "Diego Garcia-Martinez de Artola", + "author_inst": "Servicio de Microbiologia, Hospital Universitario N. S. de Candelaria" + }, + { + "author_name": "Rafaela Gonzalez-Montelongo", + "author_inst": "Genomics Division, Instituto Tecnologico y de Energias Renovables" + }, + { + "author_name": "Agustin Valenzuela-Fernandez", + "author_inst": "Laboratorio de Inmunologia Celular y Viral, Unidad de Farmacologia, Facultad de Medicina & IUETSPC, Universidad de La Laguna" + }, + { + "author_name": "Laura Ciuffreda", + "author_inst": "Research Unit, Hospital Universitario N. S. de Candelaria" + }, + { + "author_name": "Carlos Flores", + "author_inst": "Research Unit, Hospital Universitario N.S. de Candelaria" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.24.20138867", "rel_title": "Associations of ambient air pollutants and meteorological factors with COVID-19 transmission in 31 Chinese provinces: A time-series study", @@ -1376489,57 +1375104,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.22.20132910", - "rel_title": "Insufficient social distancing may be related to a future COVID-19 outbreak in Ijui-Brazil: Predictions of further social interventions.", - "rel_date": "2020-06-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.22.20132910", - "rel_abs": "The coronavirus disease initiated in 2019 (COVID-19) has proven to be highly contagious and quickly became a pandemic. Nowadays, it presents higher transmission rates worldwide, chiefly in small Brazilian cities, as Ijui. Located in the northwestern of the State of Rio Grande do Sul (RS) with 83,475 inhabitants, Ijui was selected to receive a population-based survey organized in five steps, involving 2,222 subjects. Subjects were tested for the presence of antibodies against coronavirus (SARS-CoV-2) and answered questions regarding social distance adherence (SDA), daily preventive routine (DPR), comorbidities, and sociodemographic characteristics. In parallel, the local government registered the official COVID-19 cases in Ijui, and the mobile social distancing index (MSDI) was also registered. In this study, we demonstrate the decrease in the levels of SDA, DPR and MSDI before the beginning of COVID-19 community transmission in Ijui. Also, we provide predictions for cases, hospitalization, and deaths in the city. We concluded that the insufficient social distancing, evidenced by different methods, might have a strong relationship with the rapid increase of COVID-19 cases in Ijui. Our study predicts a closer outbreak of community infection of COVID-19, which could be avoided or attenuated if the levels of the social distancing in the population increase.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Thiago Gomes Heck", - "author_inst": "Universidade Regional do Noroeste do Estado do Rio Grande do Sul (Uniju\u00ed)" - }, - { - "author_name": "Rafael Zancan Frantz", - "author_inst": "Regional University of Northwestern Rio Grande do Sul State (UNIJU\u00ed)" - }, - { - "author_name": "Matias Nunes Frizzo", - "author_inst": "Universidade Regional do Noroeste do Estado do Rio Grande do Sul (Uniju\u00ed)" - }, - { - "author_name": "Carlos Henrique Ramires Fran\u00e7ois", - "author_inst": "Universidade Regional do Noroeste do Estado do Rio Grande do Sul (Uniju\u00ed)" - }, - { - "author_name": "Mirna Stela Ludwig", - "author_inst": "Universidade Regional do Noroeste do Estado do Rio Grande do Sul (Uniju\u00ed)" - }, - { - "author_name": "Marilia Arndt Mesenburg", - "author_inst": "Universidade Federal de Pelotas e Universidade Federal de Ci\u00eancias da Sa\u00fade de Porto Alegre" - }, - { - "author_name": "Giovano Pereira Buratti", - "author_inst": "Universidade Regional do Noroeste do Estado do Rio Grande do Sul (Uniju\u00ed)" - }, - { - "author_name": "L\u00edgia Beatriz Bento Franz", - "author_inst": "Universidade Regional do Noroeste do Estado do Rio Grande do Sul (Uniju\u00ed)" - }, - { - "author_name": "Evelise Moraes Berlezi", - "author_inst": "Universidade Regional do Noroeste do Estado do Rio Grande do Sul (Uniju\u00ed)" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.20.20135186", "rel_title": "Determination of COVID-19 parameters for an agent-based model: Easing or tightening control strategies", @@ -1377483,6 +1376047,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2020.06.21.20137000", + "rel_title": "Health Condition and Test Availability as Predictors of Adults' Mental Health during the COVID-19 Pandemic", + "rel_date": "2020-06-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.21.20137000", + "rel_abs": "BackgroundResearch identifying adults mental health during the COVID-19 pandemic relies solely on demographic predictors without examining adults health status during the COVID-19 pandemic as a potential predictor.\n\nMethodsAn online survey of 669 adults in Malaysia was conducted during May 2-8, 2020, six weeks after a Movement Control Order (MCO) was issued.\n\nFindingsAdults health condition had curvilinear relationships (horizontally reversed J-shaped) with insomnia, anxiety, depression and distress. Reported test availability for COVID-19 (from \"strongly disagree\" to \"strongly agree\") also had curvilinear relationships (horizontally reversed J-shaped) with anxiety and depression. Younger adults reported worse mental health, but people from various religions and ethnic groups did not differ significantly in reported mental health.\n\nInterpretationAdults with worse health conditions had more mental health problems, especially adults at the lower end of the health spectrum. Test availability negatively predicted anxiety and depression, especially for adults experiencing poor COVID-19 test availability. The significant predictions of health condition and COVID-19 test availability suggest a new direction for the literature to identify psychiatric risk factors directly from health related variables during a pandemic.\n\nFundingTsinghua University-INDITEX Sustainable Development Fund (Project No. TISD201904).", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Huiyang Dai", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Stephen X. Zhang", + "author_inst": "University of Adelaide" + }, + { + "author_name": "Kim Hoe Looi", + "author_inst": "Xiamen University - Malaysia" + }, + { + "author_name": "Rui Su", + "author_inst": "Xiamen University - Malaysia" + }, + { + "author_name": "Jizhen Li", + "author_inst": "Tsinghua Univerisity" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.06.21.20136820", "rel_title": "Mental health and health behaviours before and during the COVID-19 lockdown: Longitudinal analyses of the UK Household Longitudinal Study", @@ -1377839,33 +1376438,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.21.20136929", - "rel_title": "Derivation and Validation of Clinical Prediction Rule for COVID-19 Mortality in Ontario, Canada", - "rel_date": "2020-06-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.21.20136929", - "rel_abs": "BackgroundSARS-CoV-2 is currently causing a high mortality global pandemic. However, the clinical spectrum of disease caused by this virus is broad, ranging from asymptomatic infection to cytokine storm with organ failure and death. Risk stratification of individuals with COVID-19 would be desirable for management, prioritization for trial enrollment, and risk stratification. We sought to develop a prediction rule for mortality due to COVID-19 in individuals with diagnosed infection in Ontario, Canada.\n\nMethodsData from Ontarios provincial iPHIS system were extracted for the period from January 23 to May 15, 2020. Both logistic regression-based prediction rules, and a rule derived using a Cox proportional hazards model, were developed in half the study and validated in remaining patients. Sensitivity analyses were performed with varying approaches to missing data.\n\nResults21,922 COVID-19 cases were reported. Individuals assigned to the derivation and validation sets were broadly similar. Age and comorbidities (notably diabetes, renal disease and immune compromise) were strong predictors of mortality. Four point-based prediction rules were derived (base case, smoking excluded as a predictor, long-term care excluded as a predictor, and Cox model based). All rules displayed excellent discrimination (AUC for all rules > 0.92) and calibration (both by graphical inspection and P > 0.50 by Hosmer-Lemeshow test) in the derivation set. All rules performed well in the validation set and were robust to random replacement of missing variables, and to the assumption that missing variables indicated absence of the comorbidity or characteristic in question.\n\nConclusionsWe were able to use a public health case-management data system to derive and internally validate four accurate, well-calibrated and robust clinical prediction rules for COVID-19 mortality in Ontario, Canada. While these rules need external validation, they may be a useful tool for clinical management, risk stratification, and clinical trials.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "David Fisman", - "author_inst": "University of Toronto" - }, - { - "author_name": "Amy L. Greer", - "author_inst": "University of Guelph" - }, - { - "author_name": "Ashleigh Tuite", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.22.20137141", "rel_title": "Spectrum of innate and adaptive immune response to SARS CoV 2 infection across asymptomatic, mild and severe cases; a longitudinal cohort study", @@ -1379025,6 +1377597,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.23.20138099", + "rel_title": "Age-structured non-pharmaceutical interventions for optimal control of COVID-19 epidemic", + "rel_date": "2020-06-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.23.20138099", + "rel_abs": "In an epidemic, individuals can widely differ in the way they spread the infection, for instance depending on their age or on the number of days they have been infected for. The latter allows to take into account the variation of infectiousness as a function of time since infection. In the absence of pharmaceutical interventions such as a vaccine or treatment, non-pharmaceutical interventions (e.g. social distancing) are of great importance to mitigate the pandemic. We propose a model with a double continuous structure by host age and time since infection. By applying optimal control theory to our age-structured model, we identify a solution minimizing deaths and costs associated with the implementation of the control strategy itself. This strategy depends on the age heterogeneity between individuals and consists in a relatively high isolation intensity over the older populations during a hundred days, followed by a steady decrease in a way that depends on the cost associated to a such control. The isolation of the younger population is weaker and occurs only if the cost associated with the control is relatively low. We show that the optimal control strategy strongly outperforms other strategies such as uniform constant control over the whole populations or over its younger fraction. These results bring new facts the debate about age-based control interventions and open promising avenues of research, for instance of age-based contact tracing.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Quentin Richard", + "author_inst": "IRD" + }, + { + "author_name": "Samuel Alizon", + "author_inst": "CNRS" + }, + { + "author_name": "Marc Choisy", + "author_inst": "IRD" + }, + { + "author_name": "Mircea T. Sofonea", + "author_inst": "Univ. Montpellier" + }, + { + "author_name": "Ramses Djidjou-Demasse", + "author_inst": "The French National Research Institute for Development (IRD)" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.22.20137810", "rel_title": "On Dynamical Analysis of the Data-DrivenSIR model (COVID-19 Outbreak in Indonesia)", @@ -1379373,73 +1377980,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.23.20137521", - "rel_title": "SARS CoV-2 Serosurvey in Addis Ababa, Ethiopia", - "rel_date": "2020-06-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.23.20137521", - "rel_abs": "The global COVID-19 pandemic caused by SARS CoV-2 is causing both mortality/morbidity and collateral social and economic damage related to public panic and aggressive public policy measures to contain the disease worldwide.(1) The epidemic appears to have taken hold much more slowly in sub-Saharan Africa than most of the world.(2) Antibody testing to evaluate the population proportion previously infected with SARS CoV-2 has the potential to guide public policy, but has not been reported so far for sub-Saharan Africa.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "John H Kempen", - "author_inst": "Massachusetts Eye and Ear/Harvard Medical School" - }, - { - "author_name": "Aida Abashawl", - "author_inst": "5.\tBerhan Public Health and Eye Care Consultancy" - }, - { - "author_name": "Hilkiah Kinfemichael", - "author_inst": "MyungSung Medical School" - }, - { - "author_name": "Mesfin Nigussie Difabachew", - "author_inst": "International Clinical Laboratories" - }, - { - "author_name": "Christopher J Kempen", - "author_inst": "MyungSung Christian Medical Center (MCM) Eye Unit, Addis Ababa, Ethiopia" - }, - { - "author_name": "Melaku Tesfaye Debele", - "author_inst": "International Clinical Laboratories, Addis Ababa" - }, - { - "author_name": "Abel A Menkir", - "author_inst": "MyungSung Medical College, Addis Ababa, Ethiopia" - }, - { - "author_name": "Maranatha T Assefa", - "author_inst": "MyungSung Medical College, Addis Ababa, Ethiopia" - }, - { - "author_name": "Eyob H Asfaw", - "author_inst": "MyungSung Medical College, Addis Ababa, Ethiopia" - }, - { - "author_name": "Leul B Habtegabriel", - "author_inst": "MyungSung Medical College, Addis Ababa, Ethiopia" - }, - { - "author_name": "Yohannes Sitotaw Addisie", - "author_inst": "Ethiopia Biotechnology Institute" - }, - { - "author_name": "Eric J Nilles", - "author_inst": "Brigham and Women's Hospital/Harvard Medical School" - }, - { - "author_name": "Joseph Craig Longenecker", - "author_inst": "Kuwait University, Health Sciences Center, Faculty of Medicine; Faculty of Public Health" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.16.155457", "rel_title": "Loss of pH switch unique to SARS-CoV2 supports unfamiliar virus pathology", @@ -1380551,6 +1379091,29 @@ "type": "new results", "category": "pathology" }, + { + "rel_doi": "10.1101/2020.06.19.20135640", + "rel_title": "On Linear Growth in COVID-19 Cases", + "rel_date": "2020-06-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.19.20135640", + "rel_abs": "We present an elementary model of COVID-19 propagation that makes explicit the connection between testing strategies and rates of transmission and the linear growth in new cases observed in many parts of the world. An essential feature of the model is that it captures the population-level response to the infection statistics information provided by governments and other organisations. The conclusions from this model have important implications regarding benefits of wide-spread testing for the presence of the virus, something that deserves greater attention.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Michael Grinfeld", + "author_inst": "University of Strathclyde" + }, + { + "author_name": "Paul A Mulheran", + "author_inst": "University of Strathclyde" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.18.20115873", "rel_title": "Thrombotic microvascular injury is not mediated by thrombotic microangiopathy despite systemic complement activation in Covid-19 patients", @@ -1380983,65 +1379546,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.18.20132571", - "rel_title": "Transcriptomic profiling of disease severity in patients with COVID-19 reveals role of blood clotting and vasculature related genes", - "rel_date": "2020-06-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.18.20132571", - "rel_abs": "COVID-19 caused by SARS-CoV-2 manifests as a range of symptoms. Understanding the molecular mechanisms responsible for immuno-pathogenesis of disease is important for treatment and management of COVID-19. We examined host transcriptomes in moderate and severe COVID-19 cases with a view to identifying pathways that affect its progression. RNA extracted from whole blood of COVID-19 cases was analysed by microarray analysis. Moderate and severe cases were compared with healthy controls and differentially regulated genes (DEGs) categorized into cellular pathways.\n\nDEGs in COVID-19 cases were mostly related to host immune activation and cytokine signaling, pathogen uptake, host defenses, blood and vasculature genes, and SARS-CoV-2- and other virus-affected pathways. The DEGs in these pathways were increased in severe compared with moderate cases. In a severe COVID-19 patient with an unfavourable outcome we observed dysregulation of genes in platelet homeostasis and cardiac conduction and fibrin clotting with disease progression.\n\nCOVID-19 morbidity is associated with cytokine activation, cardiovascular risk and thrombosis. We identified DEGs related to dysregulation of blood clotting and homeostasis, platelet activation pathways and to be associated with disease progression. These can be biomarkers of disease progression and also potential targets for treatment interventions in COVID-19.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Kiran Iqbal Masood", - "author_inst": "The Aga Khan University, Pakistan" - }, - { - "author_name": "Syed Faisal Mahmood", - "author_inst": "The Aga Khan University" - }, - { - "author_name": "Saba Shahid", - "author_inst": "The Aga Khan University, Pakistan" - }, - { - "author_name": "Nosheen Nasir", - "author_inst": "The Aga Khan University, Pakistan" - }, - { - "author_name": "Najia Ghanchi", - "author_inst": "The Aga Khan University, Pakistan" - }, - { - "author_name": "Asghar Nasir", - "author_inst": "The Aga Khan University, Pakistan" - }, - { - "author_name": "Bushra Jamil", - "author_inst": "The Aga Khan University, Pakistan" - }, - { - "author_name": "Iffat Khanum", - "author_inst": "The Aga Khan University, Pakistan" - }, - { - "author_name": "Safina Razzak", - "author_inst": "The Aga Khan University, Pakistan" - }, - { - "author_name": "Akbar Kanji", - "author_inst": "The Aga Khan University, Pakistan" - }, - { - "author_name": "Zahra Hasan", - "author_inst": "The Aga Khan University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.21.20132449", "rel_title": "Intrafamilial Exposure to SARS-CoV-2 Induces Cellular Immune Response without Seroconversion", @@ -1381941,6 +1380445,69 @@ "type": "new results", "category": "genetics" }, + { + "rel_doi": "10.1101/2020.06.22.164384", + "rel_title": "Functional characterization of SARS-CoV-2 infection suggests a complex inflammatory response and metabolic alterations", + "rel_date": "2020-06-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.22.164384", + "rel_abs": "Covid-19, caused by the SARS-CoV-2 virus, has reached the category of a worldwide pandemic. Even though intensive efforts, no effective treatments or a vaccine are available. Molecular characterization of the transcriptional response in Covid-19 patients could be helpful to identify therapeutic targets. In this study, RNAseq data from peripheral blood mononuclear cell samples from Covid-19 patients and healthy controls was analyzed from a functional point of view using probabilistic graphical models. Two networks were built: one based on genes differentially expressed between healthy and infected individuals and another one based on the 2,000 most variable genes in terms of expression in order to make a functional characterization. In the network based on differentially expressed genes, two inflammatory response nodes with different tendencies were identified, one related to cytokines and chemokines, and another one related to bacterial infections. In addition, differences in metabolism, which were studied in depth using Flux Balance Analysis, were identified. SARS-CoV2-infection caused alterations in glutamate, methionine and cysteine, and tetrahydrobiopterin metabolism. In the network based on 2,000 most variable genes, also two inflammatory nodes with different tendencies between healthy individuals and patients were identified. Similar to the other network, one was related to cytokines and chemokines. However, the other one, lower in Covid-19 patients, was related to allergic processes and self-regulation of the immune response. Also, we identified a decrease in T cell node activity and an increase in cell division node activity. In the current absence of treatments for these patients, functional characterization of the transcriptional response to SARS-CoV-2 infection could be helpful to define targetable processes. Therefore, these results may be relevant to propose new treatments.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Lucia Trilla-Fuertes", + "author_inst": "Biomedica Molecular Medicine SL." + }, + { + "author_name": "Ricardo Ramos-Ruiz", + "author_inst": "Parque Cientifico de Madrid" + }, + { + "author_name": "Natalia Blanca-Lopez", + "author_inst": "Hospital Infanta Leonor" + }, + { + "author_name": "Elena Lopez-Camacho", + "author_inst": "Biomedica Molecular Medicine SL" + }, + { + "author_name": "Laura Martin-Pedraza", + "author_inst": "Hospital Infanta Leonor" + }, + { + "author_name": "Pablo Ryan Murua", + "author_inst": "Hospital Infanta Leonor" + }, + { + "author_name": "Mariana Diaz-Almiron", + "author_inst": "Hospital Universitario La Paz" + }, + { + "author_name": "Carlos Llorens", + "author_inst": "Biotechvana, Parc Cientific, Universitat de Valencia" + }, + { + "author_name": "Toni Gabaldon", + "author_inst": "BSC-IRB" + }, + { + "author_name": "Andres Moya", + "author_inst": "Universitat de Valencia" + }, + { + "author_name": "Juan Angel Fresno", + "author_inst": "Hospital Universitario La Paz" + }, + { + "author_name": "Angelo Gamez-Pozo", + "author_inst": "Hospital Universitaio La Paz" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.06.21.163550", "rel_title": "Mathematical modeling explains differential SARS CoV-2 kinetics in lung and nasal passages in remdesivir treated rhesus macaques", @@ -1382372,49 +1380939,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.06.22.133355", - "rel_title": "Companion vaccine Bioinformatic design tool reveals limited functional genomic variability of SARS-Cov-2 Spike Receptor Binding Domain", - "rel_date": "2020-06-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.22.133355", - "rel_abs": "BackgroundTracking the genetic variability of Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) is a crucial challenge. Mainly to identify target sequences in order to generate robust vaccines and neutralizing monoclonal antibodies, but also to track viral genetic temporal and geographic evolution and to mine for variants associated with reduced or increased disease severity. Several online tools and bioinformatic phylogenetic analyses have been released, but the main interest lies in the Spike protein, which is the pivotal element of current vaccine design, and in the Receptor Binding Domain, that accounts for most of the neutralizing the antibody activity.\n\nMethodsHere, we present an open-source bioinformatic protocol, and a web portal focused on SARS-CoV-2 single mutations and minimal consensus sequence building as a companion vaccine design tool. Furthermore, we provide immunogenomic analyses to understand the impact of the most frequent RBD variations.\n\nResultsResults on the whole GISAID sequence dataset at the time of the writing (October 2020) reveals an emerging mutation, S477N, located on the central part of the Spike protein Receptor Binding Domain, the Receptor Binding Motif. Immunogenomic analyses revealed some variation in mutated epitope MHC compatibility, T-cell recognition, and B-cell epitope probability for most frequent human HLAs.\n\nConclusionsThis work provides a framework able to track down SARS-CoV-2 genomic variability.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Alice Massacci", - "author_inst": "Takis srl, Rome" - }, - { - "author_name": "Eleonora Sperandio", - "author_inst": "Biostatistics, Bioinformatics and Clinical Trial Center, IRCCS Regina Elena National Cancer Institute" - }, - { - "author_name": "Mariano Maffei", - "author_inst": "EvviVax srl" - }, - { - "author_name": "Fabio Palombo", - "author_inst": "Neomatrix srl, Rome" - }, - { - "author_name": "Luigi Aurisicchio", - "author_inst": "Takis srl, Rome" - }, - { - "author_name": "Gennaro Ciliberto", - "author_inst": "Scientific Direction IRCCS Regina Elena National Cancer Institute" - }, - { - "author_name": "Matteo Pallocca", - "author_inst": "IRCSS Regina Elena National Cancer Institute" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "confirmatory results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.06.17.20134262", "rel_title": "COVID-19 Outpatient Screening: a Prediction Score for Adverse Events", @@ -1383838,6 +1382362,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.20.20136234", + "rel_title": "Belgian Covid-19 Mortality, Excess Deaths, Number of Deaths per Million, and Infection Fatality Rates (8 March - 9 May 2020)", + "rel_date": "2020-06-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.20.20136234", + "rel_abs": "ObjectiveScrutiny of COVID-19 mortality in Belgium over the period 8 March - 9 May 2020 (Weeks 11-19), using number of deaths per million, infection fatality rates, and the relation between COVID-19 mortality and excess death rates.\n\nDataPublicly available COVID-19 mortality (2020); overall mortality (2009 - 2020) data in Belgium and demographic data on the Belgian population; data on the nursing home population; results of repeated sero-prevalence surveys in March-April 2020.\n\nStatistical methodsReweighing, missing-data handling, rate estimation, visualization.\n\nResultsBelgium has virtually no discrepancy between COVID-19 reported mortality (confirmed and possible cases) and excess mortality. There is a sharp excess death peak over the study period; the total number of excess deaths makes April 2020 the deadliest month of April since WWII, with excess deaths far larger than in early 2017 or 2018, even though influenza-induced January 1951 and February 1960 number of excess deaths were similar in magnitude. Using various sero-prevalence estimates, infection fatality rates (IFRs; fraction of deaths among infected cases) are estimated at 0.38 - 0.73% for males and 0.20 - 0.39% for females in the non-nursing home population (non-NHP), and at 0.79 - 1.52% for males and 0.88 - 1.31% for females in the entire population. Estimates for the NHP range from 38 to 73% for males and over 22 to 37% for females. The IFRs rise from nearly 0% under 45 years, to 4.3% and 13.2% for males in the non-NHP and the general population, respectively, and to 1.5% and 11.1% for females in the non-NHP and general population, respectively.\n\nThe IFR and number of deaths per million is strongly influenced by extensive reporting and the fact that 66.0% of the deaths concerned NH residents. At 764 (our re-estimation of the figure 735, presented by \"Our World in Data\"), the number of COVID-19 deaths per million led the international ranking on May 9, 2020, but drops to 262 in the non-NHP. The NHP is very specific: age-related increased risk; highly prevalent comorbidities that, while non-fatal in themselves, exacerbate COVID-19; larger collective households that share inadvertent vectors such as caregivers and favor clustered outbreaks; initial lack of protective equipment, etc. High-quality health care countries have a relatively older but also more frail population [1], which is likely to contribute to this result.\n\nThumbnail summary: What this paper addsCOVID-19 mortality and its relation to excess deaths, case fatality rates (CFRs), infection fatality rates (IFRs), and number of deaths per million are constantly being reported for a large number of countries globally.\n\nThis study adds detailed insight in the Belgian situation over the period 8 March - 9 May 2020 (Week 11-Week 19).\n\nBelgium has virtually no discrepancy between COVID-19 reported mortality (confirmed and possible cases) and excess mortality. This, combined with a high fraction of possible cases that is COVID-19 related [2] provides a basis for using all COVID-19 cases and thus not only the confirmed ones, in IFR estimation.\n\nAgainst each of the years from 2009 and 2019 and the average thereof, there is a strong excess death peak in 2020, which nearly entirely coincides with confirmed plus possible COVID-19 cases. The excess death/COVID-19 peak rises well above seasonal fluctuations seen in the first trimester during the most recent decade (induced in part by seasonal influenza). In the second week of April 2020, twice as many people died than in the corresponding week of the reference year. April 2020 was the deadliest month of April since WWII, although January 1951 and February 1960 saw similar figures. More recently, in the winter of 2017-2018, there was 4.6% excess mortality in Belgium (70,215 actual deaths; 3093 more than the Be-MOMO-model prediction). In the winter of 2016-2017, there was an excess of 3284 deaths (4.9% excess mortality) https://epistat.wiv-isp.be/docs/momo/Be-MOMO%20winter%202017-18%20report_FR.pdf.\n\nAt 764 (our estimate), the number of COVID-19 deaths per million leads the international ranking, but drops sharply to 262 in the non-nursing home population.\n\nCFR is not a good basis for international comparison, except as a tool in estimating global infection fatality rates [2]. These authors used asymptotic models to derive IFR as a limit of CFR. CFR is strongly influenced by testing strategy, and in several studies the delay between case confirmation and deaths is not accounted for. The handling of possible cases is ambiguous at best. We do not consider it here.\n\nBias and precision in estimation of IFR is influenced by difficulties surrounding the estimation of sero-prevalence, such as sensitivity and specificity of the tests used [3], time to IgM and in particular IgG seroconversion [4], and potential selection bias occurring in data from residual sample surveys. A sensitivity analysis is undertaken by augmenting one primary with three auxiliary estimates of sero-prevalence.\n\nBecause in Belgium there is a very close agreement between excess mortality on the one hand and confirmed and possible COVID-19 cases combined on the other, and because an international study [2] suggested that a fraction as high as 0.9 of possible cases could be attributable to COVID-19 [5], it is a reasonable choice to use all COVID-19 cases in IFR estimation. This encompasses a large fraction of deaths occurring in nursing homes. The IFR values obtained align with international values [2]. Using various sero-prevalence estimates, IFRs across all ages are estimated at 0.38 - 0.73% for males and 0.20 - 0.39% for females in the non-nursing home population (non-NHP), and at 0.79 - 1.52% for males and 0.88 - 1.31% for females in the entire population. Estimates for the NHP range from 38 to 73% for males and over 22 to 37% for females. The IFRs rise from nearly 0% under 45 years, to 4.3% and 13.2% for males in the non-NHP and the general population, respectively, and to 1.5% and 11.1% for females in the non-NHP and general population, respectively.\n\nThe IFR is strongly influenced by extensive death cases reporting and the fact that 66.0% of the deaths concerned NH residents. Apart from a strong age-related gradient, also for each age category, IFRs are substantially higher in males than in females Because of these dependencies, IFRs should be considered in an age, gender, and sub-population specific manner. The same proviso is made for the number of deaths per million.\n\nAn important such population is the NHP because of a specific cocktail: age-related increased risk; highly prevalent comorbidities that, while non-fatal in themselves, exacerbate COVID-19; larger collective households that share inadvertent vectors such as caregivers; initial lack of protective equipment, etc. High-quality health care countries have a relatively older but also more frail population [1], which might contribute.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Geert Molenberghs", + "author_inst": "Universiteit Hasselt and KU Leuven" + }, + { + "author_name": "Christel Faes", + "author_inst": "Universiteit Hasselt" + }, + { + "author_name": "Johan Verbeeck", + "author_inst": "Universiteit Hasselt" + }, + { + "author_name": "Patrick Deboosere", + "author_inst": "Vrije Universiteit Brussel" + }, + { + "author_name": "Steven Abrams", + "author_inst": "Universiteit Hasselt and Universiteit Antwerpen" + }, + { + "author_name": "Lander Willem", + "author_inst": "Universiteit Antwerpen" + }, + { + "author_name": "Jan Aerts", + "author_inst": "Universiteit Hasselt" + }, + { + "author_name": "Heidi Theeten", + "author_inst": "Universiteit Antwerpen" + }, + { + "author_name": "Brecht Devleesschauwer", + "author_inst": "Sciensano" + }, + { + "author_name": "Natalia Bustos Sierra", + "author_inst": "Sciensano" + }, + { + "author_name": "Francoise Renard", + "author_inst": "Sciensano" + }, + { + "author_name": "Sereina Herzog", + "author_inst": "Universiteit Antwerpen" + }, + { + "author_name": "Patrick Lusyne", + "author_inst": "Statistics Belgium" + }, + { + "author_name": "Johan Van der Heyden", + "author_inst": "Sciensano" + }, + { + "author_name": "Herman Van Oyen", + "author_inst": "Sciensano" + }, + { + "author_name": "Pierre Van Damme", + "author_inst": "Universiteit Antwerpen" + }, + { + "author_name": "Niel Hens", + "author_inst": "Hasselt University and University of Antwerp" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.19.20136069", "rel_title": "Global years of life lost to COVID-19", @@ -1384230,49 +1382837,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.06.19.20135996", - "rel_title": "The support needs of Australian primary health care nurses during the COVID-19 pandemic", - "rel_date": "2020-06-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.19.20135996", - "rel_abs": "AimTo identify Australian primary healthcare nurses immediate support needs during the COVID-19 pandemic.\n\nBackgroundCOVID-19 has had widespread implications for primary healthcare nurses. Supporting these nurses capacity to deliver quality care ensures that ongoing health needs can be met.\n\nMethodsPrimary healthcare nurses were recruited to an online survey via social media and professional organisations in April 2020.\n\nResultsSix-hundred and thirty-seven responses were included in analysis. Participants provided 1213 statements about perceived supports required to provide quality clinical care. From these, seven key categories emerged, namely; personal protective equipment, communication, funding, industrial issues, self-care, workplace factors and valuing nurses.\n\nConclusionA number of key issues relating to personal health and safety, care quality, and job security need to be addressed to support primary healthcare nurses during the COVID-19 pandemic. Addressing these support issues can assist in retaining nurses and optimising the role of primary healthcare nurses during a pandemic.\n\nImplications for nursing managementResponding to the needs of primary healthcare nurses has the potential to facilitate their role in providing community based healthcare. This knowledge can guide the provision of support for primary healthcare nurses during the current pandemic, as well as informing planning for future health crises.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Elizabeth Halcomb", - "author_inst": "University of Wollongong" - }, - { - "author_name": "Anna Williams", - "author_inst": "University of Notre Dame, Sydney" - }, - { - "author_name": "Christine Ashley", - "author_inst": "University of Wollongong" - }, - { - "author_name": "Susan McInnes", - "author_inst": "University of Wollongong" - }, - { - "author_name": "Catherine Stephen", - "author_inst": "University of Wollongong" - }, - { - "author_name": "Kaara Ray Calma", - "author_inst": "University of Wollongong" - }, - { - "author_name": "Sharon James", - "author_inst": "University of Wollongong" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "nursing" - }, { "rel_doi": "10.1101/2020.06.19.20134908", "rel_title": "ApoE e4e4 genotype and mortality with COVID-19 in UK Biobank", @@ -1385224,6 +1383788,113 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.06.19.20134767", + "rel_title": "Clinical practice guidelines and recommendations in the context of the COVID-19 pandemic: systematic review and critical appraisal", + "rel_date": "2020-06-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.19.20134767", + "rel_abs": "BackgroundThe number of published clinical practice guidelines and recommendations related to SARS-CoV-2 infections causing COVID-19 has rapidly increased. However, insufficient consideration of appropriate methodologies in the guideline development could lead to misleading information, uncertainty among professionals, and potentially harmful actions for patients.\n\nPurposeRapid systematic review of clinical practice guidelines and recommendations in the context of COVID-19 to explore if basic methodological standards of guideline development have been met.\n\nData sourcesMEDLINE [PubMed], CINAHL [Ebsco], Trip and manual search; from Feb 1st 2020 until April 27th 2020.\n\nStudy selectionAll types of healthcare workers providing any kind of healthcare to any patient population in any setting.\n\nData extractionAt least two reviewers independently extracted guideline characteristics, conducted critical appraisal according to The Appraisal of Guidelines for Research and Evaluation Instrument (AGREE II) and classified the guidelines using the Association of the Scientific Medical Societies (AWMF) Guidance Manual and Rules for Guideline Development. We plan six-month updates (living review).\n\nData synthesisThere were 1342 titles screened and 188 guidelines included. The highest average AGREE II domain score was 89% for scope and purpose, the lowest for rigor of development (25%). Only eight guidelines (4%) were based on a systematic literature search and a structured consensus process by representative experts (classified as the highest methodological quality, S3 according to AWMF). Patients were only included in the development of one guideline. A process for regular updates was described in 27 guidelines (14%).\n\nLimitationsMethodological focus only.\n\nConclusionsDespite clear scope, most publications fell short of basic methodological standards of guideline development. Future research should monitor the evolving methodological quality of the guidelines and their updates over time.\n\nRegistration/PublicationThe protocol was published at www.researchgate.net, DOI: 10.13140/RG.2.2.21293.51689. Preliminary results are publicly available on medRxiv.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Tanja A Stamm", + "author_inst": "Medical University of Vienna, Austria" + }, + { + "author_name": "Margaret R Andrews", + "author_inst": "Medical University of Vienna, Austria" + }, + { + "author_name": "Erika Mosor", + "author_inst": "Medical University of Vienna, Austria" + }, + { + "author_name": "Valentin Ritschl", + "author_inst": "Medical University of Vienna, Austria" + }, + { + "author_name": "Linda C Li", + "author_inst": "University of British Columbia, Canada" + }, + { + "author_name": "Jasmin K Ma", + "author_inst": "University of British Columbia, Canada" + }, + { + "author_name": "Adalberto Campo Arias", + "author_inst": "University of Magdalena, Santa Marta, Colombia" + }, + { + "author_name": "Sarah Baker", + "author_inst": "University of Sheffield, UK" + }, + { + "author_name": "Nicola W Burton", + "author_inst": "Griffith University, Mt. Gravatt, Australia" + }, + { + "author_name": "Mohammad Eghbali", + "author_inst": "University of Social Welfare and Rehabilitation Sciences, Tehran, Iran" + }, + { + "author_name": "Natalia Fernandez", + "author_inst": "University of Michigan, United States" + }, + { + "author_name": "Ricardo Ferreira", + "author_inst": "Centro Hospitalar e Universitario de Coimbra, Portugal" + }, + { + "author_name": "Gabriele Gaebler", + "author_inst": "Austrian Association of Dietitians, Vienna, Austria" + }, + { + "author_name": "Souzi Makri", + "author_inst": "The Cyprus League Against Rheumatism and Platform Organization for People for Rheumatic diseases in Southern Europe, Nicosia, Cyprus" + }, + { + "author_name": "Sandra Mintz", + "author_inst": "Children's Hospital Los Angeles, Los Angeles, CA, United States" + }, + { + "author_name": "Rikke Moe", + "author_inst": "Diakonhjemmet Hospital, Oslo, Norway" + }, + { + "author_name": "Elizabeth Morasso", + "author_inst": "UCLA Health, Los Angeles, CA, United States" + }, + { + "author_name": "Susan L Murphy", + "author_inst": "University of Michigan, MI, United States" + }, + { + "author_name": "Simiso Ntuli", + "author_inst": "University of Johannesburg, Johannesburg, Gauteng, South Africa" + }, + { + "author_name": "Maisa Omara", + "author_inst": "Medical University of Vienna, Austria" + }, + { + "author_name": "Miguel Simancas Pallares", + "author_inst": "University of North Carolina at Chapel Hill, NC, United States" + }, + { + "author_name": "Jen Horonieff", + "author_inst": "Savvy Cooperative, Queens, NY, USA" + }, + { + "author_name": "Gerald Gartlehner", + "author_inst": "Cochrane Austria, Department for Evidence-based Medicine and Evaluation, Danube University Krems, Austria" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2020.06.18.20134486", "rel_title": "Covid-19 Pandemic- Pits and falls of major states of India.", @@ -1385552,57 +1384223,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.18.20134346", - "rel_title": "The Relationship between the Global Burden of Influenza from 2017-2019 and COVID-19", - "rel_date": "2020-06-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.18.20134346", - "rel_abs": "BackgroundSARS-CoV-2 and influenza are lipid-enveloped viruses with differential morbidity and mortality but shared modes of transmission. With a descriptive epidemiological framing, we assessed whether historical patterns of regional influenza burden are reflected in the observed heterogeneity in COVID-19 cases across regions of the world.\n\nMethodsWeekly surveillance data reported in FluNet from January 2017-December 2019 for influenza and World Health Organization for COVID-19 (to May 31, 2020) across the seven World Bank regions were used to assess the total and annual number of influenza and COVID-19 cases per country, within and across all regions, to generate comparative descending ranks from highest to lowest burden of disease.\n\nResultsAcross regions, rankings of influenza and COVID-19 were relatively consistent. Europe and Central Asia and North America ranked first and second for COVID-19 and second and first for influenza, respectively. East Asia and the Pacific traditionally ranked higher for influenza with recent increases in COVID-19 consistent with influenza season. Across regions, Sub-Saharan Africa ranked amongst the least affected by both influenza and COVID-19.\n\nConclusionConsistency in the regional distribution of the burden of COVID-19 and influenza suggest shared individual, structural, and environmental determinants of transmission. Using a descriptive epidemiological framework to assess shared regional trends for rapidly emerging respiratory pathogens with better studied respiratory infections may provide further insights into the differential impacts of non-pharmacologic interventions and intersections with environmental conditions. Ultimately, forecasting trends and informing interventions for novel respiratory pathogens like COVID-19 should leverage epidemiologic patterns in the relative burden of past respiratory pathogens as prior information.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Stefan D Baral", - "author_inst": "JHSPH" - }, - { - "author_name": "Katherine B Rucinski", - "author_inst": "JHSPH" - }, - { - "author_name": "Jean Olivier Twahirwa Rwema", - "author_inst": "JHSPH" - }, - { - "author_name": "Amrita Rao", - "author_inst": "JHSPH" - }, - { - "author_name": "Neia Prata Menezes", - "author_inst": "JHSPH" - }, - { - "author_name": "Daouda Diouf", - "author_inst": "Enda Sant\u00e9" - }, - { - "author_name": "Adeeba Kamarulzaman", - "author_inst": "Universiti Malaya" - }, - { - "author_name": "Nancy Phaswana-Mafuya", - "author_inst": "North West University" - }, - { - "author_name": "Sharmistha Mishra", - "author_inst": "University of Toronto" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.18.20134478", "rel_title": "The influence of comorbidity on the severity of COVID-19 disease: systematic review and analysis", @@ -1387226,6 +1385846,133 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.18.160614", + "rel_title": "Mechanism and inhibition of SARS-CoV-2 PLpro", + "rel_date": "2020-06-19", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.18.160614", + "rel_abs": "Coronaviruses, including SARS-CoV-2, encode multifunctional proteases that are essential for viral replication and evasion of host innate immune mechanisms. The papain-like protease PLpro cleaves the viral polyprotein, and reverses inflammatory ubiquitin and anti-viral ubiquitin-like ISG15 protein modifications1,2. Drugs that target SARS-CoV-2 PLpro (hereafter, SARS2 PLpro) may hence be effective as treatments or prophylaxis for COVID-19, reducing viral load and reinstating innate immune responses3. We here characterise SARS2 PLpro in molecular and biochemical detail. SARS2 PLpro cleaves Lys48-linked polyubiquitin and ISG15 modifications with high activity. Structures of PLpro bound to ubiquitin and ISG15 reveal that the S1 ubiquitin binding site is responsible for high ISG15 activity, while the S2 binding site provides Lys48 chain specificity and cleavage efficiency. We further exploit two strategies to target PLpro. A repurposing approach, screening 3727 unique approved drugs and clinical compounds against SARS2 PLpro, identified no compounds that inhibited PLpro consistently or that could be validated in counterscreens. More promisingly, non-covalent small molecule SARS PLpro inhibitors were able to inhibit SARS2 PLpro with high potency and excellent antiviral activity in SARS-CoV-2 infection models.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Theresa Klemm", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, A" + }, + { + "author_name": "Gregor Ebert", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, A" + }, + { + "author_name": "Dale J Calleja", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, A" + }, + { + "author_name": "Cody C Allison", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, A" + }, + { + "author_name": "Lachlan W Richardson", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, A" + }, + { + "author_name": "Jonathan P Bernardini", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, A" + }, + { + "author_name": "Bernadine G C Lu", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, A" + }, + { + "author_name": "Nathan W Kuchel", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, A" + }, + { + "author_name": "Christoph Grohmann", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, A" + }, + { + "author_name": "Yuri Shibata", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, A" + }, + { + "author_name": "Zhong Yan Gan", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, A" + }, + { + "author_name": "James P Cooney", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, A" + }, + { + "author_name": "Marcel Doerflinger", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, A" + }, + { + "author_name": "Amanda E Au", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, A" + }, + { + "author_name": "Timothy R Blackmore", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, A" + }, + { + "author_name": "Paul P Geurink", + "author_inst": "Oncode Institute and Department of Chemical Immunology, Leiden University Medical Centre, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands." + }, + { + "author_name": "Huib Ovaa", + "author_inst": "Oncode Institute and Department of Chemical Immunology, Leiden University Medical Centre, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands." + }, + { + "author_name": "Janet Newman", + "author_inst": "Commonwealth Scientific and Industrial Research Organisation (CSIRO), Biomedical Program, Parkville, Victoria 3052, Australia." + }, + { + "author_name": "Alan Riboldi-Tunnicliffe", + "author_inst": "Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, VIC 3168, Australia." + }, + { + "author_name": "Peter E Czabotar", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, A" + }, + { + "author_name": "Jeffrey P Mitchell", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, A" + }, + { + "author_name": "Rebecca Feltham", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, A" + }, + { + "author_name": "Bernhard C Lechtenberg", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, A" + }, + { + "author_name": "Kym N Lowes", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, A" + }, + { + "author_name": "Grant Dewson", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, A" + }, + { + "author_name": "Marc Pellegrini", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, A" + }, + { + "author_name": "Guillaume Lessene", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, A" + }, + { + "author_name": "David Komander", + "author_inst": "The Walter and Eliza Hall Institute of Medical Research and Department of Medical Biology, University of Melbourne, 1G Royal Parade, Parkville, Victoria 3052, A" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.06.18.160671", "rel_title": "Identification of a critical horseshoe-shaped region in the nsp5 (Mpro, 3CLpro) protease interdomain loop (IDL) of coronavirus mouse hepatitis virus (MHV)", @@ -1387782,73 +1386529,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.06.19.158717", - "rel_title": "No evidence of coronaviruses or other potentially zoonotic viruses in Sunda pangolins (Manis javanica) entering the wildlife trade via Malaysia.", - "rel_date": "2020-06-19", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.19.158717", - "rel_abs": "The legal and illegal trade in wildlife for food, medicine and other products is a globally significant threat to biodiversity that is also responsible for the emergence of pathogens that threaten human and livestock health and our global economy. Trade in wildlife likely played a role in the origin of COVID-19, and viruses closely related to SARS-CoV-2 have been identified in bats and pangolins, both traded widely. To investigate the possible role of pangolins as a source of potential zoonoses, we collected throat and rectal swabs from 334 Sunda pangolins (Manis javanica) confiscated in Peninsular Malaysia and Sabah between August 2009 and March 2019. Total nucleic acid was extracted for viral molecular screening using conventional PCR protocols used to routinely identify known and novel viruses in extensive prior sampling (>50,000 mammals). No sample yielded a positive PCR result for any of the targeted viral families - Coronaviridae, Filoviridae, Flaviviridae, Orthomyxoviridae and Paramyxoviridae. In light of recent reports of coronaviruses including a SARS-CoV-2 related virus in Sunda pangolins in China, the lack of any coronavirus detection in our upstream market chain samples suggests that these detections in downstream animals more plausibly reflect exposure to infected humans, wildlife or other animals within the wildlife trade network. While confirmatory serologic studies are needed, it is likely that Sunda pangolins are incidental hosts of coronaviruses. Our findings further support the importance of ending the trade in wildlife globally.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Jimmy Lee", - "author_inst": "EcoHealth Alliance, 460 West 34th Street, 17th Floor, New York, NY 10001-2320" - }, - { - "author_name": "Tom Hughes", - "author_inst": "EcoHealth Alliance, 460 West 34th Street, 17th Floor, New York, NY 10001-2320" - }, - { - "author_name": "Mei-Ho Lee", - "author_inst": "EcoHealth Alliance, 460 West 34th Street, 17th Floor, New York, NY 10001-2320" - }, - { - "author_name": "Hume Field", - "author_inst": "EcoHealth Alliance, 460 West 34th Street, 17th Floor, New York, NY 10001-2320" - }, - { - "author_name": "Jeffrine Japning Rovie-Ryan", - "author_inst": "National Wildlife Forensic Laboratory, Department of Wildlife and National Parks (PERHILITAN), Peninsular Malaysia, KM 10, Jalan Cheras, 56100, Kuala Lumpur, Ma" - }, - { - "author_name": "Frankie Thomas Sitam", - "author_inst": "National Wildlife Forensic Laboratory, Department of Wildlife and National Parks (PERHILITAN), Peninsular Malaysia, KM 10, Jalan Cheras, 56100, Kuala Lumpur, Ma" - }, - { - "author_name": "Symphorosa Sipangkui", - "author_inst": "Sabah Wildlife Department, 5th Floor, B Block, Wisma MUIS, 88100, Kota Kinabalu, Sabah, Malaysia." - }, - { - "author_name": "Senthilvel K.S.S. Nathan", - "author_inst": "Sabah Wildlife Department, 5th Floor, B Block, Wisma MUIS, 88100, Kota Kinabalu, Sabah, Malaysia." - }, - { - "author_name": "Diana Ramirez", - "author_inst": "Sabah Wildlife Department, 5th Floor, B Block, Wisma MUIS, 88100, Kota Kinabalu, Sabah, Malaysia." - }, - { - "author_name": "Subbiah Vijay Kumar", - "author_inst": "Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia." - }, - { - "author_name": "Helen Lasimbang", - "author_inst": "Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia." - }, - { - "author_name": "Jonathan H. Epstein", - "author_inst": "EcoHealth Alliance, 460 West 34th Street, 17th Floor, New York, NY 10001-2320" - }, - { - "author_name": "Peter Daszak", - "author_inst": "EcoHealth Alliance, 460 West 34th Street, 17th Floor, New York, NY 10001-2320" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.06.19.161802", "rel_title": "An in-silico based clinical insight on the effect of noticeable CD4 conserved residues of SARS-CoV-2 on the CD4-MHC-I interactions", @@ -1388952,6 +1387632,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.15.20132308", + "rel_title": "Trace, Quarantine, Test, Isolate and Treat: A Kerala Model of Covid-19 Response", + "rel_date": "2020-06-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.15.20132308", + "rel_abs": "Kerala reported the first three cases of coronavirus in India in late January. Kerala, one of the Indias most densely populated states, which makes its success in fighting the Covid-19 all the more commendable. Moreover, an estimated 17% of its 35 million population employed or lives elsewhere, more than 1 million tourists visit each year, and hundreds of students study abroad, including in China. All of this mobility makes the state more vulnerable to contagious outbreaks. What is the strategy behind the success story? This paper compares the situation of COVID-19 pandemic in major states and Kerala by the different phase of lockdown, and also highlights Keralas fight against the pandemic. We used publicly available data from https://www.covid19india.org/ and Covid-19 Daily Bulletin (Jan 31-May 31), Directorate of Health Services, Kerala (https://dashboard.kerala.gov.in/). We calculate the phase-wise period prevalence rate (PPR) and the case fatality rate (CFR) of the last phase. Compared to other major states, Kerala showed better response in preventing pandemic. The equation for the Keralas success has been simple, prioritized testing, widespread contact tracing, and promoting social distance. They also imposed uncompromising controls, were supported by an excellent healthcare system, government accountability, transparency, public trust, civil rights and importantly the decentralized governance and strong grass-root level institutions. The \"proactive\" measures taken by Kerala such as early detection of cases and extensive social support measures can be a \"model for India and the world\".", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Sulaiman KM", + "author_inst": "International institute for Population Sciences- Mumbai" + }, + { + "author_name": "Muhammad T", + "author_inst": "International Institute for Population Sciences, Mumbai" + }, + { + "author_name": "Muhammad Rishad AP", + "author_inst": "International institute for Population Sciences- Mumbai" + }, + { + "author_name": "Afsal K", + "author_inst": "International institute for Population Sciences- Mumbai" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.06.16.20132803", "rel_title": "Development and validation of the Elecsys Anti-SARS-CoV-2 immunoassay as a highly specific tool for determining past exposure to SARS-CoV-2", @@ -1389308,45 +1388019,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.16.20133207", - "rel_title": "Downsides of face masks and possible mitigation strategies: a systematic review and meta-analysis", - "rel_date": "2020-06-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.16.20133207", - "rel_abs": "ObjectiveTo identify, appraise, and synthesise studies evaluating the downsides of wearing facemasks in any setting. We also discuss potential strategies to mitigate these downsides.\n\nMethodsPubMed, Embase, CENTRAL, EuropePMC were searched (inception-18/5/2020), and clinical registries were searched via CENTRAL. We also did forward-backward citation search of the included studies. We included randomised controlled trials and observational studies comparing facemask use to any active intervention or to control. Two author pairs independently screened articles for inclusion, extracted data and assessed the quality of included studies. The primary outcomes were compliance, discomforts, harms, and adverse events of wearing facemasks.\n\nFindingsWe screened 5471 articles, including 37 (40 references); 11 were meta-analysed. For mask wear adherence, 47% more people wore facemasks in the facemask group compared to control; adherence was significantly higher (26%) in the surgical/medical mask group than in N95/P2 group. The largest number of studies reported on the discomfort and irritation outcome (20-studies); fewest reported on the misuse of masks, and none reported on mask contamination or risk compensation behaviour. Risk of bias was generally high for blinding of participants and personnel and low for attrition and reporting biases.\n\nConclusionThere are insufficient data to quantify all of the adverse effects that might reduce the acceptability, adherence, and effectiveness of face masks. New research on facemasks should assess and report the harms and downsides. Urgent research is also needed on methods and designs to mitigate the downsides of facemask wearing, particularly the assessment of alternatives such as face shields.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Mina Bakhit", - "author_inst": "Bond University" - }, - { - "author_name": "Natalia Krzyzaniak", - "author_inst": "Bond University" - }, - { - "author_name": "Anna Mae Scott", - "author_inst": "Bond University" - }, - { - "author_name": "Justin Clark", - "author_inst": "Bond University" - }, - { - "author_name": "Paul Glasziou", - "author_inst": "Bond University" - }, - { - "author_name": "Chris Del Mar", - "author_inst": "Bond University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.06.17.20134114", "rel_title": "Prevalence, specificity, and clinical association of anti-phospholipid antibodies in COVID-19 patients: are the antibodies really guilty?", @@ -1390374,6 +1389046,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, + { + "rel_doi": "10.1101/2020.06.16.20132688", + "rel_title": "Assessing the impact of coordinated COVID-19 exit strategies across Europe", + "rel_date": "2020-06-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.16.20132688", + "rel_abs": "As rates of new COVID-19 cases decline across Europe due to non-pharmaceutical interventions such as social distancing policies and lockdown measures, countries require guidance on how to ease restrictions while minimizing the risk of resurgent outbreaks. Here, we use mobility and case data to quantify how coordinated exit strategies could delay continental resurgence and limit community transmission of COVID-19. We find that a resurgent continental epidemic could occur as many as 5 weeks earlier when well-connected countries with stringent existing interventions end their interventions prematurely. Further, we found that appropriate coordination can greatly improve the likelihood of eliminating community transmission throughout Europe. In particular, synchronizing intermittent lockdowns across Europe meant half as many lockdown periods were required to end community transmission continent-wide.\n\nOne Sentence SummaryEU coordination in easing restrictions is key to preventing resurgent COVID-19 outbreaks and stopping community transmission.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Nick Warren Ruktanonchai", + "author_inst": "University of Southampton" + }, + { + "author_name": "Jessica Floyd", + "author_inst": "University of Southampton" + }, + { + "author_name": "Shengjie Lai", + "author_inst": "University of Southampton" + }, + { + "author_name": "Corrine Warren Ruktanonchai", + "author_inst": "University of Southampton" + }, + { + "author_name": "Adam Sadilek", + "author_inst": "Google, Inc" + }, + { + "author_name": "Pedro Rente-Lourenco", + "author_inst": "Vodafone, Inc" + }, + { + "author_name": "Xue Ben", + "author_inst": "Google, Inc" + }, + { + "author_name": "Alessandra Carioli", + "author_inst": "University of Southampton" + }, + { + "author_name": "Joshua Gwinn", + "author_inst": "University of Kentucky" + }, + { + "author_name": "Jessica Steele", + "author_inst": "University of Southampton" + }, + { + "author_name": "Olivia Prosper", + "author_inst": "University of Tennessee" + }, + { + "author_name": "Aaron Schneider", + "author_inst": "Google, Inc" + }, + { + "author_name": "Andrew Oplinger", + "author_inst": "Google, Inc" + }, + { + "author_name": "Paul Eastham", + "author_inst": "Google, Inc" + }, + { + "author_name": "Andrew J Tatem", + "author_inst": "University of Southampton" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.18.20131417", "rel_title": "Leveraging wearable technology to predict the risk of COVID-19 infection.", @@ -1390802,49 +1389549,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.16.20133215", - "rel_title": "The first proof of the capability of wastewater surveillance for COVID-19 in India through the detection of the genetic material of SARS-CoV-2", - "rel_date": "2020-06-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.16.20133215", - "rel_abs": "we made the first ever successful effort from India to detect the genetic material of SARS-CoV-2 viruses to understand the capability and application of WBE surveillance in India. Sampling was carried out on 8 and 27 May, 2020 from Old Pirana Waste Water Treatment Plant (WWTP) at Ahmedabad, Gujarat with 106 million liters per day (MLD) capacity receiving effluent of Civil Hospital treating COVID-19 patient. All three i.e. ORF1ab, N and S genes of SARS-CoV-2 were discerned in the influents with no gene spotted in the effluent collected on 8 and 27 May 2020. Temporal difference between 8 and 27 May 2020 samples was of 10x in gene copy loading with corresponding change of 2x in the number active COVID-19 patient in the city. Number of gene copies was found comparable to that reported in the untreated wastewaters of Australia, China and Turkey and lower than that of the USA, France and Spain. This study, being the first from India and probably among the first ten reports in the world of gene detection of SARS-CoV-2 in the environmental samples, aims to assist concerned authorities and policymakers to formulate and/or upgrade the COVID-19 surveillance to have explicit picture of phase of the pandemic. While infectious SARS-CoV-2 has yet to be identified in the aquatic environment, the virus potentially enters the wastewater stream from patient excretions and thus can be a great tool for pandemic monitoring.\n\nHIGHLIGHTS{square} First ever report of the presence of gene of SARS-CoV-2 in the wastewater in India.\n{square}CT value is explicitly indicative of the increase of COVID-19 patient in the vicinity.\n{square}All three i.e. ORF1ab, N and S genes of SARS-CoV-2 were discerned in the influents.\n{square}None of three genes were spotted in the effluent collected on 8 and 27 May 2020.\n{square}Wastewater surveillance conclusively specified temporal difference in COVID-19 load.\n{square}Temporal difference was 10x and 2x in gene copies and COVID-19 patient, respectively.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Manish Kumar", - "author_inst": "Indian Institute of Technology Gandhinagar, India" - }, - { - "author_name": "Arbind K Patel", - "author_inst": "Indian Institute of Technology Gandhinagar, Gujarat, India" - }, - { - "author_name": "Anil V Shah", - "author_inst": "Gujarat Pollution Control Board, Gandhinagar, India" - }, - { - "author_name": "Janvi Raval", - "author_inst": "Gujarat Biotechnology Research Centre" - }, - { - "author_name": "Neha Rajpara", - "author_inst": "Gujarat Biotechnology Research Centre" - }, - { - "author_name": "Madhvi Joshi", - "author_inst": "Gujarat Biotechnology Research Centre" - }, - { - "author_name": "Chaitanya G Joshi", - "author_inst": "Gujarat Biotechnology Research Centre, Gujarat" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.16.20133116", "rel_title": "Mental health during the COVID-19 pandemic in two longitudinal UK population cohorts", @@ -1392208,6 +1390912,113 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.06.17.158006", + "rel_title": "Genomic surveillance of SARS-CoV-2 reveals community transmission of a major lineage during the early pandemic phase in Brazil", + "rel_date": "2020-06-18", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.17.158006", + "rel_abs": "Despite all efforts to control the COVID-19 spread, the SARS-CoV-2 reached South America within three months after its first detection in China, and Brazil became one of the hotspots of COVID-19 in the world. Several SARS-CoV-2 lineages have been identified and some local clusters have been described in this early pandemic phase in Western countries. Here we investigated the genetic diversity of SARS-CoV-2 during the early phase (late February to late April) of the epidemic in Brazil. Phylogenetic analyses revealed multiple introductions of SARS-CoV-2 in Brazil and the community transmission of a major B.1.1 lineage defined by two amino acid substitutions in the Nucleocapsid and ORF6. This SARS-CoV-2 Brazilian lineage was probably established during February 2020 and rapidly spread through the country, reaching different Brazilian regions by the middle of March 2020. Our study also supports occasional exportations of this Brazilian B.1.1 lineage to neighboring South American countries and to more distant countries before the implementation of international air travels restrictions in Brazil.", + "rel_num_authors": 23, + "rel_authors": [ + { + "author_name": "Paola Cristina Resende", + "author_inst": "Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), FIOCRUZ, Rio de Janeiro, Brazil" + }, + { + "author_name": "Edson Delatorre", + "author_inst": "Departamento de Biologia. Centro de Ciencias Exatas, Naturais e da Saude, Universidade Federal do Espirito Santo, Alegre, Brazil" + }, + { + "author_name": "Tiago Graf", + "author_inst": "Instituto Goncalo Moniz, FIOCRUZ, Salvador, Brazil." + }, + { + "author_name": "Daiana Mir", + "author_inst": "Unidad de Genomica y Bioinformatica, Centro Universitario Regional del Litoral Norte, Universidad de la Republica, Salto, Uruguay" + }, + { + "author_name": "Fernando C Motta", + "author_inst": "Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), FIOCRUZ, Rio de Janeiro, Brazil" + }, + { + "author_name": "Luciana Appolinario", + "author_inst": "Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), FIOCRUZ, Rio de Janeiro, Brazil" + }, + { + "author_name": "Anna Carolina D Paixao", + "author_inst": "Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), FIOCRUZ, Rio de Janeiro, Brazil" + }, + { + "author_name": "Maria Ogrzewalska", + "author_inst": "Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), FIOCRUZ, Rio de Janeiro, Brazil" + }, + { + "author_name": "Braula Caetano", + "author_inst": "Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), FIOCRUZ, Rio de Janeiro, Brazil" + }, + { + "author_name": "Mirleide C Santos", + "author_inst": "Instituto Evandro Chagas, Belem, Para" + }, + { + "author_name": "Jessylene Almeida Ferreira", + "author_inst": "Instituto Evandro Chagas, Belem, Para" + }, + { + "author_name": "Edivaldo C Souza Junior", + "author_inst": "Instituto Evandro Chagas, Belem, Para" + }, + { + "author_name": "Sandro Patroca Silva", + "author_inst": "Instituto Evandro Chagas, Belem, Para" + }, + { + "author_name": "Sandra B Fernandes", + "author_inst": "Laboratorio Central de Saude Publica do Estado de Santa Catarina (LACEN-SC), Florianopolis, Santa Catarina, Brazil" + }, + { + "author_name": "Lucas Alves Vianna", + "author_inst": "Laboratorio Central de Saude Publica do Estado Espirito Santo (LACEN-ES). Vitoria, Espirito Santo, Brazil" + }, + { + "author_name": "Larissa Costa", + "author_inst": "Laboratorio Central de Saude Publica do Distrito Federal (LACEN-DF). Brasilia, Distrito Federal, Brazil" + }, + { + "author_name": "Jean Ferro", + "author_inst": "Laboratorio Central de Saude Publica de Alagoas (LACEN-AL). Maceio, Alagoas, Brazil" + }, + { + "author_name": "Vanessa Nardy", + "author_inst": "Laboratorio Central de Saude Publica da Bahia (LACEN-BA). Salvador, Bahia, Brazil" + }, + { + "author_name": "Julio Croda", + "author_inst": "Fiocruz Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil" + }, + { + "author_name": "Wanderson K Oliveira", + "author_inst": "Hospital das Forcas Armadas, Ministerio da Defesa, Brasilia, Distrito Federal, Brazil" + }, + { + "author_name": "Andr\u00e9 Luis de Abreu", + "author_inst": "Coordenadoria Geral de Laboratorios - Ministerio da Saude, Brasilia, Distrito Federal, Brazil" + }, + { + "author_name": "Gonzalo Bello", + "author_inst": "Laboratorio de AIDS e Imunologia Molecular, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil" + }, + { + "author_name": "Marilda M Siqueira", + "author_inst": "Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute (IOC), FIOCRUZ, Rio de Janeiro, Brazil" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "evolutionary biology" + }, { "rel_doi": "10.1101/2020.06.18.159202", "rel_title": "Divergent SARS-CoV-2-specific T and B cell responses in severe but not mild COVID-19", @@ -1392588,165 +1391399,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.06.15.20130328", - "rel_title": "Can we trust the prediction model? Demonstrating the importance of external validation by investigating the COVID-19 Vulnerability (C-19) Index across an international network of observational healthcare datasets", - "rel_date": "2020-06-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.15.20130328", - "rel_abs": "BackgroundSARS-CoV-2 is straining healthcare systems globally. The burden on hospitals during the pandemic could be reduced by implementing prediction models that can discriminate between patients requiring hospitalization and those who do not. The COVID-19 vulnerability (C-19) index, a model that predicts which patients will be admitted to hospital for treatment of pneumonia or pneumonia proxies, has been developed and proposed as a valuable tool for decision making during the pandemic. However, the model is at high risk of bias according to the Prediction model Risk Of Bias ASsessment Tool and has not been externally validated.\n\nMethodsWe followed the OHDSI framework for external validation to assess the reliability of the C-19 model. We evaluated the model on two different target populations: i) 41,381 patients that have SARS-CoV-2 at an outpatient or emergency room visit and ii) 9,429,285 patients that have influenza or related symptoms during an outpatient or emergency room visit, to predict their risk of hospitalization with pneumonia during the following 0 to 30 days. In total we validated the model across a network of 14 databases spanning the US, Europe, Australia and Asia.\n\nFindingsThe internal validation performance of the C-19 index was a c-statistic of 0.73 and calibration was not reported by the authors. When we externally validated it by transporting it to SARS-CoV-2 data the model obtained c-statistics of 0.36, 0.53 (0.473-0.584) and 0.56 (0.488-0.636) on Spanish, US and South Korean datasets respectively. The calibration was poor with the model under-estimating risk. When validated on 12 datasets containing influenza patients across the OHDSI network the c-statistics ranged between 0.40-0.68.\n\nInterpretationThe results show that the discriminative performance of the C-19 model is low for influenza cohorts, and even worse amongst COVID-19 patients in the US, Spain and South Korea. These results suggest that C-19 should not be used to aid decision making during the COVID-19 pandemic. Our findings highlight the importance of performing external validation across a range of settings, especially when a prediction model is being extrapolated to a different population. In the field of prediction, extensive validation is required to create appropriate trust in a model.", - "rel_num_authors": 36, - "rel_authors": [ - { - "author_name": "Jenna M Reps", - "author_inst": "Janssen R&D" - }, - { - "author_name": "Chungsoo Kim", - "author_inst": "Department of Biomedical Sciences, Ajou University Graduate School of Medicine, Suwon, Republic of Korea" - }, - { - "author_name": "Ross D. Williams", - "author_inst": "Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands" - }, - { - "author_name": "Aniek F Markus", - "author_inst": "Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands" - }, - { - "author_name": "Cynthia Yang", - "author_inst": "Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands" - }, - { - "author_name": "Talita Duarte Salles", - "author_inst": "Fundacio Institut Universitari per a la recerca a l'Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol)" - }, - { - "author_name": "Thomas Falconer", - "author_inst": "Department of Biomedical Informatics, Columbia University, New York, NY" - }, - { - "author_name": "Jitendra Jonnagaddala", - "author_inst": "School of Public Health and Community Medicine, UNSW Sydney" - }, - { - "author_name": "Andrew Williams", - "author_inst": "Tufts Institute for Clinical Research and Health Policy Studies, Boston, MA, 02111, USA" - }, - { - "author_name": "Sergio Fernandez-Bertolin", - "author_inst": "Fundacio Institut Universitari per a la recerca a l'Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol)" - }, - { - "author_name": "Scott L DuVall", - "author_inst": "Department of Veterans Affairs, USA; University of Utah, USA" - }, - { - "author_name": "Kristin Kostka", - "author_inst": "Real World Solutions, IQVIA, Cambridge, MA, United States" - }, - { - "author_name": "Gowtham Rao", - "author_inst": "Janssen Research & Development, Titusville, NJ, USA" - }, - { - "author_name": "Azza Shoaibi", - "author_inst": "Janssen Research & Development, Titusville, NJ, USA" - }, - { - "author_name": "Anna Ostropolets", - "author_inst": "Department of Biomedical Informatics, Columbia University, New York, NY" - }, - { - "author_name": "Matthew E Spotnitz", - "author_inst": "Department of Biomedical Informatics, Columbia University, New York, NY" - }, - { - "author_name": "Lin Zhang", - "author_inst": "School of Public Health, Peking Union Medical College, Beijing, China" - }, - { - "author_name": "Paula Casajust", - "author_inst": "Department of Real-World Evidence, Trial Form Support, Barcelona, Spain" - }, - { - "author_name": "Ewout Steyerberg", - "author_inst": "Department of Public Health, Erasmus University Medical Center, Rotterdam, The Netherlands" - }, - { - "author_name": "Fredrik Nyberg", - "author_inst": "School of Public Health and Community Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg Gothenburg, Sweden" - }, - { - "author_name": "Benjamin Skov Kaas-Hansen", - "author_inst": "Clinical Pharmacology Unit, Zealand University Hospital, Roskilde, Denmark" - }, - { - "author_name": "Young Hwa Choi", - "author_inst": "Department of Infectious Diseases, Ajou University School of Medicine, Suwon, Republic of Korea" - }, - { - "author_name": "Daniel Morales", - "author_inst": "ivision of Population Health and Genomics, University of Dundee, UK" - }, - { - "author_name": "Siaw-Teng Liaw", - "author_inst": "School of Public Health and Community Medicine, UNSW Sydney" - }, - { - "author_name": "Maria Tereza Fernandes Abrahao", - "author_inst": "Faculty of Medicine, University of Sao Paulo, Sao Paulo, Brazil" - }, - { - "author_name": "Carlos Areia", - "author_inst": "Nuffield Department of Clinical Neurosciences, University of Oxford" - }, - { - "author_name": "Michael E Matheny", - "author_inst": "Department of Veterans Affairs, USA; Vanderbilt University, USA" - }, - { - "author_name": "Maria Aragon", - "author_inst": "Fundacio Institut Universitari per a la recerca a l'Atencio Primaria de Salut Jordi Gol i Gurina (IDIAPJGol)" - }, - { - "author_name": "Rae Woong Park", - "author_inst": "Department of Biomedical Informatics, Ajou University School of Medicine, Suwon, Republic of Korea" - }, - { - "author_name": "George Hripcsak", - "author_inst": "Department of Biomedical Informatics, Columbia University, New York, NY" - }, - { - "author_name": "Christian G Reich", - "author_inst": "Real World Solutions, IQVIA, Cambridge, MA, United States" - }, - { - "author_name": "Marc A Suchard", - "author_inst": "Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA, USA" - }, - { - "author_name": "Seng Chan You", - "author_inst": "Department of Biomedical Informatics, Ajou University School of Medicine, Suwon, Republic of Korea" - }, - { - "author_name": "Patrick B Ryan", - "author_inst": "Janssen Research & Development, Titusville, NJ, USA" - }, - { - "author_name": "Daniel Prieto-Alhambra", - "author_inst": "Centre for Statistics in Medicine, NDORMS, University of Oxford" - }, - { - "author_name": "Peter R Rijnbeek", - "author_inst": "Department of Medical Informatics, Erasmus University Medical Center, Rotterdam, The Netherlands" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.06.15.20131672", "rel_title": "Diagnostic accuracy of six commercial SARS-CoV-2 IgG/total antibody assays and identification of SARS-CoV-2 neutralizing antibodies in convalescent sera", @@ -1393974,6 +1392626,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.15.20132050", + "rel_title": "Modeling the Post-Containment Elimination of Transmission of COVID-19", + "rel_date": "2020-06-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.15.20132050", + "rel_abs": "Roughly six months into the COVID-19 pandemic, many countries have managed to contain the spread of the virus by means of strict containment measures including quarantine, tracing and isolation of patients as well strong restrictions on population mobility. Here we propose an extended SEIR model to explore the dynamics of containment and then explore scenarios for the local extinction of the disease. We present both the deterministic and stochastic version fo the model and derive the [R]0 and the probability of local extinction after relaxation (elimination of transmission) of containment, [P]0. We show that local extinctions are possible without further interventions, with reasonable probability, as long as the number of active cases is driven to single digits and strict control of case importation is maintained. The maintenance of defensive behaviors, such as using masks and avoiding agglomerations are also important factors. We also explore the importance of population immunity even when above the herd immunity threshold.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Flavio Codeco Coelho", + "author_inst": "Fundacao Getulio Vargas" + }, + { + "author_name": "Luiz Max Carvalho", + "author_inst": "Fundacao Getulio Vargas" + }, + { + "author_name": "Raquel M Lana", + "author_inst": "Fundacao Oswaldo Cruz" + }, + { + "author_name": "Oswaldo G Cruz", + "author_inst": "Fundacao Oswaldo Cruz" + }, + { + "author_name": "Leonardo S Bastos", + "author_inst": "Fundacao Oswaldo Cruz" + }, + { + "author_name": "Claudia T Codeco", + "author_inst": "Fundacao Oswaldo Cruz" + }, + { + "author_name": "Marcelo F C Gomes", + "author_inst": "Fundacao Oswaldo Cruz" + }, + { + "author_name": "Daniel Villela", + "author_inst": "Fundacao Oswaldo Cruz" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.15.20131979", "rel_title": "Mobility network modeling explains higher SARS-CoV-2 infection rates among disadvantaged groups and informs reopening strategies", @@ -1394242,61 +1392941,6 @@ "type": "new results", "category": "systems biology" }, - { - "rel_doi": "10.1101/2020.06.17.157982", - "rel_title": "Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding", - "rel_date": "2020-06-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.17.157982", - "rel_abs": "The receptor binding domain (RBD) of the SARS-CoV-2 spike glycoprotein mediates viral attachment to ACE2 receptor, and is a major determinant of host range and a dominant target of neutralizing antibodies. Here we experimentally measure how all amino-acid mutations to the RBD affect expression of folded protein and its affinity for ACE2. Most mutations are deleterious for RBD expression and ACE2 binding, and we identify constrained regions on the RBDs surface that may be desirable targets for vaccines and antibody-based therapeutics. But a substantial number of mutations are well tolerated or even enhance ACE2 binding, including at ACE2 interface residues that vary across SARS-related coronaviruses. However, we find no evidence that these ACE2-affinity enhancing mutations have been selected in current SARS-CoV-2 pandemic isolates. We present an interactive visualization and open analysis pipeline to facilitate use of our dataset for vaccine design and functional annotation of mutations observed during viral surveillance.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Tyler N Starr", - "author_inst": "Fred Hutch Cancer Research Center" - }, - { - "author_name": "Allison J Greaney", - "author_inst": "Fred Hutch Cancer Research Center" - }, - { - "author_name": "Sarah K Hilton", - "author_inst": "Fred Hutch Cancer Research Center" - }, - { - "author_name": "Katharine HD Crawford", - "author_inst": "Fred Hutch Cancer Research Center" - }, - { - "author_name": "Mary Jane Navarro", - "author_inst": "University of Washington" - }, - { - "author_name": "John E Bowen", - "author_inst": "University of Washington" - }, - { - "author_name": "M Alejandra Tortorici", - "author_inst": "University of Washington" - }, - { - "author_name": "Alexandra C Walls", - "author_inst": "University of Washington" - }, - { - "author_name": "David Veesler", - "author_inst": "University of Washington" - }, - { - "author_name": "Jesse D Bloom", - "author_inst": "Fred Hutchinson Cancer Research Center" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.16.155887", "rel_title": "Detection of SARS-CoV-2 RNA by multiplex RT-qPCR", @@ -1395556,6 +1394200,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.13.20129841", + "rel_title": "Field-deployable, rapid diagnostic testing of saliva samples for SARS-CoV-2.", + "rel_date": "2020-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.13.20129841", + "rel_abs": "Rapid, scalable, point-of-need, COVID-19 diagnostic testing is necessary to safely re-open economies and prevent future outbreaks. We developed an assay that detects single copies of SARS-CoV-2 virus directly from saliva and swab samples in 30 min using a simple, one-step protocol that utilizes only a heat block and microcentrifuge tube prefilled with a mixture containing the necessary reagents and has a sensitivity and specificity of 97% and 100%, respectively.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Shan Wei", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Esther Kohl", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Alexandre Djandji", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Stephanie Morgan", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Susan Whittier", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Mahesh Mansukhani", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Raymond Yeh", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Juan Carlos Alejaldre", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Elaine Fleck", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Mary D'Alton", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Yousin Suh", + "author_inst": "Columbia University Irving Medical Center" + }, + { + "author_name": "Zev Williams", + "author_inst": "Columbia University Irving Medical Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.14.20128876", "rel_title": "Snapshot PCR Surveillance for SARS-CoV-2 in Hospital Staff in England", @@ -1396016,33 +1394723,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2020.06.13.20130310", - "rel_title": "COVID-19: a crash test for biomedical publishing?", - "rel_date": "2020-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.13.20130310", - "rel_abs": "The effect of COVID-19 on biomedical publishing (BP) (i.e. scientific biomedical periodicals continuously published by research communities or commercial publishers) has not been deeply explored. To estimate the immediate COVID-19 impact on BP, we have assessed PubMed-indexed articles about COVID-19 (PMIAC) from December 2019 to April 2020. PMIAC have been classified according to publication date, country, and journals for evaluation of time-, region- and scientometric-dependant impact of COVID-19 on BP and have been curated manually (i.e. each entry has been individually analyzed). PMIAC analysis reflects geographic and temporal parameters of outbreak spread. A major BP problem is related to the fact that only 40% of articles report/review/analyze data. Another BP weakness is the clusterization of \"highly-trusted\" publications according to countries of origin and \"highly impacting\" journals. Finally, a problem highlighted by COVID-19 crisis is the increased specification of biomedical research. To solve the problem, analytical reviews integrating data from different areas of biology and medicine are required. The data on PMIAC suggest priority of \"what is published\" over \"where it is published\" and \"who are the authors\". We believe that our brief analysis may help to shape forthcoming BP to become more effective in solving immediate problems resulted from global threats.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ivan Y Iourov", - "author_inst": "Mental Health Research Center" - }, - { - "author_name": "Maria A Zelenova", - "author_inst": "Mental Health Research Center" - }, - { - "author_name": "Svetlana G Vorsanova", - "author_inst": "Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.06.13.20130252", "rel_title": "Prevalence of IgG antibodies to SARS-CoV-2 in Wuhan -implications for the ability to produce long-lasting protective antibodies against SARS-CoV-2", @@ -1396794,6 +1395474,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "primary care research" }, + { + "rel_doi": "10.1101/2020.06.14.20130682", + "rel_title": "Development and validation of a tool to appraise guidelines on SARS-CoV-2 infection prevention strategies in healthcare workers", + "rel_date": "2020-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.14.20130682", + "rel_abs": "BackgroundClinical guidelines on infection prevention strategies in healthcare workers (HCWs) play an important role in protecting them during the SARS-CoV-2 pandemic. Poorly constructed guidelines that are not comprehensive and are ambiguous may compromise HCWs safety. We aimed to develop and validate a tool to appraise guidelines on infection prevention strategies in HCWs.\n\nMethodsA 3-stage, web-based, Delphi consensus-building process among a panel of diverse HCWs and healthcare managers was utilised. We validated the tool by appraising 40 international, specialty-specific and procedure-specific guidelines along with national guidelines from countries with a wide range of gross national income.\n\nResultsOverall consensus ([≥]75%) was reached at the end of three rounds for all six domains included in the tool. The chosen domains allowed appraisal of guidelines in relation to general characteristics (domain-1), recommendations on engineering (domain-2) and administrative aspects (domain 4-6) of infection prevention, as well as personal protection equipment (PPE) use (domain-3). The appraisal tool performed well across all domains and inter-rater agreement was excellent. All included guidelines performed relatively better in domains 1-3 compared with domains 4-6 and this was more evident in guidelines originating from lower income countries.\n\nConclusionThe guideline appraisal tool was robust and easy to use. Recommendations on engineering aspects of infection prevention, administrative measures that promote optimal PPE use and HCW wellbeing were generally lacking in assessed guidelines. This tool may enable health systems to adopt high quality HCW infection prevention guidelines during SARS-CoV-2 pandemic and may also provide a framework for future guideline development.\n\nFundingNo funding received.\n\nKey SummaryWe developed and validated a guideline-appraisal tool by appraising 40 different guidelines from countries with varying GNI. This tool may help healthcare systems to adopt high-quality HCW infection-prevention guidelines during COVID-19 pandemic and may also provide a guideline development framework.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Ashwin Subramaniam", + "author_inst": "Peninsula Health" + }, + { + "author_name": "Mallikarjuna Reddy", + "author_inst": "Peninsula Health, Calvary Hospital" + }, + { + "author_name": "Alexander Zubarev", + "author_inst": "Peninsula Health" + }, + { + "author_name": "Umesh Kadam", + "author_inst": "Werribee Hospital, Casey Hospital" + }, + { + "author_name": "Zheng Jie Lim", + "author_inst": "Ballarat Base Hospital" + }, + { + "author_name": "Chris Anstey", + "author_inst": "Griffith University University of Queensland" + }, + { + "author_name": "Shailesh Bihari", + "author_inst": "Flinders University andMedical Centre" + }, + { + "author_name": "Jumana Haji", + "author_inst": "Aster CMI Hospital Bangalore" + }, + { + "author_name": "Subhathra Karunanithi", + "author_inst": "Valley Medical Group, New Jersey" + }, + { + "author_name": "Jinghang Luo", + "author_inst": "Western Health" + }, + { + "author_name": "Neil Mara", + "author_inst": "NHS" + }, + { + "author_name": "Saikat Mitra", + "author_inst": "National University Hospital, Singapore" + }, + { + "author_name": "Kollengode Ramanathan", + "author_inst": "National University Hospital Singapore" + }, + { + "author_name": "Arvind Rajamani", + "author_inst": "Nepean Clinical School University of Sydney" + }, + { + "author_name": "Francesca Rubulotta", + "author_inst": "Imperial College London" + }, + { + "author_name": "Erik Svensk", + "author_inst": "Sundsvall hospital, Sundsvall, Sweden" + }, + { + "author_name": "Kiran Shekar", + "author_inst": "The Prince Charles Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.06.13.20130294", "rel_title": "Impact of social distancing measures for preventing coronavirus disease 2019 : A systematic review and meta-analysis protocol", @@ -1397066,133 +1395829,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.13.20130088", - "rel_title": "Compassionate Use of Tocilizumab in Severe SARS-CoV2 Pneumonia. When late administration is too late.", - "rel_date": "2020-06-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.13.20130088", - "rel_abs": "IntroductionTocilizumab is an interleukin 6 receptor antagonist which has been used for the treatment of severe SARS-CoV-2 pneumonia (SSP), aiming to ameliorate the cytokine release syndrome (CRS) -induced acute respiratory distress syndrome (ARDS). However, there is no data about the best moment for its administration along the course of the disease.\n\nMethodsWe provided tocilizumab on a compassionate-use basis to patients with SSP hospitalized (excluding intensive care and intubated cases) who required oxygen support to have a saturation >93%. Primary endpoint was intubation or death after 24 hours of its administration. Patients received at least one dose of 400 mg intravenous tocilizumab during March 8-2020, through April 20-2020.\n\nFindingsA total of 207 patients were studied and 186 analysed. The mean age was 65 years and 68% were male. A co-existing condition was present in 68 % of cases. At baseline, 114 (61%) required oxygen support with FiO2 >0.5 % and 72 (39%) [≤]0.5%. Early administration of tocilizumab, when the need of oxygen support was still below FiO2 [≤]0.5%, was significantly more effective than given it in advanced stages (FiO2 >0.5 %), achieving lower rates of intubation or death (13% vs 37% repectively, p<0{middle dot}001).\n\nInterpretationThe benefit of tocilizumab in severe SARS-Cov-2 pneumonia is only expected when it is administrated before the need of high oxygen support.\n\nFundingNone.", - "rel_num_authors": 28, - "rel_authors": [ - { - "author_name": "Miguel Gorgolas", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - }, - { - "author_name": "Alfonso Cabello", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - }, - { - "author_name": "Laura Prieto Perez", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - }, - { - "author_name": "Felipe Villar Alvarez", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - }, - { - "author_name": "Beatriz Alvarez Alvarez", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - }, - { - "author_name": "Maria Jesus Rodriguez Nieto", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - }, - { - "author_name": "Irene Carrillo Acosta", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - }, - { - "author_name": "Itziar Fernandez Ormaechea", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - }, - { - "author_name": "Aws Al-Hayani", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - }, - { - "author_name": "Pilar Carballosa", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - }, - { - "author_name": "Silvia Calpena Martinez", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - }, - { - "author_name": "Farah Ezzine de Blas", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - }, - { - "author_name": "Marina Castellanos Gonzalez", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - }, - { - "author_name": "Alba Naya Prieto", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - }, - { - "author_name": "Marta Lopez de las Heras", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - }, - { - "author_name": "Marcel Jose Rodriguez Guzman", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - }, - { - "author_name": "Ana Cordero Guijarro", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - }, - { - "author_name": "Antonio Broncano Lavado", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - }, - { - "author_name": "Alicia Macias Valcayo", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - }, - { - "author_name": "Marta Martin Garcia", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - }, - { - "author_name": "Javier Becares Martinez", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - }, - { - "author_name": "Ricardo Fernandez Roblas", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - }, - { - "author_name": "Miguel A Piris Pinilla", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - }, - { - "author_name": "Jose Fortes Alen", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - }, - { - "author_name": "Olga Sanchez Pernaute", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - }, - { - "author_name": "Fredeswinda Romero Bueno", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - }, - { - "author_name": "Sarah Heili Frades", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - }, - { - "author_name": "German Peces Barba Romero", - "author_inst": "Hospital Universitario Fundacion Jimenez Diaz - Universidad Autonoma de Madrid" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.14.20130666", "rel_title": "Impact of weather indicators on the COVID-19 outbreak: A multi-state study in India", @@ -1398396,6 +1397032,37 @@ "type": "new results", "category": "genetics" }, + { + "rel_doi": "10.1101/2020.06.15.20131375", + "rel_title": "COVID-19 IN INDIA: MODELLING, FORECASTING AND STATE-WISE COMPARISON", + "rel_date": "2020-06-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.15.20131375", + "rel_abs": "COVID-19 has turned the whole world upside down economically and socially. COVID-19 pandemic has caused around five crores of cases and three lakhs deaths globally as of 27 May 2020. This paper adopts four mathematical growth models. Basic models are encouraged because these models can make predictions with the available data and variables in the current scenario of COVID-19 pandemic. The best-fitted model is identified in accordance with the value of the coefficient of determination. As per the best model, there might be greater than 16 lakhs cases at the infection end in India. After predicting the future size of the pandemic, we analyzed how the disease severity varies among the Indian states and union territories using Case Fatality Rates (CFR).", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Ankitha Jose", + "author_inst": "St. Thomas College, Palai" + }, + { + "author_name": "Ashid Salim", + "author_inst": "St.Thomas College , Palai" + }, + { + "author_name": "Noel George", + "author_inst": "p value solutions , palai" + }, + { + "author_name": "Silpa Subhash", + "author_inst": "Cochin University of Science and Technology, Kerala, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.11.147025", "rel_title": "COVID-19-related coagulopathy, is transferrin a missing link?", @@ -1398872,81 +1397539,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.06.16.153403", - "rel_title": "Oral drug repositioning candidates and synergistic remdesivir combinations for the prophylaxis and treatment of COVID-19", - "rel_date": "2020-06-16", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.16.153403", - "rel_abs": "The ongoing pandemic caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), necessitates strategies to identify prophylactic and therapeutic drug candidates for rapid clinical deployment. A high-throughput, high-content imaging assay of human HeLa cells expressing the SARS-CoV-2 receptor ACE2 was used to screen ReFRAME, a best-in-class drug repurposing library. From nearly 12,000 compounds, we identified 66 compounds capable of selectively inhibiting SARS-CoV-2 replication in human cells. Twenty-four of these drugs show additive activity in combination with the RNA-dependent RNA polymerase inhibitor remdesivir and may afford increased in vivo efficacy. We also identified synergistic interaction of the nucleoside analog riboprine and a folate antagonist 10-deazaaminopterin with remdesivir. Overall, seven clinically approved drugs (halofantrine, amiodarone, nelfinavir, simeprevir, manidipine, ozanimod, osimertinib) and 19 compounds in other stages of development may have the potential to be repurposed as SARS-CoV-2 oral therapeutics based on their potency, pharmacokinetic and human safety profiles.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Malina A. Bakowski", - "author_inst": "Calibr, a division of The Scripps Research Institute" - }, - { - "author_name": "Nathan Beutler", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Emily Chen", - "author_inst": "Calibr, a division of The Scripps Research Institute" - }, - { - "author_name": "Tu-Trinh H. Nguyen", - "author_inst": "Calibr, a division of The Scripps Research Institute" - }, - { - "author_name": "Melanie G. Kirkpatrick", - "author_inst": "Calibr, a division of The Scripps Research Institute" - }, - { - "author_name": "Mara Parren", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Linlin Yang", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "James Ricketts", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Anil K. Gupta", - "author_inst": "Calibr, a division of The Scripps Research Institute" - }, - { - "author_name": "Mitchell V. Hull", - "author_inst": "Calibr, a division of The Scripps Research Institute" - }, - { - "author_name": "Peter G. Schultz", - "author_inst": "Calibr, a division of The Scripps Research Institute" - }, - { - "author_name": "Dennis R. Burton", - "author_inst": "The Scripps Research Institute" - }, - { - "author_name": "Arnab K. Chatterjee", - "author_inst": "Calibr, a division of The Scripps Research Institute" - }, - { - "author_name": "Case W. McNamara", - "author_inst": "Calibr, a division of The Scripps Research Institute" - }, - { - "author_name": "Thomas F. Rogers", - "author_inst": "Scripps Research" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.15.153064", "rel_title": "Array-based analysis of SARS-CoV-2, other coronaviruses, and influenza antibodies in convalescent COVID-19 patients", @@ -1400274,6 +1398866,65 @@ "type": "new results", "category": "neuroscience" }, + { + "rel_doi": "10.1101/2020.06.15.151647", + "rel_title": "Genome-wide mapping of therapeutically-relevant SARS-CoV-2 RNA structures", + "rel_date": "2020-06-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.15.151647", + "rel_abs": "SARS-CoV-2 is a betacoronavirus with a linear single-stranded, positive-sense RNA genome of [~]30 kb, whose outbreak caused the still ongoing COVID-19 pandemic. The ability of coronaviruses to rapidly evolve, adapt, and cross species barriers makes the development of effective and durable therapeutic strategies a challenging and urgent need. As for other RNA viruses, genomic RNA structures are expected to play crucial roles in several steps of the coronavirus replication cycle. Despite this, only a handful of functionally conserved structural elements within coronavirus RNA genomes have been identified to date.\n\nHere, we performed RNA structure probing by SHAPE-MaP to obtain a single-base resolution secondary structure map of the full SARS-CoV-2 coronavirus genome. The SHAPE-MaP probing data recapitulate the previously described coronavirus RNA elements (5' UTR, ribosomal frameshifting element, and 3' UTR), and reveal new structures. Secondary structure-restrained 3D modeling of highly-structured regions across the SARS-CoV-2 genome allowed for the identification of several putative druggable pockets. Furthermore, [~]8% of the identified structure elements show significant covariation among SARS-CoV-2 and other coronaviruses, hinting at their functionally-conserved role. In addition, we identify a set of persistently single-stranded regions having high sequence conservation, suitable for the development of antisense oligonucleotide therapeutics.\n\nCollectively, our work lays the foundation for the development of innovative RNA-targeted therapeutic strategies to fight SARS-related infections.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Ilaria Manfredonia", + "author_inst": "University of Groningen" + }, + { + "author_name": "Chandran Nithin", + "author_inst": "International Institute of Molecular and Cell Biology (Warsaw)" + }, + { + "author_name": "Almudena Ponce-Salvatierra", + "author_inst": "International Institute of Molecular and Cell Biology (Warsaw)" + }, + { + "author_name": "Pritha Ghosh", + "author_inst": "Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology" + }, + { + "author_name": "Tomasz K. Wirecki", + "author_inst": "Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology" + }, + { + "author_name": "Tycho Marinus", + "author_inst": "University of Groningen" + }, + { + "author_name": "Natacha S. Ogando", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Eric J Snijder", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Martijn J van Hemert", + "author_inst": "Leiden University Medical Center" + }, + { + "author_name": "Janusz M. Bujnicki", + "author_inst": "International Institute of Molecular and Cell Biology (Warsaw)" + }, + { + "author_name": "Danny Incarnato", + "author_inst": "Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "genetics" + }, { "rel_doi": "10.1101/2020.06.15.152587", "rel_title": "Microscopy-based assay for semi-quantitative detection of SARS-CoV-2 specific antibodies in human sera", @@ -1400738,81 +1399389,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.12.20129098", - "rel_title": "Laboratory Testing Implications of Risk-Stratification and Management for Improving Clinical Outcomes of COVID-19 Patients", - "rel_date": "2020-06-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.12.20129098", - "rel_abs": "The high mortality rate of COVID-19 patients is mainly caused by the progression from mild to critical illness. To identify the key laboratory indicators and stratify high-risk COVID-19 patients with progression to severe/critical illness, we compared 474 moderate patients and 74 severe/critical patients. The laboratory indicators, including lactate dehydrogenase (LDH), monocytes percentage, etc. were significantly higher in the severe/critical patients (P <0.001) and showed a noticeable change at about a week before the diagnosis. Based on these indicators, we constructed a risk-stratification model, which can accurately grade the severity of patients with COVID-19 (accuracy = 0.96, 95% CI: 0.94 - 0.989, sensitivity = 0.98, specificity = 0.84). Also, compared with non-COVID-19 viral pneumonia, we found that COVID-19 had weaker dysfunction to the heart, liver, and kidney. The prognostic model based on laboratory indicators could help to diagnose, monitor, and predict severity at an early stage to those patients with COVID-19.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Caidong Liu", - "author_inst": "Department of laboratory medicine, Nanjing First Hospital, Nanjing Medical University" - }, - { - "author_name": "Ziyu Wang", - "author_inst": "Department of Bioinformatics, Nanjing Medical University" - }, - { - "author_name": "Jie Li", - "author_inst": "Department of Bioinformatics, Nanjing Medical University" - }, - { - "author_name": "Changgang Xiang", - "author_inst": "Department of laboratory medicine, First People's Hospital of Jiangxia District of Wuhan" - }, - { - "author_name": "Lingxiang Wu", - "author_inst": "Department of Bioinformatics, Nanjing Medical University" - }, - { - "author_name": "Wei Wu", - "author_inst": "Department of Bioinformatics, Nanjing Medical University" - }, - { - "author_name": "Weiye Hou", - "author_inst": "Department of laboratory medicine, Nanjing First Hospital, Nanjing Medical University" - }, - { - "author_name": "Huiling Sun", - "author_inst": "General clinical research center, Nanjing First Hospital, Nanjing Medical University" - }, - { - "author_name": "Youli Wang", - "author_inst": "Department of laboratory medicine, Nanjing First Hospital, Nanjing Medical University" - }, - { - "author_name": "Zhenling Nie", - "author_inst": "Department of laboratory medicine, Nanjing First Hospital, Nanjing Medical University" - }, - { - "author_name": "Yingdong Gao", - "author_inst": "Department of laboratory medicine, Nanjing First Hospital, Nanjing Medical University" - }, - { - "author_name": "Ruisheng Zhang", - "author_inst": "Department of laboratory medicine, Nanjing First Hospital, Nanjing Medical University" - }, - { - "author_name": "Xinyi Xia", - "author_inst": "COVID-19 Research Center, Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine" - }, - { - "author_name": "qianghu wang", - "author_inst": "Nanjing medical university" - }, - { - "author_name": "Shukui Wang", - "author_inst": "Department of laboratory medicine, Nanjing First Hospital, Nanjing Medical University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.12.20129254", "rel_title": "Upper-room ultraviolet air disinfection might help to reduce COVID-19 transmission in buildings", @@ -1401980,6 +1400556,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.12.20129536", + "rel_title": "High Incidence of Venous Thrombosis in Patients with Moderate to Severe COVID-19", + "rel_date": "2020-06-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.12.20129536", + "rel_abs": "COVID-19 predisposes to venous thromboembolism and there are multiple data regarding high incidence of venous thrombosis in critical COVID-19 patients, however reports on this complication in less severe patients are not widely available.\n\nThe aim of this study was to investigate the incidence of deep-vein thrombosis (DVT) in patients with moderate to severe COVID-19 and to assess the prevalence of DVT with lung computerized tomography (lung CT) exams, clinical information and lab data. This study examined 75 consecutive patients with moderate to severe COVID-19, with specific exclusions.\n\nMETHODSAlmost all patients (pts) admitted to our hospital in the first half of May underwent comprehensive vein ultrasonography. 75 pts (aged 27-92 y, median - 63 y, 36 males and 39 females) with moderate to severe COVID-19 were included in our study.\n\nRESULTSSpontaneous echo contrast (decreased blood velocity and blood stasis) was detected in common femoral veins in 53 pts (70.7%). DVT was found in 15 pts (20%). The vast majority of those with DVT (13 pts, 86.7%) had thrombi only in calf veins and ileofemoral thrombosis was detected in 2 pts with DVT (13.3%). There was no significant observed difference between DVT and non-DVT patients with respect to age, underlying diseases, lung CT scores and SpaO2 at admission. There was also no significant observed difference between DVT and non-DVT patients with respect to both \"time from symptoms onset to admission\" and with respect to the majority of lab data.\n\nHowever, a significant difference was observed in D-dimer level (1.87 {+/-} 1.62 vs 0.51 {+/-} 0,4 mcg/mL p<0.0001) and C-reactive protein (116.9 {+/-} 83,6 and 65.1 {+/-} 64.98 mg/L, p = 0.014) for patients with DVT and patients without DVT respectably (Receiver operating characteristics (ROC) curve analysis revealed that the level of D-dimer [≥] 0.69 mcg/mL is the predictor of DVT with a sensitivity of 76.9%, a specificity of 77.6%, p < 0.001 (AUC area under curve = 0.7944). Logistic regression confirmed that D-dimer is an independent predictor of DVT and patients with D-dimer [≥] 0.69 mcg/mL have odds ratio (OR) of developing DVT = 5.1 (confidence interval [CI] 1.9 - 13.5)).\n\nCONCLUSIONPatients with moderate to severe COVID-19 show high incidence of DVT, indicating that moderate to severe COVID-19 patients may require an early administration of anticoagulation therapy as part of their treatment. Such therapy may be continued after hospital discharge. Based on these findings, these patients may also require a follow-up with vein ultrasonography after recovery to rule out DVT.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Oleg B Kerbikov", + "author_inst": "Federal State Clinical Research Hospital FMBA of Russia" + }, + { + "author_name": "Pavel Yu Orekhov", + "author_inst": "Federal State Clinical Research Hospital FMBA of Russia" + }, + { + "author_name": "Ekaterina N Borskaya", + "author_inst": "Burnasyan Federal Medical Biophysical Center FMBA of Russia" + }, + { + "author_name": "Natalia S Nosenko", + "author_inst": "Federal State Clinical Research Hospital FMBA of Russia" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.12.20129213", "rel_title": "ASSESSING THE POTENTIAL IMPACT OF TRANSMISSION DURING PROLONGED VIRAL SHEDDING ON THE EFFECT OF LOCKDOWN RELAXATION ON COVID-19", @@ -1402260,25 +1400867,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.11.20128991", - "rel_title": "Transformed time series analysis of first-wave COVID-19: universal similarities found in the Group of Twenty (G20) Countries", - "rel_date": "2020-06-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20128991", - "rel_abs": "As of April 30, 2020, the number of cumulative confirmed coronavirus disease 2019 (COVID-19) cases exceeded 3 million worldwide and 1 million in the US with an estimated fatality rate of more than 7 percent. Because the patterns of the occurrence of new confirmed cases and deaths over time are complex and seemingly country-specific, estimating the long-term pandemic spread is challenging. I developed a simple transformation algorithm to investigate the characteristics of the case and death time series per nation, and described the universal similarities observed in the transformed time series of 19 nations in the Group of Twenty (G20). To investigate the universal similarities among the cumulative profiles of confirmed cases and deaths of 19 individual nations in the G20, a transformation algorithm of the time series data sets was developed with open-source software programs. The algorithm was used to extract and analyze statistical information from daily updated COVID-19 pandemic data sets from the European Centre for Disease Prevention and Control (ECDC). Two new parameters for each nation were suggested as factors for time-shifting and time-scaling to define reduced time, which was used to quantify the degree of universal similarities among nations. After the cumulative confirmed case and death profiles of a nation were transformed by using reduced time, most of the 19 nations, with few exceptions, had transformed profiles that closely converged to those of Italy after the onset of cases and deaths. The initial profiles of the cumulative confirmed cases per nation universally showed 3-4 week latency periods, during which the total number of cases remained at approximately ten. The latency period of the cumulative number of deaths was approximately half the latency number of cumulative cases, and subsequent uncontrollable increases in human deaths seemed unavoidable because the coronavirus had already widely spread. Immediate governmental actions, including responsive public-health policy-making and enforcement, are observed to be critical to minimize (and possibly stop) further infections and subsequent deaths. In the pandemic spread of infectious viral diseases, such as COVID-19 studied in this work, different nations show dissimilar and seemingly uncorrelated time series profiles of infected cases and deaths. After these statistical phenomena were viewed as identical events occurring at a distinct rate in each country, the reported algorithm of the data transformation using the reduced time revealed a nation-independent, universal profile (especially initial periods of the pandemic spread) from which a nation-specific, predictive estimation could be made and used to assist in immediate public-health policy-making.\n\nO_TEXTBOXResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSThe open data set were obtained from the website of the European Center for Disease Control and Prevention (ECDC). Although the data include the number of new cases and deaths per day per nation, extracting any apparent correlations between unique time-series of nations in different continents is challenging. Nevertheless, cumulative and non-cumulative statistics are, in principle, equivalent, and hence one can be obtained from the other. Because the non-cumulative profiles report instantaneous variations in the pandemic time series, estimation of future trends by extrapolating recent data is often intractable and limited to short-term extrapolations.\n\nAdded value of this studyA data transformation method for the cumulative confirmed cases (CCC) and cumulative confirmed deaths (CCD) was developed and used to directly compare the pandemic statuses of multiple nations, especially G20 nations. This model requires data for the nation with the greatest CCC and CCD (especially, during the initial burst of 90-120 days), which, in the case of the COVID-19 pandemic spread, is Italy. Two parameters for time-shifting (m) and time-scaling ({beta}) are newly introduced and used to define the reduced time{tau} . After the transformation, most nations cumulative profiles converge with those of Italy regardless of their geographical locations.\n\nImplications of all the available evidenceThe discovery of the universality of the transformed CCC and CCD profiles of multiple countries provides new insight into analyzing pandemic time series, including the current COVID-19 pandemic spread. By shifting and scaling a nations pandemic data into the reduced time frame, the nations CCC and CCD profiles can be predicted as long as the reference countrys cumulative data are available in the linear time domain. After the extraction of meaningful information from the transformed data, the overall implication is that most nations will reach the same state as Italys current state soon, depending on a specific nations population and human dynamics.\n\nC_TEXTBOX", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Albert S Kim", - "author_inst": "University of Hawaii at Manoa" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.06.11.20128793", "rel_title": "Optimal size of sample pooling for RNA pool testing: an avant-garde for scaling up SARS CoV 2 testing", @@ -1403354,6 +1401942,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.12.20129791", + "rel_title": "Dynamics of psychological responses to Covid-19 in India: A longitudinal study", + "rel_date": "2020-06-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.12.20129791", + "rel_abs": "To curb the spread of the novel coronavirus, India announced a nationwide lockdown on 24th March 2020 for 21 days, later extended for a longer time. This long period of lockdown greatly disrupted routine life and likely affecting citizens psychological well-being. The psychological toll of the pandemic on Indians is documented. However, no study has assessed whether the psychological toll changed over time due to repeated extensions of the lockdown. We followed up 159 Indian adults during the first two months of the lockdown to assess any change in their anxiety, stress, and depressive symptoms. Multilevel linear regression models of repeated observations nested within individuals, adjusted for socio-demographic covariates, showed that anxiety ({beta}=0.81, CI: 0.03, 1.60), stress ({beta}=0.51, CI: 0.32, 0.70), and depressive symptoms ({beta}=0.37, CI: 0.13, 0.60) increased over time during the lockdown. This increase was higher among women than men independent of covariates. Individual resilience was negatively associated with the psychological outcomes. This suggests that the state needs to address the current mental health impacts of a long-drawn out lockdown and its long-term sequelae. Disproportionate burden on women needs immediate attention. Sustainable change requires addressing the root causes driving the gender inequalities in psychological distress during such crises.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Anvita Gopal", + "author_inst": "Indian Institute of Technology Gandhinagar" + }, + { + "author_name": "Anupam Joya Sharma", + "author_inst": "IIT Gandhinagar" + }, + { + "author_name": "Malavika Ambale Subramanyam", + "author_inst": "IIT Gandhinagar" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.06.12.20129650", "rel_title": "Burnout among healthcare professionals during COVID-19 pandemic: a cross-sectional study", @@ -1403650,29 +1402265,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.09.20120139", - "rel_title": "Prevalence and Predictors of General Psychiatric Disorders and Loneliness during COVID-19 in the United Kingdom: Results from the Understanding Society UKHLS", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.09.20120139", - "rel_abs": "Despite ample research on the prevalence of specific psychiatric disorders during COVID-19, we know little about how the pandemic affects the general wellbeing of a wider population. The study investigates the prevalence and predictors of general psychiatric disorders measured by the 12-item General Health Questionnaire (GHQ-12) and frequency of loneliness during COVID-19 in the United Kingdom, a country heavily hit by the pandemic. We analyzed 15,530 respondents of the first large-scale, nationally representative survey of COVID-19 in a developed country, the first wave of Understanding Society COVID-19 Study. Results show that 29.2% of the respondents score 4 or more, the caseness threshold, on the general psychiatric disorder measure, and 35.86% of the respondents sometimes or often feel lonely. Regression analyses show that those who have or had COVID-19-related symptoms are more likely to develop general psychiatric disorders and are lonelier. Women and people in their 20s have higher risks of general psychiatric disorders and loneliness, while having a job and living with a partner are protective factors. This study showcases the general psychiatric disorders and loneliness of broader members of the society during COVID-19 and the underlying social disparities.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Lambert Zixin Li", - "author_inst": "Stanford University" - }, - { - "author_name": "Senhu Wang", - "author_inst": "University of Cambridge" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.06.10.20084715", "rel_title": "Estimating the COVID-19 epidemic trajectory and hospital capacity requirements in South West England: a mathematical modelling framework", @@ -1404744,6 +1403336,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.09.20126573", + "rel_title": "Retarded logistic equation as a universal dynamic model for the spread of COVID-19", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.09.20126573", + "rel_abs": "In this work we propose the retarded logistic equation as a dynamic model for the spread of COVID-19 all over the world. This equation accounts for asymptomatic transmission, pre-symptomatic or latent transmission as well as contact tracing and isolation, and leads to a transparent definition of the instantaneous reproduction number R. For different parameter values, the model equation admits different classes of solutions. These solution classes correspond to, inter alia, containment of the outbreak via public health measures, exponential growth despite public health measures, containment despite reopening and second wave following reopening. We believe that the spread of COVID in every localized area such as a city, district or county can be accounted for by one of our solution classes. In regions where R > 1 initially despite aggressive epidemic management efforts, we find that if the mitigation measures are sustained, then it is still possible for R to dip below unity when far less than the regions entire population is affected, and from that point onwards the outbreak can be driven to extinction in time. We call this phenomenon partial herd immunity. Our analysis indicates that COVID-19 is an extremely vicious and unpredictable disease which poses unique challenges for public health authorities, on account of which \"case races\" among various countries and states do not serve any purpose and present delusive appearances while ignoring significant determinants.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "B Shayak", + "author_inst": "Cornell University" + }, + { + "author_name": "Mohit M Sharma", + "author_inst": "Weill Cornell Medicine" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.11.20091322", "rel_title": "A study on the appropriate use of topdown approachfor stepping up economic activities in districts ofdifferent States/Union Territories in India", @@ -1405032,61 +1403647,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.10.20127266", - "rel_title": "Resource requirements for reintroducing elective surgery in England during the COVID-19 pandemic: a modelling study", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.10.20127266", - "rel_abs": "BackgroundThe response to COVID-19 has required cancellation of all but the most urgent surgeries, including many cancer operations. We estimated the number of cancelled surgical procedures in the National Health Service (NHS) in England due to COVID-19 and how this deficit would change over time once elective surgery was reintroduced.\n\nMethodsModelling study using Hospital Episode Statistics (HES) data from 2014 to 2019. Using NHS England definitions, surgical procedures were grouped into four classes of urgency. We calculated time-weighted average numbers of surgical procedures from 1st March 2020 and extrapolated to 28th February 2021 informed by activity in previous years. We estimated the procedure deficit using multiple conservative assumptions and then modelled the reintroduction of elective surgery between 1st June 2020 and 28th February 2021, estimating the resources required to achieve this. Costs of surgery were calculated using NHS reference costs. Estimates are reported with 95% confidence intervals.\n\nFindings4,547,534 (3,318,195 - 6,250,771) patients with pooled mean age of 53.5 years were expected to undergo surgery in the NHS in England between 1st March 2020 and 28th February 2021. Due to COVID-19, 749,248 (513,565 - 1,077,448) surgical procedures were cancelled by 31st May 2020. As current guidelines require a gradual reintroduction of elective surgery, this deficit will increase further and 2,270,178 (1,453,057 - 3,363,472) patients will be awaiting surgery by 28th February 2021. The cost of these delayed procedures is {pound}4,688,318,443 ({pound}2,726,364,240 - {pound}7,070,166,056). However, the safe delivery of surgery during the pandemic will require substantial extra resources including personal protective equipment and universal preoperative screening, leading to additional costs of {pound}606,252,901 ({pound}521,159,931 - {pound}730,720,808).\n\nInterpretationReintroduction of elective surgery during the pandemic response in NHS England will be associated with substantial treatment delays for many patients, and a large increase in treatment costs.\n\nFundingNIHR (DRF-2018-11-ST2-062) to AJF.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Alexander J Fowler", - "author_inst": "William Harvey Research Institute, Queen Mary, University of London, UK" - }, - { - "author_name": "Tom D Dobbs", - "author_inst": "Reconstructive Surgery & Regenerative Medicine Research Group, Institute of Life Sciences, Swansea University Medical School, Swansea, UK" - }, - { - "author_name": "Yize I Wan", - "author_inst": "William Harvey Research Institute, Queen Mary University of London, UK." - }, - { - "author_name": "Ryan Laloo", - "author_inst": "Leeds Vascular Institute, Leeds General Infirmary, UK" - }, - { - "author_name": "Sarah Hui", - "author_inst": "William Harvey Research Institute, Queen Mary University of London, UK" - }, - { - "author_name": "Dmitri Nepogodiev", - "author_inst": "Academic Department of Surgery, University of Birmingham, UK" - }, - { - "author_name": "Aneel Bhangu", - "author_inst": "Academic Department of Surgery, University of Birmingham, UK" - }, - { - "author_name": "Iain Whitaker", - "author_inst": "Reconstructive Surgery & Regenerative Medicine Research Group, Institute of Life Sciences, Swansea University Medical School, Swansea, UK" - }, - { - "author_name": "Rupert M Pearse", - "author_inst": "William Harvey Research Institute, Queen Mary University of London, UK." - }, - { - "author_name": "Tom EF Abbott", - "author_inst": "William Harvey Research Institute, Queen Mary University of London, UK" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "surgery" - }, { "rel_doi": "10.1101/2020.06.10.20127290", "rel_title": "Priority Setting of Ventilators in the COVID-19 Pandemic from the public's perspective", @@ -1406158,6 +1404718,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.10.20127837", + "rel_title": "Persistent SARS-CoV-2 replication in severe COVID-19", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.10.20127837", + "rel_abs": "BackgroundThe diagnosis of SARS-CoV-2 infection is based on viral RNA detection by real-time RT-PCR (rRT-PCR) in respiratory samples. This detection can remain positive for weeks without implying virus viability.\n\nMethodsWe have performed cell culture to assess viral replication in 106 respiratory samples rRT-PCR positive for SARS-CoV-2 from 105 patients with COVID-19. Fifty were samples from 50 patients with mild forms of COVID-19 who did not require hospital admission. Fifty-six samples were obtained from 55 hospitalized patients with severe pneumonia. Samples were obtained at different time points covering the time from clinical diagnosis to the follow up during hospital care.\n\nResultsIn 49 samples (49/106, 46.2%) a cytopathic effect (CPE) was detected in cell culture. Our study demonstrates that while in patients with mild COVID-19, viral viability is maintained in fact up to 10 days in patients with severe COVID-19 the virus can remain viable for up to 32 days after the onset of symptoms. Patients with severe COVID-19 as compared with mild cases, presented infective virus in a significantly higher proportion in samples with moderate or low viral load (Ct value > 26): 22/46 (47.8%) versus 7/38 (18.4%), (p <0.01), respectively.\n\nConclusionsPersistent SARS-CoV-2 replication could be demonstrated in severe COVID-19 cases for periods up to 32 days after the onset of symptoms and even at high Ct values. COVID-19 severity is a more determining factor for viral viability than the time elapsed since the onset of symptoms or the Ct value obtained in the RT-PCR assay.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Maria Dolores Folgueira", + "author_inst": "Hospital Universitario 12 de Octubre" + }, + { + "author_name": "Joanna Luczkowiak", + "author_inst": "Instituto de Investigacion Hospital 12 de Octubre" + }, + { + "author_name": "Fatima Lasala", + "author_inst": "Instituto de Investigacion Hospital 12 de Octubre" + }, + { + "author_name": "Alfredo Perez-Rivilla", + "author_inst": "Hospital Universitario 12 de Octubre" + }, + { + "author_name": "Rafael Delgado", + "author_inst": "Hospital Universitario 12 de Octubre" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.08.20125369", "rel_title": "First Clinical Use of Lenzilumab to Neutralize GM-CSF in Patients with Severe and Critical COVID-19 Pneumonia", @@ -1406590,45 +1405185,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.10.20127589", - "rel_title": "Effect of social distancing on COVID-19 incidence and mortality in the US", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.10.20127589", - "rel_abs": "Social distancing policies were implemented in most US states as a containment strategy against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The effectiveness of these policy interventions on morbidity and mortality remains unknown. Our analysis examined the associations between statewide policies and objective measures of social distancing, and objective social distancing and COVID-19 incidence and mortality. We used nationwide, de-identified smartphone GPS data to estimate county-level social distancing. COVID-19 incidence and mortality data were from the Johns Hopkins Coronavirus Resource Center. Generalized linear mixed models were used to estimate incidence rate ratios (IRRs) and 95% confidence intervals (CIs) for the association between objective social distancing and COVID-19 incidence and mortality. Stay-at-home orders were associated with a 35% increase in social distancing. Higher social distancing was associated with a 29% reduction in COVID-19 incidence (adjusted IRR 0.71; 95% CI 0.57-0.87) and a 35% reduction in COVID-19 mortality (adjusted IRR 0.65; 95% CI 0.55-0.76). These findings provide evidence to inform ongoing national discussions on the effectiveness of these public health measures and the potential implications of returning to normal social activity.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Trang VoPham", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Matthew D Weaver", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Jaime E Hart", - "author_inst": "Harvard Medical School" - }, - { - "author_name": "Mimi Ton", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Emily White", - "author_inst": "Fred Hutchinson Cancer Research Center" - }, - { - "author_name": "Polly A Newcomb", - "author_inst": "Fred Hutchinson Cancer Research Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.10.20127795", "rel_title": "On the increasing role of older adolescents and younger adults during the SARSCoV2 epidemic in Mexico, April 20 to May 24, 2020", @@ -1407536,6 +1406092,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2020.06.11.20128132", + "rel_title": "The curvilinear relationship between the age of adults and their mental health in Iran after its peak of COVID-19 cases", + "rel_date": "2020-06-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20128132", + "rel_abs": "The emerging body of research on the predictors of mental health in the COVID-19 pandemic has revealed contradictory findings, which prevent effective psychiatry screening for mental health assistance. This study aims to identify the predictors of nonsomatic pain, depression, anxiety, and distress, especially focusing on age as a nonlinear predictor. We conducted a survey of 474 adults in Iran during April 1-10, 2020, when Iran had just passed its first peak of the COVID-19 pandemic with new confirmed cases. We found that Age had a curvilinear relationship with nonsomatic pain, depression, and anxiety. Age was associated with pain, depression, and anxiety disorders negatively among adults younger than 45 years, but positively among seniors older than 70 years. Adults who were female, unsure about their chronic diseases, and exercised less per day were more likely to have mental health issues. This study advances the use of age as an effective predictor by uncovering a curvilinear relationship between individuals age and mental health issues by using a sample of adults across a wide spectrum of ages. We hope future research on mental health during COVID-19 pays more attention to nonlinear predictors.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Jiyao Chen", + "author_inst": "Oregon State University" + }, + { + "author_name": "Stephen X. Zhang", + "author_inst": "University of Adelaide" + }, + { + "author_name": "Yifei Wang", + "author_inst": "Tongji University" + }, + { + "author_name": "Asghar Afshar Jahanshahi", + "author_inst": "Pontificia Universidad Catolica del Peru" + }, + { + "author_name": "Maryam Mokhtari Dinani", + "author_inst": "Alzahra University" + }, + { + "author_name": "Abbas Nazarian Madavani", + "author_inst": "Shahid Rajaee Teacher Training University" + }, + { + "author_name": "Khaled Nawaser", + "author_inst": "Arvandan Non-profit Higher Education Institute" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.06.11.20127936", "rel_title": "Corona Virus Disease 2019 (COVID-19): Knowledge, attitudes, practices (KAP) and misconceptions in the general population of Katsina State, Nigeria", @@ -1407952,41 +1406551,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.11.20128165", - "rel_title": "Easing social distancing index after COVID-19 pandemic", - "rel_date": "2020-06-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.11.20128165", - "rel_abs": "ContextEasing social distancing (ESD) is a global public health issue in post-pandemic period of COVID-19 and requires a simple index for real time assessment.\n\nObjectiveWe aimed to develop a simple index for ESD to quantify the impacts of social distancing for reducing confirmed infected cases, optimal triage and care of patients for recovery, and critical care capacity for reducing death from COVID-19.\n\nDesign, Setting, and ParticipantsData on the retrospective cohort of 185 countries with reported numbers on confirmed cases, recovery, and death from COVID-19 were retrieved from publicity available repository. Up to May 31, a total of 5,844,136 confirmed cases, 2,639,961 recovered, and 327,487 deaths were reported globally.\n\nMain Outcome MeasuresThe ESD index measured by cumulative number of COVID-19 cases and recovery and case-fatality rate.\n\nResultsWe developed a simple index for the guidance of easing social distancing (ESD). If the ESD index is less than 1, ESD would be considered. The global ESD index declined from 3.87 at peak in March to 1.35 by the end of May, consisting of 56.76% countries/regions (105/185) with the ESD lower than one.\n\nConclusion and RelevanceThis simple ESD index provides a quantitative assessment on whether and when to ease social distancing from local to global community.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Li-Sheng Chen", - "author_inst": "School of Oral Hygiene, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan" - }, - { - "author_name": "Ming-Fang Yen", - "author_inst": "School of Oral Hygiene, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan" - }, - { - "author_name": "Chao-Chih Lai", - "author_inst": "Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan; Emergency Department of Taipei City Hos" - }, - { - "author_name": "Chen-Yang Hsu", - "author_inst": "Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan; Dachung Hospital, Miaoli, Taiwan" - }, - { - "author_name": "Hsiu-Hsi Chen", - "author_inst": "Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei, Taiwan" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.11.20127993", "rel_title": "Reusable Gowns for routine use in hospital and laboratory: a necessity arising of COVID-19 Pandemic", @@ -1409406,6 +1407970,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.06.12.148692", + "rel_title": "Structural basis for potent neutralization of SARS-CoV-2 and role of antibody affinity maturation", + "rel_date": "2020-06-12", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.12.148692", + "rel_abs": "SARS-CoV-2 is a betacoronavirus virus responsible for the COVID-19 pandemic. Here, we determined the X-ray crystal structure of a potent neutralizing monoclonal antibody, CV30, isolated from a patient infected with SARS-CoV-2, in complex with the receptor binding domain (RBD). The structure reveals CV30s epitope overlaps with the human ACE2 receptor binding site thus providing the structural basis for its neutralization by preventing ACE2 binding.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Nicholas K Hurlburt", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Yu-Hsin Wan", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Andrew B Stuart", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Junli Feng", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Andrew T McGuire", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Leonidas Stamatatos", + "author_inst": "Fred Hutchinson Cancer Research Center" + }, + { + "author_name": "Marie Pancera", + "author_inst": "Fred Hutchinson Cancer Research Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.06.12.148726", "rel_title": "The D614G mutation in the SARS-CoV-2 spike protein reduces S1 shedding and increases infectivity", @@ -1409926,53 +1408533,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, - { - "rel_doi": "10.1101/2020.06.10.20127258", - "rel_title": "Knowledge, attitudes, and practices among the general population during COVID-19 outbreak in Iran: A national cross-sectional survey", - "rel_date": "2020-06-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.10.20127258", - "rel_abs": "BackgroundCOVID-19, which emerged in December 2019, is the largest pandemic ever to occur. During the early phase, little was known about public awareness relating to Coronavirus disease. This study was designed to determine knowledge, attitudes and practices (KAP) among the Iranian public towards COVID-19.\n\nMethodsA cross-sectional online survey was carried out in Iran from 2 March to 8 April 2020 using a self-administered questionnaire on 1,480 people. COVID-19-related KAP questions were adapted from other internationally validated questionnaires specific to infectious diseases.\n\nResultsAll participants were aware of COVID-19. When asked unprompted, 80% of respondents could correctly cite fever, difficulty breathing and cough as signs/symptoms of COVID-19. Most of our sample population knew that by staying at home and staying isolated (95.3%, 95 % CI: 94.2-96.3) as well as constant hand washing and using disinfectants (92.5%, 95 % CI: 91.1-93.8) could prevent COVID-19. However, there was also widespread misconceptions such as the belief that COVID-19 can be transmitted by wild animals (58%, 95 % CI: 55.5-60.5) and by air (48.3%, 95 % CI: 45.7-50.8). Unprompted, self-reported actions taken to avoid COVID-19 infection included hand washing with soap and water (95.4%, 95 % CI: 94.3-96.4), avoiding crowded places (93%, 95 % CI: 91.7-94.3), cleaning hands with other disinfectants (80.9 %, 95 % CI: 78.9-82.9), and covering mouths and noses when coughing and sneezing (76.1 %, 95 % CI: 73.9-78.2). The internet and social media (94.5%, 95 % CI: 93.3-95.6) were the main Coronavirus information sources. However, the most trusted information sources on Coronavirus were health and medical professionals (79.3%, 95 % CI: 77.2-81.3). The majority of participants (77.0%, 95 % CI: 74.8-79.1) wanted more information about Coronavirus to be available.\n\nConclusionOur findings suggest that peoples knowledge and attitude towards COVID-19 at the time of its outbreak was of a high level. Therefore, health systems should use multiple ways, such as mass media, phone applications, electronic, print, and tele-education to increase KAP related to COVID-19.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Edris Kakemam", - "author_inst": "Tabriz University of Medical Sciences" - }, - { - "author_name": "DJavad Ghoddoosi-Nejad", - "author_inst": "Birjand University of Medical Sciences" - }, - { - "author_name": "Zahra Chegini", - "author_inst": "Qazvin University of Medical Sciences" - }, - { - "author_name": "Khalil Momeni", - "author_inst": "Ilam University of Medical Sciences" - }, - { - "author_name": "Hamid Salehinia", - "author_inst": "Birjand University of Medical sciences" - }, - { - "author_name": "Soheil Hassanipour", - "author_inst": "Guilan University of Medical Sciences" - }, - { - "author_name": "Hosein Ameri", - "author_inst": "Shahid Sadoughi University of Medical Sciences" - }, - { - "author_name": "Morteza Arab-Zozani", - "author_inst": "Birjand University of Medical Sciences" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "medical education" - }, { "rel_doi": "10.1101/2020.06.09.20126722", "rel_title": "Work-related and Personal Factors Associated with Mental Well-being during COVID-19 Response: A Survey of Health Care and Other Workers", @@ -1411088,6 +1409648,165 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.09.20126813", + "rel_title": "Population-scale Longitudinal Mapping of COVID-19 Symptoms, Behavior, and Testing Identifies Contributors to Continued Disease Spread in the United States", + "rel_date": "2020-06-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.09.20126813", + "rel_abs": "Summary ParagraphDespite social distancing and shelter-in-place policies, COVID-19 continues to spread in the United States. A lack of timely information about factors influencing COVID-19 spread and testing has hampered agile responses to the pandemic. We developed How We Feel, an extensible web and mobile application that aggregates self-reported survey responses, to fill gaps in the collection of COVID-19-related data. How We Feel collects longitudinal and geographically localized information on users health, behavior, and demographics. Here we report results from over 500,000 users in the United States from April 2, 2020 to May 12, 2020. We show that self-reported surveys can be used to build predictive models of COVID-19 test results, which may aid in identification of likely COVID-19 positive individuals. We find evidence among our users for asymptomatic or presymptomatic presentation, as well as for household and community exposure, occupation, and demographics being strong risk factors for COVID-19. We further reveal factors for which users have been SARS-CoV-2 PCR tested, as well as the temporal dynamics of self-reported symptoms and self-isolation behavior in positive and negative users. These results highlight the utility of collecting a diverse set of symptomatic, demographic, and behavioral self-reported data to fight the COVID-19 pandemic.", + "rel_num_authors": 36, + "rel_authors": [ + { + "author_name": "William E Allen", + "author_inst": "Harvard University" + }, + { + "author_name": "Han Altae-Tran", + "author_inst": "MIT" + }, + { + "author_name": "James Briggs", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Xin Jin", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Glen McGee", + "author_inst": "Harvard University" + }, + { + "author_name": "Rumya Raghavan", + "author_inst": "Broad Institute of MIT and Harvard" + }, + { + "author_name": "Andy Shi", + "author_inst": "Harvard University" + }, + { + "author_name": "Mireille Kamariza", + "author_inst": "Harvard University" + }, + { + "author_name": "Nicole Nova", + "author_inst": "Stanford University" + }, + { + "author_name": "Albert Pereta", + "author_inst": "The How We Feel Project" + }, + { + "author_name": "Chris Danford", + "author_inst": "The How We Feel Project" + }, + { + "author_name": "Amine Kamel", + "author_inst": "The How We Feel Project" + }, + { + "author_name": "Patrik Gothe", + "author_inst": "The How We Feel Project" + }, + { + "author_name": "Evrhet Milam", + "author_inst": "The How We Feel Project" + }, + { + "author_name": "Jean Aurambault", + "author_inst": "The How We Feel Project" + }, + { + "author_name": "Thorben Primke", + "author_inst": "The How We Feel Project" + }, + { + "author_name": "Claire Li", + "author_inst": "The How We Feel Project" + }, + { + "author_name": "Josh Inkenbrandt", + "author_inst": "The How We Feel Project" + }, + { + "author_name": "Tuan Huynh", + "author_inst": "The How We Feel Project" + }, + { + "author_name": "Evan Chen", + "author_inst": "The How We Feel Project" + }, + { + "author_name": "Christina Lee", + "author_inst": "The How We Feel Project" + }, + { + "author_name": "Michael Croatto", + "author_inst": "The How We Feel Project" + }, + { + "author_name": "Helen Bentley", + "author_inst": "The How We Feel Project" + }, + { + "author_name": "Wendy Lu", + "author_inst": "The How We Feel Project" + }, + { + "author_name": "Robert Murray", + "author_inst": "The How We Feel Project" + }, + { + "author_name": "Mark Travassos", + "author_inst": "University of Maryland School of Medicine" + }, + { + "author_name": "John Openshaw", + "author_inst": "Stanford University" + }, + { + "author_name": "Brent Coull", + "author_inst": "Harvard University" + }, + { + "author_name": "Casey Greene", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Ophir Shalem", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Gary King", + "author_inst": "Harvard University" + }, + { + "author_name": "Ryan Probasco", + "author_inst": "The How We Feel Project" + }, + { + "author_name": "David Cheng", + "author_inst": "The How We Feel Project" + }, + { + "author_name": "Ben Silbermann", + "author_inst": "The How We Feel Project" + }, + { + "author_name": "Feng Zhang", + "author_inst": "MIT" + }, + { + "author_name": "Xihong Lin", + "author_inst": "Harvard University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.09.20126292", "rel_title": "COVID-19 and associations with frailty and multimorbidity: a prospective analysis of UK Biobank participants", @@ -1411392,49 +1410111,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.06.11.140285", - "rel_title": "ROBOCOV: An affordable open-source robotic platform for COVID-19 testing by RT-qPCR", - "rel_date": "2020-06-11", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.11.140285", - "rel_abs": "Current global pandemic due to the SARS-CoV-2 has struggled and pushed the limits of global health systems. Supply chain disruptions and scarce availability of commercial laboratory reagents have motivated worldwide actors to search for alternative workflows to cope with the demand.\n\nWe have used the OT-2 open-source liquid-handling robots (Opentrons, NY), RNA extraction and RT-qPCR reagents to set-up a reproducible workflow for RT-qPCR SARS-CoV-2 testing. We developed a framework with a template and several functions and classes that allow the creation of customized RT-qPCR automated circuits. As a proof of concept, we provide data obtained by a fully-functional tested code using the MagMax Pathogen RNA/DNA kit and the MagMax Viral/Pathogen II kit (Thermo Fisher Scientific, MA) on the Kingfisher Flex instrument (Thermo Fisher Scientific, MA). With these codes available is easy to create new stations or circuits from scratch, adapt existing ones to changes in the experimental protocol, or perform fine adjustments to fulfil special needs.\n\nThe affordability of this platform makes it accessible for most laboratories and hospitals with a bioinformatician, democratising automated SARS-CoV-2 PCR testing and increasing, temporarily or not, the capacity of carrying out tests. It also confers flexibility, as this platform is not dependant on any particular commercial kit and can be quickly adapted to protocol changes or other special needs.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Jos\u00e9 Luis Villanueva-Ca\u00f1as", - "author_inst": "Hospital Cl\u00ednic de Barcelona" - }, - { - "author_name": "Eva Gonzalez-Roca", - "author_inst": "Hospital Cl\u00ednic de Barcelona" - }, - { - "author_name": "Aitor Gastaminza Unanue", - "author_inst": "Independent engineer" - }, - { - "author_name": "Esther Titos", - "author_inst": "Hospital Cl\u00ednic de Barcelona" - }, - { - "author_name": "Miguel Juli\u00e1n Mart\u00ednez Yoldi", - "author_inst": "Hospital Cl\u00ednic de Barcelona" - }, - { - "author_name": "Andrea Vergara G\u00f3mez", - "author_inst": "Hospital Cl\u00ednic de Barcelona" - }, - { - "author_name": "Joan Ant\u00f3n Puig Butill\u00e9", - "author_inst": "Hospital Cl\u00ednic de Barcelona" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.06.11.146522", "rel_title": "Shielding and Beyond: The Roles of Glycans in SARS-CoV-2 Spike Protein", @@ -1412818,6 +1411494,53 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.06.09.142125", + "rel_title": "Unravelling the debate on heme effects in COVID-19 infections", + "rel_date": "2020-06-10", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.09.142125", + "rel_abs": "The SARS-CoV-2 outbreak was recently declared a worldwide pandemic. Infection triggers the respiratory tract disease COVID-19, which is accompanied by serious changes of clinical biomarkers such as hemoglobin and interleukins. The same parameters are altered during hemolysis, which is characterized by an increase in labile heme. We present two approaches that aim at analyzing a potential link between available heme and COVID-19 pathogenesis. Four COVID-19 related proteins, i.e. the host cell proteins ACE2 and TMPRSS2 as well as the viral protein 7a and S protein, were identified as potential heme binders. We also performed a detailed analysis of the common pathways induced by heme and SARS-CoV-2 by superimposition of knowledge graphs covering heme biology and COVID-19 pathophysiology. Herein, focus was laid on inflammatory pathways, and distinct biomarkers as the linking elements. Finally, the results substantially improve our understanding of COVID-19 infections and disease progression of patients with different clinical backgrounds and expand the diagnostic and treatment options.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Marie-Therese Hopp", + "author_inst": "Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn" + }, + { + "author_name": "Daniel Domingo-Fernandez", + "author_inst": "Fraunhofer SCAI" + }, + { + "author_name": "Yojana Gadiya", + "author_inst": "Fraunhofer Institute for Algorithms and Scientific Computing" + }, + { + "author_name": "Milena S Detzel", + "author_inst": "Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn" + }, + { + "author_name": "Benjamin F Schmalohr", + "author_inst": "Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn" + }, + { + "author_name": "Francel Steinbock", + "author_inst": "Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn" + }, + { + "author_name": "Diana Imhof", + "author_inst": "Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn" + }, + { + "author_name": "Martin Hofmann-Apitius", + "author_inst": "Fraunhofer SCAI" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.06.09.143271", "rel_title": "Differential expression of COVID-19-related genes in European Americans and African Americans", @@ -1413206,41 +1411929,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.08.20125062", - "rel_title": "Principles and Practice of SARS-CoV-2 Decontamination of N95 Masks with UV-C", - "rel_date": "2020-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20125062", - "rel_abs": "A mainstay of personal protective equipment (PPE) during the COVID-19 pandemic is the N95 filtering facepiece respirator. N95 respirators are commonly used to protect healthcare workers from respiratory pathogens, including the novel coronavirus SARS-CoV-2, and are increasingly employed by other frontline workers and the general public. Under routine circumstances, these masks are disposable, single-use items, but extended use and reuse practices have been broadly enacted to alleviate critical supply shortages during the COVID-19 pandemic. While extended-time single use presents a low risk of pathogen transfer, repeated donning and doffing of potentially contaminated masks presents increased risk of pathogen transfer. Therefore, efficient and safe decontamination methods for N95 masks are needed to reduce the risk of reuse and mitigate local supply shortages. Here we review the available literature concerning use of germicidal ultraviolet-C (UV-C) light to decontaminate N95 masks. We propose a practical method for repeated point-of-use decontamination using commercially-available UV-C crosslinker boxes from molecular biology laboratories to expose each side of the mask to 800-1200 mJ/cm2 of UV-C. We measure the dose that penetrated to the interior of the respirators and model the potential germicidal action on SARS-CoV-2. Our experimental results, in combination with modeled data, suggest that a two-minute UV-C treatment cycle should induce a >3-log-order reduction in viral bioburden on the surface of the respirators, and a 2-log order reduction throughout the interior. The resulting exposure is 100-fold less than the dose expected to damage the masks, facilitating repeated decontamination. As such, UV-C germicidal irradiation (UVGI) is a practical strategy for small-scale point-of-use decontamination of N95s.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Thomas Huber", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Olivia Goldman", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Alexander E. Epstein", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Gianna Stella", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Thomas P. Sakmar", - "author_inst": "Rockefeller University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.07.20124859", "rel_title": "Impact of Timing of and Adherence to Social Distancing Measures on COVID-19 Burden in the US: A Simulation Modeling Approach", @@ -1414636,6 +1413324,89 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.06.08.139329", + "rel_title": "The hypothalamus as a hub for putative SARS-CoV-2 brain infection", + "rel_date": "2020-06-09", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.08.139329", + "rel_abs": "Most patients with COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), display neurological symptoms, and respiratory failure in certain cases could be of extra-pulmonary origin. Hypothalamic neural circuits play key roles in sex differences, diabetes, hypertension, obesity and aging, all risk factors for severe COVID-19, besides being connected to olfactory/gustative and brainstem cardiorespiratory centers. Here, human brain gene-expression analyses and immunohistochemistry reveal that the hypothalamus and associated regions express angiotensin-converting enzyme 2 and transmembrane proteinase, serine 2, which mediate SARS-CoV-2 cellular entry, in correlation with genes or pathways involved in physiological functions or viral pathogenesis. A post-mortem patient brain shows viral invasion and replication in both the olfactory bulb and the hypothalamus, while animal studies indicate that sex hormones and metabolic diseases influence this susceptibility.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Sreekala Nampoothiri", + "author_inst": "Inserm UMR-S 1172" + }, + { + "author_name": "Florent Sauve", + "author_inst": "Inserm UMR-S 1172" + }, + { + "author_name": "Gaetan Ternier", + "author_inst": "Inserm UMR-S 1172" + }, + { + "author_name": "Daniela Fernandois", + "author_inst": "Inserm UMR-S 1172" + }, + { + "author_name": "Caio Coelho", + "author_inst": "Inserm UMR-S 1172" + }, + { + "author_name": "Monica Imbernon", + "author_inst": "Inserm UMR-S 1172" + }, + { + "author_name": "Eleonora Deligia", + "author_inst": "Inserm UMR-S 1172" + }, + { + "author_name": "Romain Perbet", + "author_inst": "Inserm UMR-S 1172" + }, + { + "author_name": "Vincent Florent", + "author_inst": "Inserm UMR-S 1172" + }, + { + "author_name": "Marc Baroncini", + "author_inst": "Inserm UMR-S 1172" + }, + { + "author_name": "Florence Pasquier", + "author_inst": "Inserm UMR-S 1172" + }, + { + "author_name": "Francois Trottein", + "author_inst": "Institut Pasteur de Lille" + }, + { + "author_name": "Claude-Alain Maurage", + "author_inst": "Inserm UMR-S 1172" + }, + { + "author_name": "Virginie Mattot", + "author_inst": "Inserm UMR-S 1172" + }, + { + "author_name": "Paolo Giacobini", + "author_inst": "Inserm UMR-S 1172" + }, + { + "author_name": "S. Rasika", + "author_inst": "Inserm UMR-S 1172" + }, + { + "author_name": "Vincent Prevot", + "author_inst": "Inserm UMR-S 1172" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "neuroscience" + }, { "rel_doi": "10.1101/2020.06.08.107011", "rel_title": "Molecular modelling predicts SARS-CoV-2 ORF8 protein and human complement Factor 1 catalytic domain sharing common binding site on complement C3b", @@ -1415139,81 +1413910,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.06.07.20121939", - "rel_title": "Mortality Analysis of COVID-19 Confirmed cases in Pakistan", - "rel_date": "2020-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.07.20121939", - "rel_abs": "IntroductionCOVID-19, a novel disease, appeared in December 2019 in China and rapidly spread across the world. Till second week of April 2020, high incidence (2.9/100,000) and cases fatality rates (1.7%)was observed in Pakistan.\n\nThis study was conducted to determine temporal and spatial distribution of first 100 deaths attributed to COVID-19 in Pakistan and their associated demographic factors.\n\nMethodWe conducted a descriptive epidemiological analysis of first 100 deaths reported among RT-PCR confirmed COVID-19 cases. Demographic, epidemiological and risk factors information was obtained associated comorbidities and clinical signs and symptoms were recorded and frequencies were determined.\n\nResultsA total of 100 mortalities with overall Case Fatality Rate 1.67% (CFR) were analysed. Median age of patients was 64.5 years (IQR: 54-70) with 75% (n = 75) Males. Among all deaths reported, 71 (71%) cases had one or more documented comorbidities at the time of diagnosis. Most frequently reported co-morbidities were; hypertension (67 %), followed by Diabetes Mellitus 945%) and Ischemic Heart Diseases (27%). First death was reported on 18 March 2020 and the most frequent presenting symptoms were shortness of breath (87%) and fever (79%). Median duration of illness was eight days (IQR: 4-11 days), median delay reaching hospital to seek health care was three days (IQR: 0-6 days) while median duration of hospital stay was also three days (IQR: 1-7 days). Among all reported deaths, 62% were attributed to local transmission as these cases had no history of international travel. The most affected age group was 60-69 years while no death reported in age group below 20 years.\n\nConclusionHigh CFR among old age group and its association with co-morbidities (chronic disease) suggests targeted interventions such as social distancing and strict quarantine measure for elderly and morbid people. Comparative studies among deaths and recovered patients are recommended to explore further disease dynamics.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Ambreen Chaudhry", - "author_inst": "National Institute of Health" - }, - { - "author_name": "Aamer Ikram", - "author_inst": "National Institute of Health" - }, - { - "author_name": "Mirza Amir Baig", - "author_inst": "Field Epidemiology and Laboratory Training Program" - }, - { - "author_name": "Muhammad Salman", - "author_inst": "National Institute of Health" - }, - { - "author_name": "Tamkeen Ghafoor", - "author_inst": "Field Epidemiology and Laboratory Training Program" - }, - { - "author_name": "Zakir Hussain", - "author_inst": "Field Epidemiology and Laboratory Training Program" - }, - { - "author_name": "Mumtaz Ali Khan", - "author_inst": "National Institute of Health" - }, - { - "author_name": "Jamil Ahmad Ansari", - "author_inst": "National Institute of Health" - }, - { - "author_name": "Asif Syed", - "author_inst": "Field Epidemiology and Laboratory Training Program" - }, - { - "author_name": "Wasif Javed", - "author_inst": "Field Epidemiology and Laboratory Training Program" - }, - { - "author_name": "Ehsan Larik", - "author_inst": "Field Epidemiology and Laboratory Training Program" - }, - { - "author_name": "Muhammad Mohsan Wattoo", - "author_inst": "Field Epidemiology and Laboratory Training Program" - }, - { - "author_name": "Naveed Masood", - "author_inst": "Field Epidemiology and Laboratory Training" - }, - { - "author_name": "zeeshan Iqbal Baig", - "author_inst": "Field Epidemiology and Laboratory Training Program" - }, - { - "author_name": "Khurram Akram", - "author_inst": "Field Epidemiology and Laboratory Training Program" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.06.05.20094482", "rel_title": "Hospital practice in COVID-19 times: Perceptions of the midwifery interns in Peru", @@ -1416601,6 +1415297,101 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.08.20124792", + "rel_title": "Serological Analysis of New York City COVID19 Convalescent Plasma Donors", + "rel_date": "2020-06-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20124792", + "rel_abs": "The development of neutralizing antibodies (nAb) against SARS-CoV-2, following infection or vaccination, is likely to be critical for the development of sufficient population immunity to drive cessation of the COVID19 pandemic. A large number of serologic tests, platforms and methodologies are being employed to determine seroprevalence in populations to select convalescent plasmas for therapeutic trials, and to guide policies about reopening. However, tests have substantial variability in sensitivity and specificity, and their ability to quantitatively predict levels of nAb is unknown. We collected 370 unique donors enrolled in the New York Blood Center Convalescent Plasma Program between April and May of 2020. We measured levels of antibodies in convalescent plasma using commercially available SARS-CoV-2 detection tests and in-house ELISA assays and correlated serological measurements with nAb activity measured using pseudotyped virus particles, which offer the most informative assessment of antiviral activity of patient sera against viral infection. Our data show that a large proportion of convalescent plasma samples have modest antibody levels and that commercially available tests have varying degrees of accuracy in predicting nAb activity. We found the Ortho Anti-SARS-CoV-2 Total Ig and IgG high throughput serological assays (HTSAs), as well as the Abbott SARS-CoV-2 IgG assay, quantify levels of antibodies that strongly correlate with nAb assays and are consistent with gold-standard ELISA assay results. These findings provide immediate clinical relevance to serology results that can be equated to nAb activity and could serve as a valuable roadmap to guide the choice and interpretation of serological tests for SARS-CoV-2.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Larry L Luchsinger", + "author_inst": "New York Blood Center" + }, + { + "author_name": "Brett Ransegnola", + "author_inst": "New York Blood Center" + }, + { + "author_name": "Daniel Jin", + "author_inst": "New York Blood Center" + }, + { + "author_name": "Frauke Muecksch", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Yiska Weisblum", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Weili Bao", + "author_inst": "New York Blood Center" + }, + { + "author_name": "Parakkal Jovvian George", + "author_inst": "New York Blood Center" + }, + { + "author_name": "Marilis Rodriguez", + "author_inst": "New York Blood Center" + }, + { + "author_name": "Nancy Tricoche", + "author_inst": "New York Blood Center" + }, + { + "author_name": "Fabian Schmidt", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Chengjie Gao", + "author_inst": "New York Blood Center" + }, + { + "author_name": "Shabnam Jawahar", + "author_inst": "New York Blood Center" + }, + { + "author_name": "Mouli Pal", + "author_inst": "New York Blood Center" + }, + { + "author_name": "Emily Schnall", + "author_inst": "New York Blood Center" + }, + { + "author_name": "Huan Zhang", + "author_inst": "New York Blood Center" + }, + { + "author_name": "Donna Strauss", + "author_inst": "New York Blood Center" + }, + { + "author_name": "Karina Yazdanbakhsh", + "author_inst": "New York Blood Center" + }, + { + "author_name": "Christopher D Hillyer", + "author_inst": "New York Blood Center" + }, + { + "author_name": "Paul D Bieniasz", + "author_inst": "Rockefeller University" + }, + { + "author_name": "Theodora Hatziioannou", + "author_inst": "Rockefeller University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.08.20125245", "rel_title": "Effects of Tocilizumab on Mortality in Hospitalized Patients with COVID-19: A Multicenter Cohort Study", @@ -1416917,141 +1415708,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.08.20124305", - "rel_title": "Time-series plasma cell-free DNA analysis reveals disease severity of COVID-19 patients", - "rel_date": "2020-06-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.08.20124305", - "rel_abs": "Clinical symptoms of coronavirus disease 2019 (COVID-19) range from asymptomatic to severe pneumonia and death. Detection of individuals at high risk for critical condition is crucial for control of the disease. Herein, for the first time, we profiled and analyzed plasma cell-free DNA (cfDNA) of mild and severe COVID-19 patients. We found that in comparison between mild and severe COVID-19 patients, Interleukin-37 signaling was one of the most relevant pathways; top significantly altered genes included POTEH, FAM27C, SPATA48, which were mostly expressed in prostate and testis; adrenal glands, small intestines and liver were tissues presenting most differentially expressed genes. Our data thus revealed potential tissue involvement, provided insights into mechanism on COVID-19 progression, and highlighted utility of cfDNA as a noninvasive biomarker for disease severity inspections.\n\nOne Sentence SummaryCfDNA analysis in COVID-19 patients reveals severity-related tissue damage.", - "rel_num_authors": 30, - "rel_authors": [ - { - "author_name": "Xinping Chen", - "author_inst": "Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational M" - }, - { - "author_name": "Yu Lin", - "author_inst": "BGI-Shenzhen, Shenzhen, 518083, Guangdong, China" - }, - { - "author_name": "Tao Wu", - "author_inst": "Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational M" - }, - { - "author_name": "Jinjin Xu", - "author_inst": "BGI-Shenzhen, Shenzhen, 518083, Guangdong, China" - }, - { - "author_name": "Zhichao Ma", - "author_inst": "Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational M" - }, - { - "author_name": "Kun Sun", - "author_inst": "Shenzhen Bay Laboratory" - }, - { - "author_name": "Hui Li", - "author_inst": "Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational M" - }, - { - "author_name": "Yuxue Luo", - "author_inst": "BGI-Shenzhen, Shenzhen, 518083, Guangdong, China; School of Medicine, South China University of Technology, Guangzhou 510006, Guangdong, China" - }, - { - "author_name": "Chen Zhang", - "author_inst": "Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational M" - }, - { - "author_name": "Fang Chen", - "author_inst": "BGI-Shenzhen, Shenzhen, 518083, Guangdong, China" - }, - { - "author_name": "Jiao Wang", - "author_inst": "Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational M" - }, - { - "author_name": "Tingyu Kuo", - "author_inst": "BGI-Shenzhen, Shenzhen, 518083, Guangdong, China; BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, Guangdong, China" - }, - { - "author_name": "Xiaojuan Li", - "author_inst": "Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational M" - }, - { - "author_name": "Chunyu Geng", - "author_inst": "BGI-Shenzhen, Shenzhen, 518083, Guangdong, China" - }, - { - "author_name": "Feng Lin", - "author_inst": "Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational M" - }, - { - "author_name": "Chaojie Huang", - "author_inst": "BGI-Shenzhen, Shenzhen, 518083, Guangdong, China" - }, - { - "author_name": "Junjie Hu", - "author_inst": "Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational M" - }, - { - "author_name": "Jianhua Yin", - "author_inst": "BGI-Shenzhen, Shenzhen, 518083, Guangdong, China" - }, - { - "author_name": "Ming Liu", - "author_inst": "Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational M" - }, - { - "author_name": "Ye Tao", - "author_inst": "BGI-Shenzhen, Shenzhen, 518083, Guangdong, China" - }, - { - "author_name": "Jiye Zhang", - "author_inst": "Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational M" - }, - { - "author_name": "Rijing Ou", - "author_inst": "BGI-Shenzhen, Shenzhen, 518083, Guangdong, China" - }, - { - "author_name": "Furong Xiao", - "author_inst": "Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational M" - }, - { - "author_name": "Huanming Yang", - "author_inst": "BGI-Tianjin;Prince Aljawhra Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University" - }, - { - "author_name": "Jian Wang", - "author_inst": "BGI-Shenzhen, Shenzhen, 518083, Guangdong, China; James D. Watson Institute of Genome Sciences, Hangzhou 310058, China" - }, - { - "author_name": "Xun Xu", - "author_inst": "BGI-Shenzhen, Shenzhen, 518083, Guangdong, China; Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen, 518120, China" - }, - { - "author_name": "Shengmiao Fu", - "author_inst": "Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational M" - }, - { - "author_name": "Xin Jin", - "author_inst": "BGI-Shenzhen, Shenzhen, 518083, Guangdong, China; School of Medicine, South China University of Technology, Guangzhou 510006, Guangdong, China" - }, - { - "author_name": "Hongyan Jiang", - "author_inst": "Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Hainan Provincial Key Laboratory of Cell and Molecular Genetic Translational M" - }, - { - "author_name": "Ruoyan Chen", - "author_inst": "BGI-Shenzhen, Shenzhen, 518083, Guangdong, China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.07.20124966", "rel_title": "Covid-19 Incidence Rate Evolution Modeling using Dual Wave Gaussian-Lorentzian Composite Functions", @@ -1417871,6 +1416527,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.03.20120261", + "rel_title": "Association Between ACEIs or ARBs Use and Clinical Outcomes in COVID-19 Patients: A Systematic Review and Meta-analysis", + "rel_date": "2020-06-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.03.20120261", + "rel_abs": "ImportanceThere is a controversy regarding whether or not to continue angiotensin-converting enzyme inhibitors (ACEIs) and angiotensin receptor blockers (ARBs) in patients with coronavirus disease 2019 (COVID-19).\n\nObjectiveTo evaluate the association between ACEIs or ARBs use and clinical outcomes in COVID-19 patients.\n\nData SourcesSystematic search of the PubMed, Embase, Scopus, Web of Science, and Cochrane Central Register of Controlled Trials from database inception to May 31, 2020. We also searched the preprint servers medRxiv and SSNR for additional studies.\n\nStudy SelectionObservational studies and randomized controlled trials reporting the effect of ACEIs or ARBs use on clinical outcomes of adult patients with COVID-19.\n\nData Extraction and SynthesisRisk of bias of observational studies were evaluated using the Newcastle-Ottawa Scale. Meta-analyses were performed using a random-effects models and effects expressed as Odds ratios (OR) and mean differences with their 95% confidence interval (95%CI). If available, adjusted effects were pooled.\n\nMain Outcomes and MeasuresThe primary outcome was all-cause mortality and secondary outcomes were COVID-19 severity, hospital discharge, hospitalization, intensive care unit admission, mechanical ventilation, length of hospital stay, and troponin, creatinine, procalcitonin, C-reactive protein (CRP), interleukin-6 (IL-6), and D-dimer levels.\n\nResults40 studies (21 cross-sectional, two case-control, and 17 cohorts) involving 50615 patients were included. ACEIs or ARBs use was not associated with all-cause mortality overall (OR 1.11, 95%CI 0.77-1.60, p=0.56), in subgroups by study design and using adjusted effects. ACEI or ARB use was independently associated with lower COVID-19 severity (aOR 0.56, 95%CI 0.37-0.87, p<0.01). No significant associations were found between ACEIs or ARBs use and hospital discharge, hospitalization, mechanical ventilation, length of hospital stay, and biomarkers.\n\nConclusions and RelevanceACEIs or ARBs use was not associated with higher all-cause mortality in COVID-19. However, ACEI or ARB use was independently associated with lower COVID-19 severity. Our results support the current international guidelines to continue the use of ACEIs and ARBs in COVID-19 patients with hypertension.\n\nKey pointsO_ST_ABSQuestionC_ST_ABSWhat is the association between angiotensin-converting enzyme inhibitors (ACEIs) or angiotensin receptor blockers (ARBs) use and clinical outcomes in coronavirus disease 2019 (COVID-19) patients?\n\nFindingsIn this systematic review and meta-analysis of 40 observational studies, the use of ACEIs or ARBs was not associated with higher all-cause mortality in COVID-19 patients. Additionally, ACEIs or ARBs use was independently associated with lower COVID-19 severity.\n\nMeaningThese results support the current international guidelines to continue the use of ACEIs and ARBs in COVID-19 patients with hypertension.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Carlos Diaz-Arocutipa", + "author_inst": "Universidad San Ignacio de Loyola" + }, + { + "author_name": "Jose Saucedo-Chinchay", + "author_inst": "Programa de Atencion Domiciliaria - Essalud" + }, + { + "author_name": "Adrian V. Hernandez", + "author_inst": "University of Connecticut" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2020.06.04.20119131", "rel_title": "Social distancing across vulnerability, race, politics, and employment: How different Americans changed behaviors before and after major COVID-19 policy announcements", @@ -1418299,41 +1416982,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.04.20122325", - "rel_title": "Sub-weekly cycle uncovers the hidden link of 1atmospheric pollution to Kawasaki Disease", - "rel_date": "2020-06-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20122325", - "rel_abs": "Anthropogenic pollution has frequently been linked to myriad human ailments despite clear mechanistic links are yet lacking, a fact that severely downgraded its actual relevance. Now a prominent unnoticed sub-weekly cycle (SWC) of 3.5 days is uncovered in the long-term epidemiological records of Kawasaki disease (KD) in Japan, a mysterious vasculitis of yet unknown origin. After ruling out the effect of reporting biases, the analysis of Light Detection and Ranging (LIDAR) atmospheric profiles further confirms that this variability is linked to atmospheric particles with an aerodynamic diameter less than 1 {micro}m. SWC accounts for 20% of the variance in KD and its contribution is stable throughout the entire epidemiological record dating back to 1970, both at the prefecture level and for entire Japan. KD maxima in 2010-2016 always occur in full synchrony with LIDAR particle arrival in diverse locations such as Tokyo, Toyama and Tsukuba as well as for the entire of Japan. Rapid intrusion of aerosols from heights up to 6km to the surface is observed with KD admissions co-varying with their metal chemical composition. While regional intensity of winds has not changed in the interval 1979-2015, our study instead points for the first time to increased anthropogenic pollution as a necessary co-factor in the occurrence of KD and sets the field to associate other similar human vasculitis.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Xavier Rodo", - "author_inst": "ISGlobal" - }, - { - "author_name": "Albert Navarro Gallinad", - "author_inst": "ADAPT Centre, Trinity College Dublin, Dublin, Ireland." - }, - { - "author_name": "Tomoko Kojima", - "author_inst": "Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto, Japan" - }, - { - "author_name": "Joan Ballester", - "author_inst": "ISGlobal, Barcelona, Spain" - }, - { - "author_name": "Silvia Borras", - "author_inst": "Climate and Health (CLIMA) Program, ISGlobal, Barcelona, Catalonia, Spain." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.04.20122416", "rel_title": "Drug-Drug interactions between COVID-19 treatments and antipsychotics drugs: integrated evidence from 4 databases and a systematic review", @@ -1419765,6 +1418413,65 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.06.06.138339", + "rel_title": "SARS-CoV-2 Whole Genome Amplification and Sequencing for Effective Population-Based Surveillance and Control of Viral Transmission", + "rel_date": "2020-06-08", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.06.138339", + "rel_abs": "BackgroundWith the gradual reopening of economies and resumption of social life, robust surveillance mechanisms should be implemented to control the ongoing COVID-19 pandemic. Unlike RT-qPCR, SARS-CoV-2 Whole Genome Sequencing (cWGS) has the added advantage of identifying cryptic origins of the virus, and the extent of community-based transmissions versus new viral introductions, which can in turn influence public health policy decisions. However, practical and cost considerations of cWGS should be addressed before it can be widely implemented.\n\nMethodsWe performed shotgun transcriptome sequencing using RNA extracted from nasopharyngeal swabs of patients with COVID-19, and compared it to targeted SARS-CoV-2 full genome amplification and sequencing with respect to virus detection, scalability, and cost-effectiveness. To track virus origin, we used open-source multiple sequence alignment and phylogenetic tools to compare the assembled SARS-CoV-2 genomes to publicly available sequences.\n\nResultsWe show a significant improvement in whole genome sequencing data quality and viral detection using amplicon-based target enrichment of SARS-CoV-2. With enrichment, more than 99% of the sequencing reads mapped to the viral genome compared to an average of 0.63% without enrichment. Consequently, a dramatic increase in genome coverage was obtained using significantly less sequencing data, enabling higher scalability and significant cost reductions. We also demonstrate how SARS-CoV-2 genome sequences can be used to determine their possible origin through phylogenetic analysis including other viral strains.\n\nConclusionsSARS-CoV-2 whole genome sequencing is a practical, cost-effective, and powerful approach for population-based surveillance and control of viral transmission in the next phase of the COVID-19 pandemic.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Divinlal Harilal", + "author_inst": "Al Jalila Genomics Center, Al Jalila Childrens Hospital, Dubai, United Arab Emirates" + }, + { + "author_name": "Sathishkumar Ramaswamy", + "author_inst": "Al Jalila Genomics Center, Al Jalila Childrens Hospital, Dubai, United Arab Emirates" + }, + { + "author_name": "Tom Loney", + "author_inst": "College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates." + }, + { + "author_name": "Hanan Alsuwaidi", + "author_inst": "Mohammed Bin Rashid University of Medicine and Health Sciences" + }, + { + "author_name": "Hamda Khansaheb", + "author_inst": "Dubai Health Authority" + }, + { + "author_name": "Abdulmajeed AlKhajeh", + "author_inst": "Dubai Health Authority" + }, + { + "author_name": "Rupa Varghese", + "author_inst": "Microbiology and Infection Control Unit, Pathology and Genetics Department, Latifa Women and Children Hospital, Dubai Health Authority, Dubai, United Arab Emira" + }, + { + "author_name": "Zulfa Deesi", + "author_inst": "Microbiology and Infection Control Unit, Pathology and Genetics Department, Latifa Women and Children Hospital, Dubai Health Authority, Dubai, United Arab Emira" + }, + { + "author_name": "Norbert Nowotny", + "author_inst": "Institute of Virology, University of Veterinary Medicine Vienna, Vienna, Austria." + }, + { + "author_name": "Alawi Alsheikh-Ali", + "author_inst": "College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates." + }, + { + "author_name": "Ahmad Abou Tayoun", + "author_inst": "Al Jalila Genomics Center, Al Jalila Childrens Hospital, and College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United " + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.06.08.137331", "rel_title": "Effects of Renin-Angiotensin Inhibition on ACE2 and TMPRSS2 Expression", @@ -1420161,73 +1418868,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.05.20123745", - "rel_title": "Combined oropharyngeal/nasal swab is equivalent to nasopharyngeal sampling for SARS-CoV-2 diagnostic PCR", - "rel_date": "2020-06-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.05.20123745", - "rel_abs": "BackgroundEarly 2020, a COVID-19 epidemic became a public health emergency of international concern. To address this pandemic broad testing with an easy, comfortable and reliable testing method is of utmost concern. The nasopharyngeal (NP) swab sampling is the reference method though hampered by international supply shortages. A new oropharyngeal/nasal (OP/N) sampling method was investigated using the more readily available throat swab.\n\nMethodsIn this prospective observational study 36 COVID-19 patients were tested with both a NP and combined OP/N swab for SARS-CoV-2 RNA by PCR. In hospitalized suspect patients, who tested negative on both swabs, extensive retesting was performed. The sensitivity of NP versus combined OP/N swab sampling on admission and the correlation between viral RNA loads recovered was investigated.\n\nResults35 patients were diagnosed with SARS-CoV-2 by means of either NP or OP/N sampling. The paired swabs were both positive in 31 patients. The one patient who tested negative on both NP and OP/N swab on admission, was ultimately diagnosed on bronchoalveolar lavage fluid. A strong correlation was found between the viral RNA loads of the paired swabs (r = 0.76; P < 0.05). The sensitivity of NP and OP/N analysis in hospitalized patients (n = 28) was 89.3% and 92.7% respectively.\n\nConclusionsThis study demonstrates equivalence of NP and OP/N sampling for detection of SARS-CoV-2 by means of rRT-PCR. Sensitivity of both NP and OP/N sampling is very high in hospitalized patients.", - "rel_num_authors": 13, - "rel_authors": [ - { - "author_name": "Tania Desmet", - "author_inst": "Ghent University Hospital" - }, - { - "author_name": "Peter De Paepe", - "author_inst": "Ghent University Hospital" - }, - { - "author_name": "Jerina Boelens", - "author_inst": "Ghent University Hospital" - }, - { - "author_name": "Liselotte Coorevits", - "author_inst": "Ghent University Hospital" - }, - { - "author_name": "Elizaveta Padalko", - "author_inst": "Ghent University Hospital" - }, - { - "author_name": "Stien Vandendriessche", - "author_inst": "Ghent University Hospital" - }, - { - "author_name": "Isabel Leroux-Roels", - "author_inst": "Ghent University Hospital" - }, - { - "author_name": "Annelies Aerssens", - "author_inst": "Ghent University Hospital" - }, - { - "author_name": "Steven Callens", - "author_inst": "Ghent University Hospital" - }, - { - "author_name": "Eva Van Braeckel", - "author_inst": "Ghent University Hospital" - }, - { - "author_name": "Thomas Malfait", - "author_inst": "Ghent University Hospital" - }, - { - "author_name": "Frank Vermassen", - "author_inst": "Ghent University Hospital" - }, - { - "author_name": "Bruno Verhasselt", - "author_inst": "Ghent University Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.05.20123349", "rel_title": "An environmental determinant of viral respiratory disease", @@ -1421019,6 +1419659,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.06.04.20122606", + "rel_title": "COVID-19 and HIV co-infection: a living systematic evidence map of current research", + "rel_date": "2020-06-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20122606", + "rel_abs": "The world currently faces two ongoing devastating pandemics. These are the new severe acute respiratory syndrome coronavirus 2/coronavirus disease 2019 (SARS-CoV-2/COVID-19) and the prior human immunodeficiency virus/acquired immune deficiency syndrome (HIV/AIDS) pandemics. The literature regarding the confluence of these global plagues expands at pace. A systematic search of the literature considering COVID-19 and HIV co-infection was performed.\n\nAfter five months, from the beginning of the COVID-19 pandemic, there were at least thirty-five studies reported from thirteen countries. These ranged from individual case reports and series to cohort studies. Based on studies that could be extrapolated to the general population, co-infected individuals with suppressed HIV viral loads did not have disproportionate COVID-19 sickness and death. At least four patients, newly diagnosed with HIV recovered from COVID-19. Current evidence suggests that co-infected patients should be treated like the general population.\n\nThis ongoing living systematic evidence map of contemporary primary SARS-CoV-2 and HIV co-infection research provides a platform for researchers, policy makers, clinicians and others to more quickly discover and build relevant insights.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Gwinyai Masukume", + "author_inst": "Division of Epidemiology and Biostatistics, University of the Witwatersrand, School of Public Health, Johannesburg, South Africa" + }, + { + "author_name": "Witness Mapanga", + "author_inst": "Non-Communicable Diseases Research (NCDR) Division of the Wits Health Consortium, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Sou" + }, + { + "author_name": "Doreen Sindisiwe van Zyl", + "author_inst": "Private practitioner, Johannesburg, South Africa" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "hiv aids" + }, { "rel_doi": "10.1101/2020.06.05.20122820", "rel_title": "A systematic review of convalescent plasma treatment for COVID19", @@ -1421339,133 +1420006,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.06.07.137802", - "rel_title": "Neuropilin-1 facilitates SARS-CoV-2 cell entry and provides a possible pathway into the central nervous system", - "rel_date": "2020-06-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.07.137802", - "rel_abs": "The causative agent of the current pandemic and coronavirus disease 2019 (COVID-19) is the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)1. Understanding how SARS-CoV-2 enters and spreads within human organs is crucial for developing strategies to prevent viral dissemination. For many viruses, tissue tropism is determined by the availability of virus receptors on the surface of host cells2. Both SARS-CoV and SARS-CoV-2 use angiotensin-converting enzyme 2 (ACE2) as a host receptor, yet, their tropisms differ3-5. Here, we found that the cellular receptor neuropilin-1 (NRP1), known to bind furin-cleaved substrates, significantly potentiates SARS-CoV-2 infectivity, which was inhibited by a monoclonal blocking antibody against the extracellular b1b2 domain of NRP1. NRP1 is abundantly expressed in the respiratory and olfactory epithelium, with highest expression in endothelial cells and in the epithelial cells facing the nasal cavity. Neuropathological analysis of human COVID-19 autopsies revealed SARS-CoV-2 infected NRP1-positive cells in the olfactory epithelium and bulb. In the olfactory bulb infection was detected particularly within NRP1-positive endothelial cells of small capillaries and medium-sized vessels. Studies in mice demonstrated, after intranasal application, NRP1-mediated transport of virus-sized particles into the central nervous system. Thus, NRP1 could explain the enhanced tropism and spreading of SARS-CoV-2.", - "rel_num_authors": 28, - "rel_authors": [ - { - "author_name": "Ludovico Cantuti-Castelvetri", - "author_inst": "TU Munich" - }, - { - "author_name": "Ravi Ohja", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Liliana Pedro", - "author_inst": "TU Munich" - }, - { - "author_name": "Minou Djannatian", - "author_inst": "TU Munich" - }, - { - "author_name": "Jonas Franz", - "author_inst": "University of Goettingen" - }, - { - "author_name": "Suvi Kuivanen", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Katri Kallio", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Tugberg Kaya", - "author_inst": "TU Munich" - }, - { - "author_name": "Maria Anastasina", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Teemu Smura", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Lev Levanov", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Leonora Szirovicza", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Allan Tobi", - "author_inst": "University of Tartu" - }, - { - "author_name": "Hannimari Kallio-Kokko", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Pamela Osterlund", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Merja Joensuu", - "author_inst": "University of Queensland" - }, - { - "author_name": "Frederic Meunier", - "author_inst": "University of Queensland" - }, - { - "author_name": "Sarah Butcher", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Martin Winkler", - "author_inst": "University of Goettingen" - }, - { - "author_name": "Brit Mollenhauer", - "author_inst": "University of Goettingen" - }, - { - "author_name": "Ari Helenius", - "author_inst": "ETH Zuerich" - }, - { - "author_name": "Ozgun Gokce", - "author_inst": "LMU Munich" - }, - { - "author_name": "Tambet Teesalu", - "author_inst": "University of Tartu" - }, - { - "author_name": "Jussi Hepojoki", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Olli Vapalahti", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Christine Stadelmann", - "author_inst": "University of Goettingen" - }, - { - "author_name": "Giuseppe Balistreri", - "author_inst": "University of Helsinki" - }, - { - "author_name": "Mikael Simons", - "author_inst": "TU Munich" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.06.06.138149", "rel_title": "Rapid inactivation of SARS-CoV-2 with Deep-UV LED irradiation", @@ -1422957,6 +1421497,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.06.02.20119834", + "rel_title": "Decontamination of face masks and filtering facepiece respirators via ultraviolet germicidal irradiation, hydrogen peroxide vaporisation, and use of dry heat inactivates an infectious SARS-CoV-2 surrogate virus.", + "rel_date": "2020-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.02.20119834", + "rel_abs": "BackgroundIn the context of the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, the supply of personal protective equipment remains under severe strain. To address this issue, re-use of surgical face masks and filtering facepiece respirators has been recommended; prior decontamination is paramount to their re-use.\n\nAimWe aim to provide information on the effects of three decontamination procedures on porcine respiratory coronavirus (PRCV)-contaminated masks and respirators, presenting a stable model for infectious coronavirus decontamination of these typically single-use-only products.\n\nMethodsSurgical masks and filtering facepiece respirator coupons and straps were inoculated with infectious PRCV and submitted to three decontamination treatments, UV irradiation, vaporised H2O2, and dry heat treatment. Viruses were recovered from sample materials and viral titres were measured in swine testicle cells.\n\nFindingsUV irradiation, vaporised H2O2 and dry heat reduced infectious PRCV by more than three orders of magnitude on mask and respirator coupons and rendered it undetectable in all decontamination assays.\n\nConclusionThis is the first description of stable disinfection of face masks and filtering facepiece respirators contaminated with an infectious SARS-CoV-2 surrogate using UV irradiation, vaporised H2O2 and dry heat treatment. The three methods permit demonstration of a loss of infectivity by more than three orders of magnitude of an infectious coronavirus in line with the FDA policy regarding face masks and respirators. It presents advantages of uncomplicated manipulation and utilisation in a BSL2 facility, therefore being easily adaptable to other respirator and mask types.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Louisa F Ludwig-Begall", + "author_inst": "Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liege Uni" + }, + { + "author_name": "Constance Wielick", + "author_inst": "Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liege Uni" + }, + { + "author_name": "Lorene Dams", + "author_inst": "Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liege Uni" + }, + { + "author_name": "Hans Nauwynck", + "author_inst": "Laboratory of Virology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium" + }, + { + "author_name": "Pierre-Francois Demeuldre", + "author_inst": "Department of Hospital Pharmacy, The University Hospital Center, University of Liege, Liege, Belgium" + }, + { + "author_name": "Aurore Napp", + "author_inst": "Department of Hospital Pharmacy, The University Hospital Center, University of Liege, Liege, Belgium" + }, + { + "author_name": "Jan Laperre", + "author_inst": "Centexbel Textile Research Centre, Grace-Hollogne, Belgium" + }, + { + "author_name": "Eric Haubruge", + "author_inst": "TERRA Research Centre, Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium" + }, + { + "author_name": "Etienne Thiry", + "author_inst": "Veterinary Virology and Animal Viral Diseases, Department of Infectious and Parasitic Diseases, FARAH Research Centre, Faculty of Veterinary Medicine, Liege Uni" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.06.02.20120220", "rel_title": "Overview on COVID-19 outbreak indicators across Brazilian federative units", @@ -1423333,25 +1421924,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "emergency medicine" }, - { - "rel_doi": "10.1101/2020.06.01.20119560", - "rel_title": "Covid-19 Epidemiological Factor Analysis: Identifying Principal Factors with Machine Learning", - "rel_date": "2020-06-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20119560", - "rel_abs": "Based on a subset of Covid-19 Wave 1 cases at a time point near TZ+3m (April, 2020), we perform an analysis of the influencing factors for the epidemics impacts with several different statistical methods. The consistent conclusion of the analysis with the available data is that apart from the policy and management quality, being the dominant factor, the most influential factors among the considered were current or recent universal BCG immunization and the prevalence of smoking.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Serge Dolgikh", - "author_inst": "National Aviation University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.06.02.20119859", "rel_title": "The hidden variable in the dynamics of transmission of COVID-19: A Henon map approach", @@ -1424339,6 +1422911,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.02.20120568", + "rel_title": "A Model for the Testing and Tracing Needed to Suppress COVID-19", + "rel_date": "2020-06-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.02.20120568", + "rel_abs": "This paper presents the first analytical model for calculating how many tests and tracing needed to suppress COVID-19 transmission. The number of people needs to be tested daily is given by: O_FD O_INLINEFIG[Formula 1]C_INLINEFIGM_FD(1)C_FD Where\n\nN is the size of the population in consideration\n\nAr is the attack rate at any given time\n\nTp is the test-positive rate\n\n {rho}is the percentage of infectious people that have to be detected per day. To make the effective reproduction number Re below 1,{rho} must satisfy the following equation: O_FD O_INLINEFIG[Formula 2]C_INLINEFIGM_FD(2)C_FD\n\nWhere\n\nR0 is the basic reproduction number,\n\nS/N is the percentage of the susceptible population over the entire population,\n\nD is the length of the infectious period, and\n\n{eta}is the percentage of close contacts that have to be traced.\n\nThis model provides insights and guidance to deploy the testing and tracing resources optimally. An Excel model is attached to facilitate easy calculation of the number of tests and tracing needed. This model is also applicable to any infectious disease that can be suppressed by testing and tracing.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Victor Wang", + "author_inst": "Aimtop Ventures" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.02.20117341", "rel_title": "Analysis of the outbreak of COVID-19 in Japan on the basis of an SIQR model", @@ -1424691,57 +1423282,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.06.04.20121848", - "rel_title": "An Agent Based Model methodology for assessing spread and health systems burden for Covid-19 using a synthetic population from India", - "rel_date": "2020-06-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20121848", - "rel_abs": "ObjectivesTo evaluate the transmission dynamics and health systems burden of COVID-19 with and without interventions, using an Agent Based Modeling (ABM) approach on a localized synthetic population.\n\nStudy designA synthetic population of Rangareddy district, Telangana state, India, with 5,48,323 agents and simulated using an ABM approach for three different scenarios.\n\nMethodsThe patterns and trends of the COVID-19 in terms of infected, admitted, critical cases requiring intensive care and/ or ventilator support, mortality and recovery were examined. The model was simulated over a period of 365 days for a no lockdown scenario and two Non-Pharmaceutical Intervention (NPI) scenarios i.e., 50% lockdown and 75% lockdown scenarios.\n\nResultsResults revealed that the peak values and slope of the curve declined as NPI became more stringent. The peak values could facilitate policymakers to plan the required capacity to accommodate influx of hospitalizations.\n\nConclusionsABM provides better insight into projections compared to compartmental models. The results could provide a platform for researchers and modelers to explore using ABM approach for COVID-19 projections with inclusion of interventions and health system preparedness.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Narassima MS", - "author_inst": "Amrita Vishwa Vidyapeetham" - }, - { - "author_name": "Guru Rajesh Jammy", - "author_inst": "Society for Health, Allied Research and Education (SHARE-INDIA), Telangana, India." - }, - { - "author_name": "Rashmi Pant", - "author_inst": "Society for Health Allied Research and Education (SHARE-INDIA)" - }, - { - "author_name": "Lincoln Choudhury", - "author_inst": "Krashapana Consultancy Private limited, New Delhi, India." - }, - { - "author_name": "Aadharsh R", - "author_inst": "Amrita Vishwa Vidyapeetham" - }, - { - "author_name": "Vijay Yeldandi", - "author_inst": "Society for Health, Allied Research and Education (SHARE-INDIA), Telangana, India." - }, - { - "author_name": "Anbuudayasankar SP", - "author_inst": "Amrita Vishwa Vidyapeetham" - }, - { - "author_name": "Rangasami P", - "author_inst": "Amrita Vishwa Vidyapeetham" - }, - { - "author_name": "Denny John", - "author_inst": "Department of Public Health, Amrita Institute of Medical Sciences and Research Centre, Amrita Vishwa Vidyapeetham, Kochi, Kerala, India" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.04.20122028", "rel_title": "Geographical Variation in COVID-19 Cases, Prevalence, Recovery and Fatality Rate by Phase of National Lockdown in India, March 14-May 29, 2020", @@ -1426189,6 +1424729,165 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.06.05.135921", + "rel_title": "SARS-CoV-2 neutralizing human recombinant antibodies selected from pre-pandemic healthy donors binding at RBD-ACE2 interface", + "rel_date": "2020-06-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.05.135921", + "rel_abs": "COVID-19 is a severe acute respiratory disease caused by SARS-CoV-2, a novel betacoronavirus discovered in December 2019 and closely related to the SARS coronavirus (CoV). Both viruses use the human ACE2 receptor for cell entry, recognizing it with the Receptor Binding Domain (RBD) of the S1 subunit of the viral spike (S) protein. The S2 domain mediates viral fusion with the host cell membrane. Experience with SARS and MERS coronaviruses has shown that potent monoclonal neutralizing antibodies against the RBD can inhibit the interaction with the virus cellular receptor (ACE2 for SARS) and block the virus cell entry. Assuming that a similar strategy would be successful against SARS-CoV-2, we used phage display to select from the human naive universal antibody gene libraries HAL9/10 anti-SARS-CoV-2 spike antibodies capable of inhibiting interaction with ACE2. 309 unique fully human antibodies against S1 were identified. 17 showed more than 75% inhibition of spike binding to cells expressing ACE2 in the scFv-Fc format, assessed by flow cytometry and several antibodies showed even an 50% inhibition at a molar ratio of the antibody to spike protein or RBD of 1:1. All 17 scFv-Fc were able to bind the isolated RBD, four of them with sub-nanomolar EC50. Furthermore, these scFv-Fc neutralized active SARS-CoV-2 virus infection of VeroE6 cells. In a final step, the antibodies neutralizing best as scFv-Fc were converted into the IgG format. The antibody STE73-2E9 showed neutralization of active SARS-CoV-2 with an IC50 0.43 nM and is binding to the ACE2-RBD interface. Universal libraries from healthy human donors offer the advantage that antibodies can be generated quickly and independent from the availability of material from recovered patients in a pandemic situation.", + "rel_num_authors": 36, + "rel_authors": [ + { + "author_name": "Federico Bertoglio", + "author_inst": "TU Braunschweig" + }, + { + "author_name": "Doris Meier", + "author_inst": "TU Braunschweig" + }, + { + "author_name": "Nora Langreder", + "author_inst": "TU Braunschweig" + }, + { + "author_name": "Stephan Steinke", + "author_inst": "TU Braunschweig" + }, + { + "author_name": "Ulfert Rand", + "author_inst": "Helmholtz Centre for Infection Research" + }, + { + "author_name": "Luca Simonelli", + "author_inst": "Istituto di Ricerca in Biomedicina, Universita della Svizzera italiana" + }, + { + "author_name": "Philip Alexander Heine", + "author_inst": "TU Braunschweig" + }, + { + "author_name": "Rico Ballmann", + "author_inst": "TU Braunschweig" + }, + { + "author_name": "Kai-Thomas Schneider", + "author_inst": "TU Braunschweig" + }, + { + "author_name": "Kristian Daniel Ralph Roth", + "author_inst": "TU Braunschweig" + }, + { + "author_name": "Maximilian Ruschig", + "author_inst": "TU Braunschweig" + }, + { + "author_name": "Peggy Riese", + "author_inst": "Helmholtz Centre for Infection Research" + }, + { + "author_name": "Kathrin Eschke", + "author_inst": "Helmholtz Centre for Infection Research" + }, + { + "author_name": "Yeonsu Kim", + "author_inst": "Helmholtz Centre for Infection Research" + }, + { + "author_name": "Dorina Schaeckermann", + "author_inst": "TU Braunschweig" + }, + { + "author_name": "Mattia Pedotti", + "author_inst": "Istituto di Ricerca in Biomedicina, Universita della Svizzera italiana" + }, + { + "author_name": "Philipp Kuhn", + "author_inst": "YUMAB GmbH" + }, + { + "author_name": "Susanne Zock-Emmenthal", + "author_inst": "TU Braunschweig" + }, + { + "author_name": "Johannes Woehrle", + "author_inst": "BioCopy GmbH" + }, + { + "author_name": "Normann Kilb", + "author_inst": "BioCopy GmbH" + }, + { + "author_name": "Tobias Herz", + "author_inst": "BioCopy GmbH" + }, + { + "author_name": "Marlies Becker", + "author_inst": "TU Braunschweig" + }, + { + "author_name": "Martina Grashoff", + "author_inst": "Helmholtz Centre for Infection Research" + }, + { + "author_name": "Esther Veronika Wenzel", + "author_inst": "TU Braunschweig" + }, + { + "author_name": "Giulio Russo", + "author_inst": "TU Braunschweig" + }, + { + "author_name": "Andrea Kroeger", + "author_inst": "Helmholtz Centre for Infection Research" + }, + { + "author_name": "Linda Brunotte", + "author_inst": "Westfaelische Wilhelms-Universitaet Muenster" + }, + { + "author_name": "Stephan Ludwig", + "author_inst": "Westfaelische Wilhelms-Universitaet Muenster" + }, + { + "author_name": "Viola Fuehner", + "author_inst": "TU Braunschweig" + }, + { + "author_name": "Stefan Daniel Kraemer", + "author_inst": "BioCopy GmbH" + }, + { + "author_name": "Stefan Duebel", + "author_inst": "TU Braunschweig" + }, + { + "author_name": "Luca Varani", + "author_inst": "Istituto di Ricerca in Biomedicina" + }, + { + "author_name": "Guenter Roth", + "author_inst": "BioCopy GmbH" + }, + { + "author_name": "Luka Cicin-Sain", + "author_inst": "Helmholtz Centre for Infection Research" + }, + { + "author_name": "Maren Schubert", + "author_inst": "TU Braunschweig" + }, + { + "author_name": "Michael Hust", + "author_inst": "TU Braunschweig" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biochemistry" + }, { "rel_doi": "10.1101/2020.06.05.136481", "rel_title": "SARS-CoV-2 infection leads to acute infection with dynamic cellular and inflammatory flux in the lung that varies across nonhuman primate species", @@ -1426756,49 +1425455,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, - { - "rel_doi": "10.1101/2020.06.04.20122564", - "rel_title": "Adverse effects of COVID-19 related lockdown on pain, physical activity and psychological wellbeing in people with chronic pain", - "rel_date": "2020-06-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.04.20122564", - "rel_abs": "Countries across the world imposed lockdown restrictions during the COVID-19 pandemic. It has been proposed that lockdown conditions disproportionately impact those living with chronic pain, requiring adaptation to treatment and care strategies. We investigated how lockdown restrictions in the United Kingdom impacted individuals with chronic pain (N = 431) relative to a healthy control group (N = 88) using an online survey. In accordance with the fear-avoidance model, we hypothesised increases in perceived pain and psychological distress that would be mediated by pain catastrophizing. Survey questions answered during the lockdown period, probing patients self-perceived changes retrospectively, revealed that people with chronic pain perceived increases in their pain severity compared to before lockdown. They were also more adversely affected by lockdown compared to pain-free individuals, demonstrating greater increases in anxiety and depressed mood, increased loneliness and reduced levels of physical exercise. Pain catastrophizing was found to be an important factor in predicting the extent of self-perceived increases in pain, and accounted for the relationship between decreased mood and pain. Perceived decreases in levels of physical exercise also independently predicted perceptions of increased pain. Interestingly, actual changes in pain symptoms (measured at two time points at pre- and post-lockdown in a subgroup, N = 85) did not change significantly on average, but those reporting increases also demonstrated greater baseline levels of pain catastrophizing. Overall, the findings suggest that remote pain management provision to target reduction of catastrophizing and increases to physical activity could be beneficial for chronic pain patients in overcoming the adverse effects of lockdown.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Nicholas Fallon", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Christopher Brown", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Hannah Twiddy", - "author_inst": "Walton Centre NHS Foundation Trust" - }, - { - "author_name": "Eleanor Brian", - "author_inst": "University of Liverpool" - }, - { - "author_name": "Bernhard Frank", - "author_inst": "Walton Centre NHS Foundation Trust" - }, - { - "author_name": "Turo Nurmikko", - "author_inst": "Walton Centre NHS Foundation Trust" - }, - { - "author_name": "Andrej Stancak", - "author_inst": "University of Liverpool" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pain medicine" - }, { "rel_doi": "10.1101/2020.06.05.135954", "rel_title": "Mega-phylogeny sheds light on SARS-CoV-2 spatial phylogenetic structure", @@ -1427690,6 +1426346,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.02.20120352", + "rel_title": "Testing the effects of the timing of application of preventative procedures against COVID-19: An insight for future measures such as local emergency brakes.", + "rel_date": "2020-06-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.02.20120352", + "rel_abs": "As many countries plan to lift lockdown measures aimed at suppression of COVID-19, data from early regional epidemics in Italy were analysed to ascertain the effectiveness of the timing of preventative measures. The cumulative caseload data were extracted from regional epidemics in Italy. Epidemic features in regions where lockdown was applied early were compared to those where lockdown was applied later for statistical differences. There were statistically significant differences in the timing of the peak, the cumulative incidence at peak and the case/km2 at peak between regions where the lockdown had been applied early and those where it was applied late. The peak occurred 7 days earlier with four times less cases/km2 in regions where the lockdown was applied within 10 days of the start of the epidemic. Cumulative caseloads, cases/km2 and/or the number of days into an epidemic can be used to plan future localised suppression measures as part of a national post-lockdown policy. There were 350 (95% confidence interval (CI) 203) cumulative cases and 2.4 (CI 1.1) cases/km2 on day 8 of the regional epidemics.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Francis Scullion", + "author_inst": "Veterinary Services" + }, + { + "author_name": "Geraldine Scullion", + "author_inst": "Veterinary Services" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.31.126615", "rel_title": "An exploration of the SARS-CoV-2 spike receptor binding domain (RBD), a complex palette of evolutionary and structural features", @@ -1428118,137 +1426797,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.06.04.135012", - "rel_title": "Olfactory transmucosal SARS-CoV-2 invasion as port of Central Nervous System entry in COVID-19 patients", - "rel_date": "2020-06-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.04.135012", - "rel_abs": "The newly identified severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19, a pandemic respiratory disease presenting with fever, cough, and often pneumonia. Moreover, thromboembolic events throughout the body including the central nervous system (CNS) have been described. Given first indication for viral RNA presence in the brain and cerebrospinal fluid and in light of neurological symptoms in a large majority of COVID-19 patients, SARS-CoV-2-penetrance of the CNS is likely. By precisely investigating and anatomically mapping oro- and pharyngeal regions and brains of 32 patients dying from COVID-19, we not only describe CNS infarction due to cerebral thromboembolism, but also demonstrate SARS-CoV-2 neurotropism. SARS-CoV-2 enters the nervous system via trespassing the neuro-mucosal interface in the olfactory mucosa by exploiting the close vicinity of olfactory mucosal and nervous tissue including delicate olfactory and sensitive nerve endings. Subsequently, SARS-CoV-2 follows defined neuroanatomical structures, penetrating defined neuroanatomical areas, including the primary respiratory and cardiovascular control center in the medulla oblongata.", - "rel_num_authors": 29, - "rel_authors": [ - { - "author_name": "Jenny Meinhardt", - "author_inst": "Charite - Universitaetsmedizin Berlin" - }, - { - "author_name": "Josefine Radke", - "author_inst": "Charite - Universitaetsmedizin Berlin" - }, - { - "author_name": "Carsten Dittmayer", - "author_inst": "Charite" - }, - { - "author_name": "Ronja Mothes", - "author_inst": "Charite" - }, - { - "author_name": "Jonas Franz", - "author_inst": "University Medical Center, Goettingen" - }, - { - "author_name": "Michael Laue", - "author_inst": "Robert Koch Institute Berlin" - }, - { - "author_name": "Julia Schneider", - "author_inst": "Charite" - }, - { - "author_name": "Sebastian Bruenink", - "author_inst": "Charite" - }, - { - "author_name": "Olga Hassan", - "author_inst": "Charite" - }, - { - "author_name": "Werner Stenzel", - "author_inst": "Charite" - }, - { - "author_name": "Marc Windgassen,", - "author_inst": "Charite" - }, - { - "author_name": "Larissa Roessler", - "author_inst": "Charite" - }, - { - "author_name": "Hans-Hilmar Goebel", - "author_inst": "Charite" - }, - { - "author_name": "Hubert Martin", - "author_inst": "Charite" - }, - { - "author_name": "Andreas Nitsche", - "author_inst": "Robert Koch Institute Berlin" - }, - { - "author_name": "Walter Schulz-Schaeffer", - "author_inst": "University of the Saarland" - }, - { - "author_name": "Samy Hakroush", - "author_inst": "University Medical Center Goettingen, Germany" - }, - { - "author_name": "Martin S Winkler", - "author_inst": "University Medical Center Goettingen, Germany" - }, - { - "author_name": "Bjoern Tampe", - "author_inst": "University Medical Center Goettingen, Germany" - }, - { - "author_name": "Sefer Elezkurtaj", - "author_inst": "Charite" - }, - { - "author_name": "David Horst", - "author_inst": "Charite" - }, - { - "author_name": "Lars Oesterhelweg", - "author_inst": "Charite" - }, - { - "author_name": "Michael Tsokos", - "author_inst": "Charite" - }, - { - "author_name": "Barbara Ingold Heppner", - "author_inst": "DRK Kliniken Berlin" - }, - { - "author_name": "Christine Stadelmann", - "author_inst": "University Medical Center, Goettingen" - }, - { - "author_name": "Christian Drosten", - "author_inst": "Charite Universitaetsmedizin" - }, - { - "author_name": "Victor M Corman", - "author_inst": "Charite - Universitaetsmedizin Berlin" - }, - { - "author_name": "Helena Radbruch", - "author_inst": "Charite - Universitaetsmedizin Berlin" - }, - { - "author_name": "Frank L Heppner", - "author_inst": "Charite - Universitaetsmedizin Berlin" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "neuroscience" - }, { "rel_doi": "10.1101/2020.06.04.128751", "rel_title": "Integrated genomic view of SARS-CoV-2 in India", @@ -1429404,6 +1427952,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.06.02.20120147", + "rel_title": "Estimating critical care capacity needs and gaps in Africa during the COVID-19 pandemic", + "rel_date": "2020-06-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.02.20120147", + "rel_abs": "ObjectiveThe purpose of this analysis was to describe national critical care capacity shortages for 52 African countries and to outline needs for each country to adequately respond to the COVID-19 pandemic.\n\nMethodsA modified SECIR compartment model was used to estimate the number of severe COVID-19 cases at the peak of the outbreak. Projections of the number of hospital beds, ICU beds, and ventilators needed at outbreak peak were generated for four scenarios - if 30, 50, 70, or 100% of patients with severe COVID-19 symptoms seek health services--assuming that all people with severe infections would require hospitalization, that 4.72% would require ICU admission, and that 2.3% would require mechanical ventilation.\n\nFindingsAcross the 52 countries included in this analysis, the average number of severe COVID-19 cases projected at outbreak peak was 138 per 100,000 (SD: 9.6). Comparing current national capacities to estimated needs at outbreak peak, we found that 31of 50 countries (62%) do not have a sufficient number of hospital beds per 100,000 people if 100% of patients with severe infections seek out health services and assuming that all hospital beds are empty and available for use by patients with COVID-19. If only 30% of patients seek out health services then 10 of 50 countries (20%) do not have sufficient hospital bed capacity. The average number of ICU beds needed at outbreak peak across the 52 included countries ranged from 2 per 100,000 people (SD: 0.1) when 30% of people with severe COVID-19 infections access health services to 6.5 per 100,000 (SD: 0.5) assuming 100% of people seek out health services. Even if only 30% of severely infected patients seek health services at outbreak peak, then 34 of 48 countries (71%) do not have a sufficient number of ICU beds per 100,000 people to handle projected need. Only four countries (Cabo Verde, Egypt, Gabon, and South Africa) have a sufficient number of ventilators to meet projected national needs if 100% of severely infected individuals seek health services assuming all ventilators are functioning and available for COVID-19 patients, while 35 other countries require two or more additional ventilators per 100,000 people.\n\nConclusionThe majority of countries lack sufficient ICU bed and ventilator capacity to care for the projected number of patients with severe COVID-19 infections at outbreak peak even if only 30% of severely infected patients seek health services.\n\nThis analysis reveals there is an urgent need to allocate resources and increase critical care capacity in these countries.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Jessica Craig", + "author_inst": "CDDEP" + }, + { + "author_name": "Erta Kalanxhi", + "author_inst": "CDDEP" + }, + { + "author_name": "Gilbert Osena", + "author_inst": "CDDEP" + }, + { + "author_name": "Isabel Frost", + "author_inst": "CDDEP" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2020.06.02.20120295", "rel_title": "Increased serum levels of sCD14 and sCD163 indicate a preponderant role for monocytes in COVID-19 immunopathology", @@ -1429744,45 +1428323,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.29.20117143", - "rel_title": "Detection of lung hypoperfusion in Covid-19 patients during recovery by digital imaging quantification", - "rel_date": "2020-06-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.29.20117143", - "rel_abs": "PurposeA large number of patients affected by the SARS-Cov-2 virus worldwide undergo recovery of symptoms in about one month. Among these patients, the healing process is still under observation, with some patients in need of careful clinical monitoring. While the radiological findings have been shown to regress almost completely, little knowledge is available at the moment about other complications in the lung and in other organs. We then investigated the lung perfusion conditions in patients affected by COVID-19 during recovery.\n\nMethodWe retrospectively studied 20 patients, from 14 to 60 days after resolution of the COVID-19 symptoms, using chest CT. In a subgroup of 5 patients contrasted CT was used. Beside normal radiological evaluation of lung tissue, perfusion conditions were evaluated by digital image processing in the lung volume automatically segmented.\n\nResultsPulmonary lung evaluation showed that COVID-19 pneumonia almost completely regressed, with mild focal areas affected by fibrous stripes. In patients that reported dyspnea, lung CT showed complete resolution of interstitial changes. Quantification of lung perfusion condition by contrasted CT, showed that dyspnea in 3 patients was associated with areas of hypoperfusion, while in 2 patients not reporting dyspnea perfusion conditions were comparable to normal controls.\n\nConclusionsAlthough we obtained preliminary data, this is the first report on quantitative evaluation of hypoperfused lung tissue detected in recovering COVID-19 patients. These results suggest the need to further investigate these patients and to redefine the role of CT evaluation for diagnostic purposes as well as for evaluation of potential treatments.\n\nFundingThis was an academic study that received no direct funding.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Gianluigi Patelli", - "author_inst": "Bolognini Hospital - ASST Bergamo Est" - }, - { - "author_name": "Silvia Paganoni", - "author_inst": "Bolognini Hospital - ASST Bergamo Est" - }, - { - "author_name": "Francesca Besana", - "author_inst": "Bolognini Hospital - ASST Bergamo Est" - }, - { - "author_name": "Mattia Ronzoni", - "author_inst": "D/Vision Lab srl" - }, - { - "author_name": "Simone Manini", - "author_inst": "D/Vision Lab srl" - }, - { - "author_name": "Andrea Remuzzi", - "author_inst": "University of Bergamo" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.06.01.20119271", "rel_title": "Prevalence and mortality of Lung Comorbidities Among Patients with COVID-19: A systematic review and meta-analysis", @@ -1430538,6 +1429078,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, + { + "rel_doi": "10.1101/2020.06.01.20119230", + "rel_title": "Who do not wash their hands during the Covid-19 pandemic? Social media use as a potential predictor", + "rel_date": "2020-06-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20119230", + "rel_abs": "This study predicts handwashing behavior during the Covid-19 pandemic. An analysis of 674 adults in Malaysia identifies their time spent on social media per day as a key predictor of handwashing. The association between time spent on social media and handwashing substantially depends on gender and the number of children in the same household. Additional predictors include age and health condition. This study helps identify specific target groups for health communication on hand hygiene via peoples use of social media, which can be a key channel for health communication campaigns during a pandemic.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Stephen X. Zhang", + "author_inst": "University of Adelaide" + }, + { + "author_name": "Lorenz Graf-Vlachy", + "author_inst": "ESCP" + }, + { + "author_name": "Rui Su", + "author_inst": "Xiamen University Malaysia" + }, + { + "author_name": "Jizhen Li", + "author_inst": "Tsinghua University" + }, + { + "author_name": "Kim Hoe Looi", + "author_inst": "Xiamen University Malaysia" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.05.30.20118109", "rel_title": "Development and Prospective Validation of a Transparent Deep Learning Algorithm for Predicting Need for Mechanical Ventilation", @@ -1430946,77 +1429521,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.31.20118315", - "rel_title": "Cytokine biomarkers of COVID-19", - "rel_date": "2020-06-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.31.20118315", - "rel_abs": "We used a new strategy to screen cytokines associated with SARS-CoV-2 infection. Cytokines that can classify populations in different states of SARS-CoV-2 infection were first screened in cross-sectional serum samples from 184 subjects by 2 statistical analyses. The resultant cytokines were then analyzed for their interrelationships and fluctuating features in sequential samples from 38 COVID-19 patients. Three cytokines, M-CSF, IL-8 and SCF, which were clustered into 3 different correlation groups and had relatively small fluctuations during SARS-CoV-2 infection, were selected for the construction of a multiclass classification model. This model discriminated healthy individuals and asymptomatic and nonsevere patients with accuracy of 77.4% but was not successful in classifying severe patients. Further searching led to a single cytokine, hepatocyte growth factor (HGF), which classified severe from nonsevere COVID-19 patients with a sensitivity of 84.6% and a specificity of 97.9% under a cutoff value of 1128 pg/ml. The level of this cytokine did not increase in nonsevere patients but was significantly elevated in severe patients. Considering its potent antiinflammatory function, we suggest that HGF might be a new candidate therapy for critical COVID-19. In addition, our new strategy provides not only a rational and effective way to focus on certain cytokine biomarkers for infectious diseases but also a new opportunity to probe the modulation of cytokines in the immune response.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Hai-Jun Deng", - "author_inst": "Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Quan-Xin Long", - "author_inst": "Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Bei-Zhong Liu", - "author_inst": "Yongchuan Hospital Affiliated to Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Ji-Hua Ren", - "author_inst": "Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Pu Liao", - "author_inst": "Laboratory department, Chongqing People Hospital, Chongqing, China" - }, - { - "author_name": "Jing-Fu Qiu", - "author_inst": "School of Public Health and Management, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Xiao-Jun Tang", - "author_inst": "School of Public Health and Management, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Yong Zhang", - "author_inst": "School of Public Health and Management, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Ni Tang", - "author_inst": "Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Yin-Yin Xu", - "author_inst": "Yongchuan Hospital Affiliated to Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Zhan Mo", - "author_inst": "Yongchuan Hospital Affiliated to Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Juan Chen", - "author_inst": "Key Laboratory of Molecular Biology on Infectious Diseases, Ministry of Education, Chongqing Medical University, Chongqing, China" - }, - { - "author_name": "Jieli Hu", - "author_inst": "Chongqing Medical University" - }, - { - "author_name": "Ai-Long Huang", - "author_inst": "The Key Laboratory of Molecular Biology of Infectious Diseases designated by the Chinese Ministry of" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.30.20117721", "rel_title": "A comparative evaluation of dye-based and probe-based RT-qPCR assay for the screening of SARS-CoV-2 using individual and pooled-sample testing.", @@ -1431872,6 +1430376,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.31.20118414", + "rel_title": "Dynamics and Prediction of the COVID-19 Epidemics in the US:a Compartmental Model with Deep Learning Enhancement", + "rel_date": "2020-06-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.31.20118414", + "rel_abs": "BackgroundCompartmental models dominate epidemic modeling. Estimations of transmission parameters between compartments are typically done through stochastic parameterization processes that depend upon detailed statistics on transmission characteristics, which are economically and resource-wide expensive to collect. We apply deep learning techniques as a lower data dependency alternative to estimate transmission parameters of a customized compartmental model, for the purposes of simulating the dynamics of the US COVID-19 epidemics and projecting its further development.\n\nMethodsWe construct a compartmental model. We develop a multistep deep learning methodology to estimate the models transmission parameters. We then feed the estimated transmission parameters to the model to predict the development of the US COVID-19 epidemics for 35 and 42 days. Epidemics are considered suppressed when the basic reproduction number (R0) becomes less than one.\n\nResultsThe deep learning-enhanced compartmental model predicts that R0 will become less than one around June 19 to July 3, 2020, at which point the epidemics will effectively start to die out, and that the US \"Infected\" population will peak round June 18 to July 2, 2020 between 1{middle dot}34 million and 1{middle dot}41 million individual cases. The models also predict that the number of accumulative confirmed cases will cross the 2 million mark around June 10 to 11, 2020.\n\nConclusionsCurrent compartmental models require stochastic parameterization to estimate the transmission parameters. These models effectiveness depends upon detailed statistics on transmission characteristics. As an alternative, deep learning techniques are effective in estimating these stochastic parameters with greatly reduced dependency on data particularity.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "QI DENG", + "author_inst": "Zhejiang Normal University; Cofintelligence Fintech Co. Ltd." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.02.131102", "rel_title": "Brief Communication: Magnetic Immuno-Detection of SARS-CoV-2 specific Antibodies", @@ -1432240,33 +1430763,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.06.02.130955", - "rel_title": "Sarbecovirus comparative genomics elucidates gene content of SARS-CoV-2 and functional impact of COVID-19 pandemic mutations", - "rel_date": "2020-06-03", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.02.130955", - "rel_abs": "Despite its overwhelming clinical importance, the SARS-CoV-2 gene set remains unresolved, hindering dissection of COVID-19 biology. Here, we use comparative genomics to provide a high-confidence protein-coding gene set, characterize protein-level and nucleotide-level evolutionary constraint, and prioritize functional mutations from the ongoing COVID-19 pandemic. We select 44 complete Sarbecovirus genomes at evolutionary distances ideally-suited for protein-coding and non-coding element identification, create whole-genome alignments, and quantify protein-coding evolutionary signatures and overlapping constraint. We find strong protein-coding signatures for all named genes and for 3a, 6, 7a, 7b, 8, 9b, and also ORF3c, a novel alternate-frame gene. By contrast, ORF10, and overlapping-ORFs 9c, 3b, and 3d lack protein-coding signatures or convincing experimental evidence and are not protein-coding. Furthermore, we show no other protein-coding genes remain to be discovered. Cross-strain and within-strain evolutionary pressures largely agree at the gene, amino-acid, and nucleotide levels, with some notable exceptions, including fewer-than-expected mutations in nsp3 and Spike subunit S1, and more-than-expected mutations in Nucleocapsid. The latter also shows a cluster of amino-acid-changing variants in otherwise-conserved residues in a predicted B-cell epitope, which may indicate positive selection for immune avoidance. Several Spike-protein mutations, including D614G, which has been associated with increased transmission, disrupt otherwise-perfectly-conserved amino acids, and could be novel adaptations to human hosts. The resulting high-confidence gene set and evolutionary-history annotations provide valuable resources and insights on COVID-19 biology, mutations, and evolution.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Irwin Jungreis", - "author_inst": "MIT; Broad Institute of MIT and Harvard, Cambridge, MA" - }, - { - "author_name": "Rachel Sealfon", - "author_inst": "Center for Computational Biology, Flatiron Institute, New York, NY" - }, - { - "author_name": "Manolis Kellis", - "author_inst": "MIT" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.05.31.20107862", "rel_title": "Environmental Contamination of SARS-CoV-2 in a Non-Healthcare Setting Revealed by Sensitive Nested RT-PCR", @@ -1433354,6 +1431850,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.31.20118703", + "rel_title": "The Mathematics of Testing with Application to Prevalence of COVID-19", + "rel_date": "2020-06-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.31.20118703", + "rel_abs": "We formulate three basic assumptions that should ideally guide any well-designed COVID-19 prevalence study. We provide, on the basis of these assumptions alone, a full derivation of mathematical formulas required for statistical analysis of testing data. In particular, we express the disease prevalence in a population through those for its homogeneous subpopulations. Although some of these formulas are routinely employed in prevalence studies, the study design often contravenes the assumptions upon which these formulas vitally depend. We also designed a natural prevalence estimator from the testing data and studied some of its properties. The results are equally valid for diseases other than COVID-19 as well as in non-epidemiological settings.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Leonid Hanin", + "author_inst": "Idaho State University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.06.01.20118935", "rel_title": "Trauma-spectrum symptoms among the Italian general population in the time of the COVID-19 outbreak.", @@ -1433894,49 +1432409,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.06.01.20118505", - "rel_title": "Pulmonary Thromboembolic Disease in Patients with COVID-19 Undergoing Computed Tomography Pulmonary Angiography (CTPA): Incidence and Relationship with Pulmonary Parenchymal Abnormalities", - "rel_date": "2020-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20118505", - "rel_abs": "PurposeThis study aims to report the incidence, severity and extent of pulmonary thromboembolic disease (PTD) in patients with confirmed COVID-19 who have undergone CT pulmonary angiography (CTPA) in a tertiary centre.\n\nMaterials and MethodsThis is a retrospective analysis of all patients undergoing CTPA between 23rd March 2020 and 19th April 2020 in a tertiary centre. The presence of PTD, location and involved pulmonary lobes were documented. The pattern and extent of pulmonary parenchymal abnormalities including the presence of fibrosis, lymph node enlargement and pleural effusion were evaluated by two experienced observers independently and consensus was achieved for the most disparate results. Inter-observer agreement was assessed using Kappa statistics. Student t-test, Chi square and Mann-Whitney U tests were used to compare imaging features between PTD and non-PTD sub-groups.\n\nResultsDuring the study period, 2157 patients were confirmed with COVID-19, 297/2157 (13.8%) had CT imaging, 100/2157 (4.6%) were CTPA studies, 93 studies were analysed, excluding suboptimal studies. Overall incidence of PTD was 41/93 (44%) with a third of patients showing segmental and subsegmental PTD (n = 28/93, 30%,). D-dimer was elevated in 90/93 (96.8%) of cases. High Wells score did not differentiate between PE and non-PE groups (p = 0.801). The inter-observer agreement was fair (Kappa = 0.659) for parenchymal pattern and excellent (Kappa = 0.816) for severity. Lymph node enlargement was found in 34/93 of cases (36.6%) with 29/34 (85.3%) showing no additional source of infection. Fibrosis was seen in 16/93 (17.2%) of cases, mainly demonstrating fibrotic organising pneumonia.\n\nConclusionThere is a high incidence of PTD in COVID-19 patients undergoing CTPA, complicated by lack of a valid risk stratification tool. Our data indicates a much higher suspicion of PTD is needed in severe COVID-19 patients. The concomitant presence of fibrotic features on CT indicates the need for follow-up for evaluation of chronic pulmonary complications.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Cheng Fang", - "author_inst": "Kings College Hospital NHS Foundation Trust" - }, - { - "author_name": "Giorgio Garzillo", - "author_inst": "Kings College Hospital NHS Foundation Trust" - }, - { - "author_name": "Bhavna Batohi", - "author_inst": "Kings College Hospital NHS Foundation Trust" - }, - { - "author_name": "James T Teo", - "author_inst": "Kings College Hospital NHS Foundation Trust" - }, - { - "author_name": "Marko Berovic", - "author_inst": "Kings College Hospital NHS Foundation Trust" - }, - { - "author_name": "Paul Sidhu", - "author_inst": "Kings College Hospital NHS Foundation Trust" - }, - { - "author_name": "Hasti Robbie", - "author_inst": "Kings College Hospital NHS Foundation Trust" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.06.01.20119040", "rel_title": "Factors associated with adherence to self-isolation and lockdown measures in the UK; a cross-sectional survey", @@ -1434928,6 +1433400,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.06.01.20119768", + "rel_title": "Association between NSAIDs use and adverse clinical outcomes among adults hospitalised with COVID-19 in South Korea: A nationwide study", + "rel_date": "2020-06-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20119768", + "rel_abs": "BACKGROUNDNon-steroidal anti-inflammatory drugs (NSAIDs) may exacerbate COVID-19 and worsen associated outcomes by upregulating the enzyme that SARS-CoV-2 binds to enter cells. However, to our knowledge, no study has examined the association between NSAID use and the risk of COVID-19-related outcomes among hospitalised patients.\n\nMETHODSWe conducted a population-based cohort study using South Koreas nationwide healthcare database, which contains data of all subjects who received a test for COVID-19 (n=69,793) as of April 8, 2020. We identified a cohort of adults hospitalised with COVID-19, where cohort entry was the date of hospitalisation. NSAIDs users were those prescribed NSAIDs in the 7 days before and including the date of cohort entry and non-users were those not prescribed NSAIDs during this period. Our primary outcome was a composite of in-hospital death, intensive care unit admission, mechanical ventilation use, and sepsis; our secondary outcome was cardiovascular or renal complications. We conducted logistic regression analysis to estimate odds ratio (OR) with 95% confidence intervals (CI) using inverse probability of treatment weighting to minimize potential confounding.\n\nFINDINGSOf 1,824 adults hospitalised with COVID-19 (mean age 490 years, standard deviation 19 0 years; female 59%), 354 were NSAIDs users and 1,470 were non-users. Compared with non-use, NSAIDs use was associated with increased risks of the primary composite outcome (OR 1 65, 95% CI 1-21-2-24) and of cardiovascular or renal complications (OR 187, 95% CI 1-25-2-80). Our main findings remained consistent when we extended the exposure ascertainment window to include the first three days of hospitalisation (OR 187, 95% CI 1 06-3 29).\n\nINTERPRETATIONUse of NSAIDs, compared with non-use, is associated with worse outcomes among hospitalised COVID-19 patients. While awaiting the results of confirmatory studies, we suggest NSAIDs be used with caution among patients with COVID-19 as the harms associated with their use may outweigh their benefits in this population.\n\nFUNDINGGovernment-wide R&D Fund for Infectious Disease Research (HG18C0068).", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Han Eol Jeong", + "author_inst": "School of Pharmacy, Sungkyunkwan University" + }, + { + "author_name": "Hyesung Lee", + "author_inst": "School of Pharmacy, Sungkyunkwan University" + }, + { + "author_name": "Hyun Joon Shin", + "author_inst": "Division of General Internal Medicine, Department of Medicine, Brigham and Women's Hospital, Department of Global Health and Social Medicine, Harvard Medical Sc" + }, + { + "author_name": "Young June Choe", + "author_inst": "Hallym University College of Medicine" + }, + { + "author_name": "Kristian B Filion", + "author_inst": "Departments of Medicine and Epidemiology, Biostatistics and Occupational Health, McGill University and Centre for Clinical Epidemiology, Lady Davis Institute" + }, + { + "author_name": "Ju-Young Shin", + "author_inst": "School of Pharmacy, Sungkyunkwan University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.27.20114538", "rel_title": "COVID-19 containment in the Caribbean: the experience of Small Island Developing States", @@ -1435400,57 +1433911,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2020.05.29.20114199", - "rel_title": "Effect of Dry Heat and Autoclave Decontamination Cycles on N95 FFRs", - "rel_date": "2020-06-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.29.20114199", - "rel_abs": "Current shortages of Filtering Facepiece Respirators (FFRs) have created a demand for effective methods for N95 decontamination and reuse. Before implementing any reuse strategy it is important to determine what effects the proposed method has on the physical functioning of the FFR. Here we investigate the effects of two potential methods for decontamination; dry heat at 95 {degrees}C, and autoclave treatments. We test both fit and filtration efficiency for each method. For the dry heat treatment we consider the 3M 1860, 3M 1870, and 3M8210+ models. After five cycles of the dry heating method, all three FFR models pass both fit and filtration tests, showing no degradation. For the autoclave tests we consider the 3M 1870, and the 3M 8210+. We find significant degradation of the FFRs following the 121 {degrees}C autoclave cycles. The molded mask tested (3M 8210+) failed fit testing after just 1 cycle in the autoclave. The pleated (3M 1870) mask passed fit testing for 5 cycles, but failed filtration testing. The 95 {degrees}C dry heat cycle is scalable to over a thousand masks per day in a hospital setting, and is above the temperature which has been shown to achieve the requisite 3 log kill of SARS-CoV-2[1], making it a promising method for N95 decontamination and reuse.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Cole Meisenhelder", - "author_inst": "Harvard University" - }, - { - "author_name": "Lo\u00efc Anderegg", - "author_inst": "Harvard University" - }, - { - "author_name": "Andrew Preecha", - "author_inst": "Harvard University" - }, - { - "author_name": "Chiu Oan Ngooi", - "author_inst": "Harvard University" - }, - { - "author_name": "Lei Liao", - "author_inst": "4C Air" - }, - { - "author_name": "Wang Xiao", - "author_inst": "4C Air" - }, - { - "author_name": "Steven Chu", - "author_inst": "Stanford University" - }, - { - "author_name": "Yi Cui", - "author_inst": "Stanford University" - }, - { - "author_name": "John M Doyle", - "author_inst": "Harvard University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.05.31.20114991", "rel_title": "The ABO blood group locus and a chromosome 3 gene cluster associate with SARS-CoV-2 respiratory failure in an Italian-Spanish genome-wide association analysis", @@ -1437126,6 +1435586,69 @@ "type": "new results", "category": "biophysics" }, + { + "rel_doi": "10.1101/2020.06.02.130161", + "rel_title": "An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction", + "rel_date": "2020-06-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.02.130161", + "rel_abs": "SARS-CoV-2 is the etiologic agent of COVID-19, currently causing a devastating pandemic for which pharmacological interventions are urgently needed. The virus enters host cells through an interaction between the spike glycoprotein and the angiotensin converting enzyme 2 (ACE2) receptor. Directly preventing this interaction presents an attractive possibility for suppressing SARS-CoV-2 replication. Here we report the isolation and characterization of an alpaca-derived single domain antibody fragment, Ty1, that specifically targets the receptor binding domain (RBD) of the SARS-CoV-2 spike, directly preventing ACE2 engagement. The nanobody binds with high affinity in the low nM range to the RBD, occluding ACE2. A cryo-electron microscopy structure of the bound complex at 2.9 \u00c5 resolution reveals that Ty1 binds to an epitope on the RBD accessible in both the \u2018up\u2019 and \u2018down\u2019 conformations and that Ty1 sterically hinders RBD-ACE2 binding. This 12.8 kDa nanobody does not need an Fc domain to neutralize SARS-CoV-2, and can be expressed in high quantities in bacteria, presenting opportunities for manufacturing at scale. Ty1 is therefore an excellent candidate as an intervention against COVID-19.Competing Interest StatementThe authors have declared no competing interest.View Full Text", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Leo Hanke", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Maria Laura Perez Vidakovics", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Daniel Sheward", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Hrishikesh Das", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Tim Schulte", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Ainhoa Moliner Morro", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Martin Corcoran", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Adnane Achour", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Gunilla Karlsson Hedestam", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "B. Martin H\u00e4llberg", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Ben Murrell", + "author_inst": "Karolinska Institutet" + }, + { + "author_name": "Gerald M McInerney", + "author_inst": "Karolinska Institutet" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.06.02.129775", "rel_title": "Optimizing the molecular diagnosis of Covid-19 by combining RT-PCR and a pseudo-convolutional machine learning approach to characterize virus DNA sequences", @@ -1437566,33 +1436089,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.06.01.20118885", - "rel_title": "Modelling testing frequencies required for early detection of a SARS-CoV-2 outbreak on a university campus", - "rel_date": "2020-06-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.06.01.20118885", - "rel_abs": "BackgroundEarly detection and risk mitigation efforts are essential for averting large outbreaks of SARS-CoV-2. Active surveillance for SARS-CoV-2 can aid in early detection of outbreaks, but the testing frequency required to identify an outbreak at its earliest stage is unknown. We assess what testing frequency is required to detect an outbreak before there are 10 detectable infections.\n\nMethodsA dynamic compartmental transmission model of SARS-CoV-2 was developed to simulate spread among a university community. After introducing a single infection into a fully susceptible population, we calculate the probability of detecting at least one case on each succeeding day with various NAT testing frequencies (daily testing achieving 25%, 50%, 75%, and 100% of the population tested per month) assuming an 85% test sensitivity. A proportion of infected individuals (varied from 1-60%) are assumed to present to health services (HS) for symptomatic testing. We ascertain the expected number of detectable infections in the community when there is a > 90% probability of detecting at least 1 case. Sensitivity analyses examine impact of transmission rates (Rt = 0 = 2, 2.5,3), presentation to HS (1%/5%/30%/60%), and pre-existing immunity (0%/10%)\n\nResultsAssuming an 85% test sensitivity, identifying an outbreak with 90% probability when the expected number of detectable infections is 9 or fewer requires NAT testing of 100% of the population per month; this result holds for all transmission rates and all levels of presentation at health services we considered. If 1% of infected people present at HS and Rt=0=3, testing 75%/50%/25% per month could identify an outbreak when the expected numbers of detectable infections are 12/17/30 respectively; these numbers decline to 9/11/12 if 30% of infected people present at HS. As proportion of infected individuals present at health services increases, the marginal impact of active surveillance is reduced. Higher transmission rates result in shorter time to detection but also rapidly escalating cases without intervention. Little differences were observed with 10% pre-existing immunity.\n\nConclusionsWidespread testing of 100% of the campus population every month is required to detect an outbreak when there are fewer than 9 detectable infections for the scenarios examined, but high presentation of symptomatic people at HS can compensate in part for lower levels of testing. Early detection is necessary, but not sufficient, to curtail disease outbreaks; the proposed testing rates would need to be accompanied by case isolation, contact tracing, quarantine, and other risk mitigation and social distancing interventions.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Natasha Martin", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Robert T Schooley", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Victor De Gruttola", - "author_inst": "Harvard University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.06.01.20118901", "rel_title": "Rapid systematic review on clinical evidence of chloroquine and hydroxychloroquine in COVID-19: critical assessment and recommendation for future clinical trials", @@ -1438512,6 +1437008,57 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.06.01.127589", + "rel_title": "Reconstructing SARS-CoV-2 response signaling and regulatory networks", + "rel_date": "2020-06-01", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.06.01.127589", + "rel_abs": "Several molecular datasets have been recently compiled to characterize the activity of SARS-CoV-2 within human cells. Here we extend computational methods to integrate several different types of sequence, functional and interaction data to reconstruct networks and pathways activated by the virus in host cells. We identify key proteins in these networks and further intersect them with genes differentially expressed at conditions that are known to impact viral activity. Several of the top ranked genes do not directly interact with virus proteins. We experimentally tested treatments for a number of the predicted targets. We show that blocking one of the predicted indirect targets significantly reduces viral loads in stem cell-derived alveolar epithelial type II cells (iAT2s).\n\nSoftware and interactive visualizationhttps://github.com/phoenixding/sdremsc", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Jun Ding", + "author_inst": "McGill University" + }, + { + "author_name": "Jose Lugo-Martinez", + "author_inst": "Carnegie Mellon University" + }, + { + "author_name": "Ye Yuan", + "author_inst": "Shanghai Jiao Tong University" + }, + { + "author_name": "Jessie Huang", + "author_inst": "Boston University" + }, + { + "author_name": "Adam Joseph Hume", + "author_inst": "Boston University" + }, + { + "author_name": "Ellen L Suder", + "author_inst": "Boston University" + }, + { + "author_name": "Elke Muhlberger", + "author_inst": "Boston University" + }, + { + "author_name": "Darrell N. Kotton", + "author_inst": "Boston University" + }, + { + "author_name": "Ziv Bar-Joseph", + "author_inst": "Carnegie Mellon University" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "systems biology" + }, { "rel_doi": "10.1101/2020.05.31.126813", "rel_title": "Covid-19 pandemic and the unprecedented mobilisation of scholarly efforts prompted by a health crisis: Scientometric comparisons across SARS, MERS and 2019-nCov literature", @@ -1439011,65 +1437558,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2020.05.31.126136", - "rel_title": "A distinct phylogenetic cluster of Indian SARS-CoV-2 isolates", - "rel_date": "2020-05-31", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.31.126136", - "rel_abs": "From an isolated epidemic, COVID-19 has now emerged as a global pandemic. The availability of genomes in the public domain following the epidemic provides a unique opportunity to understand the evolution and spread of the SARS-CoV-2 virus across the globe. The availability of whole genomes from multiple states in India prompted us to analyse the phylogenetic clusters of genomes in India. We performed whole-genome sequencing for 64 genomes making a total of 361 genomes from India, followed by phylogenetic clustering, substitution analysis, and dating of the different phylogenetic clusters of viral genomes. We describe a distinct phylogenetic cluster (Clade I / A3i) of SARS-CoV-2 genomes from India, which encompasses 41% of all genomes sequenced and deposited in the public domain from multiple states in India. Globally 3.5% of genomes, which till date could not be mapped to any distinct known cluster fall in this newly defined clade. The cluster is characterized by a core set of shared genetic variants - C6312A (T2016K), C13730T (A88V/A97V), C23929T, and C28311T (P13L). Further, the cluster is also characterized by a nucleotide substitution rate of 1.4 x 10-3 variants per site per year, lower than the prevalent A2a cluster, and predominantly driven by variants in the E and N genes and relative sparing of the S gene. Epidemiological assessments suggest that the common ancestor emerged in the month of February 2020 and possibly resulted in an outbreak followed by countrywide spread, as evidenced by the low divergence of the genomes from across the country. To the best of our knowledge, this is the first comprehensive study characterizing the distinct and predominant cluster of SARS-CoV-2 in India.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Sofia Banu", - "author_inst": "CSIR Centre for Cellular and Molecular Biology" - }, - { - "author_name": "Bani Jolly", - "author_inst": "CSIR Institute of Genomics and Integrative Biology" - }, - { - "author_name": "Payel Mukherjee", - "author_inst": "CSIR Centre for Cellular and Molecular Biology" - }, - { - "author_name": "Priya Singh", - "author_inst": "CSIR Centre for Cellular and Molecular Biology" - }, - { - "author_name": "Shagufta Khan", - "author_inst": "CSIR Centre for Cellular and Molecular Biology" - }, - { - "author_name": "Lamuk Zaveri", - "author_inst": "CSIR Centre for Cellular and Molecular Biology" - }, - { - "author_name": "Sakshi Shambhavi", - "author_inst": "CSIR Centre for Cellular and Molecular Biology" - }, - { - "author_name": "Namami Gaur", - "author_inst": "CSIR Centre for Cellular and Molecular Biology" - }, - { - "author_name": "Rakesh K Mishra", - "author_inst": "CSIR Centre for Cellular and Molecular Biology" - }, - { - "author_name": "Vinod Scaria", - "author_inst": "CSIR Institute of Genomics & Integrative Biology" - }, - { - "author_name": "Divya Tej Sowpati", - "author_inst": "CSIR Centre for Cellular and Molecular Biology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.05.30.125856", "rel_title": "Sofosbuvir protects human brain organoids against SARS-CoV-2", @@ -1440153,6 +1438641,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.30.20117291", + "rel_title": "EasyCOV : LAMP based rapid detection of SARS-CoV-2 in saliva", + "rel_date": "2020-05-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.30.20117291", + "rel_abs": "Covid-19 crisis showed us that rapid massive virus detection campaign is a key element in SARS-CoV-2 pandemic response. The classical RT-PCR laboratory platforms must be complemented with rapid and simplified technologies to enhance efficiency of large testing strategies.\n\nTo this aim, we developed EasyCOV, a direct saliva RT-LAMP based SARS-CoV-2 virus detection assay that do not requires any RNA extraction step. It allows robust and rapid response under safe and easy conditions for healthcare workers and patients.\n\nEasyCOV test was assessed under double blind clinical conditions (93 asymptomatic healthcare worker volonteers, 10 actively infected patients, 20 former infected patients tested during late control visit). EasyCOV results were compared with classical laboratory RT-PCR performed on nasopharyngeal samples.\n\nOur results show that compared with nasopharyngeal laboratory RT-PCR, EasyCOV SARS-CoV-2 detection test has a sensitivity of 72.7%. Measured on healthcare worker population the specificity was 95.7%. LAMP technology on saliva is clearly able to identify subjects with infectivity profile. Among healthcare worker population EasyCOV test detected one presymptomatic subject.\n\nBecause it is simple, rapid and painless for patients, EasyCOV saliva SARS-Cov-2 detection test may be useful for large screening of general population.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Nicolas L'Helgouach", + "author_inst": "Sys2diag CNRS / ALCEDIAG" + }, + { + "author_name": "Pierre Champigneux", + "author_inst": "Sys2diag CNRS / ALCEDIAG" + }, + { + "author_name": "Francisco Santos-Schneider", + "author_inst": "Sys2diag CNRS / ALCEDIAG" + }, + { + "author_name": "Laurence Molina", + "author_inst": "Sys2diag CNRS / ALCEDIAG" + }, + { + "author_name": "Julien Espeut", + "author_inst": "Sys2diag CNRS / ALCEDIAG" + }, + { + "author_name": "Mellis Alali", + "author_inst": "Sys2diag CNRS / ALCEDIAG" + }, + { + "author_name": "Julie Baptiste", + "author_inst": "Sys2diag CNRS / ALCEDIAG" + }, + { + "author_name": "Lise Cardeur", + "author_inst": "Sys2diag CNRS / ALCEDIAG" + }, + { + "author_name": "Benjamin Dubuc", + "author_inst": "Sys2diag CNRS / ALCEDIAG" + }, + { + "author_name": "Vincent Foulongne", + "author_inst": "Virology Dpt University Hospital Montpellier" + }, + { + "author_name": "Florence Galtier", + "author_inst": "CIC University Hospital Montpellier" + }, + { + "author_name": "Alain Makinson", + "author_inst": "Infectious diseases dpt University Hospital Montpellier" + }, + { + "author_name": "Gregory Marin", + "author_inst": "DIM clinical research unit University Hospital Montpellier" + }, + { + "author_name": "Marie-Chritine Picot", + "author_inst": "DIM clinical research unit University Hospital Montpellier" + }, + { + "author_name": "Alexandra Prieux-Lejeune", + "author_inst": "Sys2diag CNRS / ALCEDIAG, Montpellier, France" + }, + { + "author_name": "Marine Quenot", + "author_inst": "Sys2diag CNRS / ALCEDIAG, Montpellier, France" + }, + { + "author_name": "Francisco Jesus Checa-Robles", + "author_inst": "Sys2diag CNRS / ALCEDIAG, Montpellier, France" + }, + { + "author_name": "Nicolas Salvetat", + "author_inst": "Sys2diag CNRS / ALCEDIAG, Montpellier, France" + }, + { + "author_name": "Diana Vetter", + "author_inst": "Sys2diag CNRS / ALCEDIAG, Montpellier, France" + }, + { + "author_name": "Jacques Reynes", + "author_inst": "Infectious diseases dpt University Hospital Montpellier" + }, + { + "author_name": "Franck Molina", + "author_inst": "Sys2diag CNRS / ALCEDIAG, Montpellier, France" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.28.20115741", "rel_title": "Chloroquine, hydroxychloroquine, and COVID-19: systematic review and narrative synthesis of efficacy and safety", @@ -1440557,97 +1439144,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2020.05.29.20116376", - "rel_title": "Early transmission of SARS-CoV-2 in South Africa: An epidemiological and phylogenetic report", - "rel_date": "2020-05-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.29.20116376", - "rel_abs": "BackgroundThe emergence of a novel coronavirus, SARS-CoV-2, in December 2019, progressed to become a world pandemic in a few months and reached South Africa at the beginning of March. To investigate introduction and understand the early transmission dynamics of the virus, we formed the South African Network for Genomics Surveillance of COVID (SANGS_COVID), a network of ten government and university laboratories. Here, we present the first results of this effort, which is a molecular epidemiological study of the first twenty-one SARS-CoV-2 whole genomes sampled in the first port of entry, KwaZulu-Natal (KZN), during the first month of the epidemic. By combining this with calculations of the effective reproduction number (R), we aim to shed light on the patterns of infections that define the epidemic in South Africa.\n\nMethodsR was calculated using positive cases and deaths from reports provided by the four major provinces. Molecular epidemiology investigation involved sequencing viral genomes from patients in KZN using ARCTIC protocols and assembling whole genomes using meticulous alignment methods. Phylogenetic analysis was performed using maximum likelihood (ML) and Bayesian trees, lineage classification and molecular clock calculations.\n\nFindingsThe epidemic in South Africa has been very heterogeneous. Two of the largest provinces, Gauteng, home of the two large metropolis Johannesburg and Pretoria, and KwaZulu-Natal, home of the third largest city in the country Durban, had a slow growth rate on the number of detected cases. Whereas, Western Cape, home of Cape Town, and the Eastern Cape provinces the epidemic is spreading fast. Our estimates of transmission potential for South Africa suggest a decreasing transmission potential towards R=1 since the first cases and deaths have been reported. However, between 06 May and 18 May 2020, we estimate that R was on average 1.39 (1.04-2.15, 95% CI). We also demonstrate that early transmission in KZN, and most probably in all main regions of SA, was associated with multiple international introductions and dominated by lineages B1 and B. The study also provides evidence for locally acquired infections in a hospital in Durban within the first month of the epidemic, which inflated early mortality in KZN.\n\nInterpretationThis first report of SANGS_COVID consortium focuses on understanding the epidemic heterogeneity and introduction of SARS-CoV-2 strains in the first month of the epidemic in South Africa. The early introduction of SARS-CoV-2 in KZN included caused a localized outbreak in a hospital, provides potential explanations for the initially high death rates in the province. The current high rate of transmission of COVID-19 in the Western Cape and Eastern Cape highlights the crucial need to strength local genomic surveillance in South Africa.\n\nFundingUKZN Flagship Program entitled: Afrocentric Precision Approach to Control Health Epidemic, by a research Flagship grant from the South African Medical Research Council (MRC-RFA-UFSP-01- 2013/UKZN HIVEPI, by the the Technology Innovation Agency and the the Department of Science and Innovation and by National Human Genome Re- search Institute of the National Institutes of Health under Award Number U24HG006941. H3ABioNet is an initiative of the Human Health and Heredity in Africa Consortium (H3Africa).\n\nResearch in context Evidence before this studyWe searched PubMed, BioRxiv and MedRxiv for reports on epidemiology and phylogenetic analysis using whole genome sequencing (WGS) of SARS-CoV-2. We used the following keywords: SARS-CoV-2, COVID-19, 2019-nCoV or novel coronavirus and transmission genomics, epidemiology, phylogenetic or reproduction number. Our search identified an important lack of molecular epidemiology studies in the southern hemisphere, with only a few reports from Latin America and one in Africa. In other early transmission reports on SARS-CoV-2 infections in Africa, authors focused on transmission dynamics, but molecular and phylogenetic methods were missing.\n\nAdded value of this studyWith a growing sampling bias in the study of transmission genomics of the SARS-CoV-2 pandemic, it is important for us to report high-quality whole genome sequencing (WGS) of local SARS-CoV-2 samples and in-depth phylogenetic analyses of the first month of infection in South-Africa. In our molecular epidemiological investigation, we identify the early transmission routes of the infection in the KZN and report thirteen distinct introductions from many locations and a cluster of localized transmission linked to a healthcare setting that caused most of the initial deaths in South Africa. Furthermore, we formed a national consortium in South Africa, funded by the Department of Science and Innovation and the South African Medical Research Council, to capacitate ten local laboratories to produce and analyse SARS-CoV-2 data in near real time.\n\nImplications of all the available evidenceThe COVID-19 pandemic is progressing around the world and in Africa. Early transmission genomics and dynamics of SARS-CoV-2 throw light on the early stages of the epidemic in a given region. This facilitates the investigation of localized outbreaks and serves to inform public health responses in South Africa.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Jennifer Giandhari", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South " - }, - { - "author_name": "Sureshnee Pillay", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South " - }, - { - "author_name": "Eduan Wilkinson", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South " - }, - { - "author_name": "Houriiyah Tegally", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South " - }, - { - "author_name": "Ilya Sinayskiy", - "author_inst": "Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa" - }, - { - "author_name": "Maria Schuld", - "author_inst": "Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa" - }, - { - "author_name": "Jos\u00e9 Louren\u00e7o", - "author_inst": "University of Oxford" - }, - { - "author_name": "Benjamin Chimukangara", - "author_inst": "University of KwaZulu Natal" - }, - { - "author_name": "Richard John Lessells", - "author_inst": "Infectious Diseases Department, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa" - }, - { - "author_name": "Yunus Moosa", - "author_inst": "Infectious Diseases Department, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa" - }, - { - "author_name": "Inbal Gazy", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South " - }, - { - "author_name": "Maryam Fish", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South " - }, - { - "author_name": "Lavanya Singh", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South " - }, - { - "author_name": "Khulekani Sedwell Khanyile", - "author_inst": "KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South " - }, - { - "author_name": "Vagner Fonseca", - "author_inst": "Laboratorio de Genetica Celular e Molecular, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil" - }, - { - "author_name": "Marta Giovanetti", - "author_inst": "Fundacao Oswaldo Cruz" - }, - { - "author_name": "Luiz Carlos Junior Alcantara", - "author_inst": "Instituto Oswaldo Cruz" - }, - { - "author_name": "Francesco Petruccione", - "author_inst": "Quantum Research Group, School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa" - }, - { - "author_name": "Tulio de Oliveira", - "author_inst": "University of KwaZulu-Natal" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.27.120402", "rel_title": "Genomic analysis of early SARS-CoV-2 strains introduced in Mexico", @@ -1441695,6 +1440191,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2020.05.28.20115832", + "rel_title": "COVID-19 higher morbidity and mortality in Chinese regions with lower air quality", + "rel_date": "2020-05-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.28.20115832", + "rel_abs": "We investigated the geographical character of the COVID-19 infection in China and correlated it with satellite- and ground-based measurements of air quality. Controlling for population size, we found more viral infections in those areas afflicted by high Carbon Monoxide, formaldehyde, PM 2.5, and Nitrogen Dioxide values. Higher mortality was also correlated with relatively poor air quality. Air pollution appears to be a risk factor for the incidence of this disease, similar to smoking. This suggests the detrimental impact of air pollution in these types of respiratory epidemics.\n\nShort summaryO_LIThere is a significant correlation between air pollution and COVID-19 spread and mortality in China.\nC_LIO_LIThe correlation stands at a second-order administration level, after controlling for varying population densities and removing Wuhan and Hubei from the dataset.\nC_LIO_LILiving in an area with low air quality is a risk factor for becoming infected and dying from this new form of coronavirus.\nC_LI", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Riccardo Pansini", + "author_inst": "Yunnan University of Finance and Economics" + }, + { + "author_name": "Davide Fornacca", + "author_inst": "Institute of Eastern-Himalaya Biodiversity Research, Dali University, Yunnan, China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.29.123455", "rel_title": "The representation of women as authors of submissions to ecology journals during the COVID-19 pandemic", @@ -1442095,33 +1440614,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.29.20116657", - "rel_title": "Loneliness during lockdown: trajectories and predictors during the COVID-19 pandemic in 35,712 adults in the UK", - "rel_date": "2020-05-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.29.20116657", - "rel_abs": "There are increasing worries that lockdowns and \"stay-at-home\" orders due to the COVID-19 pandemic could lead to a rise in loneliness, which is recognised as a major public health concern. But profiles of loneliness during the pandemic and risk factors remain unclear.\n\nData from 35,712 UK adults in the UCL COVID-19 Social Study (a panel study collecting data weekly during the pandemic) were analysed from 21/03/2020-03/05/2020. The sample was well-stratified and weighted to population proportions of gender, age, ethnicity, education and geographical location. Growth mixture modelling was used to identify the latent classes of loneliness growth trajectories and their predictors.\n\nAnalyses revealed four classes, with the baseline loneliness level ranging from low to high. In the first six weeks of lockdown, loneliness levels increased in the highest loneliness group, decreased in the lowest loneliness group, and stayed relatively constant in the middle two groups. Younger adults (OR = 2.17-6.81), women (OR = 1.59), people with low income (OR = 1.3), the economically inactive (OR = 1.3-2.04) and people with mental health conditions (OR = 5.32) were more likely to be in highest loneliness class relative to the lowest. Further, living with others or in a rural area, and having more close friends or greater social support were protective.\n\nPerceived levels of loneliness in the first few weeks of lockdown during COVID-19 were relatively stable in the UK, but for many people these levels were high with no signs of improvement. Results suggest that more efforts are needed to address loneliness, especially amongst young people.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Feifei Bu", - "author_inst": "University College London" - }, - { - "author_name": "Andrew Steptoe", - "author_inst": "University College London" - }, - { - "author_name": "Daisy Fancourt", - "author_inst": "University College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.05.29.20116889", "rel_title": "Serum proteomics in COVID-19 patients: Altered coagulation and complement status as a function of IL-6 level", @@ -1442985,6 +1441477,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.27.20114371", + "rel_title": "Covid19db -- An online database of trials of medicinal products to prevent or treat COVID-19, with a specific focus on drug repurposing", + "rel_date": "2020-05-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.27.20114371", + "rel_abs": "BackgroundThe global pandemic caused by SARS-CoV-2 virus has prompted an unprecedented international effort to seek medicines for prevention and treatment of infection. Drug repurposing has played a key part in this response. The rapid increase in trial activity has raised questions about efficiency and lack of coordination. Our objective was to develop a user-friendly, open access database to monitor and rapidly identify trials of medicinal products.\n\nMethodsUsing the US clinicaltrials.gov (NCT) registry, the EU Clinical Trials Register (EUCTR) and the WHO International Clinical Trials Registry Platform (WHO ICTRP), we identified all COVID-19 trials of medicinal products. Trials that were out of scope and duplicates were excluded. A manual encoding was performed to ascertain key information (e.g. trial aim, type of intervention etc). The database, Covid19db, is published online at: http://www.redo-project.org/covid19db/.\n\nResultsDescriptive statistics of the database from April 4th 2020 through to August 18th show an increase from 186 to 1618 trials, or an average of 10.5 new trials registered per day. Over this period, the proportion of trials including a repurposing arm decreased slightly (from a maximum of 75% to 64% at the end of the covered period) as did the proportion of trials aiming to prevent infection (from a maximum of 16% to 13%). The most popular trial intervention is hydroxychloroquine (212 trials), followed by azithromycin (64 trials), tocilizumab, favipiravir and chloroquine (145 trials). Total planned enrolment is 1064556 participants as of 18th August 2020.\n\nConclusionswe have developed an open access and regularly updated tool to monitor clinical trials of medicinal products to prevent or treat infection by SARS-CoV-2 globally. Our analysis shows a high number of me-too trials, in particular for some repurposed drugs, such as hydroxychloroquine, azithromycin and tocilizumab, substantiating calls for better coordination and better use of trial resources.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Pan Pantziarka", + "author_inst": "Anticancer Fund" + }, + { + "author_name": "Liese Vandeborne", + "author_inst": "Anticancer Fund" + }, + { + "author_name": "Lydie Meheus", + "author_inst": "Anticancer Fund" + }, + { + "author_name": "Gauthier Bouche", + "author_inst": "Anticancer Fund" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.27.20114983", "rel_title": "A call for governments to pause Twitter censorship: a cross-sectional study using Twitter data as social-spatial sensors of COVID-19/SARS-CoV-2 research diffusion", @@ -1443265,53 +1441788,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.27.20114728", - "rel_title": "Lessons from movement ecology for the return to work: modeling contacts and the spread of COVID-19", - "rel_date": "2020-05-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.27.20114728", - "rel_abs": "Human behavior (movement, social contacts) plays a central role in the spread of pathogens like SARS- CoV-2. The rapid spread of SARS-CoV-2 was driven by global human movement, and initial lockdown measures aimed to localize movement and contact in order to slow spread. Thus, movement and contact patterns need to be explicitly considered when making reopening decisions, especially regarding return to work. Here, as a case study, we consider the initial stages of resuming research at a large research university, using approaches from movement ecology and contact network epidemiology. First, we develop a dynamical pathogen model describing movement between home and work; we show that limiting social contact, via reduced people or reduced time in the workplace are fairly equivalent strategies to slow pathogen spread. Second, we develop a model based on spatial contact patterns within a specific office and lab building on campus; we show that restricting on-campus activities to labs (rather than labs and offices) could dramatically alter (modularize) contact network structure and thus, potentially reduce pathogen spread by providing a workplace mechanism to reduce contact. Here we argue that explicitly accounting for human movement and contact behavior in the workplace can provide additional strategies to slow pathogen spread that can be used in conjunction with ongoing public health efforts.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Allison K Shaw", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Lauren A White", - "author_inst": "University of Maryland College Park" - }, - { - "author_name": "Matthew Michalska-Smith", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Elizabeth T Borer", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Meggan E Craft", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Eric W Seabloom", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Emilie Snell-Rood", - "author_inst": "University of Minnesota" - }, - { - "author_name": "Michael Travisano", - "author_inst": "University of Minnesota" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.26.20113258", "rel_title": "Belief in Conspiracy Theory about COVID-19 Predicts Mental Health and Well-being -- A Study of Healthcare Staff in Ecuador", @@ -1444183,6 +1442659,53 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.05.29.123612", + "rel_title": "SARS-CoV-2 transmission chains from genetic data: a Danish case study", + "rel_date": "2020-05-29", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.29.123612", + "rel_abs": "Background The COVID-19 pandemic caused by the SARS-CoV-2 virus started in China in December 2019 and has since spread globally. Information about the spread of the virus in a country can inform the gradual reopening of a country and help to avoid a second wave of infections. Denmark is currently opening up after a lockdown in mid-March.Methods We perform a phylogenetic analysis of 742 publicly available Danish SARS-CoV-2 genome sequences and put them into context using sequences from other countries.Result Our findings are consistent with several introductions of the virus to Denmark from independent sources. We identify several chains of mutations that occurred in Denmark and in at least one case find evidence that the virus spread from Denmark to other countries. A number of the mutations found in Denmark are non-synonymous, and in general there is a considerable variety of strains. The proportions of the most common haplotypes is stable after lockdown.Conclusion Our work shows how genetic data can be used to identify routes of introduction of a virus into a region and provide alternative means for verifying existing assumptions. For example, our analysis supports the hypothesis that the virus was brought to Denmark by skiers returning from Ischgl. On the other hand, we identify transmission chains suggesting that Denmark was part of a network of countries among which the virus was being transmitted; thus challenging the common narrative that Denmark only got infected from abroad. Our analysis does not indicate that the major haplotypes appearing in Denmark have a different degree of virality. Our methods can be applied to other countries, regions or even highly localised outbreaks. When used in real-time, we believe they can serve to identify transmission events and supplement traditional methods such as contact tracing.Competing Interest StatementThe authors have declared no competing interest.View Full Text", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Andreas Bluhm", + "author_inst": "University of Copenhagen" + }, + { + "author_name": "Matthias Christandl", + "author_inst": "University of Copenhagen" + }, + { + "author_name": "Fulvio Gesmundo", + "author_inst": "University of Copenhagen" + }, + { + "author_name": "Frederik Ravn Klausen", + "author_inst": "University of Copenhagen" + }, + { + "author_name": "Laura Mancinska", + "author_inst": "University of Copenhagen" + }, + { + "author_name": "Vincent Steffan", + "author_inst": "University of Copenhagen" + }, + { + "author_name": "Daniel Stilck Franca", + "author_inst": "University of Copenhagen" + }, + { + "author_name": "Albert Werner", + "author_inst": "University of Copenhagen" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.05.28.122366", "rel_title": "Evidence of significant natural selection in the evolution of SARS-CoV-2 in bats, not humans", @@ -1444519,113 +1443042,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.28.121533", - "rel_title": "Structures of human antibodies bound to SARS-CoV-2 spike reveal common epitopes and recurrent features of antibodies", - "rel_date": "2020-05-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.28.121533", - "rel_abs": "Neutralizing antibody responses to coronaviruses focus on the trimeric spike, with most against the receptor-binding domain (RBD). Here we characterized polyclonal IgGs and Fabs from COVID-19 convalescent individuals for recognition of coronavirus spikes. Plasma IgGs differed in their degree of focus on RBD epitopes, recognition of SARS-CoV, MERS-CoV, and mild coronaviruses, and how avidity effects contributed to increased binding/neutralization of IgGs over Fabs. Electron microscopy reconstructions of polyclonal plasma Fab-spike complexes showed recognition of both S1A and RBD epitopes. A 3.4[A] cryo-EM structure of a neutralizing monoclonal Fab-S complex revealed an epitope that blocks ACE2 receptor-binding on \"up\" RBDs. Modeling suggested that IgGs targeting these sites have different potentials for inter-spike crosslinking on viruses and would not be greatly affected by identified SARS-CoV-2 spike mutations. These studies structurally define a recurrent anti-SARS-CoV-2 antibody class derived from VH3-53/VH3-66 and similarity to a SARS-CoV VH3-30 antibody, providing criteria for evaluating vaccine-elicited antibodies.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "Christopher O Barnes", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Anthony P West Jr.", - "author_inst": "California Institute Technology" - }, - { - "author_name": "Kathryn Huey-Tubman", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Magnus A.G. Hoffmann", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Naima G. Sharaf", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Pauline R. Hoffman", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Nicholas Koranda", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Harry B. Gristick", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Christian Gaebler", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Frauke Muecksch", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Julio C Cetrulo Lorenzi", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Shlomo Finkin", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Thomas Hagglof", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Arlene Hurley", - "author_inst": "California Institute of Technology" - }, - { - "author_name": "Katrina G Millard", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Yiska Weisblum", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Fabian Schmidt", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Theodora Hatziioannou", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Paul D Bieniasz", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Marina Caskey", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Davide Robbiani", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Michel C Nussenzweig", - "author_inst": "Rockefeller University" - }, - { - "author_name": "Pamela J Bjorkman", - "author_inst": "California Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.05.28.118059", "rel_title": "An enhanced isothermal amplification assay for viral detection", @@ -1445653,6 +1444069,105 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.05.28.121640", + "rel_title": "Single-dose replicating RNA vaccine induces neutralizing antibodies against SARS-CoV-2 in nonhuman primates", + "rel_date": "2020-05-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.28.121640", + "rel_abs": "The ongoing COVID-19 pandemic, caused by infection with SARS-CoV-2, is having a dramatic and deleterious impact on health services and the global economy. Grim public health statistics highlight the need for vaccines that can rapidly confer protection after a single dose and be manufactured using components suitable for scale-up and efficient distribution. In response, we have rapidly developed repRNA-CoV2S, a stable and highly immunogenic vaccine candidate comprised of an RNA replicon formulated with a novel Lipid InOrganic Nanoparticle (LION) designed to enhance vaccine stability, delivery and immunogenicity. We show that intramuscular injection of LION/repRNA-CoV2S elicits robust anti-SARS-CoV-2 spike protein IgG antibody isotypes indicative of a Type 1 T helper response as well as potent T cell responses in mice. Importantly, a single-dose administration in nonhuman primates elicited antibody responses that potently neutralized SARS-CoV-2. These data support further development of LION/repRNA-CoV2S as a vaccine candidate for prophylactic protection from SARS-CoV-2 infection.", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Jesse H Erasmus", + "author_inst": "University of Washington" + }, + { + "author_name": "Amit P Khandhar", + "author_inst": "HDT Bio Corp" + }, + { + "author_name": "Alexandra C Walls", + "author_inst": "University of Washington" + }, + { + "author_name": "Emily A Hemann", + "author_inst": "University of Washington" + }, + { + "author_name": "Patience Murapa", + "author_inst": "University of Washington" + }, + { + "author_name": "Jacob Archer", + "author_inst": "University of Washington" + }, + { + "author_name": "Shanna Leventhal", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Jim Fuller", + "author_inst": "University of Washington" + }, + { + "author_name": "Thomas Lewis", + "author_inst": "University of Washington" + }, + { + "author_name": "Kevin E Draves", + "author_inst": "University of Washington" + }, + { + "author_name": "Samantha Randall", + "author_inst": "PAI Life Sciences" + }, + { + "author_name": "Kathryn A Guerriero", + "author_inst": "University of Washington" + }, + { + "author_name": "Malcolm S Duthie", + "author_inst": "HDT Bio Corp" + }, + { + "author_name": "Darrick Carter", + "author_inst": "HDT Bio Corp" + }, + { + "author_name": "Steven G Reed", + "author_inst": "HDT Bio Corp" + }, + { + "author_name": "David W Hawman", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Heinz Feldmann", + "author_inst": "National Institute of Allergy and Infectious Diseases" + }, + { + "author_name": "Michael Gale Jr.", + "author_inst": "University of Washington" + }, + { + "author_name": "David Veesler", + "author_inst": "University of Washington" + }, + { + "author_name": "Peter Berglund", + "author_inst": "HDT Bio Corp" + }, + { + "author_name": "Deborah Heydenburg Fuller", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.05.26.118190", "rel_title": "Comparison of the NeuMoDX, Diasorin Simplexa, Cepheid and Roche CDC SARS-CoV 2 EUA assays using nasopharyngeal/nasal swabs in universal transport media (UTM) and sputum and tracheal aspirates", @@ -1446061,93 +1444576,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.26.20111120", - "rel_title": "THE LOW-HARM SCORE FOR PREDICTING MORTALITY IN PATIENTS DIAGNOSED WITH COVID-19: A MULTICENTRIC VALIDATION STUDY", - "rel_date": "2020-05-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20111120", - "rel_abs": "- ImportanceMany COVID-19 prognostic factors for disease severity have been identified and many scores have already been proposed to predict death and other outcomes. However, hospitals in developing countries often cannot measure some of the variables that have been reported as useful.\n\n- ObjectiveTo assess the sensitivity, specificity, and predictive values of the novel LOW-HARM score (Lymphopenia, Oxygen saturation, White blood cells, Hypertension, Age, Renal injury, and Myocardial injury).\n\n- DesignThe score was designed using data from already published cohorts of patients diagnosed with COVID-19. Afterwards, it was calculated it in 438 consecutive hospital admissions at twelve different institutions in ten different cities in Mexico.\n\n- SettingTwelve hospitals in ten different cities in Mexico.\n\n- ParticipantsData from 438 patients was collected. Data from 400 patients (200 deaths and 200 survivors) was included in the analysis.\n\n- ExposureAll patients had an infection with SARS-CoV-2 confirmed by PCR.\n\n- Main OutcomeThe sensitivity, specificity, and predictive values of different cut-offs of the LOW-HARM score to predict death.\n\n- ResultsMean scores at admission and their distributions were significantly lower in patients who were discharged compared to those who died during their hospitalization 10 (SD: 17) vs 70 (SD: 28). The overall AUC of the model was 95%. A cut-off > 65 points had a specificity of 98% and a positive predictive value of 96%. More than a third of the cases (36%) in the sample had a LOW-HARM score > 65 points.\n\n- Conclusions and relevanceThe LOW-HARM score measured at admission is highly specific and useful for predicting mortality. It is easy to calculate and can be updated with individual clinical progression.\n\nKEY POINTSO_ST_ABSQuestionC_ST_ABSIs it possible to predict mortality in patients diagnosed with COVID-19 using easy-to-access and easy-to-measure variables?\n\nFindingsThe LOW-HARM score (Lymphopenia, Oxygen saturation, White blood cells, Hypertension, Age, Renal injury, and Myocardial injury) is a one-hundred-point score that, when measured at admission, had an overall AUC of 95% for predicting mortality. A cut-off of [≥] 65 points had a specificity of 98% and a positive predictive value of 96%.\n\nMeaningThe LOW-HARM score measured at admission is highly specific and useful for predicting mortality in patients diagnosed with COVID-19. In our sample, more than a third of patients met the proposed cut-off.", - "rel_num_authors": 18, - "rel_authors": [ - { - "author_name": "Adrian Soto-Mota", - "author_inst": "The University of Oxford" - }, - { - "author_name": "Braulio A. Marfil Garza", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" - }, - { - "author_name": "Erick Martinez Rodriguez", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" - }, - { - "author_name": "Jose Omar Barreto Rodriguez", - "author_inst": "Instituto Nacional de Enfermedades Respiratorias." - }, - { - "author_name": "Alicia Estela Lopez Romo", - "author_inst": "Sistema de Salud Christus Muguerza" - }, - { - "author_name": "Paolo Alberti Minutti", - "author_inst": "Centro Medico Nacional Siglo XXI" - }, - { - "author_name": "Juan Vicente Alejandre Loya", - "author_inst": "Centro Medico Nacional Occidente" - }, - { - "author_name": "Felix Emmanuel Perez Talavera", - "author_inst": "Centro Medico Nacional Occidente" - }, - { - "author_name": "Freddy Jose Avila-Cervera", - "author_inst": "Hospital Regional de Alta Especialidad de la Peninsula de Yucatan" - }, - { - "author_name": "Adriana Nohemi Velazquez Burciaga", - "author_inst": "Universidad Anahuac" - }, - { - "author_name": "Oscar Morado Aramburo", - "author_inst": "Hospital de la Beneficencia Espanola, San Luis Potosi." - }, - { - "author_name": "Luis Alberto Pina Olguin", - "author_inst": "Hospital Regional de Alta Especialidad del Bajio" - }, - { - "author_name": "Adrian Soto-Rodriguez", - "author_inst": "Universidad del Valle de Mexico" - }, - { - "author_name": "Andres Castaneda Prado", - "author_inst": "Centro de Investigacion en Politicas, Poblacion y Salud." - }, - { - "author_name": "Patricio Santillan-Doherty", - "author_inst": "Instituto Nacional de Enfermedades Respiratorias" - }, - { - "author_name": "Juan O Galindo Galindo", - "author_inst": "Sistema de Salud Christus Muguerza" - }, - { - "author_name": "Daniel Hernandez Gordillo", - "author_inst": "Centro Medico Nacional Occidente" - }, - { - "author_name": "Juan Gutierrez Mejia", - "author_inst": "Instituto Nacional de Ciencias Medicas y Nutricion Salvador Zubiran" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "emergency medicine" - }, { "rel_doi": "10.1101/2020.05.26.20113720", "rel_title": "Combining fine-scale social contact data with epidemic modelling reveals interactions between contact tracing, quarantine, testing and physical distancing for controlling COVID-19", @@ -1447031,6 +1445459,153 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.05.27.118117", + "rel_title": "Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease", + "rel_date": "2020-05-27", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.27.118117", + "rel_abs": "COVID-19, caused by SARS-CoV-2, lacks effective therapeutics. Additionally, no antiviral drugs or vaccines were developed against the closely related coronavirus, SARS-CoV-1 or MERS-CoV, despite previous zoonotic outbreaks. To identify starting points for such therapeutics, we performed a large-scale screen of electrophile and non-covalent fragments through a combined mass spectrometry and X-ray approach against the SARS-CoV-2 main protease, one of two cysteine viral proteases essential for viral replication. Our crystallographic screen identified 71 hits that span the entire active site, as well as 3 hits at the dimer interface. These structures reveal routes to rapidly develop more potent inhibitors through merging of covalent and non-covalent fragment hits; one series of low-reactivity, tractable covalent fragments was progressed to discover improved binders. These combined hits offer unprecedented structural and reactivity information for on-going structure-based drug design against SARS-CoV-2 main protease.", + "rel_num_authors": 33, + "rel_authors": [ + { + "author_name": "Alice Douangamath", + "author_inst": "Diamond Light Source Ltd." + }, + { + "author_name": "Daren Fearon", + "author_inst": "Diamond Light Source Ltd." + }, + { + "author_name": "Paul Gehrtz", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Tobias Krojer", + "author_inst": "University of Oxford" + }, + { + "author_name": "Petra Lukacik", + "author_inst": "Diamond Light Source Ltd." + }, + { + "author_name": "C. David Owen", + "author_inst": "Diamond Light Source Ltd." + }, + { + "author_name": "Efrat Resnick", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Claire Strain-Damerell", + "author_inst": "Diamond Light Source Ltd" + }, + { + "author_name": "Anthony aimon", + "author_inst": "Diamond Light Source Ltd. & Research Complex at Harwell" + }, + { + "author_name": "P\u00e9ter \u00c1br\u00e1nyi-Balogh", + "author_inst": "Hungarian Academy of Sciences Research Centre for Natural Sciences" + }, + { + "author_name": "Jose Branda\u00f5-Neto", + "author_inst": "Diamond Light Source Ltd., Research Complex at Harwell" + }, + { + "author_name": "Anna Carberry", + "author_inst": "Diamond Light Source Ltd." + }, + { + "author_name": "Gemma Davison", + "author_inst": "Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer" + }, + { + "author_name": "Alexandre Dias", + "author_inst": "Diamond Light Source Ltd." + }, + { + "author_name": "Thomas D Downes", + "author_inst": "University of York" + }, + { + "author_name": "Louise Dunnett", + "author_inst": "Diamond Light Source Ltd." + }, + { + "author_name": "Michael Fairhead", + "author_inst": "University of Oxford" + }, + { + "author_name": "James D Firth", + "author_inst": "University of York" + }, + { + "author_name": "S. Paul Jones", + "author_inst": "University of York" + }, + { + "author_name": "Aaron Keely", + "author_inst": "Hungarian Academy of Sciences Research Centre for Natural Sciences" + }, + { + "author_name": "Gy\u00f6rgy M Keser\u00fc", + "author_inst": "Hungarian Academy of Sciences Research Centre for Natural Sciences" + }, + { + "author_name": "Hanna F Klein", + "author_inst": "University of York" + }, + { + "author_name": "Matthew P Martin", + "author_inst": "Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer" + }, + { + "author_name": "Martin E.M. Noble", + "author_inst": "Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer" + }, + { + "author_name": "Ailsa Powell", + "author_inst": "Diamond Light Source Ltd." + }, + { + "author_name": "Rambabu Reddi", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Rachael Skyner", + "author_inst": "Diamond Light Source Ltd." + }, + { + "author_name": "Matthew Snee", + "author_inst": "Diamond Light Source Ltd." + }, + { + "author_name": "Michael J Waring", + "author_inst": "Cancer Research UK Drug Discovery Unit, Newcastle University Centre for Cancer" + }, + { + "author_name": "Conor Wild", + "author_inst": "Diamond Light Source Ltd" + }, + { + "author_name": "Nir London", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Frank von Delft", + "author_inst": "Diamond Light Source Ltd., Research Complex at Harwell, University of Oxford, University of Johannesburg" + }, + { + "author_name": "Martin A Walsh", + "author_inst": "Diamond Light Source Ltd., Research Complex at Harwell" + } + ], + "version": "1", + "license": "cc_by", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2020.05.27.117184", "rel_title": "Morphological Cell Profiling of SARS-CoV-2 Infection Identifies Drug Repurposing Candidates for COVID-19", @@ -1447451,57 +1446026,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.05.26.20109595", - "rel_title": "Efficacy and harms of remdesivir for the treatment of COVID-19: a systematic review and meta-analysis", - "rel_date": "2020-05-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.26.20109595", - "rel_abs": "BackgroundWe evaluated the efficacy and safety of remdesivir for the treatment of COVID-19.\n\nMethodsSystematic review in five engines, pre-print webpages and RCT registries until May 22, 2020 for randomized controlled trials (RCTs) and observational studies evaluating remdesivir on confirmed, COVID-19 adults with pneumonia and/or respiratory insufficiency. Primary outcomes were all-cause mortality, clinical improvement or recovery, need for invasive ventilation, and serious adverse events (SAE). Secondary outcomes included length of hospital stay, progression of pneumonia, and adverse events (AE). Inverse variance random effects meta-analyses were performed.\n\nResultsTwo placebo-controlled RCTs (n=1300) and two case series (n=88) were included. All studies used remdesivir 200mg IV the first day and 100mg IV for 9 more days, and followed up until 28 days. Wang et al. RCT was stopped early due to AEs; ACTT-1 was preliminary reported at 15-day follow up. Time to clinical improvement was not decreased in Wang et al. RCT, but median time to recovery was decreased by 4 days in ACTT-1. Remdesivir did not decrease all-cause mortality (RR 0.71, 95%CI 0.39 to 1.28) and need for invasive ventilation at 14 days (RR 0.57, 95%CI 0.23 to 1.42), but had fewer SAEs (RR 0.77, 95%CI 0.63 to 0.94). AEs were similar between remdesivir and placebo arms. Risk of bias ranged from some concerns to high risk in RCTs.\n\nInterpretationThere is paucity of adequately powered and fully reported RCTs evaluating effects of remdesivir in adult, hospitalized COVID-19 patients. Remdesivir should not be recommended for the treatment of severe COVID-19.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Alejandro Piscoya", - "author_inst": "Universidad San Ignacio de Loyola" - }, - { - "author_name": "Luis F. Ng-Sueng", - "author_inst": "Universidad Peruana de Ciencias Aplicadas" - }, - { - "author_name": "Angela Parra del Riego", - "author_inst": "Universidad Peruana de Ciencias Aplicadas" - }, - { - "author_name": "Renato Cerna-Viacava", - "author_inst": "Universidad Peruana de Ciencias Aplicadas" - }, - { - "author_name": "Vinay Pasupuleti", - "author_inst": "MedErgy Health Group Inc." - }, - { - "author_name": "Yuani M Roman", - "author_inst": "University of Connecticut" - }, - { - "author_name": "Priyaleela Thota", - "author_inst": "Hemex Health Inc." - }, - { - "author_name": "C. Michael White", - "author_inst": "University of Connecticut" - }, - { - "author_name": "Adrian V Hernandez", - "author_inst": "University of Connecticut" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.26.20111617", "rel_title": "Mobility-Guided Modeling of the COVID-19 Pandemic in Metro Manila", @@ -1448645,6 +1447169,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "oncology" }, + { + "rel_doi": "10.1101/2020.05.22.20106476", + "rel_title": "The impact of lockdown measures on COVID-19: a worldwide comparison", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20106476", + "rel_abs": "ObjectiveWe aimed to determine which aspects of the COVID-19 national response are independent predictors of COVID-19 mortality and case numbers.\n\nDesignComparative observational study between nations using publicly available data.\n\nSettingWorldwide Participants Covid-19 patients\n\nInterventionsStringency of 11 lockdown policies recorded by the Blavatnik School of Government database and earliness of each policy relative to first recorded national cases\n\nMain outcome measuresAssociation with log10 National deaths (LogD) and log10 National cases (LogC) on the 29th April 2020 corrected for predictive demographic variables\n\nResultsEarly introduction was associated with reduced mortality (n=137) and case numbers (n=150) for every policy aside from testing policy, contact tracing and workplace closure. Maximum policy stringency was only found to be associated with reduced mortality (p=0{middle dot}003) or case numbers (p=0{middle dot}010) for international travel restrictions. A multivariate model, generated using demographic parameters (r2=0{middle dot}72 for LogD and r2=0{middle dot}74 for LogC), was used to assess the timing of each policy. Early introduction of first measure (significance p=0{middle dot}048, regression coefficient {beta}=-0{middle dot}004, 95% confidence interval 0 to -0{middle dot}008), early international travel restrictions (p=0{middle dot}042, {beta}=-0{middle dot}005, -0{middle dot}001 to - 0{middle dot}009) and early public information (p=0{middle dot}021, {beta}=-0{middle dot}005, -0{middle dot}001 to -0{middle dot}009) were associated with reduced LogC. Early introduction of first measure (p=0{middle dot}003, {beta}=-0{middle dot}007, -0{middle dot}003 to -0{middle dot}011), early international travel restrictions (p=0{middle dot}003, {beta}=-0{middle dot}008, -0{middle dot}004 to-0{middle dot}012), early public information (p=0{middle dot}003, {beta}=-0{middle dot}007, 0{middle dot}003 to -0{middle dot}011), early generalised workplace closure (p=0{middle dot}031, {beta}=-0{middle dot}012, -0{middle dot}002 to -0{middle dot}022) and early generalised school closure (p=0{middle dot}050, {beta}=-0{middle dot}012, 0 to -0{middle dot}024) were associated with reduced LogC.\n\nConclusionsAt this stage in the pandemic, early institution of public information, international travel restrictions, and workplace closure are associated with reduced COVID-19 mortality and maintaining these policies may help control the pandemic.\n\nWhat is already known on this topicThe COVID-19 pandemic has spread rapidly throughout the world and presented vast healthcare, economic and political challenges. Many nations have recently passed the peak of their infection rate, and are weighing up relaxation of lockdown strategies. Though the effect of individual lockdown policies can be estimated by modelling, little is known about the impact of individual policies on population case numbers or mortality through comparison of differing strategies between nations. A PubMed search was carried out on the 14/5/20 using keywords including \"novel coronavirus-infected pneumonia\", \"2019-nCoV\", \"Sars-Cov-2\", \"Covid-19\", \"lockdown\",\" policy\", \"social distancing\", \"isolation\", \"quarantine\" and \"contact tracing\" returned 258 studies in total. Following scanning of the above results, we found 19 studies that have examined the effect of lockdown within a region, which have demonstrated a reduction in case numbers after the introduction of a lockdown. There are no previous studies that have compared the effectiveness of government lockdowns between nations to determine the effectiveness of specific policies.\n\nWhat this study addsThis study examines the corollary between government policy and COVID-19 case numbers and mortality, correct as of the 29th of April 2020, for every nation that there is available date within the Blavatnik School of Government database on COVID-19 policy. The study demonstrates that early generalised school closure, early generalised workplace closure, early restriction of international travel and early public information campaigns are independently associated with reduced national COVID-19 mortality. The maximum stringency of individual lockdown policies were not associated with reduced case numbers or mortality. Early reintroduction of these policies may be most effective in a relapse of the pandemic, though, school closure, workplace closure and restriction of international travel carry heavy politico-economic implications. There was no measurable effect of maximum stringency of lockdown policy on outcome at this point in time, indicating that early timing of lockdown introduction is of greater importance than its stringency, provided that the resultant viral reproductive rate is less than 1.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Dimitris I Papadopoulos", + "author_inst": "Chelsea and Westminister NHS Trust" + }, + { + "author_name": "Ivo Donkov", + "author_inst": "Chelsea and Westminister NHS Trust" + }, + { + "author_name": "Konstantinos Charitopoulos", + "author_inst": "Chelsea and Westminister NHS Trust" + }, + { + "author_name": "Samuel Bishara", + "author_inst": "Chelsea and Westminister NHS Trust" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.05.18.20106245", "rel_title": "SARS-CoV-2-reactive interferon-\u03b3-producing CD8+ T cells in patients hospitalized with Coronavirus viral disease-2019", @@ -1449057,25 +1447612,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.19.20106492", - "rel_title": "A modified SEIR Model with Confinement and Lockdown of COVID-19 for Costa Rica", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20106492", - "rel_abs": "The fast moving post-modern society allows for individuals to move fast in and between different countries, making it a perfect situation for the spread of emerging diseases. COVID-19 emerged with properties of a highly contagious disease, that has spread rapidly around the world. SIR/SEIR models are generally used to explain the dynamics of epidemics, however Coronavirus has shown dynamics with constant non-pharmaceutical interventions, making it difficult to model with these simple models. We extend an SEIR model to include a confinement compartment (SEICR) and use this to explain data from COVID-19 epidemic in Costa Rica. Then we discuss possible second wave of infection by adding a time varying function in the model to simulate cyclic interventions.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Tomas de-Camino-Beck", - "author_inst": "Automata Innovations" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.19.20106427", "rel_title": "Comparing dynamics and determinants of SARS-CoV-2 transmissions among health care workers of adult and pediatric settings in central Paris", @@ -1450215,6 +1448751,105 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.19.20106997", + "rel_title": "Hydroxychloroquine alone or in combination with azithromycin to prevent major clinical events in hospitalised patients with coronavirus infection (COVID-19): rationale and design of a randomised, controlled clinical trial", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20106997", + "rel_abs": "IntroductionHydroxychloroquine and its combination with azithromycin have been suggested to improve viral clearance in patients with COVID-19, but its effect on clinical outcomes remains uncertain.\n\nMethods and analysisWe describe the rationale and design of an open-label pragmatic multicentre randomised (concealed) clinical trial of 7 days of hydroxychloroquine (400 mg BID) plus azithromycin (500 mg once daily), hydroxychloroquine 400 mg BID, or standard of care for moderately severe hospitalised patients with suspected or confirmed COVID-19 (in-patients with up to 4L/minute oxygen supply through nasal catheter). Patients are randomised in around 50 recruiting sites and we plan to enrol 630 patients with COVID-19. The primary endpoint is a 7-level ordinal scale measured at 15-days: 1)not hospitalised, without limitations on activities; 2)not hospitalised, with limitations on activities; 3)hospitalised, not using supplementary oxygen; 4)hospitalised, using supplementary oxygen; 5)hospitalised, using high-flow nasal cannula or non-invasive ventilation; 6)hospitalised, on mechanical ventilation; 7)death. Secondary endpoints are the ordinal scale at 7 days, need for mechanical ventilation and rescue therapies during 15 days, need of high-flow nasal cannula or non-invasive ventilation during 15 days, length of hospital stay, in-hospital mortality, thromboembolic events, occurrence of acute kidney injury, and number of days free of respiratory support at 15 days. Secondary safety outcomes include prolongation of QT interval on electrocardiogram, ventricular arrhythmias, and liver toxicity. The main analysis will consider all patients with confirmed COVID-19 in the groups they were randomly assigned.\n\nEthics and disseminationThis study has been approved by Brazils National Ethic Committee (CONEP) and National Health Surveillance Agency (ANVISA). An independent data monitoring committee will perform interim analyses and evaluate adverse events throughout the trial. Results will be submitted for publication after enrolment and follow-up are complete, as well as presented and reported to local health agencies.\n\nClinicalTrials.gov identifierNCT04322123\n\nO_LSTStrengths and limitations of this studyC_LSTO_LIPragmatic randomised controlled trial of 7 days of hydroxychloroquine plus azithromycin, hydroxychloroquine or standard of care for moderately severe in-patients with suspected or confirmed COVID-19\nC_LIO_LIMulticentre: around 50 recruiting sites in Brazil with planned enrolment of 630 patients (1:1:1)\nC_LIO_LIThe primary endpoint is a 7-level ordinal scale ([1] not hospitalised, without limitations on activities; [2] not hospitalised, with limitations on activities; [3] hospitalised, not using supplementary oxygen; [4] hospitalised, using supplementary oxygen; [5] hospitalised, using high-flow nasal cannula or non-invasive ventilation; [6] hospitalised, on mechanical ventilation; [7] death) measured at 15 days.\nC_LIO_LIOpen label design (no placebo)\nC_LI", + "rel_num_authors": 21, + "rel_authors": [ + { + "author_name": "Alexandre B Cavalcanti", + "author_inst": "HCor Research Institute, Sao Paulo, Brazil" + }, + { + "author_name": "Fernando G Zampieri", + "author_inst": "HCor" + }, + { + "author_name": "Luciani CP Azevedo", + "author_inst": "Hospital Sirio Libanes Research and Education Institute, Sao Paulo, Brazil" + }, + { + "author_name": "Regis G Rosa", + "author_inst": "Hospital Moinhos de Vento, Porto Alegre,Brazil" + }, + { + "author_name": "Alvaro Avezum", + "author_inst": "Hospital Alemao Oswaldo Cruz, Sao Paulo, Brazil" + }, + { + "author_name": "Viviane C Veiga", + "author_inst": "BP - A Beneficencia Portuguesa de Sao Paulo, Sao Paulo, Brazil" + }, + { + "author_name": "Renato D Lopes", + "author_inst": "Duke University Medical Center - Duke Clinical Research Institute - Durham, North Carolina, USA." + }, + { + "author_name": "Leticia Kawano-Dourado", + "author_inst": "HCor Research Institute, Sao Paulo, Brazil" + }, + { + "author_name": "Lucas P Damiani", + "author_inst": "HCor Research Institute, Sao Paulo, Brazil" + }, + { + "author_name": "Adriano J Pereira", + "author_inst": "Academic Research Organization, Hospital Israelita Albert Einstein, Sao Paulo, Brazil" + }, + { + "author_name": "Ary Serpa Neto", + "author_inst": "Intensive Care Unit, Hospital Israelita Albert Einstein, Sao Paulo, Brazil" + }, + { + "author_name": "Remo Furtado", + "author_inst": "Intensive Care Unit, Hospital Israelita Albert Einstein, Sao Paulo, Brazil" + }, + { + "author_name": "Bruno Tomazini", + "author_inst": "Hospital Sirio Libanes Research and Education Institute, Sao Paulo, Brazil" + }, + { + "author_name": "Fernando A Bozza", + "author_inst": "Brazilian Research in Intensive Care Network (BRICNet), Sao Paulo, Brazil." + }, + { + "author_name": "Israel S Maia", + "author_inst": "Brazilian Research in Intensive Care Network (BRICNet), Sao Paulo, Brazil." + }, + { + "author_name": "Maicon Falavigna", + "author_inst": "Hospital Moinhos de Vento, Porto Alegre, Brazil" + }, + { + "author_name": "Thiago C Lisboa", + "author_inst": "HCor Research Institute, Sao Paulo, Brazil" + }, + { + "author_name": "Henrique Fonseca", + "author_inst": "Academic Research Organization, Hospital Israelita Albert Einstein, Sao Paulo, Brazil" + }, + { + "author_name": "Flavia R Machado", + "author_inst": "Brazilian Research in Intensive Care Network (BRICNet), Sao Paulo, Brazil." + }, + { + "author_name": "Otavio Berwanger", + "author_inst": "Academic Research Organization, Hospital Israelita Albert Einstein, Sao Paulo, Brazil" + }, + { + "author_name": "COALITION COVID-19 Brazil I Investigators", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.19.20106906", "rel_title": "Efficacy and Safety of Hydroxychloroquine and Chloroquine for COVID-19: A systematic review", @@ -1450559,45 +1449194,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.24.20107193", - "rel_title": "Using HoloLens\u2122 to reduce staff exposure to aerosol generating procedures during a global pandemic", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20107193", - "rel_abs": "RATIONALECOVID-19 poses a unique challenge; caring for patients with a novel, infectious disease whilst protecting staff. Some interventions used to give oxygen therapy are aerosol generating procedures. Staff delivering such interventions require PPE and are exposed to a significant viral load resulting in sick days and even death. We aim to reduce this risk using an augmented-reality communication device: The HoloLens by Microsoft.\n\nOBJECTIVESIn a tertiary centre in London we aim to implement HoloLens technology, allowing other medical staff to remotely join the consulting clinician when in a high-risk patient area delivering oxygen therapy. The study primary outcome was to reduce the exposure to staff and demonstrate non-inferiority staff satisfaction when compared to not using the device. Our secondary outcome was to reduce extrapolated PPE costs when using the device.\n\nMETHODSOur study was conducted in March and April 2020, within a respiratory unit delivering aerosolising oxygen therapies (High flow nasal oxygen, Continuous positive airway pressure and non-invasive ventilation) to patients with suspected or confirmed COVID-19 infection.\n\nMEASUREMENTSSelf-reported questionnaires to assess satisfaction in key areas of patient care. An infrared people counting device was also used to assess staff in and out of the unit.\n\nMAIN RESULTSMean self-reported time in the high-risk zone was less when using HoloLens (2.69 hours) compared to usual practice (3.96 hours) although this difference was not statistically significant (p = 0.3657). HoloLens showed non-inferiority when compared to usual practice in staff satisfaction score for all domains. Furthermore, mean staff satisfaction score encouragingly improved when using HoloLens. Self-reported PPE counts from this study showed 12 staff members changing PPE 25.8 times per shift, almost double the 13.5 times in the HoloLens count.\n\nCONCLUSIONSWe have demonstrated HoloLens can reduce the number of staff exposed to aerosol generating areas in a novel infectious disease. Our results show it did not impair communication, medical staff availability or end of life care. HoloLens technology may also reduce the use of PPE, which has equipment availability and cost benefits. This study provides grounding for further use of the HoloLens device by bringing a bedside experience to experts remote to the situation.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "John J Cafferkey", - "author_inst": "Imperial College Healthcare NHS Trust" - }, - { - "author_name": "Dominic OP Hampson", - "author_inst": "Division of Respiratory Medicine, Imperial College Healthcare NHS Trust, London UK" - }, - { - "author_name": "Clare Ross", - "author_inst": "Division of Respiratory Medicine, Imperial College Healthcare NHS Trust, London UK" - }, - { - "author_name": "Angad S Kooner", - "author_inst": "Cutrale Perioperative and Ageing Research Group, Department of Bioengineering, Imperial College London" - }, - { - "author_name": "Guy FJ Martin", - "author_inst": "Department of Surgery and Cancer, Imperial College London, London UK" - }, - { - "author_name": "James M Kinross", - "author_inst": "Department of Surgery and Cancer, Imperial College London, London UK" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "respiratory medicine" - }, { "rel_doi": "10.1101/2020.05.19.20107102", "rel_title": "COVID-19: A Chronological Review of the Neurological Repercussions - What do We Know by May, 2020?", @@ -1451537,6 +1450133,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.24.20111724", + "rel_title": "COVID-19: Impact of Obesity and Diabetes in Disease Severity", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20111724", + "rel_abs": "BackgroundThe Coronavirus disease 2019 (COVID-19) pandemic is straining the healthcare system, particularly for patients with severe outcomes who require admittance to the intensive care unit (ICU). This study aimed to investigate the potential associations of obesity and diabetes with COVID-19 severe outcomes, assessed as ICU admittance.\n\nSubjectsDemographic and patient characteristics from a retrospective cohort of 1158 patients hospitalized with COVID-19 in a single center in Kuwait, along with their medical history, were analyzed. Univariate and multivariate analyses were performed to explore the associations between different variables and ICU admittance.\n\nResultsFrom the 1158 hospitalized patients, 271 (23.4%) had diabetes, 236 (20.4%) had hypertension and 104 (9%) required admittance into the ICU. From patients with available measurements, 157 (21.6%) had body mass index (BMI)[≥]25 kg/m2. Univariate analysis showed that overweight (BMI=25.0-29.9 kg/m2), obesity class I (BMI=30-34.9 kg/m2) and morbid obesity (BMI[≥]40 kg/m2) associated with ICU admittance (odds ratio (OR) [95% confidence intervals (CI)]: 2.45 [1.26-4.74] p-value=0.008; OR [95% CI]: 3.51 [1.60-7.69] p-value=0.002; and OR [95% CI]: 5.18 [1.50-17.85] p-value=0.009], respectively). Patients with diabetes were more likely to be admitted to ICU (OR [95% CI]: 9.38 [5.49-16.02]). Two models for multivariate regression analysis were used, assessing either BMI or diabetes on ICU outcomes. In the BMI model, class I obesity and morbid obesity were associated with ICU admittance (adjusted OR (AOR) [95% CI]: 2.7 [1.17-6.20] p-value=0.019 and AOR [95% CI]: 3.95 [1.00-15.20] p-value=0.046, respectively). In the diabetes model, diabetes was associated with higher ICU admittance (AOR [95% CI]: 5.49 [3.13-9.65] p-value<0.001) whereas hypertension had a protective effect on ICU admittance (AOR [95% CI]: 0.51 (0.28-0.91).\n\nConclusionsIn our cohort, overweight, obesity and diabetes in patients with COVID-19 were associated with ICU admittance, putting these patients at higher risk of poor outcomes.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Salman K. Al-Sabah", + "author_inst": "COVID-19 Research Group, Jaber Al-Ahmad Al-Sabah Hospital, Kuwait" + }, + { + "author_name": "Mohannad Al-Haddad", + "author_inst": "COVID-19 Research Group, Jaber Al-Ahmad Al-Sabah Hospital, Kuwait" + }, + { + "author_name": "Sarah Al Youha", + "author_inst": "Jaber Al-Ahmad Al-Sabah Hospital" + }, + { + "author_name": "Mohammad H. Jamal", + "author_inst": "COVID-19 Research Group, Jaber Al-Ahmad Al-Sabah Hospital, Kuwait" + }, + { + "author_name": "Sulaiman AlMazeedi", + "author_inst": "COVID-19 Research Group, Jaber Al-Ahmad Al-Sabah Hospital, Kuwait" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.19.20107391", "rel_title": "Syndromic Surveillance for COVID-19 in Canada", @@ -1451977,41 +1450608,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.25.20109470", - "rel_title": "Seroprevalence of antibodies against SARS-CoV-2 among public community and health-care workers in Alzintan City of Libya", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.25.20109470", - "rel_abs": "A study was conducted to determine the seroprevalence of antibodies against SARS-CoV-2 among public community and health care workers in Alzintan City, Libya. During the period from 2/4/2020 to 18/5/2020, a total of 219 blood samples were collected and analyzed for the presence of antibodies against SARS-CoV-2. Collection of samples were divided in two categories; random samples from public community and samples from health care workers belonging to two Governmental hospitals and one private clinic. One Step Novel Coronavirus (COVID-19) IgM/IgG Antibody Test was used. Out of the 219 samples tested, 6 (2.74%) samples were seropositive for SARS-CoV-2. All health-care workers were tested negative. All positive cases were females and 5 of them aged between 44 to 75 years and one aged 32 years. The prevalence in young females ([≤]40 years) was 1.4% in total young females tested in the study and 1.75% in young females taken from public community. The prevalence in older females aged ([≤] 40 years), was 11.1% in total females tested and 13.9% in females taken from public community. In conclusion, the preliminary investigation of SARS-CoV-2 revealed considerable prevalence in Alzintan City although the disease seems to be in its mild form. Active surveillance studies with high number of samples using both virological and serological tests are in urgent need.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "ABDULWAHAB M. KAMMON", - "author_inst": "University of Tripoli" - }, - { - "author_name": "Ali A. El-Arabi", - "author_inst": "Al-Zintan University" - }, - { - "author_name": "Esadk A. Erhouma", - "author_inst": "Al-Zintan University" - }, - { - "author_name": "Taha M. Mehemed", - "author_inst": "Al-Zintan University" - }, - { - "author_name": "Othman A. Mohamed", - "author_inst": "Al-Zintan University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.25.20111757", "rel_title": "Association between Cardiovascular Burden and Requirement of Intensive Care among Patients with Mild COVID-19", @@ -1453267,6 +1451863,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.24.20111799", + "rel_title": "Effect of various treatment modalities on the novel coronavirus (nCOV-2019) infection in humans: a systematic review & meta-analysis", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20111799", + "rel_abs": "Background and aimSeveral therapeutic agents have been investigated for the treatment of novel Coronavirus-2019 (nCOV-2019). We aimed to conduct a systematic review and meta-analysis to assess the effect of various treatment modalities in nCOV-2019 patients.\n\nMethodsAn extensive literature search was conducted before 22 May 2020 in PubMed, Google Scholar, Cochrane library databases. Quality assessment was performed using Newcastle Ottawa Scale. A fixed-effect model was applied if I2 <50%, else the results were combined using random-effect model. Risk Ratio (RR) or Standardized Mean Difference (SMD) along-with 95% Confidence Interval (95%CI) were used to pool the results. Between study heterogeneity was explored using influence and sensitivity analyses & publication bias was assessed using funnel plots. Entire statistical analysis was conducted in R version 3.6.2.\n\nResultsEighty-one studies involving 44 in vitro and 37 clinical studies including 8662 nCOV-2019 patients were included in the review. Lopinavir-Ritonavir compared to controls was significantly associated with shorter mean time to clinical improvement (SMD -0.32; 95%CI -0.57 to -0.06) and Remdesivir compared to placebo was significantly associated with better overall clinical improvement (RR 1.17; 95%CI 1.07 to 1.29). Hydroxychloroquine was associated with less overall clinical improvement (RR 0.88; 95%CI 0.79 to 0.98) and longer time to clinical improvement (SMD 0.64; 95%CI 0.33 to 0.94), It additionally had higher all-cause mortality (RR 1.6; 95%CI 1.26 to 2.03) and more total adverse events (RR 1.84; 95% CI 1.58 to 2.13).\n\nConclusionOur meta-analysis suggests that except in vitro studies, no treatment till now has shown clear-cut benefit on nCOV-2019 patients. Lopinavir-Ritonavir and Remdesivir have shown some benefits in terms less time to clinical improvement and better overall clinical improvement. Hydroxychloroquine use has a risk of higher mortality and adverse events. Results from upcoming large clinical trials must be awaited to draw any profound conclusions.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Shubham Misra", + "author_inst": "All India Institute of Medical Sciences, New Delhi, India" + }, + { + "author_name": "Manabesh Nath", + "author_inst": "All India Institute of Medical Sciences, New Delhi, India" + }, + { + "author_name": "Vijay Hadda", + "author_inst": "All India Institute of Medical Sciences, New Delhi, India" + }, + { + "author_name": "Deepti Vibha", + "author_inst": "All India Institute of Medical Sciences, New Delhi, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.25.20110239", "rel_title": "In Vitro Efficacy of Povidone-Iodine Nasal And Oral Antiseptic Preparations Against Severe Acute Respiratory Syndrome-Coronavirus 2 (SARS-CoV-2)", @@ -1453747,25 +1452374,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "genetic and genomic medicine" }, - { - "rel_doi": "10.1101/2020.05.25.20112938", - "rel_title": "What Can We Learn from the Time Evolution of COVID-19 Epidemic in Slovenia?", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.25.20112938", - "rel_abs": "A recent work (DOI 10.1101/2020.05.06.20093310) indicated that temporarily splitting larger populations into smaller groups can efficiently mitigate the spread of SARS-CoV-2 virus. The fact that, soon afterwards, on May 15, 2020, the two million people Slovenia was the first European country proclaiming the end of COVID-19 epidemic within national borders may be relevant from this perspective. Motivated by this evolution, in this paper we investigate the time dynamics of coronavirus cases in Slovenia with emphasis on how efficient various containment measures act to diminish the number of COVID-19 infections. Noteworthily, the present analysis does not rely on any speculative theoretical assumption; it is solely based on raw epidemiological data. Out of the results presented here, the most important one is perhaps the finding that, while imposing drastic curfews and travel restrictions reduce the infection rate k by a factor of four with respect to the unrestricted state, they only improve the{kappa} -value by ~ 15% as compared to the much bearable state of social and economical life wherein (justifiable) wearing face masks and social distancing rules are enforced/followed. Significantly for behavioral and social science, our analysis of the time dependence{kappa} ={kappa} (t) may reveal an interesting self-protection instinct of the population, which became manifest even before the official lockdown enforcement.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Ioan Baldea", - "author_inst": "Heidelberg University" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.23.20111211", "rel_title": "Are we #stayinghome to Flatten the Curve?", @@ -1454537,6 +1453145,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.05.24.20112318", + "rel_title": "Utility of Pan-Family Assays for Rapid Viral Screening: Reducing Delays in Public Health Responses During Pandemics", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20112318", + "rel_abs": "BackgroundThe SARS-CoV-2 pandemic has highlighted deficiencies in the testing capacity of many developed countries during the early stages of emerging pandemics. Here we describe the potential for pan-family viral assays to improve early accessibility of large-scale nucleic acid testing.\n\nMethodsCoronaviruses and SARS-CoV-2 were used as a case-study for investigating the utility of pan-family viral assays during the early stages of a novel pandemic. Specificity of a pan-coronavirus (Pan-CoV) assay for viral detection was assessed using the frequency of common human coronavirus (HCoV) species in key populations. A reported Pan-CoV assay was assessed to determine sensitivity to SARS-CoV-2 and 59 other coronavirus species. The resilience of the primer target regions of this assay to mutation was assessed in 8893 high quality SARS-CoV-2 genomes to predict ongoing utility during pandemic progression.\n\nFindingsDue to infection with common HCoV species, a Pan-CoV assay would return a false positive for as few as 1% of asymptomatic adults, but up to 30% of immunocompromised patients displaying symptoms of respiratory disease. Two of the four reported pan-coronavirus assays would have identified SARS-CoV-2 and we demonstrate that with small adjustments to the primers, these assays can accommodate novel variation observed in animal coronaviruses. The assay target region of one well established Pan-CoV assay is highly resistant to mutation compared to regions targeted by other widely applied SARS-CoV-2 RT-PCR assays.\n\nInterpretationPan-family assays have the potential to greatly assist management of emerging public health emergencies through prioritization of high-resolution testing or isolation measures, despite limitations in test specificity due to cross-reactivity with common pathogens. Targeting highly conserved genomic regions make pan-family assays robust and resilient to mutation of a given virus. This approach may be applicable to other viral families and has utility as part of a strategic stockpile of tests maintained to better contain spread of novel diseases prior to the widespread availability of specific assays.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Michael Erlichster", + "author_inst": "MX3 Diagnostics" + }, + { + "author_name": "Gursharan Chana", + "author_inst": "MX3 Diagnostics" + }, + { + "author_name": "Daniela Zantomio", + "author_inst": "Austin Health" + }, + { + "author_name": "Benjamin Goudey", + "author_inst": "IBM Research Australia" + }, + { + "author_name": "Efstratios Skafidas", + "author_inst": "MX3 Diagnostics" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.24.20111245", "rel_title": "IgG serology in health care and administrative staff populations from 7 hospital representative of different exposures to SARS-CoV-2 in Lombardy, Italy", @@ -1454893,49 +1453536,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.05.23.20111443", - "rel_title": "COVID-19 in Latin America: Contrasting phylodynamic inference with epidemiological surveillance.", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.23.20111443", - "rel_abs": "BackgroundSARS-CoV-2 revealed important gaps in infectious disease surveillance. Molecular epidemiology can help monitoring and adapting traditional surveillance to surpass those limitations. This work aims to contrast data driven from traditional surveillance with parameters inferred from molecular epidemiology in Latin America (LATAM)\n\nMethodsWe obtained epidemiological data up to 4th June, 2020. We estimated Effective Reproductive Number (Re) and epidemic curves using maximum likelihood (ML). SARS-CoV-2 genomes were obtained from GISAID up to June 4th 2020. We aligned sequences, generated a ML phylogenetic tree, and ran a coalescent model Birth Death SIR. Phylodynamic analysis was performed for inferring Re, number of infections and date of introduction.\n\nFindingsA total of 1,144,077 cases were reported up to 4th June 2020. Countries with the largest cumulative cases were Chile, Peru and Panama. We found at least 18 different lineages circulating, with a predominance of B.1 and B.1.1. We inferred an underestimation of the daily incident cases. When contrasting observed and inferred Re, we did not find statistically significant differences except for Chile and Mexico. Temporal analysis of the introduction of SARS-CoV-2 suggested a detection lag of at least 21 days.\n\nInterpretationOur results support that epidemiological and genomic surveillance are two complementary approaches. Even with a low number of genomes proper estimations of Re could be performed. We suggest that countries, especially developing countries, should consider to add genomic surveillance to their systems for monitoring and adapting epidemiological control of SARS-CoV-2.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Diana M. Rojas-Gallardo", - "author_inst": "Fundacion Universitaria Autonoma de las Americas" - }, - { - "author_name": "Sandra C. Garzon-Castano", - "author_inst": "Fundacion Universitaria Autonoma de las Americas" - }, - { - "author_name": "Natalia Millan", - "author_inst": "Fundacion Universitaria Autonoma de las Americas" - }, - { - "author_name": "Erika V. Jimenez-Posada", - "author_inst": "Fundacion Universitaria Autonoma de las Americas" - }, - { - "author_name": "Marlen Martinez-Gutierrez", - "author_inst": "Universidad Cooperativa de Colombia" - }, - { - "author_name": "Julian Ruiz-Saenz", - "author_inst": "Universidad Cooperativa de Colombia" - }, - { - "author_name": "Jaime A. Cardona-Ospina", - "author_inst": "Fundacion Universitaria Autonoma de las Americas" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.25.114199", "rel_title": "The novel Coronavirus enigma: Phylogeny and mutation analyses of SARS-CoV-2 viruses circulating in India during early 2020.", @@ -1455891,6 +1454491,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.20.20095406", + "rel_title": "Modeling the dynamics of COVID-19 using Q-SEIR model with age-stratified infection probability", + "rel_date": "2020-05-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.20.20095406", + "rel_abs": "We explore the advantage of age-stratifying the population as an improvement on the quarantine-modified SEIR model. We hypothesize that this would project lower cases of infection for the Philippines because of our countrys low median age. We introduce the variable U that is multiplied to the incubation rate{sigma} when exposed individuals become infected. U is the dot product of the proxy infection probabilities stratified per age group (F) and the population stratified per age group (P) divided by the total population, similar to calculating mathematical expectation. Proxies were taken from two data sets: Hubei, China with a calculated value of UCHN = 0.4447 and Quezon City, Philippines with UQC = 0.5074. When the majority age group, represented by the median age, is far from the age group with the highest number of infections the number of infected individuals decreases and produces a delayed peaking effect. This new method gives a much lower estimate on peak number of infected cases by 65.2% compared with age-stratification alone; and by 75.2% compared with Q-SEIR alone.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Joshua Frankie Rayo", + "author_inst": "University of the Philippines Diliman" + }, + { + "author_name": "Romulo de Castro", + "author_inst": "Center for Informatics, University of San Agustin, Philippines" + }, + { + "author_name": "Jesus Emmanuel Sevilleja", + "author_inst": "National Center for Mental Health, Philippines" + }, + { + "author_name": "Vena Pearl Bongolan", + "author_inst": "University of the Philippines Diliman" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.22.20098350", "rel_title": "A phenomenological algorithm for short-range predictions of the Covid-19 pandemics 2020", @@ -1456359,77 +1454990,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.22.20102525", - "rel_title": "Study on the expression levels of antibodies against SARS-CoV-2 at different period of disease and its related factors in 192 cases of COVID-19 patients", - "rel_date": "2020-05-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20102525", - "rel_abs": "BackgroundIn 2020, the current outbreak of Coronavirus Disease 2019(COVID-19) has constituted a global pandemic. But the question about the immune mechanism of patients with COVID-19 is unclear and cause particular concern to the world. Here, we launched a follow-up analysis of antibodies against SARS-CoV-2 of 192 COVID-19 patients, aiming to depict a kinetics profile of antibodies against SARS-CoV-2 and explore the related factors of antibodies expression against SARS-CoV-2 in COVID-19 patient.\n\nMethodsA total of 192 COVID-19 patients enrolled in the designated hospital of Guangzhou, Guangzhou Eighth Peoples Hospital, from January to February 2020 were selected as the study cohort. A cohort of 130 COVID-19 suspects who had been excluded from SARS-CoV-2 infected by negative RT-PCR result and 209 healthy people were enrolled in this study. Detection of IgM and IgG against SARS-CoV-2 were performed by Chemiluminescence immunoassay in different groups.\n\nResultsIt has been found that the seroconversion time of IgM against SARS-CoV-2 in most patients was 5-10 days after the symptoms onset, and then rose rapidly, reaching a peak around 2 to 3 weeks, and the median peak concentration was 2.705 AU / mL. The peak of IgM maintained within one week, and then enters the descending channel. IgG seroconverted later than or synchronously with IgM, reaching peaks around 3 to 4 weeks.The median peak concentration was 33.998AU / ml,which was higher than that of IgM. IgM titers begins to gradually decrease after reaching the peak in the 4th week, after the 8th week, a majority of IgM in patients serum started to turn negative. On the contrary, titers of IgG began to decline slightly after the fifth week, and more than 90% of results of patients were positive after 8 weeks. Additionally, the concentration of antibodies positively correlated with the severity of the disease and the duration of virus exist in host.\n\nConclusionWe depict a kinetics profile of antibodies against SARS-CoV-2 in COVID-19 patients and found out that the levels of antibodies were related to the disease severity, age, gender and virus clearance or continuous proliferation of COVID-19 patients.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Jingyi Ou", - "author_inst": "Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou,China" - }, - { - "author_name": "Mingkai Tan", - "author_inst": "Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou,China" - }, - { - "author_name": "Haolan He", - "author_inst": "Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou,China" - }, - { - "author_name": "Haiyan Tan", - "author_inst": "Department of Laboratory Medicine, Guangzhou Baiyun District Maternal and Child Health Hospital, Guangzhou, China" - }, - { - "author_name": "Jiewen Mai", - "author_inst": "Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou,China." - }, - { - "author_name": "Yaoxiang Long", - "author_inst": "Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou,China." - }, - { - "author_name": "Xiaowen Jiang", - "author_inst": "Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou,China." - }, - { - "author_name": "Qing He", - "author_inst": "Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou,China." - }, - { - "author_name": "Ying Huang", - "author_inst": "Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou,China." - }, - { - "author_name": "Yan Li", - "author_inst": "Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou,China." - }, - { - "author_name": "Renshen Chen", - "author_inst": "Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou,China." - }, - { - "author_name": "Liya Li", - "author_inst": "Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou,China." - }, - { - "author_name": "Fang Li", - "author_inst": "Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou,China." - }, - { - "author_name": "Yaling Shi", - "author_inst": "Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou,China" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.20.20107847", "rel_title": "MACHINE LEARNING PREDICTION FOR COVID 19 PANDEMIC IN INDIA", @@ -1457221,6 +1455781,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.20.20107797", + "rel_title": "Spread of COVID-19: Investigation of universal features in real data", + "rel_date": "2020-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.20.20107797", + "rel_abs": "We present results on the existence of various common patterns in the growth of the total number of patients affected by COVID-19, a disease acquired through infection by a novel coronavirus, in different countries. For this purpose we propose a scaling model that can have general applicability in the understanding of real data of epidemics. This is analogous to the finite-size scaling, a technique used in the literature of phase transition to identify universality classes. In the disease model, the size of a system is proportional to the volume of the population, within a geographical region, that have been infected at the death of the epidemic or are eventually going to be infected when an epidemic ends. Outcome of our study, for COVID-19, via application of this model, suggests that in most of the countries, after the onset of spread, the growths are described by rapid exponential function, for significantly long periods. In addition to accurately identifying this superuniversal feature, we point out that the model is helpful in grouping countries into universality classes, based on the late time behavior, characterized by physical distancing practices, in a natural way. This feature of the model can provide direct comparative understanding of the effectiveness of lockdown-like social measures adopted in different places.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Subir K. Das", + "author_inst": "Jawaharlal Nehru Centre for Advanced Scientific Research" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.20.20108449", "rel_title": "Risk factors affecting COVID-19 case fatality rate: A quantitative analysis of top 50 affected countries", @@ -1457585,29 +1456164,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.20.20107573", - "rel_title": "Modelling information-dependent social behaviors in response to lockdowns: the case of COVID-19 epidemic in Italy", - "rel_date": "2020-05-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.20.20107573", - "rel_abs": "The COVID-19 pandemic started in January 2020 has not only threatened world public health, but severely impacted almost every facet of lives including behavioral and psychological aspects. In this paper we focus on the human element and propose a mathematical model to investigate the effects on the COVID-19 epidemic of social behavioral changes in response to lockdowns. We consider a SEIR-like epidemic model where that contact and quarantine rates are assumed to depend on the available information and rumors about the disease status in the community. The model is applied to the case of COVID-19 epidemic in Italy. We consider the period that stretches between Bebruary 24, 2020 when the first bulletin by the Italian Civil Brotection was reported and May 18, 2020 when the lockdown restrictions have been mostly removed. The role played by the information-related parameters is determined by evaluating how they affect suitable outbreak-severity indicators. We estimated that citizens compliance with mitigation measures played a decisive role in curbing the epidemic curve by preventing a duplication of deaths and about 46% more contagions.\n\nSubject class: 92D30, 34C60", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Bruno Buonomo", - "author_inst": "University of Naples Federico II" - }, - { - "author_name": "Rossella Della Marca", - "author_inst": "University of Parma" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.19.20107409", "rel_title": "A pattern categorization of CT findings to predict outcome of COVID-19 pneumonia", @@ -1458871,6 +1457427,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.24.20112045", + "rel_title": "Reaching collective immunity for COVID-19: an estimate with a heterogeneous model based on the data for Italy", + "rel_date": "2020-05-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.24.20112045", + "rel_abs": "BackgroundAt the current stage of COVID-19 pandemic, forecasts become particularly important regarding the possibility that the total incidence could reach the level where the disease stops spreading because a considerable portion of the population has become immune and collective immunity could be reached. Such forecasts are valuable because the currently undertaken restrictive measures prevent mass morbidity but do not result in the development of a robust collective immunity. Thus, in the absence of efficient vaccines and medical treatments, lifting restrictive measures carries the risk that a second wave of the epidemic could occur.\n\nMethodsWe developed a heterogeneous model of COVID-19 dynamics. The model accounted for the differences in the infection risk across subpopulations, particularly the age-depended susceptibility to the disease. Based on this model, an equation for the minimal number of infections was calculated as a condition for the epidemic to start declining. The basic reproductive number of 2.5 was used for the disease spread without restrictions. The model was applied to COVID-19 data from Italy.\n\nFindingsWe found that the heterogeneous model of epidemic dynamics yielded a lower proportion, compared to a homogeneous model, for the minimal incidence needed for the epidemic to stop. When applied to the data for Italy, the model yielded a more optimistic assessment of the minimum total incidence needed to reach collective immunity: 43% versus 60% estimated with a homogeneous model.\n\nInterpretationBecause of the high heterogeneity of COVID-19 infection risk across the different age groups, with a higher susceptibility for the elderly, homogeneous models overestimate the level of collective immunity needed for the disease to stop spreading. This inaccuracy can be corrected by the homogeneous model introduced here. To improve the estimate even further additional factors should be considered that contribute to heterogeneity, including social and professional activity, gender and individual resistance to the pathogen.\n\nFundingThis work was supported by a grant from the Ministry of Education and Science of the Russian Federation, a unique project identifier RFMEFI60819X0278.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Andrey Gerasimov", + "author_inst": "I.M. Sechenov First Moscow State Medical University" + }, + { + "author_name": "Georgy Lebedev", + "author_inst": "I.M. Sechenov First Moscow State Medical University; Federal Research Institute for Health Organization and Informatics, Moscow, Russia" + }, + { + "author_name": "Mikhail Lebedev", + "author_inst": "I.M. Sechenov First Moscow State Medical University; National Research University Higher School of Economics, Moscow, Russia" + }, + { + "author_name": "Irina Semenycheva", + "author_inst": "I.M. Sechenov First Moscow State Medical University" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.24.20112094", "rel_title": "Sociodemographic predictors of outcomes in COVID-19: examining the impact of ethnic disparities in Northern Nevada", @@ -1459263,37 +1457850,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "respiratory medicine" }, - { - "rel_doi": "10.1101/2020.05.21.20108969", - "rel_title": "ASSESSMENT OF WORKERS PERSONAL VULNERABILITY TO COVID-19 USING COVID-AGE", - "rel_date": "2020-05-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20108969", - "rel_abs": "Decisions on fitness for employment that entails a risk of contracting Covid-19 require an assessment of the workers personal vulnerability should infection occur. Using recently published UK data, we have developed a risk model that provides estimates of personal vulnerability to Covid-19 according to sex, age, ethnicity, and various comorbidities. Vulnerability from each risk factor is quantified in terms of its equivalence to added years of age. Addition of the impact from each risk factor to an individuals true age generates their \"Covid-age\", a summary measure representing the age of a healthy UK white male with equivalent vulnerability. We discuss important limitations of the model, including current scientific uncertainties and limitations on generalisability beyond the UK setting and its use beyond informing assessments of individual vulnerability in the workplace. As new evidence becomes available, some of these limitations can be addressed. The model does not remove the need for clinical judgement or for other important considerations when managing occupational risks from Covid-19.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "David Coggon", - "author_inst": "MRC Lifecourse Epidemiology Unit, University of Southampton, UK" - }, - { - "author_name": "Peter Croft", - "author_inst": "Keele University, UK" - }, - { - "author_name": "Paul Cullinan", - "author_inst": "Imperial College (NHLI) and Royal Brompton Hospital, UK" - }, - { - "author_name": "Anthony Williams", - "author_inst": "Working Fit Ltd, Temple Ewell, Kent UK" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "occupational and environmental health" - }, { "rel_doi": "10.1101/2020.05.22.20108845", "rel_title": "Clinical and molecular characterization of COVID-19 hospitalized patients", @@ -1460421,6 +1458977,33 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.05.23.104919", + "rel_title": "In silico Proteome analysis of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)", + "rel_date": "2020-05-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.23.104919", + "rel_abs": "Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (2019-nCoV), is a positive-sense, single-stranded RNA coronavirus. The virus is the causative agent of coronavirus disease 2019 (COVID-19) and is contagious through human-to-human transmission. The present study reports sequence analysis, complete coordinate tertiary structure prediction and in silico sequence-based and structure-based functional characterization of full SARS-CoV-2 proteome based on the NCBI reference sequence NC_045512 (29903 bp ss-RNA) which is identical to GenBank entry MN908947 and MT415321. The proteome includes 12 major proteins namely orf1ab polyprotein (includes 15 proteins), surface glycoprotein, ORF3a protein, envelope protein, membrane glycoprotein, ORF6 protein, ORF7a protein, orf7b, ORF8, Nucleocapsid phosphoprotein and ORF10 protein. Each protein of orf1ab polyprotein group has been studied separately. A total of 25 polypeptides have been analyzed out of which 15 proteins are not yet having experimental structures and only 10 are having experimental structures with known PDB IDs. Out of 15 newly predicted structures six (6) were predicted using comparative modeling and nine (09) proteins having no significant similarity with so far available PDB structures were modeled using ab-initio modeling. Structure verification using recent tools QMEANDisCo 4.0.0 and ProQ3 for global and local (per-residue) quality estimates indicate that the all-atom model of tertiary structure of high quality and may be useful for structure-based drug designing targets. The study has identified nine major targets (spike protein, envelop protein, membrane protein, nucleocapsid protein, 2-O-ribose methyltransferase, endoRNAse, 3-to-5 exonuclease, RNA-dependent RNA polymerase and helicase) for which drug design targets could be considered. There are other 16 nonstructural proteins (NSPs), which may also be percieved from the drug design angle. The protein structures have been deposited to ModelArchive. Tunnel analysis revealed the presence of large number of tunnels in NSP3, ORF 6 protein and membrane glycoprotein indicating a large number of transport pathways for small ligands influencing their reactivity.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Chittaranjan Baruah", + "author_inst": "Post Graduate Department of Zoology, Darrang College, Tezpur-784001, Assam, India" + }, + { + "author_name": "Papari Devi", + "author_inst": "TCRP Foundation Guwahati-781005, Assam, India" + }, + { + "author_name": "Dhirendra K Sharma", + "author_inst": "School of Biological Science, University of Science & Technology, Meghalaya-793101, India" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.05.22.20110809", "rel_title": "Succumbing to the COVID-19 Pandemic: Healthcare Workers not Satisfied and Intend to Leave Their Jobs", @@ -1460713,61 +1459296,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.22.20110551", - "rel_title": "Anti-SARS-CoV-2 IgG antibodies are associated with reduced viral load", - "rel_date": "2020-05-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.22.20110551", - "rel_abs": "Anti-SARS-CoV-2 antibodies have been described, but correlation with virologic outcomes is limited. Here, we find anti-SARS-CoV-2 IgG to be associated with reduced viral load. High viral loads were rare in individuals who had seroconverted. Higher viral load on admission was associated with increased 30-day mortality (OR 4.20 [95% CI: 1.62-10.86]).", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Andrew Bryan", - "author_inst": "University of Washington School of Medicine" - }, - { - "author_name": "Susan L Fink", - "author_inst": "University of Washington School of Medicine" - }, - { - "author_name": "Meghan A Gattuso", - "author_inst": "Aquaelis" - }, - { - "author_name": "Gregory Pepper", - "author_inst": "University of Washington" - }, - { - "author_name": "Anu Chaudhary", - "author_inst": "University of Washington School of Medicine" - }, - { - "author_name": "Mark Wener", - "author_inst": "University of Washington School of Medicine" - }, - { - "author_name": "Chihiro Morishima", - "author_inst": "University of Washington School of Medicine" - }, - { - "author_name": "Keith Jerome", - "author_inst": "University of Washington School of Medicine" - }, - { - "author_name": "Patrick C Mathias", - "author_inst": "University of Washington School of Medicine" - }, - { - "author_name": "Alexander L Greninger", - "author_inst": "University of Washington" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.22.20110304", "rel_title": "Importations of COVID-19 into African countries and risk of onward spread", @@ -1461579,6 +1460107,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.21.20108621", + "rel_title": "A pandemic at the Tunisian scale. Mathematical modelling of reported and unreported COVID-19 infected cases", + "rel_date": "2020-05-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20108621", + "rel_abs": "Starting from the city of Wuhan in China in late December 2019, the pandemic quickly spread to the rest of the world along the main intercontinental air routes. At the time of writing this article, there are officially about five million infections and more than 300 000 deaths. Statistics vary widely from country to country, revealing significant differences in anticipation and management of the crisis. We propose to examine the COVID-19 epidemic in Tunisia through mathematical models, which aim to determine the actual number of infected cases and to predict the course of the epidemic. As of May 11, 2020, there are officially 1032 COVID-19 infected cases in Tunisia. 45 people have died. Using a mathematical model based on the number of reported infected cases, the number of deaths, and the effect of the 18-day delay between infection and death, this study estimates the actual number of COVID-19 cases in Tunisia as 2555 cases. This paper analyses the evolution of the epidemic in Tunisia using population dynamics with an SEIR model combining susceptible cases S(t), asymptomatic infected cases A(t), reported infected cases V(t), and unreported infected cases U(t). This work measures the basic reproduction number [Formula], which is the average number of people infected by a COVID-19 infected person. The model predicts an [Formula]. Strict containment measures have led to a significant reduction in the reproduction rate. Contact tracing and respect for isolation have an impact: at the current time, we compute that Tunisia has an [Formula] (95% CI 0.14-0.70). These values depend on physical separation and can vary over time depending on the management of suspicious cases. Their objective estimation and the study of their evolution are however necessary to understand the pandemic and to reduce their unintended damage (due to an absence of symptoms, or the confusion of certain symptoms with less contagious diseases, or unavailable or unreliable tests).", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Ines Abdeljaoued-Tej", + "author_inst": "BIMS Laboratory, LR16IPT09, Institut Pasteur de Tunis, University of Tunis El Manar, Tunisia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.21.108035", "rel_title": "Methods of inactivation of SARS-CoV-2 for downstream biological assays", @@ -1462123,61 +1460670,6 @@ "type": "new results", "category": "cell biology" }, - { - "rel_doi": "10.1101/2020.05.21.109322", - "rel_title": "The emergence of SARS-CoV-2 in Europe and the US", - "rel_date": "2020-05-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.21.109322", - "rel_abs": "Accurate understanding of the global spread of emerging viruses is critically important for public health response and for anticipating and preventing future outbreaks. Here, we elucidate when, where and how the earliest sustained SARS-CoV-2 transmission networks became established in Europe and the United States (US). Our results refute prior findings erroneously linking cases in January 2020 with outbreaks that occurred weeks later. Instead, rapid interventions successfully prevented onward transmission of those early cases in Germany and Washington State. Other, later introductions of the virus from China to both Italy and Washington State founded the earliest sustained European and US transmission networks. Our analyses reveal an extended period of missed opportunity when intensive testing and contact tracing could have prevented SARS-CoV-2 from becoming established in the US and Europe.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Michael Worobey", - "author_inst": "Department of Ecology and Evolutionary Biology, University of Arizona" - }, - { - "author_name": "Jonathan Pekar", - "author_inst": "Department of Biomedical Informatics, University of California San Diego" - }, - { - "author_name": "Brendan B. Larsen", - "author_inst": "Department of Ecology and Evolutionary Biology, University of Arizona" - }, - { - "author_name": "Martha I. Nelson", - "author_inst": "Fogarty International Center, National Institutes of Health" - }, - { - "author_name": "Verity Hill", - "author_inst": "Institute of Evolutionary Biology, University of Edinburgh" - }, - { - "author_name": "Jeffrey B. Joy", - "author_inst": "Department of Medicine, University of British Columbia" - }, - { - "author_name": "Andrew Rambaut", - "author_inst": "Institute of Evolutionary Biology, University of Edinburgh" - }, - { - "author_name": "Marc A. Suchard", - "author_inst": "David Geffen School of Medicine at UCLA" - }, - { - "author_name": "Joel O. Wertheim", - "author_inst": "Department of Medicine, University of California San Diego" - }, - { - "author_name": "Philippe Lemey", - "author_inst": "KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Evolutionary Virology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2020.05.20.106401", "rel_title": "Deep immune profiling of COVID-19 patients reveals patient heterogeneity and distinct immunotypes with implications for therapeutic interventions", @@ -1463413,6 +1461905,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.21.20109678", + "rel_title": "Flattening the curve and the effect of atypical events on mitigation measures in Mexico: a modeling perspective", + "rel_date": "2020-05-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.21.20109678", + "rel_abs": "On 23 and 30 March 2020 the Mexican Federal government implemented social distancing measures to mitigate the COVID-19 epidemic. We use a mathematical model to explore atypical transmission events within the confinement period, triggered by the timing and strength of short time perturbations of social distancing. We show that social distancing measures were successful in achieving a significant reduction of the effective contact rate in the early weeks of the intervention. However, \"flattening the curve\" had an undesirable effect, since the epidemic peak was delayed too far, almost to the government preset day for lifting restrictions (01 June 2020). If the peak indeed occurs in late May or early June, then the events of childrens day and mothers day may either generate a later peak (worst case scenario), a long plateau with relatively constant but high incidence (middle case scenario) or the same peak date as in the original baseline epidemic curve, but with a post-peak interval of slower decay.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Mario Santana-Cibrian", + "author_inst": "CONACYT - Instituto de Matematicas UNAM-Juriquilla" + }, + { + "author_name": "Manuel Adrian Acuna-Zegarra", + "author_inst": "Departamento de Matematicas, Universidad de Sonora" + }, + { + "author_name": "Jorge X. Velasco-Hernandez", + "author_inst": "Universidad Nacional Autonoma de Mexico" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.21.20109389", "rel_title": "COVID-19 Confirmed Case Incidence Age Shift to Young Persons Age 0-19 and 20-39 Years Over Time: Washington State March - April 2020", @@ -1463757,53 +1462276,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.18.20104703", - "rel_title": "COVID-19 in China: Risk Factors and R0 Revisited", - "rel_date": "2020-05-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20104703", - "rel_abs": "The COVID-19 epidemic had spread rapidly through China and subsequently has proliferated globally leading to a pandemic situation around the globe. Human-to-human transmissions, as well as asymptomatic transmissions of the infection, have been confirmed. As of April 3rd public health crisis in China due to COVID-19 is potentially under control. We compiled a daily dataset of case counts, mortality, recovery, temperature, population density, and demographic information for each prefecture during the period of January 11 to April 07, 2020 (excluding Wuhan from our analysis due to missing data). Understanding the characteristics of spatiotemporal clustering of the COVID-19 epidemic and R0 is critical in effectively preventing and controlling the ongoing global pandemic. The prefectures were grouped based on several relevant features using unsupervised machine learning techniques. We performed a computational analysis utilizing the reported cases in China to estimate the revised R0 among different regions for prevention planning in an ongoing global pandemic. Finally, our results indicate that the impact of temperature and demographic (different age group percentage compared to the total population) factors on virus transmission may be characterized using a stochastic transmission model. Such predictions will help prioritize segments of a given community/region for action and provide a visual aid in designing prevention strategies for a specific geographic region. Furthermore, revised estimation and our methodology will aid in improving the human health consequences of COVID-19 elsewhere.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Irtesam Mahmud Khan", - "author_inst": "BUET" - }, - { - "author_name": "Wenyi Zhang", - "author_inst": "Center for Disease Control and Prevention of PLA" - }, - { - "author_name": "Sumaira Zafar", - "author_inst": "Asian Institute of Technology" - }, - { - "author_name": "Yong Wang", - "author_inst": "Center for Disease Control and Prevention of PLA" - }, - { - "author_name": "Junyu He", - "author_inst": "Zhejiang University" - }, - { - "author_name": "Hailon Sun", - "author_inst": "Center for Disease Control and Prevention of PLA" - }, - { - "author_name": "Ubydul Haque", - "author_inst": "University of North Texas Health Science Center" - }, - { - "author_name": "M. Sohel Rahman", - "author_inst": "BUET" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.18.20105395", "rel_title": "The COVID-19 Pandemic Predominantly Hits Poor Neighborhoods, or does it? Evidence from Germany", @@ -1464939,6 +1463411,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.05.21.109546", + "rel_title": "A high-throughput neutralizing antibody assay for COVID-19 diagnosis and vaccine evaluation", + "rel_date": "2020-05-22", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.21.109546", + "rel_abs": "Virus neutralization remains the gold standard for determining antibody efficacy. Therefore, a high-throughput assay to measure SARS-CoV-2 neutralizing antibodies is urgently needed for COVID-19 serodiagnosis, convalescent plasma therapy, and vaccine development. Here we report on a fluorescence-based SARS-CoV-2 neutralization assay that detects SARS-CoV-2 neutralizing antibodies in COVID-19 patient specimens and yields comparable results to plaque reduction neutralizing assay, the gold standard of serological testing. Our approach offers a rapid platform that can be scaled to screen people for antibody protection from COVID-19, a key parameter necessary to safely reopen local communities.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Antonio E. Muruato", + "author_inst": "University of Texas Medical Branch, Galveston TX, USA" + }, + { + "author_name": "Camila R. Fontes-Garfias", + "author_inst": "University of Texas Medical Branch, Galveston TX, USA" + }, + { + "author_name": "Ping Ren", + "author_inst": "University of Texas Medical Branch, Galveston TX, USA" + }, + { + "author_name": "Mariano A Garcia-Blanco", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Vineet D Menachery", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Xuping D Xie", + "author_inst": "University of Texas Medical Branch" + }, + { + "author_name": "Pei-Yong Shi", + "author_inst": "University of Texas Medical Branch" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.05.20.107243", "rel_title": "A modular framework for the development of targeted Covid-19 blood transcript profiling panels", @@ -1465331,41 +1463846,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2020.05.21.109298", - "rel_title": "Recombinant SARS-CoV-2 spike proteins for sero-surveillance and epitope mapping", - "rel_date": "2020-05-22", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.21.109298", - "rel_abs": "The newly emergent SARS-CoV-2 coronavirus is closely related to SARS-CoV which emerged in 2002. Studies on coronaviruses in general, and SARS in particular, have identified the virus spike protein (S) as being central to virus tropism, to the generation of a protective antibody response and to the unambiguous detection of past infections. As a result of this centrality SARS-CoV-2 S protein has a role in many aspects of research from vaccines to diagnostic tests. We describe a number of recombinant forms of SARS-CoV-2 S expressed in commonly available expression systems and their preliminary use in diagnostics and epitope mapping. These sources may find use in the current and future analysis of the virus and the Covid-19 disease it causes.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Sophie M Jegouic", - "author_inst": "University of Reading" - }, - { - "author_name": "Silvia Loureiro", - "author_inst": "University of Reading" - }, - { - "author_name": "Michelle Thom", - "author_inst": "The Pirbright Institute" - }, - { - "author_name": "Deepa Paliwal", - "author_inst": "University of Reading" - }, - { - "author_name": "Ian M Jones", - "author_inst": "University of Reading" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.05.19.20095901", "rel_title": "Dramatic reduction of psychiatric emergency consultations during lockdown linked to COVID-19 in Paris and suburbs", @@ -1466493,6 +1464973,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.17.20104554", + "rel_title": "The true case fatality of COVID19: An analytical solution", + "rel_date": "2020-05-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.17.20104554", + "rel_abs": "The exact risk of dying from COVID-19 has remained elusive and a topic of debate. In this study, the observed case fatality rates of 46 different countries are hypothesized to be dependent on their testing rates. An analytical test to this hypothesis suggests that the case fatality rate of COVID-19 could be consistent to a certain degree across all countries and states. The current global fatality rate is estimated to be around 1% and expected to converge between 1-3% when the pandemic ends. This model can be helpful to estimate the true infection rate for individual countries.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Syamantak Khan", + "author_inst": "Stanford University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.19.20103788", "rel_title": "Prevalence of Mental Health Problems During Virus Epidemics in the General Public, Health Care Workers and Survivors: A Rapid Review of the Evidence", @@ -1467037,45 +1465536,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.05.20.20103200", - "rel_title": "The Hybrid Forecasting Method SVR-ESAR forCovid-19", - "rel_date": "2020-05-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.20.20103200", - "rel_abs": "We know that SARS-Cov2 produces the new COVID-19 disease, which is one of the most dangerous pandemics of modern times. This pandemic has critical health and economic consequences, and even the health services of the large, powerful nations may be saturated. Thus, forecasting the number of infected persons in any country is essential for controlling the situation. In the literature, different forecasting methods have been published, attempting to solve the problem. However, a simple and accurate forecasting method is required for its implementation in any part of the world. This paper presents a precise and straightforward forecasting method named SVR-ESAR (Support Vector regression hybridized with the classical Exponential smoothing and ARIMA). We applied this method to the infected time series in four scenarios, which we have taken for the Github repository: the Whole World, China, the US, and Mexico. We compared our results with those of the literature showing the proposed method has the best accuracy.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Juan Frausto-Solis", - "author_inst": "National Technological Institute of Mexico/IT Cd Madero" - }, - { - "author_name": "Jose Enrique Olvera Vazquez", - "author_inst": "National Technological Institute of Mexico/IT Cd Madero" - }, - { - "author_name": "Juan Javier Gonzalez-Barbosa", - "author_inst": "National Technological Institute of Mexico/IT Cd Madero" - }, - { - "author_name": "Guadalupe Castilla-Valdez", - "author_inst": "National Technological Institute of Mexico/IT Cd Madero" - }, - { - "author_name": "Juan Paulo Sanchez-Hernandez", - "author_inst": "Universidad Politecnica del Estado de Morelos" - }, - { - "author_name": "Joaquin Perez-Ortega", - "author_inst": "National Technological Institute of Mexico/CENIDET" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.05.21.20105106", "rel_title": "Analysis of Covid-19 and non-Covid-19 viruses including influenza viruses to see the influence of intensive preventive measures among Japanese", @@ -1468119,6 +1466579,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.05.17.20104885", + "rel_title": "Extension of a SIR model for modelling the propagation of Covid-19 in several countries.", + "rel_date": "2020-05-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.17.20104885", + "rel_abs": "BackgroundSeveral epidemiologic models have been published to forecast the spread of the COVID-19 pandemic yet there are still uncertainties regarding their accuracy. We report the main features of the development of a novel freely accessible model intended to urgently help researchers and decision makers to predict the evolution of the pandemic in their country.\n\nMethods and findingsWe built a SIR-type compartmental model with additional compartments and features. We made the hypothesis that the number of contagious individuals in the population was negligible as compared to the population size. We introduced a compartment D corresponding to the deceased patients and a compartment L representing the group of individuals who will die but who will not infect anybody (due to social or medical isolation). Our model integrated a time-dependent transmission rate, whose variations can be thought to be related to the public measures taken by each country and a cosine function to incorporate a periodic weekly component linked to the way in which numbers of cases and deaths are counted and reported, which can change from day to day.\n\nThe model was able to accurately capture the different changes in the dynamics of the pandemic for nine different countries whatever the type of pandemic spread or containment measures. The model provided very accurate forecasts in the relatively short term (10 days).\n\nConclusionsIn early evaluation of the performance of our model, we found a high level of accuracy between prediction and observed data, regardless of the country. The model should be used by the community to help public health decisions as we will refine it over time and further investigate its performance.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Marc Lavielle", + "author_inst": "Inria" + }, + { + "author_name": "Matthieu Faron", + "author_inst": "Gustave Roussy" + }, + { + "author_name": "jeremie lefevre", + "author_inst": "sorbonne universite" + }, + { + "author_name": "Jean-David Zeitoun", + "author_inst": "Centre Epidemiologie Clinique, Hotel Dieu" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.17.20104976", "rel_title": "A structured model for COVID-19 spread: modelling age and healthcare inequities", @@ -1468471,101 +1466962,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.18.20105155", - "rel_title": "The Dynamic Changes of Antibodies against SARS-CoV-2 during the Infection and Recovery of COVID-19", - "rel_date": "2020-05-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20105155", - "rel_abs": "Deciphering the dynamic changes of antibodies against SARS-CoV-2 is essential for understanding the immune response in COVID-19 patients. By comprehensively analyzing the laboratory findings of 1,850 patients, we describe the dynamic changes of the total antibody, spike protein (S)-, receptor-binding domain (RBD)-, and nucleoprotein (N)- specific IgM and IgG levels during SARS-CoV-2 infection and recovery. Our results indicate that the S-, RBD-, and N- specific IgG generation of severe/critical COVID-19 patients is one week later than mild/moderate cases, while the levels of these antibodies are 1.5-fold higher in severe/critical patients during hospitalization (P<0.01). The decrease of these IgG levels indicates the poor outcome of severe/critical patients. The RBD- and S-specific IgG levels are 2-fold higher in virus-free patients (P<0.05). Notably, we found that the patients who got re-infected had a low level of protective antibody on discharge. Therefore, our evidence proves that the dynamic changes of antibodies could provide an important reference for diagnosis, monitoring, and treatment, and shed new light on the precise management of COVID-19.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Kening Li", - "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China" - }, - { - "author_name": "Min Wu", - "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China" - }, - { - "author_name": "Bin Huang", - "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China" - }, - { - "author_name": "Aifang Zhong", - "author_inst": "Medical Technical Support Division, the 904th Hospital, Changzhou, Jiangsu 213003, China" - }, - { - "author_name": "Lu Li", - "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China" - }, - { - "author_name": "Yun Cai", - "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China" - }, - { - "author_name": "Lingxiang Wu", - "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China" - }, - { - "author_name": "Mengyan Zhu", - "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China" - }, - { - "author_name": "Jie Li", - "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China" - }, - { - "author_name": "Ziyu Wang", - "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China" - }, - { - "author_name": "Wei Wu", - "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China" - }, - { - "author_name": "Wanlin Li", - "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China" - }, - { - "author_name": "Bakwatanisa Bosco", - "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China" - }, - { - "author_name": "Zhenhua Gan", - "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China" - }, - { - "author_name": "Zhihua Wang", - "author_inst": "Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China" - }, - { - "author_name": "Qinghua Qiao", - "author_inst": "Medical and Technical Support Department, Pingdingshan Medical District, the 989th Hospital of Joint Logistic Support Force, Pingdingshan, Henan, 467000, China" - }, - { - "author_name": "Jian Wu", - "author_inst": "COVID-19 Research Center, Institute of Laboratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, Jiangsu 210002, China" - }, - { - "author_name": "qianghu wang", - "author_inst": "Nanjing medical university" - }, - { - "author_name": "Shukui Wang", - "author_inst": "Department of Laboratory Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu 210006, China" - }, - { - "author_name": "Xinyi Xia", - "author_inst": "Joint Expert Group for COVID-19, Wuhan Huoshenshan Hospital, Wuhan, Hubei 430100, China" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.18.20105247", "rel_title": "An acceptable method to evaluate the analytical performance of real-time fluorescent RT-PCR targeting SARS-CoV-2", @@ -1469753,6 +1468149,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.19.20107268", + "rel_title": "A simple criterion to design optimal nonpharmaceutical interventions for epidemic outbreaks", + "rel_date": "2020-05-21", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.19.20107268", + "rel_abs": "To mitigate the COVID-19 pandemic, much emphasis exists on implementing non-pharmaceutical interventions to keep the reproduction number below one. But using that objective ignores that some of these interventions, like bans of public events or lockdowns, must be transitory and as short as possible because of their significative economic and societal costs. Here we derive a simple and mathematically rigorous criterion for designing optimal transitory non-pharmaceutical interventions. We find that reducing the reproduction number below one is sufficient but not necessary. Instead, our criterion prescribes the required reduction in the reproduction number according to the maximum health services capacity. To explore the implications of our theoretical results, we study the non-pharmaceutical interventions implemented in 16 cities during the COVID-19 pandemic. In particular, we estimate the minimal reduction of the contact rate in each city that is necessary to control the epidemic optimally. We also compare the optimal start of the intervention with the start of the actual interventions applied in each city. Our results contribute to establishing a rigorous methodology to guide the design of non-pharmaceutical intervention policies.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Marco Tulio Angulo", + "author_inst": "CONACyT - Institute of Mathematics, UNAM." + }, + { + "author_name": "Fernando Casta\u00f1os", + "author_inst": "Department of Automatic Control, CINVESTAV-IPN" + }, + { + "author_name": "Rodrigo Moreno-Morton", + "author_inst": "Universidad Nacional Autonoma de Mexico, Faculty of Sciences" + }, + { + "author_name": "Jorge X. Velasco-Hernandez", + "author_inst": "Universidad Nacional Autonoma de Mexico" + }, + { + "author_name": "Jaime A. Moreno", + "author_inst": "Institute of Engineering, UNAM." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.19.20107433", "rel_title": "Analyzing the Effect of Temperature on the Outspread of COVID-19 around the Globe", @@ -1470045,57 +1468476,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.15.20103531", - "rel_title": "IL6 inhibition in critically ill COVID-19 patients is associated with increased secondary infections", - "rel_date": "2020-05-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.15.20103531", - "rel_abs": "BackgroundAnti-inflammatory therapies such as IL-6 inhibition have been proposed for COVID-19 in a vacuum of evidence-based treatment. However, abrogating the inflammatory response in infectious diseases may impair a desired host response and predispose to secondary infections.\n\nMethodsWe retrospectively reviewed the medical record of critically ill COVID-19 patients during an 8-week span and compared the prevalence of secondary infection and outcomes in patients who did and did not receive tocilizumab. Additionally, we included representative histopathologic post-mortem findings from several COVID-19 cases that underwent autopsy at our institution.\n\nResults111 patients were identified, of which 54 had received tocilizumab while 57 had not. Receiving tocilizumab was associated with a higher risk of secondary bacterial (48.1% vs. 28.1%, p=0.029 and fungal (5.6% vs. 0%, p=0.112) infections. Consistent with higher number of infections, patients who received tocilizumab had higher mortality (35.2% vs. 19.3%, p=0.020). Seven cases underwent autopsy. In 3 cases who received tocilizumab, there was evidence of pneumonia on pathology. Of the 4 cases that had not been given tocilizumab, 2 showed evidence of aspiration pneumonia and 2 exhibited diffuse alveolar damage.\n\nConclusionsExperimental therapies are currently being applied to COVID-19 outside of clinical trials. Anti-inflammatory therapies such as anti-IL-6 therapy have the potential to impair viral clearance, predispose to secondary infection, and cause harm. We seek to raise physician awareness of these issues and highlight the need to better understand the immune response in COVID-19.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Lucas M Kimmig", - "author_inst": "University of Chicago" - }, - { - "author_name": "David Wu", - "author_inst": "University of Chicago" - }, - { - "author_name": "Matthew Gold", - "author_inst": "University of Chicago" - }, - { - "author_name": "Natasha N Pettit", - "author_inst": "University of Chicago" - }, - { - "author_name": "David Pitrak", - "author_inst": "University of Chicago" - }, - { - "author_name": "Jeffrey Mueller", - "author_inst": "University of Chicago" - }, - { - "author_name": "Aliya N Husain", - "author_inst": "University of Chicago" - }, - { - "author_name": "Ece A Mutlu", - "author_inst": "Rush University" - }, - { - "author_name": "Gokhan M Mutlu", - "author_inst": "University of Chicago" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.05.16.20103853", "rel_title": "COVID-19 in London, a Case Series Demonstrating Late Improvement in Survivors", @@ -1470847,6 +1469227,109 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.05.20.106609", + "rel_title": "Tiger team: a panel of human neutralizing mAbs targeting SARS-CoV-2 spike at multiple epitopes", + "rel_date": "2020-05-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.20.106609", + "rel_abs": "The novel highly transmissible human coronavirus SARS-CoV-2 is the causative agent of the COVID-19 pandemic. Thus far, there is no approved therapeutic drug, specifically targeting this emerging virus. Here we report the isolation and characterization of a panel of human neutralizing monoclonal antibodies targeting the SARS-CoV-2 receptor binding domain (RBD). These antibodies were selected from a phage display library constructed using peripheral circulatory lymphocytes collected from patients at the acute phase of the disease. These neutralizing antibodies are shown to recognize distinct epitopes on the viral spike RBD, therefore they represent a promising basis for the design of efficient combined post-exposure therapy for SARS-CoV-2 infection.", + "rel_num_authors": 22, + "rel_authors": [ + { + "author_name": "Tal Noy-Porat", + "author_inst": "Israel Institute for Biological Research" + }, + { + "author_name": "Efi Makdasi", + "author_inst": "Israel Institute for Biological Research" + }, + { + "author_name": "Ron Alcalay", + "author_inst": "Israel Institute for Biological Research" + }, + { + "author_name": "Adva Mechaly", + "author_inst": "Israel Institute for Biological Research" + }, + { + "author_name": "Yinon Levy", + "author_inst": "Israel Institute for Biological Research" + }, + { + "author_name": "Adi Bercovich-Kinori", + "author_inst": "Israel Institute for Biological Research" + }, + { + "author_name": "Ayelet Zauberman", + "author_inst": "Israel Institute for Biological Research" + }, + { + "author_name": "Hadas Tamir", + "author_inst": "Israel Institute for Biological Research" + }, + { + "author_name": "Yfat Yahalom-Ronen", + "author_inst": "Israel Institute for Biological Research" + }, + { + "author_name": "Eyal Epstein", + "author_inst": "Israel Institute for Biological Research" + }, + { + "author_name": "Hagit Achdout", + "author_inst": "Israel Institute for Biological Research" + }, + { + "author_name": "Sharon Melamed", + "author_inst": "Israel Institute for Biological Research" + }, + { + "author_name": "Theodor Chitlaru", + "author_inst": "Israel Institute for Biological Research" + }, + { + "author_name": "Shay Weiss", + "author_inst": "Israel Institute for Biological Research" + }, + { + "author_name": "Eldar Peretz", + "author_inst": "Israel Institute for Biological Research" + }, + { + "author_name": "Osnat Rosen", + "author_inst": "Israel Institute for Biological Research" + }, + { + "author_name": "Nir Paran", + "author_inst": "Israel Institute for Biological Research" + }, + { + "author_name": "Shmuel Yitzhaki", + "author_inst": "Israel Institute for Biological Research" + }, + { + "author_name": "Shmuel C. Shapira", + "author_inst": "Israel Institute for Biological Research" + }, + { + "author_name": "Tomer Israely", + "author_inst": "Israel Institute for Biological Research" + }, + { + "author_name": "Ohad Mazor", + "author_inst": "Israel Institute for Biological Research" + }, + { + "author_name": "Ronit Rosenfeld", + "author_inst": "Israel Institute for Biological Research" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.05.19.104513", "rel_title": "Prediction of the virus incubation period for COVID-19 and future outbreaks", @@ -1471287,113 +1469770,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.05.20.105247", - "rel_title": "A replication-competent vesicular stomatitis virus for studies of SARS-CoV-2 spike-mediated cell entry and its inhibition", - "rel_date": "2020-05-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.20.105247", - "rel_abs": "There is an urgent need for vaccines and therapeutics to prevent and treat COVID-19. Rapid SARS-CoV-2 countermeasure development is contingent on the availability of robust, scalable, and readily deployable surrogate viral assays to screen antiviral humoral responses, and define correlates of immune protection, and to down-select candidate antivirals. Here, we describe a highly infectious recombinant vesicular stomatitis virus bearing the SARS-CoV-2 spike glycoprotein S as its sole entry glycoprotein that closely resembles the authentic agent in its entry-related properties. We show that the neutralizing activities of a large panel of COVID-19 convalescent sera can be assessed in high-throughput fluorescent reporter assay with rVSV-SARS-CoV-2 S and that neutralization of the rVSV and authentic SARS-CoV-2 by spike-specific antibodies in these antisera is highly correlated. Our findings underscore the utility of rVSV-SARS-CoV-2 S for the development of spike-specific vaccines and therapeutics and for mechanistic studies of viral entry and its inhibition.", - "rel_num_authors": 23, - "rel_authors": [ - { - "author_name": "M Eugenia Dieterle", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Denise Haslwanter", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Robert H Bortz III", - "author_inst": "Albert Einstein College Of Medicine" - }, - { - "author_name": "Ariel S Wirchnianski", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Gorka Lasso", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Olivia Vergnolle", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Shawn A Abbasi", - "author_inst": "U.S. Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "J Maximilian Fels", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Ethan Laudermilch", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Catalina Florez", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Amanda Mengotto", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Duncan Kimmel", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Ryan J Malonis", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "George Georgiev", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Jose Quiroz", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Jason Barnhill", - "author_inst": "United States Marine Academy at West Point" - }, - { - "author_name": "Liise-Anne Pirofski", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Johanna P Daily", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "John M Dye", - "author_inst": "U.S. Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Jonathan R Lai", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Andrew S Herbert", - "author_inst": "U.S. Army Medical Research Institute of Infectious Diseases" - }, - { - "author_name": "Kartik Chandran", - "author_inst": "Albert Einstein College of Medicine" - }, - { - "author_name": "Rohit K Jangra", - "author_inst": "Albert Einstein College of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.05.18.103184", "rel_title": "In-Vivo Toxicity Studies and In-Vitro Inactivation of SARS-CoV-2 by Povidone-iodine In-situ Gel Forming Formulations", @@ -1472433,6 +1470809,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.18.20097220", + "rel_title": "Hyperpyrexia leading to death in a patient with severe COVID-19 disease", + "rel_date": "2020-05-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.18.20097220", + "rel_abs": "We describe here the clinical course of a 42 year old male with severe COVID 19 disease treated at a private hospital in Mumbai, India. This patient with very high inflammatory markers at admission was treated with supportive care, mechanical ventilation, anticoagulation, hydroxychloroquine, corticosteroids, tocilizumab, intravenous insulin, antibiotics, sedation and paralysis. There was sustained improvement in his respiratory status and decline in ventilator settings with decline and normalization of CRP, D dimer and PCT. However high fever persisted that did not respond to paracetamol and NSAIDS. On day 8 of admission his axillary temperature touched 107F followed by rapid clinical deterioration and death within the next 12 hours, Blood cultures were consistently sterile. While death was related to hyperpyrexia, the cause of this hyperpyrexia is uncertain.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Tanu Singhal", + "author_inst": "Kokilaben Dhirubhai Ambani Hospital and Medical Research Institute" + }, + { + "author_name": "Sourabh Phadtare", + "author_inst": "Kokilaben Dhirubhai Ambani Hospital and Medical Research Institute" + }, + { + "author_name": "Sunil Pai", + "author_inst": "Kokilaben Dhirubhai Ambani Hospital and Medical Research Institute" + }, + { + "author_name": "Amit Raodeo", + "author_inst": "Kokilaben Dhirubhai Ambani Hospital and Medical Research Institute" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.16.20099408", "rel_title": "Serological prevalence of antibodies to SARS CoV-2 amongst cancer centre staff", @@ -1472693,25 +1471100,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.15.20103077", - "rel_title": "Mathematical Modeling and Simulation of SIR Model for COVID-2019 Epidemic Outbreak: A Case Study of India", - "rel_date": "2020-05-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.15.20103077", - "rel_abs": "The present study discusses the spread of COVID-2019 epidemic of India and its end by using SIR model. Here we have discussed about the spread of COVID-2019 epidemic in great detail using Euler's method. The Eulers method is a method for solving the ordinary differential equations. The SIR model has the combination of three ordinary differential equations. In this study, we have used the data of COVID-2019 Outbreak of India on 8 May, 2020. In this data, we have used 135710 susceptible cases, 54340 infectious cases and 1830 reward/removed cases for the initial level of experimental purpose. Data about a wide variety of infectious diseases has been analyzed with the help of SIR model. Therefore, this model has been already well tested for infectious diseases by various scientists and researchers. Using the data to the number of COVID-2019 outbreak cases in India the results obtained from the analysis and simulation of this proposed SIR model showing that the COVID-2019 epidemic cases increase for some time and there after this outbreak decrease. The results obtained from the SIR model also suggest that the Eulers method can be used to predict transmission and prevent the COVID-2019 epidemic in India. Finally, from this study, we have found that the outbreak of COVID-2019 epidemic in India will be at its peak on 25 May 2020 and after that it will work slowly and on the verge of ending in the first or second week of August 2020.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Dr. Ramjeet Singh Yadav", - "author_inst": "Ashoka Institute of Technology and Management, Varanasi, UP, India" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.18.20101840", "rel_title": "Depression and loneliness during COVID-19 restrictions in the United States, and their associations with frequency of social and sexual connections", @@ -1473691,6 +1472079,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.12.20098970", + "rel_title": "Agent-Based Simulation for Evaluation of Contact-Tracing Policies Against the Spread of SARS-CoV-2", + "rel_date": "2020-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20098970", + "rel_abs": "BackgroundMany countries have already gone through several infection waves and mostly managed to successfully stop the exponential spread of SARS-CoV-2 through bundles of restrictive measures. Still, the danger of further waves of infections is omnipresent and it is apparent that every containment policy must be carefully evaluated and possibly replaced by a different, less restrictive policy, before it can be lifted. Tracing of contacts and consequential breaking of infection chains is a promising strategy to help containing the disease, although its precise impact on the epidemic is unknown.\n\nObjectiveIn this work we aim to quantify the impact of tracing on the containment of the disease and investigate the dynamic effects involved.\n\nDesignWe developed an agent-based model that validly depicts the spread of the disease and allows for exploratory analysis of containment policies. We apply this model to quantify the impact of divverent variants of contact tracing in Austria and to derive general conclusions on contract tracing.\n\nResultsThe study displays that strict tracing can supplement up to 5% reduction of infectivity and that household quarantine comes at the smallest price regarding preventively quarantined people.\n\nLimitationsThe results are limited by the validity of the modeling assumptions, model parameter estimates, and the quality of the parametrization data.\n\nConclusionsThe study shows that tracing is indeed an efficient measure to keep case numbers low but comes at a high price if the disease is not well contained. Therefore, contact tracing must be executed strictly and adherence within the population must be held up to prevent uncontrolled outbreaks of the disease.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Martin Richard Bicher", + "author_inst": "TU Wien" + }, + { + "author_name": "Claire Rippinger", + "author_inst": "dwh GmbH" + }, + { + "author_name": "Christoph Urach", + "author_inst": "dwh GmbH" + }, + { + "author_name": "Dominik Brunmeir", + "author_inst": "dwh GmbH" + }, + { + "author_name": "Uwe Siebert", + "author_inst": "UMIT University for Health Sciences, Institute of Public Health, Medical Decision Making and Health Technology Assessment" + }, + { + "author_name": "Niki Popper", + "author_inst": "TU Wien" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.12.20099036", "rel_title": "Stepping out of lockdown should start with school re-openings while maintaining distancing measures. Insights from mixing matrices and mathematical models.", @@ -1474179,81 +1472606,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.13.20100404", - "rel_title": "Clinical characteristics and early outcomes in patients with COVID-19 treated with tocilizumab at a United States academic center", - "rel_date": "2020-05-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.13.20100404", - "rel_abs": "We describe early outcomes in 11 COVID-19 patients treated with the IL-6 receptor inhibitor tocilizumab. While C-reactive protein decreased, neither clinical improvement nor reduced temperature or oxygen requirements was observed in most patients. Our findings contrast with prior reports and raise questions about tocilizumab use in severe COVID-19.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Casey Allison Rimland", - "author_inst": "Medical Scientist Training Program, University of North Carolina at Chapel Hill (UNC), Chapel Hill, NC" - }, - { - "author_name": "Camille E Morgan", - "author_inst": "Medical Scientist Training Program, University of North Carolina at Chapel Hill (UNC), Chapel Hill, NC; \tDepartment of Epidemiology, UNC Gillings School of Glob" - }, - { - "author_name": "Griffin J Bell", - "author_inst": "Department of Epidemiology, UNC Gillings School of Global Public Health, Chapel Hill, NC" - }, - { - "author_name": "Min K Kim", - "author_inst": "Division of Infectious Diseases, Department of Medicine, UNC School of Medicine, Chapel Hill, NC" - }, - { - "author_name": "Tanner Hedrick", - "author_inst": "Department of Pharmacy, UNC Medical Center, Chapel Hill, NC" - }, - { - "author_name": "Ashley Marx", - "author_inst": "Department of Pharmacy, UNC Medical Center, Chapel Hill, NC" - }, - { - "author_name": "Brian Bramson", - "author_inst": "Division of Infectious Diseases, Department of Medicine, UNC School of Medicine, Chapel Hill, NC" - }, - { - "author_name": "Heidi Swygard", - "author_inst": "Division of Infectious Diseases, UNC School of Medicine, Chapel Hill, NC, USA" - }, - { - "author_name": "Sonia Napravnik", - "author_inst": "Department of Epidemiology, UNC Gillings School of Global Public Health, Chapel Hill, NC; Division of Infectious Diseases, Department of Medicine, UNC School of" - }, - { - "author_name": "John L Schmitz", - "author_inst": "Department of Pathology and Laboratory Medicine, UNC School of Medicine, Chapel Hill, NC" - }, - { - "author_name": "Shannon S Carson", - "author_inst": "Division of Pulmonary Diseases and Critical Care Medicine, Department of Medicine, UNC School of Medicine, Chapel Hill, NC" - }, - { - "author_name": "William A Fischer", - "author_inst": "Division of Pulmonary Diseases and Critical Care Medicine, Department of Medicine, UNC School of Medicine, Chapel Hill, NC" - }, - { - "author_name": "Joseph J Eron", - "author_inst": "Division of Infectious Diseases, Department of Medicine, UNC School of Medicine, Chapel Hill, NC" - }, - { - "author_name": "Cynthia L Gay", - "author_inst": "Division of Infectious Diseases, Department of Medicine, UNC School of Medicine, Chapel Hill, NC" - }, - { - "author_name": "Jonathan B Parr", - "author_inst": "Division of Infectious Diseases, Department of Medicine, UNC School of Medicine, Chapel Hill, NC" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.13.20100206", "rel_title": "Comparison of SARS-CoV-2 detection in nasopharyngeal swab and saliva", @@ -1475029,6 +1473381,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.14.20101675", + "rel_title": "Reproducing SARS-CoV-2 epidemics byregion-specific variables and modeling contacttracing App containment", + "rel_date": "2020-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20101675", + "rel_abs": "Targeted contact-tracing through mobile phone apps has been proposed as an instrument to help contain the spread of COVID-19 and manage the lifting of nation-wide lockdowns currently in place in USA and Europe. However, there is an ongoing debate on its potential efficacy, especially in the light of region-specific demographics.\n\nWe built an expanded SIR model of COVID-19 epidemics that accounts for region-specific population densities, and we used it to test the impact of a contact-tracing app in a number of scenarios. Using demographic and mobility data from Italy and Spain, we used the model to simulate scenarios that vary in baseline contact rates, population densities and fraction of app users in the population.\n\nOur results show that, in support of efficient isolation of symptomatic cases, app-mediated contact-tracing can successfully mitigate the epidemic even with a relatively small fraction of users, and even suppress altogether with a larger fraction of users. However, when regional differences in population density are taken into consideration, the epidemic can be significantly harder to contain in higher density areas, highlighting potential limitations of this intervention in specific contexts.\n\nThis work corroborates previous results in favor of app-mediated contact-tracing as mitigation measure for COVID-19, and draws attention on the importance of region-specific demographic and mobility factors to achieve maximum efficacy in containment policies.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Alberto Ferrari", + "author_inst": "FROM research foundation" + }, + { + "author_name": "Enrico Santus", + "author_inst": "Bayer, Decision Science & Advanced Analytics for MA, PV & RA Division." + }, + { + "author_name": "Davide Cirillo", + "author_inst": "Barcelona Supercomputing Center (BSC), C/ Jordi Girona 29, 08034, Barcelona,Spain." + }, + { + "author_name": "Miguel Ponce-de-Leon", + "author_inst": "Barcelona Supercomputing Center (BSC), C/ Jordi Girona 29, 08034, Barcelona,Spain." + }, + { + "author_name": "Nicola Marino", + "author_inst": "Women's Brain Project (WBP), Gunterhausen, Switzerland" + }, + { + "author_name": "Maria Teresa Ferretti", + "author_inst": "Women's Brain Project (WBP), Gunterhausen, Switzerland" + }, + { + "author_name": "Antonella Santuccione Chadha", + "author_inst": "Women's Brain Project (WBP), Gunterhausen, Switzerland" + }, + { + "author_name": "Nikolaos Mavridis", + "author_inst": "Interactive Robots and Media Laboratory (IRLM), United Arab Emirates." + }, + { + "author_name": "Alfonso Valencia", + "author_inst": "Barcelona Supercomputing Center (BSC), C/ Jordi Girona 29, 08034, Barcelona,Spain." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.14.20101642", "rel_title": "Knowledge of novel coronavirus (SARS-COV-2) among a Georgian population", @@ -1475337,37 +1473740,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.14.20101873", - "rel_title": "COVID Faster R-CNN: A Novel Framework to Diagnose Novel Coronavirus Disease (COVID-19) in X-Ray Images", - "rel_date": "2020-05-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20101873", - "rel_abs": "COVID-19 or novel coronavirus disease, which has already been declared as a worldwide pandemic, at first had an outbreak in a small town of China, named Wuhan. More than two hundred countries around the world have already been affected by this severe virus as it spreads by human interaction. Moreover, the symptoms of novel coronavirus are quite similar to the general flu. Screening of infected patients is considered as a critical step in the fight against COVID-19. Therefore, it is highly relevant to recognize positive cases as early as possible to avoid further spreading of this epidemic. However, there are several methods to detect COVID-19 positive patients, which are typically performed based on respiratory samples and among them one of the critical approach which is treated as radiology imaging or X-Ray imaging. Recent findings from X-Ray imaging techniques suggest that such images contain relevant information about the SARS-CoV-2 virus. In this article, we have introduced a Deep Neural Network (DNN) based Faster Regions with Convolutional Neural Networks (Faster R-CNN) framework to detect COVID-19 patients from chest X-Ray images using available open-source dataset. Our proposed approach provides a classification accuracy of 97.36%, 97.65% of sensitivity, and a precision of 99.28%. Therefore, we believe this proposed method might be of assistance for health professionals to validate their initial assessment towards COVID-19 patients.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Kabid Hassan Shibly", - "author_inst": "Dhaka International University (DIU)" - }, - { - "author_name": "Samrat Kumar Dey", - "author_inst": "Dhaka International University (DIU)" - }, - { - "author_name": "Md. Tahzib Ul Islam", - "author_inst": "Dhaka International University (DIU)" - }, - { - "author_name": "Md. Mahbubur Rahman", - "author_inst": "Military Institute of Science and Technology (MIST)" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.05.14.20101758", "rel_title": "Semantic and geographical analysis of Covid-19 trials reveals a fragmented clinical research landscape likely to impair informativeness.", @@ -1476439,6 +1474811,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.16.20098657", + "rel_title": "Empirical Assessment of COVID-19 Crisis Standards of Care Guidelines", + "rel_date": "2020-05-19", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.16.20098657", + "rel_abs": "BackgroundSeveral states have released Crisis Standards of Care (CSC) guidelines for the allocation of scarce critical care resources. Most guidelines rely on Sequential Organ Failure Assessment (SOFA) scores to maximize lives saved, but states have adopted different stances on whether to maximize long-term outcomes (life-years saved) by accounting for patient comorbidities.\n\nMethodsWe compared 4 representative state guidelines with varying approaches to comorbidities and analyzed how CSC prioritization correlates with clinical outcomes. We included 27 laboratory-confirmed COVID-19 patients admitted to ICUs at Brigham and Womens Hospital from March 12 to April 3, 2020. We compared prioritization algorithms from New York, which assigns priority based on SOFA alone; Maryland, which uses SOFA plus severe comorbidities; Pennsylvania, which uses SOFA plus major and severe comorbidities; and Colorado, which uses SOFA plus a modified Charlson comorbidity index.\n\nResultsIn pairwise comparisons across all possible pairs, we found that state guidelines frequently resulted in tie-breakers based on age or lottery: New York 100% of the time (100% resolved by lottery), Pennsylvania 86% of the time (18% by lottery), Maryland 93% of the time (35% by lottery), and Colorado: 32% of the time (10% by lottery). The prioritization algorithm with the strongest correlation with 14-day outcomes was Colorado (rs = -0.483. p = 0.011) followed by Maryland (rs = -0. 394, p =0.042), Pennsylvania (rs = -0.382, p = 0.049), and New York (rs = 0). An alternative model using raw SOFA scores alone was moderately correlated with outcomes (rs = -0.448, p = 0.019).\n\nConclusionsState guidelines for scarce resource allocation frequently resulted in identical priority scores, requiring tie-breakers based on age or lottery. These findings suggest that state CSC guidelines should be further assessed empirically to understand whether they meet their goals.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Julia L. Jezmir", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Maheetha Bharadwaj", + "author_inst": "Harvard Medical School" + }, + { + "author_name": "Sandeep P. Kishore", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Marisa Winkler", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Bradford Diephuis", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Edy Y. Kim", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "William B. Feldman", + "author_inst": "Brigham and Women's Hospital" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "medical ethics" + }, { "rel_doi": "10.1101/2020.05.18.20105171", "rel_title": "Upper airway gene expression differentiates COVID-19 from other acute respiratory illnesses and reveals suppression of innate immune responses by SARS-CoV-2", @@ -1477063,121 +1475478,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.05.18.102038", - "rel_title": "Neutralizing antibody and soluble ACE2 inhibition of a replication-competent VSV-SARS-CoV-2 and a clinical isolate of SARS-CoV-2.", - "rel_date": "2020-05-18", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.18.102038", - "rel_abs": "Antibody-based interventions against SARS-CoV-2 could limit morbidity, mortality, and possibly disrupt epidemic transmission. An anticipated correlate of such countermeasures is the level of neutralizing antibodies against the SARS-CoV-2 spike protein, yet there is no consensus as to which assay should be used for such measurements. Using an infectious molecular clone of vesicular stomatitis virus (VSV) that expresses eGFP as a marker of infection, we replaced the glycoprotein gene (G) with the spike protein of SARS-CoV-2 (VSV-eGFP-SARS-CoV-2) and developed a high-throughput imaging-based neutralization assay at biosafety level 2. We also developed a focus reduction neutralization test with a clinical isolate of SARS-CoV-2 at biosafety level 3. We compared the neutralizing activities of monoclonal and polyclonal antibody preparations, as well as ACE2-Fc soluble decoy protein in both assays and find an exceptionally high degree of concordance. The two assays will help define correlates of protection for antibody-based countermeasures including therapeutic antibodies, immune {gamma}-globulin or plasma preparations, and vaccines against SARS-CoV-2. Replication-competent VSV-eGFP-SARS-CoV-2 provides a rapid assay for testing inhibitors of SARS-CoV-2 mediated entry that can be performed in 7.5 hours under reduced biosafety containment.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "James Brett Case", - "author_inst": "Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA." - }, - { - "author_name": "Paul W Rothlauf", - "author_inst": "Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA; Program in Virology, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Rita E Chen", - "author_inst": "Departments of Medicine, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA." - }, - { - "author_name": "Zhuoming Liu", - "author_inst": "Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA." - }, - { - "author_name": "Haiyan Zhao", - "author_inst": "Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA." - }, - { - "author_name": "Arthur S Kim", - "author_inst": "Departments of Medicine, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA." - }, - { - "author_name": "Louis-Marie Bloyet", - "author_inst": "Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA." - }, - { - "author_name": "Qiru Zeng", - "author_inst": "Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA." - }, - { - "author_name": "Stephen Tahan", - "author_inst": "Washington University in St. Louis School of Medicine" - }, - { - "author_name": "Lindsay Droit", - "author_inst": "Departments of Molecular Microbiology, Pathology & Immunology, Washington University School of Medicine, St. Louis, MO, USA." - }, - { - "author_name": "Ma. Xenia G. Ilagan", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Michael A Tartell", - "author_inst": "Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA; Program in Virology, Harvard Medical School, Boston, MA, USA" - }, - { - "author_name": "Gaya K Amarasinghe", - "author_inst": "Departments of Molecular Microbiology, Pathology & Immunology, Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA" - }, - { - "author_name": "Jeffrey P Henderson", - "author_inst": "Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA." - }, - { - "author_name": "Shane Miersch", - "author_inst": "The Donnelly Centre, University of Toronto, Toronto, Canada." - }, - { - "author_name": "Mart Ustav", - "author_inst": "The Donnelly Centre, University of Toronto, Toronto, Canada." - }, - { - "author_name": "Sachdev Sidhu", - "author_inst": "The Donnelly Centre, University of Toronto, Toronto, Canada." - }, - { - "author_name": "Herbert W Virgin", - "author_inst": "Vir Biotechnology, San Francisco, CA, USA." - }, - { - "author_name": "David Wang", - "author_inst": "Washington University School of Medicine" - }, - { - "author_name": "Siyuan Ding", - "author_inst": "Washington University in St. Louis School of Medicine" - }, - { - "author_name": "Davide Corti", - "author_inst": "Humabs Biomed SA, subsidiary of Vir Biotechnology" - }, - { - "author_name": "Elitza S Theel", - "author_inst": "Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA." - }, - { - "author_name": "Daved H Fremont", - "author_inst": "Departments of Molecular Microbiology, Pathology & Immunology, Biochemistry & Molecular Biophysics, and The Andrew M. and Jane M. Bursky Center for Human Immuno" - }, - { - "author_name": "Michael S Diamond", - "author_inst": "Departments of Medicine, Molecular Microbiology, Biochemistry & Molecular Biophysics, and The Andrew M. and Jane M. Bursky Center for Human Immunology & Immunot" - }, - { - "author_name": "Sean P. J. Whelan", - "author_inst": "Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA." - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.05.18.101691", "rel_title": "Repurposing of Miglustat to inhibit the coronavirus Severe Acquired Respiratory Syndrome SARS-CoV-2", @@ -1478413,6 +1476713,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.11.20092916", + "rel_title": "Prevalence of SARS-CoV-2 infection in the Luxembourgish population: the CON-VINCE study.", + "rel_date": "2020-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20092916", + "rel_abs": "BACKGROUNDThe World Health Organization declared the outbreak of coronavirus disease to be a public health emergency of international concern on January 30, 2020. The first SARS-CoV-2 infection was subsequently detected in Luxembourg on February 29, 2020. Representative population-based data, including asymptomatic individuals for assessing the viral spread and immune response was, however, lacking worldwide.\n\nMETHODSUsing a panel-based method, we recruited a representative sample of the Luxembourgish population based on age, gender and residency for testing for SARS-CoV-2 infection and antibody status in order to define prevalence irrespective of clinical symptoms. Participants were contacted via email to fill an online questionnaire before biosampling at local laboratories. Participants provided information related to clinical symptoms, epidemiology, socioeconomic and psychological assessments and underwent biosampling, rRT-PCR testing and serology for SARS-CoV-2.\n\nRESULTSA total of 1862 individuals were included for our representative sample of the general Luxembourgish population. We detected an ongoing SARS-CoV-2 infection based on rRT-PCR in 5 participants. h Four of the SARS-CoV-2 infected participants were oligosymptomatic and one was asymptomatic. Overall, 35 participants (1.97%) had developed a positive IgG response, of whom 11 self-reported to have previously received a positive rRT-PCR diagnosis of SARS-CoV-2 infection. Our data indicate a prevalence of 0.3% for active SARS-CoV-2 infection in the Luxembourgish population between 18 and 79 years of age.\n\nCONCLUSIONSLuxembourgish residents show a low rate of acute infections after 7 weeks of confinement and present with an antibody profile indicative of a more recent immune response to SARS-CoV-2. All infected individuals were oligo- or asymptomatic. Bi-weekly follow-up visits over the next 2 months will inform about the viral spread by oligo- and asymptomatic carriers and the individual changes in the immune profile.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Chantal J. Snoeck", + "author_inst": "Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, L-4354 Luxembourg" + }, + { + "author_name": "Michel Vaillant", + "author_inst": "Competence Center for Methodology and Statistics, Luxembourg Institute of Health. Strassen L-1445 Luxembourg" + }, + { + "author_name": "Tamir Abdelrahman", + "author_inst": "Department of Microbiology, Laboratoire national de sant\u00e9, Dudelange, L-3555, Luxembourg" + }, + { + "author_name": "Venkata P. Satagopam", + "author_inst": "Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-Belval, Luxembourg" + }, + { + "author_name": "Jonathan D. Turner", + "author_inst": "Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, L-4354 Luxembourg" + }, + { + "author_name": "Katy Beaumont", + "author_inst": "Integrated Biobank of Luxembourg (IBBL), Dudelange, L-3555 Luxembourg" + }, + { + "author_name": "Clarissa P. C. Gomes", + "author_inst": "Clinical and Experimental Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-Belval, Luxembourg" + }, + { + "author_name": "Joelle Veronique Fritz", + "author_inst": "Luxembourg Institute of Health" + }, + { + "author_name": "Valerie E. Schr\u00f6der", + "author_inst": "Department of Neurology, Centre Hospitalier de Luxembourg, Luxembourg, L-1210 Clinical and Experimental Neuroscience, Luxembourg Centre for Systems Biomedicine" + }, + { + "author_name": "Anne Kaysen", + "author_inst": "Clinical and Experimental Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-Belval, Luxembourg" + }, + { + "author_name": "Lukas Pavelka", + "author_inst": "Department of Neurology, Centre Hospitalier de Luxembourg, Luxembourg, L-1210 Clinical and Experimental Neuroscience, Luxembourg Centre for Systems Biomedicine " + }, + { + "author_name": "Lara Stute", + "author_inst": "Department of Neurology, Centre Hospitalier de Luxembourg, Luxembourg, L-1210 Clinical and Experimental Neuroscience, Luxembourg Centre for Systems Biomedicine " + }, + { + "author_name": "Guilherme Ramos Meyers", + "author_inst": "Clinical and Experimental Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-Belval, Luxembourg" + }, + { + "author_name": "Laure Pauly", + "author_inst": "Clinical and Experimental Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-Belval, Luxembourg" + }, + { + "author_name": "Maxime Hansen", + "author_inst": "Department of Neurology, Centre Hospitalier de Luxembourg, Luxembourg, L-1210 Transversal Translational Medicine, Luxembourg Institute of Health, Strassen, Luxe" + }, + { + "author_name": "Claire Pauly", + "author_inst": "Department of Neurology, Centre Hospitalier de Luxembourg, Luxembourg, L-1210 Clinical and Experimental Neuroscience, Luxembourg Centre for Systems Biomedicine " + }, + { + "author_name": "Gloria A. Aguayo", + "author_inst": "Population Health Department, Luxembourg Institute of Health. Strassen L-1445 Luxembourg" + }, + { + "author_name": "Magali Perquin", + "author_inst": "Population Health Department, Luxembourg Institute of Health. Strassen L-1445 Luxembourg" + }, + { + "author_name": "Anne-Marie Hanff", + "author_inst": "Transversal Translational Medicine, Luxembourg Institute of Health, Strassen, Luxembourg" + }, + { + "author_name": "Soumyabrata Ghosh", + "author_inst": "Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-Belval, Luxembourg" + }, + { + "author_name": "Manon Gantenbein", + "author_inst": "Clinical and Epidemiological Investigation Center (CIEC), Luxembourg Institute of Health. Strassen L-1445 Luxembourg" + }, + { + "author_name": "Laetitia Huiart", + "author_inst": "Population Health Department, Luxembourg Institute of Health. Strassen L-1445 Luxembourg" + }, + { + "author_name": "Markus Ollert", + "author_inst": "Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, L-4354 Luxembourg Department of Dermatology and Allergy Center, Odense R" + }, + { + "author_name": "Rejko Kr\u00fcger", + "author_inst": "Transversal Translational Medicine, Luxembourg Institute of Health, Strassen, Luxembourg Department of Neurology, Centre Hospitalier de Luxembourg, Luxembourg, " + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.15.20102798", "rel_title": "The effect of ambient temperature on worldwide COVID-19 cases and deaths - an epidemiological study", @@ -1478961,57 +1477372,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health systems and quality improvement" }, - { - "rel_doi": "10.1101/2020.05.11.20098053", - "rel_title": "Parasites and their protection against COVID-19- Ecology or Immunology?", - "rel_date": "2020-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20098053", - "rel_abs": "BackgroundDespite the high infectivity of SARS-CoV-2, the incidence of COVID-19 in Africa has been slower than predicted. We aimed to investigate a possible association between parasitic infections and COVID-19.\n\nMethodsAn ecological study in which we analysed WHO data on COVID-19 cases in comparison to WHO data on helminths and malaria cases using correlation, regression, and Geographical Information Services analyses.\n\nResultsOf the global 3.34 million COVID-19 cases and 238,628 deaths as at May 4th 2020, Africa reported 0.029/3.3 million (0.88%) cases and 1,064/238,628 (0.45%) deaths. In 2018, Africa reported 213/229 million (93%) of all malaria cases, 204/229 million (89%) of schistosomiasis cases, and 271/1068 million (25%) of soil-transmitted helminth cases globally. In contrast, Europe reported 1.5/3.3 million (45%) of global COVID-19 cases and 142,667/238,628 (59%) deaths. Europe had 5.8/1068 million (0.55%) soil-transmitted helminths cases and no malaria/schistosomiasis cases in 2018. We found an inverse correlation between the incidence of COVID-19 and malaria (r -0.17, p =0.002) and COVID-19 and soil-transmitted helminths (r -0.25, p <0.001). Malaria-endemic countries were less likely to have COVID-19 (OR 0.51, 95% CI 0.29-0.90; p =0.02). Similarly, countries endemic for soil-transmitted helminths were less likely to have COVID-19 (OR 0.24, 95% CI 0.13-0.44; p <0.001), as were countries endemic for schistosomiasis (OR 0.22, 95% CI 0.11-0.45; p<0.001).\n\nConclusionsOne plausible hypothesis for the comparatively low COVID-19 cases/deaths in parasite-endemic areas is immunomodulation induced by parasites. Studies to elucidate the relationship between parasitic infections and susceptibility to COVID-19 at an individual level are warranted.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Kenneth Ssebambulidde", - "author_inst": "Infectious Diseases Institute, College of Health Sciences, Makerere University" - }, - { - "author_name": "Ivan Segawa", - "author_inst": "Makerere Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda" - }, - { - "author_name": "Kelvin M Abuga", - "author_inst": "Kenya Medical Research Institute Centre for Geographic Medicine Research-Coast, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya" - }, - { - "author_name": "Vivian Nakate", - "author_inst": "Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda" - }, - { - "author_name": "Anthony Kayiira", - "author_inst": "St Francis Hospital Nsambya, Kampala, Uganda" - }, - { - "author_name": "Jayne Ellis", - "author_inst": "London School of Hygiene and Tropical Medicine, London, UK" - }, - { - "author_name": "Lillian Tugume", - "author_inst": "Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda" - }, - { - "author_name": "Agnes N Kiragga", - "author_inst": "Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda" - }, - { - "author_name": "David B Meya", - "author_inst": "Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.14.20102533", "rel_title": "Heg.IA: An intelligent system to support diagnosis of Covid-19 based on blood tests", @@ -1479851,6 +1478211,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.14.20102459", + "rel_title": "Early transmission of COVID-19 has an optimal temperature but late transmission decreases in warm climate", + "rel_date": "2020-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.14.20102459", + "rel_abs": "The COVID-19 novel virus, as an emerging highly pathogenic agent, has caused a pandemic. Revealing the influencing factors affecting transmission of COVID-19 is essential to take effective control measures. Several previous studies suggested that the spread of COVID-19 was likely associated with temperature and/or humidity. But, a recent extensive review indicated that conclusions on associations between climate and COVID-19 were elusive with high uncertainty due to caveats in most previous studies, such as limitations in time and space, data quality and confounding factors. In this study, by using a more extensive global dataset covering 578 time series from China, USA, Europe and the rest of the world, we show that climate show distinct impacts on early and late transmission of COVID-19 in the world after excluding the confounding factors. The early transmission ability of COVID-19 peakedaround 6.3{degrees}C without or with little human intervention, but the later transmission ability was reduced in high temperature conditions under human intervention, probably driven by increased control efficiency of COVID-19. The transmission ability was positively associated with the founding population size of early reported cases and population size of a location. Our study suggested that with the coming summer seasons, the transmission risk of COVID-19 would increase in the high-latitude or high-altitude regions but decrease in low-latitude or low-altitude regions; human intervention is essential in containing the spread of COVID-19 around the world.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "xinru wan", + "author_inst": "State Key Laboratory of Integrated Management on Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences" + }, + { + "author_name": "Chaoyuan Cheng", + "author_inst": "State Key Laboratory of Integrated Management on Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences" + }, + { + "author_name": "zhibin zhang", + "author_inst": "State Key Laboratory of Integrated Management on Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.13.20096826", "rel_title": "Transmission dynamics of the COVID-19 epidemic in India, and evaluating the impact of asymptomatic carriers and role of expanded testing in the lockdown exit strategy: a modelling approach", @@ -1480175,153 +1478562,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.05.11.20098459", - "rel_title": "Distinct systems serology features in children, elderly and COVID patients", - "rel_date": "2020-05-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20098459", - "rel_abs": "SARS-CoV-2, the pandemic coronavirus that causes COVID-19, has infected millions worldwide, causing unparalleled social and economic disruptions. COVID-19 results in higher pathogenicity and mortality in the elderly compared to children. Examining baseline SARS-CoV-2 cross-reactive coronavirus immunological responses, induced by circulating human coronaviruses, is critical to understand such divergent clinical outcomes. The cross-reactivity of coronavirus antibody responses of healthy children (n=89), adults (n=98), elderly (n=57), and COVID-19 patients (n=19) were analysed by systems serology. While moderate levels of cross-reactive SARS-CoV-2 IgG, IgM, and IgA were detected in healthy individuals, we identified serological signatures associated with SARS-CoV-2 antigen-specific Fc{gamma} receptor binding, which accurately distinguished COVID-19 patients from healthy individuals and suggested that SARS-CoV-2 induces qualitative changes to antibody Fc upon infection, enhancing Fc{gamma} receptor engagement. Vastly different serological signatures were observed between healthy children and elderly, with markedly higher cross-reactive SARS-CoV-2 IgA and IgG observed in elderly, whereas children displayed elevated SARS-CoV-2 IgM, including receptor binding domain-specific IgM with higher avidity. These results suggest that less-experienced humoral immunity associated with higher IgM, as observed in children, may have the potential to induce more potent antibodies upon SARS-CoV-2 infection. These key insights will inform COVID-19 vaccination strategies, improved serological diagnostics and therapeutics.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Kevin J. Selva", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Carolien E. van de Sandt", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Melissa M. Lemke", - "author_inst": "University of Michigan" - }, - { - "author_name": "Christina Y. Lee", - "author_inst": "University of Michigan" - }, - { - "author_name": "Suzanne K. Shoffner", - "author_inst": "University of Michigan" - }, - { - "author_name": "Brendon Y. Chua", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Thi H.O. Nguyen", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Louise C. Rowntree", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Luca Hensen", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Marios Koutsakos", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Chinn Yi Wong", - "author_inst": "University of Melbourne" - }, - { - "author_name": "David C. Jackson", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Katie L. Flanagan", - "author_inst": "Launceston General Hospital, Launceston" - }, - { - "author_name": "Jane Crowe", - "author_inst": "Deepdene Surgery" - }, - { - "author_name": "Allen C. Cheng", - "author_inst": "Monash University" - }, - { - "author_name": "Denise L. Doolan", - "author_inst": "James Cook University" - }, - { - "author_name": "Fatima Amanat", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Florian Krammer", - "author_inst": "Icahn School of Medicine at Mount Sinai" - }, - { - "author_name": "Keith Chappell", - "author_inst": "University of Queensland" - }, - { - "author_name": "Naphak Modhiran", - "author_inst": "University of Queensland" - }, - { - "author_name": "Daniel Watterson", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Paul Young", - "author_inst": "University of Queensland" - }, - { - "author_name": "Bruce Wines", - "author_inst": "University of Melbourne" - }, - { - "author_name": "P. Mark Hogarth", - "author_inst": "Burnet Institute" - }, - { - "author_name": "Robyn Esterbauer", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Hannah G. Kelly", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Hyon-Xhi Tan", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Jennifer A. Juno", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Adam K. Wheatley", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Stephen J. Kent", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Kelly B. Arnold", - "author_inst": "University of Michigan" - }, - { - "author_name": "Katherine Kedzierska", - "author_inst": "University of Melbourne" - }, - { - "author_name": "Amy W. Chung", - "author_inst": "University of Melbourne" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.14.20102061", "rel_title": "Bounding the Predictive Values of COVID-19 Antibody Tests", @@ -1481109,6 +1479349,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "ophthalmology" }, + { + "rel_doi": "10.1101/2020.05.11.20098442", + "rel_title": "SARS-CoV-2 seroprevalence trends in healthy blood donors during the COVID-19 Milan outbreak", + "rel_date": "2020-05-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20098442", + "rel_abs": "ObjectivesThe Milan metropolitan area in Northern Italy was among the most severely hit by the SARS-CoV-2 outbreak. The epidemiological trends of mild COVID-19 are however still unknown. The aim of this study was to examine the seroprevalence of SARS-CoV-2 infection in healthy asymptomatic adults, the risk factors, and laboratory correlates.\n\nDesignWe conducted a cross-sectional study during the outbreak. Presence of anti-SARS-CoV-2 IgM/IgG antibodies against the Nucleocapsid protein was assessed by a lateral flow immunoassay.\n\nSettingBlood center at a leading academic hospital serving as COVID-19 referral center.\n\nParticipantsWe considered a random sample of blood donors since the start of the outbreak (February 24th to April 8th 2020, n=789).\n\nMain outcome measuresThe main outcome was the prevalence of IgG/IgM anti-SARS-CoV-2 antibodies.\n\nResultsThe test had a 98.3% specificity and 100% sensitivity, and for IgG+ was validated in a subset by an independent ELISA against the Spike protein (N=34, P<0.001). At the start of the outbreak, the overall seroprevalence of SARS-CoV-2 was 4.6% (2.3 to 7.9; P<0.0001 vs. 120 historical controls). During the study period characterized by a gradual implementation of social distancing measures, there was a progressive increase in seroprevalence to 7.1% (4.4 to 10.8), due to a rise in IgG+ to 5% (2.8 to 8.2; P=0.004 for trend, adjusted weekly increase 2.7{+/-}1.3%), but not of IgM+ (P=NS). At multivariate logistic regression analysis, seroconversion to IgG+ was more frequent in younger (P=0.043), while recent infections (IgM+) in older individuals (P=0.002). IgM+ was independently associated with higher triglycerides, eosinophils, and lymphocytes (P<0.05).\n\nConclusionsSARS-CoV-2 infection was already circulating in Milan at the outbreak start. Social distancing may have been more effective in younger individuals, and by the end of April 4.4-10.8% of healthy adults had evidence of seroconversion. Asymptomatic infection may affect lipid profile and blood count.\n\nSUMMARY BOXO_ST_ABSWhat is already know on this topicC_ST_ABSO_LISARS-CoV-2 causes COVID-19, associated with a high mortality rate, but may be asymptomatic in a still undefined fraction of individuals.\nC_LIO_LICOVID-19 is associated with altered hematological, inflammatory and biochemical parameters, but the laboratory correlates of non-severe infection are unknown.\nC_LIO_LIA severe COVID-19 outbreak severely hit Milan at the end of February 2020, but the number of infected individuals and risk factors remain unclear.\nC_LI\n\nWhat this study addsO_LISARS-CoV-2 was already circulating in Milan at the COVID-19 outbreak start on February 2020, with only 1 in 20 infected individuals being symptomatic and diagnosed.\nC_LIO_LISocial distancing may have been more effective in reducing new infections in younger individuals, and by the end of April 4.4-10.8% of healthy asymptomatic adults had evidence of seroconversion.\nC_LIO_LIAsymptomatic infection may affect lipid profile and be associated with higher circulating lymphocytes and eosinophils.\nC_LI", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Luca Valenti", + "author_inst": "University of Milan" + }, + { + "author_name": "Annalisa Bergna", + "author_inst": "University of Milan" + }, + { + "author_name": "Serena Pelusi", + "author_inst": "University of Milan" + }, + { + "author_name": "Federica Facciotti", + "author_inst": "Istituto Europeo di Oncologia" + }, + { + "author_name": "Alessia Lai", + "author_inst": "University of Milan" + }, + { + "author_name": "Maciej Tarkowski", + "author_inst": "University of Milan" + }, + { + "author_name": "Alessandra Berzuini", + "author_inst": "Fondazione IRCCS Ca' Granda" + }, + { + "author_name": "Flavio Caprioli", + "author_inst": "University of Milan" + }, + { + "author_name": "Luigi Santoro", + "author_inst": "Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico" + }, + { + "author_name": "Guido Baselli", + "author_inst": "Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico" + }, + { + "author_name": "Carla Della Ventura", + "author_inst": "University of Milan" + }, + { + "author_name": "Elisa Erba", + "author_inst": "Fondazione IRCCS Ca' Granda" + }, + { + "author_name": "Silvano Bosari", + "author_inst": "Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico" + }, + { + "author_name": "Massimo Galli", + "author_inst": "University of Milan" + }, + { + "author_name": "Gianguglielmo Zehender", + "author_inst": "University of Milan" + }, + { + "author_name": "Daniele Prati", + "author_inst": "Fondazione IRCCS Ca' Granda Ospedale Policlinico Milano" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.12.20098921", "rel_title": "Behavioural change towards reduced intensity physical activity is disproportionately prevalent among adults with serious health issues or self-perception of high risk during the UK COVID-19 lockdown.", @@ -1481509,33 +1479828,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.05.12.20099085", - "rel_title": "Understanding the indoor pre-symptomatic transmission mechanism of COVID-19", - "rel_date": "2020-05-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20099085", - "rel_abs": "Discovering the mechanism that enables pre-symptomatic individuals to transmit the SARS-CoV-2 virus has a significant impact on the possibility of controlling COVID-19 pandemic. To this end, we have developed an evidence based quantitative mechanistic mathematical model. The model explicitly tracks the dynamics of contact and airborne transmission between individuals indoors, and was validated against the observed fundamental attributes of the epidemic, the secondary attack rate (SAR) and serial interval distribution. Using the model we identified the dominant driver of pre-symptomatic transmission, which was found to be contact route, while the contribution of the airborne route is negligible. We provide evidence that a combination of rather easy to implement measures of frequent hand washing, cleaning fomites and avoiding physical contact decreases the risk of infection by an order of magnitude, similarly to wearing masks and gloves.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Yehuda Arav", - "author_inst": "Israel Institute for Biological Research" - }, - { - "author_name": "Ziv Klausner", - "author_inst": "Israel Institute for Biological Research" - }, - { - "author_name": "Eyal Fattal", - "author_inst": "Israeli Institute for Biological Research" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.14.096107", "rel_title": "Molecular conservation and Differential mutation on ORF3a gene in Indian SARS-CoV2 genomes", @@ -1482459,6 +1480751,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.13.20099796", + "rel_title": "Adjusted fatality rates of COVID19 pandemic: a comparison across countries", + "rel_date": "2020-05-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.13.20099796", + "rel_abs": "BackgroundA key impact measure of COVID-19 pandemic is the case fatality rate (CFR), but estimating it during an epidemic is challenging as the true number of cases may remain elusive.\n\nObjectiveTo estimate the CFR applying a delay-adjusted method across countries, exploring differences to simple methods and potential correlation to country level variables.\n\nMethodsSecondary analysis of publicly available data from countries with [≥]500 cases by April 30th. We calculated CFR adjusting for delay time from diagnosis to death and using simple methods for comparison. We performed a random effects meta-analysis to pooling CFRs for all countries and for those with high testing coverage and low positivity rate. We explored correlation of adjusted CFR with age structure and health care resources at country level.\n\nResultsWe included 107 countries and the Diamond Princess cruise-ship. The overall delay adjusted CFR was 2.8% (95%CI: 2.1 to 3.1) while naive CFR was 5.1% (95%CI: 4.1 to 6.2). In countries with high testing coverage/low positivity rate the pooled adjusted CFR was 2.1% (95%CI: 1.5 to 3.0), there was a correlation with age over 65 years ({beta} = 0.12; 95%CI: 0.06 to 0.18), but not with number of physician or critical care beds. Naive method underestimated the CFR of the CFR with a median of 1.3% across countries.\n\nConclusionOur best estimation of CFR across countries is 2% and varies according to the aged population size. Modelers and policy makers may consider these results to assess the impact of lockdowns or other mitigation policies.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Carlos Canelo-Aybar", + "author_inst": "Cochrane Iberoamerican" + }, + { + "author_name": "Jessica Beltran", + "author_inst": "Cochrane Iberoamerica" + }, + { + "author_name": "Marilina Santero", + "author_inst": "Cochrane Iberoamerica" + }, + { + "author_name": "Pablo Alonso-Coello", + "author_inst": "Cochrane Iberoamerica" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.13.20099838", "rel_title": "COVID-19 Healthcare Demand Projections: Arizona", @@ -1482715,45 +1481038,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.13.20099614", - "rel_title": "Dynamic liver function indexes monitoring and clinical characteristics in three types of COVID-19 patients", - "rel_date": "2020-05-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.13.20099614", - "rel_abs": "Background & AimsThe abnormal liver function and even liver failure related death were reported in the COVID-19 patients, but less of studies focus on the dynamic liver function changes. We analysed the liver function indexes of COVID-19 patients to explore the characteristics of liver function changes in patients with different severity.\n\nMethodsThis study included 54 moderate, 50 severe, and 31 death nucleic acid-confirmed COVID-19 patients hospitalized at the central hospital of Wuhan, China. Epidemiological histories, clinical features, imaging materials, medications and especially major liver function laboratory tests were collected for analysis.\n\nResultsThe clinical symptoms did not present any significant difference in the patients at admission, but the older male patients had pronounced mortality risk. The normal ratio of ALT, TB, and DBIL of moderate patients was 96.3%, 94.44%, and 98.15% separately at the first test, but 59.26% of patients showed declined ALB levels. The normal ratio of all liver function indexes declined after admission, but most abnormalities were mild (1-2 times of upper limit unit) and went back normal before discharge. In severe patients, the normal ratio of ALB dropped down to 30.61% at admission along with the dramatic impaired normal ratio of bilirubin at the second test. The severe patients liver function dysfunction was worse than the moderate patients but without a significant difference. The dead patients showed a significantly higher level of DBIL, AST, GGT and CRP than other groups patients in the final test, along with the hypoalbuminemia. What is worse, 16.13% of non-survivors were diagnosed with liver failure. No medication was found to be related to ALT, AST, and GGT abnormality in our study.\n\nConclusionIn moderate and severe patients, liver dysfunction was mild. Patients widely presented lower level of ALB. The higher level of bilirubin, AST, and GGT was likely to indicate the worse outcome. Dynamic monitoring of liver function indexes could be considered and liver failure related death should be noticed and prevented in the early stage.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Cheng Chen", - "author_inst": "Institute of Liver Diseases, Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China" - }, - { - "author_name": "Jie Jiang", - "author_inst": "1.\tDepartment of Respiratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China" - }, - { - "author_name": "Xiaoxiao Xu", - "author_inst": "1.\tDepartment of Respiratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China" - }, - { - "author_name": "Yiyang Hu", - "author_inst": "1.\tInstitute of Liver Diseases, Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China" - }, - { - "author_name": "Yi Hu", - "author_inst": "1.\tDepartment of Respiratory, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Hubei, China" - }, - { - "author_name": "Yu Zhao", - "author_inst": "1.\tInstitute of Liver Diseases, Shuguang Hospital affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "gastroenterology" - }, { "rel_doi": "10.1101/2020.05.13.20100636", "rel_title": "The SARS-CoV-2 T-cell immunity is directed against the spike, membrane, and nucleocapsid protein and associated with COVID 19 severity", @@ -1483649,6 +1481933,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.05.12.20099358", + "rel_title": "SARS-CoV-2 Detection in Istanbul Wastewater Treatment Plant Sludges", + "rel_date": "2020-05-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20099358", + "rel_abs": "Following the announcement of SARS-CoV-2 worldwide pandemic spread by WHO on March 11, 2020, wastewater based epidemiology received great attention in several countries: The Netherlands [Medama et al., 2020; K-Lodder et al., 2020], USA [Wu et al., 2020; Memudryi et al., 2020], Australia [Ahmed et al., 2020], France [Wurtzer et al., 2020], China [Wang et al., 2020], Spain [Randazzo et al., 2020; Walter et al., 2020], Italy (La Rosa et al., 2020; Rimoldi et al., 2020) and Israel [Or et al., 2020], performed analysis in wastewaters by using different virus concentration techniques. Turkey took its place among these countries on 7th of May, 2020 by reporting SARS-CoV-2 RT-qPCR levels at the inlet of seven (7) major municipal wastewater treatment plants (WWTPs) of Istanbul [Alpaslan Kocamemi et al., 2020], which is a metropole with 15.5 million inhabitants and a very high population density (2987 persons/km2) and having about 65 % of Covid-19 cases in Turkey. Sludges that are produced in WWTPs should be expected to contain SARS-CoV-2 virus as well. There has not yet been any study for the fate of SAR-CoV-2 in sludges generated from WWTPs. Knowledge about the existing of SARS-CoV-2 in sludge may be useful for handling the sludge during its dewatering, stabilizing and disposal processes. This information will also be valuable in case of sludges that are used as soil conditioners in agriculture or sent to landfill disposal.\n\nIn wastewater treatment plants, generally two different types of sludges are generated; primary sludge (PS) and waste activated sludge (WAS). PS forms during the settling of wastewater by gravity in the primary settling tanks. Little decomposition occurs during primary sludge formation. Since most of the inorganic part of the wastewater is removed in the earlier grit removal process, the PS consists of mainly organic material that settles. The PS is about 1-2 % solids by weight. In the biological treatment part of the WWTPs, the biomass that forms in the anaerobic, anoxic and oxic zones of the process is settled in final clarifiers by gravity and returned to the beginning of the biological process so that it is not washed off. The waste activated sludge (WAS) is the excess part of the biomass that grows in this secondary treatment process. It has to be removed from the process not to increase the mixed liquor suspended solids concentration (bacteria concentration) in the secondary process more than a fixed value. The WAS is about 0.6 - 0.9 % solids by weight.\n\nThis work aims to find whether SARS-CoV-19 is present in the PS and WAS before it is dewatered and sent to anaerobic or aerobic digester processes or to thermal drying operations.\n\nFor this purpose, on the 7th of May 2020, two (2) PS samples were collected from Ambarli and Tuzla WWTPs, seven (7) WAS samples were collected from Terkos, Ambarli, Atakoy I & II, Pasakoy II, Buyukcekmece and Tuzla I WWTPs. Polyethylene glycol 8000 (PEG 8000) adsorption [Wu et al., 2020] SARS-Cov-2 concentration method was used for SARS-CoV-2 concentration after optimization. [Alpaslan Kocamemi et al., 2020]. Real time RT-PCR diagnostic panel validated by US was used to quantify SARS-CoV-2 RNA in primary and waste activated sludge samples taken from WWTPs in Istanbul. All samples were tested positive. Titers of SARS-CoV-2 have been detected ranging copies between 1.17x104 to 4.02x104 per liter.\n\nO_LSTValue of the DataC_LSTO_LIThe dataset provides information about SARS-CoV-19 in primary and waste activated sludges generated in WWTPs.\nC_LIO_LIAs being the first study in the world, the dataset presented is expected to be beneficial in handling the sludge during its dewatering, stabilizing and disposal processes\nC_LI\n\nData DescriptionSARS-CoV-2 copy numbers per liter measured for sludge samples from WWTPs were summarized in Table 1 and shown in Figure 1 together with SARS-CoV-2 copy numbers observed in an earlier study [Alpaslan Kocamemi et al., 2020] in the influent of the WWTPs from which the sludge samples were taken.\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@1647aa7org.highwire.dtl.DTLVardef@1b09df2org.highwire.dtl.DTLVardef@518f39org.highwire.dtl.DTLVardef@92061forg.highwire.dtl.DTLVardef@cfe4b2_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1.C_FLOATNO O_TABLECAPTIONSARS-CoV-2 RT-qPCR results of sludges taken from Istanbul WWTPs\n\nC_TABLECAPTION C_TBL O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=129 SRC=\"FIGDIR/small/20099358v1_fig1.gif\" ALT=\"Figure 1\">\nView larger version (18K):\norg.highwire.dtl.DTLVardef@af6ccaorg.highwire.dtl.DTLVardef@10f7150org.highwire.dtl.DTLVardef@d83bbborg.highwire.dtl.DTLVardef@3980c8_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1.C_FLOATNO SAR-CoV-2 Levels in primary and waste activated sludges of Istanbul WWTPs.\n\nC_FIG To the best of our knowledge, no study has yet been reported the presence of SARS-CoV-2 in primary sludge (PS) and waste activated sludge (WAS) samples. Herein we report the results of SARS-CoV-2 presence in two (2) PS and seven (7) WAS samples from WWTPs in Istanbul. A total of nine (9) sludge samples were collected on the 7th May of 2020 and investigated for presence of SARS-CoV-2 with RT-qPCR methodology. SARS-CoV-2 genome was detected quantitatively from all samples. Sludge samples presented CT ranging from 33.5 to 35.8. Titers of SARS-CoV-2 have been detected ranging from 1.17x104 to 4.02x104 per liter.\n\nThe detected numbers of SARS-CoV-2 in PS samples were found similar to those observed for WAS samples. SARS-CoV-2 copy numbers detected in PS and WAS on 7th of May, 2020 are greater than the copy numbers observed in the influent of these WWTPs on 21st April, 2020 [Alpaslan Kocamemi, 2020]. By considering the fact that the number of cases reported for Istanbul on the 7th of May, 2020 is less than the cases reported for the 21st April, 2020, it may be concluded that SARS-CoV-2 concentrations are more in both primary and waste activated sludge.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Bilge Alpaslan Kocamemi", + "author_inst": "Marmara University" + }, + { + "author_name": "Halil Kurt", + "author_inst": "Saglik Bilimleri University" + }, + { + "author_name": "Ahmet Sait", + "author_inst": "Ministry of Agriculture and Forestry, Republic of Turkey" + }, + { + "author_name": "Fahriye Sarac", + "author_inst": "Ministry of Agriculture and Forestry, Republic of Turkey" + }, + { + "author_name": "Ahmet Mete Saatci", + "author_inst": "Turkish Water Institute" + }, + { + "author_name": "Bekir Pakdemirli", + "author_inst": "Ministry of Agriculture and Forestry" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.12.20099739", "rel_title": "Progression, recovery and fatality in patients with SARS-CoV-2 related pneumonia in Wuhan, China: a single-centered, retrospective, observational study", @@ -1484137,81 +1482460,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.13.20101006", - "rel_title": "Loss of Taste and Smell as Distinguishing Symptoms of COVID-19", - "rel_date": "2020-05-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.13.20101006", - "rel_abs": "Olfactory and taste dysfunctions have emerged as symptoms of COVID-19. Among individuals with COVID-19 enrolled in a household study, loss of taste and/or smell was the fourth most commonly reported symptom (26/42; 62%), and among household contacts, it had the highest positive predictive value (83%; 95% CI: 55-95%) for COVID-19. These findings support consideration of loss of taste and/or smell in possible case identification and testing prioritization for COVID-19.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Patrick Dawson", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Elizabeth M. Rabold", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Rebecca L. Laws", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Erin E. Conners", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Radhika Gharpure", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Sherry Yin", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Sean Buono", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Trivikram Dasu", - "author_inst": "City of Milwaukee Health Department Laboratory" - }, - { - "author_name": "Sanjib Bhattacharyya", - "author_inst": "City of Milwaukee Health Department Laboratory" - }, - { - "author_name": "Ryan P. Westergaard", - "author_inst": "Wisconsin Department of Health Services" - }, - { - "author_name": "Ian W. Pray", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Dongni Ye", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Scott A. Nabity", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Jacqueline E. Tate", - "author_inst": "Centers for Disease Control and Prevention" - }, - { - "author_name": "Hannah L. Kirking", - "author_inst": "Centers for Disease Control and Prevention" - } - ], - "version": "1", - "license": "cc0", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.13.20100925", "rel_title": "Differential Redistribution of Activated Monocyte and Dendritic Cell Subsets to the Lung Associates with Severity of COVID-19", @@ -1485343,6 +1483591,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.09.20096677", + "rel_title": "Depression and anxiety during 2019 coronavirus disease pandemic in Saudi Arabia: a cross-sectional study", + "rel_date": "2020-05-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.09.20096677", + "rel_abs": "AimsThe emergence of the COVID-19 global pandemic, with a high transmission and mortality rate, has created an extraordinary crisis worldwide. Such an unusual situation may have an undesirable impact on the mental health of individuals which, in turn, may influence their outcomes. This study aimed to explore the influence of the COVID-19 pandemic on the psychological disposition of residents of the Kingdom of Saudi Arabia.\n\nMethodsA cross-sectional study using an online survey was conducted in Saudi Arabia between 27 March and 27 April 2020. The Patient Health Questionnaire (PHQ-9) and Generalised Anxiety Disorder-7 (GAD-7) were used to assess depression and anxiety. Logistic regression analysis was used to identify predictors of these.\n\nResultsA total of 2,081 individuals participated in the study. The prevalence of depression and anxiety among the study participants was 9.4% and 7.3%, respectively. Non-Saudi residents, individuals aged 50 years and above, divorced people, retired people, university students, and those with an income between 2,000 and 10,000 SR were at higher risk of developing depression. Saudi individuals, married people, the unemployed, and those with a high income (> 10,000 RS) were at higher risk of developing anxiety.\n\nConclusionWe found that there is a wide range of Saudi residents who are at higher risk of developing mental illness during the current COVID-19 pandemic. Policymakers and mental healthcare providers are advised to provide continuous monitoring of the psychological consequences during this pandemic and provide the required health support.\n\nWhat is already known about this subject?- The emergence of the COVID-19 global pandemic, with a high transmission and mortality rate, has created an extraordinary crisis worldwide.\n- The COVID-19 pandemic might have an undesirable impact on the mental health of individuals.\n\n\nWhat does this article add?- Depression and anxiety are common among the Saudi population.\n- A considerable proportion of the Saudi population is concerned about contracting COVID-19 or transmitting it to family members.\n- Unemployed individuals and university students are at higher risk of depression and anxiety.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Hamad S Alyami", + "author_inst": "Department of Pharmaceutics, College of Pharmacy, Najran University, Najran, Saudi Arabia." + }, + { + "author_name": "Abdallah Y Naser", + "author_inst": "Faculty of Pharmacy, Isra University, Amman, Jordan." + }, + { + "author_name": "Eman Zmaily Dahmash", + "author_inst": "Faculty of Pharmacy, Isra University, Amman, Jordan." + }, + { + "author_name": "Mohammed H Alyami", + "author_inst": "Department of Pharmaceutics, College of Pharmacy, Najran University, Najran, Saudi Arabia." + }, + { + "author_name": "Musfer S Alyami", + "author_inst": "King Khalid University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.05.10.20093161", "rel_title": "Psychological Distress during the COVID-19 pandemic in France: a national assessment of at-risk populations", @@ -1485899,45 +1484182,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.10.20097543", - "rel_title": "Estimating the extent of true asymptomatic COVID-19 and its potential for community transmission: systematic review and meta-analysis", - "rel_date": "2020-05-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.10.20097543", - "rel_abs": "BackgroundThe prevalence of true asymptomatic COVID-19 cases is critical to policy makers considering the effectiveness of mitigation measures against the SARS-CoV-2 pandemic. We aimed to synthesize all available research on the asymptomatic rates and transmission rates where possible.\n\nMethodsWe searched PubMed, Embase, Cochrane COVID-19 trials, and Europe PMC (which covers pre-print platforms such as MedRxiv). We included primary studies reporting on asymptomatic prevalence where: (a) the sample frame includes at-risk population, and (b) there was sufficiently long follow up to identify pre-symptomatic cases. Meta-analysis used fixed effect and random effects models. We assessed risk of bias by combination of questions adapted from risk of bias tools for prevalence and diagnostic accuracy studies.\n\nResultsWe screened 998 articles and included nine low risk-of-bias studies from six countries that tested 21,035 at-risk people, of which 559 were positive and 83 were asymptomatic. Diagnosis in all studies was confirmed using a RT-qPCR test. The proportion of asymptomatic cases ranged from 4% to 41%. Meta-analysis (fixed effect) found that the proportion of asymptomatic cases was 15% (95% CI: 12% - 18%) overall; higher in non-aged care 16% (13% - 19%), and lower in long-term aged care 8% (3% - 18%). Four studies provided direct evidence of forward transmission of the infection by asymptomatic cases but suggested considerably lower rates than symptomatic cases.\n\nDiscussionOur estimates of the prevalence of asymptomatic COVID-19 cases and asymptomatic transmission rates are lower than many highly publicized studies, but still sufficient to warrant policy attention. Further robust epidemiological evidence is urgently needed, including in sub-populations such as children, to better understand the importance of asymptomatic cases for driving spread of the pandemic.\n\nFundingOB is supported by NHMRC Grant APP1106452. PG is supported by NHMRC Australian Fellowship grant 1080042. KB was supported by NHMRC Fellowship grant 1174523. All authors had full access to all data and agreed to final manuscript to be submitted for publication. There was no funding source for this study.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Oyungerel Byambasuren", - "author_inst": "Bond University" - }, - { - "author_name": "Magnolia Cardona", - "author_inst": "Bond University" - }, - { - "author_name": "Katy Bell", - "author_inst": "University of Sydney" - }, - { - "author_name": "Justin Clark", - "author_inst": "Bond University" - }, - { - "author_name": "Mary-Louise McLaws", - "author_inst": "UNSW Sydney" - }, - { - "author_name": "Paul Glasziou", - "author_inst": "Bond University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.09.20096859", "rel_title": "Sensitivity of UK Covid-19 deaths to the timing of suppression measures and their relaxation", @@ -1486992,6 +1485236,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "geriatric medicine" }, + { + "rel_doi": "10.1101/2020.05.11.20097725", + "rel_title": "A Systems Approach to Assess Transport and Diffusion of Hazardous Airborne Particles in a Large Surgical Suite: Potential Impacts on Viral Airborne Transmission", + "rel_date": "2020-05-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.11.20097725", + "rel_abs": "Airborne transmission of viruses, such as the coronavirus 2 (SARS-CoV-2), in hospital systems are under debate: it has been shown that transmission of SARS-CoV-2 virus goes beyond droplet dynamics that is limited to 3-6 feet, but it is unclear if the airborne viral load is significant enough to ensure transmission of the disease. Surgical smoke can act as a carrier for tissue particles, viruses, and bacteria. To quantify airborne transmission from a physical point of view, we consider surgical smoke produced by thermal destruction of tissue during the use of electrosurgical instruments as a marker of airborne particle diffusion-transportation. Surgical smoke plumes are also known to be dangerous for human health, especially to surgical staff who receive long-term exposure over the years. There are limited quantified metrics reported on long-term effects of surgical smoke on staffs health. The purpose of this paper is to provide a mathematical framework and experimental protocol to assess the transport and diffusion of hazardous airborne particles in every large operating room suite. Measurements from a network of air quality sensors gathered during a clinical study provide validation for the main part of the model. Overall, the model estimates staff exposure to airborne contamination from surgical smoke and biological material. To address the clinical implication over a long period of time, the systems approach is built upon previous work on multi-scale modeling of surgical flow in a large operating room suite and takes into account human behavior factors.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Marc Garbey", + "author_inst": "The Houston Methodist Research Institute" + }, + { + "author_name": "Guillaume Joerger", + "author_inst": "ORintelligence, GEPROVAS" + }, + { + "author_name": "Shannon Furr", + "author_inst": "ORintelligence" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2020.05.11.20097790", "rel_title": "COVID-19: a retrospective cohort study with focus on the over-80s and hospital-onset disease", @@ -1487508,37 +1485779,6 @@ "type": "new results", "category": "pathology" }, - { - "rel_doi": "10.1101/2020.05.15.097501", - "rel_title": "Traffic-derived particulate matter and angiotensin-converting enzyme 2 expression in human airway epithelial cells", - "rel_date": "2020-05-15", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.15.097501", - "rel_abs": "Background The mechanism for the association between traffic-derived particulate matter less than 10 microns (PM10) and cases of COVID-19 disease reported in epidemiological studies is unknown. To infect cells, the spike protein of SARS-CoV-2 interacts with angiotensin-converting enzyme 2 (ACE2) on host airway cells. Increased ACE2 expression in lower airway cells in active smokers, suggests a potential mechanism whereby PM10 increases vulnerability to COVID-19 disease.Objective To assess the effect of traffic-derived PM10 on human airway epithelial cell ACE2 expression in vitro.Methods PM10 was collected from Marylebone Road (London) using a kerbside impactor. A549 and human primary nasal epithelial cells were cultured with PM10 for 2 h, and ACE2 expression (median fluorescent intensity; MFI) assessed by flow cytometry. We included cigarette smoke extract as a putative positive control. Data were analysed by either Mann-Whitney test, or Kruskal-Wallis with Dunn\u2019s multiple comparisons test.Results PM10 at 10 \u03bcg/mL, and 20 \u03bcg/mL increased ACE2 expression in A549 cells (P<0.05, 0.01 vs. medium control, respectively). Experiments using a single PM10 concentration (10 \u03bcg/mL), found increased ACE2 expression in both A549 cells (control vs. PM10, median (IQR) MFI; 470 (0.1 to 1114) vs 6217 (5071 to 8506), P<0.01), and in human primary epithelial cells (0 (0 to 591) vs. 4000 (2610 to 7853), P<0.05). Culture of A549 cells with 5% cigarette smoke extract increased ACE2 expression (n=4, 0 (0 to 28) vs. 9088 (7557 to 15831, P<0.05).Conclusion Traffic-related PM10 increases the expression of the receptor for SARS-CoV-2 in human respiratory epithelial cells.Competing Interest StatementThe authors have declared no competing interest.View Full Text", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Lisa Miyashita", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Gary Foley", - "author_inst": "Queen Mary University of London" - }, - { - "author_name": "Sean Semple", - "author_inst": "University of Sterling, UK" - }, - { - "author_name": "Jonathan Grigg", - "author_inst": "Queen Mary University of London" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2020.05.15.095794", "rel_title": "Phylogenetic Analysis of SARS-CoV-2 Genomes in Turkey", @@ -1489038,6 +1487278,45 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.05.14.095661", + "rel_title": "Growth factor receptor signaling inhibition prevents SARS-CoV-2 replication", + "rel_date": "2020-05-14", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.14.095661", + "rel_abs": "SARS-CoV-2 infections are rapidly spreading around the globe. The rapid development of therapies is of major importance. However, our lack of understanding of the molecular processes and host cell signaling events underlying SARS-CoV-2 infection hinder therapy development. We employed a SARS-CoV-2 infection system in permissible human cells to study signaling changes by phospho-proteomics. We identified viral protein phosphorylation and defined phosphorylation-driven host cell signaling changes upon infection. Growth factor receptor (GFR) signaling and downstream pathways were activated. Drug-protein network analyses revealed GFR signaling as key pathway targetable by approved drugs. Inhibition of GFR downstream signaling by five compounds prevented SARS-CoV-2 replication in cells, assessed by cytopathic effect, viral dsRNA production, and viral RNA release into the supernatant. This study describes host cell signaling events upon SARS-CoV-2 infection and reveals GFR signaling as central pathway essential for SARS-CoV-2 replication. It provides with novel strategies for COVID-19 treatment.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Kevin Klann", + "author_inst": "Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany" + }, + { + "author_name": "Denisa Bojkova", + "author_inst": "Institute of Medical Virology, University Hospital Frankfurt, Frankfurt am Main, Germany" + }, + { + "author_name": "Georg Tascher", + "author_inst": "Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany" + }, + { + "author_name": "Sandra Ciesek", + "author_inst": "Institute of Medical Virology, University Hospital Frankfurt, Frankfurt am Main, Germany; German Centre for Infection Research (DZIF), External partner site Fra" + }, + { + "author_name": "Christian Muench", + "author_inst": "Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany; Frankfurt Cancer Institute, Frankfurt am Main, Germany; Cardio" + }, + { + "author_name": "Jindrich Cinatl", + "author_inst": "Institute of Medical Virology, University Hospital Frankfurt, Frankfurt am Main, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "systems biology" + }, { "rel_doi": "10.1101/2020.05.13.094839", "rel_title": "Patient DNA cross-reactivity of CDC SARS-nCoV2 extraction control leads to potential false negative results", @@ -1489490,45 +1487769,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.05.14.092767", - "rel_title": "ACE2-Variants Indicate Potential SARS-CoV-2-Susceptibility in Animals: An Extensive Molecular Dynamics Study", - "rel_date": "2020-05-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.14.092767", - "rel_abs": "Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) emerged in late 2019 and since evolved into a global threat with nearly 4.4 million infected people and over 290,000 confirmed deaths worldwide.1 SARS-CoV-2 is an enveloped virus presenting spike (S) glycoproteins on its outer surface. Binding of S to host cell angiotensin converting enzyme 2 (ACE2) is thought to be critical for cellular entry. The host range of the virus extends far beyond humans and non-human primates. Natural and experimental infections have confirmed high susceptibility of cats, ferrets, and hamsters, whereas dogs, mice, rats, pigs, and chickens seem refractory to SARS-CoV-2 infection. To investigate the reason for the variable susceptibility observed in different species, we have developed molecular descriptors to efficiently analyze our dynamic simulation models of complexes between SARS-CoV-2 S and ACE2. Based on our analyses we predict that: (i) the red squirrel is likely susceptible to SARS-CoV-2 infection and (ii) specific mutations in ACE2 of dogs, rats, and mice render them susceptible to SARS-CoV-2 infection.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Szymon Pach", - "author_inst": "Institute of Pharmacy, Molecular Drug Design, Freie Universitaet Berlin, Germany" - }, - { - "author_name": "Trung Ngoc Nguyen", - "author_inst": "Institute of Pharmacy, Molecular Drug Design, Freie Universitaet Berlin, Germany" - }, - { - "author_name": "Jakob Trimpert", - "author_inst": "Institut fuer Virologie, Freie Universitaet Berlin, Germany" - }, - { - "author_name": "Dusan Kunec", - "author_inst": "Institut fuer Virologie, Freie Universitaet Berlin, Germany" - }, - { - "author_name": "Nikolaus Osterrieder", - "author_inst": "Institut fuer Virologie, Freie Universitaet Berlin, Germany" - }, - { - "author_name": "Gerhard Wolber", - "author_inst": "Institute of Pharmacy, Molecular Drug Design, Freie Universitaet Berlin, Germany" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2020.05.11.20098061", "rel_title": "Health literacy of inland population in the mitigation phase 3.2. of COVID-19's pandemic in Portugal - a descriptive cohort study", @@ -1490512,6 +1488752,157 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.12.20099879", + "rel_title": "Early Safety Indicators of COVID-19 ConvalescentPlasma in 5,000 Patients", + "rel_date": "2020-05-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.12.20099879", + "rel_abs": "BackgroundConvalescent plasma is the only antibody based therapy currently available for COVID-19 patients. It has robust historical precedence and sound biological plausibility. Although promising, convalescent plasma has not yet been shown to be safe as a treatment for COVID-19.\n\nMethodsThus, we analyzed key safety metrics after transfusion of ABO-compatible human COVID-19 convalescent plasma in 5,000 hospitalized adults with severe or life-threatening COVID-19, with 66% in the intensive care unit, as part of the US FDA Expanded Access Program for COVID-19 convalescent plasma.\n\nResultsThe incidence of all serious adverse events (SAEs) in the first four hours after transfusion was <1%, including mortality rate (0.3%). Of the 36 reported SAEs, there were 25 reported incidences of related SAEs, including mortality (n=4), transfusion-associated circulatory overload (TACO; n=7), transfusion-related acute lung injury (TRALI; n=11), and severe allergic transfusion reactions (n=3). However, only 2 (of 36) SAEs were judged as definitely related to the convalescent plasma transfusion by the treating physician. The seven-day mortality rate was 14.9%.\n\nConclusionGiven the deadly nature of COVID-19 and the large population of critically-ill patients included in these analyses, the mortality rate does not appear excessive. These early indicators suggest that transfusion of convalescent plasma is safe in hospitalized patients with COVID-19.\n\nBrief SummaryAfter transfusion of COVID-19 convalescent plasma in 5,000 patients, the incidence of serious adverse events was <1% and the seven-day incidence of mortality was 14.9%.", + "rel_num_authors": 34, + "rel_authors": [ + { + "author_name": "Michael Joyner", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "R. Scott Wright", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "DeLisa Fairweather", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Jonathon Senefeld", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Katelyn Bruno", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Stephen Klassen", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Rickey Carter", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Allan Klompas", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Chad Wiggins", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "John RA Shepherd", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Robert Rea", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Emily Whelan", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Andrew Clayburn", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Matthew Spiegel", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Patrick Johnson", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Elizabeth Lesser", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Sarah Baker", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Kathryn Larson", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Juan Ripoll Sanz", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Kylie Andersen", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "David Hodge", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Katie Kunze", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Matthew Buras", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Matthew Vogt", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Vitaly Herasevich", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Joshua Dennis", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Riley Regimbal", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Philippe Bauer", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Janis Blair", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Camille van Buskirk", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Jeffrey Winters", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "James Stubbs", + "author_inst": "Mayo Clinic" + }, + { + "author_name": "Nigel Paneth", + "author_inst": "Michigan State University" + }, + { + "author_name": "Arturo Casadevall", + "author_inst": "Johns Hopkins University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.10.20097147", "rel_title": "Hidden periods, duration and final size of COVID-19 pandemic", @@ -1490736,29 +1489127,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.12.091314", - "rel_title": "Meta-analysis of transcriptomes of SARS-Cov2 infected human lung epithelial cells identifies transmembrane serine proteases co-expressed with ACE2 and biological processes related to viral entry, immunity, inflammation and cellular stress.", - "rel_date": "2020-05-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.12.091314", - "rel_abs": "The COVID-19 pandemic resulting from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which emerged in December 2019 in the Chinese city of Wuhan in the province Hubei has placed immense burden on national economies and global health. At present neither vaccination nor therapies are available although several antiviral agents such as remdesivir, originally an Ebola drug, nelfinavir, an HIV-1 protease inhibitor and other drugs such as lopinavir have been evaluated. Here, we performed a meta-analysis of RNA-sequencing data from three studies employing human lung epithelial cells. Of these one focused on lung epithelial cells infected with SARS-CoV-2. We aimed at identifying genes co-expressed with angiotensin I converting enzyme 2 (ACE2) the human cell entry receptor of SARS-CoV-2, and unveiled several genes correlated or inversely correlated with high significance, among the most significant of these was the transmembrane serine protease 4 (TMPRSS4). Serine proteases are known to be involved in the infection process by priming the virus spike protein. Pathway analysis revealed papilloma virus infection amongst the most significantly correlated pathways. Gene Ontologies revealed regulation of viral life cycle, immune responses, pro-inflammatory responses-several interleukins such as IL6, IL1, IL20 and IL33, IFI16 regulating the interferon response to a virus, chemo-attraction of macrophages, last and not least cellular stress resulting from activated Reactive Oxygen Species. We believe that this dataset will aid in a better understanding of the molecular mechanism(s) underlying COVID-19.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Wasco Wruck", - "author_inst": "Heinrich-Heine-University" - }, - { - "author_name": "James Adjaye", - "author_inst": "Heinrich Heine University Duesseldorf" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.05.11.089409", "rel_title": "An integrated in silico immuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets", @@ -1491922,6 +1490290,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.08.20095893", + "rel_title": "Association of Vitamin D Deficiency and Treatment with COVID-19 Incidence", + "rel_date": "2020-05-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20095893", + "rel_abs": "ImportanceVitamin D treatment has been found to decrease incidence of viral respiratory tract infection, especially in vitamin D deficiency. It is unknown whether COVID-19 incidence is associated with vitamin D deficiency and treatment.\n\nObjectiveTo examine whether vitamin D deficiency and treatment are associated with testing positive for COVID-19.\n\nDesignRetrospective cohort study\n\nSettingUniversity of Chicago Medicine\n\nParticipantsPatients tested for COVID-19 from 3/3/2020-4/10/2020. Vitamin D deficiency was defined by the most recent 25-hydroxycholecalciferol <20ng/ml or 1,25-dihydroxycholecalciferol <18pg/ml within 1 year before COVID-19 testing. Treatment was defined by the most recent vitamin D type and dose, and treatment changes between the time of the most recent vitamin D level and time of COVID-19 testing. Vitamin D deficiency and treatment changes were combined to categorize vitamin D status at the time of COVID-19 testing as likely deficient (last-level-deficient/treatment-not-increased), likely sufficient(last-level-not-deficient/treatment-not-decreased), or uncertain deficiency(last-level-deficient/treatment-increased or last-level-not-deficient/treatment-decreased).\n\nMain Outcomes and MeasuresThe main outcome was testing positive for COVID-19. Multivariable analysis tested whether the most recent vitamin D level and treatment changes after that level were associated with testing positive for COVID-19 controlling for demographic and comorbidity indicators. Bivariate analyses of associations of treatment with vitamin D deficiency and COVID-19 were performed.\n\nResultsAmong 4,314 patients tested for COVID-19, 499 had a vitamin D level in the year before testing. Vitamin D status at the time of COVID-19 testing was categorized as likely deficient for 127(25%) patients, likely sufficient for 291(58%) patients, and uncertain for 81(16%) patients. In multivariate analysis, testing positive for COVID-19 was associated with increasing age(RR(age<50)=1.05,p<0.021;RR(age[≥]50)=1.02,p<0.064)), non-white race(RR=2.54,p<0.01) and being likely vitamin D deficient (deficient/treatment-not-increased:RR=1.77,p<0.02) as compared to likely vitamin D sufficient(not-deficient/treatment-not-decreased), with predicted COVID-19 rates in the vitamin D deficient group of 21.6%(95%CI[14.0%-29.2%]) versus 12.2%(95%CI[8.9%-15.4%]) in the vitamin D sufficient group. Vitamin D deficiency declined with increasing vitamin D dose, especially of vitamin D3. Vitamin D dose was not significantly associated with testing positive for COVID-19.\n\nConclusions and RelevanceVitamin D deficiency that is not sufficiently treated is associated with COVID-19 risk. Testing and treatment for vitamin D deficiency to address COVID-19 warrant aggressive pursuit and study.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "David O Meltzer", + "author_inst": "The University of Chicago" + }, + { + "author_name": "Thomas J Best", + "author_inst": "The University of Chicago" + }, + { + "author_name": "Hui Zhang", + "author_inst": "The University of Chicago" + }, + { + "author_name": "Tamara Vokes", + "author_inst": "The University of Chicago" + }, + { + "author_name": "Vineet Arora", + "author_inst": "The University of Chicago" + }, + { + "author_name": "Julian Solway", + "author_inst": "The University of Chicago" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.11.20092114", "rel_title": "Systemic hypoferraemia and severity of hypoxaemic respiratory failure in COVID-19", @@ -1492158,45 +1490565,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.09.20096099", - "rel_title": "Healthcare workers preparedness for COVID-19 pandemic in the occupied Palestinian territory: a cross-sectional survey", - "rel_date": "2020-05-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.09.20096099", - "rel_abs": "BackgroundThe coronavirus disease 19 (COVID-19) pandemic threatens to overwhelm the capacity of the vulnerable healthcare system in the occupied Palestinian territory (oPt). Sufficient training of healthcare workers (HCWs) in how to manage COVID-19 and the provision of personal protective equipment (PPE) to enable them to do so will be key tools in allowing oPt to mount a credible response to the crisis.\n\nMethodsA cross-sectional study was conducted using a validated online questionnaire. Data collection occurred between March 30, 2020 and April 12, 2020. The primary outcomes were availability of PPE and HCWs preparedness in oPt for COVID-19 pandemic. The secondary outcome was the regional and hospital differences in oPt in terms of availability of PPE and HCWs preparedness.\n\nResultsOf 138 respondents, only 38 HCWs (27.5%) always had access to facemasks when needed and 15 (10.9%) for isolation gowns. The vast majority of HCWs did not find eye protection (n=128, 92.8%), N95 respirators (n=132, 95.7%), and face shields (n=127, 92%) always available. Compared to HCWs in West Bank, those in the Gaza Strip were significantly less likely to have access to alcohol sanitizers (p=0.026) and gloves (p <0.001). On average, governmental hospitals were significantly less likely to have all appropriate PPE measures than non-governmental institutions (p = 0.001). As for preparedness, only 16 (11.6%) surveyed felt confident in dealing with a potential COVID-19 case. With 57 (41.3%) having received any COVID-19 related training and 57 (41.3%) not having a local hospital protocol.\n\nConclusionHCWs in oPt are underprepared and severely lacking adequate PPE provision. The lack of local protocols, and training has left HCWs confidence exceedingly low. The lack of PPE provision will exacerbate spread of COVID-19 and deepen the crisis, whilst putting HCWs at risk.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Osaid Alser", - "author_inst": "Ministry of Health, Gaza, occupied Palestinian territory and OxPal Medlink, UK." - }, - { - "author_name": "Heba Alghoul", - "author_inst": "Faculty of Medicine, Islamic University of Gaza, occupied Palestinian territory." - }, - { - "author_name": "Zahra Alkhateeb", - "author_inst": "Vertex Pharmaceuticals, Boston, USA." - }, - { - "author_name": "Ayah Hamdan", - "author_inst": "Harvard T.H. Chan School of Public Health, Boston, USA." - }, - { - "author_name": "Loai Albarqouni", - "author_inst": "Institute for Evidence-Based Healthcare, Faculty of Health Sciences & Medicine, Bond University, Australia." - }, - { - "author_name": "Kiran Saini", - "author_inst": "Medical Sciences Division, University of Oxford and OxPal Medlink, UK." - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.09.20096719", "rel_title": "Brazil Health Care System preparation against COVID-19", @@ -1493200,6 +1491568,81 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.05.12.092387", + "rel_title": "Comparison of SARS-CoV-2 Indirect and Direct Detection Methods", + "rel_date": "2020-05-13", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.12.092387", + "rel_abs": "The COVID-19 pandemic caused by the SARS-CoV-2 virus has placed extensive strain on RNA isolation and RT-qPCR reagents. Rapid development of new test kits has helped to alleviate these shortages. However, comparisons of these new detection systems are largely lacking. Here, we compare indirect methods that require RNA extraction, and direct RT-qPCR on patient samples. For RNA isolation we compared four different companies (Qiagen, Invitrogen, BGI and Norgen Biotek). For detection we compared two recently developed Taqman-based modules (BGI and Norgen Biotek), a SYBR green-based approach (NEB Luna Universal One-Step Kit) with published and newly-developed primers, and clinical results (Seegene STARMag RNA extraction system and Allplex 2019-nCoV RT-qPCR assay). Most RNA isolation procedures performed similarly, and while all RT-qPCR modules effectively detected purified viral RNA, the BGI system proved most sensitive, generating comparable results to clinical diagnostic data, and identifying samples ranging from 65 copies - 2.1x105 copies of viral Orf1ab/l. However, the BGI detection system is [~]4x more expensive than other options tested here. With direct RT-qPCR we found that simply adding RNase inhibitor greatly improved sensitivity, without need for any other treatments (e.g. lysis buffers or boiling). The best direct methods were [~]10 fold less sensitive than indirect methods, but reduce sample handling, as well as assay time and cost. These studies will help guide the selection of COVID-19 detection systems and provide a framework for the comparison of additional systems.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Rod Bremner", + "author_inst": "Lunefeld Tanenbaum Research Institute" + }, + { + "author_name": "Joel D Pearson", + "author_inst": "Lunenfeld Tanenbaum Research Institute" + }, + { + "author_name": "Daniel Trcka", + "author_inst": "Lunenfeld Tanenbaum Research Institute" + }, + { + "author_name": "Sharon J Hyduk", + "author_inst": "Toronto General Hospital Research Institute, University Health Network" + }, + { + "author_name": "Marie-Ming Aynaud", + "author_inst": "Lunenfeld Tanenbaum Research Institute" + }, + { + "author_name": "J. Javier Hernandez", + "author_inst": "Lunenfeld Tanenbaum Research Institute" + }, + { + "author_name": "Filippos Peidis", + "author_inst": "Lunenfeld Tanenbaum Research Institute" + }, + { + "author_name": "Suying Lu", + "author_inst": "Lunenfeld Tanenbaum Research Institute" + }, + { + "author_name": "Kin Chan", + "author_inst": "Lunenfeld Tanenbaum Research Institute" + }, + { + "author_name": "Jim Woodgett", + "author_inst": "Lunenfeld Tanenbaum Research Institute" + }, + { + "author_name": "Tony Mazzulli", + "author_inst": "Department of Microbiology, Sinai Health System/University Health Network" + }, + { + "author_name": "Liliana Attisano", + "author_inst": "University of Toronto" + }, + { + "author_name": "Laurence Pelletier", + "author_inst": "Lunenfeld Research Institute" + }, + { + "author_name": "Myron I Cybulsky", + "author_inst": "Toronto General Hospital Research Institute, University Health Network" + }, + { + "author_name": "Jeffrey L Wrana", + "author_inst": "Samuel Lunenfeld Research Inst." + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.05.13.093609", "rel_title": "Evaluation Of SYBR Green Real Time PCR For Detecting SARS-CoV-2 From Clinical Samples", @@ -1493736,25 +1492179,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.05.13.092577", - "rel_title": "Lung Disease Network Reveals the Impact of Comorbidity on SARS-CoV-2 infection", - "rel_date": "2020-05-13", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.13.092577", - "rel_abs": "Higher mortality of COVID19 patients with comorbidity is the formidable challenge faced by the health care system. In response to the present crisis, understanding the molecular basis of comorbidity is essential to accelerate the development of potential drugs. To address this, we have measured the genetic association between COVID19 and various lung disorders and observed a remarkable resemblance. 141 lung disorders directly or indirectly linked to COVID19 result in a high-density disease-disease association network that shows a small-world property. The clustering of many lung diseases with COVID19 demonstrates a greater complexity and severity of SARS-CoV-2 infection. Furthermore, our results show that the functional protein-protein interaction modules involved RNA and protein metabolism, substantially hijacked by SARS-CoV-2, are connected to several lung disorders. Therefore we recommend targeting the components of these modules to inhibit the viral growth and improve the clinical conditions in comorbidity.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Asim Bikas Das", - "author_inst": "National Institute of Technology Warangal" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "systems biology" - }, { "rel_doi": "10.1101/2020.05.12.092379", "rel_title": "Comparison of the Accula SARS-CoV-2 Test with a Laboratory-Developed Assay for Detection of SARS-CoV-2 RNA in Clinical Nasopharyngeal Specimens", @@ -1494654,6 +1493078,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.08.20094953", + "rel_title": "Predicting Long-term Evolution of COVID-19 by On-going Data using Bayesian Susceptible-Infected-Removed Model", + "rel_date": "2020-05-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20094953", + "rel_abs": "In this study, we propose a novel statistical method to predict a long-term epidemic evolution based on a on-going data. We developed a Bayesian framework for the Susceptible-Infected-Removed model (Bayesian SIR), and estimated its underlying parameters based on day-by-day timeseries of the cumulative number of infectious individuals. The new Baysian framework extends the deterministic SIR model to a probabilistic form, which provides an accurate estimation of the underlying system by a short and noisy data. We applied it to the data reported on the Coronavirus Disease 2019 (COVID-19), and made a month long prediction on its evolution. Our simulated test using past timeseries to predict the current data gives a reasonable reliablity of the proposed method. Our analysis of the current data detected and warned a rising trend in the countries in Central Asia, Middle East, and South America, while United States or European countries, which have already experienced large numbers of infected cases, are predicted to slow down in the increase.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Shohei Hidaka", + "author_inst": "Japan Advanced Institute of Science and Technology" + }, + { + "author_name": "Takuma Torii", + "author_inst": "Japan Advanced Institute of Science and Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.08.20095489", "rel_title": "COVID-19: Predictive Mathematical Models for the Number of Deaths in South Korea, Italy, Spain, France, UK, Germany, and USA", @@ -1495034,45 +1493481,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.08.20093229", - "rel_title": "Placental pathology in COVID-19", - "rel_date": "2020-05-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20093229", - "rel_abs": "ObjectivesTo describe histopathologic findings in the placentas of women with COVID-19 during pregnancy.\n\nMethodsPregnant women with COVID-19 delivering between March 18, 2020 and May 5, 2020 were identified. Placentas were examined and compared to historical controls and women with placental evaluation for a history of melanoma.\n\nResults16 placentas from patients with SARS-CoV-2 were examined (15 with live birth in the 3rd trimester 1 delivered in the 2nd trimester after intrauterine fetal demise). Compared to controls, third trimester placentas were significantly more likely to show at least one feature of maternal vascular malperfusion (MVM), including abnormal or injured maternal vessels, as well as delayed villous maturation, chorangiosis, and intervillous thrombi. Rates of acute and chronic inflammation were not increased.\n\nThe placenta from the patient with intrauterine fetal demise showed villous edema and a retroplacental hematoma.\n\nConclusionsRelative to controls, COVID-19 placentas show increased prevalence of features of maternal vascular malperfusion (MVM), a pattern of placental injury reflecting abnormalities in oxygenation within the intervillous space associated with adverse perinatal outcomes. Only 1 COVID-19 patient was hypertensive despite the association of MVM with hypertensive disorders and preeclampsia. These changes may reflect a systemic inflammatory or hypercoagulable state influencing placental physiology.\n\nKey PointsO_LIThe placentas of women infected with SARS-CoV2 have higher rates maternal vascular malperfusion features compared to controls.\nC_LIO_LIMaternal vascular malperfusion has been associated with adverse perinatal outcomes, such as preeclampsia, fetal growth restriction, preterm birth, and stillbirth.\nC_LIO_LIAs the placentas of women with SARS-CoV2 show reproducible histopathologic abnormalities, these findings suggest increased antenatal surveillance for women with COVID-19 may be warranted.\nC_LI", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Elisheva D Shanes", - "author_inst": "Northwestern University" - }, - { - "author_name": "Leena B Mithal", - "author_inst": "Ann and Robert H. Lurie Children's Hospital of Chicago and Northwestern University" - }, - { - "author_name": "Sebastian Otero", - "author_inst": "Ann and Robert H. Lurie Children's Hospital of Chicago" - }, - { - "author_name": "Hooman A Azad", - "author_inst": "Northwestern University" - }, - { - "author_name": "Emily S Miller", - "author_inst": "Northwestern University" - }, - { - "author_name": "Jeffery A Goldstein", - "author_inst": "Northwestern University" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2020.05.11.088500", "rel_title": "Pericyte-specific vascular expression of SARS-CoV-2 receptor ACE2 - implications for microvascular inflammation and hypercoagulopathy in COVID-19 patients", @@ -1496239,6 +1494647,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.08.20037556", + "rel_title": "A Research on the Results of Viral Nucleic Acid Tests and CT Imaging Variation of Patients with COVID-19", + "rel_date": "2020-05-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.08.20037556", + "rel_abs": "BackgroundCoronavirus disease 2019 (COVID-19) has become a global health problem. We aim to investigate the changes in the results of viral nucleic acid tests on pharyngeal swabs and feces of patients with COVID-19 and CT imaging of lungs as the disease progresses.\n\nMethodsSeven patients with COVID-19 in the third affiliated hospital of Sun Yat-sen University Yuedong Hospital were retrospectively enrolled with clinical features, including imaging staging, and performance characteristics of viral nucleic acid test results of pharyngeal swabs and feces. The dynamic changes of these features were observed during hospitalization, and therapeutic effect and prognosis of patients were evaluated.\n\nResultsThe results of seven cases with COVID-19 were positive for viral nucleic acid tests on pharyngeal swabs early after the onset of symptoms, and then turned negative; while the results of viral nucleic acid tests on feces were persistently positive in the mid-term clinical treatment and recovery period. And the viral nucleic acid test results were capricious in three cases. Pulmonary CT imaging showed characteristic changes in early, advanced and recovery phases.\n\nConclusionThe application of viral nucleic acid detection and pulmonary CT imaging can be used for screening of suspected cases. Fecal nucleic acid test should be recommended as the reference of discharge standard, in order to minimize the risk of transmission from digestive tract.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Meng Xu", + "author_inst": "the Third Affiliated Hospital of Sun Yat-sen University Yuedong Hospital" + }, + { + "author_name": "Xun Liu", + "author_inst": "the Third Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Chuhong Su", + "author_inst": "Southern Medical University, Guangzhou, China" + }, + { + "author_name": "Yuping Zeng", + "author_inst": "the Third Affiliated Hospital of Sun Yat-sen University Yuedong Hospital, Meizhou, China;" + }, + { + "author_name": "Jinqian Zhang", + "author_inst": "the Third Affiliated Hospital of Sun Yat-sen University Yuedong Hospital, Meizhou, China" + }, + { + "author_name": "Xuwen Li", + "author_inst": "the Third Affiliated Hospital of Sun Yat-sen University Yuedong Hospital, Meizhou, China" + }, + { + "author_name": "Guirong Liu", + "author_inst": "The Third Affiliated Hospital of Sun Yat-sen University Yuedong Hospital, Meizhou, China" + }, + { + "author_name": "Jinjun Xie", + "author_inst": "The Third Affiliated Hospital of Sun Yat-sen University Yuedong Hospital, Meizhou, China" + }, + { + "author_name": "Hongyong Liu", + "author_inst": "the Third Affiliated Hospital of Sun Yat-sen University Yuedong Hospital, Meizhou, China" + }, + { + "author_name": "Yusheng Jie", + "author_inst": "the third affiliated hospital of Sun Yat-sen university" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.05.20092064", "rel_title": "Evaluating the serological status of COVID-19 patients using an indirect immunofluorescent assay, France.", @@ -1496595,69 +1495058,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.07.20094888", - "rel_title": "SARS-CoV-2 Infection Associated Hemophagocytic Lymphohistiocytosis: An autopsy series with clinical and laboratory correlation.", - "rel_date": "2020-05-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20094888", - "rel_abs": "BackgroundA subset of COVID-19 patients exhibit clinical features of cytokine storm. However, clinicopathologic features diagnostic of hemophagocytic lymphohistiocytosis (HLH) have not been reported. Pathologic studies to date have largely focused on the pulmonary finding of diffuse alveolar damage (DAD). To this aim, we study the reticuloendothelial organs of four consecutive patients dying of COVID-19 and correlate with clinical and laboratory parameters to detect HLH.\n\nMethodsAutopsies restricted to chest and abdomen were performed on four patients who succumbed to COVID-19. Spleen, liver, and multiple pulmonary hilar/mediastinal lymph nodes were sampled in all cases. Bone marrow was obtained by rib squeeze in a subset of cases. Routine H&E staining as well as immunohistochemical staining for CD163 was performed to detect hemophagocytosis. Clinical and laboratory results from pre-mortem blood samples were used to calculate H-scores.\n\nFindingsAll four cases demonstrated DAD within the lungs. Three of the four cases had histologic evidence of hemophagocytosis within pulmonary hilar/mediastinal lymph nodes. One case showed hemophagocytosis in the spleen but none showed hemophagocytosis in liver or bone marrow. Lymphophagocytosis was the predominant form of hemophagocytosis observed. One patient showed diagnostic features of HLH with an H-score of 217 while a second patient was likely HLH with a partial H-score of 145 due to missing triglyceride level. Both patients exhibited high fever and early onset rise in serum ferritin; however, neither bicytopenia, pancytopenia, nor hypofibrinogenemia were observed in either. The remaining two patients had H-scores of 131 and 96.\n\nInterpretationThis is the first report of SARS-CoV-2 associated HLH. Identification of HLH in a subset of patients with severe COVID-19 will inform clinical trials of therapeutic strategies.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Andrey Prilutskiy", - "author_inst": "Boston Medical Center" - }, - { - "author_name": "Michael Kritselis", - "author_inst": "Boston Medical Center" - }, - { - "author_name": "Artem Shevtsov", - "author_inst": "Boston Medical Center" - }, - { - "author_name": "Ilyas Yambayev", - "author_inst": "Boston Medical Center" - }, - { - "author_name": "Charitha Vadlamudi", - "author_inst": "Boston Medical Center" - }, - { - "author_name": "Qing Zhao", - "author_inst": "Boston Medical Center" - }, - { - "author_name": "Yachana Kataria", - "author_inst": "Boston Medical Center" - }, - { - "author_name": "Shayna Sarosiek", - "author_inst": "Boston Medical Center" - }, - { - "author_name": "Adam Lerner", - "author_inst": "Boston Medical Center" - }, - { - "author_name": "John Mark Sloan", - "author_inst": "Boston Medical Center" - }, - { - "author_name": "Karen Quillen", - "author_inst": "Boston Medical Center" - }, - { - "author_name": "Eric Burks", - "author_inst": "Boston Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pathology" - }, { "rel_doi": "10.1101/2020.05.08.20093708", "rel_title": "Mental Health Status among the South Indian Pharmacy Students during Covid-19 Pandemic Quarantine Period: A Cross-Sectional Study", @@ -1497781,6 +1496181,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.07.20092353", + "rel_title": "Social Distancing is Effective at Mitigating COVID-19 Transmission in the United States", + "rel_date": "2020-05-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20092353", + "rel_abs": "COVID-19 is present in every state and over 90 percent of all counties in the United States. Decentralized government efforts to reduce spread, combined with the complex dynamics of human mobility and the variable intensity of local outbreaks makes assessing the effect of large-scale social distancing on COVID-19 transmission in the U.S.a challenge. We generate a novel metric to represent social distancing behavior derived from mobile phone data and examine its relationship with COVID-19 case reports at the county level. Our analysis reveals that social distancing is strongly correlated with decreased COVID-19 case growth rates for the 25 most affected counties in the United States, with a lag period consistent with the incubation time of SARS-CoV-2. We also demonstrate evidence that social distancing was already under way in many U.S. counties before state or local-level policies were implemented. This study strongly supports social distancing as an effective way to mitigate COVID-19 transmission in the United States.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Hamada Badr", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Hongru Du", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Max Marshall", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Ensheng Dong", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Marietta Squire", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Lauren Marie Gardner", + "author_inst": "Johns Hopkins University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.04.20091272", "rel_title": "Spread of Covid-19 in the United States is controlled", @@ -1498257,57 +1496696,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.06.20092957", - "rel_title": "Associations with covid-19 hospitalisation amongst 406,793 adults: the UK Biobank prospective cohort study", - "rel_date": "2020-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20092957", - "rel_abs": "OBJECTIVESTo identify the sociodemographic, lifestyle, comorbidity and antihypertensive medication associations with the development of hospitalisation with covid-19 in an English population.\n\nDESIGNProspective cohort study\n\nSETTINGThe population-based UK Biobank study was linked to English covid-19 test results.\n\nPARTICIPANTSIndividuals resident in England and alive in 2020.\n\nMAIN OUTCOME MEASURESCases (n=605) were defined by a positive covid-19 test result conducted between 16th March and 16th April 2020, during a restricted testing policy for hospitalised individuals with severe disease.\n\nRESULTSA total of 406,793 participants were included. Mean age on 1st January 2020 was 68 years (range 48 to 85 years). 55% were women. In multivariable models, major independent risk factors for hospitalisation with covid-19 were male sex (odds ratio 1.52; 95% confidence interval 1.28 to 1.81; P<0.001), South Asian ethnicity (2.02; 1.28 to 3.17; P=0.002) or black ethnicity (3.09; 2.18 to 4.38; P<0.001) compared to white ethnicity, greater residential deprivation (1.92 for most deprived quartile compared to least deprived quartile; 1.50 to 2.47; P<0.001), higher BMI (2.04 for BMI >35 compared to <25 Kg/m2; 1.50 to 2.77; P<0.001), former smoking (1.39 compared to never smoked; 1.16 to 1.66; P<0.001), and comorbidities hypertension (1.28; 1.06 to 1.53; P=0.009) and chronic obstructive pulmonary disease (1.81; 1.34 to 2.44; P<0.001). Increased risk was observed with increasing number of antihypertensive medications used rather than any individual class.\n\nCONCLUSIONUnderstanding why these factors confer increased risk of severe covid-19 in the population may help elucidate the underlying mechanisms as well as inform strategy and policy to prevent this disease and its consequences. We found no evidence of increased risk with specific classes of antihypertensive medication.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Anthony P Khawaja", - "author_inst": "Moorfields Eye Hospital and UCL Institute of Ophthalmology" - }, - { - "author_name": "Alasdair N Warwick", - "author_inst": "Institute of Cardiovascular Science, University College London" - }, - { - "author_name": "Pirro G Hysi", - "author_inst": "Department of Twin Research & Genetic Epidemiology, King's College London, St. Thomas' Hospital, London" - }, - { - "author_name": "Alan Kastner", - "author_inst": "NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London" - }, - { - "author_name": "Andrew Dick", - "author_inst": "NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London" - }, - { - "author_name": "Peng T Khaw", - "author_inst": "NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London" - }, - { - "author_name": "Adnan Tufail", - "author_inst": "NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London" - }, - { - "author_name": "Paul J Foster", - "author_inst": "NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London" - }, - { - "author_name": "Kay-Tee Khaw", - "author_inst": "Department of Public Health and Primary Care, University of Cambridge" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.05.20092395", "rel_title": "TB Prevalence Correlation to Covid- 19 Mortality", @@ -1499483,6 +1497871,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.07.20094102", + "rel_title": "Observer agreement and clinical significance of chest CT reporting in patients suspected of COVID-19", + "rel_date": "2020-05-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20094102", + "rel_abs": "ObjectivesTo assess inter-observer agreement and clinical significance of chest CT reporting in patients suspected of COVID-19.\n\nMethodsFrom 16th to 24th March 2020, 241 consecutive patients addressed to hospital for COVID-19 suspicion had both chest CT and SARS-CoV-2 RT-PCR. Eight observers (2 thoracic and 2 general senior radiologists, 2 junior radiologists and 2 emergency physicians) retrospectively categorized each CT into one out of 3 categories (evocative, compatible for COVID-19 pneumonia, and not evocative or normal). Observer agreement for categorization between all readers and pairs of readers with similar experience was evaluated with the Kappa coefficient. The results of a consensus categorization were correlated to RT-PCR.\n\nResultsObserver agreement across the 3 categories was good between all readers ({kappa} value 0.68 95%CI 0.67-0.70) and good to very good between pairs of readers (0.64-0.85). It was very good ({kappa} 0.81 95%CI 0.79-0.83), fair ({kappa} 0.32 95%CI 0.29-0.34) and good ({kappa} 0.74 95%CI 0.71-0.76) for the categories evocative, compatible and not evocative or normal, respectively. RT-PCR was positive in 97%, 50% and 27% of cases classified in the respective categories. Observer agreement was lower (p=0.045) and RT-PCR positive cases were less frequently categorized evocative in presence of an underlying pulmonary disease (p<0.001).\n\nConclusionInter-observer agreement for chest CT reporting using categorization of findings is good in patients suspected of COVID-19. Among patients considered for hospitalization in an epidemic context, CT categorized evocative is highly predictive of COVID-19, whereas the predictive value of CT decreases between the categories compatible and not evocative.\n\nKey resultsO_LIInter-observer agreement for chest CT reporting into categories is good in patients suspected of COVID-19\nC_LIO_LIChest CT can participate in estimating the likelihood of COVID-19 in patients presenting to hospital during the outbreak, CT categorized <> being highly predictive of the disease whereas up to a quarter of patients with CT <> had a positive RT-PCR in our study.\nC_LIO_LIObserver agreement is lower and CTs of positive RT-PCR cases less frequently \"evocative\" in presence of an underlying pulmonary disease\nC_LI", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Marie-Pierre Debray", + "author_inst": "APHP, Hopital Bichat, Paris, France" + }, + { + "author_name": "Helena Tarabay", + "author_inst": "APHP, Hopital Bichat, Paris, France" + }, + { + "author_name": "Lisa Males", + "author_inst": "APHP, Hopital Bichat, Paris, France" + }, + { + "author_name": "Nisrine Chalhoub", + "author_inst": "APHP, Hopital Bichat, Paris, France" + }, + { + "author_name": "Elyas Mahdjoub", + "author_inst": "APHP, Hopital Bichat, Paris, France" + }, + { + "author_name": "Thomas Pavlovsky", + "author_inst": "APHP, Hopital Bichat, Paris, France" + }, + { + "author_name": "Benoit Visseaux", + "author_inst": "APHP, Hopital Bichat, Paris, France" + }, + { + "author_name": "Donia Bouzid", + "author_inst": "APHP, Hopital Bichat, Paris, France" + }, + { + "author_name": "Raphael Borie", + "author_inst": "APHP, Hopital Bichat, Paris, France" + }, + { + "author_name": "Catherine Wackenheim", + "author_inst": "APHP, Hopital Bichat, Paris, France" + }, + { + "author_name": "Bruno Crestani", + "author_inst": "APHP, Hopital Bichat, Paris, France" + }, + { + "author_name": "Christophe Rioux", + "author_inst": "APHP, Hopital Bichat, Paris, France" + }, + { + "author_name": "Loukbi Saker", + "author_inst": "APHP, Hopital Bichat, Paris, France" + }, + { + "author_name": "Christophe Choquet", + "author_inst": "APHP, Hopital Bichat, Paris, France" + }, + { + "author_name": "Jimmy Mullaert", + "author_inst": "APHP, Hopital Bichat, Paris, France" + }, + { + "author_name": "Antoine Khalil", + "author_inst": "APHP, Hopital Bichat, Paris, France" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "radiology and imaging" + }, { "rel_doi": "10.1101/2020.05.08.20093393", "rel_title": "Voices from the frontline: findings from a thematic analysis of a rapid online global survey of maternal and newborn health professionals facing the COVID-19 pandemic", @@ -1499855,81 +1498322,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.07.20094276", - "rel_title": "Characteristics of 1,573 healthcare workers who underwent nasopharyngeal swab for SARS-CoV-2 in Milano, Lombardy, Italy", - "rel_date": "2020-05-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20094276", - "rel_abs": "BackgroundThe management of healthcare workers (HCWs) exposed to confirmed cases of COVID-19 is still a matter of debate. It is unclear whether these subjects should be tested in the absence of symptoms and if those can guide diagnosis.\n\nMethodsOccupational and clinical characteristics of all the consecutive HCWs who performed a nasopharyngeal swab for the detection of SARS-CoV-2 in a University Hospital from February 24, 2020, to March 31, 2020, were collected. Frequencies of positive tests were compared according to selected variables. Multivariable logistic regression analyses were then applied.\n\nFindingsPositive tests were 138 among 1,573 HCWs (8.8%, 95% confidence interval [CI]: 7.4-10.3), with a marked difference between symptomatic (20.2%, 95% CI: 16.7-24.1) and asymptomatic (3.7%, 95% CI: 2.7-5.1) subjects (p<0.001). Physicians were the group with the highest frequency of positive tests (10.6%, 95% CI: 8.3-13.4) whereas clerical workers and technicians displayed the lowest frequency (2.9%, 95% CI: 0.8-7.3). The likelihood of being positive increased with the number of reported symptoms and the strongest predictors of a positive test were taste and smell alterations (odds ratio [OR] = 29.7) and fever (OR = 7.21). The median time from first positive test to a negative test was 23 days (95% CI: 19-24).\n\nInterpretationIn this Italian group of HCWs exposed to confirmed cases of COVID-19 the presence of symptoms, especially taste and smell alterations and fever, was associated with SARS-CoV-2 infection. The median time to clear the virus from nasopharynx was 23 days.\n\nFundingnone related to the content of this manuscript.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSWe searched PubMed for articles published in English up to April 25, 2020, using the keywords \"SARS-CoV-2\", \"COVID-19\", \"2019-nCoV\", AND \"healthcare workers\",\"HCW\", AND \"testing\", \"nasopharyngeal swab\". We found one article: Roll-out of SARS-CoV-2 testing for healthcare workers at a large NHS Foundation Trust in the United Kingdom, March 2020 published in Euro Surveillance. Reviewing the pre-print website medRxiv with the same keywords we identified two additional studies: SARS-CoV-2 infection in Health Care Workers in a large public hospital in Madrid, Spain, during March 2020, and SARS-CoV-2 infection in 86 healthcare workers in two Dutch hospitals in March.\n\nAdded value of this studyWe showed that, even if symptomatic healthcare workers had a much higher probability of positive test, almost one third of those infected were asymptomatic. Specific symptoms, namely taste and smell alterations and fever, were strongly associated with the infection. Finally, the median time to clear the virus from nasopharynx was 23 days.\n\nImplications of all the available evidenceScreening strategies for healthcare workers exposed to COVID-19 patients should take in account the significant proportion of asymptomatic carriers and the predictive role of specific symptoms. Moreover, healthcare workers coming back to work after a positive test should be aware of the long-time of viral shedding from nasopharynx.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "ANDREA LOMBARDI", - "author_inst": "IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation" - }, - { - "author_name": "Dario Consonni", - "author_inst": "IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation" - }, - { - "author_name": "Michele Carugno", - "author_inst": "IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation" - }, - { - "author_name": "Giorgio Bozzi", - "author_inst": "IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation" - }, - { - "author_name": "Davide Mangioni", - "author_inst": "IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation" - }, - { - "author_name": "Antonio Muscatello", - "author_inst": "IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation" - }, - { - "author_name": "Valeria Castelli", - "author_inst": "IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation" - }, - { - "author_name": "Emanuele Palomba", - "author_inst": "IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation" - }, - { - "author_name": "Anna Paola Cantu'", - "author_inst": "IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation" - }, - { - "author_name": "Ferruccio Ceriotti", - "author_inst": "IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation" - }, - { - "author_name": "Basilio Tiso", - "author_inst": "IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation" - }, - { - "author_name": "Angela Cecilia Pesatori", - "author_inst": "IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation" - }, - { - "author_name": "Luciano Riboldi", - "author_inst": "IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation" - }, - { - "author_name": "Alessandra Bandera", - "author_inst": "IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation" - }, - { - "author_name": "Andrea Gori", - "author_inst": "IRCCS Ca' Granda Ospedale Maggiore Policlinico Foundation" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.07.20094227", "rel_title": "Pandemic related Health literacy - A Systematic Review of literature in COVID-19, SARS and MERS pandemics", @@ -1500973,6 +1499365,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.06.20091900", + "rel_title": "Predicting the Growth and Trend of COVID-19 Pandemic using Machine Learning and Cloud Computing", + "rel_date": "2020-05-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20091900", + "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWThe outbreak of COVID-19 Coronavirus, namely SARS-CoV-2, has created a calamitous situation throughout the world. The cumulative incidence of COVID-19 is rapidly increasing day by day. Machine Learning (ML) and Cloud Computing can be deployed very effectively to track the disease, predict growth of the epidemic and design strategies and policy to manage its spread. This study applies an improved mathematical model to analyse and predict the growth of the epidemic. An ML-based improved model has been applied to predict the potential threat of COVID-19 in countries worldwide. We show that using iterative weighting for fitting Generalized Inverse Weibull distribution, a better fit can be obtained to develop a prediction framework. This can be deployed on a cloud computing platform for more accurate and real-time prediction of the growth behavior of the epidemic. A data driven approach with higher accuracy as here can be very useful for a proactive response from the government and citizens. Finally, we propose a set of research opportunities and setup grounds for further practical applications. Predicted curves for some of the most affected countries can be seen at https://collaboration.coraltele.com/covid/.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Shreshth Tuli", + "author_inst": "IIT Delhi" + }, + { + "author_name": "Shikhar Tuli", + "author_inst": "IIT Delhi" + }, + { + "author_name": "Rakesh Tuli", + "author_inst": "UIET, Panjab University" + }, + { + "author_name": "Sukhpal Singh Gill", + "author_inst": "Queen Mary University London" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.06.20093377", "rel_title": "The RBD Of The Spike Protein Of SARS-Group Coronaviruses Is A Highly Specific Target Of SARS-CoV-2 Antibodies But Not Other Pathogenic Human and Animal Coronavirus Antibodies", @@ -1501277,61 +1499700,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.06.20093476", - "rel_title": "Sensitivity and specificity of a rapid test for assessment of exposure to SARS-CoV-2 in a community-based setting in Brazil", - "rel_date": "2020-05-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20093476", - "rel_abs": "BackgroundWhile the recommended laboratory diagnosis of COVID-19 is a molecular based assay, population-based studies to determine the prevalence of COVID-19 usually use serological assays.\n\nObjectiveTo evaluate the sensitivity and specificity of a rapid diagnostic test for COVID-19 compared to quantitative reverse transcription polymerase chain reaction (qRT-PCR).\n\nMethodsWe evaluated the sensitivity using a panel of finger prick blood samples from participants >18 years of age that had been tested for COVID-19 by qRT-PCR. For assessing specificity, we used serum samples from the 1982 Pelotas (Brazil) Birth Cohort participants collected in 2012 with no exposure to SARS-CoV-2.\n\nResultsThe sensitivity of the test was 77.1% (95% CI 66.6 - 85.6), based upon 83 subjects who had tested positive for qRT-PCR at least 10 days before the rapid diagnostic test (RDT). Based upon 100 sera samples, specificity was 98.0% (95% CI 92.9 - 99.8). There was substantial agreement (Kappa score 0.76) between the qRT-PCR results and the RDT.\n\nInterpretationThe validation results are well in line with previous assessments of the test, and confirm that it is sufficiently precise for epidemiological studies aimed at monitoring levels and trends of the COVID-19 pandemic.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Lucia C Pellanda", - "author_inst": "Universidade Federal de Ciencias da Saude de Porto Alegre" - }, - { - "author_name": "Eliana M Wendland", - "author_inst": "Universidade Federal de Ciencias da Saude de Porto Alegre" - }, - { - "author_name": "Alan JA McBride", - "author_inst": "Biotechnology Department, Centre for Technological Development, Federal University of Pelotas, Brazil" - }, - { - "author_name": "Luciana Tovo-Rodrigues", - "author_inst": "Post-graduate Program in Epidemiology, Federal University of Pelotas" - }, - { - "author_name": "Marcos RA Ferreira", - "author_inst": "Biotechnology Department, Centre for Technological Development, Federal University of Pelotas" - }, - { - "author_name": "Odir A Dellagostin", - "author_inst": "Biotechnology Department, Centre for Technological Development, Federal University of Pelotas" - }, - { - "author_name": "Mariangela F Silveira", - "author_inst": "Post-graduate Program in Epidemiology, Federal University of Pelotas" - }, - { - "author_name": "Aluisio JD Barros", - "author_inst": "Post-graduate Program in Epidemiology, Federal University of Pelotas" - }, - { - "author_name": "Pedro C Hallal", - "author_inst": "Post-graduate Program in Epidemiology, Federal University of Pelotas" - }, - { - "author_name": "Cesar G Victora", - "author_inst": "Post-graduate Program in Epidemiology, Federal University of Pelotas" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.06.20093666", "rel_title": "TAMING COVID-19 EPIDEMIC IN SAO PAULO WITH ALOGISTIC MODEL AND NON-PHARMACEUTICAL MEASURES", @@ -1502391,6 +1500759,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.06.20093070", + "rel_title": "Neutrophil calprotectin identifies severe pulmonary disease in COVID-19", + "rel_date": "2020-05-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20093070", + "rel_abs": "Severe cases of coronavirus disease 2019 (COVID-19) are regularly complicated by respiratory failure. While it has been suggested that elevated levels of blood neutrophils associate with worsening oxygenation in COVID-19, it is unknown whether neutrophils are drivers of the thrombo-inflammatory storm or simple bystanders. To better understand the potential role of neutrophils in COVID-19, we measured levels of the neutrophil activation marker S100A8/A9 (calprotectin) in hospitalized patients and determined its relationship to severity of illness and respiratory status. Patients with COVID-19 (n=172) had markedly elevated levels of calprotectin in their blood. Calprotectin tracked with other acute phase reactants including C-reactive protein, ferritin, lactate dehydrogenase, and absolute neutrophil count, but was superior in identifying patients requiring mechanical ventilation. In longitudinal samples, calprotectin rose as oxygenation worsened. When tested on day 1 or 2 of hospitalization (n=94 patients), calprotectin levels were significantly higher in patients who progressed to severe COVID-19 requiring mechanical ventilation (8039 {+/-} 7031 ng/ml, n=32) as compared to those who remained free of intubation (3365 {+/-} 3146, p<0.0001). In summary, serum calprotectin levels track closely with current and future COVID-19 severity, implicating neutrophils as potential perpetuators of inflammation and respiratory compromise in COVID-19.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Hui Shi", + "author_inst": "University of Michigan" + }, + { + "author_name": "Yu Zuo", + "author_inst": "University of Michigan" + }, + { + "author_name": "Srilakshmi Yalavarthi", + "author_inst": "University of Michigan" + }, + { + "author_name": "Kelsey Gockman", + "author_inst": "University of Michigan" + }, + { + "author_name": "Melanie Zuo", + "author_inst": "University of Michigan" + }, + { + "author_name": "Jacqueline A. Madison", + "author_inst": "University of Michigan" + }, + { + "author_name": "Christopher N. Blair", + "author_inst": "University of Michigan" + }, + { + "author_name": "Wrenn Woodard", + "author_inst": "University of Michigan" + }, + { + "author_name": "Sean P. Lezak", + "author_inst": "University of Michigan" + }, + { + "author_name": "Njira L. Lugogo", + "author_inst": "University of MIchigan" + }, + { + "author_name": "Robert J. Woods", + "author_inst": "University of Michigan" + }, + { + "author_name": "Christian Lood", + "author_inst": "University of Michigan" + }, + { + "author_name": "Jason S. Knight", + "author_inst": "University of Michigan" + }, + { + "author_name": "Yogendra Kanthi", + "author_inst": "University of Michigan" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.07.083139", "rel_title": "Pre-treatment of the clinical sample with Proteinase K allows detection of SARS-CoV-2 in the absence of RNA extraction", @@ -1503035,29 +1501474,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.05.05.20092254", - "rel_title": "County-level factors influence the trajectory of Covid-19 incidence", - "rel_date": "2020-05-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20092254", - "rel_abs": "With new cases of Covid-19 surging in the United States, we need to better understand how the spread of novel coronavirus varies across all segments of the population. We use hierarchical exponential growth curve modeling techniques to examine whether community social and economic characteristics uniquely influence the incidence of Covid-19 cases in the urban built environment. We show that, as of May 3, 2020, confirmed coronavirus infections are concentrated along demographic and socioeconomic lines in New York City and surrounding areas, the epicenter of the Covid-19 pandemic in the United States. Furthermore, we see evidence that, after the onset of the pandemic, timely enactment of physical distancing measures such as school closures is imperative in order to limit the extent of the coronavirus spread in the population. Public health authorities must impose nonpharmaceutical measures early on in the pandemic and consider community-level factors that associate with a greater risk of viral transmission.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Ashley Wendell Kranjac", - "author_inst": "Chapman University" - }, - { - "author_name": "Dinko Kranjac", - "author_inst": "University of La Verne" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.05.05.20092247", "rel_title": "Awareness, knowledge, attitude and practice towards measures for prevention of the spread of COVID-19 in the Ugandans: A nationwide online cross-sectional Survey", @@ -1504017,6 +1502433,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.05.20092155", + "rel_title": "A Divide and Conquer Strategy against the Covid-19 Pandemic?!", + "rel_date": "2020-05-09", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20092155", + "rel_abs": "The concern about (socio-)economic consequences of collective lockdowns in the Covid-19 pandemic calls for alternative strategies. We consider a divide and conquer strategy in which a high risk group (HRG) is put on strict isolation, whereas the remainder of the population is exposed to the virus, building up immunity against Covid-19. The question is whether this strategy may suppress the effective reproduction number below the critical value of [Formula] without further lockdown once the HRG is released from isolation. While this proposal appears already rather academic, we show that [Formula] can only be obtained provided that the HRG is less than ~ 20 - 30% of the total population. Hence, this strategy is likely to fail in countries with a HRG larger than the given upper bound. In addition, we argue that the maximum infection rate occurring in this strategy is likely to exceed realistic capacities of most health care systems. While the conclusion is rather negative in this regard, we emphasise that the strategy of stopping the curve at an early stage of the Covid-19 pandemic has a chance to work out. The required duration of the lockdown is estimated to be {tau} ~ 14 days/[Formula] (up to some order one factor) for [Formula], provided a systematic tracing strategy of new infections exists for the subsequent relaxation phase. In this context we also argue why [Formula] remains the crucial parameter which needs to be accurately monitored and controlled.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Patrick S. Mangat", + "author_inst": "Mannheim University of Applied Science" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.05.20092221", "rel_title": "Containing Covid-19 outbreaks with spatiallytargeted short-term lockdowns and mass-testing", @@ -1504517,41 +1502952,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.08.083816", - "rel_title": "Intra-genome variability in the dinucleotide composition of SARS-CoV-2", - "rel_date": "2020-05-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.08.083816", - "rel_abs": "CpG dinucleotides are under-represented in the genomes of single stranded RNA viruses, and coronaviruses, including SARS-CoV-2, are no exception to this. Artificial modification of CpG frequency is a valid approach for live attenuated vaccine development, and if this is to be applied to SARS-CoV-2, we must first understand the role CpG motifs play in regulating SARS-CoV-2 replication. Accordingly, the CpG composition of the newly emerged SARS-CoV-2 genome was characterised in the context of other coronaviruses. CpG suppression amongst coronaviruses does not significantly differ according to genera of virus, but does vary according to host species and primary replication site (a proxy for tissue tropism), supporting the hypothesis that viral CpG content may influence cross-species transmission. Although SARS-CoV-2 exhibits overall strong CpG suppression, this varies considerably across the genome, and the Envelope (E) open reading frame (ORF) and ORF10 demonstrate an absence of CpG suppression. While ORF10 is only present in the genomes of a subset of coronaviruses, E is essential for virus replication. Across the Coronaviridae, E genes display remarkably high variation in CpG composition, with those of SARS and SARS-CoV-2 having much higher CpG content than other coronaviruses isolated from humans. Phylogeny indicates that this is an ancestrally-derived trait reflecting their origin in bats, rather than something selected for after zoonotic transfer. Conservation of CpG motifs in these regions suggests that they have a functionality which over-rides the need to suppress CpG; an observation relevant to future strategies towards a rationally attenuated SARS-CoV-2 vaccine.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Paul Digard", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Hui-Min Lee", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Colin Sharp", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Finn Grey", - "author_inst": "University of Edinburgh" - }, - { - "author_name": "Eleanor R Gaunt", - "author_inst": "University of Edinburgh" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "evolutionary biology" - }, { "rel_doi": "10.1101/2020.05.08.085308", "rel_title": "VIRTUS: a pipeline for comprehensive virus analysis from conventional RNA-seq data", @@ -1505703,6 +1504103,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.05.04.20090274", + "rel_title": "Assessing Differential Impacts of COVID-19 on Black Communities", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20090274", + "rel_abs": "PurposeGiven incomplete data reporting by race, we used data on COVID-19 cases and deaths in US counties to describe racial disparities in COVID-19 disease and death and associated determinants.\n\nMethodsUsing publicly available data (accessed April 13, 2020), predictors of COVID-19 cases and deaths were compared between disproportionately ([≥]13%) black and all other (<13% black) counties. Rate ratios were calculated and population attributable fractions (PAF) were estimated using COVID-19 cases and deaths via zero-inflated negative binomial regression model. National maps with county-level data and an interactive scatterplot of COVID-19 cases were generated.\n\nResultsNearly ninety-seven percent of disproportionately black counties (656/677) reported a case and 49% (330/677) reported a death versus 81% (1987/2,465) and 28% (684/ 2465), respectively, for all other counties. Counties with higher proportions of black people have higher prevalence of comorbidities and greater air pollution. Counties with higher proportions of black residents had more COVID-19 diagnoses (RR 1.24, 95% CI 1.17-1.33) and deaths (RR 1.18, 95% CI 1.00-1.40), after adjusting for county-level characteristics such as age, poverty, comorbidities, and epidemic duration. COVID-19 deaths were higher in disproportionally black rural and small metro counties. The PAF of COVID-19 diagnosis due to lack of health insurance was 3.3% for counties with <13% black residents and 4.2% for counties with [≥]13% black residents.\n\nConclusionsNearly twenty-two percent of US counties are disproportionately black and they accounted for 52% of COVID-19 diagnoses and 58% of COVID-19 deaths nationally. County-level comparisons can both inform COVID-19 responses and identify epidemic hot spots. Social conditions, structural racism, and other factors elevate risk for COVID-19 diagnoses and deaths in black communities.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Greg Millett", + "author_inst": "amfAR" + }, + { + "author_name": "Austin T Jones", + "author_inst": "amfAR" + }, + { + "author_name": "David Benkeser", + "author_inst": "Emory University" + }, + { + "author_name": "Stefan D Baral", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Laina Mercer", + "author_inst": "PATH" + }, + { + "author_name": "Chris Beyrer", + "author_inst": "Johns Hopkins University" + }, + { + "author_name": "Brian Honnermann", + "author_inst": "amfAR" + }, + { + "author_name": "Elise Lankiewicz", + "author_inst": "amfAR" + }, + { + "author_name": "Lenandro Mena", + "author_inst": "University of Mississippi Medical Center" + }, + { + "author_name": "Jeffrey S Crowley", + "author_inst": "O'Neill Institute for National and Global Health Law, Georgetown University" + }, + { + "author_name": "Jennifer Sherwood", + "author_inst": "amfAR" + }, + { + "author_name": "Patrick S Sullivan", + "author_inst": "Emory University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.03.20089839", "rel_title": "Assessing COVID-19 Risk, Vulnerability and Infection Prevalence in Communities", @@ -1506243,25 +1504706,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "neurology" }, - { - "rel_doi": "10.1101/2020.05.04.20091041", - "rel_title": "The Social and Economic Factors Underlying the Impact of COVID-19 Cases and Deaths in US Counties", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20091041", - "rel_abs": "This paper uncovers the socioeconomic and health/lifestyle factors that can explain the differential impact of the coronavirus pandemic on different parts of the United States. Using a dynamic panel representation of an epidemiological model of disease spread, the paper develops a Vulnerability Index for US counties from daily reported number of cases over a 20-day period of rapid disease growth. County-level economic, demographic, and health factors are used to explain the differences in the values of this index and thereby the transmission and concentration of the disease across the country. These factors are also used to examine the number of reported deaths. The paper finds that counties with high median income have a high incidence of cases but reported lower deaths. Income inequality as measured by the Gini coefficient, is found to be associated with more deaths and more cases. The remarkable similarity in the distribution of cases across the country and the distribution of distance-weighted international passengers served by the top international airports is evidence of the spread of the virus by way of international travel. The distributions of age, race, and health risk factors such as obesity and diabetes are found to be particularly significant factors in explaining the differences in mortality across counties. Counties with better access to health care as measured by the number of primary care physicians per capita have lower deaths, and so do places with more health awareness as measured by flu vaccination prevalence. Environmental health conditions such as the amount of air pollution is found to be associated with counties with higher deaths from the virus. It is hoped that research such as these will help policymakers to develop risk factors for each region of the country to better contain the spread of infectious diseases in the future.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Nivedita Mukherji", - "author_inst": "Oakland University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.05.04.20090993", "rel_title": "TRENDS IN PERCEPTION OF COVID-19 IN POLISH INTERNET", @@ -1507585,6 +1506029,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, + { + "rel_doi": "10.1101/2020.05.05.20091587", + "rel_title": "Acceptability of app-based contact tracing for COVID-19: Cross-country survey evidence", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.05.20091587", + "rel_abs": "BackgroundThe COVID-19 pandemic is the greatest public health crisis of the last 100 years. Countries have responded with various levels of lockdown to save lives and stop health systems from being overwhelmed. At the same time, lockdowns entail large socio-economic costs. One exit strategy under consideration is a mobile phone app that traces close contacts of those infected with COVID-19. Recent research has demonstrated the theoretical effectiveness of this solution in different disease settings. However, concerns have been raised about such apps because of the potential privacy implications. This could limit the acceptability of app-based contact tracing among the general population. As the effectiveness of this approach increases strongly with app take-up, it is crucial to understand public support for this intervention.\n\nObjectivesThe objective of this study is to investigate user acceptability of a contact-tracing app in five countries hit by the pandemic.\n\nMethodsWe conducted a multi-country, large-scale (N = 5995) study to measure public support for digital contact tracing of COVID-19 infections. We ran anonymous online surveys in France, Germany, Italy, the UK and the US. We measured intentions to use a contact-tracing app across different installation regimes (voluntary installation vs. automatic installation by mobile phone providers), and studied how these intentions vary across individuals and countries.\n\nResultsWe found strong support for the app under both regimes, in all countries, across all sub-groups of the population, and irrespective of regional-level COVID-19 mortality rates. We investigated the main factors that may hinder or facilitate take-up and found that concerns about cyber security and privacy, together with lack of trust in government, are the main barriers to adoption.\n\nConclusionsEpidemiological evidence shows that app-based contact-tracing can suppress the spread of COVID-19 if a high enough proportion of the population uses the app and that it can still reduce the number of infections if take-up is moderate. Our findings show that the willingness to install the app is very high. The available evidence suggests that app-based contact tracing may be a viable approach to control the diffusion of COVID-19.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Samuel Altmann", + "author_inst": "University of Oxford" + }, + { + "author_name": "Luke Milsom", + "author_inst": "University of Oxford" + }, + { + "author_name": "Hannah Zillessen", + "author_inst": "University of Oxford" + }, + { + "author_name": "Raffaele Blasone", + "author_inst": "University of Oxford" + }, + { + "author_name": "Frederic Gerdon", + "author_inst": "University of Mannheim" + }, + { + "author_name": "Ruben Bach", + "author_inst": "University of Mannheim" + }, + { + "author_name": "Frauke Kreuter", + "author_inst": "University of Mannheim" + }, + { + "author_name": "Daniele Nosenzo", + "author_inst": "University of Nottingham" + }, + { + "author_name": "Severine Toussaert", + "author_inst": "University of Oxford" + }, + { + "author_name": "Johannes Abeler", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.05.03.20089557", "rel_title": "The Impact of Coronavirus Disease 2019 (COVID-19) on Liver Injury in China: A Systematic Review and Meta-analysis", @@ -1508101,37 +1506600,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.05.08.084384", - "rel_title": "ACE2 coding variants in different populations and their potential impact on SARS-CoV-2 binding affinity", - "rel_date": "2020-05-08", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.08.084384", - "rel_abs": "The susceptibility of different populations to the SARS-CoV-2 infection is not yet understood. A deeper analysis of the genomes of individuals from different populations might explain their risk for infection. In this study, a combined analysis of ACE2 coding variants in different populations and computational chemistry calculations are conducted in order to probe the potential effects of ACE2 coding variants on SARS-CoV-2/ACE2 binding affinity. Our study reveals novel interaction data on the variants and SARS-CoV-2. We could show that ACE2-K26R; which is more frequent in the Ashkenazi Jewish population decrease the electrostatic attraction between SARS-CoV-2 and ACE2. On the contrary, ACE2-I468V, R219C, K341R, D206G, G211R were found to increase the electrostatic attraction and increase the binding to SARS-CoV-2; ordered by the strength of binding from weakest to strongest. I468V, R219C, K341R, D206G and G211R were more frequent in East Asian, South Asian, African and African American, European and European and South Asian populations, respectively. SARS-CoV-2/ACE2 interface in the WT protein and corresponding variants is showed to be a dominated by van der Waals (vdW) interactions. All the mutations except K341R induce an increase in the vdW attractions between the ACE2 and the SARS-CoV-2. The largest increase of is observed for the R219C mutant.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Fedaa Ali", - "author_inst": "Zewail City of Science and Technology" - }, - { - "author_name": "Menattallah Elserafy", - "author_inst": "Zewail City of Science and Technology" - }, - { - "author_name": "Mohamed Alkordi", - "author_inst": "Zewail City of Science and Technology" - }, - { - "author_name": "Muhamed Amin", - "author_inst": "University of Groningen" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.05.05.078758", "rel_title": "A phylodynamic workflow to rapidly gain insights into the dispersal history and dynamics of SARS-CoV-2 lineages", @@ -1509215,6 +1507683,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nutrition" }, + { + "rel_doi": "10.1101/2020.05.03.20082818", + "rel_title": "Contact tracing and isolation of asymptomatic spreaders to successfully control the COVID-19 epidemic among healthcare workers in Milan (Italy)", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.03.20082818", + "rel_abs": "ObjectiveTo study the source, symptoms, and duration of infection, preventive measures, contact tracing and their effects on SARS-CoV-2 epidemic among healthcare workers (HCW) in 2 large hospitals and 40 external healthcare services in Milan (Italy) to propose effective measures to control the COVID-19 epidemic among healthcare workers.\n\nDesignEpidemiological observational study.\n\nSettingTwo large hospitals and 40 territorial healthcare units, with a total of 5700 workers.\n\nParticipants143 HCWs with a SARS-CoV-2 positive nasopharyngeal (NF) swab in a population made of 5,700 HCWs.\n\nMain outcome measuresClinical data on the history of exposure, contacts inside and outside of the hospital, NF swab dates and results. A daily online self-reported case report form consisting of the morning and evening body temperature and 11 other symptoms (cough, dyspnoea, discomfort, muscle pain, headache, sore throat, vomiting, diarrhoea, anosmia, dysgeusia, conjunctival hyperaemia).\n\nResultsMost workers were tested and found positive due to a close contact with a positive colleague (49%), followed by worker-initiated testing due to symptoms (and unknown contact, 28%), and a SARS-CoV-2 positive member of the family (9.8%). 10% of NF swabs performed in the framework of contact tracing resulted positive, compared to only 2.6% through random testing. The first (index) case caused a cluster of 7 positive HCWs discovered through contact tracing and testing of 250 asymptomatic HCWs. HCWs rarely reported symptoms of a respiratory infection, and up to 90% were asymptomatic or with mild symptoms in the days surrounding the positive NF swab. During the 15-day follow-up period, up to 40% of HCWs reported anosmia and dysgeusia/ageusia as moderate or heavy, more frequently than any other symptom. The time necessary for 95% of HCWs to be considered cured (between the positive and two negative NF swabs) was 30 days.\n\nConclusionHCWs represent the main source of infection in healthcare institutions, 90% are asymptomatic or with symptoms not common in a respiratory infection. The time needed to overcome the infection in 95% of workers was 30 days. Contact tracing allows identifying asymptomatic workers which would spread SARS-CoV-2 in the hospital and is a more successful strategy than random testing.\n\nWhat is already known on this topic?There are more than 3 million SARS-CoV-2 positive cases and more than 200,000 deaths attributed to coronavirus disease (COVID-19) worldwide.\n\nCommonly reported symptoms of COVID-19 include fever, cough, dyspnea, sore throat, muscle pain, discomfort, and many prevention strategies are based on identifying these symptoms of infection.\n\nThe virus can be spread even by asymptomatic patients or patients with mild symptoms, and healthcare workers (HCWs) represent 10% of overall cases and often more than 10% of hospital personnel are commonly infected.\n\nHCWs represent both a vulnerable population and an irreplaceable resource in the fight against this epidemic and further analysis is needed to show how and why they get infected and introduce successful prevention measures.\n\nWhat this study adds?The first (index) case in our study was infected by a family member, but due to close contacts with colleagues managed to infect other 7 HCWs. Contrary to a common expectation that HCWs get infected from patients, they regularly get infected by other HCWs.\n\nUp to 90% of HCWs were asymptomatic or had only mild symptoms. Random testing for SARS-CoV-2 was not efficient. Active search for suspect cases through contact tracing is the strategy of choice to identify most of the positive HCWs.\n\nMost HCWs remained asymptomatic during the 15-day follow-up period, and even in the days prior to the positive NF swab. Anosmia and ageusia/dysgeusia were reported more commonly than classic symptoms of a respiratory infection.\n\nContrary to the recommended quarantine of 14 days, 30 days were necessary for 95% of the workers to be declared cured (two negative NF swabs)", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Stefan Mandi\u0107-Raj\u010devi\u0107", + "author_inst": "Department of Health Sciences, University of Milan, Occupational Health Unit, International Centre for Rural Health and Central Health Care Management of the Sa" + }, + { + "author_name": "Federica Masci", + "author_inst": "Department of Health Sciences, University of Milan, Occupational Health Unit, International Centre for Rural Health and Central Health Care Management of the Sa" + }, + { + "author_name": "Eleonora Crespi", + "author_inst": "Department of Health Sciences, University of Milan, Occupational Health Unit, International Centre for Rural Health and Central Health Care Management of the Sa" + }, + { + "author_name": "Sara Franchetti", + "author_inst": "Department of Health Sciences, University of Milan, Occupational Health Unit, International Centre for Rural Health and Central Health Care Management of the Sa" + }, + { + "author_name": "Anna Longo", + "author_inst": "Department of Health Sciences, University of Milan, Occupational Health Unit, International Centre for Rural Health and Central Health Care Management of the Sa" + }, + { + "author_name": "Ilaria Bollina", + "author_inst": "Department of Health Sciences, University of Milan, Occupational Health Unit, International Centre for Rural Health and Central Health Care Management of the Sa" + }, + { + "author_name": "Serena Veloci", + "author_inst": "Department of Health Sciences, University of Milan, Occupational Health Unit, International Centre for Rural Health and Central Health Care Management of the Sa" + }, + { + "author_name": "Alessandro Amorosi", + "author_inst": "Department of Health Sciences, University of Milan, Occupational Health Unit, International Centre for Rural Health and Central Health Care Management of the Sa" + }, + { + "author_name": "Riccardo Baldelli", + "author_inst": "Department of Health Sciences, University of Milan, Occupational Health Unit, International Centre for Rural Health and Central Health Care Management of the Sa" + }, + { + "author_name": "Luisa Boselli", + "author_inst": "Department of Health Sciences, University of Milan, Occupational Health Unit, International Centre for Rural Health and Central Health Care Management of the Sa" + }, + { + "author_name": "Lucia Negroni", + "author_inst": "Department of Health Sciences, University of Milan, Occupational Health Unit, International Centre for Rural Health and Central Health Care Management of the Sa" + }, + { + "author_name": "Alessandro Z\u00e0", + "author_inst": "Department of Health Sciences, University of Milan, Occupational Health Unit, International Centre for Rural Health and Central Health Care Management of the Sa" + }, + { + "author_name": "Nicola Vincenzo Orfeo", + "author_inst": "Department of Health Sciences, University of Milan, Occupational Health Unit, International Centre for Rural Health and Central Health Care Management of the Sa" + }, + { + "author_name": "Giusepe Ortisi", + "author_inst": "Department of Health Sciences, University of Milan, Occupational Health Unit, International Centre for Rural Health and Central Health Care Management of the Sa" + }, + { + "author_name": "Claudio Colosio", + "author_inst": "Department of Health Sciences, University of Milan, Occupational Health Unit, International Centre for Rural Health and Central Health Care Management of the Sa" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2020.05.03.20088526", "rel_title": "Objective Olfactory Evaluation of Self-reported Olfactory Dysfunction in a Case Series of 86 COVID-19 Patients", @@ -1509599,33 +1508142,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.05.04.20090555", - "rel_title": "Laboratory findings associated with mechanical ventilation requirement and mortality among hospitalized individuals with Covid-19 in Eastern Massachusetts", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.04.20090555", - "rel_abs": "ImportanceThe coronavirus disease 2019 (COVID-19) pandemic has placed unprecedented stress on health systems across the world, and reliable estimates of risk for adverse hospital outcomes are needed.\n\nObjectiveTo quantify admission laboratory and comorbidity features associated with critical illness and mortality risk across 6 Eastern Massachusetts hospitals.\n\nDesignRetrospective cohort study using hospital course, prior diagnoses, and laboratory values.\n\nSettingEmergency department and inpatient settings from 2 academic medical centers and 4 community hospitals.\n\nParticipantsAll individuals with hospital admission and positive severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by PCR testing across these 6 hospitals through June 5, 2020.\n\nExposureCoronavirus 2 (SARS-CoV-2).\n\nMain Outcome MeasuresSevere illness defined by ICU admission, mechanical ventilation, or death.\n\nResultsAmong 2,511 hospitalized individuals who tested positive for SARS-CoV-2 (of whom 50.9% were male, 53.9% white, and 27.0% Hispanic, with mean age 62.6 years), 215 (8.6%) were admitted to the ICU, 164 (6.5%) required mechanical ventilation, and 292 (11.6%) died. L1-regression models developed in 3 of these hospitals yielded area under ROC curve (AUC) of 0.807 for severe illness and 0.847 for mortality in the 3 held-out hospitals. In total, 212/292 (78%) of the deaths occurred in the highest-risk mortality quintile.\n\nConclusions and RelevanceIn this cohort, specific admission laboratory studies in concert with sociodemographic features and prior diagnosis facilitated risk stratification among individuals hospitalized for COVID-19.\n\nFunding1R56MH115187-01\n\nTrial RegistrationNone\n\nKey PointsO_ST_ABSQuestionC_ST_ABSHow well can sociodemographic features, laboratory values, and comorbidities of individuals hospitalized with coronavirus disease 2019 (COVID-19) in Eastern Massachusetts through June 5, 2020 predict severe illness course?\n\nFindingsIn this cohort study of 2,511 hospitalized individuals positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by PCR who were admitted to one of six hospitals, 215 (8.6%) were admitted to the ICU, 164 (6.5%) required mechanical ventilation, and 292 (11.6%) died. In a risk prediction model, 212 (78%) deaths occurred in the top mortality-risk quintile.\n\nMeaningSimple prediction models may assist in risk stratification among hospitalized COVID-19 patients.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Victor M Castro", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Thomas H McCoy Jr.", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Roy H Perlis", - "author_inst": "Massachusetts General Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.04.20090209", "rel_title": "Assessment of a serological diagnostic kit of sars-cov-2 availble in Iran", @@ -1511005,6 +1509521,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.07.20055947", + "rel_title": "A 5-min RNA preparation method for COVID-19 detection with RT-qPCR", + "rel_date": "2020-05-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.07.20055947", + "rel_abs": "RNA extraction has become a bottleneck for detection of COVID-19, in part because of reagent shortages. We present here a rapid protocol that circumvents the need for RNA extraction that is compatible with RT-qPCR-based detection methods.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Alim Ladha", + "author_inst": "Broad Institute of MIT and Harvard; MIT" + }, + { + "author_name": "Julia Joung", + "author_inst": "Broad Institute of MIT and Harvard; MIT" + }, + { + "author_name": "Omar Abudayyeh", + "author_inst": "MIT" + }, + { + "author_name": "Jonathan Gootenberg", + "author_inst": "MIT" + }, + { + "author_name": "Feng Zhang", + "author_inst": "HHMI; Broad Institute of MIT and Harvard; and McGovern Institute, MIT" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.04.20076349", "rel_title": "Intensive care risk estimation in COVID-19 pneumonia based on clinical and imaging parameters: experiences from the Munich cohort", @@ -1511341,49 +1509892,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.03.20089938", - "rel_title": "Protocol for a systematic review of qualitative and quantitative effects of cardiovascular disease risk communication using heart age concepts", - "rel_date": "2020-05-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.03.20089938", - "rel_abs": "IntroductionThe concept of heart age is increasingly used for health promotion and alongside clinical guidelines for cardiovascular disease (CVD) prevention. These tools have been used by millions of consumers around the world, and many health organisations promote them as a way of encouraging lifestyle change. However, heart age tools vary widely in terms of their underlying risk models and display formats, the effectiveness of these tools compared to other CVD risk communication formats remains unclear, and doctors have raised concerns over their use to expand testing of healthy low risk adults.\n\nMethods and analysisWe aim to systematically review both qualitative and quantitative evidence of the effects of heart age when presented to patients or consumers for the purpose of CVD risk communication. Four electronic databases will be search until April 2020 and reference lists from similar review articles will be searched. Studies will be considered eligible if they meet the following criteria: (1) published from the inception of the database to April 2020, in peer-reviewed journals, (2) used an adult population (over 18 years of age) or, if not explicit regarding age, are clear that participants were not children, (3) present the concept of heart age to patients or consumers for the purpose of CVD risk communication, (4) report qualitative themes or quantitative outcomes relating to psychological and/or behavioural responses to heart age. Two reviewers will perform study selection, data extraction and quality assessment. Reporting of the review will be informed by Preferred Reporting Items for Systematic Review and Meta-Analysis guidance.\n\nEthics and disseminationEthical approval is not required as it is a protocol for a systematic review. Findings will be disseminated through peer-reviewed publications and conference presentations.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Carissa Bonner", - "author_inst": "University of Sydney" - }, - { - "author_name": "Samuel Cornell", - "author_inst": "University of Sydney" - }, - { - "author_name": "Carys Batcup", - "author_inst": "University of Sydney" - }, - { - "author_name": "Michael Fajardo", - "author_inst": "University of Sydney" - }, - { - "author_name": "Jenny Doust", - "author_inst": "University of Queensland" - }, - { - "author_name": "Kevin McGeechan", - "author_inst": "University of Sydney" - }, - { - "author_name": "Lyndal Trevena", - "author_inst": "University of Sydney" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2020.05.03.20089375", "rel_title": "Impact of hospitalised patients with COVID-19 taking Renin-Angiotensin-Aldosterone System inhibitors: a systematic review and meta-analysis", @@ -1512191,6 +1510699,145 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.06.20092999", + "rel_title": "OpenSAFELY: factors associated with COVID-19-related hospital death in the linked electronic health records of 17 million adult NHS patients.", + "rel_date": "2020-05-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.06.20092999", + "rel_abs": "BackgroundEstablishing who is at risk from a novel rapidly arising cause of death, and why, requires a new approach to epidemiological research with very large datasets and timely data. Working on behalf of NHS England we therefore set out to deliver a secure and pseudonymised analytics platform inside the data centre of a major primary care electronic health records vendor establishing coverage across detailed primary care records for a substantial proportion of all patients in England. The following results are preliminary.\n\nData sourcesPrimary care electronic health records managed by the electronic health record vendor TPP, pseudonymously linked to patient-level data from the COVID-19 Patient Notification System (CPNS) for death of hospital inpatients with confirmed COVID-19, using the new OpenSAFELY platform.\n\nPopulation17,425,445 adults.\n\nTime period1st Feb 2020 to 25th April 2020.\n\nPrimary outcomeDeath in hospital among people with confirmed COVID-19.\n\nMethodsCohort study analysed by Cox-regression to generate hazard ratios: age and sex adjusted, and multiply adjusted for co-variates selected prospectively on the basis of clinical interest and prior findings.\n\nResultsThere were 5683 deaths attributed to COVID-19. In summary after full adjustment, death from COVID-19 was strongly associated with: being male (hazard ratio 1.99, 95%CI 1.88-2.10); older age and deprivation (both with a strong gradient); uncontrolled diabetes (HR 2.36 95% CI 2.18-2.56); severe asthma (HR 1.25 CI 1.08-1.44); and various other prior medical conditions. Compared to people with ethnicity recorded as white, black people were at higher risk of death, with only partial attenuation in hazard ratios from the fully adjusted model (age-sex adjusted HR 2.17 95% CI 1.84-2.57; fully adjusted HR 1.71 95% CI 1.44-2.02); with similar findings for Asian people (age-sex adjusted HR 1.95 95% CI 1.73-2.18; fully adjusted HR 1.62 95% CI 1.431.82).\n\nConclusionsWe have quantified a range of clinical risk factors for death from COVID-19, some of which were not previously well characterised, in the largest cohort study conducted by any country to date. People from Asian and black groups are at markedly increased risk of in-hospital death from COVID-19, and contrary to some prior speculation this is only partially attributable to pre-existing clinical risk factors or deprivation; further research into the drivers of this association is therefore urgently required. Deprivation is also a major risk factor with, again, little of the excess risk explained by co-morbidity or other risk factors. The findings for clinical risk factors are concordant with policies in the UK for protecting those at highest risk. Our OpenSAFELY platform is rapidly adding further NHS patients records; we will update and extend these results regularly.", + "rel_num_authors": 31, + "rel_authors": [ + { + "author_name": "- The OpenSAFELY Collaborative", + "author_inst": "" + }, + { + "author_name": "Elizabeth Williamson", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Alex J Walker", + "author_inst": "University of Oxford" + }, + { + "author_name": "Krishnan J Bhaskaran", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Seb Bacon", + "author_inst": "University of Oxford" + }, + { + "author_name": "Chris Bates", + "author_inst": "TPP" + }, + { + "author_name": "Caroline E Morton", + "author_inst": "University of Oxford" + }, + { + "author_name": "Helen J Curtis", + "author_inst": "University of Oxford" + }, + { + "author_name": "Amir Mehrkar", + "author_inst": "University of Oxford" + }, + { + "author_name": "David Evans", + "author_inst": "University of Oxford" + }, + { + "author_name": "Peter Inglesby", + "author_inst": "University of Oxford" + }, + { + "author_name": "Jonathan Cockburn", + "author_inst": "TPP" + }, + { + "author_name": "Helen I Mcdonald", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Brian MacKenna", + "author_inst": "University of Oxford" + }, + { + "author_name": "Laurie Tomlinson", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Ian J Douglas", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Christopher T Rentsch", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Rohini Mathur", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Angel Wong", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Richard Grieve", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "David Harrison", + "author_inst": "ICNARC" + }, + { + "author_name": "Harriet Forbes", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Anna Schultze", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Richard T Croker", + "author_inst": "University of Oxford" + }, + { + "author_name": "John Parry", + "author_inst": "TPP" + }, + { + "author_name": "Frank Hester", + "author_inst": "TPP" + }, + { + "author_name": "Sam Harper", + "author_inst": "TPP" + }, + { + "author_name": "Rafael Perera", + "author_inst": "University of Oxford" + }, + { + "author_name": "Stephen Evans", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Liam Smeeth", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Ben Goldacre", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.01.20053413", "rel_title": "Development of a Clinical Decision Support System for Severity Risk Prediction and Triage of COVID-19 Patients at Hospital Admission: an International Multicenter Study", @@ -1512714,69 +1511361,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.05.07.082487", - "rel_title": "COVID-19: Viral-host interactome analyzed by network based-approach model to study pathogenesis of SARS-CoV-2 infection.", - "rel_date": "2020-05-07", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.07.082487", - "rel_abs": "BackgroundEpidemiological, virological and pathogenetic characteristics of SARS-CoV-2 infection are under evaluation. A better understanding of the pathophysiology associated with COVID-19 is crucial to improve treatment modalities and to develop effective prevention strategies. Transcriptomic and proteomic data on the host response against SARS-CoV-2 still have anecdotic character; currently available data from other coronavirus infections are therefore a key source of information.\n\nMethodsWe investigated selected molecular aspects of three human coronavirus (HCoV) infections, namely SARS-CoV, MERS-CoV and HCoV-229E, through a network based-approach. A functional analysis of HCoV-host interactome was carried out in order to provide a theoretic host-pathogen interaction model for HCoV infections and in order to translate the results in prediction for SARS-CoV-2 pathogenesis.\n\nThe 3D model of S-glycoprotein of SARS-CoV-2 was compared to the structure of the corresponding SARS-CoV, HCoV-229E and MERS-CoV S-glycoprotein. SARS-CoV, MERS-CoV, HCoV-229E and the host interactome were inferred through published protein-protein interactions (PPI) as well as gene co-expression, triggered by HCoV S-glycoprotein in host cells.\n\nResultsAlthough the amino acid sequences of the S-glycoprotein were found to be different between the various HCoV, the structures showed high similarity, but the best 3D structural overlap shared by SARS-CoV and SARS-CoV-2, consistent with the shared ACE2 predicted receptor. The host interactome, linked to the S-glycoprotein of SARS-CoV and MERS-CoV, mainly highlighted innate immunity pathway components, such as Toll Like receptors, cytokines and chemokines.\n\nConclusionsIn this paper, we developed a network-based model with the aim to define molecular aspects of pathogenic phenotypes in HCoV infections. The resulting pattern may facilitate the process of structure-guided pharmaceutical and diagnostic research with the prospect to identify potential new biological targets.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Francesco Messina", - "author_inst": "National Instritute for Infectious Diseases \"L. Spallanzani\" - IRCCS" - }, - { - "author_name": "Emanuela Giombini", - "author_inst": "National Institute for Infectious Diseases \"Lazzaro Spallanzani\" IRCCS, Rome, Italy." - }, - { - "author_name": "Chiara Agrati", - "author_inst": "National Institute for Infectious Diseases \"Lazzaro Spallanzani\" IRCCS, Rome, Italy." - }, - { - "author_name": "Francesco Vairo", - "author_inst": "National Institute for Infectious Diseases \"Lazzaro Spallanzani\" IRCCS, Rome, Italy." - }, - { - "author_name": "Tommaso Ascoli Bartoli", - "author_inst": "National Institute for Infectious Diseases \"Lazzaro Spallanzani\" IRCCS, Rome, Italy." - }, - { - "author_name": "Samir Al Moghazi", - "author_inst": "National Institute for Infectious Diseases \"Lazzaro Spallanzani\" IRCCS, Rome, Italy." - }, - { - "author_name": "Mauro Piancentini", - "author_inst": "Department of Biology, University of Rome \"Tor Vergata,\" Rome, Italy." - }, - { - "author_name": "Markus Maeurer", - "author_inst": "Champalimaud Centre for the Unknown, Lisbon, Portugal; I. Medizinische Klinik Johannes Gutenberg-Universitat, University of Mainz, 55131 Mainz, Germany." - }, - { - "author_name": "Alimuddin Zumla", - "author_inst": "Department of Infection, Division of Infection and Immunity, University College London, and National Institutes of Health and Research Biomedical Research Centr" - }, - { - "author_name": "Maria R. Capobianchi", - "author_inst": "National Institute for Infectious Diseases \"Lazzaro Spallanzani\" IRCCS, Rome, Italy." - }, - { - "author_name": "Francesco Nicola Lauria", - "author_inst": "National Institute for Infectious Diseases \"Lazzaro Spallanzani\" IRCCS, Rome, Italy." - }, - { - "author_name": "Giuseppe Ippolito", - "author_inst": "National Institute for Infectious Diseases \"Lazzaro Spallanzani\" IRCCS, Rome, Italy." - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.05.07.082909", "rel_title": "The coding capacity of SARS-CoV-2", @@ -1513752,6 +1512336,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.01.20087809", + "rel_title": "Time-adjusted Analysis Shows Weak Associations Between BCG Vaccination Policy and COVID-19 Disease Progression", + "rel_date": "2020-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20087809", + "rel_abs": "In this study, we ascertain the associations between BCG vaccination policies and progression of COVID-19 through analysis of various time-adjusted indicators either directly extracted from the incidence and death reports, or estimated as parameters of disease progression models. We observe weak correlation between BCG vaccination status and indicators related to disease reproduction characteristics. We did not find any associations with case fatality rates (CFR), but the differences in CFR estimates are at present likely dominated by differences in testing and case reporting between countries.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Katarina Bodova", + "author_inst": "Comenius University in Bratislava" + }, + { + "author_name": "Vladimir Boza", + "author_inst": "Comenius University in Bratislava" + }, + { + "author_name": "Brona Brejova", + "author_inst": "Comenius University in Bratislava" + }, + { + "author_name": "Richard Kollar", + "author_inst": "Comenius University in Bratislava" + }, + { + "author_name": "Katarina Mikusova", + "author_inst": "Comenius University in Bratislava" + }, + { + "author_name": "Tomas Vinar", + "author_inst": "Comenius University in Bratislava" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.02.20088344", "rel_title": "A new role for Biofoundries in rapid prototyping, development, and validation of automated clinical diagnostic tests for SARS-CoV-2", @@ -1514148,117 +1512771,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.05.05.079202", - "rel_title": "Neutralization of SARS-CoV-2 by destruction of the prefusion Spike", - "rel_date": "2020-05-06", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.05.079202", - "rel_abs": "There are as yet no licenced therapeutics for the COVID-19 pandemic. The causal coronavirus (SARS-CoV-2) binds host cells via a trimeric Spike whose receptor binding domain (RBD) recognizes angiotensin-converting enzyme 2 (ACE2), initiating conformational changes that drive membrane fusion. We find that monoclonal antibody CR3022 binds the RBD tightly, neutralising SARS-CoV-2 and report the crystal structure at 2.4 [A] of the Fab/RBD complex. Some crystals are suitable for screening for entry-blocking inhibitors. The highly conserved, structure-stabilising, CR3022 epitope is inaccessible in the prefusion Spike, suggesting that CR3022 binding would facilitate conversion to the fusion-incompetent post-fusion state. Cryo-EM analysis confirms that incubation of Spike with CR3022 Fab leads to destruction of the prefusion trimer. Presentation of this cryptic epitope in an RBD-based vaccine might advantageously focus immune responses. Binders at this epitope may be useful therapeutically, possibly in synergy with an antibody blocking receptor attachment.\n\nHighlightsO_LICR3022 neutralises SARS-CoV-2\nC_LIO_LINeutralisation is by destroying the prefusion SPIKE conformation\nC_LIO_LIThis antibody may have therapeutic potential alone or with one blocking receptor attachment\nC_LI", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Jiandong Huo", - "author_inst": "University of Oxford and The Rosalind Franklin Institute" - }, - { - "author_name": "Yuguang Zhao", - "author_inst": "University of Oxford." - }, - { - "author_name": "Jingshan Ren", - "author_inst": "University of Oxford." - }, - { - "author_name": "Daming Zhou", - "author_inst": "University of Oxford." - }, - { - "author_name": "Helen M E Duyvesteyn", - "author_inst": "University of Oxford" - }, - { - "author_name": "Helen M Ginn", - "author_inst": "Diamond Light Source Ltd" - }, - { - "author_name": "Loic Carrique", - "author_inst": "University of Oxford" - }, - { - "author_name": "Tomas Malinauskas", - "author_inst": "University of Oxford" - }, - { - "author_name": "Reinis R Ruza", - "author_inst": "University of Oxford" - }, - { - "author_name": "Pranav NM Shah", - "author_inst": "University of Oxford" - }, - { - "author_name": "Tiong Kit Tan", - "author_inst": "University of Oxford" - }, - { - "author_name": "Pramila Rijal", - "author_inst": "University of Oxford" - }, - { - "author_name": "Naomi Coombes", - "author_inst": "Public Health England" - }, - { - "author_name": "Kevin Bewley", - "author_inst": "Public Health England" - }, - { - "author_name": "Julika Radecke", - "author_inst": "Diamond Light Source Ltd" - }, - { - "author_name": "Neil G Paterson", - "author_inst": "Diamond Light Source Ltd" - }, - { - "author_name": "Piyasa Supasa", - "author_inst": "University of Oxford" - }, - { - "author_name": "Juthathip Mongkolsapaya", - "author_inst": "University of Oxford and Mahidol University" - }, - { - "author_name": "Gavin R Screaton", - "author_inst": "University of Oxford" - }, - { - "author_name": "Miles Carroll", - "author_inst": "Public Health England and University of Oxford" - }, - { - "author_name": "Alain Townsend", - "author_inst": "University of Oxford" - }, - { - "author_name": "Elizabeth E Fry", - "author_inst": "University of Oxford" - }, - { - "author_name": "Raymond J Owens", - "author_inst": "University of Oxford and The Rosalind Franklin Institute" - }, - { - "author_name": "David I Stuart", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.05.06.079798", "rel_title": "Applying Lexical Link Analysis to DiscoverInsights from Public Information on COVID-19", @@ -1515166,6 +1513678,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.05.03.20089482", + "rel_title": "The importance of the timing of quarantine measures before symptom onset to prevent COVID-19 outbreaks - illustrated by Hong Kong's intervention model", + "rel_date": "2020-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.03.20089482", + "rel_abs": "BackgroundThe rapid expansion of the current COVID-19 outbreak has caused a global pandemic but how quarantine-based measures can prevent or suppress an outbreak without other more intrusive interventions has not yet been determined. Hong Kong had a massive influx of travellers from mainland China, where the outbreak began, during the early expansion period coinciding with the Lunar New Year festival; however, the spread of the virus has been relatively limited even without imposing severe control measures, such as a full city lockdown. Understanding how quarantine measures in Hong Kong were effective in limiting community spread can provide us with valuable insights into how to suppress an outbreak. However, challenges exist in evaluating the effects of quarantine on COVID-19 transmission dynamics in Hong Kong due to the fact that the effects of border control have to be also taken into account.\n\nMethodsWe have developed a two-layered susceptible-exposed-infectious-quarantined-recovered (SEIQR) meta-population model which can estimate the effects of quarantine on virus transmissibility after stratifying infections into imported and subsequent community infections, in a region closely connected to the outbreaks source. We fitted the model to both imported and local confirmed case data with symptom onset from 18 January to 29 February 2020 in Hong Kong, together with daily transportation data and the transmission dynamics of COVID-19 from Wuhan and mainland China. After model fitting, epidemiological parameters and the timing of the start of quarantine for infected cases were estimated.\n\nResultsThe model estimated that the reproduction number of COVID-19 in Hong Kong was 0.76 (95% CI, 0.66 to 0.86), achieved through quarantining infected cases -0.57 days (95% CI, -4.21 - 3.88) relative to symptom onset, with an estimated incubation time of 5.43 days (95% CI, 1.30 - 9.47). However, if delaying the quarantine start by more than 1.43 days, the reproduction number would be greater than one, making community spread more likely. The model also determined the timing of the start of quarantine necessary in order to suppress an outbreak in the presence of population immunity.\n\nConclusionThe results suggest that the early quarantine for infected cases before symptom onset is a key factor to prevent COVID-19 outbreak.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Hsiang-Yu Yuan", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Guiyuan Han", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Hsiangkuo Yuan", + "author_inst": "Thomas Jefferson University Hospital" + }, + { + "author_name": "Susanne Pfeiffer", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Axiu Mao", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Lindsey Wu", + "author_inst": "London School of Hygiene and Tropical Medicine" + }, + { + "author_name": "Dirk Pfeiffer", + "author_inst": "City University of Hong Kong" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.05.03.20089854", "rel_title": "A systematic review and meta-analysis of published research data on COVID-19 infection-fatality rates", @@ -1515742,25 +1514297,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.02.20084947", - "rel_title": "Voluntary Cyclical Distancing: A potential alternative to constant level mandatory social distancing, relying on an 'infection weather report'", - "rel_date": "2020-05-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.02.20084947", - "rel_abs": "1COVID-19 has significantly changed our daily lives. Stay-at-home orders and forced closings of all non-essential businesses has had a significant impact on our economy. While it is important to ensure that the healthcare system is not overwhelmed, there are many questions that remain about the efficacy of extreme social distancing, and whether there are alternatives to mandatory lockdowns. This paper analyzes the utility of various levels of social distancing, and suggests an alternative approach using voluntary distancing informed by an infectious load index or infection weather report.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Daniel Goldman", - "author_inst": "Promote.Health" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.30.20086934", "rel_title": "Effect of Alert Level 4 on effective reproduction number: review of international COVID-19 cases", @@ -1516708,6 +1515244,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.01.20087759", + "rel_title": "Effect of Temperature on the Transmission of COVID-19: A Machine Learning Case Study in Spain", + "rel_date": "2020-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20087759", + "rel_abs": "The novel coronavirus (COVID-19) has already spread to almost every country in the world and has infected over 3 million people. To understand the transmission mechanism of this highly contagious virus, it is necessary to study the potential factors, including meteorological conditions. Here, we present a machine learning approach to study the effect of temperature, humidity and wind speed on the number of infected people in the three most populous autonomous communities in Spain. We find that there is a moderate inverse correlation between temperature and the daily number of infections. This correlation manifests for temperatures recorded up to 6 days before the onset, which corresponds well to the known mean incubation period of COVID-19. We also show that the correlation for humidity and wind speed is not significant.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Amir Abdollahi", + "author_inst": "Universitat Politecnica de Catalunya" + }, + { + "author_name": "Maryam Rahbaralam", + "author_inst": "Barcelona Supercomputing Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.05.01.20087478", "rel_title": "Antibodies to SARS/CoV-2 in arbitrarily-selected Atlanta residents", @@ -1516952,25 +1515511,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.01.20087460", - "rel_title": "Prediction of Spreads of COVID-19 in India from Current Trend", - "rel_date": "2020-05-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20087460", - "rel_abs": "The article describe modelling efforts for evaluating the current level of COVID-19 infections in India, using exponential model. The Data from 15 march 2020 to 30 April 2020 are used for validating the model, where intrinsic rise rate is kept constant. It is observed that some states of India, like MAharastra, Gujarat and Delhi have a much higher daily infection cases. This is modelled by assuming an initial higher infections, keeping rise rate same. The sudden outbursts are captured using offset of values for these three states. Data from other states like Madhya Pradesh, Uttar Pradesh and Rajasthan are also analysed and they are found to be following the same constants as India is following. Worldwide, many attempts are made to predict outburst of COVID-19 and in the model, described in this paper, turning point is not predicted, as cases in India are still rising. The developed model is based on daily confirmed infections and not on cumulative infections and rationalization is carried out for the population of various regions, while predicting infections for various states. Assigning a decay constant at this stage will be a premature exercise and keeping that in mind, exponential model predicts that India will attain 1 lakh case by 15 May 2020. The figure of 2 lakh and 3 lakh will be attained on 22 May 2020 and 26 May 2020, respectively.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Himanshu Shekhar", - "author_inst": "O/o DG(ACE)" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.05.02.20087544", "rel_title": "Evaluating growth pattern and assessing future scenario of COVID-19 epidemic of India", @@ -1518214,6 +1516754,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2020.05.02.20088492", + "rel_title": "Simulations of the spread of COVID-19 and control policies in Tunisia", + "rel_date": "2020-05-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.02.20088492", + "rel_abs": "We develop and analyze in this work an epidemiological model for COVID-19 using Tunisian data. Our aims are first to evaluate Tunisian control policies for COVID-19 and secondly to understand the effect of different screening, quarantine and containment strategies and the rule of the asymptomatic patients on the spread of the virus in the Tunisian population. With this work, we show that Tunisian control policies are efficient in screening infected and asymptomatic individuals and that if containment and curfew are maintained the epidemic will be quickly contained.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Slimane Ben Miled", + "author_inst": "Institut Pasteur de Tunis, University of Tunis el Manar" + }, + { + "author_name": "Amira Kebir", + "author_inst": "Institut Pasteur de Tunis. University of Tunis el Manar" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.30.20084780", "rel_title": "COVID-19 length of hospital stay: a systematic review and data synthesis", @@ -1518498,37 +1517061,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.05.01.20084384", - "rel_title": "A Susceptible-Infected-Removed (SIR) model of COVID-19 epidemic trend in Malaysia under Movement Control Order (MCO) using a data fitting approach", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.05.01.20084384", - "rel_abs": "BackgroundIn this work, we presented a Susceptible-Infected-Removed (SIR) epidemiological model of COVID-19 epidemic in Malaysia post- and pre-Movement Control Order (MCO). The proposed SIR model was fitted to confirmed COVID-19 cases from the official press statements to closely reflect the observed epidemic trend in Malaysia. The proposed model is aimed to provide an accurate predictive information for decision makers in assessing the public health and social measures related to COVID-19 epidemic.\n\nMethodsThe SIR model was fitted to the data by minimizing a weighted loss function; the sum of the residual sum of squares (RSS) of infected, removed and total cases. Optimized beta ({beta}),), gamma ({gamma}) parameter values) parameter values and the starting value of susceptible individuals (N) were obtained.\n\nResultsThe SIR model post-MCO indicates the peak of infection on 10 April 2020, less than 100 active cases by 8 July 2020, less than 10 active cases by 29 August 2020, and close to zero daily new case by 22 July 2020, with a total of 6562 infected cases. In the absence of MCO, the model predicts the peak of infection on 1 May 2020, less than 100 active cases by 14 February 2021, less than 10 active cases by 26 April 2021 and close to zero daily new case by 6 October 2020, with a total of 1.6 million infected cases. Conclusion: The results suggest that the present MCO has significantly reduced the number of susceptible population and the total number of infected cases. The method to fit the SIR model used in this study was found to be accurate in reflecting the observed data. The method can be used to predict the epidemic trend of COVID-19 in other countries.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Wan Nor Arifin", - "author_inst": "Universiti Sains Malaysia" - }, - { - "author_name": "Weng Howe Chan", - "author_inst": "Universiti Teknologi Malaysia" - }, - { - "author_name": "Safiya Amaran", - "author_inst": "Universiti Sultan Zainal Abidin" - }, - { - "author_name": "Kamarul Imran Musa", - "author_inst": "Universiti Sains Malaysia" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "forensic medicine" - }, { "rel_doi": "10.1101/2020.04.30.20085290", "rel_title": "Group testing for SARS-CoV-2 allows for up to 10-fold efficiency increase across realistic scenarios and testing strategies", @@ -1519664,6 +1518196,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "cardiovascular medicine" }, + { + "rel_doi": "10.1101/2020.04.30.20086611", + "rel_title": "Mathematical Model with Social Distancing Parameter for Early Estimation of COVID-19 Spread", + "rel_date": "2020-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.30.20086611", + "rel_abs": "COVID-19 is well known to everyone in the world. It has spread around the world. No vaccine or antiviral treatment is available till now. COVID-19 patients are increasing day by day. All countries have adopted social distancing as a preventive measure to reduce spread. It becomes necessary to estimate the number of peoples going to be affected with COVID-19 in advance so that necessary arrangements can be done. Mathematical models are used to provide early disease estimation based on limited parameters. In the present manuscript, a novel mathematical model with a social distancing parameter has been proposed to provide early COVID-19 spread estimation. The model has been validated with real data set. It has been observed that the proposed model is more accurate in spread estimation.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Saroj Kumar Chandra", + "author_inst": "IIITDM, Jabalpur, India" + }, + { + "author_name": "Avaneesh Singh", + "author_inst": "IIITDMJ" + }, + { + "author_name": "Manish Kumar Bajpai", + "author_inst": "IIITDMJ" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.30.20086348", "rel_title": "Beyond predicting the number of infections: predicting who is likely to be COVID negative or positive", @@ -1520104,53 +1518663,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "transplantation" }, - { - "rel_doi": "10.1101/2020.04.30.20086447", - "rel_title": "Evaluation of effects of public health interventions on COVID-19 transmission for Pakistan: A mathematical simulation study", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.30.20086447", - "rel_abs": "BackgroundIn an effort to contain the COVID-19 epidemic, many governments across the world have enforced lockdown or social distancing measures. Several outbreak models have been developed to investigate the effects of different public health strategies for COVID-19, but they have not been developed for Pakistan and other South East Asian countries, where a large proportion of global population resides.\n\nMethodsWe developed a stochastic individual contact model by extending the widely-used Susceptible-Infectious-Recovered (SIR) compartment model with additional compartments to model both anticipated mitigating effects of public health intervention strategies for Pakistan. We estimated the projected spread, number of hospitalizations, and case fatalities under no intervention and four increasingly stringent public health strategies of social distancing and self-isolation at the national and provincial levels of Pakistan.\n\nResultsOur analysis shows that without any public health interventions the expected number of cumulative case fatalities is 671,596 in Pakistan with the virus is expected to peak in terms of the number of required ICU-hospitalizations at 198,593 persons by the end of the June 2020. The estimated total numbers of cumulative case fatalities are lower for other public health strategies with strict social distancing showing the lowest number of deaths at 1,588 (Self-isolation: n=341,359; Flexible social distancing strategy: n=3,995; and Exit strategy: n=28,214). The lowest number of required ICU-hospitalization is also estimated for strict social distancing strategy (n=266 persons at the end of May 2020). Generally, the simulated effects of the different public health strategies at the provincial-level were similar to the national-level with strict social distancing showing the fewest number of case fatalities and ICU-hospitalizations.\n\nConclusionOur results indicate that case fatalities and ICU-hospitalizations for Pakistan will be high without any public health interventions. While strict social distancing can potentially prevent a large number of deaths and ICU-hospitalizations, the government faces an important dilemma of potentially severe economic downfall. Consideration of a temporary strict social distancing strategy with gradual return of the lower-risk Pakistani population, as simulated in our exit strategy scenario, may an effective compromise between public health and economy of Pakistani population.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Zulfiqar A Bhutta", - "author_inst": "Aga Khan University" - }, - { - "author_name": "Ofir Harari", - "author_inst": "Cytel Inc" - }, - { - "author_name": "Jay JH Park", - "author_inst": "University of British Columbia" - }, - { - "author_name": "Noor Zannat", - "author_inst": "Cytel Inc" - }, - { - "author_name": "Michael Zoratti", - "author_inst": "McMaster University" - }, - { - "author_name": "Timothy Churches", - "author_inst": "South Western Sydney Clinical School, UNSW Medicine" - }, - { - "author_name": "Kristian Thorlund", - "author_inst": "Cytel Inc" - }, - { - "author_name": "Edward J Mills", - "author_inst": "Cytel Inc" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.04.30.20086553", "rel_title": "Social Media Platforms for Health Communication and Research in the Face of COVID-19 Pandemic: A Cross Sectional Survey in Uganda.", @@ -1520934,6 +1519446,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.05.04.075911", + "rel_title": "Global Spread of SARS-CoV-2 Subtype with Spike Protein Mutation D614G is Shaped by Human Genomic Variations that Regulate Expression of TMPRSS2 and MX1 Genes", + "rel_date": "2020-05-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.04.075911", + "rel_abs": "COVID-19 pandemic is a major human tragedy. Worldwide, SARS-CoV-2 has already infected over 3 million and has killed about 230,000 people. SARS-CoV-2 originated in China and, within three months, has evolved to an additional 10 subtypes. One particular subtype with a non-silent (Aspartate to Glycine) mutation at 614th position of the Spike protein (D614G) rapidly outcompeted other pre-existing subtypes, including the ancestral. We assessed that D614G mutation generates an additional serine protease (Elastase) cleavage site near the S1-S2 junction of the Spike protein. We also identified that a single nucleotide deletion (delC) at a known variant site (rs35074065) in a cis-eQTL of TMPRSS2, is extremely rare in East Asians but is common in Europeans and North Americans. The delC allele facilitates entry of the 614G subtype into host cells, thus accelerating the spread of 614G subtype in Europe and North America where the delC allele is common. The delC allele at the cis-eQTL locus rs35074065 of TMPRSS2 leads to overexpression of both TMPRSS2 and a nearby gene MX1. The cis-eQTL site, rs35074065 overlaps with a transcription factor binding site of an activator (IRF1) and a repressor (IRF2). IRF1 activator can bind to variant delC allele, but IRF2 repressor fails to bind. Thus, in an individual carrying the delC allele, there is only activation, but no repression. On viral entry, IRF1 mediated upregulation of MX1 leads to neutrophil infiltration and processing of 614G mutated Spike protein by neutrophil Elastase. The simultaneous processing of 614G spike protein by TMPRSS2 and Elastase serine proteases facilitates the entry of the 614G subtype into host cells. Thus, SARS-CoV-2, particularly the 614G subtype, has spread more easily and with higher frequency to Europe and North America where the delC allele regulating expression of TMPRSS2 and MX1 host proteins is common, but not to East Asia where this allele is rare.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Chandrika Bhattacharyya", + "author_inst": "National Institute of Biomedical Genomics, Kalyani, West Bengal, India" + }, + { + "author_name": "Chitrarpita Das", + "author_inst": "National Institute of Biomedical Genomics, Kalyani, West Bengal, India" + }, + { + "author_name": "Arnab Ghosh", + "author_inst": "National Institute of Biomedical Genomics, Kalyani, West Bengal, India" + }, + { + "author_name": "Animesh K Singh", + "author_inst": "National Institute of Biomedical Genomics, Kalyani, West Bengal, India" + }, + { + "author_name": "Souvik Mukherjee", + "author_inst": "National Institute of Biomedical Genomics, Kalyani, West Bengal, India" + }, + { + "author_name": "Partha P Majumder", + "author_inst": "National Institute of Biomedical Genomics, Kalyani, West Bengal, India" + }, + { + "author_name": "Analabha Basu", + "author_inst": "National Institute of Biomedical Genomics, Kalyani, West Bengal, India" + }, + { + "author_name": "Nidhan K Biswas", + "author_inst": "National Institute of Biomedical Genomics, Kalyani, West Bengal, India" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.05.04.077842", "rel_title": "SARS-CoV-2 Spike Glycoprotein Receptor Binding Domain is Subject to Negative Selection with Predicted Positive Selection Mutations", @@ -1521266,65 +1519825,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.30.20077594", - "rel_title": "Early transmission dynamics and control of COVID-19 in a southern hemisphere setting: Lima-Peru, February 29th-March 30th, 2020 .", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.30.20077594", - "rel_abs": "The COVID-19 pandemic that emerged in Wuhan China has generated substantial morbidity and mortality impact around the world during the last four months. The daily trend in reported cases has been rapidly rising in Latin America since March 2020 with the great majority of the cases reported in Brazil followed by Peru as of April 15th, 2020. Although Peru implemented a range of social distancing measures soon after the confirmation of its first case on March 6th, 2020, the daily number of new COVID-19 cases continues to accumulate in this country. We assessed the early COVID-19 transmission dynamics and the effect of social distancing interventions in Lima, Peru.\n\nWe estimated the reproduction number, R, during the early transmission phase in Lima from the daily series of imported and autochthonous cases by the date of symptoms onset as of March 30th, 2020. We also assessed the effect of social distancing interventions in Lima by generating short-term forecasts grounded on the early transmission dynamics before interventions were put in place.\n\nPrior to the implementation of the social distancing measures in Lima, the local incidence curve by the date of symptoms onset displays near exponential growth dynamics with the mean scaling of growth parameter, p, estimated at 0.9 (95%CI: 0.9,1.0) and the reproduction number at 2.3 (95% CI: 2.0, 2.5). Our analysis indicates that school closures and other social distancing interventions have helped slow down the spread of the novel coronavirus, with the nearly exponential growth trend shifting to an approximately linear growth trend soon after the broad scale social distancing interventions were put in place by the government.\n\nWhile the interventions appear to have slowed the transmission rate in Lima, the number of new COVID-19 cases continue to accumulate, highlighting the need to strengthen social distancing and active case finding efforts to mitigate disease transmission in the region.\n\nPeru COVID-19 working group\n\n\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@113464dorg.highwire.dtl.DTLVardef@6c8ba2org.highwire.dtl.DTLVardef@434c63org.highwire.dtl.DTLVardef@4c0821org.highwire.dtl.DTLVardef@1a9c01e_HPS_FORMAT_FIGEXP M_TBL C_TBL", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Cesar V. Munayco", - "author_inst": "Centro Nacional de Epidemiologia, Prevencion y Control de Enfermedades, Peruvian Ministry of Health, Lima, Peru" - }, - { - "author_name": "Amna Tariq", - "author_inst": "Georgia State University" - }, - { - "author_name": "Richard Rothenberg", - "author_inst": "Georgia State University" - }, - { - "author_name": "Gabriela G Soto-Cabezas", - "author_inst": "Centro Nacional de Epidemiologia, Prevencion y Control de Enfermedades, Peruvian Ministry of Health, Lima, Peru" - }, - { - "author_name": "Mary F. Reyes", - "author_inst": "Centro Nacional de Epidemiologia, Prevencion y Control de Enfermedades, Peruvian Ministry of Health, Lima, Peru" - }, - { - "author_name": "Andree Valle", - "author_inst": "Centro Nacional de Epidemiologia, Prevencion y Control de Enfermedades, Peruvian Ministry of Health, Lima, Peru" - }, - { - "author_name": "Leonardo Rojas-Mezarina", - "author_inst": "Instituto Nacional de Salud, Peruvian Ministry of Health, Lima, Peru" - }, - { - "author_name": "Cesar Cabezas", - "author_inst": "Instituto Nacional de Salud, Peruvian Ministry of Health, Lima, Peru" - }, - { - "author_name": "Manuel Loayza", - "author_inst": "Centro Nacional de Epidemiologia, Prevencion y Control de Enfermedades, Peruvian Ministry of Health, Lima, Peru." - }, - { - "author_name": "- COVID-19 Peru COVID-19 working group", - "author_inst": "" - }, - { - "author_name": "Gerardo Chowell", - "author_inst": "Georgia State University" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.30.20076703", "rel_title": "TEG Max Clot Strength is Consistently Elevated and May Be Predictive of COVID-19 Status at the Time of ICU Admission", @@ -1522512,6 +1521012,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "sexual and reproductive health" }, + { + "rel_doi": "10.1101/2020.04.28.20083261", + "rel_title": "A Simple Early Warning Signal for COVID-19", + "rel_date": "2020-05-05", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20083261", + "rel_abs": "The paper provides some initial evidence that daily mortality rates (for any cause) by municipality or province can be used as a statistically reliable predictor of looming COVID-19 crises. Using recently published deaths figures for 1,689 Italian municipalities, we estimate the growth in daily mortality rates between the period 2015-2019 and 2020 by province. All provinces that experienced a major COVID-19 shock in mid-March 2020 had increases in mortality rates of 100% or above already in early February 2020. This increase was particularly strong for males and older people, two recognizable features of COVID-19. Using a panel fixed effect model, we show that the association between these early increases in mortality for any cause and the March 2020 COVID-19 shock is strong and significant. We conclude that the growth in mortality rates can be used as a statistically reliable predictor of COVID-19 crises.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Lidia Ceriani", + "author_inst": "Georgetown University, USA" + }, + { + "author_name": "Carlos Hernandez-Suarez", + "author_inst": "Colima University, Mexico" + }, + { + "author_name": "Paolo Verme", + "author_inst": "World bank group" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health economics" + }, { "rel_doi": "10.1101/2020.05.01.20081026", "rel_title": "Sensitivity of nasopharyngeal swabs and saliva for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)", @@ -1523004,49 +1521531,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "pediatrics" }, - { - "rel_doi": "10.1101/2020.04.30.20083881", - "rel_title": "Associations between psychiatric disorders, COVID-19 testing probability and COVID-19 testing results: Findings from a population-based study", - "rel_date": "2020-05-05", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.30.20083881", - "rel_abs": "ObjectiveTo compare prevalence of COVID-19 testing and test outcomes among individuals with psychiatric disorders to those without such diagnoses, and to examine the associations of testing probability and outcome with psychiatric diagnosis categories.\n\nDesignLarge population-based study to perform association analyses of psychiatric disorder diagnoses with COVID-19 testing probability and such test results, by using two-sided Fisher exact tests and logistic regressions.\n\nSettingUK Biobank.\n\nParticipants1 474 men and women of British ancestry that had been tested for COVID-19, with a mean age of 58.2 years.\n\nMain outcome measuresCOVID-19 testing probability and COVID-19 test results.\n\nResultsIndividuals with psychiatric disorders were overrepresented among the 1 474 UKB participants with test data: 23% of the COVID-19 test sample had a psychiatric diagnosis compared to 10% in the full cohort (p<0.0001). This overrepresentation persisted for each of the specific psychiatric disorders tested. Furthermore, individuals with a psychiatric disorder (p=0.01), particularly with substance use disorder (p<0.005), had negative test results significantly more often than individuals without psychiatric disorders. Sensitivity analyses confirmed our results.\n\nConclusionsIn contrast with our hypotheses, UKB participants with psychiatric disorders have been tested for COVID-19 more frequently than individuals without a psychiatric history, pleading against the notion that limited health care access is preventing them from undergoing testing. Among those tested, test outcomes were more frequently negative for UKB participants with psychiatric disorders than in others, countering arguments that people with psychiatric disorders are particularly prone to contract the virus.\n\nSUMMARY BOXO_ST_ABSWhat is already known on this topic (2-3 sentences)C_ST_ABSWe searched PubMed using the terms \"COVID-19\" combined with \"mental health\", \"psychiatric disorder\" or \"mental illness\" for all articles published in any language before April 21st, 2020. Two hundred articles were retrieved, most of which related to the Chinese experience when dealing with the pandemic, including the mental health impact of the COVID-19 pandemic on general population mental health and healthcare workers; and on advancing mental healthcare resources in times of crisis. No evidence was found on testing patterns for severe acute respiratory syndromes (e.g. COVID-19, SARS, MERS) or Ebola virus on people with psychiatric disorders.\n\nWhat this study adds (2-3 sentences)We highlight a positive association between psychiatric disorders and the likelihood of being tested for COVID-19, as well as an association between psychiatric disorders and negative results. The results thus counter arguments that patients with psychiatric disorders are suffering from limited health care access preventing them from undergoing testing. Additionally, these are important findings as they carry the potential to reduce stigma: while people in the general population may be concerned that patients with psychiatric disorders do not comply with containment measures and are susceptible to contract COVID-19, our findings may help counter such concerns.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Dennis van der Meer", - "author_inst": "NORMENT, Division of Mental Health and Addiction, Oslo University Hospital & Institute of Clinical Medicine, University of Oslo, Oslo, Norway" - }, - { - "author_name": "Justo Emilio Pinzon-Espinosa", - "author_inst": "Department of Psychiatry and Psychology, Institute of Neuroscience, Hospital Clinic of Barcelona, Spain" - }, - { - "author_name": "Bochao Danae Lin", - "author_inst": "Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands" - }, - { - "author_name": "Joeri K. Tijdink", - "author_inst": "Department of Medical Humanities, Amsterdam University Medical Center, Amsterdam, the Netherlands" - }, - { - "author_name": "Christiaan H. Vinkers", - "author_inst": "Amsterdam University Medical Center" - }, - { - "author_name": "Sinan Guloksuz", - "author_inst": "Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, Maastricht University Medical Center, Maastricht, the Netherlands" - }, - { - "author_name": "Jurjen J. Luykx", - "author_inst": "Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.04.29.20084335", "rel_title": "News from the front: Excess mortality and life expectancy in two major epicentres of the COVID-19 pandemic in Italy", @@ -1524146,6 +1522630,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.04.28.20080838", + "rel_title": "COVID-19 Pandemic Response Simulation: Impact of Non-pharmaceutical Interventions on Ending Lockdowns", + "rel_date": "2020-05-04", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20080838", + "rel_abs": "As many federal and state governments are starting to ease restrictions on non-pharmaceutical interventions (NPIs) used to flatten the curve, we developed an agent-based simulation to model the incidence of COVID-19 in King County, WA under several scenarios. While NPIs were effective in flattening the curve, any relaxation of social distancing strategies yielded a second wave. Even if daily confirmed cases dropped to one digit, daily incidence can peak again to 874 cases without import cases. Therefore, policy makers should be very cautious in reopening society.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Serin Lee", + "author_inst": "University of Washington" + }, + { + "author_name": "Zelda B Zabinsky", + "author_inst": "University of Washington" + }, + { + "author_name": "Stephen M Kofsky", + "author_inst": "UW Healthcare Analytics Lab" + }, + { + "author_name": "Shan Liu", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.04.28.20081844", "rel_title": "Enzyme immunoassay for SARS-CoV-2 antibodies in dried blood spot samples: A minimally-invasive approach to facilitate community- and population-based screening", @@ -1524790,357 +1523305,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.05.02.043554", - "rel_title": "Catalytic cleavage of HEAT and subsequent covalent binding of the tetralone moiety by the SARS-CoV-2 main protease", - "rel_date": "2020-05-04", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.02.043554", - "rel_abs": "Here we present the crystal structure of SARS-CoV-2 main protease (Mpro) covalently bound to 2-methyl-1-tetralone. This complex was obtained by co-crystallization of Mpro with HEAT (2-(((4-hydroxyphenethyl)amino)methyl)-3,4-dihydronaphthalen-1(2H)-one) in the framework of a large X-ray crystallographic screening project of Mpro against a drug repurposing library, consisting of 5632 approved drugs or compounds in clinical phase trials. Further investigations showed that HEAT is cleaved by Mpro in an E1cB-like reaction mechanism into 2-methylene-1-tetralone and tyramine. The catalytic Cys145 subsequently binds covalently in a Michael addition to the methylene carbon atom of 2-methylene-1-tetralone. According to this postulated model HEAT is acting in a pro-drug-like fashion. It is metabolized by Mpro, followed by covalent binding of one metabolite to the active site. The structure of the covalent adduct elucidated in this study opens up a new path for developing non-peptidic inhibitors.", - "rel_num_authors": 84, - "rel_authors": [ - { - "author_name": "Sebastian G\u00fcnther", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany" - }, - { - "author_name": "Patrick Y. A. Reinke", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany" - }, - { - "author_name": "Dominik Oberthuer", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany" - }, - { - "author_name": "Oleksandr Yefanov", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany" - }, - { - "author_name": "Helen Ginn", - "author_inst": "Diamond Light Source Ltd. Diamond House, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK" - }, - { - "author_name": "Susanne Meier", - "author_inst": "Universitaet Hamburg, Institut fuer Nanostruktur- und Festkoerperphysik and Hamburg Centre for Ultrafast Imaging, Universitaet Hamburg, Luruper Chaussee 149, 22" - }, - { - "author_name": "Thomas J. Lane", - "author_inst": "Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA" - }, - { - "author_name": "Kristina Lorenzen", - "author_inst": "European XFEL GmbH. Holzkoppel 4, 22869 Schenefeld, Germany" - }, - { - "author_name": "Luca Gelisio", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany" - }, - { - "author_name": "Wolfgang Brehm", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany" - }, - { - "author_name": "Ilona Dunkel", - "author_inst": "Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany" - }, - { - "author_name": "Martin Domaracky", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany" - }, - { - "author_name": "Sofiane Saouane", - "author_inst": "Deutsches Elektronen Synchrotron (DESY), Photon Science, Notkestrasse 85, 22607, Hamburg, Germany" - }, - { - "author_name": "Julia Lieske", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany" - }, - { - "author_name": "Christiane Ehrt", - "author_inst": "Universitaet Hamburg, Center for Bioinformatics, Bundesstr. 43, 20146 Hamburg, Germany" - }, - { - "author_name": "Faisal Koua", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany" - }, - { - "author_name": "Alexandra Tolstikova", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany" - }, - { - "author_name": "Thomas A. White", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany" - }, - { - "author_name": "Michael Groessler", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany" - }, - { - "author_name": "Holger Fleckenstein", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany" - }, - { - "author_name": "Fabian Trost", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany" - }, - { - "author_name": "Marina Galchenkova", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany" - }, - { - "author_name": "Yaroslav Gevorkov", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg and Vision Systems, Hamburg University of Technology, 21071 Hamburg, Germany" - }, - { - "author_name": "Chufeng Li", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany" - }, - { - "author_name": "Salah Awel", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany" - }, - { - "author_name": "Ariana Peck", - "author_inst": "Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA" - }, - { - "author_name": "P. Lourdu Xavier", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg and Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee" - }, - { - "author_name": "Miriam Barthelmess", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany" - }, - { - "author_name": "Frank Schl\u00fcnzen", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany" - }, - { - "author_name": "Nadine Werner", - "author_inst": "Universitaet Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammati" - }, - { - "author_name": "Hina Andaleeb", - "author_inst": "Universitaet Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammati" - }, - { - "author_name": "Najeeb Ullah", - "author_inst": "Universitaet Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammati" - }, - { - "author_name": "Sven Falke", - "author_inst": "Universitaet Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammati" - }, - { - "author_name": "Bruno Alves Franca", - "author_inst": "Universitaet Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammati" - }, - { - "author_name": "Martin Schwinzer", - "author_inst": "Universitaet Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammati" - }, - { - "author_name": "Hevila Brognaro", - "author_inst": "Universitaet Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology and Laboratory for Structural Biology of Infection and Inflammati" - }, - { - "author_name": "Brandon Seychell", - "author_inst": "Universitaet Hamburg, Department of Chemistry, Institute of Physical Chemistry, Grindelallee 117, 20146 Hamburg, Germany" - }, - { - "author_name": "Henry Gieseler", - "author_inst": "Universitaet Hamburg, Institut fuer Nanostruktur- und Festkoerperphysik and Hamburg Centre for Ultrafast Imaging, Universitaet Hamburg, Luruper Chaussee 149, 22" - }, - { - "author_name": "Diogo Melo", - "author_inst": "Universitaet Hamburg, Institut fuer Nanostruktur- und Festkoerperphysik and Hamburg Centre for Ultrafast Imaging, Universitaet Hamburg, Luruper Chaussee 149, 22" - }, - { - "author_name": "Jo J. Zaitsev-Doyle", - "author_inst": "Universitaet Hamburg, Institut fuer Nanostruktur- und Festkoerperphysik and Hamburg Centre for Ultrafast Imaging, Universitaet Hamburg, Luruper Chaussee 149, 22" - }, - { - "author_name": "Brenna Norton-Baker", - "author_inst": "Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany" - }, - { - "author_name": "Juraj Knoska", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany" - }, - { - "author_name": "Gisel Esperanza", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany" - }, - { - "author_name": "Aida Rahmani Mashhour", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany" - }, - { - "author_name": "Filip Guicking", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany" - }, - { - "author_name": "Vincent Hennicke", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany" - }, - { - "author_name": "Pontus Fischer", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany" - }, - { - "author_name": "Cromarte Rogers", - "author_inst": "Universitaet Hamburg, Institut fuer Nanostruktur- und Festkoerperphysik, Luruper Chaussee 149, 22761 Hamburg, Germany" - }, - { - "author_name": "Diana C. F. Monteiro", - "author_inst": "Hauptmann Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY, 14203, USA" - }, - { - "author_name": "Johanna Hakanp\u00e4\u00e4", - "author_inst": "Deutsches Elektronen Synchrotron (DESY), Photon Science, Notkestrasse 85, 22607, Hamburg, Germany" - }, - { - "author_name": "Jan Meyer", - "author_inst": "Deutsches Elektronen Synchrotron (DESY), Photon Science, Notkestrasse 85, 22607, Hamburg, Germany" - }, - { - "author_name": "Heshmat Noei", - "author_inst": "Deutsches Elektronen Synchrotron (DESY), Photon Science, Notkestrasse 85, 22607, Hamburg, Germany" - }, - { - "author_name": "Phil Gribbon", - "author_inst": "Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), screening port, Schnackenburgallee 114, 22525 Hamburg, Germany" - }, - { - "author_name": "Bernhard Ellinger", - "author_inst": "Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), screening port, Schnackenburgallee 114, 22525 Hamburg, Germany" - }, - { - "author_name": "Maria Kuzikov", - "author_inst": "Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), screening port, Schnackenburgallee 114, 22525 Hamburg, Germany" - }, - { - "author_name": "Markus Wolf", - "author_inst": "Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), screening port, Schnackenburgallee 114, 22525 Hamburg, Germany" - }, - { - "author_name": "Linlin Zhang", - "author_inst": "Institute of Biochemistry, Center for Structural and Cell Biology in Medicine and German Center for Infection Research (DZIF), Hamburg-Luebeck-Borstel-Riems Sit" - }, - { - "author_name": "Xinyuanyuan Sun", - "author_inst": "Institute of Biochemistry, Center for Structural and Cell Biology in Medicine and German Center for Infection Research (DZIF), Hamburg-Luebeck-Borstel-Riems Sit" - }, - { - "author_name": "Jonathan Pletzer-Zelgert", - "author_inst": "Universitaet Hamburg, Center for Bioinformatics, Bundesstr. 43, 20146 Hamburg, Germany" - }, - { - "author_name": "Jan Wollenhaupt", - "author_inst": "Helmholtz Zentrum Berlin, Hahn-Meitner-Platz 1, 14109 Berlin, Germany" - }, - { - "author_name": "Christian Feiler", - "author_inst": "Helmholtz Zentrum Berlin, Hahn-Meitner-Platz 1, 14109 Berlin, Germany" - }, - { - "author_name": "Manfred Weiss", - "author_inst": "Helmholtz Zentrum Berlin, Hahn-Meitner-Platz 1, 14109 Berlin, Germany" - }, - { - "author_name": "Eike-Christian Schulz", - "author_inst": "Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany" - }, - { - "author_name": "Pedram Mehrabi", - "author_inst": "Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany" - }, - { - "author_name": "Christina Schmidt", - "author_inst": "European XFEL GmbH. Holzkoppel 4, 22869 Schenefeld, Germany" - }, - { - "author_name": "Robin Schubert", - "author_inst": "European XFEL GmbH. Holzkoppel 4, 22869 Schenefeld, Germany" - }, - { - "author_name": "Huijong Han", - "author_inst": "European XFEL GmbH. Holzkoppel 4, 22869 Schenefeld, Germany" - }, - { - "author_name": "Boris Krichel", - "author_inst": "Dynamics of Viral Structures, Heinrich-Pette-Institut, Leibniz-Institut f\u00fcr Experimentelle Virologie, Martinistrasse 52, 20251 Hamburg, Germany" - }, - { - "author_name": "Yaiza Fern\u00e1ndez-Garc\u00eda", - "author_inst": "Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Strasse 74, 20359 Hamburg, Germany" - }, - { - "author_name": "Beatriz Escudero-P\u00e9rez", - "author_inst": "Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Strasse 74, 20359 Hamburg, Germany" - }, - { - "author_name": "Stephan G\u00fcnther", - "author_inst": "Bernhard Nocht Institute for Tropical Medicine, Bernhard-Nocht-Strasse 74, 20359 Hamburg, Germany" - }, - { - "author_name": "Dusan Turk", - "author_inst": "Department of Biochemistry & Molecular & Structural Biology, Jozef Stefan Institute, Jamova 39, 1 000 Ljubljana, Slovenia" - }, - { - "author_name": "Charlotte Uetrecht", - "author_inst": "Dynamics of Viral Structures, Heinrich-Pette-Institut, Leibniz-Institut f\u00fcr Experimentelle Virologie, Martinistrasse 52, 20251 Hamburg, Germany" - }, - { - "author_name": "Tobias Beck", - "author_inst": "Universitaet Hamburg, Department of Chemistry, Institute of Physical Chemistry, Grindelallee 117, 20146 Hamburg and Hamburg Centre for Ultrafast Imaging, Univer" - }, - { - "author_name": "Henning Tidow", - "author_inst": "Universitaet Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology, Martin-Luther-King-Platz 6, 20146 Hamburg, and Hamburg Centre fo" - }, - { - "author_name": "Aschwin Chari", - "author_inst": "Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Goettingen, Germany" - }, - { - "author_name": "Andrea Zaliani", - "author_inst": "Fraunhofer Institute for Molecular Biology and Applied Ecology (IME), screening port, Schnackenburgallee 114, 22525 Hamburg, Germany" - }, - { - "author_name": "Matthias Rarey", - "author_inst": "Universitaet Hamburg, Center for Bioinformatics, Bundesstr. 43, 20146 Hamburg, Germany" - }, - { - "author_name": "Russel Cox", - "author_inst": "Institute for Organic Chemistry and BMWZ, Leibniz University of Hannover, Schneiderberg 38, 30167 Hannover, Germany" - }, - { - "author_name": "Rolf Hilgenfeld", - "author_inst": "German Center for Infection Research (DZIF), Hamburg-Luebeck-Borstel, Laboratory for Antiviral Chemotherapy, Institute of Chemistry & Metabolomics and Institute" - }, - { - "author_name": "Henry N Chapman", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg and Hamburg Centre for Ultrafast Imaging, Universitaet Hamburg, Luruper Chaussee 14" - }, - { - "author_name": "Arwen R. Pearson", - "author_inst": "Universitaet Hamburg, Institut fuer Nanostruktur- und Festkoerperphysik and Hamburg Centre for Ultrafast Imaging, Universitaet Hamburg, Luruper Chaussee 149, 22" - }, - { - "author_name": "Christian Betzel", - "author_inst": "Universitaet Hamburg, Department of Chemistry, Institute of Biochemistry and Molecular Biology, Martin-Luther-King-Platz 6, 20146 Hamburg, and Hamburg Centre fo" - }, - { - "author_name": "Alke Meents", - "author_inst": "Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "biophysics" - }, { "rel_doi": "10.1101/2020.05.03.074781", "rel_title": "Missense variants in ACE2 are predicted to encourage and inhibit interaction with SARS-CoV-2 Spike and contribute to genetic risk in COVID-19", @@ -1525912,6 +1524076,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.05.03.074930", + "rel_title": "Design of an Epitope-Based Peptide Vaccine against the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2): A Vaccine Informatics Approach", + "rel_date": "2020-05-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.05.03.074930", + "rel_abs": "The recurrent and recent global outbreak of SARS-CoV-2 has turned into a global concern which has infected more than 19-million people all over the globe, and this number is increasing in hours. Unfortunate no vaccine or specific treatment is available, which make it more deadly. A vaccine-informatics approach has shown significant breakthrough in peptide-based epitope mapping and opens the new horizon in vaccine development. In this study, we have identified a total of 15 antigenic peptides (including T and B cells) in the surface glycoprotein of SARS-CoV-2 which showed non-toxic nature, non-allergenic, highly antigenic and non-mutated in other SARS-CoV-2 virus strains. The population coverage analysis has found that CD4+ T-cell peptides showed higher cumulative population coverage over to CD8+ peptides in the 16 different geographical regions of the world. We identified twelve peptides (LTDEMIAQY, WTAGAAAYY, WMESEFRVY, IRASANLAA, FGAISSVLN, VKQLSSNFG, FAMQMAYRF, FGAGAALQI, YGFQPTNGVGYQ, LPDPSKPSKR, QTQTNSPRRARS and VITPGTNTSN) that are 80% - 90% identical with experimentally determined epitopes of SARS-CoV, and this will likely be beneficial for a quick progression of the vaccine design. Moreover, docking analysis suggested that identified peptides are tightly bound in the groove of HLA molecules which can induce the T-cell response. Overall this study allows us to determine potent peptide antigen targets in surface glycoprotein on intuitive grounds which open up a new horizon in COVID-19 research. However, this study needs experimental validation by in vitro and in vivo.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Aftab Alam", + "author_inst": "Center for Interdisciplinary Research in Basic Sciences, JMI University, New Delhi-110025." + }, + { + "author_name": "Arbaaz Khan", + "author_inst": "Department of Computer Science, Jamia Millia Islamia, New Delhi-110025" + }, + { + "author_name": "Nikhat Imam", + "author_inst": "Institute of Computer Science & Information Technology, Department of Mathematics, Magadh University, Bodh Gaya (Bihar, India)." + }, + { + "author_name": "Mohd Faizan Siddiqui", + "author_inst": "International Medical Faculty, Osh State University, Osh City, 723500, Kyrgyz Republic (Kyrgyzstan)" + }, + { + "author_name": "Mohd Waseem", + "author_inst": "School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India" + }, + { + "author_name": "Md. Zubbair Malik", + "author_inst": "Jawaharlal Nehru University" + }, + { + "author_name": "Romana Ishrat", + "author_inst": "Center for Interdisciplinary Research in Basic Sciences, JMI University, New Delhi-110025." + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.05.03.074567", "rel_title": "Large scale genomic analysis of 3067 SARS-CoV-2 genomes reveals a clonal geodistribution and a rich genetic variations of hotspots mutations", @@ -1526488,25 +1524695,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.04.27.20081539", - "rel_title": "An ARIMA Model to Forecast the Spread and the Final Size of COVID-2019 Epidemic in Italy", - "rel_date": "2020-05-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20081539", - "rel_abs": "Coronavirus disease (COVID-2019) is a severe ongoing novel pandemic that is spreading quickly across the world. Italy, that is widely considered one of the main epicenters of the pandemic, has registered the highest COVID-2019 death rates and death toll in the world, to the present day. In this article I estimate an autoregressive integrated moving average (ARIMA) model to forecast the epidemic trend over the period after April 4, 2020, by using the Italian epidemiological data at national and regional level. The data refer to the number of daily confirmed cases officially registered by the Italian Ministry of Health (www.salute.gov.it) for the period February 20 to April 4, 2020. The main advantage of this model is that it is easy to manage and fit. Moreover, it may give a first understanding of the basic trends, by suggesting the hypothetic epidemics inflection point and final size.\n\nHighlights ARIMA models allow in an easy way to investigate COVID-2019 trends, which are nowadays of huge economic and social impact.\nThese data may be used by the health authority to continuously monitor the epidemic and to better allocate the available resources.\nThe results suggest that the epidemic spread inflection point, in term of cumulative cases, will be reached at the end of May.\nFurther useful and more precise forecasting may be provided by updating these data or applying the model to other regions and countries.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Gaetano Perone", - "author_inst": "University of Bergamo" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.04.28.20081687", "rel_title": "Pre-test probability for SARS-Cov-2-related Infection Score: the PARIS score", @@ -1527930,6 +1526118,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.27.20082180", + "rel_title": "Hydroxychloroquine is associated with slower viral clearance in clinical COVID-19 patients with mild to moderate disease: A retrospective study", + "rel_date": "2020-05-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20082180", + "rel_abs": "BackgroundThere is conflicting data regarding the use of hydroxychloroquine (HCQ) in COVID-19 hospitalized patients\n\nObjectiveTo assess the efficacy of HCQ in increasing SARS-CoV-2 viral clearance\n\nDesignRetrospective observational study\n\nSettingCleveland Clinic Abu Dhabi\n\nParticipantsHospitalized adult patients with confirmed SARS-CoV-2 infection\n\nInterventionNone\n\nMeasurementsThe primary outcome was the time from a confirmed positive nasopharyngeal swab to turn negative. A negative nasopharyngeal swab conversion was defined as a confirmed SARS-CoV-2 case followed by two negative results using RT-PCR assay with samples obtained 24 hours apart\n\nResults34 confirmed COVID-19 patients were included. Nineteen (55.9%) patients presented with symptoms, and 14 (41.2%) had pneumonia. Only 21 (61.8%) patients received HCQ. The time to SARS-CoV-2 negativity nasopharyngeal test was significantly longer in patients who received HCQ compared to those who did not receive HCQ (17 [13-21] vs. 10 [4-13] days, p=0.023). HCQ was independently associated with time to negativity test after adjustment for potential confounders (symptoms, pneumonia or oxygen therapy) in multivariable linear regression analysis. On day 14, 47.8% (14/23) patients tested negative in the HCQ group compared to 90.9% (10/11) patients who did not receive HCQ (p=0.016).\n\nLimitationsSmall sample size and retrospective design with a potential risk of selection bias\n\nConclusionHCQ was associated with a slower viral clearance in COVID-19 patients with mild to moderate disease. Data from ongoing randomized clinical trials with HCQ should provide a definitive answer regarding the efficacy and safety of this treatment.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Jihad Mallat", + "author_inst": "Cleveland Clinic Abu Dhabi" + }, + { + "author_name": "Fadi Hamed", + "author_inst": "Cleveland Clinic Abu Dhabi" + }, + { + "author_name": "Maher Balkis", + "author_inst": "Cleveland Clinic Abu Dhabi" + }, + { + "author_name": "Mohamed A Mohamed", + "author_inst": "Cleveland Clinic Abu Dhabi" + }, + { + "author_name": "Mohamad Mooty", + "author_inst": "Cleveland Clinic Abu Dhabi" + }, + { + "author_name": "Asim Malik", + "author_inst": "Cleveland Clinic Abu Dhabi" + }, + { + "author_name": "Ahmad Nusair", + "author_inst": "Cleveland Clinic Abu Dhabi" + }, + { + "author_name": "Fernanda Bonilla", + "author_inst": "Cleveland Clinic Abu Dhabi" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.27.20082289", "rel_title": "Seroprevalence of antibodies against SARS-CoV-2 among health care workers in a large Spanish reference hospital", @@ -1528370,41 +1526605,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.27.20074849", - "rel_title": "Performance verification of detecting COVID-19 specific antibody by using four chemiluminescence immunoassay systems", - "rel_date": "2020-05-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20074849", - "rel_abs": "BackgroundThe purpose of current study is to evaluate the analytical performance of seven kits for detecting IgM/IgG antibody of corona virus (2019-nCoV) by using four chemiluminescence immunoassay systems.\n\nMethods50 patients diagnosed with 2019-nCoV infection and 130 controls without corona virus infection from the General Hospital of Chongqing were enrolled in current retrospective study. Four chemiluminescence immunoassay systems including seven IgM/IgG antibody detection Kits for 2019-nCoV (A_IgM, A_IgG, B_IgM, B_IgG, C_IgM, C_IgG, D_Ab) were employed to detecting antibody concentration. Chi-square test, receiver operating characteristic (ROC) curve and Youdens index were demonstrated to verify the cutoff value of each detection system.\n\nResultsThe repeatability verification results of the A, B, C, and D system are all qualified. D-Ab performances best (92% sensitivity and 99.23% specificity), and B_IgM worse than other systems. Except for the system of A_IgM and C_IgG, the optimal diagnostic thresholds and cutoff value of other kits from recommendations are inconsistent with each other. B_IgM got the worst AUC and C_IgG had the best diagnostic accuracy. More importantly, B_IgG system have the highest false positive rate for testing patients with AIDS, tumor and pregnant. A_IgM system test showed highest false positive rates among elder over 90 years old.\n\nConclusionsSystems for CoVID-2019 IgM/IgG antibody test performance difference. Serum diagnosis kit of D-Ab is the most reliable detecting system for 2019-nCoV antibody, which can be used as an alternative method for nucleic acid testing.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Yafang Wan", - "author_inst": "Chongqing General Hospital" - }, - { - "author_name": "Zhijie Li", - "author_inst": "The General Hospital of Chongqing" - }, - { - "author_name": "Kun Wang", - "author_inst": "The General Hospital of Chongqing" - }, - { - "author_name": "Tian Li", - "author_inst": "The General Hospital of Chongqing" - }, - { - "author_name": "Pu Liao", - "author_inst": "The General Hospital of Chongqing" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.05.01.071688", "rel_title": "Comprehensive characterization of N- and O- glycosylation of SARS-CoV-2 human receptor angiotensin converting enzyme 2.", @@ -1529496,6 +1527696,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.04.29.20084475", + "rel_title": "Reduced COVID-19-Related Critical Illness and Death, and High Risk of Epidemic Resurgence, After Physical Distancing in Ontario, Canada", + "rel_date": "2020-05-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.29.20084475", + "rel_abs": "BackgroundInsights from epidemiological models have helped to both guide and better understand COVID-19 mitigation policies that have been adopted across the globe. Many early models focussed on initial control options and were less reliant on fitting to observed data. As the pandemic progresses, models can be used to quantify the impact that control measures have had and what may unfold when such measures are relaxed.\n\nObjectiveTo explore the impact of physical distancing measures on COVID-19 transmission in the population of Ontario, Canada.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Ashleigh Tuite", + "author_inst": "University of Toronto" + }, + { + "author_name": "Amy L Greer", + "author_inst": "University of Guelph" + }, + { + "author_name": "Steven De Keninck", + "author_inst": "Matrix Factory bvba" + }, + { + "author_name": "David N Fisman", + "author_inst": "University of Toronto" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.29.20084863", "rel_title": "Inflammatory markers in Covid-19 Patients: a systematic review and meta-analysis.", @@ -1530032,45 +1528263,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, - { - "rel_doi": "10.1101/2020.04.26.20080341", - "rel_title": "How the COVID-19 pandemic is favoring the adoption of digital technologies in healthcare: a rapid literature review", - "rel_date": "2020-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20080341", - "rel_abs": "BackgroundHealthcare is responding to the COVID-19 pandemic through the fast adoption of digital solutions and advanced technology tools. The aim of this study is to describe which digital solutions have been reported in the scientific literature and to investigate their potential impact in the fight against the COVID-19 pandemic.\n\nMethodsWe conducted a literature review searching PubMed and MedrXiv with terms considered adequate to find relevant literature on the use of digital technologies in response to COVID-19. We developed an impact score to evaluate the potential impact on COVID-19 pandemic of all the digital solutions addressed in the selected papers.\n\nResultsThe search identified 269 articles, of which 145 full-text articles were assessed and 124 included in the review after screening and impact evaluation. Of selected articles, most of them addressed the use of digital technologies for diagnosis, surveillance and prevention. We report that digital solutions and innovative technologies have mainly been proposed for the diagnosis of COVID-19. In particular, within the reviewed articles we identified numerous suggestions on the use of artificial-intelligence-powered tools for the diagnosis and screening of COVID-19. Digital technologies are useful also for prevention and surveillance measures, for example through contact-tracing apps or monitoring of internet searches and social media usage.\n\nDiscussionIt is worth taking advantage of the push given by the crisis, and mandatory to keep track of the digital solutions proposed today to implement tomorrows best practices and models of care, and to be ready for any new moments of emergency.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Davide Golinelli", - "author_inst": "DIBINEM, University of Bologna" - }, - { - "author_name": "Erik Boetto", - "author_inst": "University of Bologna" - }, - { - "author_name": "Gherardo Carullo", - "author_inst": "Department of Italian and Supranational Public Law, University of Milan, Italy" - }, - { - "author_name": "Andrea Giovanni Nuzzolese", - "author_inst": "STLab, ISTC-CNR" - }, - { - "author_name": "Maria Paola Landini", - "author_inst": "IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy" - }, - { - "author_name": "Maria Pia Fantini", - "author_inst": "DIBINEM, University of Bologna" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.04.26.20080143", "rel_title": "Projection of hospitalization by COVID-19 in Brazilfollowing different social distances policies", @@ -1531258,6 +1529450,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.27.20075085", + "rel_title": "How urgent do intravitreal anti-VEGF injections need to be to justify the risk of transmitting COVID-19? Proof-of-concept calculations to determine the Health Adjusted Life-Year (HALY) trade-off.", + "rel_date": "2020-05-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20075085", + "rel_abs": "BackgroundClinical ophthalmological guidelines encourage the assessment of potential benefits and harms when deciding whether to perform elective ophthalmology procedures during the COVID-19 pandemic, in order to minimize the risk of disease transmission.\n\nMethodWe performed probability calculations to estimate COVID-19 infection status and likelihood of disease transmission among neovascular age-related macular degeneration patients and health care workers during anti-VEGF procedures, at various community prevalence levels of COVID-19. We then applied the expected burden of COVID-19 illness and death expressed through health-adjusted life-years (HALYs) lost. We compared these results to the expected disease burden of severe visual impairment if sight protecting anti-VEGF injections were not performed.\n\nResultsOur calculations suggest a wide range of contexts where the benefits of treatment to prevent progression to severe visual impairment or blindness are greater than the expected harms to the patient and immediate health care team due to COVID-19. For example, with appropriate protective equipment the benefits of treatment outweigh harms when the chance of progression to severe visual impairment is >0.044% for all scenarios where COVID-19 prevalence was one per thousand, even when the attack rate in the clinical setting is very high (5-43%).\n\nConclusionUnless COVID-19 prevalence is very high, the reduced disease burden from avoiding visual impairment outweighs the expected HALYs lost from COVID-19 transmission. This finding is driven by the fact that HALYs lost when someone suffers severe visual impairment for 5 years are equivalent to nearly 400 moderate cases of infectious disease lasting 2 weeks each.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Matt James Boyd", + "author_inst": "Adapt Research Ltd, Reefton, New Zealand" + }, + { + "author_name": "Daniel Andrew Richard Scott", + "author_inst": "Department of Ophthalmology, Gisborne Hospital, Hauora Tairawhiti, Gisborne, New Zealand" + }, + { + "author_name": "David Michael Squirrell", + "author_inst": "Department of Ophthalmology, Greenlane Clinical Centre, Auckland District Health Board, Auckland, New Zealand" + }, + { + "author_name": "Graham Ashley Wilson", + "author_inst": "Matai Lab, Gisborne, New Zealand" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "ophthalmology" + }, { "rel_doi": "10.1101/2020.04.28.20075119", "rel_title": "Cohort profile: Preliminary experience of 500 COVID-19 postive cases at a South West London District General Hospital.", @@ -1531594,117 +1529817,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.27.20076000", - "rel_title": "The effect of a national lockdown in response to COVID-19 pandemic on the prevalence of clinical symptoms in the population", - "rel_date": "2020-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.27.20076000", - "rel_abs": "The vast and rapid spread of COVID-19 calls for immediate action from policy-makers, and indeed, many countries have implemented lockdown measures to varying degrees. Here, we utilized nationwide surveys that assess COVID-19 associated symptoms to analyse the effect of the lockdown policy in Israel on the prevalence of clinical symptoms in the population. Daily symptom surveys were distributed online and included questions regarding fever, respiratory symptoms, gastrointestinal symptoms, anosmia and ageusia. A total of 2,071,349 survey responses were analysed. We defined a single measure of symptoms, Symptoms Average (SA), as the mean number of symptoms reported by responders. Data were collected between March 15th to June 3rd, 2020. Notably, on the population level, following severe lockdown measures between March 15 th and April 20th, SA sharply declined by 83.8% (p < 0.05), as did every single symptom, including the most common symptoms reported by our responders, cough and rhinorrhea and\\or nasal congestion, which decreased by 74.1% (p < 0.05) and 69.6% (p < 0.05), respectively. Similarly, on the individual level, analysis of repeated responses from the same individuals (N = 208,637) over time also showed a decrease in symptoms during this time period. Moreover, the reduction in symptoms was observed in all cities in Israel, and in several stratifications of demographic characteristics. Different symptoms exhibit different reduction dynamics, suggesting differences in the nature of the symptoms or in the underlying medical conditions. Between May 13th and June 3rd, following several subsequent lockdown relief measures, we observed an increase in individual symptoms and in SA, which increased by 31.42%. Overall, these results demonstrate a profound decrease in a variety of clinical symptoms following the implementation of a lockdown in Israel, and an increase in the prevalence of symptoms following the loosening of lockdown restrictions. As our survey symptoms are not specific to COVID-19 infection, this effect likely represents an overall nationwide reduction in the prevalence of infectious diseases, including COVID-19. This quantification may be of major interest for COVID-19 pandemic, as many countries consider implementation of lockdown strategies.", - "rel_num_authors": 24, - "rel_authors": [ - { - "author_name": "Ayya Keshet", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Amir Gavrieli", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Hagai Rossman", - "author_inst": "Weizmann institute of science" - }, - { - "author_name": "Smadar Shilo", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Tomer Meir", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Tal Karady", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Amit Lavon", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Dmitry Kolobkov", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Iris Kalka", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Saar Shoer", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Anastasia Godneva", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Ori Cohen", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Adam Kariv", - "author_inst": "The public knowledge workshop" - }, - { - "author_name": "Ori Hoch", - "author_inst": "The public knowledge workshop" - }, - { - "author_name": "Mushon Zer-Aviv", - "author_inst": "The public knowledge workshop" - }, - { - "author_name": "Noam Castel", - "author_inst": "The public knowledge workshop" - }, - { - "author_name": "Anat Ekka Zohar", - "author_inst": "Maccabi Healthcare Services" - }, - { - "author_name": "Angela Irony", - "author_inst": "Maccabi Healthcare Services" - }, - { - "author_name": "Benjamin Geiger", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Yuval Dor", - "author_inst": "Hebrew University of Jerusalem" - }, - { - "author_name": "Dorit Hizi", - "author_inst": "The public knowledge workshop" - }, - { - "author_name": "Ran Balicer", - "author_inst": "Clalit Health Services" - }, - { - "author_name": "Varda Shalev", - "author_inst": "Maccabi Healthcare Services" - }, - { - "author_name": "Eran Segal", - "author_inst": "Weizmann Institute of Science" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.26.20080788", "rel_title": "Accounting for super-spreading gives the basic reproduction number R0 of COVID-19 that is higher than initially estimated", @@ -1532600,6 +1530712,25 @@ "type": "new results", "category": "genetics" }, + { + "rel_doi": "10.1101/2020.04.26.20081109", + "rel_title": "Modeling Return of the Epidemic: Impact of Population Structure, Asymptomatic Infection, Case Importation and Personal Contacts", + "rel_date": "2020-05-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.26.20081109", + "rel_abs": "BackgroundProactive interventions have halted the pandemic of coronavirus infected disease in some regions. However, without reaching herd immunity, the return of epidemic is possible. We investigate the impact of population structure, case importation, asymptomatic cases, and the number of contacts on a possible second wave of epidemic through mathematical modelling.\n\nMethodswe built a modified Susceptible-exposed-Infectious-Removed (SEIR) model with parameters mirroring those of the COVID-19 pandemic and reported simulated characteristics of epidemics for incidence, hospitalizations and deaths under different scenarios.\n\nResultsA larger percent of elderly people leads to higher number of hospitalizations, while a large percent of prior infection will effectively curb the epidemic. The number of imported cases and the speed of importation have small impact on the epidemic progression. However, a higher percent of asymptomatic cases slows the epidemic down and reduces the number of hospitalizations and deaths at the epidemic peak. Finally, reducing the number of contacts among young people alone has moderate effects on themselves, but little effects on the elderly population. However, reducing the number of contacts among elderly people alone can mitigate the epidemic significantly in both age groups, even though young people remain active within themselves.\n\nConclusionReducing the number of contacts among high risk populations alone can mitigate the burden of epidemic in the whole society. Interventions targeting high risk groups may be more effective in containing or mitigating the epidemic.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Xinhua Yu", + "author_inst": "University of Memphis" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.27.20081281", "rel_title": "A fundamental model and predictions for the spread of the COVID-19 epidemic", @@ -1532884,29 +1531015,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.04.30.071175", - "rel_title": "Electrostatic Characteristics of SARS-CoV-2 Spike and Human ACE2 Protein Variations Predict Mutable Binding Efficacy", - "rel_date": "2020-05-01", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.30.071175", - "rel_abs": "SARS-CoV-2 is a novel virus that is presumed to have emerged from bats to crossover into humans in late 2019. As the global pandemic ensues, scientist are working to evaluate the virus and develop a vaccine to counteract the deadly disease that has impacted lives across the entire globe. We perform computational electrostatic simulations on multiple variants of SARS-CoV-2 spike protein s1 in complex with human angiotensin-converting enzyme 2 (ACE2) variants to examine differences in electrostatic interactions across the various complexes. Calculations are performed across the physiological pH range to also examine the impact of pH on these interactions. Two of six spike protein s1 variations having greater electric forces at pH levels consistent with nasal secretions and significant variations in force across all five variants of ACE2. Five out of six spike protein s1 variations have relatively consistent forces at pH levels of the lung, and one spike protein s1 variant that has low potential across a wide range of pH. These predictions indicate that variants of SARS-CoV-2 spike proteins and human ACE2 in certain combinations could potentially play a role in increased binding efficacy of SARS-CoV-2 in vivo.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Scott P Morton", - "author_inst": "Middle Tennessee State University" - }, - { - "author_name": "Joshua L Phillips", - "author_inst": "Middle Tennessee State University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "molecular biology" - }, { "rel_doi": "10.1101/2020.04.30.070383", "rel_title": "Dysregulation in mTOR/HIF-1 signaling identified by proteo-transcriptomics of SARS-CoV-2 infected cells", @@ -1534034,6 +1532142,85 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.28.20082552", + "rel_title": "Can Nebulised Heparin Reduce Time to Extubation in SARS CoV 2 The CHARTER Study Protocol", + "rel_date": "2020-05-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.28.20082552", + "rel_abs": "IntroductionCOVID-19 is associated with the development of ARDS displaying the typical features of diffuse alveolar damage with extensive pulmonary coagulation activation resulting in fibrin deposition in the microvasculature and formation of hyaline membranes in the air sacs. The anti-coagulant actions of nebulised heparin limit fibrin deposition and progression of lung injury. Serendipitously, unfractionated heparin also inactivates the SARS-CoV-2 virus and prevents its entry into mammalian cells. Nebulisation of heparin may therefore limit both fibrin-mediated lung injury and inhibit pulmonary infection by SARS-CoV-2. For these reasons we have initiated a multi-centre international trial of nebulised heparin in patients with COVID-19.\n\nMethods and interventionMechanically ventilated patients with confirmed or strongly suspected SARS-CoV-2 infection, hypoxaemia and an acute pulmonary opacity in at least one lung quadrant on chest X-ray, will be randomised to nebulised heparin 25,000 Units every 6 hours or standard care for up to 10 days while mechanically ventilated. The primary outcome is the time to separation from invasive ventilation to day 28, where non-survivors to day 28 are treated as though not separated from invasive ventilation.\n\nEthics and disseminationThe study protocol has been submitted to the human research and ethics committee of St Vincents Hospital, Melbourne, Australia. Submission is pending in other jurisdictions. Results of this study will be published in scientific journals and presented at scientific meetings.\n\nTrial RegistrationACTRN: 12620000517976", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Barry Dixon", + "author_inst": "St.Vincents Hospital Melbourne" + }, + { + "author_name": "Roger Smith", + "author_inst": "Department of Critical Care Medicine, St Vincents Hospital (Melbourne), Victoria, Australia." + }, + { + "author_name": "Antonio Artigas", + "author_inst": "Critical Care Center, Corporaco Sanitaria Universitaria Parc Tauli CIBER Enfermedades Respiratorias, Autonomous University of Barcelona, Sabadell, Spain" + }, + { + "author_name": "John Laffey", + "author_inst": "Centre for Medical Devices, National University of Ireland Galway; Department of Intensive Care Medicine, University Hospital, Galway, Ireland" + }, + { + "author_name": "Bairbre McNicholas", + "author_inst": "Centre for Medical Devices, National University of Ireland Galway; Department of Intensive Care Medicine, University Hospital, Galway, Ireland" + }, + { + "author_name": "Eric Schmidt", + "author_inst": "Department of Critical Care Medicine, Denver Medical Centre, University of Colorado, USA." + }, + { + "author_name": "Quentin Nunes", + "author_inst": "Department of Surgery, University of Liverpool, Aintree University Hospital, UK" + }, + { + "author_name": "Mark Andrew Skidmore", + "author_inst": "Molecular & Structural Biosciences, Keele University, Staffordshire, UK" + }, + { + "author_name": "Marcelo Andrade de Lome", + "author_inst": "Molecular & Structural Biosciences, Keele University, Staffordshire, UK" + }, + { + "author_name": "John Moran", + "author_inst": "Department of Intensive Care Medicine, The Queen Elizabeth Hospital, South Australia." + }, + { + "author_name": "Frank Van Haren", + "author_inst": "Department of Intensive Care Medicine, Canberra Hospital, Australia" + }, + { + "author_name": "Gordon Doig", + "author_inst": "Northern Clinical School Intensive Care Research Unit, University of Sydney, Australia" + }, + { + "author_name": "Sachin Gupta", + "author_inst": "Intensive Care Unit, Frankston Hospital, Melbourne, Australia" + }, + { + "author_name": "Angajendra Ghosh", + "author_inst": "Intensive Care Unit, The Northern Hospital, Melbourne, Australia" + }, + { + "author_name": "Simone Said", + "author_inst": "Intensive Care Unit, The Northern Hospital, Melbourne, Australia" + }, + { + "author_name": "John Santamaria", + "author_inst": "Department of Critical Care Medicine, St Vincents Hospital, Melbourne, Victoria, Australia." + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.04.28.20082859", "rel_title": "COVID-19 and Inflammatory Bowel Diseases: risk assessment, shared molecular pathways and therapeutic challenges", @@ -1534330,25 +1532517,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.24.20078717", - "rel_title": "Full lockdown policies in Western Europe countries have no evident impacts on the COVID-19 epidemic.", - "rel_date": "2020-05-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20078717", - "rel_abs": "This phenomenological study assesses the impacts of full lockdown strategies applied in Italy, France, Spain and United Kingdom, on the slowdown of the 2020 COVID-19 outbreak. Comparing the trajectory of the epidemic before and after the lockdown, we find no evidence of any discontinuity in the growth rate, doubling time, and reproduction number trends. Extrapolating pre-lockdown growth rate trends, we provide estimates of the death toll in the absence of any lockdown policies, and show that these strategies might not have saved any life in western Europe. We also show that neighboring countries applying less restrictive social distancing measures (as opposed to police-enforced home containment) experience a very similar time evolution of the epidemic.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Thomas A. J. Meunier", - "author_inst": "Woods Hole Oceanographic Institution" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.26.20074377", "rel_title": "A statistical forecast of LOW mortality (< 400,000 deaths) due to COVID-19, for the whole WORLD.", @@ -1535244,6 +1533412,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.20.20072942", + "rel_title": "Estimating COVID-19 Prevalence in the United States: A Sample Selection Model Approach", + "rel_date": "2020-04-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.20.20072942", + "rel_abs": "BackgroundPublic health efforts to determine population infection rates from coronavirus disease 2019 (COVID-19) have been hampered by limitations in testing capabilities and the large shares of mild and asymptomatic cases. We developed a methodology that corrects observed positive test rates for non-random sampling to estimate population infection rates across U.S. states from March 31 to April 7.\n\nMethodsWe adapted a sample selection model that corrects for non-random testing to estimate population infection rates. The methodology compares how the observed positive case rate vary with changes in the size of the tested population, and applies this gradient to infer total population infection rates. Model identification requires that variation in testing rates be uncorrelated with changes in underlying disease prevalence. To this end, we relied on data on day-to-day changes in completed tests across U.S. states for the period March 31 to April 7, which were primarily influenced by immediate supply-side constraints. We used this methodology to construct predicted infection rates across each state over the sample period. We also assessed the sensitivity of the results to controls for state-specific daily trends in infection rates.\n\nResultsThe median population infection rate over the period March 31 to April 7 was 0.9% (IQR 0.64 1.77). The three states with the highest prevalence over the sample period were New York (8.5%), New Jersey (7.6%), and Louisiana (6.7%). Estimates from mod-els that control for state-specific daily trends in infection rates were virtually identical to the baseline findings. The estimates imply a nationwide average of 12 population infections per diagnosed case. We found a negative bivariate relationship (corr. = -0.51) between total per capita state testing and the ratio of population infections per diagnosed case.\n\nInterpretationThe effectiveness of the public health response to the coronavirus pandemic will depend on timely information on infection rates across different regions. With increasingly available high frequency data on COVID-19 testing, our methodology could be used to estimate population infection rates for a range of countries and subnational districts. In the United States, we found widespread undiagnosed COVID-19 infection. Expansion of rapid diagnostic and serological testing will be critical in preventing recurrent unobserved community transmission and identifying the large numbers individuals who may have some level of viral immunity.\n\nFundingSocial Sciences and Humanities Research Council.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "David Benatia", + "author_inst": "CREST - ENSAE" + }, + { + "author_name": "Raphael Godefroy", + "author_inst": "University of Montreal" + }, + { + "author_name": "Joshua Lewis", + "author_inst": "University of Montreal" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.24.20073296", "rel_title": "Emergency Medical Services resource capacity and competency amid COVID-19 in the United States: Preliminary findings from a national survey", @@ -1535584,109 +1533779,6 @@ "type": "new results", "category": "evolutionary biology" }, - { - "rel_doi": "10.1101/2020.04.30.029736", - "rel_title": "Susceptibility of tree shrew to SARS-CoV-2 infection", - "rel_date": "2020-04-30", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.30.029736", - "rel_abs": "Since SARS-CoV-2 became a pandemic event in the world, it has not only caused huge economic losses, but also a serious threat to global public health. Many scientific questions about SARS-CoV-2 and COVID-19 were raised and urgently need to be answered, including the susceptibility of animals to SARS-CoV-2 infection. Here we tested whether tree shrew, an emerging experimental animal domesticated from wild animal, is susceptible to SARS-CoV-2 infection. No clinical signs were observed in SARS-CoV-2 inoculated tree shrews during this experiment except the increasing body temperature (above 39{degrees} C) particular in female animals during infection. Low levels of virus shedding and replication in tissues occurred in all three age groups, each of which showed his own characteristics. Histopathological examine revealed that pulmonary abnormalities were mild but the main changes although slight lesions were also observed in other tissues. In summary, tree shrew is not susceptible to SARS-CoV-2 infection and may not be a suitable animal for COVID-19 related researches.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Yuan Zhao", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Junbin Wang", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical Collegeof" - }, - { - "author_name": "Dexuan Kuang", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Jingwen Xu", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Mengli Yang", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Chunxia Ma", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Siwen Zhao", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Jingmei Li", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Haiting Long", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Kaiyun Ding", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Jiahong Gao", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Jiansheng Liu", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Haixuan Wang", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Haiyan Li", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Yun Yang", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Wenhai Yu", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Jing Yang", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Yinqiu Zheng", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Daoju Wu", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Shuaiyao Lu", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Hongqi Liu", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College" - }, - { - "author_name": "Xiaozhong Peng", - "author_inst": "Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.04.29.069476", "rel_title": "SARS-CoV-2 selectively mimics a cleavable peptide of human ENaC in a strategic hijack of host proteolytic machinery", @@ -1536682,6 +1534774,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.24.20078105", + "rel_title": "A Nationwide Survey of UK cardiac surgeons view on clinical decision making during the COVID-19 pandemic", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20078105", + "rel_abs": "BackgroundNo firm recommendations are currently available to guide decision making for patients requiring cardiac surgery during the COVID-19 pandemic. Systematic appraisal of national expert consensus can be used to generate interim recommendations until data from clinical observations will become available. Hence, we aimed to collect and quantitatively appraise nationwide UK senior surgeons opinion on clinical decision making for patients requiring cardiac surgery during the COVID-19 pandemic.\n\nMethodsWe mailed a web-based questionnaire to all consultant cardiac surgeons through the Society for Cardiothoracic Surgery in Great Britain and Ireland (SCTS) mailing list on the 17th April 2020 and we pre-determined to close the survey on the 21st April 2020. This survey was primarily designed to gather information on UK surgeons opinion using 12 items. Strong consensus was predefined as an opinion shared by at least 60% of responding consultants.\n\nResultsA total of 86 consultant surgeons undertook the survey. All UK cardiac units were represented by at least one consultant. Strong consensus was achieved for the following key questions:1) before hospital admission every patient should receive nasopharyngeal swab, PCR and chest CT; 2) the use of full PPE should to be adopted in every case by the theatre team regardless patients COVID-19 status; 3) the risk of COVID-19 exposure for patients undergoing heart surgery should be considered moderate to high and likely to increase mortality if it occurs; 4) cardiac procedure should be decided based on ad-hoc multidisciplinary team discussion for every patient. The majority believed that both aortic and mitral surgery should be considered in selected cases. The role of CABG surgery during the pandemic was more controversial.\n\nConclusionsIn the current unprecedented scenario, the present survey provides information for generating interim recommendations until data from clinical observations will become available.\n\nPerspective statementSystematic appraisal of national expert consensus can be used to generate interim recommendations for patients undergoing cardiac surgery during COVID-19 pandemic until data from clinical observations will become available.\n\nCentral messageNo firm recommendations are currently available to guide decision making for patients requiring cardiac surgery during the pandemic. This can translate into significant variability in clinical practice and patients outcomes across cardiac units. Systematic appraisal of national expert consensus can represent a rapid and efficient instrument to provide support to heath policy makers and other stakeholders in generating interim recommendations until data from clinical observations will become available.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Umberto Benedetto", + "author_inst": "Bristol Heart Institute, University Hospitals bristol NHS Foundation Trust" + }, + { + "author_name": "Andrew Goodwin", + "author_inst": "South Tees Hospitals NHS Trust" + }, + { + "author_name": "Simon Kendall", + "author_inst": "South Tees Hospitals NHS Trust" + }, + { + "author_name": "Rakesh Uppal", + "author_inst": "Barts Health NHS Turst" + }, + { + "author_name": "Enoch Akowuah", + "author_inst": "South Tees Hospitals NHS Trust" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "cardiovascular medicine" + }, { "rel_doi": "10.1101/2020.04.22.20075093", "rel_title": "COVID-19 containment policies through time may cost more lives at metapopulation level", @@ -1536914,33 +1535041,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.24.20078808", - "rel_title": "Reacting to outbreaks at neighboring localities", - "rel_date": "2020-04-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20078808", - "rel_abs": "We study the dynamics of epidemics in a networked metapopulation model. In each subpopulation, representing a locality, the disease propagates according to a modified susceptible-exposed-infected-recovered (SEIR) dynamics. In the modified SEIR dynamics, individuals reduce their number of contacts as a function of the weighted sum of cumulative number of cases within the locality and in neighboring localities. We consider a scenario with two localities where disease originates in one locality and is exported to the neighboring locality via travel of exposed (latently infected) individuals. We establish a lower bound on the outbreak size at the origin as a function of the speed of spread. Using the lower bound on the outbreak size at the origin, we establish an upper bound on the outbreak size at the importing locality as a function of the speed of spread and the level of preparedness for the low mobility regime. We evaluate the critical levels of preparedness that stop the disease from spreading at the importing locality. Finally, we show how the benefit of preparedness diminishes under high mobility rates. Our results highlight the importance of preparedness at localities where cases are beginning to rise such that localities can help stop local outbreaks when they respond to the severity of outbreaks in neighboring localities.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ceyhun Eksin", - "author_inst": "Texas A&M" - }, - { - "author_name": "Martial Ndeffo-Mbah", - "author_inst": "Texas A&M" - }, - { - "author_name": "Joshua S Weitz", - "author_inst": "Georgia Institute of Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.24.20078493", "rel_title": "Forecast analysis of the epidemics trend of COVID-19 in the United States by a generalized fractional-order SEIR model", @@ -1537728,6 +1535828,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.25.20079863", + "rel_title": "Interim Analysis of Pandemic Coronavirus Disease 2019 (COVID-19) and the SARS-CoV-2 virus in Latin America and the Caribbean: Morbidity, Mortality and Molecular Testing Trends in the Region", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.25.20079863", + "rel_abs": "BackgroundThe relentless advance of the SARS-CoV-2 virus pandemic has resulted in a significant burden on countries, regardless of their socio-economic conditions. The virus has infected more than 2.5 million people worldwide, causing to date more than 150,000 deaths in over 210 countries.\n\nObjectiveThe aim of this study was to describe the trends in cases, tests and deaths related to novel coronavirus disease (COVID-19) in Latin American and Caribbean (LAC) countries.\n\nMethodologyData were retrieved from the WHO-Coronavirus Disease (COVID-2019) situation reports and the Center for Systems Science and Engineering (CSSE) databases from Johns Hopkins University. Descriptive statistics including death rates, cumulative mortality and incidence rates, as well as testing rates per population at risk were performed. A comparison analysis among countries with [≥]50 confirmed cases was performed from February 26th, 2020 to April 8th, 2020.\n\nResultsBrazil had the greatest number of cases and deaths in the region. Panama experienced a rapid increase in the number of confirmed cases with Trinidad and Tobago, Bolivia and Honduras having the highest case fatality rates. Panama and Chile conducted more tests per million inhabitants and more tests per day per million inhabitants, followed by Uruguay and El Salvador. Dominican Republic, Bolivia, Ecuador and Brazil had the highest positive test rates.\n\nConclusionsThe COVID-19 disease pandemic caused by the SARS-CoV-2 virus has progressed rapidly in LAC countries. Some countries have been affected more severely than others, with some adopting similar disease control methods to help slow down the spread of the virus. With limited testing and other resources, social distancing is needed to help alleviate the strain on already stretched health systems.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Katherine Simbana-Rivera", + "author_inst": "OneHealth Global Research Group, Universidad de las Americas, Quito, Ecuador" + }, + { + "author_name": "Lenin Gomez-Barreno", + "author_inst": "OneHealth Global Research group, Universidad de las Americas, Quito, Ecuador" + }, + { + "author_name": "Jhon Guerrero", + "author_inst": "Scientific Association of Medical Students, Universidad Central del Ecuador, Quito, Ecuador" + }, + { + "author_name": "Fernanda Simbana-Guaycha", + "author_inst": "Scientific Association of Medical Students, Universidad Central del Ecuador, Quito, Ecuador" + }, + { + "author_name": "Raul Fernandez", + "author_inst": "One Health Global research group, Universidad de las Americas, Quito, Ecuador" + }, + { + "author_name": "Andres Lopez-Cortes Sr.", + "author_inst": "Universidad UTE" + }, + { + "author_name": "Alex Lister", + "author_inst": "University of Southampton, Southampton, United Kingdom." + }, + { + "author_name": "Esteban Ortiz-Prado", + "author_inst": "OneHealth Global Research Group, Universidad De Las Americas" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.04.25.20079640", "rel_title": "COVID-19 Outcomes in Saudi Arabia and the UK: A Tale of Two Kingdoms", @@ -1538372,45 +1536519,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.28.066977", - "rel_title": "Controlling the SARS-CoV-2 outbreak, insights from large scale whole genome sequences generated across the world", - "rel_date": "2020-04-29", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.28.066977", - "rel_abs": "BackgroundSARS-CoV-2 most likely evolved from a bat beta-coronavirus and started infecting humans in December 2019. Since then it has rapidly infected people around the world, with more than 4.5 million confirmed cases by the middle of May 2020. Early genome sequencing of the virus has enabled the development of molecular diagnostics and the commencement of therapy and vaccine development. The analysis of the early sequences showed relatively few evolutionary selection pressures. However, with the rapid worldwide expansion into diverse human populations, significant genetic variations are becoming increasingly likely. The current limitations on social movement between countries also offers the opportunity for these viral variants to become distinct strains with potential implications for diagnostics, therapies and vaccines.\n\nMethodsWe used the current sequencing archives (NCBI and GISAID) to investigate 15,487 whole genomes, looking for evidence of strain diversification and selective pressure.\n\nResultsWe used 6,294 SNPs to build a phylogenetic tree of SARS-CoV-2 diversity and noted strong evidence for the existence of two major clades and six sub-clades, unevenly distributed across the world. We also noted that convergent evolution has potentially occurred across several locations in the genome, showing selection pressures, including on the spike glycoprotein where we noted a potentially critical mutation that could affect its binding to the ACE2 receptor. We also report on mutations that could prevent current molecular diagnostics from detecting some of the sub-clades.\n\nConclusionThe worldwide whole genome sequencing effort is revealing the challenge of developing SARS-CoV-2 containment tools suitable for everyone and the need for data to be continually evaluated to ensure accuracy in outbreak estimations.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Jody Phelan", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Wouter Deelder", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Daniel Ward", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Susana Campino", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Martin L Hibberd", - "author_inst": "London School of Hygiene and Tropical Medicine" - }, - { - "author_name": "Taane G Clark", - "author_inst": "London School of Hygiene and Tropical Medicine" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.04.29.067983", "rel_title": "Evaluation of 19 antiviral drugs against SARS-CoV-2 Infection", @@ -1539314,6 +1537422,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, + { + "rel_doi": "10.1101/2020.04.25.20078311", + "rel_title": "Demographic and Socio-Economic Factors, and Healthcare Resource Indicators Associated with the Rapid Spread of COVID-19 in Northern Italy: An Ecological Study", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.25.20078311", + "rel_abs": "BackgroundCOVID-19 rapidly escalated into a pandemic, threatening 213 countries, areas, and territories the world over. We aimed to identify potential province-level socioeconomic determinants of the viruss dissemination, and explain between-province differences in the speed of its spread, based on data from 36 provinces of Northern Italy.\n\nMethodsThis is an ecological study. We included all confirmed cases of SARS-CoV-2 reported between February 24th and March 30th, 2020. For each province, we calculated the trend of contagion as the relative increase in the number of individuals infected between two time endpoints, assuming an exponential growth. Pearsons test was used to correlate the trend of contagion with a set of healthcare-associated, economic, and demographic parameters by province. The viruss spread was input as a dependent variable in a stepwise OLS regression model to test the association between rate of spread and province-level indicators.\n\nFindingsMultivariate analysis showed that the spread of COVID-19 was correlated negatively with aging index (p-value=0.003), and positively with public transportation per capita (p-value=0.012), the % of private long-term care hospital beds and, to a lesser extent (p-value=0.070), the % of private acute care hospital beds (p-value=0.006).\n\nInterpretationDemographic and socioeconomic factors, and healthcare organization variables were found associated with a significant difference in the rate of COVID-19 spread in 36 provinces of Northern Italy. An aging population seemed to naturally contain social contacts. The availability of healthcare resources and their coordination could play an important part in spreading infection.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Alessandra Buja", + "author_inst": "Department of Cardiologic, Vascular and Thoracic Sciences, and Public Health, University of Padova. Via Loredan, 18, 35131, Padova, Italy." + }, + { + "author_name": "Matteo Paganini", + "author_inst": "Department of Biomedical Sciences, University of Padova." + }, + { + "author_name": "Silvia Cocchio", + "author_inst": "Department of Cardiologic, Vascular and Thoracic Sciences, and Public Health, University of Padova. Via Loredan, 18, 35131, Padova, Italy." + }, + { + "author_name": "Manuela Scioni", + "author_inst": "Statistics Department, University of Padova. Via C. Battisti, 241, 35121, Padova, Italy." + }, + { + "author_name": "Vincenzo Rebba", + "author_inst": "'Marco Fanno' Department of Economics and Management, University of Padova. Via U. Bassi, 1, 35131, Padova, Italy." + }, + { + "author_name": "Vincenzo Baldo", + "author_inst": "Department of Cardiologic, Vascular and Thoracic Sciences, and Public Health, University of Padova. Via Loredan, 18, 35131, Padova, Italy." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.04.23.20077321", "rel_title": "COVID-19 Growth Rate Decreases with Social Capital", @@ -1539834,309 +1537981,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.25.20074856", - "rel_title": "Test performance evaluation of SARS-CoV-2 serological assays", - "rel_date": "2020-04-29", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.25.20074856", - "rel_abs": "BackgroundSerological tests are crucial tools for assessments of SARS-CoV-2 exposure, infection and potential immunity. Their appropriate use and interpretation require accurate assay performance data.\n\nMethodWe conducted an evaluation of 10 lateral flow assays (LFAs) and two ELISAs to detect anti-SARS-CoV-2 antibodies. The specimen set comprised 128 plasma or serum samples from 79 symptomatic SARS-CoV-2 RT-PCR-positive individuals; 108 pre-COVID-19 negative controls; and 52 recent samples from individuals who underwent respiratory viral testing but were not diagnosed with Coronavirus Disease 2019 (COVID-19). Samples were blinded and LFA results were interpreted by two independent readers, using a standardized intensity scoring system.\n\nResultsAmong specimens from SARS-CoV-2 RT-PCR-positive individuals, the percent seropositive increased with time interval, peaking at 81.8-100.0% in samples taken >20 days after symptom onset. Test specificity ranged from 84.3-100.0% in pre-COVID-19 specimens. Specificity was higher when weak LFA bands were considered negative, but this decreased sensitivity. IgM detection was more variable than IgG, and detection was highest when IgM and IgG results were combined. Agreement between ELISAs and LFAs ranged from 75.7-94.8%. No consistent cross-reactivity was observed.\n\nConclusionOur evaluation showed heterogeneous assay performance. Reader training is key to reliable LFA performance, and can be tailored for survey goals. Informed use of serology will require evaluations covering the full spectrum of SARS-CoV-2 infections, from asymptomatic and mild infection to severe disease, and later convalescence. Well-designed studies to elucidate the mechanisms and serological correlates of protective immunity will be crucial to guide rational clinical and public health policies.", - "rel_num_authors": 72, - "rel_authors": [ - { - "author_name": "Jeffrey D. Whitman", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Joseph Hiatt", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Cody T. Mowery", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Brian R. Shy", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Ruby Yu", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Tori N. Yamamoto", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Ujjwal Rathore", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Gregory M. Goldgof", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Caroline Whitty", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Jonathan M Woo", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Antonia E. Gallman", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Tyler E. Miller", - "author_inst": "Massachusetts General Hospital/Harvard Medical School" - }, - { - "author_name": "Andrew G. Levine", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "David N. Nguyen", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Sagar P. Bapat", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Joanna Balcerek", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Sophia Bylsma", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Ana M. Lyons", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Stacy Li", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Allison Wai-yi Wong", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Eva Mae Gillis-Buck", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Zachary B. Steinhart", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Youjin Lee", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Ryan Apathy", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Mitchell J. Lipke", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Jennifer A. Smith", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Tina Zheng", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Ian C. Boothby", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Erin Isaza", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Jackie Chan", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Dante D Acenas II", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Jinwoo Lee", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Trisha A. Macrae", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Than S. Kyaw", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "David Wu", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Dianna L. Ng", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Wei Gu", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Vanessa A. York", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Haig A. Eskandarian", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Perri C. Callaway", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Lakshmi Warrier", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Mary E. Moreno", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Justine Levan", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Leonel Torres", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Lila Farrington", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Rita Loudermilk", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Kanishka Koshal", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Kelsey C. Zorn", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Wilfredo F. Garcia-Beltran", - "author_inst": "Massachusetts General Hospital" - }, - { - "author_name": "Diane Yang", - "author_inst": "Massachusetts General Hospital/Harvard Medical School" - }, - { - "author_name": "Michael G. Astudillo", - "author_inst": "Massachusetts General Hospital/Harvard Medical School" - }, - { - "author_name": "Bradley E. Bernstein", - "author_inst": "Massachusetts General Hospital/Harvard Medical School" - }, - { - "author_name": "Jeffrey A. Gelfand", - "author_inst": "Massachusetts General Hospital/Harvard Medical School" - }, - { - "author_name": "Edward T. Ryan", - "author_inst": "Massachusetts General Hospital/Harvard Medical School" - }, - { - "author_name": "Richelle C. Charles", - "author_inst": "Massachusetts General Hospital/Harvard Medical School" - }, - { - "author_name": "A. John Iafrate", - "author_inst": "Massachusetts General Hospital/Harvard Medical School" - }, - { - "author_name": "Jochen K. Lennerz", - "author_inst": "Massachusetts General Hospital/Harvard Medical School" - }, - { - "author_name": "Steve Miller", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Charles Y Chiu", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Susan L. Stramer", - "author_inst": "American Red Cross" - }, - { - "author_name": "Michael R. Wilson", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Aashish Manglik", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Chun Jimmie Ye", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Nevan J. Krogan", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Mark S. Anderson", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Jason G. Cyster", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Joel D. Ernst", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Alan H.B. Wu", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Kara L. Lynch", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Caryn Bern", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Patrick D. Hsu", - "author_inst": "University of California, Berkeley" - }, - { - "author_name": "Alexander Marson", - "author_inst": "University of California, San Francisco" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.24.20074179", "rel_title": "Liver Chemistries in Patients with Severe or Non-Severe COVID-19: a Meta-Analysis", @@ -1540848,6 +1538692,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.23.20077297", + "rel_title": "Quantifying early COVID-19 outbreak transmission in South Africa and exploring vaccine efficacy scenarios", + "rel_date": "2020-04-29", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20077297", + "rel_abs": "BackgroundCOVID-19 has emerged and spread at great speed globally and has presented one of the greatest public health challenges in modern times with no proven cure or vaccine. Africa is still early in this epidemic, therefore the spectrum of disease severity is not yet clear.\n\nMethodsWe used a mathematical model to fit to the observed cases of COVID-19 in South Africa to estimate the basic reproductive number and critical vaccination coverages to control the disease for different hypothetical vaccine efficacy scenarios. We also estimated the percentage reduction in effective contacts due to the social distancing measures implemented.\n\nResultsEarly model estimates show that COVID-19 outbreak in South Africa had a basic re-productive number of 2.95 (95% credible interval [CrI] 2.83-3.33). A vaccine with 70% efficacy had the capacity to contain COVID-19 outbreak but at very higher vaccination coverage 94.44% (95% Crl 92.44-99.92%) with a vaccine of 100% efficacy requiring 66.10% (95% Crl 64.72-69.95%) coverage. Social distancing measures put in place have so far reduced the number of social contacts by 80.31% (95% Crl 79.76-80.85%).\n\nConclusionsFindings suggest a highly efficacious vaccine would have been required to contain COVID-19 in South Africa. Therefore, the current social distancing measures to reduce contacts will remain key in controlling the infection in the absence of vaccines and other therapeutics.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Zindoga Mukandavire", + "author_inst": "Coventry University" + }, + { + "author_name": "Farai Nyabadza", + "author_inst": "University of Johannesburg" + }, + { + "author_name": "Noble J Malunguza", + "author_inst": "National University of Science and Technology, Bulawayo, Zimbabwe" + }, + { + "author_name": "Diego F Cuadros", + "author_inst": "University of Cincinnati" + }, + { + "author_name": "Tinevimbo Shiri", + "author_inst": "Liverpool School of Tropical Medicine" + }, + { + "author_name": "Godfrey Musuka", + "author_inst": "ICAP at Columbia University, Harare, Zimbabwe" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.23.20077545", "rel_title": "Influence of socio-ecological factors on COVID-19 risk: a cross-sectional study based on 178 countries/regions worldwide", @@ -1541372,165 +1539255,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.04.22.20074351", - "rel_title": "Resilient SARS-CoV-2 diagnostics workflows including viral heat inactivation", - "rel_date": "2020-04-28", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.22.20074351", - "rel_abs": "There is a worldwide need for reagents to perform SARS-CoV-2 detection. Some laboratories have implemented kit-free protocols, but many others do not have the capacity to develop these and/or perform manual processing. We provide multiple workflows for SARS-CoV-2 nucleic acid detection in clinical samples by comparing several commercially available RNA extraction methods: QIAamp Viral RNA Mini Kit (QIAgen), RNAdvance Blood/Viral (Beckman) and Mag-Bind Viral DNA/RNA 96 Kit (Omega Bio-tek). We also compared One-step RT-qPCR reagents: TaqMan Fast Virus 1-Step Master Mix (FastVirus, ThermoFisher Scientific), qPCRBIO Probe 1-Step Go Lo-ROX (PCR Biosystems) and Luna(R) Universal Probe One-Step RT-qPCR Kit (Luna, NEB). We used primer-probes that detect viral N (EUA CDC) and RdRP (PHE guidelines). All RNA extraction methods provided similar results. FastVirus and Luna proved most sensitive. N detection was more reliable than that of RdRP, particularly in samples with low viral titres. Importantly, we demonstrate that treatment of nasopharyngeal swabs with 70 degrees for 10 or 30 min, or 90 degrees for 10 or 30 min (both original variant and B 1.1.7) inactivates SARS-CoV-2 employing plaque assays, and that it has minimal impact on the sensitivity of the qPCR in clinical samples. These findings make SARS-CoV-2 testing portable to settings that do not have CL-3 facilities. In summary, we provide several testing pipelines that can be easily implemented in other laboratories and have made all our protocols and SOPs freely available at https://osf.io/uebvj/.", - "rel_num_authors": 36, - "rel_authors": [ - { - "author_name": "Maria Jose Lista", - "author_inst": "King's College London" - }, - { - "author_name": "Pedro Matos", - "author_inst": "King's College London" - }, - { - "author_name": "Thomas J.A. Maguire", - "author_inst": "King's College London" - }, - { - "author_name": "Kate Poulton", - "author_inst": "King's College London" - }, - { - "author_name": "Elena Ortiz-Zapater", - "author_inst": "King's College London" - }, - { - "author_name": "Robert Page", - "author_inst": "King's College London" - }, - { - "author_name": "Helin Sertkaya", - "author_inst": "King's College London" - }, - { - "author_name": "Ana Maria Ortega-Prieto", - "author_inst": "King's College London" - }, - { - "author_name": "Aoife O'Byrne", - "author_inst": "King's College London" - }, - { - "author_name": "Clement Bouton", - "author_inst": "King's College London" - }, - { - "author_name": "Ruth E Dickenson", - "author_inst": "King's College London" - }, - { - "author_name": "Mattia Ficarelli", - "author_inst": "King's College London" - }, - { - "author_name": "Jose M Jimenez-Guardeno", - "author_inst": "King's College London" - }, - { - "author_name": "Mark Howard", - "author_inst": "King's College London" - }, - { - "author_name": "Gilberto Betancor", - "author_inst": "King's College London" - }, - { - "author_name": "Rui Pedro Galao", - "author_inst": "King's College London" - }, - { - "author_name": "Suzanne Pickering", - "author_inst": "King's College London" - }, - { - "author_name": "Adrian W Signell", - "author_inst": "King's College London" - }, - { - "author_name": "Harry Wilson", - "author_inst": "King's College London" - }, - { - "author_name": "Penny Cliff", - "author_inst": "Viapath St Thomas'" - }, - { - "author_name": "Mark Tan Kia Ik", - "author_inst": "St Thomas' Hospital" - }, - { - "author_name": "Amita Patel", - "author_inst": "St Thomas' Hospital" - }, - { - "author_name": "Eithne MacMahon", - "author_inst": "St Thomas' Hospital" - }, - { - "author_name": "Emma Cunningham", - "author_inst": "St Thomas' Hospital" - }, - { - "author_name": "Katie Doores", - "author_inst": "King's College London" - }, - { - "author_name": "Monica Agromayor", - "author_inst": "King's College London" - }, - { - "author_name": "Juan Martin-Serrano", - "author_inst": "King's College London" - }, - { - "author_name": "Esperanza Perucha", - "author_inst": "King's College London" - }, - { - "author_name": "Hannah E Mischo", - "author_inst": "King's College London" - }, - { - "author_name": "Manu Shankar-Hari", - "author_inst": "King's College London" - }, - { - "author_name": "Rahul Batra", - "author_inst": "St Thomas' Hospital" - }, - { - "author_name": "Jonathan Edgeworth", - "author_inst": "St Thomas' Hospital" - }, - { - "author_name": "Mark Zuckerman", - "author_inst": "King's College Hospital" - }, - { - "author_name": "Michael H Malim", - "author_inst": "King's College London" - }, - { - "author_name": "Stuart Neil", - "author_inst": "King's College London" - }, - { - "author_name": "Rocio Teresa Martinez-Nunez", - "author_inst": "King's College London" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.24.20072611", "rel_title": "Clinical course and risk factors for mortality of COVID-19 patients with pre-existing cirrhosis: A multicenter cohort study", @@ -1542618,6 +1540342,49 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.24.20075838", + "rel_title": "Vitamin D Insufficiency is Prevalent in Severe COVID-19", + "rel_date": "2020-04-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.24.20075838", + "rel_abs": "BackgroundCOVID-19 is a major pandemic that has killed more than 196,000 people. The COVID-19 disease course is strikingly divergent. Approximately 80-85% of patients experience mild or no symptoms, while the remainder develop severe disease. The mechanisms underlying these divergent outcomes are unclear. Emerging health disparities data regarding African American and homeless populations suggest that vitamin D insufficiency (VDI) may be an underlying driver of COVID-19 severity. To better define the VDI-COVID-19 link, we determined the prevalence of VDI among our COVID-19 intensive care unit (ICU) patients.\n\nMethodsIn an Institutional Review Board approved study performed at a single, tertiary care academic medical center, the medical records of COVID-19 patients were retrospectively reviewed. Subjects were included for whom serum 25-hydroxycholecalcifoerol (25OHD) levels were determined. COVID-19-relevant data were compiled and analyzed. We determined the frequency of VDI among COVID-19 patients to evaluate the likelihood of a VDI-COVID-19 relationship.\n\nResultsTwenty COVID-19 patients with serum 25OHD levels were identified; 65.0% required ICU admission.The VDI prevalence in ICU patients was 84.6%, vs. 57.1% in floor patients. Strikingly, 100% of ICU patients less than 75 years old had VDI. Coagulopathy was present in 62.5% of ICU COVID-19 patients, and 92.3% were lymphocytopenic.\n\nConclusionsVDI is highly prevalent in severe COVID-19 patients. VDI and severe COVID-19 share numerous associations including hypertension, obesity, male sex, advanced age, concentration in northern climates, coagulopathy, and immune dysfunction. Thus, we suggest that prospective, randomized controlled studies of VDI in COVID-19 patients are warranted.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Frank H. Lau", + "author_inst": "Louisiana State Univ. Health Sciences Center New Orleans" + }, + { + "author_name": "Rinku Majumder", + "author_inst": "Louisiana State University Health Sciences Center New Orleans" + }, + { + "author_name": "Radbeh Torabi", + "author_inst": "Louisiana State University Health Sciences Center New Orleans" + }, + { + "author_name": "Fouad Saeg", + "author_inst": "Tulane University School of Medicine" + }, + { + "author_name": "Ryan Hoffman", + "author_inst": "Louisiana State University Health Sciences Center New Orleans" + }, + { + "author_name": "Jeffrey D. Cirillo", + "author_inst": "Texas A&M College of Medicine" + }, + { + "author_name": "Patrick Greiffenstein", + "author_inst": "Louisiana State University Health Sciences Center New Orleans" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.23.20076851", "rel_title": "Heparin-induced thrombocytopenia is associated with a high risk of mortality in critical COVID-19 patients receiving heparin-involved treatment", @@ -1543066,65 +1540833,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.04.27.064139", - "rel_title": "A Modular Framework for Multiscale Spatial Modeling of Viral Infection and Immune Response in Epithelial Tissue", - "rel_date": "2020-04-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.27.064139", - "rel_abs": "Simulations of tissue-specific effects of primary acute viral infections like COVID-19 are essential for understanding disease outcomes and optimizing therapies. Such simulations need to support continuous updating in response to rapid advances in understanding of infection mechanisms, and parallel development of components by multiple groups. We present an open-source platform for multiscale spatiotemporal simulation of an epithelial tissue, viral infection, cellular immune response and tissue damage, specifically designed to be modular and extensible to support continuous updating and parallel development. The base simulation of a simplified patch of epithelial tissue and immune response exhibits distinct patterns of infection dynamics from widespread infection, to recurrence, to clearance. Slower viral internalization and faster immune-cell recruitment slow infection and promote containment. Because antiviral drugs can have side effects and show reduced clinical effectiveness when given later during infection, we studied the effects on progression of treatment potency and time-of-first treatment after infection. In simulations, even a low potency therapy with a drug which reduces the replication rate of viral RNA greatly decreases the total tissue damage and virus burden when given near the beginning of infection. Many combinations of dosage and treatment time lead to stochastic outcomes, with some simulation replicas showing clearance or control (treatment success), while others show rapid infection of all epithelial cells (treatment failure). Thus, while a high potency therapy usually is less effective when given later, treatments at late times are occasionally effective. We illustrate how to extend the platform to model specific virus types (e.g., hepatitis C) and add additional cellular mechanisms (tissue recovery and variable cell susceptibility to infection), using our software modules and publicly-available software repository.\n\nAuthor summaryThis study presents an open-source, extensible, multiscale platform for simulating viral immune interactions in epithelial tissues, which enables the rapid development and deployment of sophisticated models of viruses, infection mechanisms and tissue types. The model is used to investigate how potential treatments influence disease progression. Simulation results suggest that drugs which interfere with virus replication (e.g., remdesivir) yield substantially better infection outcomes when administered prophylactically even at very low doses than when used at high doses as treatment for an infection that has already begun.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "T.J. Sego", - "author_inst": "Indiana University" - }, - { - "author_name": "Josua O. Aponte-Serrano", - "author_inst": "Indiana University" - }, - { - "author_name": "Juliano Ferrari Gianlupi", - "author_inst": "Indiana University" - }, - { - "author_name": "Samuel Heaps", - "author_inst": "Indiana University" - }, - { - "author_name": "Kira Breithaupt", - "author_inst": "Cognitive Science Program, Indiana University, Bloomington, IN" - }, - { - "author_name": "Lutz Brusch", - "author_inst": "Center for Information Services and High Performance Computing (ZIH), Technische Universitat Dresden" - }, - { - "author_name": "Jessica Crawshaw", - "author_inst": "School of Mathematics and Statistics, University of Melbourne" - }, - { - "author_name": "James M. Osborne", - "author_inst": "School of Mathematics and Statistics, University of Melbourne" - }, - { - "author_name": "Ellen M. Quardokus", - "author_inst": "Indiana University" - }, - { - "author_name": "Richard K. Plemper", - "author_inst": "Institute for Biomedical Sciences, Georgia State University" - }, - { - "author_name": "James A. Glazier", - "author_inst": "Indiana University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "bioengineering" - }, { "rel_doi": "10.1101/2020.04.28.065201", "rel_title": "RNA-GPS Predicts SARS-CoV-2 RNA Localization to Host Mitochondria and Nucleolus", @@ -1544132,6 +1541840,37 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.04.19.20070722", + "rel_title": "Between-centre differences for COVID-19 ICU mortality from early data in England", + "rel_date": "2020-04-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.19.20070722", + "rel_abs": "The high numbers of COVID-19 patients developing severe respiratory failure has placed exceptional demands on ICU capacity around the world. Understanding the determinants of ICU mortality is important for surge planning and shared decision making. We used early data from the COVID-19 Hospitalisation in England Surveillance System (from the start of data collection 8th February -22nd May 2020) to look for factors associated with ICU outcome in the hope that information from such timely analysis may be actionable before the outbreak peak. Immunosuppressive disease, chronic cardiorespiratory/renal disease and age were key determinants of ICU mortality in a proportional hazards mixed effects model. However variation in site-stratified random effects were comparable in magnitude suggesting substantial between-centre variability in mortality. Notwithstanding possible ascertainment and lead-time effects, these early results motivate comparative effectiveness research to understand the origin of such differences and optimise surge ICU provision.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Zhaozhi Qian", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Ahmed M Alaa", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Mihaela van der Schaar", + "author_inst": "University of Cambridge" + }, + { + "author_name": "Ari Ercole", + "author_inst": "University of Cambridge" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.04.24.20074559", "rel_title": "Comparison of Commercially Available and Laboratory Developed Assays for in vitro Detection of SARS-CoV-2 in Clinical Laboratories", @@ -1544468,49 +1542207,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.22.20075762", - "rel_title": "Proactive social distancing mitigates COVID-19 outbreaks within a month across 58 mainland China cities", - "rel_date": "2020-04-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.22.20075762", - "rel_abs": "In early 2020, cities across China enacted strict social distancing measures to contain emerging coronavirus (COVID-19) outbreaks. We estimated the speed with which these measures contained community transmission in each of 58 Chinese cities. On average, containment was achieved 7.83 days (SD 6.79 days) after the implementation of social distancing interventions, with an average reduction in the reproduction number (Rt) of 54.3% (SD 17.6%) over that time period. A single day delay in the implementation of social distancing led to a 2.41 (95% CI: 0.97, 3.86) day delay in containment. Swift social distancing interventions may thus achieve rapid containment of newly emerging COVID-19 outbreaks.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Zhanwei Du", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "xiaoke Xu", - "author_inst": "Dalian Minzu university" - }, - { - "author_name": "Lin Wang", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Spencer J. Fox", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "Benjamin J Cowling", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Alison P. Galvani", - "author_inst": "Yale School of Public Health" - }, - { - "author_name": "Lauren Ancel Meyers", - "author_inst": "The University of Texas at Austin" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.22.20071258", "rel_title": "Long period dynamics of viral load and antibodies for SARS-CoV-2 infection: an observational cohort study", @@ -1545246,6 +1542942,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.21.20073791", + "rel_title": "Understanding the asymmetric spread and case fatality rate (CFR) for COVID-19 among countries", + "rel_date": "2020-04-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20073791", + "rel_abs": "The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections are rising rapidly every day in the world, causing the disease COVID-19 with around 2 million people infected and more than 100,000 people died so far, in more than 200 countries. One of the baffling aspects of this pandemic is the asymmetric increase in cases and case fatality rate (CFR) among countries. We analyze the time series of the infection and fatality numbers and found two interesting aspects. Firstly, the rate of spread in a region is directly connected to the population density of the region where the virus is spreading. For example, the high rate of increase in cases in the United States of America (USA) is related to the high population density of New York City. This is shown by scaling the cumulative number of cases with a measure of the population density of the affected region in countries such as Italy, Spain, Germany, and the USA and we see that the curves are coinciding. Secondly, we analyzed the CFR number as a function of the number of days, since the first death, and we found that there are two clear categories among countries: one category with high CFR numbers (around 10%) and the other category with low CFR numbers (2% to 4%). When we analyzed the results, we see that countries with lower CFR numbers more or less tend to have implemented active control measures such as aggressive testing, tracking down possible infections, effective quarantine measures, etc. Moreover, we did not see any convincing correlation between mortality rates and the median age of the population.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Eldhose Iype", + "author_inst": "BITS Pilani, Dubai Campus" + }, + { + "author_name": "Sadhya Gulati", + "author_inst": "BITS Pilani, Dubai Campus" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.20.20072488", "rel_title": "A statistical forecast of LOW mortality and morbidity due to COVID-19, in ARGENTINA and other Southern Hemisphere countries.", @@ -1545510,49 +1543229,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.04.23.20076612", - "rel_title": "A systematic review of Anakinra, Tocilizumab, Sarilumab and Siltuximab for coronavirus-related infections", - "rel_date": "2020-04-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.23.20076612", - "rel_abs": "BackgroundThere is accumulating evidence for an overly activated immune response in severe Covid-19, with several studies exploring the therapeutic role of immunomodulation. Through systematic review and meta-analysis, we assess the effectiveness of specific interleukin inhibitors for the treatment of Covid-19.\n\nMethodsElectronic databases were searched on 7th January 2021 to identify studies of immunomodulatory agents (anakinra, sarilumab, siltuximab and tocilizumab) for the treatment of Covid-19. The primary outcomes were severity on an ordinal scale measured at day 15 from intervention and days to hospital discharge. Key secondary endpoints included overall mortality.\n\nResults71 studies totalling 22,058 patients were included, six were randomised trials. Most explored outcomes in patients who received tocilizumab (59/71). In prospective studies, tocilizumab was associated with improved unadjusted survival (RR 0.83 95%CI 0.72;0.96 I2 = 0.0%), but conclusive benefit was not demonstrated for other outcomes. In retrospective studies, tocilizumab was associated with less severe outcomes on an ordinal scale (Generalised odds ratio 1.34 95%CI 1.10;1.64, I2=98%) and adjusted mortality risk (HR 0.52 95%CI 0.41;0.66, I2 =76.6%). The mean difference in duration of hospitalisation was 0.36 days (95%CI -0.07;0.80, I2 =93.8%). There was substantial heterogeneity in retrospective studies, and estimates should be interpreted cautiously. Other immunomodulatory agents showed similar effects to tocilizumab, but insufficient data precluded meta-analysis by agent.\n\nConclusionTocilizumab was associated with a lower relative risk of mortality in prospective studies, but effects were inconclusive for other outcomes. Current evidence for the efficacy of anakinra, siltuximab or sarilumab in Covid-19 is insufficient, with further studies urgently needed for conclusive findings.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Fasihul Khan", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Iain Stewart", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Laura Fabbri", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Samuel Moss", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Karen Robinson", - "author_inst": "John Hopkins University" - }, - { - "author_name": "Alan R Smyth", - "author_inst": "University of Nottingham" - }, - { - "author_name": "Gisli Jenkins", - "author_inst": "University of Nottingham" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.23.20076737", "rel_title": "ICU and ventilator mortality among critically ill adults with COVID-19", @@ -1546620,6 +1544296,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.22.20074989", + "rel_title": "Heat treatment for reuse of disposable respirators during Covid-19 pandemic: Is filtration and fit adversely affected?", + "rel_date": "2020-04-25", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.22.20074989", + "rel_abs": "A number of methods for decontaminating disposable filtering face piece respirators have been explored for use in health care settings during epidemics where respirators are in short supply, such as the current Covid-19 pandemic. Heating to temperatures above 65{degrees}C has been shown to successfully inactivate the SARS-CoV-2 virus on various surfaces. Ovens or similar heating devices are likely already widely available in hospitals globally. We did a quantitative fit test on nine models of FFP2 and FFP3 respirators before and after heat treatment in an oven. These included both flat fold and moulded cup styles. All passed the initial fit test, and all but two passed the post-treatment fit test. This study demonstrates that FFP respirators can still retain both filtration efficiency and fit after wear and heat treatment, but that it is necessary to understand the probability for failure of fit after decontamination. Heat shows promise as a simple and effective way of treating FFP respirators. Further evaluation of longer-term wear and disinfection effectiveness of heat treatment should be done before widespread use.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Miranda Loh", + "author_inst": "Institute of Occupational Medicine" + }, + { + "author_name": "Ross Clark", + "author_inst": "Institute of Occupational Medicine" + }, + { + "author_name": "John W Cherrie", + "author_inst": "Institute of Occupational Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "occupational and environmental health" + }, { "rel_doi": "10.1101/2020.04.22.20075200", "rel_title": "SARS-CoV-2 RNA titers in wastewater anticipated COVID-19 occurrence in a low prevalence area", @@ -1547220,49 +1544923,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.21.20074757", - "rel_title": "Knowledge, attitude, practice and perception regarding COVID-19 among students in Bangladesh: Survey in Rajshahi University", - "rel_date": "2020-04-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20074757", - "rel_abs": "BackgroundThe number of infection and death by COVID-19 has been rapidly increasing since December 2019 in all over the world. Until now, there is no specific treatment or vaccine for this disease; WHO suggests only some protective measures like maintaining social distance, staying home, washing hands with soap or sanitizer, wearing mask etc. The objective of this study was to survey knowledge, attitude, practice and perception regarding COVID-19 among students in Rajshahi University, Bangladesh.\n\nMethodsWe collected data from 305 students of Rajshahi University for this cross-sectional study using mixed sampling from March 11 to March 19, 2020. Frequency distribution, Mann-Whitney and Kruskal-Wallis tests were used in this study.\n\nResultsOut of 305 participants, 224 (73.4%) and 81 (26.6%) were male and female students respectively. The study revealed that Rajshahi university students had average knowledge on symptoms, protective way and transmission of COVID-19. Female students were more knowledgeable than male. More than one third of the students had negative attitude to avoiding public transport and going out to public places with friends and family. The practice of students practice during our data collection period and in future was not satisfactory. More than one third of students were not keen to stay at home and avoid going to crowded places. The perception towards COVID-19 was not good; they had no idea whether the outbreak would affect their daily routine, study and financial matters, study field work and restrict leisure time of meeting family and relatives.\n\nConclusionsWe found that general knowledge, attitude, practice and perception of the university students regarding COVID-19 were not satisfactory. This indicated that the situation was worse among common people. In Bangladesh, the number of healthcare providers is insufficient. University students can be employed as potential workforce to create awareness among mass people on prevention of COVID-19.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Md. Abdul Wadood", - "author_inst": "University of Rajshahi" - }, - { - "author_name": "ASMA Mamun", - "author_inst": "University of Rajshahi" - }, - { - "author_name": "Md. Abdur Rafi", - "author_inst": "Rajshahi Medical College" - }, - { - "author_name": "Md. kamrul Islam", - "author_inst": "University of Rajshahi" - }, - { - "author_name": "Suhaili Mohd", - "author_inst": "University of Malaya" - }, - { - "author_name": "Lai Lee Lee", - "author_inst": "University of Malaya" - }, - { - "author_name": "Md. Golam Hossain", - "author_inst": "University of Rajshahi" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.22.20075184", "rel_title": "Model the transmission dynamics of COVID-19 propagation with public health intervention", @@ -1548002,6 +1545662,57 @@ "type": "new results", "category": "genetics" }, + { + "rel_doi": "10.1101/2020.04.22.056747", + "rel_title": "Comparison of commercial RT-PCR diagnostic kits for COVID-19", + "rel_date": "2020-04-24", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.22.056747", + "rel_abs": "The final months of 2019 witnessed the emergence of a novel coronavirus in the human population. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has since spread across the globe and is posing a major burden on society. Measures taken to reduce its spread critically depend on timely and accurate identification of virus-infected individuals by the most sensitive and specific method available, i.e. real-time reverse transcriptase PCR (RT-PCR). Many commercial kits have recently become available, but their performance has not yet been independently assessed.\n\nThe aim of this study was to compare basic analytical and clinical performance of selected RT-PCR kits from seven different manufacturers (Altona Diagnostics, BGI, CerTest Biotec, KH Medical, PrimerDesign, R-Biopharm AG, and Seegene).\n\nWe used serial dilutions of viral RNA to establish PCR efficiency and estimate the 95% limit of detection (LOD95%). Furthermore, we ran a panel of SARS-CoV-2-positive clinical samples (n=16) for a preliminary evaluation of clinical sensitivity. Finally, we used clinical samples positive for non-coronavirus respiratory viral infections (n=6) and a panel of RNA from related human coronaviruses to evaluate assay specificity.\n\nPCR efficiency was [≥]96% for all assays and the estimated LOD95% varied within a 6-fold range. Using clinical samples, we observed some variations in detection rate between kits. Importantly, none of the assays showed cross-reactivity with other respiratory (corona)viruses, except as expected for the SARS-CoV-1 E-gene.\n\nWe conclude that all RT-PCR kits assessed in this study may be used for routine diagnostics of COVID-19 in patients by experienced molecular diagnostic laboratories.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Puck B van Kasteren", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Bas van der Veer", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Sharon van den Brink", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Lisa Wijsman", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Jorgen de Jonge", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Anne-Marie van den Brandt", + "author_inst": "National Institute for Public Health and the Environment (RIVM)" + }, + { + "author_name": "Richard Molenkamp", + "author_inst": "Erasmus University Medical Center" + }, + { + "author_name": "Chantal B.E.M. Reusken", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Adam Meijer", + "author_inst": "National Institute for Public Health and the Environment" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.04.20.20067512", "rel_title": "Rapid identification of SARS-CoV-2-infected patients at the emergency department using routine testing", @@ -1548638,69 +1546349,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.04.20.20064899", - "rel_title": "Epidemiological characteristics of COVID-19 in medical staff members of neurosurgery departments in Hubei province: A multicentre descriptive study", - "rel_date": "2020-04-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.20.20064899", - "rel_abs": "BackgroundThe novel coronavirus (SARS-CoV-2) has infected a large number of healthcare workers in Hubei province, China. In addition to infectious and respiratory disease physicians, many doctors in other medical fields have been infected.\n\nMethodsWe prospectively collected epidemiological data on medical staff members who are working in neurosurgery departments in 107 hospitals in Hubei province through self-reported questionnaires or telephone interviews. Data of medical staff members with laboratory-confirmed coronavirus disease 2019 (COVID-19) were analysed. The final follow-up date was 1 March 2020.\n\nFindingsA total of 5,442 neurosurgery department medical staff members were surveyed. One hundred and twenty cases, involving 54 doctors and 66 nurses, were found to have been infected with SARS-CoV-2. The overall incidence was 2.2%. These cases were concentrated in 26 centres, 16 of which had admitted a total of 59 patients with COVID-19 complicated by craniocerebral disease. Medical staff members in centres receiving COVID-19 patients had a higher risk of contracting infection than those in centres not receiving COVID-19 patients (relative risk: 19.6; 95% confidence interval: 12.6-30.6). Contact with either COVID-19 patients (62.5%, 75/120) or infected colleagues (30.8%, 37/120) was the most common mode of transmission. About 78.3% (94/120) of the infected cases wore surgical masks, whereas 20.8% (25/120) failed to use protection when exposed to the source of infection. Severe infections were observed in 11.7% (14/120) of the cases, with one death (0.8%, 1/120). All the infected medical staff members had been discharged from the hospital. A total of 1,287 medical staff members were dispatched to participate in the frontline response to COVID-19 under level 2 protection of whom one was infected. Medical staff members who took inadequate protection had a higher risk of contracting infection than those using level 2 protection (relative risk: 36.9; 95% confidence interval: 5.2-263.6).\n\nConclusionsNeurosurgical staff members in Hubei province were seriously affected by COVID-19. Level 2 protection and strengthening of protective measures are likely to be effective in preventing medical workers from being infected.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Qiangping Wang", - "author_inst": "Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China, 430022" - }, - { - "author_name": "Xing Huang", - "author_inst": "Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China, 430022." - }, - { - "author_name": "Yansen Bai", - "author_inst": "Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong" - }, - { - "author_name": "Xuan Wang", - "author_inst": "Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China, 430022." - }, - { - "author_name": "Haijun Wang", - "author_inst": "Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China, 430022." - }, - { - "author_name": "Xuebin Hu", - "author_inst": "Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China, 430022." - }, - { - "author_name": "Feng Wang", - "author_inst": "Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China, 430022." - }, - { - "author_name": "Xianke Wang", - "author_inst": "Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China, 430022." - }, - { - "author_name": "Jincao Chen", - "author_inst": "Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China, 430071." - }, - { - "author_name": "Qianxue Chen", - "author_inst": "Department of Neurosurgery, Hubei Provincial People's Hospital of Wuhan University, Wuhan, China, 430060." - }, - { - "author_name": "Xiaobing Jiang Sr.", - "author_inst": "Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China, 430022." - }, - { - "author_name": "Hongyang Zhao", - "author_inst": "Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China, 430022." - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.24.059667", "rel_title": "Critical role of type III interferon in controlling SARS-CoV-2 infection, replication and spread in primary human intestinal epithelial cells", @@ -1549924,6 +1547572,341 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.19.20071373", + "rel_title": "Scalable and Resilient SARS-CoV2 testing in an Academic Centre", + "rel_date": "2020-04-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.19.20071373", + "rel_abs": "The emergence of the novel coronavirus SARS-CoV-2 has led to a pandemic infecting more than two million people worldwide in less than four months, posing a major threat to healthcare systems. This is compounded by the shortage of available tests causing numerous healthcare workers to unnecessarily self-isolate. We provide a roadmap instructing how a research institute can be repurposed in the midst of this crisis, in collaboration with partner hospitals and an established diagnostic laboratory, harnessing existing expertise in virus handling, robotics, PCR, and data science to derive a rapid, high throughput diagnostic testing pipeline for detecting SARS-CoV-2 in patients with suspected COVID-19. The pipeline is used to detect SARS-CoV-2 from combined nose-throat swabs and endotracheal secretions/ bronchoalveolar lavage fluid. Notably, it relies on a series of in-house buffers for virus inactivation and the extraction of viral RNA, thereby reducing the dependency on commercial suppliers at times of global shortage. We use a commercial RT-PCR assay, from BGI, and results are reported with a bespoke online web application that integrates with the healthcare digital system. This strategy facilitates the remote reporting of thousands of samples a day with a turnaround time of under 24 hours, universally applicable to laboratories worldwide.", + "rel_num_authors": 80, + "rel_authors": [ + { + "author_name": "Jim Aitken", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Karen Ambrose", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Sam Barrell", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Rupert Beale", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Ganka Bineva-Todd", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Dhruva Biswas", + "author_inst": "University College London" + }, + { + "author_name": "Richard Byrne", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Simon Caidan", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Peter Cherepanov", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Laura Churchward", + "author_inst": "University College London Hospitals, NHS Foundation Trust" + }, + { + "author_name": "Graham Clark", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Marg Crawford", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Laura Cubitt", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Vicky Dearing", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Christopher Earl", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Amelia Edwards", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Chris Ekin", + "author_inst": "Health Services Laboratories" + }, + { + "author_name": "Efthymios Fidanis", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Alessandra Gaiba", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Steve Gamblin", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Sonia Gandhi", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Jacki Goldman", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Robert Goldstone", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Paul R Grant", + "author_inst": "Health Services Laboratories" + }, + { + "author_name": "Maria Greco", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Judith Heaney", + "author_inst": "University College London Hospitals, NHS Foundation Trust" + }, + { + "author_name": "Steve Hindmarsh", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Catherine F Houlihan", + "author_inst": "University College London Hospitals, NHS Foundation Trust" + }, + { + "author_name": "Michael Howell", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Michael Hubank", + "author_inst": "The Institute of Cancer Research" + }, + { + "author_name": "Debbie Hughes", + "author_inst": "The Institute of Cancer Research" + }, + { + "author_name": "Rachel Instrell", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Deb Jackson", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Mariam Jamal-Hanjani", + "author_inst": "University College London" + }, + { + "author_name": "Ming Jiang", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Mark Johnson", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Leigh Jones", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Nnennaya Kanu", + "author_inst": "University College London" + }, + { + "author_name": "George Kassiotis", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Stuart Kirk", + "author_inst": "Health Services Laboratories" + }, + { + "author_name": "Svend Kjaer", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Andrew Levett", + "author_inst": "Health Services Laboratories" + }, + { + "author_name": "Lisa Levett", + "author_inst": "Health Services Laboratories" + }, + { + "author_name": "Marcel Levi", + "author_inst": "University College London Hospitals, NHS Foundation Trust" + }, + { + "author_name": "Wei-Ting Lu", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "James I MacRae", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "John Matthews", + "author_inst": "Health Services Laboratories" + }, + { + "author_name": "Laura McCoy", + "author_inst": "University College London" + }, + { + "author_name": "Catherine Moore", + "author_inst": "Public Health Wales" + }, + { + "author_name": "David Moore", + "author_inst": "University College London" + }, + { + "author_name": "Eleni Nastouli", + "author_inst": "University College London Hospitals, NHS Foundation Trust" + }, + { + "author_name": "Jerome Nicod", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Luke Nightingale", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Jessica Olsen", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Nicola OReilly", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Amar Pabari", + "author_inst": "Health Services Laboratories" + }, + { + "author_name": "Venizelos Papayannopoulos", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Namita Patel", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Nigel Peat", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Marc Pollitt", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Peter Ratcliffe", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Caetano Reis e Sousa", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Annachiara Rosa", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Rachel Rosenthal", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Chloe Roustan", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Andrew Rowan", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Gee Yen Shin", + "author_inst": "Health Services Laboratories" + }, + { + "author_name": "Daniel M Snell", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Ok-Ryul Song", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Moria Spyer", + "author_inst": "University College London" + }, + { + "author_name": "Amy Strange", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Charles Swanton", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "James M A Turner", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Melanie Turner", + "author_inst": "Health Services Laboratories" + }, + { + "author_name": "Andreas Wack", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Philip A Walker", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Sophie Ward", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Wai Keong Wong", + "author_inst": "University College London Hospitals, NHS Foundation Trust" + }, + { + "author_name": "Joshua Wright", + "author_inst": "The Francis Crick Institute" + }, + { + "author_name": "Mary Wu", + "author_inst": "The Francis Crick Institute" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2020.04.21.20073890", "rel_title": "Data-driven modeling reveals a universal dynamic underlying the COVID-19 pandemic under social distancing", @@ -1550252,49 +1548235,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.22.20076141", - "rel_title": "COVID-19: Public Compliance with and Public Support for Stay-at-Home Mitigation Strategies", - "rel_date": "2020-04-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.22.20076141", - "rel_abs": "AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSObjectivesC_ST_ABSGovernments worldwide have recommended unprecedented measures to mitigate the coronavirus disease 2019 (COVID-19) pandemic. As pressure mounts to scale back these measures, understanding public compliance with and priorities for COVID-19 mitigation is critical. The main aim of this study was to assess public compliance with and support for government-imposed stay-at-home orders in nations and cities with different COVID-19 infection and death rates.\n\nDesignIn this cross-sectional study, questionnaires were administered to nationally representative respondents from April 2-8, 2020.\n\nSettingRegions with different disease prevalence included two nations [the United States (US--high) and Australia (AU--low)] and two cities [New York (NY--high) and Los Angeles (LA--low)].\n\nParticipantsFor adults 18 years or older residing in specified regions, eligible respondents were empaneled until representative quotas were reached for age, gender, and either race and ethnicity (US, NY, LA) or ancestry (AU), matching the 2010 US or 2016 AU census. Of 8718 eligible potential respondents, 5573 (response rate, 63.9%) completed surveys (US: 3010; NY: 507; LA: 525; AU: 1531). The median age was 47 years (range, 18-89); 3039 (54.5%) were female.\n\nExposureThe prevalence of COVID-19 in each region (cumulative infections, deaths) as of April 8, 2020: US (458610, 15659), AU (5956, 45),1 NY (81803, 4571), LA (7530, 198).2\n\nMain Outcomes MeasuresPublic compliance with and attitudes regarding government-imposed stay-at-home orders were evaluated and compared between regions.\n\nResultsOf 5573 total respondents, 4560 (81.8%) reported compliance with recommended quarantine or stay-at-home policies (range of samples, 75.5%-88.2%). Despite significant disruptions of social and work life, health, and behavior, 5022 respondents (90.1%) supported government-imposed stay-at-home orders (range of samples, 88.9%-93.1%). Of these, 90.8% believe orders should last at least three more weeks or until public health or government officials recommend, with such support spanning the political spectrum.\n\nConclusionsPublic compliance with stringent quarantine and stay-at-home policies was very high, in both highly-affected (US, NY) and minimally-affected regions (AU, LA). Despite extensive disruption of respondents lives, the vast majority supported continuation of long-term government-imposed stay-at-home orders. These findings have important implications for policymakers grappling with the decision as to when to lift restrictions.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Mark \u00c9 Czeisler", - "author_inst": "School of Psychological Sciences and Turner Institute for Brain and Mental Health, Monash University, Melbourne, Victoria 3800 Australia" - }, - { - "author_name": "Mark E Howard", - "author_inst": "Institute for Breathing and Sleep, Austin Health, Melbourne, Victoria 3084 Australia" - }, - { - "author_name": "Rebecca Robbins", - "author_inst": "Division of Sleep and Circadian Disorders, Departments of Medicine and Neurology, Brigham and Women's Hospital, Boston, Massachusetts 02115 USA" - }, - { - "author_name": "Laura K Barger", - "author_inst": "Division of Sleep and Circadian Disorders, Departments of Medicine and Neurology, Brigham and Women's Hospital, Boston, Massachusetts 02115 USA" - }, - { - "author_name": "Elise R Facer-Childs", - "author_inst": "School of Psychological Sciences and Turner Institute for Brain and Mental Health, Monash University, Melbourne, Victoria 3800 Australia" - }, - { - "author_name": "Shantha MW Rajaratnam", - "author_inst": "School of Psychological Sciences and Turner Institute for Brain and Mental Health, Monash University, Melbourne, Victoria 3800 Australia" - }, - { - "author_name": "Charles A Czeisler", - "author_inst": "Division of Sleep and Circadian Disorders, Departments of Medicine and Neurology, Brigham and Women's Hospital, Boston, Massachusetts 02115 USA" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.19.20071779", "rel_title": "Performance of fabrics for home-made masks against spread of respiratory infection through droplets: a quantitative mechanistic study", @@ -1551242,6 +1549182,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "endocrinology" }, + { + "rel_doi": "10.1101/2020.04.21.20073536", + "rel_title": "Population modeling of early COVID-19 epidemic dynamics in French regions and estimation of the lockdown impact on infection rate", + "rel_date": "2020-04-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.21.20073536", + "rel_abs": "We developed a multi-level model of the French COVID-19 epidemic at the regional level. We rely on a global extended Susceptible-Exposed-Infectious-Recovered (SEIR) mechanistic model as a simplified representation of the average epidemic process, with the addition of region specific random effects. Combining several French public datasets on the early dynamics of the epidemic, we estimate region-specific key parameters conditionally on this mechanistic model through Stochastic Approximation Expectation Maximization (SAEM) optimization using Monolix software. We thus estimate the basic reproductive numbers by region before lockdown (with a national average at 2.81 with 95% Confidence Interval [2.58; 3.07]), attack rates (i.e. percentages of infected people) over time per region which range between 1.9% and 9.9% as of May 11th, 2020, and the impact of nationwide lockdown on the infection rate which decreased the transmission rate by 76% towards reproductive numbers ranging from 0.63 to 0.73 at the end of lockdown across regions. These results confirm the low population immunity, the strong effect of the lockdown on the dynamics of the epidemics and the need for further intervention when lifting the lockdown to avoid an epidemic rebound.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Melanie Prague", + "author_inst": "Univ. Bordeaux - INRIA - Inserm U1219 - SISTM Team - Vaccine Research Institute" + }, + { + "author_name": "Linda Wittkop", + "author_inst": "Univ. Bordeaux - Inria - Inserm U1219 - Vaccine Research Institute - CHU Bordeaux" + }, + { + "author_name": "Annabelle COLLIN", + "author_inst": "Inria Bordeaux Sud-Ouest, IMB, Bordeaux INP" + }, + { + "author_name": "Quentin Clairon", + "author_inst": "Univ. Bordeaux - INRIA - Inserm U1219 - SISTM Team - Vaccine Research Institute" + }, + { + "author_name": "Dan Dutartre", + "author_inst": "Inria Bordeaux" + }, + { + "author_name": "Philippe Moireau", + "author_inst": "Inria Paris Saclay, LMS, Ecole Polytechnique, CNRS, Institut Polytechnique" + }, + { + "author_name": "Rodolphe Thiebaut", + "author_inst": "Univ. Bordeaux - INRIA - Inserm U1219 - SISTM Team - Vaccine Research Institute - CHU Bordeaux" + }, + { + "author_name": "Boris Pierre Hejblum", + "author_inst": "Univ. Bordeaux - INRIA - Inserm U1219 - SISTM Team - Vaccine Research Institute" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.20.20072413", "rel_title": "Estimating the burden of SARS-CoV-2 in France", @@ -1551530,69 +1549517,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.20.20072462", - "rel_title": "ESTIMATING R0 OF SARS-COV-2 IN HEALTHCARE SETTINGS", - "rel_date": "2020-04-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.20.20072462", - "rel_abs": "To date, no specific estimate of R0 for SARS-CoV-2 is available for healthcare settings. Using inter-individual contact data, we highlight that R0 estimates from the community cannot translate directly to healthcare settings, with pre-pandemic R0 values ranging 1.3-7.7 in three illustrative healthcare institutions. This has implications for nosocomial Covid-19 control.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Laura TEMIME", - "author_inst": "Cnam" - }, - { - "author_name": "Marie-Paule Gustin", - "author_inst": "University Claude Bernard Lyon 1, Inserm" - }, - { - "author_name": "Audrey Duval", - "author_inst": "Institut Pasteur" - }, - { - "author_name": "Niccolo Buetti", - "author_inst": "Inserm" - }, - { - "author_name": "Pascal Crepey", - "author_inst": "EHESP" - }, - { - "author_name": "Didier Guillemot", - "author_inst": "Paris-Saclay University , Inserm, Institut Pasteur, AP-HP" - }, - { - "author_name": "Rodolphe Thiebaut", - "author_inst": "University of Bordeaux, Inria" - }, - { - "author_name": "Philippe Vanhems", - "author_inst": "Lyon University Hospitals" - }, - { - "author_name": "Jean-Ralph Zahar", - "author_inst": "AP-HP, Inserm" - }, - { - "author_name": "David RM Smith", - "author_inst": "Paris-Saclay University, Institut Pasteur, Cnam" - }, - { - "author_name": "Lulla Opatowski", - "author_inst": "Paris Saclay university, Inserm, Institut Pasteur" - }, - { - "author_name": "Modelling COVID-19 in hospitals REACTinG AVIESAN working group", - "author_inst": "" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.20.20072744", "rel_title": "COVID-19 pandemic scenario in India compared to China and rest of the world: a data driven and model analysis", @@ -1552624,6 +1550548,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.22.20076018", + "rel_title": "Optimal control of the COVID-19 pandemic with non-pharmaceutical interventions", + "rel_date": "2020-04-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.22.20076018", + "rel_abs": "The COVID-19 pandemic has forced societies across the world to resort to social distancing to slow the spread of the SARS-CoV-2 virus. Due to the economic impacts of social distancing, there is growing desire to relax these measures. To characterize a range of possible strategies for control and to understand their consequences, we performed an optimal control analysis of a mathematical model of SARS-CoV-2 transmission. Given that the pandemic is already underway and controls have already been initiated, we calibrated our model to data from the US and focused our analysis on optimal controls from May 2020 through December 2021. We found that a major factor that differentiates strategies that prioritize lives saved versus reduced time under control is how quickly control is relaxed once social distancing restrictions expire in May 2020. Strategies that maintain control at a high level until summer 2020 allow for tapering of control thereafter and minimal deaths, whereas strategies that relax control in the short term lead to fewer options for control later and a higher likelihood of exceeding hospital capacity. Our results also highlight that the potential scope for controlling COVID-19 until a vaccine is available depends on epidemiological parameters about which there is still considerable uncertainty, including the basic reproduction number and the effectiveness of social distancing. In light of those uncertainties, our results do not constitute a quantitative forecast and instead provide a qualitative portrayal of possible outcomes from alternative approaches to control.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Alex Perkins", + "author_inst": "University of Notre Dame" + }, + { + "author_name": "Guido Espana", + "author_inst": "University of Notre Dame" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.19.20071415", "rel_title": "Impact of control strategies on COVID-19 pandemic and the SIR model based forecasting in Bangladesh.", @@ -1553124,89 +1551071,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.04.22.046565", - "rel_title": "Functional and Genetic Analysis of Viral Receptor ACE2 Orthologs Reveals Broad Potential Host Range of SARS-CoV-2", - "rel_date": "2020-04-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.22.046565", - "rel_abs": "The pandemic of Coronavirus Disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a major global health threat. Epidemiological studies suggest that bats are the natural zoonotic reservoir for SARS-CoV-2. However, the host range of SARS-CoV-2 and intermediate hosts that facilitate its transmission to humans remain unknown. The interaction of coronavirus with its host receptor is a key genetic determinant of host range and cross-species transmission. SARS-CoV-2 uses angiotensin-converting enzyme 2 (ACE2) as the receptor to enter host cells in a species-dependent manner. It has been shown that human, palm civet, pig and bat ACE2 can support virus entry, while the murine ortholog cannot. In this study, we characterized the ability of ACE2 from diverse species to support viral entry. We found that ACE2 is expressed in a wide range of species, with especially high conservation in mammals. By analyzing amino acid residues of ACE2 critical for virus entry, based on structure of SARS-CoV spike protein interaction with human, bat, palm civet, pig and ferret ACE2, we identified approximately eighty ACE2 proteins from mammals that could potentially mediate SARS-CoV-2 entry. We chose 48 representative ACE2 orthologs among eighty orthologs for functional analysis and it showed that 44 of these mammalian ACE2 orthologs, including those of domestic animals, pets, livestock, and animals commonly found in zoos and aquaria, could bind SARS-CoV-2 spike protein and support viral entry. In contrast, New World monkey ACE2 orthologs could not bind SARS-CoV-2 spike protein and support viral entry. We further identified the genetic determinant of New World monkey ACE2 that restricts viral entry using genetic and functional analyses. In summary, our study demonstrates that ACE2 from a remarkably broad range of species can facilitate SARS-CoV-2 entry. These findings highlight a potentially broad host tropism of SARS-CoV-2 and suggest that SARS-CoV-2 might be distributed much more widely than previously recognized, underscoring the necessity to monitor susceptible hosts to prevent future outbreaks.", - "rel_num_authors": 17, - "rel_authors": [ - { - "author_name": "Yinghui Liu", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Gaowei Hu", - "author_inst": "Fudan University" - }, - { - "author_name": "Yuyan Wang", - "author_inst": "Fudan University" - }, - { - "author_name": "Xiaomin Zhao", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Fansen Ji", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Wenlin Ren", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Mingli Gong", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Xiaohui Ju", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Yuanfei Zhu", - "author_inst": "Fudan University" - }, - { - "author_name": "Xia Cai", - "author_inst": "Fudan University" - }, - { - "author_name": "Jianping Wu", - "author_inst": "Westlake University" - }, - { - "author_name": "Xun Lan", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Youhua Xie", - "author_inst": "Fudan University" - }, - { - "author_name": "Xinquan Wang", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Zhenghong Yuan", - "author_inst": "Fudan University" - }, - { - "author_name": "Rong Zhang", - "author_inst": "Fudan University" - }, - { - "author_name": "Qiang Ding", - "author_inst": "Tsinghua University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.04.23.057265", "rel_title": "Structural and biochemical characterization of nsp12-nsp7-nsp8 core polymerase complex from COVID-19 virus", @@ -1554378,6 +1552242,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, + { + "rel_doi": "10.1101/2020.04.19.20071340", + "rel_title": "Are German endoscopy units prepared for the COVID-19 pandemic? A nationwide survey", + "rel_date": "2020-04-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.19.20071340", + "rel_abs": "ObjectiveThe COVID-19 pandemic challenges health care systems worldwide. In this situation, guidelines for health care professionals in endoscopy units with increased risk of infection from inhalation of airborne droplets, conjunctival contact and faeces are urgently needed. Recently, the European Society of Gastrointestinal Endoscopy (ESGE) and the German Society for Pneumology (DGP) issued recommendations. However, real-world data on the conditions and requirements of endoscopy units to adhere to this guidance are missing.\n\nDesignWe conducted an internet-based survey among German endoscopy units from all levels of care from April 1st to 7th, 2020. The survey comprised 33 questions and was distributed electronically by the German Society of Gastroenterology, Digestive and Metabolic Diseases (DGVS) and the DGP.\n\nResultsIn total, 656 endoscopy units completed the survey. Overall, 253 units (39%) cancelled fewer than 40% of their procedures. Of note, private practices cancelled less procedures than hospital-based units. Complete separation of high-risk and COVID-19 positive patients was achieved in only 20% of the units. Procedural measures were well adopted, with 91% of the units systematically identifying patients at risk and 85% using risk-adapted personal protective equipment (PPE). For the future, shortages in PPE (81%), staff (69%) and relevant financial losses (77%) were expected.\n\nConclusionConcise definitions of non-urgent, elective interventions and endoscopic surveillance strategies are needed to better guide endoscopic activity and intervention cancellations. In the short term, a lack of PPE can constitute considerable impairment of endoscopy units operability and patient outcomes.\n\nSUMMARY BOXO_LIWhat is already known about this subject?\n- Recent data indicate a potentially important role of the gastrointestinal tract in the spreading of COVID-19.\n- Endoscopy units and their personnel are at high risk to be exposed to and to distribute COVID-19 infections.\n- Several societies have formulated guidance for endoscopy units in the current situation, but their feasibility is unclear.\n\nC_LIO_LIWhat are the new findings?\n- Endoscopic activity seems not to be limited to urgent interventions across all units as 39% of all endoscopy units cancelled less than 40% of procedures.\n- For most endoscopy units, structural conditions are insufficient to realize a complete separation of high-risk patients, which can be guaranteed by only 20% of the units.\n- The willingness to adhere to the recommendations is very high, as most endoscopy units adopted their procedures accordingly. Shortage of personal protective equipment is a critical concern in many units.\n\nC_LIO_LIHow might it impact on clinical practice in the foreseeable future?\n- An update of the current recommendations to refine practicable measures for the majority of endoscopic units is warranted.\n- A concise definition of non-urgent or elective procedures as well as postponement strategies and intervals are of utmost importance, since current data implicate that transmission of SARS-CoV-2 via the respiratory and gastrointestinal tract may be critical for public health.\n\nC_LI", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Jakob Garbe", + "author_inst": "University Hospital Halle (Saale), Department for Internal Medicine I, Germany" + }, + { + "author_name": "Stephan Eisenmann", + "author_inst": "University Hospital Halle (Saale), Department for Internal Medicine I, Germany" + }, + { + "author_name": "Clara Sophie Heidemann", + "author_inst": "University Hospital Halle (Saale), Department for Internal Medicine I, Germany" + }, + { + "author_name": "Marko Damm", + "author_inst": "University Hospital Halle (Saale), Department for Internal Medicine I, Germany" + }, + { + "author_name": "Sebastian Krug", + "author_inst": "University Hospital Halle (Saale), Department for Internal Medicine I, Germany" + }, + { + "author_name": "Steffen Walter", + "author_inst": "University Hospital Ulm, Department for Medical Psychology, Ulm, Germany" + }, + { + "author_name": "Frank Lammert", + "author_inst": "Saarland University Hospital, Department for Medicine II, Homburg, Germany" + }, + { + "author_name": "Kaid Darwiche", + "author_inst": "Ruhrland Hospital, West German Lung Center, Essen, Nordrhein-Westfalen, DE" + }, + { + "author_name": "Patrick Michl", + "author_inst": "University Hospital Halle (Saale), Department for Internal Medicine I, Germany" + }, + { + "author_name": "Jonas Rosendahl", + "author_inst": "University Hospital Halle (Saale), Department for Internal Medicine I, Germany" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "gastroenterology" + }, { "rel_doi": "10.1101/2020.04.18.20070755", "rel_title": "Detection of SARS-CoV-2 RNA by direct RT-qPCR on nasopharyngeal specimens without extraction of viral RNA", @@ -1554982,57 +1552901,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.18.20070821", - "rel_title": "Estimating the Prevalence of COVID-19 in the United States: Three Complementary Approaches", - "rel_date": "2020-04-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.18.20070821", - "rel_abs": "Effectively designing and evaluating public health responses to the ongoing COVID-19 pandemic requires accurate estimation of the prevalence of COVID-19 across the United States (US). Equipment shortages and varying testing capabilities have however hindered the usefulness of the official reported positive COVID-19 case counts. We introduce four complementary approaches to estimate the cumulative incidence of symptomatic COVID-19 in each state in the US as well as Puerto Rico and the District of Columbia, using a combination of excess influenza-like illness reports, COVID-19 test statistics, COVID-19 mortality reports, and a spatially structured epidemic model. Instead of relying on the estimate from a single data source or method that may be biased, we provide multiple estimates, each relying on different assumptions and data sources. Across our four approaches emerges the consistent conclusion that on April 4, 2020, the estimated case count was 5 to 50 times higher than the official positive test counts across the different states. Nationally, our estimates of COVID-19 symptomatic cases as of April 4 have a likely range of 2.2 to 4.9 million, with possibly as many as 8.1 million cases, up to 26 times greater than the cumulative confirmed cases of about 311,000. Extending our method to May 16, 2020, we estimate that cumulative symptomatic incidence ranges from 6.0 to 10.3 million, as opposed to 1.5 million positive test counts. The proposed combination of approaches may prove useful in assessing the burden of COVID-19 during resurgences in the US and other countries with comparable surveillance systems.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Fred S Lu", - "author_inst": "Stanford" - }, - { - "author_name": "Andre T Nguyen", - "author_inst": "University of Maryland, Baltimore County" - }, - { - "author_name": "Nicholas B Link", - "author_inst": "Boston Children's Hospital" - }, - { - "author_name": "Jessica T Davis", - "author_inst": "Northeastern University" - }, - { - "author_name": "Matteo Chinazzi", - "author_inst": "Northeastern University" - }, - { - "author_name": "Xinyue Xiong", - "author_inst": "Northeastern University" - }, - { - "author_name": "Alessandro Vespignani", - "author_inst": "Northeastern University" - }, - { - "author_name": "Marc Lipsitch", - "author_inst": "Harvard T.H. Chan School of Public Health" - }, - { - "author_name": "Mauricio Santillana", - "author_inst": "Harvard Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.20.20064873", "rel_title": "Gastrointestinal symptoms as Covid-19 onset in hospitalized Italian patients", @@ -1556352,6 +1554220,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.17.20059535", + "rel_title": "Modeling projections for COVID-19 pandemic by combining epidemiological, statistical, and neural network approaches", + "rel_date": "2020-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20059535", + "rel_abs": "As the number of people affected by COVID-19 disease caused by the novel coronavirus SARS-CoV-2 ebbs and flows in different national and sub-national regions across the world, it is evident that our lifestyle and socio-economic trajectories will have to be adapted and adjusted to the changing scenarios. Novel forecasting tools and frameworks provide an arguable advantage to facilitate this adapting and adjusting process, by promoting efficient resource management at individual and institutional levels. Based on deterministic compartment models we propose an empirical top-down modeling approach to provide epidemic forecasts and risk calculations for (local) outbreaks. We use neural networks to develop leading indicators based on available data for different regions. These indicators are not only used to assess the risk of a (new) outbreak or to determine the effectiveness of a measure at an early stage, but also in parametric models to determine an effective forecast, along with the associated uncertainty. Based on initial results, we show the performance of such an approach and its robustness against inherent disturbances in epidemiological surveillance data. We foresee such a statistical framework to drive web-based automatic platforms to democratize the dissemination of prognosis results.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Steffen Uhlig", + "author_inst": "QuoData GmbH" + }, + { + "author_name": "Kapil Nichani", + "author_inst": "QuoData GmbH" + }, + { + "author_name": "Carsten Uhlig", + "author_inst": "Akees GmbH" + }, + { + "author_name": "Kirsten Simon", + "author_inst": "QuoData GmbH" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.16.20067975", "rel_title": "LONG-TERM CLINICAL OUTCOMES IN SURVIVORS OF CORONAVIRUS OUTBREAKS AFTER HOSPITALISATION OR ICU ADMISSION: A SYSTEMATIC REVIEW AND META-ANALYSIS OF FOLLOW-UP STUDIES", @@ -1556748,37 +1554647,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.17.20069716", - "rel_title": "Years of life lost due to the psychosocial consequences of COVID19 mitigation strategies based on Swiss data", - "rel_date": "2020-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20069716", - "rel_abs": "BackgroundThe pandemic caused by COVID-19 has forced governments to implement strict social mitigation strategies to reduce the morbidity and mortality from acute infections. These strategies however carry a significant risk for mental health which can lead to increased short-term and long-term mortality and is currently not included in modelling the impact of the pandemic.\n\nMethodsWe used years of life lost (YLL) as the main outcome measure as applied to Switzerland as an exemplar. We focused on suicide, depression, alcohol use disorder, childhood trauma due to domestic violence, changes in marital status and social isolation as these are known to increase YLL in the context of imposed restriction in social contact and freedom of movement. We stipulated a minimum duration of mitigation of 3 months based on current public health plans.\n\nResultsThe study projects that the average person would suffer 0.205 YLL due to psychosocial consequence of COVID-19 mitigation measures. However, this loss would be entirely borne by 2.1% of the population, who will suffer an average 9.79 YLL.\n\nConclusionsThe results presented here are likely to underestimate the true impact of the mitigation strategies on YLL. However, they highlight the need for public health models to expand their scope in order to provide better estimates of the risks and benefits of mitigation.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Dominik Andreas Moser", - "author_inst": "University of Berne, Institute of Psychology, Switzerland; Centre Hospitalier Universitaire Vaudois, Child and Adolescent Psychiatry Service, Department of Psyc" - }, - { - "author_name": "Jennifer Glaus", - "author_inst": "Centre Hospitalier Universitaire Vaudois, Child and Adolescent Psychiatry Service, Department of Psychiatry, Switzerland" - }, - { - "author_name": "Sophia Frangou", - "author_inst": "Djavad Mowafaghian Centre for Brain Health, Department of Psychiatry, University of British Columbia, Canada; Department of Psychiatry, Icahn School of Medicine" - }, - { - "author_name": "Daniel Scott Schechter", - "author_inst": "Centre Hospitalier Universitaire Vaudois, Child and Adolescent Psychiatry Service, Switzerland; Universite de Geneve Faculte de medecine, Switzerland; New York " - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.04.17.20068908", "rel_title": "The proportion of deaths cases in confirmed patients of COVID-19 is still increasing for cumulative cases reported up to 14 April 2020", @@ -1557786,6 +1555654,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.17.20069773", + "rel_title": "The role of corticosteroids in the management of critically ill patients with coronavirus disease 2019 (COVID-19): A meta-analysis", + "rel_date": "2020-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20069773", + "rel_abs": "ObjectiveThere are no controlled studies on the role of systemic corticosteroids (CS) in patients with coronavirus disease 2019 (COVID-19). In the absence of high-quality evidence, understandably the recommendations from various organizations are cautious. Several randomized controlled trials are underway but shall take time to conclude. We therefore undertook a meta-analysis to ascertain the role of CS in the management of critically ill patients with COVID-19.\n\nData SourcesElectronic databases, including Pubmed, Cochrane library and Embase, were searched, using the keywords of interest and the PICO search technique, from inception to 12th April 2020.\n\nStudy SelectionStudies highlighting the use of CS in coronavirus infection with severe acute respiratory syndrome (SARS), Middle East Respiratory Syndrome (MERS) and COVID-19 were selected based on pre-determined inclusion criteria.\n\nData extractionData was extracted into an excel sheet and transferred to comprehensive meta-analysis software version 3, Biostat Inc., Englewood, NJ, USA, for analysis.\n\nData synthesisFive studies with SARS-CoV-2 infection were included in the meta-analysis. The rate ratio (RR) for mortality in patients with SARS-CoV-2 infection was 1.26 (95% CI: 0.96-1.65, I2: 74.46), indicating lack of benefit of CS therapy on mortality in critically ill patients with COVID-19. The RR for mortality on analysis of the three studies that particularly reported on patients with significant pulmonary compromise secondary to SARS-CoV-2 infection was neutral (RR: 0.91, 95% CI: 0.63-1.33, I2: 63.38).\n\nConclusionsThe use of CS in critically ill patients with COVID-19 did not improve or worsen mortality. Pending further information from controlled studies, CS can be used in critically ill patients with COVID-19 with critical illness related corticosteroid insufficiency and moderate to severe ARDS without the risk of increased mortality.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Kalyan Kumar Gangopadhyay", + "author_inst": "Fortis and Peerless Hospital, Kolkata, India" + }, + { + "author_name": "Jagat J Mukherjee", + "author_inst": "Apollo Gleneagles Hospital, Kolkata, India" + }, + { + "author_name": "Binayak Sinha", + "author_inst": "AMRI Hospitals, Kolkata, India" + }, + { + "author_name": "SAMIT GHOSAL", + "author_inst": "Nightingale Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.17.20069237", "rel_title": "Forecasting of COVID-19 Cases and Deaths Using ARIMA Models", @@ -1558106,53 +1556005,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.04.16.20068163", - "rel_title": "Projections for first-wave COVID-19 deaths across the US using social-distancing measures derived from mobile phones", - "rel_date": "2020-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.16.20068163", - "rel_abs": "We propose a Bayesian model for projecting first-wave COVID-19 deaths in all 50 U.S. states. Our models projections are based on data derived from mobile-phone GPS traces, which allows us to estimate how social-distancing behavior is \"flattening the curve\" in each state. In a two-week look-ahead test of out-of-sample forecasting accuracy, our model significantly outperforms the widely used model from the Institute for Health Metrics and Evaluation (IHME), achieving 42% lower prediction error: 13.2 deaths per day average error across all U.S. states, versus 22.8 deaths per day average error for the IHME model. Our model also provides an accurate, if slightly conservative, assessment of forecasting accuracy: in the same look-ahead test, 98% of data points fell within the models 95% credible intervals. Our models projections are updated daily at https://covid-19.tacc.utexas.edu/projections/.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Spencer Woody", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "Mauricio Garcia Tec", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "Maytal Dahan", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "Kelly Gaither", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "Michael Lachmann", - "author_inst": "Santa Fe Institute" - }, - { - "author_name": "Spencer Fox", - "author_inst": "University of Texas at Austin" - }, - { - "author_name": "Lauren Ancel Meyers", - "author_inst": "The University of Texas at Austin" - }, - { - "author_name": "James G Scott", - "author_inst": "University of Texas at Austin" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.20.052233", "rel_title": "Rapid and quantitative detection of COVID-19 markers in micro-liter sized samples", @@ -1559224,6 +1557076,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.17.20069245", + "rel_title": "Importance of Social Distancing: Modeling the spread of 2019-nCoV using Susceptible-Infected-Quarantined-Recovered-t model", + "rel_date": "2020-04-22", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.17.20069245", + "rel_abs": "BackgroundThe Novel Coronavirus that originated in Wuhan, Hubei, China, has raised global concerns and has been declared a pandemic. The infection shows the primary symptoms of pneumonia and has an incubation period, with the majority of people showing symptoms within 14 days. Online Social Networks are the closest simulations of real-world networks and have similar topology characteristics. This article simulates the spread and control of the nCoV-19 using the SIQR-t model to highlight the importance of self-quarantine and exercise of proper health care as a method to prevent the spread of the virus.\n\nMethodThe article uses the Susceptible-Infected-Quarantined-Recovered model with modification, introducing 14 different Infected states depending on the number of days the host has been carrying the infection. We simulate the spread of 2019-nCoV on human interaction similar graph taken from Online Social Network Epinions, of about 75000 nodes, similar to a small town or settlement. The infection rates depend on the sanitation and cleanliness these people exercise.\n\nResultsWhen people practice self-quarantine and hygiene, aided by the governmental efforts of testing and quarantine, the cumulative number of affected people fall drastically. The decrease is apparent in time-based simulations of the spread received from the study.\n\nConclusionThe 2019-nCoV is a highly infectious zoonotic virus. It has spread like a pandemic, and governments across the world have launched quarantines. The results of the SIQR-t model indicate that hygiene and social-distancing can reduce its impact and sharply decrease the infection scale. Individual efforts are key to the control.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Nipun aggarwal", + "author_inst": "Delhi Technological University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.17.20069161", "rel_title": "Mortality from COVID-19 in 12 countries and 6 states of the United States", @@ -1559564,45 +1557435,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.19.20071712", - "rel_title": "Potential magnitude of COVID-19-induced healthcare resource depletion in Ontario, Canada", - "rel_date": "2020-04-22", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.19.20071712", - "rel_abs": "BackgroundThe global spread of coronavirus disease 2019 (COVID-19) continues in several jurisdictions, causing significant strain to healthcare systems. The purpose of our study is to predict the impact of the COVID-19 pandemic on patient outcomes and the healthcare system in Ontario, Canada.\n\nMethodsWe developed an individual-level simulation to model the flow of COVID-19 patients through the Ontario healthcare system. We simulated different combined scenarios of epidemic trajectory and healthcare capacity. Outcomes include numbers of patients needing admission to the ward, Intensive Care Unit (ICU), and requiring ventilation; days to resource depletion; and numbers of patients awaiting resources and deaths associated with limited access to resources.\n\nFindingsWe demonstrate that with effective early public health measures system resources need not be depleted. For scenarios considering late or ineffective implementation of physical distancing, health system resources would be depleted within 14-26 days. Resource depletion was also avoided or delayed with aggressive measures to rapidly increase ICU, ventilator, and acute care hospital capacity.\n\nInterpretationWe found that without aggressive physical distancing measures the Ontario healthcare system would have been inadequately equipped to manage the expected number of patients with COVID-19, despite the rapid capacity increase. This overall lack of resources would have led to an increase in mortality. By slowing the spread of the disease via ongoing public health measures and having increased healthcare capacity, Ontario may have avoided catastrophic stresses to its health care system.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Kali Barrett", - "author_inst": "University Health Network" - }, - { - "author_name": "Yasin A Khan", - "author_inst": "University Health Network" - }, - { - "author_name": "Stephen Mac", - "author_inst": "Institute of Health Policy, Management and Evaluation, University of Toronto" - }, - { - "author_name": "Raphael Ximenes", - "author_inst": "Toronto Health Economics and Technology Assessment (THETA) Collaborative, University Health Network" - }, - { - "author_name": "David MJ Naimark", - "author_inst": "Sunnybrook Health Sciences Centre" - }, - { - "author_name": "Beate Sander", - "author_inst": "Toronto Health Economics and Technology Assessment (THETA) Collaborative, University Health Network" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.19.20071845", "rel_title": "The importance of timing of a population level intervention on COVID-19 mortality", @@ -1560586,6 +1558418,25 @@ "type": "new results", "category": "physiology" }, + { + "rel_doi": "10.1101/2020.04.20.052217", + "rel_title": "SARS-CoV-2 Encodes a PPxY Late Domain Motif that is Known to Enhance 1 Budding and Spread in Enveloped RNA Viruses", + "rel_date": "2020-04-21", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.20.052217", + "rel_abs": "The current COVID-19 (Coronavirus Disease-2019) pandemic is affecting the health and/or socioeconomic welfare of almost everyone in the world. Finding vaccines and therapeutics is therefore urgent, but elucidation of the molecular mechanisms that allow some viruses to cross host species boundaries, becoming a threat to human health, must also be given close attention. Here, analysis of all proteins of SARS-CoV-2 revealed a unique PPxY Late (L) domain motif, 25PPAY28, in a spike (S) protein inside a predicted hot disordered loop subject to phosphorylation and binding. PPxY motifs in enveloped RNA viruses are known to recruit Nedd4 E3 ubiquitin ligases and ultimately the ESCRT complex to enhance virus budding and release, resulting in higher viral loads, hence facilitating new infections. Interestingly, proteins of SARS-CoV-1 do not feature PPxY motifs, which could explain why SARS-CoV-2 is more contagious than SARS-CoV-1. Should an experimental assessment of this hypothesis show that the PPxY motif plays the same role in SARS-CoV-2 as it does in other enveloped RNA viruses, this motif will become a promising target for the development of novel host-oriented antiviral therapeutics for preventing S proteins from recruiting Nedd4 E3 ubiquitin ligase partners.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Halim Maaroufi", + "author_inst": "Universite Laval" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.04.21.052084", "rel_title": "Artificial intelligence predicts the immunogenic landscape of SARS-CoV-2: toward universal blueprints for vaccine designs", @@ -1561002,201 +1558853,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.15.20064931", - "rel_title": "Sequencing analysis of the spread of SARS-CoV2 in the Greater New York City region", - "rel_date": "2020-04-21", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.15.20064931", - "rel_abs": "Effective public response to a pandemic relies upon accurate measurement of the extent and dynamics of an outbreak. Viral genome sequencing has emerged as a powerful approach to link seemingly unrelated cases, and large-scale sequencing surveillance can inform on critical epidemiological parameters. Here, we report the analysis of 864 SARS-CoV-2 sequences from cases in the New York City metropolitan area during the COVID-19 outbreak in Spring 2020. The majority of cases had no recent travel history or known exposure, and genetically linked cases were spread throughout the region. Comparison to global viral sequences showed that early transmission was most linked to cases from Europe. Our data are consistent with numerous seeds from multiple sources and a prolonged period of unrecognized community spreading. This work highlights the complementary role of genomic surveillance in addition to traditional epidemiological indicators.", - "rel_num_authors": 45, - "rel_authors": [ - { - "author_name": "Matthew T Maurano", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Sitharam Ramaswami", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Paul Zappile", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Dacia Dimartino", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Ludovic Boytard", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Andre M Ribeiro-dos-Santos", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Nicholas A Vulpescu", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Gael Westby", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Guomiao Shen", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Xiaojun Feng", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Megan S Hogan", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Manon Ragonnet-Cronin", - "author_inst": "MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Imperial College London" - }, - { - "author_name": "Lily Geidelberg", - "author_inst": "MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Imperial College London" - }, - { - "author_name": "Christian Marier", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Peter Meyn", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Yutong Zhang", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "John Cadley", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Raquel Ordonez", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Raven Luther", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Emily Huang", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Emily Guzman", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Carolina Arguelles-Grande", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Kimon V Argyropoulos", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Margaret Black", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Antonio Serrano", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Melissa E Call", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Min Jae Kim", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Brendan Belovarac", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Tatyana Gindin", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Andrew Lytle", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Jared Pinnell", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Theodore Vougiouklakis", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "John Chen", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Lawrence H Lin", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Amy Rapkiewicz", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Vanessa Raabe", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Marie I Samanovic", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "George Jour", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Iman Osman", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Maria Aguero-Rosenfeld", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Mark J Mulligan", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Erik M Volz", - "author_inst": "MRC Centre for Global Infectious Disease Analysis and Department of Infectious Disease Epidemiology, Imperial College London" - }, - { - "author_name": "Paolo Cotzia", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Matija Snuderl", - "author_inst": "NYU School of Medicine" - }, - { - "author_name": "Adriana Heguy", - "author_inst": "NYU School of Medicine" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.16.20065920", "rel_title": "Outcomes of hydroxychloroquine usage in United States veterans hospitalized with Covid-19", @@ -1562396,6 +1560052,433 @@ "type": "new results", "category": "scientific communication and education" }, + { + "rel_doi": "10.1101/2020.04.19.049254", + "rel_title": "Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells", + "rel_date": "2020-04-20", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.19.049254", + "rel_abs": "The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, creates an urgent need for identifying molecular mechanisms that mediate viral entry, propagation, and tissue pathology. Cell membrane bound angiotensin-converting enzyme 2 (ACE2) and associated proteases, transmembrane protease serine 2 (TMPRSS2) and Cathepsin L (CTSL), were previously identified as mediators of SARS-CoV2 cellular entry. Here, we assess the cell type-specific RNA expression of ACE2, TMPRSS2, and CTSL through an integrated analysis of 107 single-cell and single-nucleus RNA-Seq studies, including 22 lung and airways datasets (16 unpublished), and 85 datasets from other diverse organs. Joint expression of ACE2 and the accessory proteases identifies specific subsets of respiratory epithelial cells as putative targets of viral infection in the nasal passages, airways, and alveoli. Cells that co-express ACE2 and proteases are also identified in cells from other organs, some of which have been associated with COVID-19 transmission or pathology, including gut enterocytes, corneal epithelial cells, cardiomyocytes, heart pericytes, olfactory sustentacular cells, and renal epithelial cells. Performing the first meta-analyses of scRNA-seq studies, we analyzed 1,176,683 cells from 282 nasal, airway, and lung parenchyma samples from 164 donors spanning fetal, childhood, adult, and elderly age groups, associate increased levels of ACE2, TMPRSS2, and CTSL in specific cell types with increasing age, male gender, and smoking, all of which are epidemiologically linked to COVID-19 susceptibility and outcomes. Notably, there was a particularly low expression of ACE2 in the few young pediatric samples in the analysis. Further analysis reveals a gene expression program shared by ACE2+TMPRSS2+ cells in nasal, lung and gut tissues, including genes that may mediate viral entry, subtend key immune functions, and mediate epithelial-macrophage cross-talk. Amongst these are IL6, its receptor and co-receptor, IL1R, TNF response pathways, and complement genes. Cell type specificity in the lung and airways and smoking effects were conserved in mice. Our analyses suggest that differences in the cell type-specific expression of mediators of SARS-CoV-2 viral entry may be responsible for aspects of COVID-19 epidemiology and clinical course, and point to putative molecular pathways involved in disease susceptibility and pathogenesis.", + "rel_num_authors": 103, + "rel_authors": [ + { + "author_name": "Christoph Muus", + "author_inst": "Broad Institute" + }, + { + "author_name": "Malte D Luecken", + "author_inst": "Institute of Computational Biology, Helmholtz Zentrum Munchen, Munich, Germany" + }, + { + "author_name": "Gokcen Eraslan", + "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Avinash Waghray", + "author_inst": "Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care U" + }, + { + "author_name": "Graham Heimberg", + "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Lisa Sikkema", + "author_inst": "Institute of Computational Biology, Helmholtz Zentrum Munchen, Munich, Germany" + }, + { + "author_name": "Yoshihiko Kobayashi", + "author_inst": "Department of Cell Biology, Duke University Medical School, Durham, NC 27710, USA" + }, + { + "author_name": "Eeshit Dhaval Vaishnav", + "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA Department of Biology, Massachusetts Institute of Technology, Cambridge," + }, + { + "author_name": "Ayshwarya Subramanian", + "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Christopher Smillie", + "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Karthik Jagadeesh", + "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Elizabeth Thu Duong", + "author_inst": "University of California San Diego Department of Pediatrics, Division of Respiratory Medicine" + }, + { + "author_name": "Evgenij Fiskin", + "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Elena Torlai Triglia", + "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Christophe Becavin", + "author_inst": "Universite Cote dAzur, CNRS, IPMC, Sophia-Antipolis, 06560, France" + }, + { + "author_name": "Meshal Ansari", + "author_inst": "Comprehensive Pneumology Center (CPC) / Institute of Lung Biology and Disease (ILBD), Helmholtz Zentrum Munchen, Member of the German Center for Lung Research (" + }, + { + "author_name": "Peiwen Cai", + "author_inst": "Department of Genetics and Genomic Sciences, Icahn School of Medicineat Mount Sinai, New York, NY 10029, USA" + }, + { + "author_name": "Brian Lin", + "author_inst": "Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA Departments of Internal Medicine and Pediatrics, Pulmonary and Critical Care U" + }, + { + "author_name": "Justin Buchanan", + "author_inst": "Center for Epigenomics, University of California-San Diego School of Medicine, La Jolla, CA, 92093. Department of Cellular and Molecular Medicine, University of" + }, + { + "author_name": "Jian Shu", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Adam L Haber", + "author_inst": "Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA. Klarman Cell Observatory, Broad Institute of MIT and Harv" + }, + { + "author_name": "Hattie Chung", + "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Daniel T Montoro", + "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Taylor Adams", + "author_inst": "Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine" + }, + { + "author_name": "Hananeh Aliee", + "author_inst": "Institute of Computational Biology, Helmholtz Zentrum Munchen, Member of the German Center for Lung Research (DZL), Munich, Germany" + }, + { + "author_name": "Samuel J Allon", + "author_inst": "Institute for Medical Engineering and Science & Department of Chemistry, MIT; Ragon Institute of MGH, MIT and Harvard; Broad Institute of MIT and Harvard" + }, + { + "author_name": "Zaneta Andrusivova", + "author_inst": "SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology" + }, + { + "author_name": "Ilias Angelidis", + "author_inst": "Comprehensive Pneumology Center (CPC) / Institute of Lung Biology and Disease (ILBD), Helmholtz Zentrum Munchen, Member of the German Center for Lung Research (" + }, + { + "author_name": "Orr Ashenberg", + "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Kevin Bassler", + "author_inst": "Department for Genomics & Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany" + }, + { + "author_name": "Inbal Benhar", + "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA Center for Brain Science, Harvard University, Cambridge, MA 02138 Depart" + }, + { + "author_name": "Joseph Bergenstrahle", + "author_inst": "SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology" + }, + { + "author_name": "Ludvig Bergenstrahle", + "author_inst": "SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology" + }, + { + "author_name": "Liam Bolt", + "author_inst": "Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK" + }, + { + "author_name": "Emelie Braun", + "author_inst": "Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute" + }, + { + "author_name": "Linh T Bui", + "author_inst": "Translational Genomics Research Institute, Phoenix, AZ" + }, + { + "author_name": "Mark Chaffin", + "author_inst": "Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA, USA 02142" + }, + { + "author_name": "Evgeny Chichelnitskiy", + "author_inst": "Institute of Transplant Immunology, Hannover Medical School, MHH, Carl-Neuberg Str. 1, 30625 Hannover, Germany, phone +40 511 532 9745; fax +40 511 532 8090; Ge" + }, + { + "author_name": "Joshua Chiou", + "author_inst": "Biomedical Sciences Graduate Program, University of California-San Diego, La Jolla, CA, 92093" + }, + { + "author_name": "Thomas M Conlon", + "author_inst": "Comprehensive Pneumology Center (CPC) / Institute of Lung Biology and Disease (ILBD), Helmholtz Zentrum Munchen, Member of the German Center for Lung Research (" + }, + { + "author_name": "Michael S Cuoco", + "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Marie Deprez", + "author_inst": "Universite Cote dAzur, CNRS, IPMC, Sophia-Antipolis, 06560, France" + }, + { + "author_name": "David S Fischer", + "author_inst": "Institute of Computational Biology, Helmholtz Zentrum Munchen, Munich, Germany" + }, + { + "author_name": "Astrid Gillich", + "author_inst": "Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA." + }, + { + "author_name": "Joshua Gould", + "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Austin J Gutierrez", + "author_inst": "Translational Genomics Research Institute, Phoenix, AZ" + }, + { + "author_name": "Arun C Habermann", + "author_inst": "Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN" + }, + { + "author_name": "Tyler Harvey", + "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Peng He", + "author_inst": "Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK" + }, + { + "author_name": "Xiaomeng Hou", + "author_inst": "Center for Epigenomics, University of California-San Diego School of Medicine, La Jolla, CA, 92093. Department of Cellular and Molecular Medicine, University of" + }, + { + "author_name": "Lijuan Hu", + "author_inst": "Division of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institute" + }, + { + "author_name": "Alok Jaiswal", + "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Peiyong Jiang", + "author_inst": "Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China" + }, + { + "author_name": "Theodoros Kapellos", + "author_inst": "Department for Genomics & Immunoregulation, LIMES-Institute, University of Bonn, 53115 Bonn, Germany" + }, + { + "author_name": "Christin S Kuo", + "author_inst": "Department of Pediatrics, Pulmonary Medicine, Stanford University School of Medicine, Stanford, CA." + }, + { + "author_name": "Ludvig Larsson", + "author_inst": "SciLifeLab, Department of Gene Technology, KTH Royal Institute of Technology" + }, + { + "author_name": "Michael A Leney-Greene", + "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Kyungtae Lim", + "author_inst": "Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK" + }, + { + "author_name": "Monika Litvinukova", + "author_inst": "Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom.; Cardiovascular and Metabolic Scien" + }, + { + "author_name": "Ji Lu", + "author_inst": "Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China" + }, + { + "author_name": "Leif S Ludwig", + "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA Division of Hematology / Oncology, Boston Childrens Hospital and Departm" + }, + { + "author_name": "Wendy Luo", + "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Henrike Maatz", + "author_inst": "Cardiovascular and Metabolic Sciences, Max Delbruck Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany" + }, + { + "author_name": "Elo Maddissoon", + "author_inst": "Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK" + }, + { + "author_name": "Lira Mamanova", + "author_inst": "Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK" + }, + { + "author_name": "Kasidet Manakongtreecheep", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, USA Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA Cente" + }, + { + "author_name": "Ian Mbano", + "author_inst": "Africa Health Research Institute, Durban, South Africa" + }, + { + "author_name": "Alexi M McAdams", + "author_inst": "Department of Ophthalmology, Harvard Medical School and Massachusetts Eye and Ear, Boston, MA 02114" + }, + { + "author_name": "Ross J Metzger", + "author_inst": "Vera Moulton Wall Center for Pulmonary Vascular Disease, Department of Pediatrics, Division of Cardiology, Stanford University School of Medicine, Stanford, CA" + }, + { + "author_name": "Ahmad N Nabhan", + "author_inst": "Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA." + }, + { + "author_name": "Sarah K Nyquist", + "author_inst": "Computational and Systems Biology, CSAIL, Institute for Medical Engineering and Science & Department of Chemistry, MIT; Ragon Institute of MGH, MIT and Harvard;" + }, + { + "author_name": "Jose Ordovas-Montanes", + "author_inst": "Division of Gastroenterology Boston Childrens Hospital; Program in Immunology Harvard Medical School; Harvard Stem Cell Institute; Broad Institute of MIT and Ha" + }, + { + "author_name": "Lolita Penland", + "author_inst": "Chan Zuckerberg Biohub, San Francisco, CA, USA." + }, + { + "author_name": "Olivier B Poirion", + "author_inst": "Center for Epigenomics, University of California-San Diego School of Medicine, La Jolla, CA, 92093. Department of Cellular and Molecular Medicine, University of" + }, + { + "author_name": "Segio Poli", + "author_inst": "Division of Internal Medicine - Mount Sinai Medical Center, Miami Beach, FL" + }, + { + "author_name": "CanCan Qi", + "author_inst": "Dept. of Pediatric Pulmonology and Pediatric Allergology, Beatrix Childrens Hospital, University of Groningen, University Medical Center Groningen, Groningen, T" + }, + { + "author_name": "Daniel Reichart", + "author_inst": "Department of Genetics, Harvard Medical School, Boston, MA, United States.; Department of Cardiology, University Heart&Vascular Center, University of Hamburg, H" + }, + { + "author_name": "Ivan Rosas", + "author_inst": "Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine" + }, + { + "author_name": "Jonas Schupp", + "author_inst": "Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine" + }, + { + "author_name": "Rahul Sinha", + "author_inst": "Institute for Stem Cell Biology and Regenerative Medicine, Department of Pathology, Stanford University School of Medicine, Stanford, CA" + }, + { + "author_name": "Rene V Sit", + "author_inst": "Chan Zuckerberg Biohub, San Francisco, CA, USA." + }, + { + "author_name": "Kamil Slowikowski", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, USA Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA Cente" + }, + { + "author_name": "Michal Slyper", + "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Neal Smith", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, USA Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA Cente" + }, + { + "author_name": "Alex Sountoulidis", + "author_inst": "Stockholm University, Department of Molecular Biosciences, The Wenner-Gren Institute" + }, + { + "author_name": "Maximilian Strunz", + "author_inst": "Comprehensive Pneumology Center (CPC) / Institute of Lung Biology and Disease (ILBD), Helmholtz Zentrum Munchen, Member of the German Center for Lung Research (" + }, + { + "author_name": "Dawei Sun", + "author_inst": "Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN, UK" + }, + { + "author_name": "Carlos Talavera-Lopez", + "author_inst": "Cellular Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom" + }, + { + "author_name": "Peng Tan", + "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Jessica Tantivit", + "author_inst": "Broad Institute of MIT and Harvard, Cambridge, MA, USA Center for Cancer Research, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA Cente" + }, + { + "author_name": "Kyle J Travaglini", + "author_inst": "Department of Biochemistry and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA." + }, + { + "author_name": "Nathan R Tucker", + "author_inst": "Precision Cardiology Laboratory, The Broad Institute, Cambridge, MA, USA 02142 Masonic Medical Research Institute, Utica, NY, USA 13501" + }, + { + "author_name": "Katherine Vernon", + "author_inst": "Department of Medicine, Brigham and Womens Hospital and Harvard Medical School, Boston, MA, USA Broad Institute of MIT and Harvard, Cambridge, MA, USA" + }, + { + "author_name": "Marc H Wadsworth III", + "author_inst": "Institute for Medical Engineering and Science, Department of Chemistry & Koch Institute for Integrative Cancer Research, MIT; Ragon Institute of MGH, MIT and Ha" + }, + { + "author_name": "Julia Waldman", + "author_inst": "Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA" + }, + { + "author_name": "Xiuting Wang", + "author_inst": "Department of Genetics and Genomic Sciences, Icahn School of Medicineat Mount Sinai, New York, NY 10029, USA" + }, + { + "author_name": "Wenjun Yan", + "author_inst": "Center for Brain Science, Harvard University, Cambridge, MA 02138 Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138" + }, + { + "author_name": "Ali Onder Yildirim", + "author_inst": "Comprehensive Pneumology Center (CPC) / Institute of Lung Biology and Disease (ILBD), Helmholtz Zentrum Munchen, Member of the German Center for Lung Research (" + }, + { + "author_name": "William Zhao", + "author_inst": "Department of Genetics and Genomic Sciences, Icahn School of Medicineat Mount Sinai, New York, NY 10029, USA" + }, + { + "author_name": "Carly G K Ziegler", + "author_inst": "Harvard-MIT Health Sciences and Technology, Institute for Medical Engineering and Science, Koch Institute for Integrative Cancer Research, MIT; Broad Institute " + }, + { + "author_name": "Aviv Regev", + "author_inst": "MIT and Broad Inst. of MIT & Harvard" + }, + { + "author_name": "- The NHLBI LungMAP Consortium", + "author_inst": "-" + }, + { + "author_name": "- The Human Cell Atlas Lung Biological Network", + "author_inst": "-" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.04.20.046920", "rel_title": "Leverging Deep Learning to Simulate Coronavirus Spike proteins has the potential to predict future Zoonotic sequences", @@ -1562796,65 +1560879,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.04.20.051581", - "rel_title": "Boceprevir, GC-376, and calpain inhibitors II, XII inhibit SARS-CoV-2 viral replication by targeting the viral main protease", - "rel_date": "2020-04-20", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.20.051581", - "rel_abs": "A novel coronavirus SARS-CoV-2, also called novel coronavirus 2019 (nCoV-19), started to circulate among humans around December 2019, and it is now widespread as a global pandemic. The disease caused by SARS-CoV-2 virus is called COVID-19, which is highly contagious and has an overall mortality rate of 6.96% as of May 4, 2020. There is no vaccine or antiviral available for SARS-CoV-2. In this study, we report our discovery of inhibitors targeting the SARS-CoV-2 main protease (Mpro). Using the FRET-based enzymatic assay, several inhibitors including boceprevir, GC-376, and calpain inhibitors II, and XII were identified to have potent activity with single-digit to submicromolar IC50 values in the enzymatic assay. The mechanism of action of the hits was further characterized using enzyme kinetic studies, thermal shift binding assays, and native mass spectrometry. Significantly, four compounds (boceprevir, GC-376, calpain inhibitors II and XII) inhibit SARS-CoV-2 viral replication in cell culture with EC50 values ranging from 0.49 to 3.37 M. Notably, boceprevir, calpain inhibitors II and XII represent novel chemotypes that are distinct from known Mpro inhibitors. A complex crystal structure of SARS-CoV-2 Mpro with GC-376, determined at 2.15 [A] resolution with three monomers per asymmetric unit, revealed two unique binding configurations, shedding light on the molecular interactions and protein conformational flexibility underlying substrate and inhibitor binding by Mpro. Overall, the compounds identified herein provide promising starting points for the further development of SARS-CoV-2 therapeutics.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Chunlong Ma", - "author_inst": "University of Arizona" - }, - { - "author_name": "Michael D Sacco", - "author_inst": "University of South Florida" - }, - { - "author_name": "Brett Hurst", - "author_inst": "Utah State University" - }, - { - "author_name": "Julia A Townsend", - "author_inst": "University of Arizona" - }, - { - "author_name": "Yanmei Hu", - "author_inst": "University of Arizona" - }, - { - "author_name": "Tommy Szeto", - "author_inst": "University of Arizona" - }, - { - "author_name": "Xiujun Zhang", - "author_inst": "University of South Florida" - }, - { - "author_name": "Bart Tarbet", - "author_inst": "Utah State University" - }, - { - "author_name": "Michael T Marty", - "author_inst": "University of Arizona" - }, - { - "author_name": "Yu Chen", - "author_inst": "University of South Florida" - }, - { - "author_name": "Jun Wang", - "author_inst": "University of Arizona" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "pharmacology and toxicology" - }, { "rel_doi": "10.1101/2020.04.20.050138", "rel_title": "Interplay of host regulatory network on SARS-CoV-2 binding and replication machinery", @@ -1563954,6 +1561978,89 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.14.20065276", + "rel_title": "Hydroxychloroquine Versus COVID-19: A Rapid Systematic Review and Meta-Analysis", + "rel_date": "2020-04-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20065276", + "rel_abs": "BackgroundCoronavirus Disease 2019 (COVID-19) has become a major global issue with rising the number of infected individuals and mortality in recent months. Among all therapeutic approaches, arguments have raised about hydroxychloroquine (HCQ) efficacy in the treatment of COVID-19. We carried out a systematic review and meta-analysis overcome the controversies regarding the effectiveness of hydroxychloroquine in the treatment of COVID-19.\n\nMethodsA systematic search was performed in PubMed, Scopus, Embase, Cochrane Library, Web of Science, Google Scholar and medRxiv pre-print database using all available MeSH terms for COVID-19 and hydroxychloroquine up to July 19, 2020. Studies focused on the effectiveness of HCQ with/without azithromycin (AZM) in confirmed COVID-19 patients were entered into the study. Two researchers have independently evaluated quality assessment of the studies and abstracted data for data extraction. Extracted data were analyzed using CMA v. 2.2.064. Heterogeneity was assessed using the I-squared (I2) test, and fixed/random-effects model was used when appropriate for pooling of studies.\n\nResultsOut of 26 studies entered into our systematic review, 21 studies including 14 comparative studies with control group and seven observational studies containing 103,486 participants have entered into the meta-analysis. The results of the meta-analysis on comparative studies indicated no significant clinical effectiveness (negative in RT-PCR evaluation) for HCQ regimen in the treatment of COVID-19 in comparison to control group (RR: 1.03, 95% CI, 0.79-1.34). The same result was observed for the combination of HCQ+azithromycin (RR: 1.26, 95% CI, 0.91-1.74). No significant differences were found for both HCQ (RR: 0.92, 95% CI, 0.72-1.16) and HCQ+AZM (RR: 1.72, 95% CI, 0.86-3.42) mortality rate; however, mortality was affected by age differences according to meta-regression analysis (P<0.000001). No substantial difference was observed for disease exacerbation (RR: 1.23, 95% CI, 0.65-2.30) between HCQ group and controls. Also, radiological findings significantly improved in the HCQ group (OR: 0.32, 95% CI, 0.11-0.98). Odds of known HCQ adverse effects (diarrhea, vomiting, blurred vision, rash, headache, etc.) occurred in the HCQ regimen group was approximately 3.5 times of control group (OR: 3.40, 95% CI, 1.65-6.98), but no substantial differences were found regarding intubation odds between HCQ group and control group (OR: 2.11, 95% CI, 0.31-14.03). Meta-analysis indicated no significant prophylactic effects for HCQ (OR: 0.40, 95% CI, 0.04-3.65)\n\nConclusionThis systematic review and meta-analysis showed no clinical benefits regarding HCQ treatment with/without azithromycin for COVID-19 patients. Although mortality rate was not significantly different between cases and controls, frequency of adverse effects was substantially higher in HCQ regimen group. However, due to that most of the studies were non-randomized and results were not homogenous, selection bias was unavoidable and further large randomized clinical trials following comprehensive meta-analysis should be taken into account in order to achieve more reliable findings. Also, it is worth mentioning that if this work does not allow to quantify a \"value\" of the HCQ, it allows at least to know what is not the HCQ and that it would be prudent not to continue investing in this direction.", + "rel_num_authors": 17, + "rel_authors": [ + { + "author_name": "Amir Shamshirian", + "author_inst": "Mazandaran University of Medical Sciences" + }, + { + "author_name": "Amirhossein Hessami", + "author_inst": "Mazandaran University of Medical Sciences" + }, + { + "author_name": "Keyvan Heydari", + "author_inst": "Mazandaran University of Medical Sciences" + }, + { + "author_name": "Reza Alizadeh-Navaei", + "author_inst": "Mazandaran University of Medical Sciences" + }, + { + "author_name": "Mohammad Ali Ebrahimzadeh", + "author_inst": "Mazandaran University of Medical Sciences" + }, + { + "author_name": "George W YIP", + "author_inst": "National University of Singapore" + }, + { + "author_name": "Roya Ghasemian", + "author_inst": "Mazandaran University of Medical Sciences" + }, + { + "author_name": "Meghdad Sedaghat", + "author_inst": "Shahid Beheshti University of Medical Sciences" + }, + { + "author_name": "Hananeh Baradaran", + "author_inst": "Tehran university of medical sciences" + }, + { + "author_name": "Soheil Mohammadi Yazdi", + "author_inst": "Kashan University of Medical Sciences" + }, + { + "author_name": "Elham Aboufazeli", + "author_inst": "IRAN NAJO Pharmaceutical Company" + }, + { + "author_name": "Hamed Jafarpour", + "author_inst": "Mazandaran University of Medical Sciences" + }, + { + "author_name": "Ehsan Dadgostar", + "author_inst": "Halal research center of IRI" + }, + { + "author_name": "Behnaz Tirandazi", + "author_inst": "Iran University of Medical Sciences" + }, + { + "author_name": "Keyvan Karimifar", + "author_inst": "Mashhad University of Medical Sciences" + }, + { + "author_name": "Aida Eftekhari", + "author_inst": "Mashhad University of Medical Sciences" + }, + { + "author_name": "Danial Shamshirian", + "author_inst": "Shahid Beheshti University of Medical Sciences" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.15.20067157", "rel_title": "Epidemiology, clinical course, and outcomes of critically ill adults with COVID-19 in New York City: a prospective cohort study", @@ -1564458,77 +1562565,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.04.14.20060160", - "rel_title": "Patient-derived mutations impact pathogenicity of SARS-CoV-2", - "rel_date": "2020-04-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20060160", - "rel_abs": "The sudden outbreak of the severe acute respiratory syndrome-coronavirus (SARS-CoV-2) has spread globally with more than 1,300,000 patients diagnosed and a death toll of 70,000. Current genomic survey data suggest that single nucleotide variants (SNVs) are abundant. However, no mutation has been directly linked with functional changes in viral pathogenicity. We report functional characterizations of 11 patient-derived viral isolates. We observed diverse mutations in these viral isolates, including 6 different mutations in the spike glycoprotein (S protein), and 2 of which are different SNVs that led to the same missense mutation. Importantly, these viral isolates show significant variation in cytopathic effects and viral load, up to 270-fold differences, when infecting Vero-E6 cells. Therefore, we provide direct evidence that the SARS-CoV-2 has acquired mutations capable of substantially changing its pathogenicity.", - "rel_num_authors": 14, - "rel_authors": [ - { - "author_name": "Hangping Yao", - "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Z" - }, - { - "author_name": "Xiangyun Lu", - "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Z" - }, - { - "author_name": "Qiong Chen", - "author_inst": "Life Sciences Institute, Zhejiang University" - }, - { - "author_name": "Kaijin Xu", - "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Z" - }, - { - "author_name": "Yu Chen", - "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Z" - }, - { - "author_name": "Linfang Cheng", - "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Z" - }, - { - "author_name": "Fumin Liu", - "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Z" - }, - { - "author_name": "Zhigang Wu", - "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Z" - }, - { - "author_name": "Haibo Wu", - "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Z" - }, - { - "author_name": "Changzhong Jin", - "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Z" - }, - { - "author_name": "Min Zheng", - "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Z" - }, - { - "author_name": "Nanping Wu", - "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, First Affiliated Hospital, Z" - }, - { - "author_name": "Chao Jiang", - "author_inst": "Life Sciences Institute, Zhejiang University" - }, - { - "author_name": "Lanjuan Li", - "author_inst": "State Key Laboratory for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.16.20067611", "rel_title": "The focus and timing of COVID-19 pandemic control measures under healthcare resource constraints", @@ -1565592,6 +1563628,101 @@ "type": "new results", "category": "pathology" }, + { + "rel_doi": "10.1101/2020.04.13.20063784", + "rel_title": "Comparative dynamic aerosol efficiencies of three emergent coronaviruses and the unusual persistence of SARS-CoV-2 in aerosol suspensions", + "rel_date": "2020-04-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.13.20063784", + "rel_abs": "The emergent coronavirus, designated severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is a zoonotic pathogen that has demonstrated remarkable transmissibility in the human population and is the etiological agent of a current global pandemic called COVID-191. We measured the dynamic (short-term) aerosol efficiencies of SARS-CoV-2 and compared the efficiencies with two other emerging coronaviruses, SARS-CoV (emerged in 2002) and Middle Eastern respiratory syndrome CoV (MERS-CoV; emerged starting in 2012). We also quantified the long-term persistence of SARS-CoV-2 and its ability to maintain infectivity when suspended in aerosols for up to 16 hours.", + "rel_num_authors": 20, + "rel_authors": [ + { + "author_name": "Alyssa C Fears", + "author_inst": "Tulane School of Medicine, Tulane National Primate Research Center" + }, + { + "author_name": "William B Klimstra", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Paul Duprex", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Amy Hartman", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Scott C. Weaver", + "author_inst": "World Reference Center for Emerging Viruses and Arboviruses, Institute for Human Infections and Immunity, University of Texas Medical Branch" + }, + { + "author_name": "Ken S. Plante", + "author_inst": "World Reference Center for Emerging Viruses and Arboviruses, Institute for Human Infections and Immunity, University of Texas Medical Branch" + }, + { + "author_name": "Divya Mirchandani", + "author_inst": "World Reference Center for Emerging Viruses and Arboviruses, Institute for Human Infections and Immunity, University of Texas Medical Branch G" + }, + { + "author_name": "Jessica Plante", + "author_inst": "World Reference Center for Emerging Viruses and Arboviruses, Institute for Human Infections and Immunity, University of Texas Medical Branch G" + }, + { + "author_name": "Patricia V. Aguilar", + "author_inst": "Department of Pathology and Center for Tropical Diseases, University of Texas Medical Branch" + }, + { + "author_name": "Diana Fernandez", + "author_inst": "Department of Pathology and Center for Tropical Diseases, University of Texas Medical Branch" + }, + { + "author_name": "Aysegul Nalca", + "author_inst": "USAMRIID" + }, + { + "author_name": "Allison Totura", + "author_inst": "USAMRIID" + }, + { + "author_name": "David Dyer", + "author_inst": "USAMRIID" + }, + { + "author_name": "Brian Kearney", + "author_inst": "USAMRIID" + }, + { + "author_name": "Matthew Lackemeyer", + "author_inst": "National Institutes of Health, National Institute of Allergy and Infectious Diseases, Integrated Research Facility" + }, + { + "author_name": "J. Kyle Bohannon", + "author_inst": "National Institutes of Health, National Institute of Allergy and Infectious Diseases, Integrated Research Facility" + }, + { + "author_name": "Reed Johnson", + "author_inst": "National Institutes of Health, National Institute of Allergy and Infectious Diseases, Integrated Research Facility" + }, + { + "author_name": "Robert F Garry", + "author_inst": "Tulane School of Medicine, Tulane National Primate Research Center" + }, + { + "author_name": "Doug S Reed", + "author_inst": "University of Pittsburgh" + }, + { + "author_name": "Chad J Roy", + "author_inst": "Tulane School of Medicine, Tulane National Primate Research Center" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.13.20064162", "rel_title": "Mesenchymal stromal cells for COVID-19: A living systematic review protocol", @@ -1566360,25 +1564491,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.14.20065706", - "rel_title": "Has mortality due to other causes increased during the Covid-19 pandemic? Early evidence from England and Wales", - "rel_date": "2020-04-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20065706", - "rel_abs": "BackgroundThe Covid-19 pandemic has claimed many lives in the UK and globally. The objective of this paper is to study whether the number of deaths not registered as covid-19-related has increased compared to what would have been expected in the absence of the pandemic. This may be a result of some covid-19 deaths being unreported or spillover effects on other causes of death (or both). Reasons behind this might include covid-19 underreporting, avoiding visits to hospitals or GPs, and the effects of the lockdown.\n\nMethodsI used weekly ONS data on the number of deaths in England and Wales that did not officially involve covid-19 over the period 2015-2020. Simply observing trends is not sufficient as spikes in deaths may occasionally occur. I thus followed a differences-in-differences econometric approach to study whether there was a relative increase in deaths not registered as covid-19-related during the pandemic, compared to a control. As an additional approach, an interrupted time series model was also used.\n\nResultsResults suggest that there are an additional 968 weekly deaths that officially did not involve covid-19, compared to what would have otherwise been expected. This increase is also confirmed by the interrupted time series analysis.\n\nDiscussionThe number of deaths not officially involving covid-19 has demonstrated an absolute and relative increase during the pandemic. It is possible that some people are dying from covid-19 without being diagnosed, and that there are excess deaths due to other causes as a result of the pandemic. Analysing the cause of death for any excess non-covid-19 deaths will shed light upon the reasons for the increase in such deaths and will help design appropriate policy responses to save lives.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Sotiris Vandoros", - "author_inst": "King's College London" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.15.20067207", "rel_title": "A cross-sectional study of patients presenting for hospital-based screening for COVID-19: risk of disease, and healthcare access preferences.", @@ -1567258,6 +1565370,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.11.037473", + "rel_title": "Multiscale three-dimensional pathology findings of COVID-19 diseased lung using high-resolution cleared tissue microscopy", + "rel_date": "2020-04-17", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.11.037473", + "rel_abs": "The study of pulmonary samples from individuals who have died as a direct result of COVID-19 infection is vital to our understanding of the pathogenesis of this disease. Histopathologic studies of lung tissue from autopsy of patients with COVID-19 specific mortality are only just emerging. All existing reports have relied on traditional 2-dimensional slide-based histological methods for specimen preparation. However, emerging methods for high-resolution, massively multiscale imaging of tissue microstructure using fluorescence labeling and tissue clearing methods enable the acquisition of tissue histology in 3-dimensions, that could open new insights into the nature of SARS-Cov-2 infection and COVID-19 disease processes. In this article, we present the first 3-dimensional images of lung autopsy tissues taken from a COVID-19 patient, including 3D \"virtual histology\" of cubic-millimeter volumes of the diseased lung, providing unique insights into disease processes contributing to mortality that could inform frontline treatment decisions.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Guang Li", + "author_inst": "Tulane University" + }, + { + "author_name": "Sharon E Fox", + "author_inst": "LSU Health Sciences Center - New Orleans" + }, + { + "author_name": "Brian Summa", + "author_inst": "Tulane University" + }, + { + "author_name": "Bihe Hu", + "author_inst": "Tulane University" + }, + { + "author_name": "Carola Wenk", + "author_inst": "Tulane University" + }, + { + "author_name": "Aibek Akmatbekov", + "author_inst": "LSU Health Sciences Center - New Orleans" + }, + { + "author_name": "Jack L Harbert", + "author_inst": "LSU Health Sciences Center - New Orleans" + }, + { + "author_name": "Richard S. Vander Heide", + "author_inst": "LSU Health Sciences Center - New Orleans" + }, + { + "author_name": "J. Quincy Brown", + "author_inst": "Tulane University" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "pathology" + }, { "rel_doi": "10.1101/2020.04.14.20064766", "rel_title": "The end of the social confinement in Spain and the COVID-19 re-emergence risk", @@ -1567730,101 +1565893,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.04.14.20064733", - "rel_title": "Chest Computed Tomography for the Diagnosis of Patients with Coronavirus Disease 2019 (COVID-19): A Rapid Review and Meta-Analysis", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20064733", - "rel_abs": "BackgroundThe outbreak of the coronavirus disease 2019 (COVID-19) has had a massive impact on the whole world. Computed tomography (CT) has been widely used in the diagnosis of this novel pneumonia. This study aims to understand the role of CT for the diagnosis and the main imaging manifestations of patients with COVID-19.\n\nMethodsWe conducted a rapid review and meta-analysis on studies about the use of chest CT for the diagnosis of COVID-19. We comprehensively searched databases and preprint servers on chest CT for patients with COVID-19 between 1 January 2020 and 31 March 2020. The primary outcome was the sensitivity of chest CT imaging. We also conducted subgroup analyses and evaluated the quality of evidence using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach.\n\nResultsA total of 104 studies with 5694 patients were included. Using RT-PCR results as reference, a meta-analysis based on 64 studies estimated the sensitivity of chest CT imaging in COVID-19 was 99% (95% CI, 0.97-1.00). If case reports were excluded, the sensitivity in case series was 96% (95% CI, 0.93-0.99). The sensitivity of CT scan in confirmed patients under 18 years old was only 66% (95% CI, 0.11-1.00). The most common imaging manifestation was ground-glass opacities (GGO) which was found in 75% (95% CI, 0.68-0.82) of the patients. The pooled probability of bilateral involvement was 84% (95% CI, 0.81-0.88). The most commonly involved lobes were the right lower lobe (84%, 95% CI, 0.78-0.90) and left lower lobe (81%, 95% CI, 0.74-0.87). The quality of evidence was low across all outcomes.\n\nConclusionsIn conclusion, this meta-analysis indicated that chest CT scan had a high sensitivity in diagnosis of patients with COVID-19. Therefore, CT can potentially be used to assist in the diagnosis of COVID-19.", - "rel_num_authors": 20, - "rel_authors": [ - { - "author_name": "Meng Lv", - "author_inst": "Lanzhou University" - }, - { - "author_name": "Mengshu Wang", - "author_inst": "Department of Radiology, The First Affiliated Hospital, Lanzhou University" - }, - { - "author_name": "Nan Yang", - "author_inst": "Department of Respiratory Medicine; Children's Hospital of Chongqing Medical University" - }, - { - "author_name": "Xufei Luo", - "author_inst": "School of Public Health of Lanzhou University, Lanzhou" - }, - { - "author_name": "Wei Li", - "author_inst": "Department of Radiology; Children's Hospital of Chongqing Medical University" - }, - { - "author_name": "Xin Chen", - "author_inst": "Department of Radiology; Children's Hospital of Chongqing Medical University" - }, - { - "author_name": "Yunlan Liu", - "author_inst": "School of Public Health, Lanzhou University" - }, - { - "author_name": "Mengjuan Ren", - "author_inst": "School of Public Health, Lanzhou University" - }, - { - "author_name": "Xianzhuo Zhang", - "author_inst": "The First School of Clinical Medicine, Lanzhou University" - }, - { - "author_name": "Ling Wang", - "author_inst": "School of Public Health, Lanzhou University" - }, - { - "author_name": "Yanfang Ma", - "author_inst": "Evidence-based Medicine Center, School of Basic Medical Sciences, Lanzhou University" - }, - { - "author_name": "Junqiang Lei", - "author_inst": "Department of Radiology, The First Affiliated Hospital, Lanzhou University" - }, - { - "author_name": "Toshio Fukuoka", - "author_inst": "Emergency and Critical Care Center, the Department of General Medicine, Department of Research and Medical Education at Kurashiki Central Hospital" - }, - { - "author_name": "Hyeong Sik Ahn", - "author_inst": "Department of Preventive Medicine, Korea University College of Medicine" - }, - { - "author_name": "Myeong Soo Lee", - "author_inst": "Korea Institute of Oriental Medicine, Daejeon, Korea" - }, - { - "author_name": "Zhengxiu Luo", - "author_inst": "Department of Respiratory Medicine; Children's Hospital of Chongqing Medical University" - }, - { - "author_name": "Yaolong Chen", - "author_inst": "Evidence-based Medicine Center, School of Basic Medical Sciences, Lanzhou University" - }, - { - "author_name": "Enmei Liu", - "author_inst": "Department of Respiratory Medicine; Children's Hospital of Chongqing Medical University" - }, - { - "author_name": "Jinhui Tian", - "author_inst": "Evidence-based Medicine Center, School of Basic Medical Sciences, Lanzhou University" - }, - { - "author_name": "Xiaohui Wang", - "author_inst": "School of Public Health, Lanzhou University" - } - ], - "version": "1", - "license": "", - "type": "PUBLISHAHEADOFPRINT", - "category": "radiology and imaging" - }, { "rel_doi": "10.1101/2020.04.16.044016", "rel_title": "A Large-scale Drug Repositioning Survey for SARS-CoV-2 Antivirals", @@ -1568956,6 +1567024,97 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.14.20065664", + "rel_title": "Application of Telemedicine During the Coronavirus Disease Epidemics: A Rapid Review and Meta-Analysis", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20065664", + "rel_abs": "BackgroundAs COVID-19 has become a global pandemic, early prevention and control of the epidemic is extremely important. Telemedicine, which includes medical advice given over telephone, Internet, mobile phone applications or other similar ways, may be an efficient way to reduce transmission and pressure on medical institutions.\n\nMethodsWe searched MEDLINE, Web of science, Embase, Cochrane, CBM, CNKI and Wanfang databases for literature on the use of telemedicine for COVID-19, SARS and MERS. from their inception to March 31st, 2020. We included studies about the content of the consultation (such as symptoms, therapy and prevention, policy, public service), screening of suspected cases, the provision of advice given to those people who may have symptoms or contact history. We conducted meta-analyses on the main outcomes of the studies.\n\nResultsA total of 2041 articles were identified after removing duplicates. After reading the full texts, we finally included nine studies. People were most concerned about symptoms (64.2%), epidemic situation and public problems (14.5%), and psychological problems (10.3%) during COVID-19 epidemic. During the SARS epidemic, the proportions of people asking for consultation for symptoms, prevention and therapy, and psychological problems were 35.0%, 22.0%, and 23.0%, respectively. Two studies demonstrated that telemedicine can be used to screen the suspected patients and give advice. One study emphasized the limited possibilities to follow up people calling hotlines and difficulties in identifying all suspect cases.\n\nConclusionsTelemedicine services should focus on the issues that the public is most concerned about, such as then symptoms, prevention and treatment of the disease, and provide reasonable advice to patients with symptoms or people with epidemic history.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Yelei Gao", + "author_inst": "Children's Hospital of Chongqing Medical University, Chongqing, China" + }, + { + "author_name": "Rui Liu", + "author_inst": "Children's Hospital of Chongqing Medical University, Chongqing 400014, China" + }, + { + "author_name": "Qi Zhou", + "author_inst": "The First School of Clinical Medicine, Lanzhou University, Lanzhou 730000, China" + }, + { + "author_name": "Xingmei Wang", + "author_inst": "Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University" + }, + { + "author_name": "Liping Huang", + "author_inst": "Children's Hospital of Chongqing Medical University, Chongqing 400014, China" + }, + { + "author_name": "Qianling Shi", + "author_inst": "The First School of Clinical Medicine,Lanzhou University,Lanzhou 730000,China" + }, + { + "author_name": "Zijun Wang", + "author_inst": "Lanzhou University" + }, + { + "author_name": "Shuya Lu", + "author_inst": "Department of Pediatric, Sichuan Provincial People's Hospital, University of Electronic Science a" + }, + { + "author_name": "Weiguo Li", + "author_inst": "Children's Hospital of Chongqing Medical University, Chongqing 400014, China" + }, + { + "author_name": "Yanfang Ma", + "author_inst": "Evidence-based Medicine Center,School of Basic Medical Sciences,Lanzhou University,Lanzhou 730000,China" + }, + { + "author_name": "Xufei Luo", + "author_inst": "School of Public Health, Lanzhou University, Lanzhou 730000, China" + }, + { + "author_name": "Toshio Fukuoka", + "author_inst": "Emergency and Critical Care Center, the Department of General Medicine, Department of Research and Medical Education at Kurashiki Central Hospital, Japan" + }, + { + "author_name": "Hyeong Sik Ahn", + "author_inst": "Department of Preventive Medicine, Korea University College of Medicine, Seoul, Korea" + }, + { + "author_name": "Myeong Soo Lee", + "author_inst": "Korea Institute of Oriental Medicine, Daejeon, Korea" + }, + { + "author_name": "Zhengxiu Luo", + "author_inst": "Children's Hospital of Chongqing Medical University, Chongqing 400014, China" + }, + { + "author_name": "Enmei Liu", + "author_inst": "Children's Hospital of Chongqing Medical University,Chongqing 400014,China" + }, + { + "author_name": "Yaolong Chen", + "author_inst": "School of Public Health, Lanzhou University, Lanzhou 730000, China" + }, + { + "author_name": "Chang Shu", + "author_inst": "Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University, Chongqing 400014, China" + }, + { + "author_name": "Daiyin Tian", + "author_inst": "Department of Respiratory Medicine, Children's Hospital of Chongqing Medical University, Chongqing 400014, China" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.14.20065557", "rel_title": "Failing our Most Vulnerable: COVID-19 and Long-Term Care Facilities in Ontario", @@ -1569348,33 +1567507,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.14.20064501", - "rel_title": "What influences COVID-19 infection rates: A statistical approach to identify promising factors applied to infection data from Germany", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.14.20064501", - "rel_abs": "The recent COVID-19 pandemic is of big and world-wide concern. There is an intense discussion and uncertainty which factors and sanctions can reduce infection rates. The overall aim is to prevent an overload of the medical system. Even within one country, there is frequently a strong local variability in both - political sanctions as well as other local factors - which may influence infection rates. The main focus of study is analysis and interpretation of recent temporal developments (infection rates). We present a statistical framework designed to identify local factors which reduce infection rates. The approach is robust with respect to the number of undetected infection cases. We apply the framework to spatio-temporal infection data from Germany. In particular, we demonstrate that (1) infection rates are in average significantly decreasing in Germany; (2) there is a high spatial variability of these rates, and (3) both, early emergence of first infections and high local infection densities has led to strong recent decays in infection rates, suggesting that psychological effects (such as awareness of danger) lead to behaviour changes that reduce infection rates. However, the full potential of the presented method cannot yet be exploited, since more precise spatio-temporal data, such as local cell phone-based mobility data, are not yet available. In the nearest future, the presented framework could be applied to data from other countries at any state of infection, even during the exponential phase of the growth of infection rates.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Moritz Mercker", - "author_inst": "BIONUM - Consultants in biological and biomedical statistics, Hamburg, Germany" - }, - { - "author_name": "Uwe Betzin", - "author_inst": "User Experience Consultant, Schriesheim, Germany" - }, - { - "author_name": "Dennis Wilken", - "author_inst": "Institute of Geosciences, Kiel University, Kiel, Germany" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.14.20064840", "rel_title": "Estimate of Covid-19 prevalence using imperfect data", @@ -1570146,6 +1568278,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.12.20060079", + "rel_title": "Serum Mycoplasma Pneumoniae IgG in COVID-19: A Protective Factor", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.12.20060079", + "rel_abs": "BackgroundA correlation between prior exposure to Mycoplasma pneumoniae (IgG positive) and better clinical response to COVID-19 was elusive.\n\nMethodsA retrospective review of all COVID-19 infected patients treated at Wuhan Union Hospital from Feb 1 to Mar 20 was carried out. Continuous variables were described as mean, median, and interquartile range (IQR), while categorical variables were compared by X2 test or Fishers exact test between COVID-19 infected patients with mycoplasma lgG (-) and mycoplasma lgG (+).\n\nResultsStatistically significant differences were shown in terms of laboratory test results. COVID-19 infected patients with mycoplasma lgG positivity had a higher lymphocyte count and percentage (p=0.026, p=0.017), monocyte count and percentage (p=0.028, p=0.006) and eosinophil count and percentage (p=0.039, p=0.007), and a lower neutrophil count and percentage (p=0.044, p=0.006) than COVID-19 infected patients without mycoplasma lgG. Other routine blood tests, including coagulation tests, blood biochemistry and infection-related biomarkers did not significantly differ except for thrombin time (p=0.001) and lactate dehydrogenase (p=0.008). Furthermore, requirement and use of a nasal catheter or oxygen mask was significantly lower in COVID-19 infected patients with mycoplasma lgG positivity (p=0.029).\n\nConclusionsOur findings indicate that mycoplasma IgG positivity is a potential protective factor for SARS-CoV-2 infection.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Bobin Mi", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Lang Chen", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Adriana C. Panayi", + "author_inst": "Brigham and Women's Hospital" + }, + { + "author_name": "Yuan Xiong", + "author_inst": "Wuhan Union Hospital" + }, + { + "author_name": "Guohui Liu", + "author_inst": "Wuhan Union Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.15.20057786", "rel_title": "RAPID SEROLOGICAL TESTS HAVE A ROLE IN ASYMPTOMATIC HEALTH WORKERS COVID-19 SCREENING", @@ -1570462,29 +1568629,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "radiology and imaging" }, - { - "rel_doi": "10.1101/2020.04.12.20062695", - "rel_title": "Shut it down: a cross country panel analysis on the efficacy of lockdown measures", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.12.20062695", - "rel_abs": "Coronavirus pandemic outbreak from China in the December 2019 and since then has quickly spread all over the world. National governments introduced policies aimed to reduce the probability to contract the virus, such as lockdown measures, in order to limit the outbreak. Lockdown fostered a debate about the effective need and the optimal duration of such measures. Indeed, these policies have a high price, being characterized by the alt of many productive activities. The aim of this note is to provide preliminary evidences about the efficacy of lockdown measures all over the world, by the means of a panel data quantitative analysis. Our results confirm the efficacy of such measures, and that the average time to have effects in terms of a reduction of cases is of about ten days. Furthermore the beneficial effects of a lockdown keep reducing the new cases with a linear trend for at least the ten successive days.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Vincenzo Alfano", - "author_inst": "University of Napoli Federico II" - }, - { - "author_name": "Salvatore Ercolano", - "author_inst": "University of Basilicata" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.04.11.20062125", "rel_title": "Coronavirus epidemic: prediction and controlling measures", @@ -1571264,6 +1569408,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.16.20061127", + "rel_title": "Outcomes of the 2019 Novel Coronavirus in patients with or without a history of cancer - a multi-centre North London experience", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.16.20061127", + "rel_abs": "BackgroundFour months after the first known case of the 2019 novel coronavirus disease (COVID-19), on the 11th March 2020, the WHO declared the outbreak a pandemic and acknowledged the potential to overwhelm national healthcare systems. The high prevalence and associated healthcare, social and economic challenges of COVID-19 suggest this pandemic is likely to have a major impact on cancer management, and has been shown to potentially have worse outcomes in this cohort of vulnerable patients (1). This study aims to compare the outcomes of reverse transcriptase polymerase chain reaction (RT-PCR) confirmed COVID-19 positive disease in patients with or without a history of cancer.\n\nMethodWe retrospectively collected clinical, pathological and radiological characteristics and outcomes of COVID-19 RT-PCR positive cancer patients treated consecutively in four different North London hospitals (cohort A). Outcomes recorded included morbidity, mortality and length of hospital stay. All clinically relevant outcomes were then compared to consecutively admitted COVID-19 positive patients, without a history of cancer (cohort B), treated at the primary centre during the same time period (12th March-7th April 2020).\n\nResultsA total of 52 electronic patient records during the study time period were reviewed. Cohort A (median age 76 years, 56% males) and cohort B (median age 58 years, 62% male) comprised of 26 patients each. With the exclusion of cancer, both had a median of 2 comorbidities. Within cohort A, the most frequent underlying cancer was colorectal (5/26) and prostate cancer (5/26), and 77% of patients in Cohort A had received previous anti-cancer therapy. The most common presenting symptoms were cough and pyrexia in both cohorts. Frequent laboratory findings included lymphopenia, anaemia and elevated CRP in both cohorts, whilst hypokalaemia, hypoalbuminaemia and hypoproteinaemia was predominantly seen amongst patients with cancer. Median duration of admission was 7 days in both cohorts. The mortality rate was the same in both cohorts (23%), with median age of mortality of 80 years. Of cancer patients who died, all were advanced stage, had been treated with palliative intent and had received anti-cancer therapy within 13 days of admission.\n\nConclusionOld age, late stage of cancer diagnosis and multiple co-morbidities adversely influence the outcome of patients with COVID-19 positive patients. Whilst extra caution is warranted in the administration of anti-cancer therapies pertaining to the risk of immune-suppression, this data does not demonstrate a higher risk to cancer patients compared to their non-cancer counterparts.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Nalinie Joharatnam-Hogan", + "author_inst": "University College London Hospital" + }, + { + "author_name": "Daniel Hochhauser", + "author_inst": "University College London Hospital NHS Foundation Trust" + }, + { + "author_name": "Kai-Keen Shiu", + "author_inst": "University College London Hospital NHS Foundation Trust" + }, + { + "author_name": "Hannah Rush", + "author_inst": "University College London" + }, + { + "author_name": "Valerie Crolley", + "author_inst": "North Middlesex University Hospital NHS Trust" + }, + { + "author_name": "Emma Butcher", + "author_inst": "University College London" + }, + { + "author_name": "Anand Sharma", + "author_inst": "Mount Vernon Hospital" + }, + { + "author_name": "Aun Muhammad", + "author_inst": "Whittington Hospital" + }, + { + "author_name": "Nikhil Vasdev", + "author_inst": "Lister Hospital" + }, + { + "author_name": "Muhammad Anwar", + "author_inst": "Princess Alexandra Hospital" + }, + { + "author_name": "Ganna Kantser", + "author_inst": "North Middlesex University Hospital" + }, + { + "author_name": "Aramita Saha", + "author_inst": "North Middlesex University Hospital" + }, + { + "author_name": "Fharat Raja", + "author_inst": "North Middlesex University Hospital" + }, + { + "author_name": "John Bridgewater", + "author_inst": "University College London Hospital NHS Foundation Trust" + }, + { + "author_name": "Khurum Khan", + "author_inst": "University College London Hospital NHS Trust" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.12.20062828", "rel_title": "Estimation of airborne viral emission: quanta emission rate of SARS-CoV-2 for infection risk assessment", @@ -1571640,25 +1569859,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.13.20063610", - "rel_title": "The December 2019 New Corona Virus Disease (SARS-CoV-2) Outbreak: A Behavioral Infectious Disease Policy Model", - "rel_date": "2020-04-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.13.20063610", - "rel_abs": "It is critical to understand the impact of distinct policy interventions to the ongoing coronavirus disease pandemic. I develop a flexible behavioral, dynamic, and sectorial epidemic policy model comprising both endogenous virus transmission and public health and citizen responses. Applicable to the full epidemic cycle including confinement, deconfinement, and resurgence, the model allows exploring the multivariate impact of distinct policy interventions, including general and targeted testing and social contact reduction efforts. Using a cross-sectional calibration to data on the ongoing coronavirus disease outbreak about reported cases and deaths, tests performed, and social interactions from six countries (South Korea, Germany, Italy, France, Sweden, and the United States), I demonstrate how early, rapid, and extensive buildup of testing and social contact reduction efforts interplay to suppress the outbreak. I then use the model to show and quantify limits to the extent of deconfinement and illustrate the critical role of targeted approaches for managing post peak deconfinement and resurgence. To aid necessary public and expert understanding of outbreak control strategies the model is accessible in the form of a web-based management flight simulator.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Jeroen Struben", - "author_inst": "emlyon business school" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.13.20063628", "rel_title": "The Effect of Stay-at-Home Orders on COVID-19 Infections in the United States", @@ -1572406,6 +1570606,29 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.13.20064253", + "rel_title": "Population simulations of COVID-19 outbreaks provide tools for risk assessment and continuity planning", + "rel_date": "2020-04-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.13.20064253", + "rel_abs": "Essential industrial sectors, healthcare systems, and government agencies must continue operations despite the risk of COVID-19 infection. They need tools to assess risks associated with operations, so they can devise emergency plans. We developed a population-based simulator to study COVID-19 outbreaks in enclosed environments and evaluate the effectiveness of preventative measures and action plans, such as pre-dispatch quarantine and removal of symptomatic cases.\n\nAvailabilityThe simulation tool is publicly available at http://github.com/ictr/covid19-outbreak-simulator and is free for non-commercial use.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Bo Peng", + "author_inst": "Baylor College of Medicine" + }, + { + "author_name": "Christopher I Amos", + "author_inst": "Baylor College of Medicine" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.13.20064220", "rel_title": "Severe underestimation of COVID-19 case numbers: effect of epidemic growth rate and test restrictions", @@ -1572674,65 +1570897,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.12.20062869", - "rel_title": "Cardiovascular Diseases and COVID-19 Mortality and Intensive Care Unit Admission: A Systematic Review and Meta-analysis", - "rel_date": "2020-04-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.12.20062869", - "rel_abs": "BackgroundHigh rate of cardiovascular disease (CVD) have been reported among patients with novel coronavirus disease (COVID-19). Meanwhile there were controversies among different studies about CVD burden in COVID-19 patients. Hence, we aimed to study CVD burden among COVID-19 patients, using a systematic review and meta-analysis.\n\nMethodsWe have systematically searched databases including PubMed, Embase, Cochrane Library, Scopus, Web of Science as well as medRxiv pre-print database. Hand searched was also conducted in journal websites and Google Scholar. Meta-analyses were carried out for Odds Ratio (OR) of mortality and Intensive Care Unit (ICU) admission for different CVDs. We have also performed a descriptive meta-analysis on different CVDs.\n\nResultsFifty-six studies entered into meta-analysis for ICU admission and mortality outcome and 198 papers for descriptive outcomes, including 159,698 COVID-19 patients. Results of meta-analysis indicated that acute cardiac injury, (OR: 13.29, 95% CI 7.35-24.03), hypertension (OR: 2.60, 95% CI 2.11-3.19), heart Failure (OR: 6.72, 95% CI 3.34-13.52), arrhythmia (OR: 2.75, 95% CI 1.43-5.25), coronary artery disease (OR: 3.78, 95% CI 2.42-5.90), and cardiovascular disease (OR: 2.61, 95% CI 1.89-3.62) were significantly associated with mortality. Arrhythmia (OR: 7.03, 95% CI 2.79-17.69), acute cardiac injury (OR: 15.58, 95% CI 5.15-47.12), coronary heart disease (OR: 2.61, 95% CI 1.09-6.26), cardiovascular disease (OR: 3.11, 95% CI 1.59-6.09), and hypertension (OR: 1.95, 95% CI 1.41-2.68) were also significantly associated with ICU admission in COVID-19 patients.\n\nConclusionFindings of this study revealed a high burden of CVDs among COVID-19 patients, which was significantly associated with mortality and ICU admission. Proper management of CVD patients with COVID-19 and monitoring COVID-19 patients for acute cardiac conditions is highly recommended to prevent mortality and critical situations.\n\nGraphical abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=143 SRC=\"FIGDIR/small/20062869v2_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (22K):\norg.highwire.dtl.DTLVardef@21e53corg.highwire.dtl.DTLVardef@150dcc6org.highwire.dtl.DTLVardef@1ce7f21org.highwire.dtl.DTLVardef@1fc5fd7_HPS_FORMAT_FIGEXP M_FIG C_FIG", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Amirhossein Hessami", - "author_inst": "Mazandaran University of Medical Sciences" - }, - { - "author_name": "Amir Shamshirian", - "author_inst": "Mazandaran University of Medical Sciences" - }, - { - "author_name": "Keyvan Heydari", - "author_inst": "Mazandaran University of Medical Sciences" - }, - { - "author_name": "Fatemeh Pourali", - "author_inst": "Mazandaran University of Medical Sciences" - }, - { - "author_name": "Reza Alizadeh-Navaei", - "author_inst": "Mazandaran University of Medical Sciences" - }, - { - "author_name": "Mahmood Moosazadeh", - "author_inst": "Mazandaran University of Medical Sciences" - }, - { - "author_name": "Saeed Abrotan", - "author_inst": "Mazandaran University of Medical Sciences" - }, - { - "author_name": "Layla Shojaei", - "author_inst": "University of Southern California" - }, - { - "author_name": "Sogol Sedighi", - "author_inst": "Shiraz University of Medical Sciences" - }, - { - "author_name": "Danial Shamshirian", - "author_inst": "Shahid Beheshti University of Medical Sciences" - }, - { - "author_name": "Nima Rezaei", - "author_inst": "Tehran University of Medical Sciences" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.11.20061994", "rel_title": "Identifying common pharmacotherapies associated with reduced COVID-19 morbidity using electronic health records", @@ -1573623,6 +1571787,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.10.20061267", + "rel_title": "Public perceptions and experiences of social distancing and social isolation during the COVID-19 pandemic: A UK-based focus group study", + "rel_date": "2020-04-15", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20061267", + "rel_abs": "OBJECTIVEExplore the perceptions and experiences of the UK public of social distancing and social isolation measures related to the COVID-19 pandemic.\n\nDESIGNQualitative study comprising five focus groups carried out online during the early stages of the UKs social distancing and isolation measures (5-12 days post lockdown).\n\nSETTINGOnline video-conferencing\n\nPARTICIPANTS27 participants, all UK residents aged 18 years and older, representing a range of gender, ethnic, age and occupational backgrounds.\n\nRESULTSThe social distancing and isolation associated with COVID-19 policy has had having substantial negative impacts on the mental health and wellbeing of the UK public within a short time of policy implementation. It has disproportionately negatively affected those in low-paid or precarious employment. Practical social and economic losses - the loss of (in-person) social interaction, loss of income and loss of structure and routine - led to psychological and emotional losses - the loss of motivation, loss of meaning, and loss of self-worth. Participants reported high adherence to distancing and isolation guidelines but reported seeing or hearing of non-adherence in others. A central concern for participants was the uncertainty duration of the measures, and their ability to cope longer-term. Some participants felt they would have lingering concerns over social contact while others were eager to return to high levels of social activity.\n\nCONCLUSIONSA rapid response is necessary in terms of public health programming to mitigate the mental health impacts of COVID-19 social distancing and isolation. Initial high levels of support for, and adherence to, social distancing and isolation is likely to wane over time, particularly where end dates are uncertain. Social distancing and isolation exit strategies must account for the fact that, although some individuals will voluntarily or habitually continue to socially distance, others will seek high levels of social engagement as soon as possible.\n\nO_TEXTBOXWhat is already known on this topic\n\nO_LIAdherence to non-pharmaceutical interventions during pandemics is lower where people have low trust in government and where people perceive themselves at relatively low risk from the disease\nC_LIO_LIThere is a need for evidence on public perceptions and experiences of the psychological and social public experiences of COVID-19 related social distancing and isolation, and its relation to adherence.\nC_LI\n\nWhat this study adds\n\nO_LIPeople lack trust in government and perceive themselves at low personal risk,but closely adhere to social distancing and isolation measures motivated by social conscience, and are critical of non-adherence in others.\nC_LIO_LIPopulation-wide social distancing and isolation can have significant negative social and psychological impacts within a short time of policy implementation.\nC_LIO_LIKey concerns during social distancing and isolation are uncertainty of duration and ability to cope longer-term.\nC_LIO_LIAt the end of pandemic lockdowns, some individuals will likely voluntarily or habitually continue to socially distance, while others will likely seek high levels of social engagement as soon as possible.\nC_LI\n\nC_TEXTBOX", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Simon N Williams", + "author_inst": "Swansea University" + }, + { + "author_name": "Christopher J Armitage", + "author_inst": "University of Manchester" + }, + { + "author_name": "Tova Tampe", + "author_inst": "Independent Consultant, World Health Organization" + }, + { + "author_name": "Kimberly Dienes", + "author_inst": "University of Manchester" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.04.11.20061697", "rel_title": "Surveillance by age-class and prefecture for emerging infectious febrile diseases with respiratory symptoms, including COVID-19", @@ -1573967,49 +1572162,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.11.20062372", - "rel_title": "Self-Collected Oral Fluid and Nasal Swabs Demonstrate Comparable Sensitivity to Clinician Collected Nasopharyngeal Swabs for Covid-19 Detection", - "rel_date": "2020-04-15", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.11.20062372", - "rel_abs": "BackgroundCurrently, there is a pandemic caused by the 2019 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes Covid-19. We wanted to compare specimen types and collection methods to explore if a simpler to collect specimen type could expand access to testing.\n\nMethodsWe recruited individuals recently tested for SARS-CoV-2 infection through a \"drive-through\" testing program. In participants homes, we assessed the performance of self-collected oral fluid swab specimens with and without clinician supervision, clinician-supervised self-collected mid-turbinate (nasal) swab specimens, and clinician-collected nasopharyngeal swab specimens. We tested specimens with a validated reverse transcription-quantitative polymerase chain reaction assay for the detection of SARS-CoV-2 and measured cycle threshold values. Symptom status and date of onset of symptoms was also recorded for each participant.\n\nResultsWe recruited 45 participants. The median age of study participant was 42 years old (Interquartile range, 31 to 52 years). Of the participants, 29 had at least one specimen test positive for SARS-CoV-2. Of those, 21 (73%) of 29 reported active symptoms. By specimen type and home-based collection method, clinician-supervised self-collected oral fluid swab specimens detected 26 (90%) of 29 infected individuals, clinician-supervised self-collected nasal swab specimens detected 23 (85%) of 27, clinician-collected posterior nasopharyngeal swab specimens detected 23 (79%) of 29, and unmonitored self-collected oral fluid swab specimens detected 19 (66%) of 29. Despite nasopharyngeal swabs being considered the gold standard, 4 participants tested negative by clinician-collected nasopharyngeal swab and positive by the 3 other specimen types. Additionally, false negative results by each sample type were seen to generally not overlap.\n\nConclusionsSupervised self-collected oral fluid and nasal swab specimens performed similarly to, if not better than clinician-collected nasopharyngeal swab specimens for the detection of SARS-CoV-2 infection. No sample type captured all SARS-CoV-2 infections, suggesting potential heterogeneity in the distribution of viral load in different parts of the respiratory tract between individuals. Supervised self-collection performed comparably to clinician collection and would allow for rapid expansion of testing capacity in the United States by reducing the need for trained healthcare workers, reducing exposure of healthcare workers, and reducing the amount of PPE (personal protective equipment) being used for testing during a critical shortage.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Noah Kojima", - "author_inst": "UCLA" - }, - { - "author_name": "Fred Turner", - "author_inst": "Curative Inc" - }, - { - "author_name": "Vlad Slepnev", - "author_inst": "Curative Inc" - }, - { - "author_name": "Agatha Bacelar", - "author_inst": "Curative Inc" - }, - { - "author_name": "Laura Deming", - "author_inst": "Curative Inc" - }, - { - "author_name": "Siri Kodeboyina", - "author_inst": "Curative Inc" - }, - { - "author_name": "Jeffrey D Klausner", - "author_inst": "UCLA Health" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.11.20061333", "rel_title": "A survey-based study on the knowledge, attitude, and the practices pertaining to the 2019 novel Corona Virusinfection amongst undergraduate medical students in India", @@ -1574921,6 +1573073,85 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.04.15.042085", + "rel_title": "TMPRSS2 and furin are both essential for proteolytic activation and spread of SARS-CoV-2 in human airway epithelial cells and provide promising drug targets", + "rel_date": "2020-04-15", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.15.042085", + "rel_abs": "In December 2019, a novel coronavirus named SARS-CoV-2 first reported in Wuhan, China, emerged and rapidly spread to numerous other countries globally, causing the current pandemic. SARS-CoV-2 causes acute infection of the respiratory tract (COVID-19) that can result in severe disease and lethality. Currently, there is no approved antiviral drug for treating COVID-19 patients and there is an urgent need for specific antiviral therapies and vaccines.\n\nIn order for SARS-CoV-2 to enter cells, its surface glycoprotein spike (S) must be cleaved at two different sites by host cell proteases, which therefore represent potential drug targets. In the present study we investigated which host cell proteases activate the SARS-CoV-2 S protein in Calu-3 human airway epithelial cells. We show that S can be cleaved by both the proprotein convertase furin at the S1/S2 site and the transmembrane serine protease 2 (TMPRSS2) at the S2 site. We demonstrate that TMPRSS2 is essential for activation of SARS-CoV-2 S in Calu-3 cells through antisense-mediated knockdown of TMPRSS2 expression. Further, we show that SARS-CoV-2 replication can be efficiently inhibited by two synthetic inhibitors of TMPRSS2 and also by the broad range serine protease inhibitor aprotinin. Additionally, SARS-CoV-2 replication was also strongly inhibited by the synthetic furin inhibitor MI-1851. Combining various TMPRSS2 inhibitors with MI-1851 produced more potent antiviral activity against SARS-CoV-2 than an equimolar amount of any single serine protease inhibitor. In contrast, inhibition of endosomal cathepsins by E64d did not affect virus replication.\n\nOur data demonstrate that both TMPRSS2 and furin are essential for SARS-CoV-2 activation in human airway cells and are promising drug targets for the treatment of COVID-19 either by targeting one of these proteases alone or by a combination of furin and TMPRSS2 inhibitors. Therefore, this approach has a high therapeutic potential for treatment of COVID-19.", + "rel_num_authors": 16, + "rel_authors": [ + { + "author_name": "Dorothea Bestle", + "author_inst": "Institute of Virology, Philipps-University, Marburg, Germany" + }, + { + "author_name": "Miriam Ruth Heindl", + "author_inst": "Institute of Virology, Philipps-University, Marburg, Germany" + }, + { + "author_name": "Hannah Limburg", + "author_inst": "Institute of Virology, Philipps-University, Marburg, Germany" + }, + { + "author_name": "Thuy Van Lam van", + "author_inst": "Institute of Pharmaceutical Chemistry, Philipps-University, Marburg, Germany" + }, + { + "author_name": "Oliver Pilgram", + "author_inst": "Institute of Pharmaceutical Chemistry, Philipps-University, Marburg, Germany" + }, + { + "author_name": "Hong Moulton", + "author_inst": "Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, USA" + }, + { + "author_name": "David A. Stein", + "author_inst": "Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, USA" + }, + { + "author_name": "Kornelia Hardes", + "author_inst": "Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany" + }, + { + "author_name": "Markus Eickmann", + "author_inst": "Institute of Virology, Philipps-University, Marburg, Germany" + }, + { + "author_name": "Olga Dolnik", + "author_inst": "Institute of Virology, Philipps-University, Marburg, Germany" + }, + { + "author_name": "Cornelius Rohde", + "author_inst": "Institute of Virology, Philipps-University, Marburg, Germany" + }, + { + "author_name": "Stephan Becker", + "author_inst": "Institute of Virology, Philipps-University, Marburg, Germany" + }, + { + "author_name": "Hans-Dieter Klenk", + "author_inst": "Institute of Virology, Philipps-University, Marburg, Germany" + }, + { + "author_name": "Wolfgang Garten", + "author_inst": "Institute of Virology, Philipps-University, Marburg, Germany" + }, + { + "author_name": "Torsten Steinmetzer", + "author_inst": "Institute of Pharmaceutical Chemistry, Philipps-University, Marburg, Germany" + }, + { + "author_name": "Eva Bottcher-Friebertshauser", + "author_inst": "Institute of Virology, Philipps-University, Marburg, Germany" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.04.14.039925", "rel_title": "Multidrug treatment with nelfinavir and cepharanthine against COVID-19", @@ -1575489,45 +1573720,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.04.08.20058180", - "rel_title": "Impact of COVID-19 pandemic on severity of illness and resources required during intensive care in the greater New York City area", - "rel_date": "2020-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20058180", - "rel_abs": "ObjectiveDescribe the changes in patient population, bed occupancy, severity of illness and ventilator requirements across a large health system in the greater New York City area during the pandemic response in comparison with the 2019 baseline.\n\nDesignObservational, descriptive study of ICUs monitored by a tele-ICU system across Northwell Health. Inclusion criteria: All patients admitted to Northwell Health tele-ICUs during 2019 and between March 23, 2020 and April 6, 2020.\n\nExposureA data extract was developed to collect data every hour for each ICU bed in the Northwell tele-critical care program as a quality reporting initiative to understand ICU capacity and resource utilization. A similar extract was developed for each hour of 2019.\n\nMain Outcomes and MeasuresAverage of any given hour during the pre-COVID-19 and pandemic periods for the following metrics: proportion of beds occupied, proportion of ventilated patients, severity of illness (measured by the ICU Discharge Readiness Score (DRS)), and length of stay (LOS).\n\nResultsHourly analysis of data from 186 ICU beds from 14 ICUs and 9 hospitals were included, representing 10,714 patients in 2019 and 465 patients between March 23 and April 6, 2020. Average hourly occupancy increased from 64% to 78%, while the proportion of patients invasively ventilated increased from 33.9% to 84.2%. Median DRS (severity of illness score) increased from 1.08 (IQR: 0.24-6.98) to 39.38 (IQR: 12.00-71.28). Proportion of patients with Hispanic ethnicity doubled (7.8% to 16.6%; p<0.01) and proportion of female patients decreased from 46.3% to 32.9% (p<0.01).\n\nConclusions and RelevanceIn addition to the expected increase in ICU occupancy and ventilator requirements, this large group of ICUs in midst of the COVID-19 epidemic are faced with managing a cohort of ICU patients with a dramatically higher severity of illness than their typical census.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Omar Badawi", - "author_inst": "Philips Healthcare" - }, - { - "author_name": "Xinggang Liu", - "author_inst": "Philips Healthcare" - }, - { - "author_name": "Iris Berman", - "author_inst": "Northwell Health" - }, - { - "author_name": "Pamela J Amelung", - "author_inst": "Philips Healthcare" - }, - { - "author_name": "Martin Doerfler", - "author_inst": "Northwell Health" - }, - { - "author_name": "Saurabh Chandra", - "author_inst": "Northwell Health" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "intensive care and critical care medicine" - }, { "rel_doi": "10.1101/2020.04.09.20059634", "rel_title": "Bayesian Adaptive Clinical Trials for Anti-Infective Therapeutics during Epidemic Outbreaks", @@ -1576271,6 +1574463,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.10.20061036", + "rel_title": "A novel high specificity COVID-19 screening method based on simple blood exams and artificial intelligence", + "rel_date": "2020-04-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20061036", + "rel_abs": "BackgroundThe SARS-CoV-2 virus responsible for COVID-19 poses a significant challenge to healthcare systems worldwide. Despite governmental initiatives aimed at containing the spread of the disease, several countries are experiencing unmanageable increases in the demand for ICU beds, medical equipment, and larger testing capacity. Efficient COVID-19 diagnosis enables healthcare systems to provide better care for patients while protecting caregivers from the disease. However, many countries are constrained by the limited amount of test kits available, lack of equipment and trained professionals. In the case of patients visiting emergency rooms (ERs) with a suspect of COVID-19, prompt diagnosis may improve the outcome and even provide information for efficient hospital management. In such a context, a quick, inexpensive and readily available test to perform an initial triage in ERs could help to smooth patient flow, provide better patient care, and reduce the backlog of exams.\n\nMethodsIn this Case-control quantitative study, we developed a strategy backed by artificial intelligence to perform an initial screening of suspect COVID-19 patients. We developed a machine learning classifier that takes widely available simple blood exams as input and classifies samples as likely to be positive (having SARS-CoV-2) or negative (not having SARS-CoV-2). Based on this initial classification, positive cases can be referred for further highly sensitive testing (e.g. CT scan, or specific antibodies). We used publicly available data from the Albert Einstein Hospital in Brazil from 5,644 patients. Focusing on simple blood exam figures as main predictors, a sample of 599 subjects that had the fewest missing values for 16 common exams were selected. From these 599 patients, 81 tested positive for SARS-CoV-2 (determined by RT-PCR). Based on the reduced dataset, we built an artificial intelligence classification framework, ER-CoV, aiming at determining if suspect patients arriving in ER were likely to be negative for SARS-CoV-2, that is, to predict if that suspect patient is negative for COVID-19. The primary goal of this investigation is to develop a classifier with high specificity and high negative predictive values, with reasonable sensitivity.\n\nFindingsWe identified that our AI framework achieved an average specificity of 85.98% [95%CI: 84.94 - 86.84] and negative predictive value (NPV) of 94.92% [95%CI: 94.37% - 95.37%]. Those values are completely aligned with our goal of providing an effective low-cost system to triage suspect patients in ERs. As for sensitivity, our model achieved an average of 70.25% [95%CI: 66.57% - 73.12%] and positive predictive value (PPV) of 44.96% [95%CI: 43.15% - 46.87%]. The area under the curve (AUC) of the receiver operating characteristic (ROC) was 86.78% [95%CI: 85.65% - 87.90%]. An error analysis (inspection of which patients were misclassified) identified that, on average, 28% of the false negative results would have been hospitalized anyway; thus the model is making mistakes for severe cases that would not be overlooked, partially mitigating the fact that the test is not highly sensitive. All code for our AI model, called ER-CoV is publicly available at https://github.com/soares-f/ER-CoV.\n\nInterpretationBased on the capacity of our model to accurately predict which cases are negative from suspect patients arriving in emergency rooms, we envision that this framework may play an important role in patient triage. Probably the most important outcome is related to testing availability, which at this point is extremely low in many countries. Considering the achieved specificity, we could reduce by at least 90% the number of SARS-CoV-2 tests performed in emergency rooms, with around 5% chance of getting a false negative. The second important outcome is related to patient management in hospitals. Patients predicted as positive by our framework could be immediately separated from other patients while waiting for the results of confirmatory tests. This could reduce the spread rate within hospitals since in many of them all suspect cases are kept in the same ward. In Brazil, where the data was collected, rate infection is starting to quickly spread and the lead time of a SARS-CoV-2 may be up to 2 weeks.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Felipe Soares", + "author_inst": "University of Sheffield" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "health informatics" + }, { "rel_doi": "10.1101/2020.04.10.20061069", "rel_title": "Optimal Control applied to a SEIR model of 2019-nCoV with social distancing", @@ -1576627,37 +1574838,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.10.20060673", - "rel_title": "COVID-19 lockdowns cause global air pollution declines with implications for public health risk", - "rel_date": "2020-04-14", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.10.20060673", - "rel_abs": "The lockdown response to COVID-19 has caused an unprecedented reduction in global economic activity. We test the hypothesis that this has reduced tropospheric and ground-level air pollution concentrations using satellite data and a network of >10,000 air quality stations. After accounting for the effects of meteorological variability, we find remarkable declines in ground-level nitrogen dioxide (NO2: -29 % with 95% confidence interval -44% to -13%), ozone (O3: -11%; -20% to -2%) and fine particulate matter (PM2.5: -9%; -28% to 10%) during the first two weeks of lockdown (n = 27 countries). These results are largely mirrored by satellite measures of the troposphere although long-distance transport of PM2.5 resulted in more heterogeneous changes relative to NO2. Pollutant anomalies were related to short-term health outcomes using empirical exposure-response functions. We estimate that there was a net total of 7400 (340 to 14600) premature deaths and 6600 (4900 to 7900) pediatric asthma cases avoided during two weeks post-lockdown. In China and India alone, the PM2.5-related avoided premature mortality was 1400 (1100 to 1700) and 5300 (1000 to 11700), respectively. Assuming that the lockdown-induced deviations in pollutant concentrations are maintained for the duration of 2020, we estimate 0.78 (0.09 to 1.5) million premature deaths and 1.6 (0.8 to 2) million pediatric asthma cases could be avoided globally. While the state of global lockdown is not sustainable, these findings illustrate the potential health benefits gained from reducing \"business as usual\" air pollutant emissions from economic activities. Explore trends here: www.covid-19-pollution.zsv.co.za\n\nSignificance statementThe global response to the COVID-19 pandemic has resulted in unprecedented reductions in economic activity. We find that lockdown events have reduced air pollution levels by approximately 20% across 27 countries. The reduced air pollution levels come with a substantial health co-benefit in terms of avoided premature deaths and pediatric asthma cases that accompanied the COVID-19 containment measures.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Zander S Venter", - "author_inst": "Norwegian Institute for Nature Research" - }, - { - "author_name": "Kristin Aunan", - "author_inst": "CICERO Center for International Climate Research" - }, - { - "author_name": "Sourangsu Chowdhury", - "author_inst": "Max Planck Institute for Chemistry" - }, - { - "author_name": "Jos Lelieveld", - "author_inst": "Max Planck Institute for Chemistry" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.10.20060681", "rel_title": "A Stratified Model to Quantify the Effects of Containment Policies on the Spread of COVID-19", @@ -1577701,6 +1575881,57 @@ "type": "new results", "category": "molecular biology" }, + { + "rel_doi": "10.1101/2020.04.09.20059154", + "rel_title": "COVID-19 pandemic in the African continent: forecasts of cumulative cases, new infections, and mortality", + "rel_date": "2020-04-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20059154", + "rel_abs": "BackgroundThe epidemiology of COVID-19 remains speculative in Africa. To the best of our knowledge, no study, using robust methodology provides its trajectory for the region or accounts for local context. This paper is the first systematic attempt to provide prevalence, incidence, and mortality estimates across Africa.\n\nMethodsCaseloads and incidence forecasts are from a co-variate-based instrumental variable regression model. Fatality rates from Italy and China were applied to generate mortality estimates after making relevant health system and population-level characteristics related adjustments between each of the African countries.\n\nResultsBy June 30 2020, around 16.3 million people in Africa will contract COVID-19 (95% CI 718,403 to 98,358,799). Northern and Eastern Africa will be the most and least affected areas. Cumulative cases by June 30 are expected to reach around 2.9 million (95% CI 465,028 to 18,286,358) in Southern Africa, 2.8 million (95% CI 517,489 to 15,056,314) in Western Africa, and 1.2 million (95% CI 229,111 to 6,138,692) in Central Africa. Incidence for the month of April 2020 is expected to be highest in Djibouti, 32.8 per 1000 (95% CI 6.25 to 171.77), while Morocco will experience among the highest fatalities (1,045 deaths, 95% CI 167 to 6,547).\n\nConclusionLess urbanized countries with low levels of socio-economic development (hence least connected to the world), are likely to register lower and slower transmissions at the early stages of an epidemic. However, the same enabling factors that worked for their benefit can hinder interventions that have lessened the impact of COVID-19 elsewhere.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Tom Achoki", + "author_inst": "School of Health Systems and Public Health, University of Pretoria, South Africa" + }, + { + "author_name": "Uzma Alam", + "author_inst": "Africa Institute for Health Policy Foundation, Kenya" + }, + { + "author_name": "Lawrence Were", + "author_inst": "Department of Health Sciences & Department of Global Health, Boston University, Boston, MA." + }, + { + "author_name": "Tesfaye Gebremedhin", + "author_inst": "Department of Economics, Faculty of Business, Government and Law, University of Canberra." + }, + { + "author_name": "Flavia Senkubuge", + "author_inst": "School of Health Systems and Public Health, University of Pretoria, South Africa" + }, + { + "author_name": "Abaleng Lesego", + "author_inst": "Kudu Communications - Health Services" + }, + { + "author_name": "Shuangzhe Liu", + "author_inst": "Faculty of Science and Technology, University of Canberra" + }, + { + "author_name": "Richard Wamai", + "author_inst": "Department of Cultures, Societies and Global Studies, and Integrated Initiative for Global Health, Northeastern University" + }, + { + "author_name": "Yohannes Kinfu", + "author_inst": "Faculty of Health, University of Canberra, Australia" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.04.12.038216", "rel_title": "Detection of spreader nodes and ranking of interacting edges in Human-SARS-CoV protein interaction network", @@ -1578009,109 +1576240,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.12.037580", - "rel_title": "Single Nucleus Multiomic Profiling Reveals Age-Dynamic Regulation of Host Genes Associated with SARS-CoV-2 Infection", - "rel_date": "2020-04-14", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.12.037580", - "rel_abs": "Respiratory failure is the leading cause of COVID-19 death and disproportionately impacts adults more than children. Here, we present a large-scale snATAC-seq dataset (90,980 nuclei) of the human lung, generated in parallel with snRNA-seq (46,500 nuclei), from healthy donors of ~30 weeks, ~3 years and ~30 years of age. Focusing on genes implicated in SARS-CoV-2 cell entry, we observed an increase in the proportion of alveolar epithelial cells expressing ACE2 and TMPRSS2 in adult compared to young lungs. Consistent with expression dynamics, 10 chromatin peaks linked to TMPRSS2 exhibited significantly increased activity with age and harbored IRF and STAT binding sites. Furthermore, we identified 14 common sequence variants in age-increasing peaks with predicted regulatory function, including several associated with respiratory traits and TMPRSS2 expression. Our findings reveal a plausible contributor to why children are more resistant to COVID-19 and provide an epigenomic basis for transferring this resistance to older populations.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Allen Wang", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Joshua A Chiou", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Olivier B Poirion", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Justin Buchanan", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Michael J Valdez", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Jamie M Verheyden", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Xiaomeng Hou", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Jacklyn M Newsome", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Parul Kudtarkar", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Dina A Faddah", - "author_inst": "Vertex Phamaceuticals" - }, - { - "author_name": "Kai Zhang", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Randee E Young", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Justinn Barr", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Ravi Misra", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Heidie Huyck", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Lisa Rogers", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Cory Poole", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Gloria Pryhuber", - "author_inst": "University of Rochester Medical Center" - }, - { - "author_name": "Kyle J Gaulton", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Sebastian Preissl", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Xin Sun", - "author_inst": "University of California San Diego" - }, - { - "author_name": "- NHLBI LungMap Consortium", - "author_inst": "-" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "genomics" - }, { "rel_doi": "10.1101/2020.04.10.20060442", "rel_title": "Possibilities of exponential or Sigmoid growth of Covid19 data in different states of India", @@ -1579159,6 +1577287,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.09.20058859", + "rel_title": "Epidemic prevention and control measures in China significantly curbed the epidemic of COVID-19 and influenza", + "rel_date": "2020-04-14", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20058859", + "rel_abs": "At the end of 2019, an outbreak of unknown pathogen pneumonia occurred in China, then it was named corona virus disease 2019 (COVID-19). With the rapid spread of COVID-19, a series of strict prevention and control measures were implemented to cut the spread of the epidemic. Influenza as a respiratory tract infection disease as COVID-19 might also be controlled. To assess the effects, we used the total passenger numbers sent in mainland China from 2018 to 2020 and the daily number of railway passenger (DNRP) flow in 2020 during Spring Festival travel rush to reflect the population movement and further to analyze newly and cumulative confirmed COVID-19 and influenza. We found that with implementing the series measures on COVID-19, not only COVID-19, but also influenza mitigated in China. The prevention and control measures for COVID-19 might be used in controlling respiratory tract diseases, and reducing the national health economic burden. When other countries issue measures on COVID-19 and influenza, they should consider adopting more aggressive epidemic prevention and control strategies.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Xiang Sha Kong", + "author_inst": "Peking University People's Hospital" + }, + { + "author_name": "Feng Liu", + "author_inst": "Peking University People's Hospital" + }, + { + "author_name": "Hai Bo Wang", + "author_inst": "Peking University Clinical Research Institute" + }, + { + "author_name": "Rui Feng Yang", + "author_inst": "Peking University People's Hospital" + }, + { + "author_name": "Dong Bo Chen", + "author_inst": "Peking University People's Hospital" + }, + { + "author_name": "Xiao Xiao Wang", + "author_inst": "Peking University People's Hospital" + }, + { + "author_name": "Feng Min Lu", + "author_inst": "Peking University People's Hospital, School of Basic Medical Sciences" + }, + { + "author_name": "Hui Ying Rao", + "author_inst": "Peking University People's Hospital" + }, + { + "author_name": "Hong Song Chen", + "author_inst": "Peking University People's Hospital" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.09.20059626", "rel_title": "Neutrophil extracellular traps (NETs) as markers of disease severity in COVID-19", @@ -1579447,25 +1577626,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.04.10.036020", - "rel_title": "Analysis of Ten Microsecond simulation data of SARS-CoV-2 dimeric main protease", - "rel_date": "2020-04-12", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.10.036020", - "rel_abs": "The dimeric main protease of SARS-CoV-2, has become a crucial target for inhibiting/modulating its catalytic activity. However, understanding of its conformational change, and atomistic flexibility, is very much lucrative for designing/developing small molecules. Fortunately, huge data has been revealed by a research group, performed about ten-microsecond molecular dynamics to paving the way for understanding the structural complexity of protease. Herein, we have done the basic structural analysis, advanced flexibility and conformational analysis like PCA, for revealing out the regions and residues, which are mostly flexible and likely to be responsible for different conformation of protease protein.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Rimon Parves", - "author_inst": "University of Science and Technology, Chittagong" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "bioinformatics" - }, { "rel_doi": "10.1101/2020.04.10.036418", "rel_title": "The SARS-CoV-2 receptor-binding domain elicits a potent neutralizing response without antibody-dependent enhancement", @@ -1580545,6 +1578705,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.07.20056184", + "rel_title": "Modelling the impact of COVID-19 in Australia to inform transmission reducing measures and health system preparedness", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.07.20056184", + "rel_abs": "BackgroundThe ability of global health systems to cope with increasing numbers of COVID-19 cases is of major concern. In readiness for this challenge, Australia has drawn on clinical pathway models developed over many years in preparation for influenza pandemics. These models have been used to estimate health care requirements for COVID-19 patients, in the context of broader public health measures.\n\nMethodsAn age and risk stratified transmission model of COVID-19 infection was used to simulate an unmitigated epidemic with parameter ranges reflecting uncertainty in current estimates of transmissibility and severity. Overlaid public health measures included case isolation and quarantine of contacts, and broadly applied social distancing. Clinical presentations and patient flows through the Australian health care system were simulated, including expansion of available intensive care capacity and alternative clinical assessment pathways.\n\nFindingsAn unmitigated COVID-19 epidemic would dramatically exceed the capacity of the Australian health system, over a prolonged period. Case isolation and contact quarantine alone will be insufficient to constrain case presentations within a feasible level of expansion of health sector capacity. Overlaid social restrictions will need to be applied at some level over the course of the epidemic to ensure that systems do not become overwhelmed, and that essential health sector functions, including care of COVID-19 patients, can be maintained. Attention to the full pathway of clinical care is needed to ensure access to critical care.\n\nInterpretationReducing COVID-19 morbidity and mortality will rely on a combination of measures to strengthen and extend public health and clinical capacity, along with reduction of overall infection transmission in the community. Ongoing attention to maintaining and strengthening the capacity of health care systems and workers to manage cases is needed.\n\nFundingAustralian Government Department of Health Office of Health Protection, Australian Government National Health and Medical Research Council", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Robert Moss", + "author_inst": "Modelling and Simulation Unit, Melbourne School of Population and Global Health, The University of Melbourne" + }, + { + "author_name": "James Wood", + "author_inst": "School of Public Health and Community Medicine, UNSW Sydney" + }, + { + "author_name": "Damien Brown", + "author_inst": "Victorian Infectious Diseases Laboratory Epidemiology Unit at The Peter Doherty Institute for Infection and Immunity; The University of Melbourne and Royal Melb" + }, + { + "author_name": "Freya Shearer", + "author_inst": "Modelling and Simulation Unit, Melbourne School of Population and Global Health, The University of Melbourne" + }, + { + "author_name": "Andrew J Black", + "author_inst": "School of Mathematical Sciences, University of Adelaide" + }, + { + "author_name": "Allen Cheng", + "author_inst": "Infection Prevention and Healthcare Epidemiology Unit, Alfred Health; School of Public Health and Preventive Medicine, Monash University" + }, + { + "author_name": "James M McCaw", + "author_inst": "School of Mathematics and Statistics, The University of Melbourne" + }, + { + "author_name": "Jodie McVernon", + "author_inst": "The Peter Doherty Institute for Infection and Immunity" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.06.20055863", "rel_title": "Outbreak dynamics of COVID-19 in China and the United States", @@ -1580825,29 +1579032,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.04.09.20059014", - "rel_title": "How much India detecting SARS-CoV-2 Infections? A model-based estimation", - "rel_date": "2020-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20059014", - "rel_abs": "Background and RationaleAmid SARS-CoV-2 outbreak, the low number of infections for a population size of 1.38 billion is widely discussed, but with no definite answers.\n\nMethodsWe used the model proposed by Bommer and Vollmer to assess the quality of official case records. The infection fatality rates were taken from Verity et al (2020). Age distribution of the population for India and states are taken from the Census of India (2011). Reported number of deaths and SARS-CoV-2 confirmed cases from https://www.covid19india.org. The reported numbers of samples tests were collected from the reports of the Indian Council for Medical Research (ICMR).\n\nResultsThe findings suggest that India is detecting just 3.6% of the total number of infections with a huge variation across its states. Among 13 states which have more than 100 COVID-19 cases, the detection rate varies from 81.9% (of 410 estimated infections) in Kerala to 0.8% (of 35487 estimated infections) in Madhya Pradesh and 2.4% (of 7431 estimated infections) in Gujarat.\n\nConclusionAs the study reports a lower number of deaths and higher recovery rates in the states with a high detection rate, thus suggest that India must enhance its testing capacity and go for widespread testing. Late detection puts patients in greater need of mechanical ventilation and ICU care, which imposes greater costs on the health system. The country should also adopt population-level random testing to assess the prevalence of the infection.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Srinivas Goli", - "author_inst": "The University of Western Australia" - }, - { - "author_name": "K.S. James", - "author_inst": "International Institute for Population Sciences (IIPS)" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.04.06.20055467", "rel_title": "COVID-19: Tracking the Pandemic with A Simple Curve Approximation Tool (SCAT)", @@ -1581827,6 +1580011,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.09.20059006", + "rel_title": "Effectiveness of quarantine measure on transmission dynamics of COVID-19 in Hong Kong", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20059006", + "rel_abs": "The rapid expansion of COVID-19 has caused a global pandemic. Although quarantine measures have been used widely, the critical steps among them to suppress the outbreak without a huge social-economic loss remain unknown. Hong Kong, unlike other regions in the world, had a massive number of travellers from Mainland China during the early expansion period, and yet the spread of virus has been relatively limited. Understanding the effect of control measures to reduce the transmission in Hong Kong can improve the control of the virus spreading.\n\nWe have developed a susceptible-exposed-infectious-quarantined-recovered (SEIQR) meta-population model that can stratify the infections into imported and subsequent local infections, and therefore to obtain the control effects on transmissibility in a region with many imported cases. We fitted the model to both imported and local confirmed cases with symptom onset from 18 January to 29 February 2020 in Hong Kong with daily transportation data and the transmission dynamics from Wuhan and Mainland China.\n\nThe model estimated that the reproductive number was dropped from 2.32 to 0.76 (95% CI, 0.66 to 0.86) after an infected case was estimated to be quarantined half day before the symptom onset, corresponding to the incubation time of 5.43 days (95% CI, 1.30-9.47). If the quarantine happened about one day after the onset, community spread would be likely to occur, indicated by the reproductive number larger than one. The results suggest that the early quarantine for a suspected case before the symptom onset is a key factor to suppress COVID-19.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Hsiang-Yu Yuan", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Axiu Mao", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Guiyuan Han", + "author_inst": "City University of Hong Kong" + }, + { + "author_name": "Hsiangkuo Yuan", + "author_inst": "Thomas Jefferson University Hospital" + }, + { + "author_name": "Dirk Pfeiffer", + "author_inst": "City University of Hong Kong" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.06.20055327", "rel_title": "Analysing and comparing the COVID-19 data: The closed cases of Hubei and South Korea, the dark March in Europe, the beginning of the outbreak in South America", @@ -1582091,57 +1580310,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.08.20058040", - "rel_title": "Blood glucose is a representative of the clustered indicators of multi-organ injury for predicting mortality of COVID-19 in Wuhan, China", - "rel_date": "2020-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20058040", - "rel_abs": "BackgroundConcomitance with diabetes is associated with high mortality in critical conditions. Patients with previous diabetes are more vulnerable to COVID-19. However, new-onset COVID-19-related diabetes (CRD) and its relevance have scarcely been reported. This study investigates new-onset CRD and its correlation with poor outcomes or death in patients with COVID-19.\n\nMethodsWe performed a single center, retrospective case series study in 120 patients with laboratory confirmed COVID-19 at a university hospital. Fasting blood glucose (FBG) [≥]7.0 mmol/L for two times during hospitalization and without a history of diabetes were defined as CRD. The Critical status was defined as admitted to intensive care unit (ICU) or death.\n\nResultsAfter excluding patients with a history of diabetes, chronic heart, kidney, and liver disease, 69 patients with COVID-19 were included in the final analysis. Of the 69 patients, 23 were Moderate, 20 were Severe, and 26 were Critical (including 16 deceased patients). The prevalence of CRD in Critical and Moderate+Severe patients was 53.85% and 13.95%, respectively. Kaplan-Meier survival analysis revealed a significantly higher mortality rate in patients with CRD (P=0.0019). Multivariable analysis indicated that CRD was an independent predictor for death (HR = 3.75, 95% CI 1.26-11.15). Cluster analysis suggested that indicators for multi-organ injury were interdependent, and more proximities of FBG with indicators for multi-organ injury was present.\n\nConclusionOur results suggest that new onset COVID-19-related diabetes is an indicator of multi-organ injury and predictor for poor outcomes and death in COVID- 19 patients. As it is easy to perform for clinical practices and even self-monitoring, glucose testing will be much helpful for predicting poor outcomes to facilitate appropriate intensive care in patients with COVID-19.\n\nFundingNational Key Research and Development Program of China; The Beijing Science and Technology Project.\n\nSignificance of this studyO_ST_ABSEvidence before this studyC_ST_ABSConcomitance with diabetes is associated with high mortality in critical conditions. Patients with previous diabetes are more vulnerable to COVID-19. However, new-onset COVID-19-related diabetes (CRD) and its relevance have scarcely been reported. Recently, an international group of leading diabetes researchers participating in the CoviDIAB Project have established a global registry of patients with Covid-19-related diabetes (covidiab.e-dendrite.com).\n\nAdded value of this study?New-onset diabetes in COVID-19 defined as CRD was investigated. Correlation between CRD and poor outcomes or death in patients with COVID-19 was found. About half of the Critical patients have new onset CRD. CRD is the representative of the clustered indicators of multi-organ injury and is the predictor for poor outcomes and death.\n\nHow might these results change the focus of research or clinical practice?Our results suggest that new onset diabetes is an indicator of multi-organ injury and predictor for poor outcomes and death in COVID-19 patients. The study of CRD may also uncover novel mechanisms of disease.", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "Jin-Kui Yang", - "author_inst": "Beijing Tongren Hospital, Capital Medical University" - }, - { - "author_name": "Jian-Min Jin", - "author_inst": "Beijing Tongren Hospital" - }, - { - "author_name": "Shi Liu", - "author_inst": "Wuhan Union Hospital" - }, - { - "author_name": "Peng Bai", - "author_inst": "Beijing Tongren Hospital" - }, - { - "author_name": "Wei He", - "author_inst": "Beijing Tongren Hospital" - }, - { - "author_name": "Fei Wu", - "author_inst": "Wuhan Union Hospital" - }, - { - "author_name": "Xiao-Fang Liu", - "author_inst": "Beijing Tongren Hospital" - }, - { - "author_name": "Zhong-Lin Chai", - "author_inst": "Monash University" - }, - { - "author_name": "De-Min Han", - "author_inst": "Beijing Tongren Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.09.034967", "rel_title": "Comparative ACE2 variation and primate COVID-19 risk", @@ -1583005,6 +1581173,20 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.04.09.20057257", + "rel_title": "Assessing the risk of spread of COVID-19 to the Asia Pacificregion", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20057257", + "rel_abs": "During the early stages of an emerging disease outbreak, governments are required to make critical decisions on how to respond appropriately, despite limited data being available to inform these decisions. Analytical risk assessment is a valuable approach to guide decision-making on travel restrictions and border measures during the early phase of an outbreak, when transmission is primarily contained within a source country. Here we introduce a modular framework for estimating the importation risk of an emerging disease when the direct travel route is restricted and the risk stems from indirect importation via intermediary countries. This was the situation for Australia in February 2020. The framework was specifically developed to assess the importation risk of COVID-19 into Australia during the early stages of the outbreak from late January to mid-February 2020. The dominant importation risk to Australia at the time of analysis was directly from China, as the only country reporting uncontained transmission. However, with travel restrictions from mainland China to Australia imposed from February 1, our framework was designed to consider the importation risk from China into Australia via potential intermediary countries in the Asia Pacific region. The framework was successfully used to contribute to the evidence base for decisions on border measures and case definitions in the Australian context during the early phase of COVID-19 emergence and is adaptable to other contexts for future outbreak response.", + "rel_num_authors": 0, + "rel_authors": null, + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.04.11.036855", "rel_title": "Evaluation of heating and chemical protocols for inactivating SARS-CoV-2", @@ -1583313,45 +1581495,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health informatics" }, - { - "rel_doi": "10.1101/2020.04.07.20057224", - "rel_title": "UV light dosage distribution over irregular respirator surfaces. Methods and implications for safety", - "rel_date": "2020-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.07.20057224", - "rel_abs": "Background and ObjectivesThe SARS-CoV-2 pandemic has led to a global decrease in personal protective equipment (PPE), especially filtering facepiece respirators (FFRs). Ultraviolet-C wavelength is a promising way of decontamination, however adequate dosimetry is needed to ensure balance between over and underexposed areas and provide reliable results. Our study demonstrates that UVGI light irradiance varies significantly on different respirator angles and propose a method to decontaminate several masks at once ensuring appropriate dosage in shaded zones.\n\nMethodsAn UVGI irradiator was built with internal dimensions of 69.5 x 55 x 33 cm with three 15W UV lamps. Inside, a grating of 58 x 41 x 15 cm was placed to hold the masks. Two different flat fold respirator models were used to assess irradiance, four of model Aura 9322 3M of dimensions 17 x 9 x 4cm (tri-fold), and two of model SAFE 231FFP3NR (bi-fold) with dimensions 17 x 6 x 5 cm. A spectrometer STN-SilverNova was employed to verify wavelength spectrum and surface irradiance. A simulation was performed to find the irradiance pattern inside the box and the six masks placed inside. These simulations were carried out using the software DIALUX EVO 8.2.\n\nResultsThe data obtained reveal that the irradiance received inside the manufactured UVGI-irradiator depends not only on the distance between the lamps plane and the base of the respirators but also on the orientation and shape of the masks. This point becomes relevant in order to assure that all the respirators inside the chamber receive the correct dosage.\n\nConclusionIrradiance over FFR surfaces depend on several factors such as distance and angle of incidence of the light source. Careful irradiance measurement and simulation can ensure reliable dosage in the whole mask surface, balancing overexposure. Closed box systems might provide a more reliable, reproducible UVGI dosage than open settings.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Aurora Baluja", - "author_inst": "Department of Anesthesiology and Critical Care. FIDIS Health Research Institute. Hospital Clinico Universitario de Santiago de Compostela" - }, - { - "author_name": "Justo Arines", - "author_inst": "Photonics4Life research group, Optics Area, Department of Applied Physics, Universidade de Santiago de Compostela" - }, - { - "author_name": "Ramon Vilanova", - "author_inst": "Iberman Group. University Hospital. Santiago de Compostela. Spain" - }, - { - "author_name": "Julio Corti\u00f1as", - "author_inst": "Department of Anaesthesiology and Critical Care. Hospital Clinico Universitario. FIDIS Health Research Institute. Santiago de Compostela, Spain" - }, - { - "author_name": "Carmen Bao-Varela", - "author_inst": "Photonics4Life research group, Optics Area, Department of Applied Physics, Universidade de Santiago de Compostela" - }, - { - "author_name": "Maria Teresa Flores-Arias", - "author_inst": "Photonics4Life research group, Optics Area, Department of Applied Physics, Universidade de Santiago de Compostela" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health policy" - }, { "rel_doi": "10.1101/2020.04.08.20057984", "rel_title": "Assessing the Hospital Surge Capacity of the Kenyan Health System in the Face of the COVID-19 Pandemic", @@ -1584179,6 +1582322,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.09.20049288", + "rel_title": "Know Your Epidemic, Know Your Response: Covid-19 in the United States", + "rel_date": "2020-04-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20049288", + "rel_abs": "We document that during the week of March 10-16, the Covid-19 pandemic fundamentally affected the perceptions of U.S. residents about the health risks and socioeconomic consequences entailed by the pandemic. During this week, it seems, \"everything changed.\" Not only did the pandemic progress rapidly across the United States, but U.S. residents started to realize that the threat was real: increasing Covid-19 caseloads heightened perceptions of infection risks and excess mortality risks, concerns about the economic implications increased substantially, and behavioral responses became widespread as the pandemic expanded rapidly in the U.S. In early to mid-March 2020, average perceptions about the coronavirus infection risks are broadly consistent with projections about the pandemic, while expectations about dying conditional on infection and expectations about Covid-19-related excess mortality during the next months are possibly too pessimistic. However, some aspects of Covid-19 perceptions are disconcerting from the perspective of implementing and sustaining an effective societal response to the pandemic. For instance, the education gradient in expected infection risks entails the possibility of having different perceptions of the reality of the pandemic between people with and without a college education, potentially resulting in two different levels of behavioral and policy-responses across individuals and regions. Unless addressed by effective health communication that reaches individuals across all social strata, some of the misperceptions about Covid-19 epidemic raise concerns about the ability of the United States to implement and sustain the widespread and harsh policies that are required to curtail the pandemic. Our analyses also reveal perceptions of becoming infected with the virus, and dying from Covid-19, were driven upwards by a rapidly increasing national caseload, and perceptions of the economic consequences and the adaptation of social distancing were affected by both national and state-level cases.", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Alberto Ciancio", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Fabrice K\u00e4mpfen", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Iliana V. Kohler", + "author_inst": "University of Pennsylvania" + }, + { + "author_name": "Daniel Bennett", + "author_inst": "University of Southern California" + }, + { + "author_name": "W\u00e4ndi Bruine de Bruin", + "author_inst": "University of Southern California" + }, + { + "author_name": "Jill Darling", + "author_inst": "University of Southern California" + }, + { + "author_name": "Arie Kapteyn", + "author_inst": "University of Southern California" + }, + { + "author_name": "J\u00e4rgen Maurer", + "author_inst": "University of Lausanne" + }, + { + "author_name": "Hans-Peter Kohler", + "author_inst": "University of Pennsylvania" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.04.07.20056804", "rel_title": "Non-specific Primers Reveal False-negative Risk in Detection of COVID-19 Infections", @@ -1584483,37 +1582677,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.04.07.20055723", - "rel_title": "SARS-CoV-2 infection in Health Care Workers in a large public hospital in Madrid, Spain, during March 2020", - "rel_date": "2020-04-11", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.07.20055723", - "rel_abs": "BackgroundOn January 31st the first case of COVID-19 was detected in Spain, an imported case from Germany in Canary Islands, and thereafter on February 25th the first case was detected in Madrid. The first case of COVID-19 was confirmed at the Hospital Universitario 12 de Octubre on March 1st, a large public hospital with 1200 beds, covering an area over 400000 inhabitants in southern Madrid. During March 2020 highly active circulation of SARS-CoV-2 was experienced in Madrid with 24090 cases officially reported by March 29th.\n\nMethodsSince the beginning of the epidemics the Occupational Health and Safety Service (OHSS) organized the consulting and testing of the hospital personnel with confirmed exposure and also those presenting symptoms suggestive of viral respiratory infection. For molecular diagnosis of SARS-CoV-2 infection both nasopharyngeal and oropharyngeal swabs were obtained from suspected cases and processed at the Microbiology Laboratory by automatized specific PCR methods that was operative from February 25th as part of the preparedness.\n\nResultsFrom a total of 6800 employees of the hospital, 2085 (30,6 %) were tested during the period 1-29 March 2020, some of them repeatedly (2286 total samples). The first HCW infected was confirmed on March 9th. A total of 791 HCW and personnel were confirmed to be infected by March 29th, representing 38% of those tested and 11,6 % of all the hospital workers. The proportion of infected individuals was estimated among the different groups of occupational exposure and the evolution of the cases during the expansive epidemic wave was compared between HCW and those patients attending at the Emergency Department (ER) during the same period and adjusted by the same age range. There were no statistically significant differences in the proportion of SARS- CoV-2 positive PCR detection between HCW from high risk areas involved in close contact with COVID-19 patients in comparison with clerical, administrative or laboratory personnel without direct contact with patients. The curves of evolution of accumulated cases between patients and HCW during March 2020 showed an almost parallel shape.\n\nDiscussionThe recommendation from our OHSS did not include testing of asymptomatic cases but was highly proactive in testing even patients with minor symptoms therefore, a high proportion of HCW and non-sanitary personnel was tested in March 2020 during the rapid period of expansion of the epidemics in Madrid, accounting for a total of 30,6 % of the hospital employees. Most of the COVID-19 cases among the hospital HCW and personnel were mild and managed at home under self-isolation measures, however 23 (3%) required hospitalization mostly due to severe bilateral interstitial pneumonia, two of those cases required mechanical ventilation at the ICU. No fatalities occurred during the study period.\n\nAlthough there were some cases of highly probable transmission from COVID-19 patients to HCWs, mainly at the first phase of the epidemics, there were no significant differences on the infection rates of HCW and hospital personnel that can be related to working in areas of high exposure risk. Furthermore, the evolution of cases during the same time period (March 2020) between patients attending the ER and hospital staff suggests that both groups were driven by the same dynamics. This experience is similar to the communicated from Wuhan verified by the WHO Joint Mission and also from recent experiences at hospital in the Netherlands, where most of the infections of HCW were related to household or community contacts.\n\nSignificanceSince the collective of hospital HCW are exhaustively screened in specific centers, their rate of infection for SARS-CoV-2 could be an indicator of the epidemic dynamics in the community. There appears to be a close connection between HCW infection and the driving forces of transmission in the community. Although we cannot exclude an additional risk factor of infection by SARS-CoV-2 due to the fact of the hospital environment, the similar proportions of positive cases among all the areas of the hospital and the evolutive wave of infection, as compared with the community, are clear arguments against a major factor of occupational risk. Exhaustive testing, such as the one carried out in our institution, covering over one third of all the workers, could be used as a reference of the population infected in the community. Since a significant proportion of COVID-19 cases can be asymptomatic and not all the hospital employees were actually tested, it is highly likely that this 11,6 % is a minimum estimation of the impact of SARS-CoV-2 circulation in Madrid during the first 4 weeks of the epidemics. This is in high and clear contrast with the official figures circulating at national and international levels. This has important implications to more precisely estimate the actual number of cases in the community and to develop public health policies for containment, treatment and recovery.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Maria Dolores Folgueira", - "author_inst": "Hospital Universitario 12 de Octubre, Madrid, Spain" - }, - { - "author_name": "Carmen Munoz-Ruiperez", - "author_inst": "Hospital Universitario 12 de Octubre, Madrid, Spain" - }, - { - "author_name": "Miguel Angel Alonso-Lopez", - "author_inst": "Hospital Universitario 12 de Octubre, Madrid, Spain" - }, - { - "author_name": "Rafael Delgado", - "author_inst": "Hospital Universitario 12 de Octubre, Madrid, Spain" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.04.06.20055657", "rel_title": "Two mechanisms for accelerated diffusion of COVID-19 outbreaks in regions with high intensity of population and polluting industrialization: the air pollution-to-human and human-to-human transmission dynamics", @@ -1585537,6 +1583700,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.08.20057281", + "rel_title": "Spatial modeling cannot currently differentiate SARS-CoV-2 coronavirus and human distributions on the basis of climate in the United States", + "rel_date": "2020-04-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.08.20057281", + "rel_abs": "The SARS-CoV-2 coronavirus is wreaking havoc globally, yet knowledge of its biology is limited. Climate and seasonality influence the distributions of many diseases, and studies suggest a link between SARS-CoV-2 and cool weather. One such study, building species distribution models (SDMs), predicted SARS-CoV-2 risk may remain concentrated in the Northern Hemisphere, shifting northward in summer months. Others have highlighted issues with SARS-CoV-2 SDMs, notably: the primary niche of the virus is the host it infects, climate may be a weak distributional predictor, global prevalence data have issues, and the virus is not in a population equilibrium. While these issues should be considered, climate still may be important for predicting the future distribution of SARS-CoV-2. To further examine if there is a link, we model with raw cases and population scaled cases for SARS-CoV-2 county-level data from the United States. We show that SDMs built from population scaled cases data cannot be distinguished from control models built from raw human population data, while SDMs built on raw data fail to predict the current known distribution of cases in the US. The population scaled analyses indicate that climate may not play a central role in current US viral distribution and that human population density is likely a primary driver. Still, we do find slightly more population scaled viral cases in cooler areas. This coupled with our geographically constrained focus make it so we cannot rule out climate as a partial driver of the US SARS-CoV-2 distribution. Climates role on SARS-CoV-2 should continue to be cautiously examined, but at this time we should assume that SARS-CoV-2 can spread anywhere in the US.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Robert S Harbert", + "author_inst": "Stonehill College" + }, + { + "author_name": "Seth W Cunningham", + "author_inst": "American Museum of Natural History" + }, + { + "author_name": "Michael Tessler", + "author_inst": "American Museum of Natural History" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.07.20052340", "rel_title": "COVID-19 UK Lockdown Forecasts and R0", @@ -1585781,41 +1583971,6 @@ "type": "new results", "category": "microbiology" }, - { - "rel_doi": "10.1101/2020.04.07.20057315", - "rel_title": "Clinical analysis and early differential diagnosis of suspected pediatric patients with 2019 novel coronavirus infection", - "rel_date": "2020-04-10", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.07.20057315", - "rel_abs": "BackgroundWe aimed to identify clinical features of coronavirus disease 2019 (COVID-19) in children and evaluate the role of procalcitonin in early differential diagnosis.\n\nMethodsA retrospective analysis was performed on all suspected pediatric cases.\n\nResults39 (50.6%) of 77 suspected cases were comfirmed, 4 (5.2%) of them had viral coinfection. Compared with non-COVID-19 group (n=33), COVID-19 confirmed group (n=39) had fewer fever(OR[95% CI]0.467[0.314-0.694]; P=.000) and symptoms of acute respiratory infection (0.533[0.36-0.788]; P=.001), more asymptomatic (13.568[1.895-96.729]; P=.000), and more family cluster infections (5.077[2.224-11.591]; P=.000), while computed tomography had more positive findings of viral pneumonia (1.822[1.143-2.906]; P=.008). Age (6.9[3.6-10.5] vs 5[2.1-7.6]; P=. 088) and gender were statistically insignificant. Procalcitonin (0.05[0.029-0.076] vs 0.103[0.053-0.21]; P= 000) of COVID-19 alone group (n=35) was significantly reduced. While compared with coinfection group (n=4), procalcitonin (0.05[0.029-0.076] vs 0.144[0.109-2.26]; P=.010) was also reduced. The area under curve of model is 0.834 ([95% CI][0.741-0.926]; P=.000). Procalcitonin as a differential indicator of COVID-19 alone, its area under curve is 0.809 ([0.710-0.909]; P=.000). The optimal cut-off value is 0.1 ng/mL, the sensitivity, specificity, positive and negative predictive value of differentiating are 65.9%, 78.6%, 82.9%, and 59.2%, respectively.\n\nConclusionsAsymptoms or mild symptoms, positive computed tomography findings and family cluster infection are the main clinical features of COVID-19 in children. With good performance, procalcitonin can provide an important basis for differentiating COVID-19 alone and other viral infection or viral coinfection.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Denggao Peng", - "author_inst": "The Third People's Hospital of Shenzhen" - }, - { - "author_name": "Jing Zhang", - "author_inst": "The Third People's Hospital of Shenzhen" - }, - { - "author_name": "Yingqi Xu", - "author_inst": "The Third People's Hospital of Shenzhen" - }, - { - "author_name": "Zhichao Liu", - "author_inst": "The Third People's Hospital of Shenzhen" - }, - { - "author_name": "Pengyao Wu", - "author_inst": "The Third People's Hospital of Shenzhen" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "pediatrics" - }, { "rel_doi": "10.1101/2020.04.08.013516", "rel_title": "Understanding the B and T cells epitopes of spike protein of severe respiratory syndrome coronavirus-2: A computational way to predict the immunogens", @@ -1586707,6 +1584862,49 @@ "type": "new results", "category": "immunology" }, + { + "rel_doi": "10.1101/2020.04.09.20056325", + "rel_title": "Evaluation of nine commercial SARS-CoV-2 immunoassays", + "rel_date": "2020-04-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.09.20056325", + "rel_abs": "Due to urgency and demand, numerous severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunoassays are rapidly being developed and placed on the market with limited validation on clinical samples. Thorough validation of serological tests are required to facilitate their use in the accurate diagnosis of SARS-CoV-2 infection, confirmation of molecular results, contact tracing, and epidemiological studies. This study evaluated the sensitivity and specificity of nine commercially available serological tests. These included three enzyme-linked immunosorbent assays (ELISAs) and six point-of-care (POC) lateral flow tests. The assays were validated using serum samples from: i) SARS-CoV-2 PCR-positive patients with a documented first day of disease; ii) archived sera obtained from healthy individuals before the emergence of SARS-CoV-2 in China; iii) sera from patients with acute viral respiratory tract infections caused by other coronaviruses or non-coronaviruses; and iv) sera from patients positive for dengue virus, cytomegalovirus and Epstein Barr virus. The results showed 100% specificity for the Wantai SARS-CoV-2 Total Antibody ELISA, 93% for the Euroimmun IgA ELISA, and 96% for the Euroimmun IgG ELISA with sensitivities of 90%, 90%, and 65%, respectively. The overall performance of the POC tests according to manufacturer were in the rank order of AutoBio Diagnostics > Dynamiker Biotechnology = CTK Biotech > Artron Laboratories > Acro Biotech [≥] Hangzhou Alltest Biotech. Overall, these findings will facilitate selection of serological assays for the detection SARS-CoV-2-specific antibodies towards diagnosis as well as sero-epidemiological and vaccine development studies.", + "rel_num_authors": 7, + "rel_authors": [ + { + "author_name": "Ria Lassauni\u00e8re", + "author_inst": "Statens Serum Institut, Copenhagen, Denmark" + }, + { + "author_name": "Anders Frische", + "author_inst": "Statens Serum Institut, Copenhagen, Denmark" + }, + { + "author_name": "Zitta B Harboe", + "author_inst": "Nordsjaellands Hospital, Copenhagen, Denmark" + }, + { + "author_name": "Alex CY Nielsen", + "author_inst": "Rigshospitalet, Copenhagen, Denmark" + }, + { + "author_name": "Anders Fomsgaard", + "author_inst": "Statens Serum Institut, Copenhagen, Denmark" + }, + { + "author_name": "Karen A Krogfelt", + "author_inst": "Roskilde University, Roskilde, Denmark and Statens Serum Institut, Copenhagen, Denmark" + }, + { + "author_name": "Charlotte S J\u00f8rgensen", + "author_inst": "Statens Serum Institut" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.06.028712", "rel_title": "Confronting the COVID-19 Pandemic with Systems Biology", @@ -1587483,45 +1585681,6 @@ "type": "new results", "category": "immunology" }, - { - "rel_doi": "10.1101/2020.04.07.028589", - "rel_title": "The IMPDH inhibitor merimepodib suppresses SARS-CoV-2 replication in vitro.", - "rel_date": "2020-04-09", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.07.028589", - "rel_abs": "The ongoing COVID-19 pandemic continues to pose a major public health burden around the world. The novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected over one million people worldwide as of April, 2020, and has led to the deaths of nearly 300,000 people. No approved vaccines or treatments in the USA currently exist for COVID-19, so there is an urgent need to develop effective countermeasures. The IMPDH inhibitor merimepodib (MMPD) is an investigational antiviral drug that acts as a noncompetitive inhibitor of IMPDH. It has been demonstrated to suppress replication of a variety of emerging RNA viruses. We report here that MMPD suppresses SARS-CoV-2 replication in vitro. After overnight pretreatment of Vero cells with 10 M of MMPD, viral titers were reduced by 4 logs of magnitude, while pretreatment for 4 hours resulted in a 3-log drop. The effect is dose-dependent, and concentrations as low as 3.3 M significantly reduced viral titers when the cells were pretreated prior to infection. The results of this study provide evidence that MMPD may be a viable treatment option for COVID-19.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Natalya Bukreyeva", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Emily K Mantlo", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Rachel A Sattler", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Cheng Huang", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Slobodan Paessler", - "author_inst": "University of Texas Medical Branch" - }, - { - "author_name": "Jerry Zeldis", - "author_inst": "ViralClear, a subsidiary of BioSig, Inc." - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.04.07.029090", "rel_title": "Absence of SARS-CoV-2 infection in cats and dogs in close contact with a cluster of COVID-19 patients in a veterinary campus", @@ -1588769,6 +1586928,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.06.20055194", + "rel_title": "Acute kidney injury in patients hospitalized with COVID-19 in Wuhan, China: A single-center retrospective observational study", + "rel_date": "2020-04-08", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.06.20055194", + "rel_abs": "BackgroundThe kidney may be affected in coronavirus-2019 disease (COVID-19). This study assessed the predictors and outcomes of acute kidney injury (AKI) among individuals with COVID-19.\n\nMethodsThis observational study, included data on all patients with clinically confirmed COVID-19 admitted to Hankou Hospital, Wuhan, China from January 5 to March 8, 2020. Data were extracted from clinical and laboratory records. Follow-up was censored on March 8, 2020.\n\nThis is a single-center, retrospective, observational study. Patients clinically confirmed COVID-19 and admitted to Hankou Hospital, Wuhan, China from January 5 to March 8, 2020 were enrolled. We evaluated the association between changes in the incidence of AKI and COVID-19 disease and clinical outcomes by using logistic regression models.\n\nResultsA total of 287 patients, 55 with AKI and 232 without AKI, were included in the analysis. Compared to patients without AKI, AKI patients were older, predominantly male, and were more likely to present with hypoxia and have pre-existing hypertension and cerebrovascular disease. Moreover, AKI patients had higher levels of white blood cells, D-dimer, aspartate aminotransferase, total bilirubin, creatine kinase, lactate dehydrogenase, procalcitonin, C-reactive protein, a higher prevalence of hyperkalemia, lower lymphocyte counts, and higher chest computed tomographic scores. The incidence of stage 1 AKI was 14.3%, and the incidence of stage 2 or 3 AKI was 4.9%. Patients with AKI had substantially higher mortality.\n\nConclusionsAKI is an important complication of COVID-19. Older age, male, multiple pre-existing comorbidities, lymphopenia, increased infection indicators, elevated D-dimer, and impaired heart and liver functions were the risk factors of AKI. AKI patients who progressed to stages 2 or 3 AKI had a higher mortality rate. Prevention of AKI and monitoring of kidney function is very important for COVID-19 patients.\n\nTrial registrationNCT04316299(03/19/2020)", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Guanhua Xiao", + "author_inst": "Department of Respiratory and Critical Care Medicine, Chronic Airways Diseases Laboratory, Nanfang Hospital, Southern Medical University" + }, + { + "author_name": "Hongbin Hu", + "author_inst": "Department of Critical Care Medicine, Nanfang Hospital, Southern Medical University" + }, + { + "author_name": "Feng Wu", + "author_inst": "Department of Critical Care Medicine, Nanfang Hospital, Southern Medical University" + }, + { + "author_name": "Tong Sha", + "author_inst": "Department of Critical Care Medicine, Nanfang Hospital, Southern Medical University" + }, + { + "author_name": "Qiaobing Huang", + "author_inst": "Guangdong Provincial Key Laboratory of Shock and Microcirculation, School of Basic Medical Sciences, Southern Medical University" + }, + { + "author_name": "Haijun Li", + "author_inst": "Department of Radiology, Hankou Hospital of Wuhan" + }, + { + "author_name": "Jiafa Han", + "author_inst": "Department of Radiology, Hankou Hospital of Wuhan" + }, + { + "author_name": "Wenhong Song", + "author_inst": "Department of Radiology, Hankou Hospital of Wuhan" + }, + { + "author_name": "Zhongqing Chen", + "author_inst": "Department of Critical Care Medicine, Nanfang Hospital, Southern Medical University" + }, + { + "author_name": "Zhenhua Zeng", + "author_inst": "Nanfang Hospital ofouthern Medical University" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.04.06.20055103", "rel_title": "The impact of early social distancing at COVID-19 Outbreak in the largest Metropolitan Area of Brazil.", @@ -1589060,25 +1587274,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.03.20052845", - "rel_title": "Use Crow-AMSAA Method to predict the cases of the Coronavirus 19 in Michigan and U.S.A", - "rel_date": "2020-04-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.03.20052845", - "rel_abs": "The Crow-AMSAA method is used in engineering reliability world to predict the failures and evaluate the reliability growth. The author intents to use this model in the prediction of the Coronavirus 19 (COVID19) cases by using the daily reported data from Michigan, New York City, U.S.A and other countries. The piece wise Crow-AMSAA (CA) model fits the data very well for the infected cases and deaths at different phases while the COVID19 outbreak starting. The slope {beta} of the Crow-AMSAA line indicates the speed of the transmission or death rate. The traditional epidemiological model is based on the exponential distribution, but the Crow-AMSAA is the Non Homogeneous Poisson Process (NHPP) which can be used to modeling the complex problem like COVID19, especially when the various mitigation strategies such as social distance, isolation and locking down were implemented by the government at different places.\n\nSummaryThis paper is to use piece wise Crow-AMSAA method to fit the COVID19 confirmed cases in Michigan, New York City, U.S.A and other countries.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Yanshuo Wang", - "author_inst": "LLLW LLC" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.05.20054361", "rel_title": "Population-level COVID-19 mortality risk for non-elderly individuals overall and for non-elderly individuals without underlying diseases in pandemic epicenters", @@ -1590030,6 +1588225,181 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.04.07.20054585", + "rel_title": "Proteomic and Metabolomic Characterization of COVID-19 Patient Sera", + "rel_date": "2020-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.07.20054585", + "rel_abs": "Severe COVID-19 patients account for most of the mortality of this disease. Early detection and effective treatment of severe patients remain major challenges. Here, we performed proteomic and metabolomic profiling of sera from 46 COVID-19 and 53 control individuals. We then trained a machine learning model using proteomic and metabolomic measurements from a training cohort of 18 non-severe and 13 severe patients. The model correctly classified severe patients with an accuracy of 93.5%, and was further validated using ten independent patients, seven of which were correctly classified. We identified molecular changes in the sera of COVID-19 patients implicating dysregulation of macrophage, platelet degranulation and complement system pathways, and massive metabolic suppression. This study shows that it is possible to predict progression to severe COVID-19 disease using serum protein and metabolite biomarkers. Our data also uncovered molecular pathophysiology of COVID-19 with potential for developing anti-viral therapies.", + "rel_num_authors": 40, + "rel_authors": [ + { + "author_name": "Bo Shen", + "author_inst": "Department of clinical laboratory, Taizhou Hospital,Wenzhou Medical Universtry, 150 Ximen Street,Linhai 317000,Zhejiang Province,China." + }, + { + "author_name": "Xiao Yi", + "author_inst": "Westlake University" + }, + { + "author_name": "Yaoting Sun", + "author_inst": "Westlake University" + }, + { + "author_name": "Xiaojie Bi", + "author_inst": "Taizhou Hospital,Wenzhou Medical Universtry ,150 Ximen Street,Linhai 317000,Zhejiang Province,China." + }, + { + "author_name": "Juping Du", + "author_inst": "Taizhou Hospital,Wenzhou Medical Universtry ,150 Ximen Street,Linhai 317000,Zhejiang Province,China." + }, + { + "author_name": "Chao Zhang", + "author_inst": "Calibra Lab at DIAN Diagnostics, 329 Jinpeng Street, Hangzhou 310030, Zhejiang Province, China." + }, + { + "author_name": "Sheng Quan", + "author_inst": "Calibra Lab at DIAN Diagnostics, 329 Jinpeng Street, Hangzhou 310030, Zhejiang Province, China." + }, + { + "author_name": "Fangfei Zhang", + "author_inst": "Westlake University" + }, + { + "author_name": "Rui Sun", + "author_inst": "Westlake University" + }, + { + "author_name": "Liujia Qian", + "author_inst": "Westlake University" + }, + { + "author_name": "Weigang Ge", + "author_inst": "Westlake University" + }, + { + "author_name": "Wei Liu", + "author_inst": "Westlake University" + }, + { + "author_name": "Shuang Liang", + "author_inst": "Westlake University" + }, + { + "author_name": "Hao Chen", + "author_inst": "Westlake University" + }, + { + "author_name": "Ying Zhang", + "author_inst": "Taizhou Hospital,Wenzhou Medical Universtry ,150 Ximen Street,Linhai 317000,Zhejiang Province,China." + }, + { + "author_name": "Jun Li", + "author_inst": "Taizhou Hospital,Wenzhou Medical Universtry ,150 Ximen Street,Linhai 317000,Zhejiang Province,China." + }, + { + "author_name": "Jiaqin Xu", + "author_inst": "Taizhou Hospital,Wenzhou Medical Universtry ,150 Ximen Street,Linhai 317000,Zhejiang Province,China." + }, + { + "author_name": "Zebao He", + "author_inst": "Taizhou Enze Medical Center (Group) Enze Hospital" + }, + { + "author_name": "Baofu Chen", + "author_inst": "Taizhou Hospital,Wenzhou Medical Universtry ,150 Ximen Street,Linhai 317000, Zhejiang Province,China." + }, + { + "author_name": "Jing Wang", + "author_inst": "Taizhou Hospital,Wenzhou Medical Universtry ,150 Ximen Street,Linhai 317000,Zhejiang Province,China." + }, + { + "author_name": "Haixi Yan", + "author_inst": "Taizhou Hospital,Wenzhou Medical Universtry ,150 Ximen Street,Linhai 317000,Zhejiang Province,China." + }, + { + "author_name": "Yufen Zheng", + "author_inst": "Taizhou Hospital,Wenzhou Medical Universtry ,150 Ximen Street,Linhai 317000,Zhejiang Province,China." + }, + { + "author_name": "Donglian Wang", + "author_inst": "Taizhou Hospital,Wenzhou Medical Universtry ,150 Ximen Street,Linhai 317000,Zhejiang Province,China." + }, + { + "author_name": "Jiansheng Zhu", + "author_inst": "Taizhou Hospital,Wenzhou Medical Universtry ,150 Ximen Street,Linhai 317000,Zhejiang Province,China." + }, + { + "author_name": "Ziqing Kong", + "author_inst": "Calibra Lab at DIAN Diagnostics, 329 Jinpeng Street, Hangzhou 310030, Zhejiang Province,China." + }, + { + "author_name": "Zhouyang Kang", + "author_inst": "Calibra Lab at DIAN Diagnostics, 329 Jinpeng Street, Hangzhou 310030, Zhejiang Province, China." + }, + { + "author_name": "Xiao Liang", + "author_inst": "Westlake University" + }, + { + "author_name": "Xuan Ding", + "author_inst": "Westlake University" + }, + { + "author_name": "Guan Ruan", + "author_inst": "Westlake University" + }, + { + "author_name": "Nan Xiang", + "author_inst": "Westlake University" + }, + { + "author_name": "Xue Cai", + "author_inst": "Westlake University" + }, + { + "author_name": "Huanhuan Gao", + "author_inst": "Westlake University" + }, + { + "author_name": "Lu Li", + "author_inst": "Westlake University" + }, + { + "author_name": "Sainan Li", + "author_inst": "Westlake University" + }, + { + "author_name": "Qi Xiao", + "author_inst": "Westlake University" + }, + { + "author_name": "Tian Lu", + "author_inst": "Westlake University" + }, + { + "author_name": "Yi Judy Zhu", + "author_inst": "Westlake University" + }, + { + "author_name": "Huafen Liu", + "author_inst": "Calibra Lab at DIAN Diagnostics, 329 Jinpeng Street, Hangzhou 310030, Zhejiang Province, China." + }, + { + "author_name": "Haixiao Chen", + "author_inst": "Taizhou Hospital,Wenzhou Medical Universtry ,150 Ximen Street,Linhai 317000, Zhejiang Province,China." + }, + { + "author_name": "Tiannan Guo", + "author_inst": "Westlake University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.03.20052787", "rel_title": "Susceptible supply limits the role of climate in the COVID-19 pandemic", @@ -1590258,41 +1588628,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.03.20052720", - "rel_title": "Mitigating COVID-19 outbreak via high testing capacity and strong transmission-intervention in the United States", - "rel_date": "2020-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.03.20052720", - "rel_abs": "Most models of the COVID-19 pandemic in the United States do not consider geographic variation and spatial interaction. In this research, we developed a travel-network-based susceptible-exposed-infectious-removed (SEIR) mathematical compartmental model system that characterizes infections by state and incorporates inflows and outflows of interstate travelers. Modeling reveals that curbing interstate travel when the disease is already widespread will make little difference. Meanwhile, increased testing capacity (facilitating early identification of infected people and quick isolation) and strict social-distancing and self-quarantine rules are most effective in abating the outbreak. The modeling has also produced state-specific information. For example, for New York and Michigan, isolation of persons exposed to the virus needs to be imposed within 2 days to prevent a broad outbreak, whereas for other states this period can be 3.6 days. This model could be used to determine resources needed before safely lifting state policies on social distancing.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Shi Chen", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Qin Li", - "author_inst": "University of Wisconsin-Madisons" - }, - { - "author_name": "Song Gao", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Yuhao Kang", - "author_inst": "University of Wisconsin-Madison" - }, - { - "author_name": "Xun Shi", - "author_inst": "Dartmouth College" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.03.20048389", "rel_title": "Management of rheumatic diseases in the times of COVID-19 pandemic- perspectives of rheumatology practitioners from India", @@ -1591180,6 +1589515,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.04.05.20054445", + "rel_title": "Efficient sample pooling strategies for COVID-19 data gathering", + "rel_date": "2020-04-07", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.05.20054445", + "rel_abs": "Sample pooling of CoViD-19 PCR tests has been recently proposed as a low cost alternative to individual tests. We show that sample pooling is efficient as long as the fraction of the population infected is relatively small. Fisher information theory suggests a rule of thumb that for low infection rates p, pooling 2/p samples is close to optimal. We present a simple strategy for survey design when not even a ballpark estimate of the infection rate is available.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Istvan Szapudi", + "author_inst": "University of Hawaii" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.04.05.20053884", "rel_title": "Study of Epidemiological Characteristics and In-silico Analysis of the Effect of Interventions in the SARS-CoV-2 Epidemic in India", @@ -1591464,41 +1589818,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "medical education" }, - { - "rel_doi": "10.1101/2020.04.03.20052936", - "rel_title": "An \"Infodemic\": Leveraging High-Volume Twitter Data to Understand Public Sentiment for the COVID-19 Outbreak", - "rel_date": "2020-04-07", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.03.20052936", - "rel_abs": "BackgroundTwitter has been used to track trends and disseminate health information during viral epidemics. On January 21, 2020, the CDC activated its Emergency Operations Center and the WHO released its first situation report about Coronavirus disease 2019 (COVID-19), sparking significant media attention. How Twitter content and sentiment has evolved in the early stages of any outbreak, including the COVID-19 epidemic, has not been described.\n\nObjectiveTo quantify and understand early changes in Twitter activity, content, and sentiment about the COVID-19 epidemic.\n\nDesignObservational study.\n\nSettingTwitter platform.\n\nParticipantsAll Twitter users who created or sent a message from January 14th to 28th, 2020.\n\nMeasurementsWe extracted tweets matching hashtags related to COVID-19 and measured frequency of keywords related to infection prevention practices, vaccination, and racial prejudice. We performed a sentiment analysis to identify emotional valence and predominant emotions. We conducted topic modeling to identify and explore discussion topics over time.\n\nResultsWe evaluated 126,049 tweets from 53,196 unique users. The hourly number of COVID-19-related tweets starkly increased from January 21, 2020 onward. Nearly half (49.5%) of all tweets expressed fear and nearly 30% expressed surprise. The frequency of racially charged tweets closely paralleled the number of newly diagnosed cases of COVID-19. The economic and political impact of the COVID-19 was the most commonly discussed topic, while public health risk and prevention were among the least discussed.\n\nConclusionTweets with negative sentiment and emotion parallel the incidence of cases for the COVID-19 outbreak. Twitter is a rich medium that can be leveraged to understand public sentiment in real-time and target public health messages based on user interest and emotion.\n\nFundingNone.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Richard J. Medford", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Sameh N. Saleh", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Andrew Sumarsono", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Trish M. Perl", - "author_inst": "University of Texas Southwestern Medical Center" - }, - { - "author_name": "Christoph U. Lehmann", - "author_inst": "University of Texas Southwestern Medical Center" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.04.05.20054254", "rel_title": "Repurposing Therapeutics for COVID-19: Rapid Prediction of Commercially available drugs through Machine Learning and Docking", @@ -1592314,6 +1590633,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.31.20045401", + "rel_title": "A case of SARS-CoV-2 carrier for 32 days with several times false negative nucleic acid tests", + "rel_date": "2020-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.31.20045401", + "rel_abs": "In 2019, a novel coronavirus (SARS-CoV-2) was first discovered in Wuhan, Hubei, China, causing severe respiratory disease in humans, and has been identified as a public health emergency of international concern. With the spread of the virus, there are more and more false negative cases of RT-PCR nucleic acid detection in the early stage of potential infection. In this paper, we collected the epidemiological history, clinical manifestations, outcomes, laboratory results and images of a SARS-CoV-2 carrier with no significant past medical history. The patient was quarantined because of her colleague had been diagnosed. After the onset of clinical symptoms, chest CT results showed patchy ground-glass opacity (GGO) in her lungs, but it took a total of nine nucleic acid tests to confirm the diagnosis, among which the first eight RT-PCR results were negative or single-target positive. In addition to coughing up phlegm during her stay in the hospital, she did not develop chills, fever, abdominal pain, diarrhea and other clinical symptoms. Since initial antiviral treatment, the lung lesions were absorbed. But the sputum nucleic acid test was still positive. In combination with antiviral and immune therapy, the patient tested negative for the virus. Notably, SARS-CoV-2 was detected only in the lower respiratory tract samples (sputum) throughout the diagnosis and treatment period. This is a confirmed case of SARS-CoV-2 infection with common symptoms, and her diagnosis has undergone multiple false negatives, suggesting that it is difficult to identify certain carriers of the virus and that such patients may also increase the spread of the SARS-CoV-2.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Lingjie Song", + "author_inst": "Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan, China." + }, + { + "author_name": "Guibao Xiao", + "author_inst": "The First People's Hospital of Ziyang City" + }, + { + "author_name": "Xianqin Zhang", + "author_inst": "Chengdu medical college" + }, + { + "author_name": "Zhan Gao", + "author_inst": "Institute of Blood Transfusion, Chinese Academy of Medical Sciences" + }, + { + "author_name": "Shixia Sun", + "author_inst": "The First People's Hospital of Ziyang City" + }, + { + "author_name": "Lin Zhang", + "author_inst": "Shaoxing Hospital, Zhejiang University School of Medicine" + }, + { + "author_name": "Youjun Feng", + "author_inst": "Zhejiang University" + }, + { + "author_name": "Guangxin Luan", + "author_inst": "Chengdu medical college" + }, + { + "author_name": "Sheng Lin", + "author_inst": "The First People's Hospital of Ziyang City" + }, + { + "author_name": "Miao He", + "author_inst": "Institute of Blood Transfusion, Chinese Academy of Medical Sciences, Chengdu, Sichuan, China." + }, + { + "author_name": "Xu Jia", + "author_inst": "Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, Sichuan, China." + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.03.20051763", "rel_title": "Virologic and clinical characteristics for prognosis of severe COVID-19: a retrospective observational study in Wuhan, China", @@ -1592778,37 +1591156,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.30.20048165", - "rel_title": "Association of BCG vaccination policy with prevalence and mortality of COVID-19", - "rel_date": "2020-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.30.20048165", - "rel_abs": "BackgroundEvidence suggests non-specific benefits of the tuberculosis vaccine bacillus Calmette-Guerin (BCG) against non-related infections. Recent studies propose such protection may extend to the novel COVID-19 as well. This is a contested hypothesis.\n\nMethodsOur ecological study confronts this hypothesis. We examine the effects of BCG vaccination on countries COVID-19 (a) cases and deaths (per million) and (b) exponential growth factors over specific periods of the pandemic. Since the BCG vaccine was derived from Mycobacterium bovis, a bacterium causing tuberculosis in cattle, having suffered from tuberculosis also may exert a non-specific protection against the COVID-19 as well. Along with BCG vaccination, we test the effect of the prevalence of tuberculosis.\n\nWe employ multiple regression and principal component analysis (PCA) to control for potentially confounding variables (n = 16).\n\nResultsBCG vaccination policy and incidence of tuberculosis is associated with a reduction in both COVID-19 cases and deaths, and the effects of these two variables are additive ({approx} 5% to 15% of total unique variance explained). The study of exponential growth factors in the initial stages of the pandemic further shows that BCG vaccination exerts a significant effect (up to 35% of unique variance explained).\n\nConclusionsOverall, these findings corroborate the hypothesis that BCG vaccination and exposure to tuberculosis may induce a non-specific protection against the novel SARS-CoV-2 infection, even after accounting for a large number of confounding influences. However, given the potential public-health benefits, our results indicate that the hypothesis deserves further attention and should not be hastily dismissed.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Giovanni Sala", - "author_inst": "Fujita Health University" - }, - { - "author_name": "Rik Chakraborti", - "author_inst": "Department of Economics, Christopher Newport University" - }, - { - "author_name": "Atsuhiko Ota", - "author_inst": "Department of Public Health, Fujita Health University School of Medicine" - }, - { - "author_name": "Tsuyoshi Miyakawa", - "author_inst": "Fujita Health University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.30.20048090", "rel_title": "COVID-19 related social distancing measures and reduction in city mobility", @@ -1593696,6 +1592043,225 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.04.02.20051284", + "rel_title": "Building an International Consortium for Tracking Coronavirus Health Status", + "rel_date": "2020-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.02.20051284", + "rel_abs": "Information is the most potent protective weapon we have to combat a pandemic, at both the individual and global level. For individuals, information can help us make personal decisions and provide a sense of security. For the global community, information can inform policy decisions and offer critical insights into the epidemic of COVID-19 disease. Fully leveraging the power of information, however, requires large amounts of data and access to it. To achieve this, we are making steps to form an international consortium, Coronavirus Census Collective (CCC, coronaviruscensuscollective.org), that will serve as a hub for integrating information from multiple data sources that can be utilized to understand, monitor, predict, and combat global pandemics. These sources may include self-reported health status through surveys (including mobile apps), results of diagnostic laboratory tests, and other static and real-time geospatial data. This collective effort to track and share information will be invaluable in predicting hotspots of disease outbreak, identifying which factors control the rate of spreading, informing immediate policy decisions, evaluating the effectiveness of measures taken by health organizations on pandemic control, and providing critical insight on the etiology of COVID-19. It will also help individuals stay informed on this rapidly evolving situation and contribute to other global efforts to slow the spread of disease.\n\nIn the past few weeks, several initiatives across the globe have surfaced to use daily self-reported symptoms as a means to track disease spread, predict outbreak locations, guide population measures and help in the allocation of healthcare resources. The aim of this paper is to put out a call to standardize these efforts and spark a collaborative effort to maximize the global gain while protecting participant privacy.", + "rel_num_authors": 51, + "rel_authors": [ + { + "author_name": "Eran Segal", + "author_inst": "Weizmann Institute of Science" + }, + { + "author_name": "Feng Zhang", + "author_inst": "Howard Hughes Medical Institute, Core Member, Broad Institute of MIT and Harvard, United States" + }, + { + "author_name": "Xihong Lin", + "author_inst": "Departments of Biostatistics and Statistics, Harvard T.H. Chan School of Public Health" + }, + { + "author_name": "Gary King", + "author_inst": "Albert J. Weatherhead III University, Institute for Quantitative Social Science, Harvard University" + }, + { + "author_name": "Ophir Shalem", + "author_inst": "Department of Genetics, Perelman School of Medicine, University of Pennsylvania, United States" + }, + { + "author_name": "Smadar Shilo", + "author_inst": "Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel" + }, + { + "author_name": "William E. Allen", + "author_inst": "Society of Fellows, Harvard University, United States" + }, + { + "author_name": "Yonatan H. Grad", + "author_inst": "Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, United States" + }, + { + "author_name": "Casey S. Greene", + "author_inst": "Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, United States" + }, + { + "author_name": "Faisal Alquaddoomi", + "author_inst": "ETH Zurich, NEXUS Personalized Health Technologies, Zurich, Switzerland" + }, + { + "author_name": "Simon Anders", + "author_inst": "Center for Molecular Biology (ZMBH), University of Heidelberg, Germany" + }, + { + "author_name": "Ran Balicer", + "author_inst": "Clalit Research Institute, Clalit Health Services, Israel" + }, + { + "author_name": "Tal Bauman", + "author_inst": "Mapping and Geo-Information Engineering, Civil and Environmental Engineering Faculty, The Technion, Israel" + }, + { + "author_name": "Ximena Bonilla", + "author_inst": "ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich, " + }, + { + "author_name": "Gisel Booman", + "author_inst": "Regen Network, Argentina" + }, + { + "author_name": "Andrew T. Chan", + "author_inst": "Massachusetts General Hospital (MGH), United States" + }, + { + "author_name": "Ori Ori Cohen", + "author_inst": "Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel" + }, + { + "author_name": "Silvano Coletti", + "author_inst": "Chelonia Applied Science, Switzerland" + }, + { + "author_name": "Natalie Davidson", + "author_inst": "ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich, " + }, + { + "author_name": "Yuval Dor", + "author_inst": "School of Medicine-IMRIC-Developmental Biology and Cancer Research, The Hebrew University" + }, + { + "author_name": "David A. Drew", + "author_inst": "Massachusetts General Hospital (MGH), United States" + }, + { + "author_name": "Olivier Elemento", + "author_inst": "Englander Institute for Precision Medicine and Department of Physiology and Biophysics, Weill Cornell Medicine, USA" + }, + { + "author_name": "Georgina Evans", + "author_inst": "Institute for Quantitative Social Science, Harvard University" + }, + { + "author_name": "Phil Ewels", + "author_inst": "Science for Life Laboratory (SciLifeLab), Department of Biochemistry and Biophysics, Stockholm University, Sweden" + }, + { + "author_name": "Joshua Gale", + "author_inst": "symptometrics.org" + }, + { + "author_name": "Amir Gavrieli", + "author_inst": "Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel" + }, + { + "author_name": "Benjamin Geiger", + "author_inst": "Department of immunology, Weizmann Institute of Science, Israel" + }, + { + "author_name": "Iman Hajirasouliha", + "author_inst": "Englander Institute for Precision Medicine and Department of Physiology and Biophysics, Weill Cornell Medicine, USA" + }, + { + "author_name": "Roman Jerala", + "author_inst": "Department of Synthetic biology and Immunology, National Institute of Chemistry, Slovenia" + }, + { + "author_name": "Andre Kahles", + "author_inst": "ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich, " + }, + { + "author_name": "Olli Kallioniemi", + "author_inst": "Science for Life Laboratory (SciLifeLab), Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden" + }, + { + "author_name": "Ayya Keshet", + "author_inst": "Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel" + }, + { + "author_name": "Gregory Landua", + "author_inst": "Regen Network, United States" + }, + { + "author_name": "Tomer Meir", + "author_inst": "Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel" + }, + { + "author_name": "Aline Muller", + "author_inst": "Luxembourg Institute of Socio-Economic Research and University of Luxembourg, Luxembourg" + }, + { + "author_name": "Long H. Nguyen", + "author_inst": "Massachusetts General Hospital (MGH), United States" + }, + { + "author_name": "Matej Oresic", + "author_inst": "School of Medical Sciences, Orebro University, Orebro, Sweden, and Turku Bioscience Centre, University of Turku and Abo Akademi University, Turku, Finland" + }, + { + "author_name": "Svetlana Ovchinnikova", + "author_inst": "Center for Molecular Biology (ZMBH), University of Heidelberg, Germany" + }, + { + "author_name": "Hedi Peterson", + "author_inst": "Institute of Computer Science, University of Tartu, Estonia, Estonia" + }, + { + "author_name": "Jay Rajagopal", + "author_inst": "Internal Medicine, Harvard Medical School, Department of Pulmonary Medicine and Critical Care, Massachusetts General Hospital (MGH), United States" + }, + { + "author_name": "Gunnar Ratsch", + "author_inst": "ETH Zurich, Department for Computer Science, Zurich, University Hospital Zurich, Medical Informatics, Zurich and SIB Swiss Institute of Bioinformatics, Zurich a" + }, + { + "author_name": "Hagai Rossman", + "author_inst": "Department of Computer Science and Applied Mathematics, and Department of Molecular Cell Biology, Weizmann Institute of Science, Israel" + }, + { + "author_name": "Johan Rung", + "author_inst": "Science for Life Laboratory (SciLifeLab), Department of Immunology, Genetics and Pathology, Uppsala university, Sweden" + }, + { + "author_name": "Andrea Sboner", + "author_inst": "Englander Institute for Precision Medicine and Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, USA" + }, + { + "author_name": "Alexandros Sigaras", + "author_inst": "Englander Institute for Precision Medicine and Department of Physiology and Biophysics, Weill Cornell Medicine, USA" + }, + { + "author_name": "Tim Spector", + "author_inst": "Kings College, United Kingdom" + }, + { + "author_name": "Ron Steinherz", + "author_inst": "Regen Network, United States" + }, + { + "author_name": "Irene Stevens", + "author_inst": "Science for Life Laboratory (SciLifeLab), Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Sweden" + }, + { + "author_name": "Jaak Vilo", + "author_inst": "Institute of Computer Science, University of Tartu, Estonia, Estonia" + }, + { + "author_name": "Paul Wilmes", + "author_inst": "Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg" + }, + { + "author_name": "CCC (Coronavirus Census Collective)", + "author_inst": "" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.04.01.20049478", "rel_title": "Differential COVID-19-attributable mortality and BCG vaccine use in countries", @@ -1593960,33 +1592526,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.31.20049452", - "rel_title": "A Covid-19 case mortality rate without time delay systematics", - "rel_date": "2020-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.31.20049452", - "rel_abs": "Concerning the two approaches to the Covid-19 case mortality rate published in the literature, namely computing the ratio of (a) the daily number of deaths to a time delayed daily number of confirmed infections; and (b) the cumulative number of deaths to confirmed infections up to a certain time, both numbers having been acquired in the middle of an outbreak, it is shown that each suffers from systematic error of a different source. We further show that in the absence of detailed knowledge of the time delay distribution of (a), the true case mortality rate is obtained by pursuing method (b) at the end of the outbreak when the fate of every case has decisively been rendered. The approach is then employed to calculate the mean case mortality rate of 13 regions of China where every case has already been resolved. This leads to a mean rate of 0.527 {+/-} 0.001 %.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Richard Lieu", - "author_inst": "University of Alabama" - }, - { - "author_name": "Siobhan Quenby", - "author_inst": "Division of Reproductive Health, Warwick Medical School, The University of Warwick, UK" - }, - { - "author_name": "Ally Bi-zhu Jiang", - "author_inst": "Shenzhen RAK wireless Technology Co., Ltd., China" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.01.20049684", "rel_title": "COVID19-Tracker: A shiny app to produce comprehensive data visualization for SARS-CoV-2 epidemic in Spain", @@ -1594726,6 +1593265,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, + { + "rel_doi": "10.1101/2020.04.01.20050203", + "rel_title": "Seeding COVID-19 across sub-Saharan Africa: an analysis of reported importation events across 40 countries", + "rel_date": "2020-04-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.01.20050203", + "rel_abs": "BackgroundThe first case of COVID-19 in sub-Saharan Africa (SSA) was reported by Nigeria on February 27, 2020. While case counts in the entire region remain considerably less than those being reported by individual countries in Europe, Asia, and the Americas, SSA countries remain vulnerable to COVID morbidity and mortality due to systemic healthcare weaknesses, less financial resources and infrastructure to address the new crisis, and untreated comorbidities. Variation in preparedness and response capacity as well as in data availability has raised concerns about undetected transmission events.\n\nMethodsConfirmed cases reported by SSA countries were line-listed to capture epidemiological details related to early transmission events into and within countries. Data were retrieved from publicly available sources, including institutional websites, situation reports, press releases, and social media accounts, with supplementary details obtained from news articles. A data availability score was calculated for each imported case in terms of how many indicators (sex, age, travel history, date of arrival in country, reporting date of confirmation, and how detected) could be identified. We assessed the relationship between time to first importation and overall Global Health Security Index (GHSI) using Cox regression. K-means clustering grouped countries according to healthcare capacity and health and demographic risk factors.\n\nResultsA total of 13,201 confirmed cases of COVID-19 were reported by 48 countries in SSA during the 54 days following the first known introduction to the region. Out of the 2516 cases for which travel history information was publicly available, 1129 (44.9%) were considered importation events. At the regional level, imported cases tended to be male (65.0%), were a median 41.0 years old (Range: 6 weeks - 88 years), and most frequently had recent travel history from Europe (53.1%). The median time to reporting an introduction was 19 days; a countrys time to report its first importation was not related to GHSI, after controlling for air traffic. Countries that had, on average, the highest case fatality rates, lowest healthcare capacity, and highest probability of premature death due to non-communicable diseases were among the last to report any cases.\n\nConclusionsCountries with systemic, demographic, and pre-existing health vulnerabilities to severe COVID-related morbidity and mortality are less likely to report any cases or may be reporting with limited public availability of information. Reporting on COVID detection and response efforts, as well as on trends in non-COVID illness and care-seeking behavior, is critical to assessing direct and indirect consequences and capacity needs in resource-constrained settings. Such assessments aid in the ability to make data-driven decisions about interventions, country priorities, and risk assessment.\n\nKey MessagesO_LIWe line-listed epidemiological indicators for the initial cases reported by 48 countries in sub-Saharan Africa by reviewing and synthesizing information provided by official institutional outlets and news sources.\nC_LIO_LIOur findings suggest that countries with the largest proportions of untreated comorbidities, as measured by probability of premature death due to non-communicable diseases, and the fewest healthcare resources tended to not be reporting any cases at one-month post-introduction into the region.\nC_LIO_LIUsing data availability as a measure of gaps in detection and reporting and relating them to COVID-specific parameters for morbidity and mortality provides a measure of vulnerability.\nC_LIO_LIAccurate and available information on initial cases in seeding local outbreaks is key to projecting case counts and assessing the potential impact of intervention approaches, such that support for local data teams will be important as countries make decisions about control strategies.\nC_LI", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Laura A Skrip", + "author_inst": "Institute for Disease Modeling" + }, + { + "author_name": "Prashanth Selvaraj", + "author_inst": "Institute for Disease Modeling" + }, + { + "author_name": "Brittany Hagedorn", + "author_inst": "Institute for Disease Modeling" + }, + { + "author_name": "Andre Lin Ou\u00e9draogo", + "author_inst": "Institute for Disease Modeling" + }, + { + "author_name": "Navideh Noori", + "author_inst": "Institute for Disease Modeling" + }, + { + "author_name": "Dina Mistry", + "author_inst": "Institute for Disease Modeling" + }, + { + "author_name": "Jamie Bedson", + "author_inst": "Consultant to the Bill & Melinda Gates Foundation" + }, + { + "author_name": "Laurent H\u00e9bert-Dufresne", + "author_inst": "University of Vermont" + }, + { + "author_name": "Samuel V Scarpino", + "author_inst": "Northeastern University" + }, + { + "author_name": "Benjamin Muir Althouse", + "author_inst": "Institute for Disease Modeling" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.04.01.20050138", "rel_title": "Epidemiological Characteristics of COVID-19: A Systemic Review and Meta-Analysis", @@ -1595046,49 +1593640,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.04.02.20050922", - "rel_title": "Inferring COVID-19 spreading rates and potential change points for case number forecasts", - "rel_date": "2020-04-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.04.02.20050922", - "rel_abs": "As COVID-19 is rapidly spreading across the globe, short-term modeling forecasts provide time-critical information for decisions on containment and mitigation strategies. A main challenge for short-term forecasts is the assessment of key epidemiological parameters and how they change when first interventions show an effect. By combining an established epidemiological model with Bayesian inference, we analyze the time dependence of the effective growth rate of new infections. Focusing on the COVID-19 spread in Germany, we detect change points in the effective growth rate that correlate well with the times of publicly announced interventions. Thereby, we can quantify the effect of interventions, and we can incorporate the corresponding change points into forecasts of future scenarios and case numbers. Our code is freely available and can be readily adapted to any country or region.\n\nIntroductionWhen faced with the outbreak of a novel epidemic like COVID-19, rapid response measures are required by individuals as well as by society as a whole to mitigate the spread of the virus. During this initial, time-critical period, neither the central epidemiological parameters, nor the effectiveness of interventions like cancellation of public events, school closings, and social distancing are known.\n\nRationaleAs one of the key epidemiological parameters, we infer the spreading rate{lambda} from confirmed COVID-19 case numbers at the example of Germany by combining Bayesian inference based on Markov-Chain Monte-Carlo sampling with a class of SIR (Susceptible-Infected-Recovered) compartmental models from epidemiology. Our analysis characterizes the temporal change of the spreading rate and, importantly, allows us to identify potential change points and to provide short-term forecast scenarios based on various degrees of social distancing. A detailed description is provided in the accompanying paper, and the models, inference, and predictions are available on github. While we apply it to Germany, our approach can be readily adapted to other countries or regions.\n\nResultsIn Germany, interventions to contain the outbreak were implemented in three steps over three weeks: Around March 9, large public events like soccer matches were cancelled. On March 16, schools and childcare facilities as well as many non-essential stores were closed. One week later, on March 23, a far-reaching contact ban (\"Kontaktsperre\"), which included the prohibition of even small public gatherings as well as the further closing of restaurants and non-essential stores, was imposed by the government authorities.\n\nFrom the observed case numbers of COVID-19, we can quantify the impact of these measures on the disease spread (Fig. 0). Based on our analysis, which includes data until April 21, we have evidence of three change points: the first changed the spreading rate from{lambda} 0 = 0.43 (95 % credible interval (CI: [0.35, 0.51])) to{lambda} 1 = 0.25 (CI: [0.20, 0.30]), and occurred around March 6 (CI: March 2 to March 9); the second change point resulted in{lambda} 2 = 0.15 (CI: [0.12, 0.20]), and occurred around March 15 (CI: March 13 to March 17). Both changes in{lambda} slowed the spread of the virus, but still implied exponential growth (Fig. 0, red and orange traces). To contain the disease spread, and turn from exponential growth to a decline of new cases, a further decrease in{lambda} was necessary. Our analysis shows that this transition has been reached by the third change point that resulted in{lambda} 3 = 0.09 (CI: [0.06, 0.12]) around March 23 (CI: March 20 to March 25).\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC=\"FIGDIR/small/20050922v3_fig0.gif\" ALT=\"Figure 0\">\nView larger version (39K):\norg.highwire.dtl.DTLVardef@1176ccorg.highwire.dtl.DTLVardef@8e7739org.highwire.dtl.DTLVardef@13549baorg.highwire.dtl.DTLVardef@17b5d36_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 0.C_FLOATNO Bayesian analysis of the German COVID-19 data (blue diamonds) reveals three change points that match the timing of publicly announced interventions. A: The inferred effective growth rate (difference between spreading and recovery rate,{lambda} * ={lambda} - ) for an SIR model with weekly reporting modulation and reporting delay that includes scenarios with one, two or three change points (red, orange, green; fitted to case reports until March 25, April 1 and April 9, respectively). The timing of the inferred change points in growth rate is consistent with the timing of German governmental interventions (depicted as *, **, and * * *). B: Comparing inferred models with the actual new reported cases per day reveals the effectiveness of governmental interventions. After the first two interventions, the number of new cases still grew exponentially (red, orange); only after the third intervention did the number of new cases start to saturate (green) or even to decline (gray, data until April 21). This illustrates that the future development strongly depends on our distancing behavior. Note the delay between a change point and the observation of changes in the number of new cases of almost two weeks a combination of reporting delay and a minimal period of evidence accumulation.\n\nC_FIG With this third change point,{lambda} transitioned below the critical value where the spreading rate{lambda} balances the recovery rate , i.e. the effective growth rate{lambda} * ={lambda} - {approx} 0 (Fig. 0, gray traces). Importantly,{lambda} * = 0 presents the watershed between exponential growth or decay. Given the delay of approximately two weeks between an intervention and first inference of the induced changes in{lambda} *, future interventions such as lifting restrictions warrant careful consideration.\n\nOur detailed analysis shows that, in the current phase, reliable short- and long-term forecasts are very difficult as they critically hinge on how the epidemiological parameters change in response to interventions: In Fig. 0 already the three example scenarios quickly diverge from each other, and consequently span a considerable range of future case numbers. Thus, any uncertainty on the magnitude of our social distancing in the past two weeks can have a major impact on the case numbers in the next two weeks. Beyond two weeks, the case numbers depend on our future behavior, for which we have to make explicit assumptions. In the main paper we illustrate how the precise magnitude and timing of potential change points impact the forecast of case numbers (Fig. 2).\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC=\"FIGDIR/small/20050922v3_fig2.gif\" ALT=\"Figure 2\">\nView larger version (28K):\norg.highwire.dtl.DTLVardef@24b42corg.highwire.dtl.DTLVardef@1b0dcc8org.highwire.dtl.DTLVardef@6ef54aorg.highwire.dtl.DTLVardef@a9f26c_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 2.C_FLOATNO The timing and effectiveness of interventions strongly impact future COVID-19 cases. A: We assume three different scenarios for interventions starting on March 16: (I, red) no social distancing, (II, orange) mild social distancing, or (III, green) strict social distancing. B: Delaying the restrictions has a major impact on case numbers: strict restrictions starting on March 16 (green), five days later (magenta) or five days earlier (gray). C: Comparison of the time span over which interventions ramp up to full effect. For all ramps that are centered around the same day, the resulting case numbers are fairly similar. However, a sudden change of the spreading rate can cause a temporary decrease of daily new cases, although{lambda} > at all times (brown).\n\nC_FIG ConclusionsWe developed a Bayesian framework to infer central epidemiological parameters and the timing and magnitude of intervention effects. Thereby, the efficiency of political and individual intervention measures for social distancing and containment can be assessed in a timely manner. We find evidence for a successive decrease of the spreading rate in Germany around March 6 and around March 15, which significantly reduced the magnitude of exponential growth, but was not sufficient to turn growth into decay. Our analysis also shows that a further decrease of the spreading rate occurred around March 23, turning exponential growth into decay. Future interventions and lifting of restrictions can be modeled as additional change points, enabling short-term forecasts for case numbers. In general, our analysis code may help to infer the efficiency of measures taken in other countries and inform policy makers about tightening, loosening and selecting appropriate rules for containment.", - "rel_num_authors": 7, - "rel_authors": [ - { - "author_name": "Jonas Dehning", - "author_inst": "Max Planck Institute for Dynamics and Self-Organization" - }, - { - "author_name": "Johannes Zierenberg", - "author_inst": "Max Planck Institute for Dynamics and Self-Organization" - }, - { - "author_name": "Frank Paul Spitzner", - "author_inst": "Max Planck Institute for Dynamics and Self-Organization" - }, - { - "author_name": "Michael Wibral", - "author_inst": "Georg August University Goettingen" - }, - { - "author_name": "Joao Pinheiro Neto", - "author_inst": "Max Planck Institute for Dynamics and Self-Organization" - }, - { - "author_name": "Michael Wilczek", - "author_inst": "Max Planck Institute for Dynamics and Self-Organization" - }, - { - "author_name": "Viola Priesemann", - "author_inst": "Max Planck Institute for Dynamics and Self-Organization" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.04.01.20050393", "rel_title": "Predicting Whom to Test is More Important Than More Tests - Modeling the Impact of Testing on the Spread of COVID-19 Virus By True Positive Rate Estimation", @@ -1596012,6 +1594563,53 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.04.04.025080", + "rel_title": "Computational analysis suggests putative intermediate animal hosts of the SARS-CoV-2", + "rel_date": "2020-04-05", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.04.025080", + "rel_abs": "The recent emerged SARS-CoV-2 may first transmit to intermediate animal host from bats before the spread to humans. The receptor recognition of ACE2 protein by SARS-CoVs or bat-originated coronaviruses is one of the most important determinant factors for the cross-species transmission and human-to-human transmission. To explore the hypothesis of possible intermediate animal host, we employed molecular dynamics simulation and free energy calculation to examine the binding of bat coronavirus with ACE2 proteins of 47 representing animal species collected from public databases. Our results suggest that intermediate animal host may exist for the zoonotic transmission of SARS-CoV-2. Furthermore, we found that tree shrew and ferret may be two putative intermediate hosts for the zoonotic spread of SARS-CoV-2. Collectively, the continuous surveillance of pneumonia in human and suspicious animal hosts are crucial to control the zoonotic transmission events caused by SARS-CoV-2.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Peng Chu", + "author_inst": "Dalian Medical University" + }, + { + "author_name": "Zheng Zhou", + "author_inst": "Dalian Medical University" + }, + { + "author_name": "Zhichen Gao", + "author_inst": "Dalian University of Technology" + }, + { + "author_name": "Ruiqi Cai", + "author_inst": "Dalian University of Technology" + }, + { + "author_name": "Sijin Wu", + "author_inst": "Ohio State University" + }, + { + "author_name": "Zhaolin Sun", + "author_inst": "Dalian Medical University" + }, + { + "author_name": "Shuyuan Chen", + "author_inst": "University of Melbourne" + }, + { + "author_name": "Yongliang Yang", + "author_inst": "Dalian University of Technology" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.04.01.020594", "rel_title": "A snapshot of SARS-CoV-2 genome availability up to 30th March, 2020 and its implications", @@ -1596292,161 +1594890,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.04.02.019075", - "rel_title": "Rapid community-driven development of a SARS-CoV-2 tissue simulator", - "rel_date": "2020-04-05", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.02.019075", - "rel_abs": "The 2019 novel coronavirus, SARS-CoV-2, is a pathogen of critical significance to international public health. Knowledge of the interplay between molecular-scale virus-receptor interactions, single-cell viral replication, intracellular-scale viral transport, and emergent tissue-scale viral propagation is limited. Moreover, little is known about immune system-virus-tissue interactions and how these can result in low-level (asymptomatic) infections in some cases and acute respiratory distress syndrome (ARDS) in others, particularly with respect to presentation in different age groups or pre-existing inflammatory risk factors. Given the nonlinear interactions within and among each of these processes, multiscale simulation models can shed light on the emergent dynamics that lead to divergent outcomes, identify actionable \"choke points\" for pharmacologic interventions, screen potential therapies, and identify potential biomarkers that differentiate patient outcomes. Given the complexity of the problem and the acute need for an actionable model to guide therapy discovery and optimization, we introduce and iteratively refine a prototype of a multiscale model of SARS-CoV-2 dynamics in lung tissue. The first prototype model was built and shared internationally as open source code and an online interactive model in under 12 hours, and community domain expertise is driving regular refinements. In a sustained community effort, this consortium is integrating data and expertise across virology, immunology, mathematical biology, quantitative systems physiology, cloud and high performance computing, and other domains to accelerate our response to this critical threat to international health. More broadly, this effort is creating a reusable, modular framework for studying viral replication and immune response in tissues, which can also potentially be adapted to related problems in immunology and immunotherapy.", - "rel_num_authors": 35, - "rel_authors": [ - { - "author_name": "Michael Getz", - "author_inst": "Indiana University" - }, - { - "author_name": "Yafei Wang", - "author_inst": "Indiana University" - }, - { - "author_name": "Gary An", - "author_inst": "University of Vermont Medical Center" - }, - { - "author_name": "Maansi Asthana", - "author_inst": "Purdue University" - }, - { - "author_name": "Andrew Becker", - "author_inst": "University of Vermont Medical Center" - }, - { - "author_name": "Chase Cockrell", - "author_inst": "University of Vermont Medical Center" - }, - { - "author_name": "Nicholson Collier", - "author_inst": "Argonne National Laboratory, University of Chicago" - }, - { - "author_name": "Morgan Craig", - "author_inst": "University of Montreal, CHU Sainte-Justine Research Centre" - }, - { - "author_name": "Courtney L. Davis", - "author_inst": "Pepperdine University" - }, - { - "author_name": "James R Faeder", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Ashlee N Ford Versypt", - "author_inst": "Oklahoma State University" - }, - { - "author_name": "Tarunendu Mapder", - "author_inst": "Indiana University School of Medicine" - }, - { - "author_name": "Juliano F Gianlupi", - "author_inst": "Indiana University" - }, - { - "author_name": "James A. Glazier", - "author_inst": "Indiana University" - }, - { - "author_name": "Sara Hamis", - "author_inst": "University of Saint Andrews" - }, - { - "author_name": "Randy Heiland", - "author_inst": "Indiana University" - }, - { - "author_name": "Thomas Hillen", - "author_inst": "University of Alberta" - }, - { - "author_name": "Dennis Hou", - "author_inst": "Rutgers University" - }, - { - "author_name": "Mohammad Aminul Islam", - "author_inst": "Oklahoma State University" - }, - { - "author_name": "Adrianne L Jenner", - "author_inst": "University of Montreal, CHU Sainte-Justine Research Centre" - }, - { - "author_name": "Furkan Kurtoglu", - "author_inst": "Indiana University" - }, - { - "author_name": "Caroline I Larkin", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Bing Liu", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Fiona Macfarlane", - "author_inst": "University of Saint Andrews" - }, - { - "author_name": "Pablo Maygrundter", - "author_inst": "Citizen Scientist" - }, - { - "author_name": "Penelope A Morel", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Aarthi Narayanan", - "author_inst": "George Mason University" - }, - { - "author_name": "Jonathan Ozik", - "author_inst": "Argonne National Laboratory, University of Chicago" - }, - { - "author_name": "Elsje Pienaar", - "author_inst": "Purdue University" - }, - { - "author_name": "Padmini Rangamani", - "author_inst": "University of California, San Diego" - }, - { - "author_name": "Ali Sinan Saglam", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Jason E Shoemaker", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Amber M Smith", - "author_inst": "University of Tennessee Health Science Center" - }, - { - "author_name": "Jordan J A Weaver", - "author_inst": "University of Pittsburgh" - }, - { - "author_name": "Paul Macklin", - "author_inst": "Indiana University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "systems biology" - }, { "rel_doi": "10.1101/2020.04.03.024216", "rel_title": "Increasing testing throughput and case detection with a pooled-sample Bayesian approach in the context of COVID-19", @@ -1597510,6 +1595953,25 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.04.01.020941", + "rel_title": "The Spike Protein S1 Subunit of SARS-CoV-2 Contains an LxxIxE-like Motif that is Known to Recruit the Host PP2A-B56 Phosphatase", + "rel_date": "2020-04-03", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.04.01.020941", + "rel_abs": "SARS-CoV-2 is highly contagious and can cause acute respiratory distress syndrome (ARDS) and multiple organ failure that are largely attributed to the cytokine storm. The surface coronavirus spike (S) glycoprotein is considered as a key factor in host specificity because it mediates infection by receptor-recognition and membrane fusion. Here, the analysis of SARS-CoV-2 S protein revealed two B56-binding LxxIxE-like motifs in S1 and S2 subunits that could recruit the host protein phosphatase 2A (PP2A). The motif in S1 subunit is absent in SARS-CoV and MERS-CoV. Phosphatases and kinases are major players in the regulation of pro-inflammatory responses during pathogenic infections. Moreover, studies have shown that viruses target PP2A in order to manipulate hosts antiviral responses. Recent researches have indicated that SARS-CoV-2 is involved in sustained host inflammation. Therefore, by controlling acute inflammation, it is possible to eliminate its dangerous effects on the host. Among efforts to fight COVID-19, the interaction between LxxIxE-like motif and the PP2A-B56-binding pocket could be a target for the discovery and/or development of a bioactive ligand inhibitor for therapeutic purposes. Indeed, a small molecule called Artepillin C (ArtC), a main compound in Brazilian honeybee green propolis, mimics the side chains of LxxLxE motif. Importantly, ArtC is known, among other effects, to have anti-inflammatory activity that makes it an excellent candidate for future clinical trials in COVID-19 patients.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Halim Maaroufi", + "author_inst": "Institut de Biologie Int\u00e9grative et des Syst\u00e8mes (IBIS) Universit\u00e9 Laval, Quebec, Canada" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.03.31.017459", "rel_title": "In silico approach for designing of a multi-epitope based vaccine against novel Coronavirus (SARS-COV-2)", @@ -1597786,41 +1596248,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.31.20049007", - "rel_title": "Harmonizing heterogeneous endpoints in COVID-19 trials without loss of information - an essential step to facilitate decision making", - "rel_date": "2020-04-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.31.20049007", - "rel_abs": "BackgroundMany trials are now underway to inform decision-makers on potential effects of treatments for COVID-19. To provide sufficient information for all involved decision-makers (clinicians, public health authorities, drug regulatory agencies) a multiplicity of endpoints must be considered. It is a challenge to generate detailed high quality evidence from data while ensuring fast availability and evaluation of the results.\n\nMethodsWe reviewed all interventional COVID-19 trials on Remdesivir, Lopinavir/ritonavir and Hydroxychloroquine registered in the National Library of Medicine (NLM) at the National Institutes of Health (NIH) and summarized the endpoints used to assess treatment effects. We propose a multistate model that harmonizes heterogeneous endpoints and differing lengths of follow-up within and between trials.\n\nResultsThere are currently, March 27, 2020, 23 registered interventional trials investigating the potential benefits of Remdesivir, Lopinavir/ritonavir and Hydroxychloroquine. The endpoints are highly heterogeneous. Follow-up for the primary endpoints ranges from four to 168 days.\n\nA detailed precisely defined endpoint has been proposed by the global network REMAP-CAP, which is specialized on community-acquired pneumonia. Their seven-category endpoint accounts for major clinical events informative for all decision-makers. Moreover, the Core Outcome Measures in Effectiveness Trials (COMET) Initiative is currently working on a core outcome set. We propose a multistate model that accommodates analysis of these recommended endpoints. The model allows for a detailed investigation of treatment effects for various endpoints over the course of time thereby harmonizing differing endpoints and lengths of follow-up.\n\nConclusionMultistate model analysis is a powerful tool to study clinically heterogeneous endpoints (mortality, discharge) as well as endpoints influencing hospital capacities (duration of hospitalization and ventilation) simultaneously over time. Our proposed model extracts all information available in the data and is - by harmonizing endpoints within and between trials - a step towards faster decision making. All ongoing clinical trials, especially those with severe cases, should accommodate primary analysis with a stacked probability plot of the major events mechanical ventilation, discharge alive and death.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Maja von Cube", - "author_inst": "Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center - University of" - }, - { - "author_name": "Marlon Grodd", - "author_inst": "Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center - University of Freiburg, Germany" - }, - { - "author_name": "Martin Wolkewitz", - "author_inst": "Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center - University of Freiburg, Germany" - }, - { - "author_name": "Derek Hazard", - "author_inst": "Institute of Medical Biometry and Statistics, Faculty of Medicine and Medical Center - University of Freiburg, Germany" - }, - { - "author_name": "Jerome Lambert", - "author_inst": "University of Paris, Paris, France; ECSTRA Team, Epidemiology and Biostatistics Sorbonne Paris Cite Research Centre UMR 1153, Inserm, Paris, France" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.28.20046151", "rel_title": "Clinical features, Diagnosis, and Treatment of COVID-19: A systematic review of case reports and case series", @@ -1598656,6 +1597083,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "endocrinology" }, + { + "rel_doi": "10.1101/2020.03.30.20048009", + "rel_title": "Flattening the curve is not enough, we need to squash it. An explainer using a simple model", + "rel_date": "2020-04-02", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.30.20048009", + "rel_abs": "BackgroundAround the world there are examples of both effective control (e.g., South Korea, Japan) and less successful control (e.g., Italy, Spain, United States) of COVID-19 with dramatic differences in the consequent epidemic curves. Models agree that flattening the curve without controlling the epidemic completely is insufficient and will lead to an overwhelmed health service. A recent model, calibrated for the UK and US, demonstrated this starkly.\n\nMethodsWe used a simple compartmental deterministic model of COVID-19 transmission in Australia, to illustrate the dynamics resulting from shifting or flattening the curve versus completely squashing it.\n\nResultsWe find that when the reproduction number is close to one, a small decrease in transmission leads to a large reduction in burden (i.e., cases, deaths and hospitalisations), but achieving this early in the epidemic through social distancing interventions also implies that the community will not reach herd immunity.\n\nConclusionsAustralia needs not just to shift and flatten the curve, but to squash it by getting the reproduction number below one. This will require Australia to achieve transmission rates at least two thirds lower than those seen in the most severely affected countries.\n\nThe knownCOVID-19 has been diagnosed in over 4,000 Australians. Up until mid-March, most were from international travel, but now we are seeing a rise in locally acquired cases.\n\nThe newThis study uses a simple transmission dynamic model to demonstrate the difference between moderate changes to the reproduction number and forcing the reproduction number below one.\n\nThe implicationsLowering local transmission is becoming important in reducing the transmission of COVID-19. To maintain control of the epidemic, the focus should be on those in the community who do not regard themselves as at risk.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Emma S McBryde", + "author_inst": "James Cook University" + }, + { + "author_name": "Michael T Meehan", + "author_inst": "James Cook University" + }, + { + "author_name": "James M Trauer", + "author_inst": "Monash University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.31.20048595", "rel_title": "Ambient nitrogen dioxide pollution and spread ability of COVID-19 in Chinese cities", @@ -1598888,57 +1597342,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2020.03.31.20047142", - "rel_title": "Clinical features and outcomes of 2019 novel coronavirus-infected patients with high plasma BNP levels", - "rel_date": "2020-04-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.31.20047142", - "rel_abs": "AimsTo explore clinical features and outcome of 2019 novel coronavirus(2019-nCoV)-infected patients with high BNP levels\n\nMethods and resultsData were collected from patients medical records, and we defined high BNP according to the plasma BNP was above > 100 pg/mL. In total,34 patients with corona virus disease 2019(COVID-19)were included in the analysis. Ten patients had high plasma BNP level. The median age for these patients was 60.5 years(interquartile range, 40-80y), and 6/10 (60%) were men. Underlying comorbidities in some patients were coronary heart disease (n=2, 20%), hypertesion (n=3,30%), heart failure (n=1,10%)and diabetes (n=2, 20%). Six (60%) patients had a history of Wuhan exposure. The most common symptoms at illness onset in patients were fever (n=7, 70%), cough (n=3, 30%), headache or fatigue(n=4,40%). These patients had higher aspartate aminotransferase(AST), troponin I, C reactive protein and lower hemoglobin, and platelet count,compared with patients with normal BNP, respectively. Compared with patients with normal BNP, patients with high BNP were more likely to develop severe pneumonia, and receive tracheal cannula, invasive mechanical ventilation, continuous renal replacement therapy, extracorporeal membrane oxygenation, and be admitted to the intensive care unit. One patient with high BNP died during the study.\n\nConclusionHigh BNP is a common condition among patients infected with 2019-nCoV. Patients with high BNP showed poor clinical outcomes", - "rel_num_authors": 9, - "rel_authors": [ - { - "author_name": "youbin liu", - "author_inst": "Department of Cardiology, Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Dehui Liu", - "author_inst": "Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Huafeng Song", - "author_inst": "Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Chunlin chen", - "author_inst": "Department of Cardiology, Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Mingfang lv", - "author_inst": "Department of Cardiology, Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Xing pei", - "author_inst": "Department of Cardiology, Guangzhou Eighth People's Hospita" - }, - { - "author_name": "Zhongwei Hu", - "author_inst": "Department of Cardiology, Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Zhihui Qin", - "author_inst": "Department of Cardiology, Guangzhou Eighth People's Hospital" - }, - { - "author_name": "Jinglong Li", - "author_inst": "Department of Cardiology, Guangzhou Eighth People's Hospital" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "cardiovascular medicine" - }, { "rel_doi": "10.1101/2020.03.30.20047803", "rel_title": "Forecasting COVID-19 impact in India using pandemic waves Nonlinear Growth Models", @@ -1599822,6 +1598225,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.30.20048132", + "rel_title": "Optimal timing for social distancing during an epidemic", + "rel_date": "2020-04-01", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.30.20048132", + "rel_abs": "Social distancing is an effective way to contain the spread of a contagious disease, particularly when facing a novel pathogen and no pharmacological interventions are available. In such cases, conventional wisdom suggests that social distancing measures should be introduced as soon as possible after the beginning of an outbreak to more effectively mitigate the spread of the disease. Using a simple epidemiological model we show that, however, there is in fact an optimal time to initiate a temporal social distancing intervention if the goal is to reduce the final epidemic size or \"flatten\" the epidemic curve. The optimal timing depends strongly on the effective reproduction number (R0) of the disease, such that as the R0 increases, the optimal time decreases non-linearly. Additionally, if pharmacological interventions (e.g., a vaccine) become available at some point during the epidemic, the sooner these interventions become available the sooner social distancing should be initiated to maximize its effectiveness. Although based on a simple model, we hope that these insights inspire further investigations within the context of more complex and data-driven epidemiological models, and can ultimately help decision makers to improve temporal social distancing policies to mitigate the spread of epidemics.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Oscar Patterson-Lomba", + "author_inst": "Analysis Group" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.30.20047472", "rel_title": "COVID-19 Epidemic in Switzerland: Growth Prediction and Containment Strategy Using Artificial Intelligence and Big Data", @@ -1600194,25 +1598616,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.30.20047894", - "rel_title": "Forecasting the CoViD19 Diffusion in Italy and the Related Occupancy of Intensive Care Units", - "rel_date": "2020-04-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.30.20047894", - "rel_abs": "This paper provides a model-based method for the forecast of the total number of currently CoVoD-19 positive individuals and of the occupancy of the available Intensive Care Units in Italy. The predictions obtained - for a time horizon of 10 days starting from March 29th - will be provided at a national as well as at a more disaggregate levels, following a criterion based on the magnitude of the phenomenon. While the Regions which have been hit the most by the pandemic have been kept separated, the less affected ones have been aggregated into homogeneous macro-areas. Results show that - within the forecast period considered (March 29th - April 7th) - all of the Italian regions will show a decreasing number of CoViD-19 positive people. Same for the number of people who will need to be hospitalized in a Intensive Care Unit (ICU). These estimates are valid under constancy of the Governments current containment policies. In this scenario, Northern Regions will remain the most affected ones and no significant outbreak are foreseen in the southern regions.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Livio Fenga", - "author_inst": "ISTAT" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.28.20046144", "rel_title": "Clinical observations of low molecular weight heparin in relieving inflammation in COVID-19 patients: A retrospective cohort study", @@ -1600988,6 +1599391,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.30.20046326", + "rel_title": "Pandemic Politics: Timing State-Level Social Distancing Responses to COVID-19", + "rel_date": "2020-03-31", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.30.20046326", + "rel_abs": "Social distancing policies are critical but economically painful measures to flatten the curve against emergent infectious diseases. As the novel coronavirus that causes COVID-19 spread throughout the United States in early 2020, the federal government issued social distancing recommendations but left to the states the most difficult and consequential decisions restricting behavior, such as canceling events, closing schools and businesses, and issuing stay-at-home orders. We present an original dataset of state-level social distancing policy responses to the epidemic and explore how political partisanship, COVID-19 caseload, and policy diffusion explain the timing of governors decisions to mandate social distancing. An event history analysis of five social distancing policies across all fifty states reveals the most important predictors are political: all else equal, Republican governors and governors from states with more Trump supporters were slower to adopt social distancing policies. These delays are likely to produce significant, on-going harm to public health.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Christopher Adolph", + "author_inst": "University of Washington" + }, + { + "author_name": "Kenya Amano", + "author_inst": "University of Washington" + }, + { + "author_name": "Bree Bang-Jensen", + "author_inst": "University of Washington" + }, + { + "author_name": "Nancy Fullman", + "author_inst": "University of Washington" + }, + { + "author_name": "John Wilkerson", + "author_inst": "University of Washington" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "health policy" + }, { "rel_doi": "10.1101/2020.03.28.20036715", "rel_title": "The first three months of the COVID-19 epidemic: Epidemiological evidence for two separate strains of SARS-CoV-2 viruses spreading and implications for prevention strategies", @@ -1601292,25 +1599730,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.03.29.20046565", - "rel_title": "Eco-epidemiological assessment of the COVID-19 epidemic in China, January-February 2020", - "rel_date": "2020-03-31", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.29.20046565", - "rel_abs": "BackgroundThe outbreak of COVID-19 in China in early 2020 provides a rich data source for exploring the ecological determinants of this new infection, which may be of relevance elsewhere.\n\nObjectivesAssessing the spread of the COVID-19 across China, in relation to associations between cases and ecological factors including population density, temperature, solar radiation and precipitation.\n\nMethodsOpen-access COVID-19 case data include 18,069 geo-located cases in China during January and February 2020, which were mapped onto a 0.25{degrees} latitude/longitude grid together with population and weather data (temperature, solar radiation and precipitation). Of 15,539 grid cells, 559 (3.6%) contained at least one case, and these were used to construct a Poisson regression model of cell-weeks. Weather parameters were taken for the preceding week given the established 5-7 day incubation period for COVID-19. The dependent variable in the Poisson model was incident cases per cell-week and exposure was cell population, allowing for clustering of cells over weeks, to give incidence rate ratios.\n\nResultsThe overall COVID-19 incidence rate in cells with confirmed cases was 0.12 per 1,000. There was a single case in 113/559 (20.2%) of cells, while two grid cells recorded over 1,000 cases. Weekly means of maximum daily temperature varied from -28.0 to 30.1 {degrees}C, minimum daily temperature from -42.4 to 23.0 {degrees}C, maximum solar radiation from 0.04 to 2.74 MJm-2 and total precipitation from 0 to 72.6 mm. Adjusted incidence rate ratios suggested brighter, warmer and drier conditions were associated with lower incidence.\n\nConclusionThough not demonstrating cause and effect, there were appreciable associations between weather and COVID-19 incidence during the epidemic in China. This does not mean the pandemic will go away with summer weather but demonstrates the importance of using weather conditions in understanding and forecasting the spread of COVID-19.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Peter Byass", - "author_inst": "Umea University" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "public and global health" - }, { "rel_doi": "10.1101/2020.03.30.20040519", "rel_title": "Inferring Timing of Infection Using Within-host SARS-CoV-2 Infection Dynamics Model: Are \"Imported Cases\" Truly Imported?", @@ -1602281,6 +1600700,97 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.03.30.015461", + "rel_title": "Potent neutralizing antibodies in the sera of convalescent COVID-19 patients are directed against conserved linear epitopes on the SARS-CoV-2 spike protein", + "rel_date": "2020-03-31", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.30.015461", + "rel_abs": "The ongoing SARS-CoV-2 pandemic demands rapid identification of immunogenic targets for the design of efficient vaccines and serological detection tools. In this report, using pools of overlapping linear peptides and functional assays, we present two immunodominant regions on the spike glycoprotein that were highly recognized by neutralizing antibodies in the sera of COVID-19 convalescent patients. One is highly specific to SARS-CoV-2, and the other is a potential pan-coronavirus target.", + "rel_num_authors": 19, + "rel_authors": [ + { + "author_name": "Chek Meng Poh", + "author_inst": "Singapore Immunology Network, Agency of Science, Technology and Research, Immunos, Biopolis, Singapore" + }, + { + "author_name": "Guillaume Carissimo", + "author_inst": "Singapore Immunology Network" + }, + { + "author_name": "Wang Bei", + "author_inst": "Singapore Immunology Network" + }, + { + "author_name": "Siti Naqiah Amrun", + "author_inst": "Singapore Immunology Network" + }, + { + "author_name": "Cheryl Yi-Pin Lee", + "author_inst": "Singapore Immunology Network" + }, + { + "author_name": "Rhonda Sin-Ling Chee", + "author_inst": "Singapore Immunology Network" + }, + { + "author_name": "Nicholas Kim-Wah Yeo", + "author_inst": "Singapore Immunology Network" + }, + { + "author_name": "Wen-Hsin Lee", + "author_inst": "Singapore Immunology Network" + }, + { + "author_name": "Yee-Sin Leo", + "author_inst": "National Centre for Infectious Diseases, Singapore" + }, + { + "author_name": "Mark I-Cheng Chen", + "author_inst": "National Centre for Infectious Diseases, Singapore" + }, + { + "author_name": "Seow-Yen Tan", + "author_inst": "Department of Infectious Diseases, Changi General Hospital, Singapore" + }, + { + "author_name": "Louis Yi Ann Chai", + "author_inst": "Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore" + }, + { + "author_name": "Shirin Kalimuddin", + "author_inst": "Department of Infectious Diseases, Singapore General Hospital, Singapore" + }, + { + "author_name": "Siew-Yee Thien", + "author_inst": "Department of Infectious Diseases, Singapore General Hospital, Singapore" + }, + { + "author_name": "Barnaby Edward Young", + "author_inst": "National Centre for Infectious Diseases, Singapore" + }, + { + "author_name": "David C. Lye", + "author_inst": "National Centre for Infectious Diseases, Singapore" + }, + { + "author_name": "Cheng-I Wang", + "author_inst": "Singapore Immunology Network" + }, + { + "author_name": "Laurent Renia", + "author_inst": "Singapore Immunology Network" + }, + { + "author_name": "Lisa FP Ng", + "author_inst": "Singapore Immunology Network" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "immunology" + }, { "rel_doi": "10.1101/2020.03.30.015164", "rel_title": "Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2 etiologic agent of global pandemic COVID-19: an in silico approach", @@ -1602761,29 +1601271,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.25.20043505", - "rel_title": "Machine Learning Approach for Confirmation of COVID-19 Cases: Positive, Negative, Death and Release", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.25.20043505", - "rel_abs": "In recent days, Covid-19 coronavirus has been an immense impact on social, economic fields in the world. The objective of this study determines if it is feasible to use machine learning method to evaluate how much prediction results are close to original data related to Confirmed-Negative-Released-Death cases of Covid-19. For this purpose, a verification method is proposed in this paper that uses the concept of Deep-learning Neural Network. In this framework, Long short-term memory (LSTM) and Gated Recurrent Unit (GRU) are also assimilated finally for training the dataset and the prediction results are tally with the results predicted by clinical doctors. The prediction results are validated against the original data based on some predefined metric. The experimental results showcase that the proposed approach is useful in generating suitable results based on the critical disease outbreak. It also helps doctors to recheck further verification of virus by the proposed method. The outbreak of Coronavirus has the nature of exponential growth and so it is difficult to control with limited clinical persons for handling a huge number of patients with in a reasonable time. So it is necessary to build an automated model, based on machine learning approach, for corrective measure after the decision of clinical doctors. It could be a promising supplementary confirmation method for frontline clinical doctors. The proposed method has a high prediction rate and works fast for probable accurate identification of the disease. The performance analysis shows that a high rate of accuracy is obtained by the proposed method.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Samir Kumar Bandyopadhyay Sr.", - "author_inst": "The Bhawanipur Education Society College, Kolkata, India" - }, - { - "author_name": "Shawni Dutta Jr.", - "author_inst": "The Bhawanipur Education Society College, Kolkata, India" - } - ], - "version": "1", - "license": "cc0_ng", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.27.20043968", "rel_title": "Evaluation of Group Testing for SARS-CoV-2 RNA", @@ -1603811,6 +1602298,57 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.27.20045203", + "rel_title": "Triage assessment of cardiorespiratory risk status based on measurement of the anaerobic threshold, and estimation by patient-reported activity limitation", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.27.20045203", + "rel_abs": "BO_SCPLOWACKGROUNDC_SCPLOWRapid triaging, as in the current COVID-19 pandemic, focuses on age and pre-existing medical conditions. In contrast, preoperative assessments use cardiopulmonary exercise testing (CPET) to categorise patients to higher and lower risk independent of diagnostic labels. Since CPET is not feasible in population-based settings, our aims included evaluation of a triage/screening tool for cardiorespiratory risk.\n\nMO_SCPLOWETHODSC_SCPLOWCPET-derived anaerobic thresholds were evaluated retrospectively in 26 patients with pulmonary arteriovenous malformations (AVMs) who represent a challenging group to risk-categorise. Pulmonary AVM-induced hypoxaemia secondary to intrapulmonary right-to-left shunts, anaemia from underlying hereditary haemorrhagic telangiectasia and metabolic equivalents derived from the 13-point Veterans Specific Activity Questionnaire (VSAQ) were evaluated as part of routine clinical care. Pre-planned analyses evaluated associations and modelling of the anaerobic threshold and patient-specific variables.\n\nRO_SCPLOWESULTSC_SCPLOWIn the 26 patients (aged 21-77, median 57 years), anaerobic threshold ranged from 7.6-24.5 (median 12.35) ml.min-1kg-1 and placed more than half of the patients (15, 57.7%) in the >11 ml.min-1kg-1 category suggested as \"lower-risk\" for intra-abdominal surgeries. Neither age nor baseline SpO2 predicted anaerobic threshold, or lower/higher risk categories, either alone or in multivariate analyses, despite baseline oxygen saturation (SpO2) ranging from 79 to 99 (median 92)%, haemoglobin from 108 to 183 (median 156)g.L-1. However, lower haemoglobin, and particularly, arterial oxygen content and oxygen pulse were associated with increased cardiorespiratory risk: Modelling a haemoglobin increase of 25g.L-1 placed a further 7/26 (26.9%) patients in a lower risk category. For patients completing the VSAQ, derived metabolic equivalents were strongly associated with anaerobic threshold enabling risk evaluations through a simple questionnaire.\n\nCO_SCPLOWONCLUSIONSC_SCPLOWBaseline exercise tolerance may override age and diagnostic labels in triage settings. These data support approaches to risk reduction by aerobic conditioning and attention to anaemia. The VSAQ is suggested as a rapid screening tool for cardiorespiratory risk assessment to implement during triage/screening.\n\nKey Messages\n\nWhat is already knownO_LIAlongside age, pre-existing medical conditions are perceived negatively during triage assessments, particularly if rare, and/or theoretically expected to influence cardiorespiratory risk;\nC_LIO_LIAnaesthetists use cardiopulmonary exercise testing to categorise patients to higher and lower risk independently to diagnostic labels, but this is not feasible in acute settings;\nC_LIO_LIPulmonary arteriovenous malformations are an exemplar of a condition where, due to expected or measured abnormalities (hypoxaemia-low PaO2 SpO2), poor physiological capacity might be predicted.\nC_LI\n\nWhat this study addsO_LINeither age nor usual SpO2 predicted lower/higher risk categories by anaerobic threshold, but haemoglobin-dependent indices of oxygen delivery to the tissues were associated with higher risk, offering opportunities for improvement by attention to anaemia and aerobic conditioning;\nC_LIO_LIBaseline exercise tolerance may override age and diagnostic labels in triage settings: the 13-point VSAQ Veterans Specific Activity Questionnaire (VSAQ) is suggested as a rapid screening tool for cardiorespiratory risk assessment.\nC_LI", + "rel_num_authors": 9, + "rel_authors": [ + { + "author_name": "Saranya Thurairatnam", + "author_inst": "Imperial College London" + }, + { + "author_name": "Filip Gawecki", + "author_inst": "Imprial College London" + }, + { + "author_name": "Timothy Strangeways", + "author_inst": "Imperial College London" + }, + { + "author_name": "Joseph Perks", + "author_inst": "Imperial College Healthcare NHS Trust" + }, + { + "author_name": "Vatshalan Santhirapala", + "author_inst": "Imperial College London" + }, + { + "author_name": "Jonathan Myers", + "author_inst": "Palo Alto Health Care System and Stanford University" + }, + { + "author_name": "Hannah C Tighe", + "author_inst": "Imperial College Healthcare NHS Trust" + }, + { + "author_name": "Luke SGE Howard", + "author_inst": "Imperial College Healthcare NHS Trust" + }, + { + "author_name": "Claire L Shovlin", + "author_inst": "Imperial College London" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2020.03.27.20045195", "rel_title": "A mathematical model of COVID-19 transmission between frontliners and the general public", @@ -1604067,37 +1602605,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.03.27.20044958", - "rel_title": "Research on the Influence of Effective Distance Between Cities on the Cross-regional Transmission of COVID-19", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.27.20044958", - "rel_abs": "The COVID-19 epidemic in China has been effectively controlled. It is of great significance to study the law of cross-regional spread of the epidemic, for the prevention and control of the COVID-19 in the future in China and other countries or regions. In this study, the cross-regional connection intensity between cities was characterized based on the probability and the effective distance of the shortest path tree, and the empirical analysis was carried out based on the high-frequency data such as the cases of COVID 19 outbreaks. It is concluded that the higher the intensity of inter-city connection, the larger scale the cross-regional spread of the epidemic.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Shanlang Lin", - "author_inst": "School of Economics and Management,Tongji University" - }, - { - "author_name": "Yanning Qiao", - "author_inst": "School of economics and management, tongji university" - }, - { - "author_name": "Junpei Huang", - "author_inst": "School of economics and management, tongji university" - }, - { - "author_name": "Na Yan", - "author_inst": "School of economics and management, tongji university" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.03.26.20044842", "rel_title": "A model to estimate regional demand for COVID-19 related hospitalizations", @@ -1605101,6 +1603608,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.26.20044693", + "rel_title": "Why estimating population-based case fatality rates during epidemics may be misleading", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20044693", + "rel_abs": "Different ways of calculating mortality ratios during epidemics can yield widely different results, particularly during the COVID-19 pandemic. We formulate both a survival probability model and an associated infection duration-dependent SIR model to define individual- and population-based estimates of dynamic mortality ratios. The key parameters that affect the dynamics of the different mortality estimates are the incubation period and the length of time individuals were infected before confirmation of infection. We stress that none of these ratios are accurately represented by the often misinterpreted case fatality ratio (CFR), the number of deaths to date divided by the total number of infected cases to date. Using available data on the recent SARS-CoV-2 outbreaks and simple assumptions, we estimate and compare the different dynamic mortality ratios and highlight their differences. Informed by our modeling, we propose a more systematic method to determine mortality ratios during epidemic outbreaks and discuss sensitivity to confounding effects and errors in the data.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Lucas B\u00f6ttcher", + "author_inst": "UCLA" + }, + { + "author_name": "Mingtao Xia", + "author_inst": "UCLA" + }, + { + "author_name": "Tom Chou", + "author_inst": "UCLA" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.22.20040758", "rel_title": "Efficacy of hydroxychloroquine in patients with COVID-19: results of a randomized clinical trial", @@ -1605477,37 +1604011,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health economics" }, - { - "rel_doi": "10.1101/2020.03.28.20046110", - "rel_title": "Which Measures are Effective in Containing COVID-19?Empirical Research Based on Prevention and Control Cases in China", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.28.20046110", - "rel_abs": "Various epidemic prevention and control measures aimed at reducing person-to-person contact has paid a certain cost while controlling the epidemic. So accurate evaluation of these measures helps to maximize the effectiveness of prevention and control while minimizing social costs. In this paper, we develop the model in Dirk Brockmann and Dirk Helbing (2013) to theoretically explain the impact mechanism of traffic control and social distancing measures on the spread of the epidemic, and empirically tests the effect of the two measures in China at the present stage using econometric approach. We found that both traffic control and social distancing measures have played a very good role in controlling the development of the epidemic. Nationally, social distancing measures are better than traffic control measures; the two measures are complementary and their combined action will play a better epidemic prevention effect; Traffic control and social distancing do not work everywhere. Traffic control only works in cities with higher GDP per capita and population size, while fails in cities with lower GDP per capita and population size. In cities with lower population size, social distancing becomes inoperative; the rapid and accurate transmission of information, a higher protection awareness of the public, and a stronger confidence of residents in epidemic prevention can promote the realization of the measure effects. The findings above verify the effectiveness and correctness of the measures implemented in China at present, at the same time, we propose that it is necessary to fully consider the respective characteristics of the two measures, cooperating and complementing each other; whats more, measures should be formulated according to the citys own situation, achieving precise epidemic prevention; Finally, we should increase the transparency of information, improve protection awareness of the public, guide emotions of the public in a proper way, enhancing public confidence.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Shanlang Lin", - "author_inst": "Tongji University" - }, - { - "author_name": "Junpei Huang", - "author_inst": "Tongji University" - }, - { - "author_name": "Ziwen He", - "author_inst": "School of economics and management, tongji university" - }, - { - "author_name": "Dandan Zhan", - "author_inst": "251227468@qq.com" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "health economics" - }, { "rel_doi": "10.1101/2020.03.29.20045187", "rel_title": "How to evaluate the success of the COVID-19 measures implemented by the Norwegian government by analyzing changes in doubling time", @@ -1606395,6 +1604898,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.26.20044271", + "rel_title": "Negligible Risk of the COVID-19 Resurgence Caused by Work Resuming in China (outside Hubei): a Statistical Probability Study", + "rel_date": "2020-03-30", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.26.20044271", + "rel_abs": "The COVID-19 outbreak in China appears to reach the late stage since late February 2020, and a stepwise restoration of economic operations is implemented. Risk assessment for such economic restoration is of significance. Here we estimated the probability of COVID-19 resurgence caused by work resuming in typical provinces/cities, and found that such probability is very limited (<5% for all the regions except Beijing). Our work may inform provincial governments to make risk level-based, differentiated control measures.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "XINMIAO FU", + "author_inst": "Fujian Normal University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.25.20043315", "rel_title": "Analysis of the scientific literature in the first 30 Days of the novel coronavirus outbreak.", @@ -1606807,29 +1605329,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.25.20043927", - "rel_title": "Dangers of ACE inhibitor and ARB usage in COVID-19: evaluating the evidence", - "rel_date": "2020-03-30", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.25.20043927", - "rel_abs": "BackgroundConcerns have been raised regarding the safety of Angiotensin Converting Enzyme Inhibitors (ACEIs) and Angiotensin Receptor Blockers (ARBs) in patients with COVID-19, based on the hypothesis that such medications may raise expression of ACE2, the receptor for SARS-CoV-2.\n\nMethodsWe conducted a literature review of studies (n=12) in experimental animals and human subjects (n=12) and evaluated the evidence regarding the impact of administration of ACEIs and ARBs on ACE2 expression. We prioritized studies that assessed ACE2 protein expression data, measured directly or inferred from ACE2 activity assays.\n\nResultsThe findings in animals are inconsistent with respect to an increase in ACE2 expression in response to treatment with ACEIs or ARBs. Control/sham animals show little to no effect in the plurality of studies. Those studies that report increases in ACE2 expression tend to involve acute injury models and/or higher doses of ACEIs or ARBS than are typically administered to patients. Data from human studies overwhelmingly imply that administration of ACEIs/ARBs does not increase ACE2 expression.\n\nConclusionAvailable evidence, in particular, data from human studies, does not support the hypothesis that ACEI/ARB use increases ACE2 expression and the risk of complications from COVID-19. We conclude that patients being treated with ACEIs and ARBs should continue their use for approved indications.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Krishna Sriram", - "author_inst": "University of California San Diego" - }, - { - "author_name": "Paul A. Insel", - "author_inst": "University of California San Diego" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "pharmacology and therapeutics" - }, { "rel_doi": "10.1101/2020.03.26.20044511", "rel_title": "Trend Analysis and Forecasting of COVID-19 outbreak in India", @@ -1607701,6 +1606200,29 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.03.25.008904", + "rel_title": "Modeling of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Proteins by Machine Learning and Physics-Based Refinement", + "rel_date": "2020-03-28", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.25.008904", + "rel_abs": "Protein structures are crucial for understanding their biological activities. Since the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), there is an urgent need to understand the biological behavior of the virus and provide a basis for developing effective therapies. Since the proteome of the virus was determined, some of the protein structures could be determined experimentally, and others were predicted via template-based modeling approaches. However, tertiary structures for several proteins are still not available from experiment nor they could be accurately predicted by template-based modeling because of lack of close homolog structures. Previous efforts to predict structures for these proteins include efforts by DeepMind and the Zhang group via machine learning-based structure prediction methods, i.e. AlphaFold and C-I-TASSER. However, the predicted models vary greatly and have not yet been subjected to refinement. Here, we are reporting new predictions from our in-house structure prediction pipeline. The pipeline takes advantage of inter-residue contact predictions from trRosetta, a machine learning-based method. The predicted models were further improved by applying molecular dynamics simulation-based refinement. We also took the AlphaFold models and refined them by applying the same refinement method. Models based on our structure prediction pipeline and the refined AlphaFold models were analyzed and compared with the C-I-TASSER models. All of our models are available at https://github.com/feiglab/sars-cov-2-proteins.", + "rel_num_authors": 2, + "rel_authors": [ + { + "author_name": "Lim Heo", + "author_inst": "Michigan State University" + }, + { + "author_name": "Michael Feig", + "author_inst": "Michigan State University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "biophysics" + }, { "rel_doi": "10.1101/2020.03.27.009480", "rel_title": "SARS-CoV-2 exhibits intra-host genomic plasticity and low-frequency polymorphic quasispecies", @@ -1608145,33 +1606667,6 @@ "type": "new results", "category": "molecular biology" }, - { - "rel_doi": "10.1101/2020.03.27.012906", - "rel_title": "RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses", - "rel_date": "2020-03-28", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.27.012906", - "rel_abs": "As the COVID-19 outbreak spreads, there is a growing need for a compilation of conserved RNA genome regions in the SARS-CoV-2 virus along with their structural propensities to guide development of antivirals and diagnostics. Using sequence alignments spanning a range of betacoronaviruses, we rank genomic regions by RNA sequence conservation, identifying 79 regions of length at least 15 nucleotides as exactly conserved over SARS-related complete genome sequences available near the beginning of the COVID-19 outbreak. We then confirm the conservation of the majority of these genome regions across 739 SARS-CoV-2 sequences reported to date from the current COVID-19 outbreak, and we present a curated list of 30 SARS-related-conserved regions. We find that known RNA structured elements curated as Rfam families and in prior literature are enriched in these conserved genome regions, and we predict additional conserved, stable secondary structures across the viral genome. We provide 106 SARS-CoV-2-conserved-structured regions as potential targets for antivirals that bind to structured RNA. We further provide detailed secondary structure models for the 5 UTR, frame-shifting element, and 3 UTR. Last, we predict regions of the SARS-CoV-2 viral genome have low propensity for RNA secondary structure and are conserved within SARS-CoV-2 strains. These 59 SARS-CoV-2-conserved-unstructured genomic regions may be most easily targeted in primer-based diagnostic and oligonucleotide-based therapeutic strategies.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ramya Rangan", - "author_inst": "Stanford University" - }, - { - "author_name": "Ivan N. Zheludev", - "author_inst": "Stanford University" - }, - { - "author_name": "Rhiju Das", - "author_inst": "Stanford University" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "genetics" - }, { "rel_doi": "10.1101/2020.03.24.20042598", "rel_title": "Disparities in Age-Specific Morbidity and Mortality from SARS-CoV-2 in China and the Republic of Korea", @@ -1609231,6 +1607726,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.23.20041863", + "rel_title": "Modelling strategies to organize healthcare workforce during pandemics: application to COVID-19", + "rel_date": "2020-03-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.23.20041863", + "rel_abs": "Protection of healthcare workforce who are at increased risk to become infected is of paramount relevance for the care of patients in the setting of a pandemic such as coronavirus disease 2019 (COVID-19). The ideal organisational strategy to protect the workforce in a situation in which social distancing cannot be maintained remains to be determined. In this study, we have mathematically modelled strategies for the employment of hospital workforce with the goal to simulate health and productivity of the workers. The models were designed to determine if desynchronization of medical teams by dichotomizing the workers may protect the workforce. Our studies model workforce productivity depending on the infection rate, the presence of reinfection and the efficiency of home office and apply our theory to the case of COVID-19. The results reveal that a desynchronization strategy in which two medical teams work alternating for 7 days increases the available workforce.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Daniel Sanchez-Taltavull", + "author_inst": "Department for Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Switzerland" + }, + { + "author_name": "Daniel Candinas", + "author_inst": "Department for Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Switzerland" + }, + { + "author_name": "Edgar Roldan", + "author_inst": "The Abdus Salam International Centre for Theoretical Physics, Trieste, Italy" + }, + { + "author_name": "Guido Beldi", + "author_inst": "Department for Visceral Surgery and Medicine, Bern University Hospital, University of Bern, Switzerland" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.22.20041145", "rel_title": "Global transmission network of SARS-CoV-2: from outbreak to pandemic", @@ -1609727,29 +1608253,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, - { - "rel_doi": "10.1101/2020.03.23.004176", - "rel_title": "Structure-based modeling of SARS-CoV-2 peptide/HLA-A02 antigens", - "rel_date": "2020-03-27", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.23.004176", - "rel_abs": "As a first step toward the development of diagnostic and therapeutic tools to fight the Coronavirus disease (COVID-19), it is important to characterize CD8+ T cell epitopes in the SARS-CoV-2 peptidome that can trigger adaptive immune responses. Here, we use RosettaMHC, a comparative modeling approach which leverages existing high-resolution X-ray structures from peptide/MHC complexes available in the Protein Data Bank, to derive physically realistic 3D models for high-affinity SARS-CoV-2 epitopes. We outline an application of our method to model 439 9mer and 279 10mer predicted epitopes displayed by the common allele HLA-A*02:01, and we make our models publicly available through an online database (https://rosettamhc.chemistry.ucsc.edu). As more detailed studies on antigen-specific T cell recognition become available, RosettaMHC models of antigens from different strains and HLA alleles can be used as a basis to understand the link between peptide/HLA complex structure and surface chemistry with immunogenicity, in the context of SARS-CoV-2 infection.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Santrupti Nerli", - "author_inst": "University of California, Santa Cruz" - }, - { - "author_name": "Nikolaos G Sgourakis", - "author_inst": "University of California, Santa Cruz" - } - ], - "version": "1", - "license": "cc_no", - "type": "new results", - "category": "immunology" - }, { "rel_doi": "10.1101/2020.03.24.005561", "rel_title": "Computational simulations reveal the binding dynamics between human ACE2 and the receptor binding domain of SARS-CoV-2 spike protein", @@ -1610797,6 +1609300,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.03.25.20043570", + "rel_title": "Acute gastrointestinal injury in critically ill patients with coronavirus disease 2019 in Wuhan, China", + "rel_date": "2020-03-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.25.20043570", + "rel_abs": "BackgroundTo investigate the prevalence and outcomes of acute gastrointestinal injury (AGI) in critically ill patients with coronavirus disease 2019 (COVID-19).\n\nMethodsIn this clinical retrospective study, demographic data, laboratory parameters, AGI grades, clinical severity and outcomes were collected. The primary endpoints were AGI incidence and 28-day mortality, the secondary endpoints were organ dysfunction and septic shock incidence.\n\nResultsFrom February 10 to March 10 2020, 83 critically ill patients of 1314 patients with COVID-19 were enrolled. Seventy-two (86.7%) patients had AGI during hospital stay, of them, 30 had AGI grade I, 35 had AGI grade II, 5 had AGI grade III, and 2 had AGI grade IV. The incidence of AGI grade II and above was 50.6%. As of March 16, 40 (48.2%) patients died within 28 days of admission, the median hospital stay was 12.0 days, ranging from 3 days to 27 days. Multiple organ dysfunction syndrome developed in 58 (69.9%) patients, septic shock in 16 (19.3%) patients. Patients with worse AGI grades had worse clinical variables, higher septic shock incidence and 28-day mortality. Sequential organ failure assessment scores (SOFA) (95% CI, 1.374-2.860; P <0.001), white blood cell (WBC) counts (95% CI, 1.037-1.379; P =0.014), duration of mechanical ventilation (MV) (95% CI, 1.020-1.340; P =0.025) were risk factors for the development of AGI grade II and above. Non-survivors were accompanied by higher incidence of AGI grade III to IV than survivors (17.5% vs. 0.0%, P =0.004).\n\nConclusionsThe AGI incidence was 86.7%, and hospital mortality was 48.2% in critically ill patients with COVID-19. SOFA scores, WBC counts, and duration of MV were risk factors for the development of AGI grade II and above. Patients with worse AGI grades had worse clinical severity variables, higher septic shock incidence and 28-day mortality.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Jia-Kui Sun", + "author_inst": "Nanjing First Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "intensive care and critical care medicine" + }, { "rel_doi": "10.1101/2020.03.24.20043026", "rel_title": "A Computational Model for Estimating the Progression of COVID-19 Cases in the US West and East Coasts", @@ -1611121,41 +1609643,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "otolaryngology" }, - { - "rel_doi": "10.1101/2020.03.24.20042796", - "rel_title": "Reproducibility and reporting practices in COVID-19 preprint manuscripts", - "rel_date": "2020-03-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.24.20042796", - "rel_abs": "The novel coronavirus, COVID-19, has sparked an outflow of scientific research seeking to understand the virus, its spread, and best practices in prevention and treatment. If this international research effort is going to be as swift and effective as possible, it will need to rely on a principle of open science. When researchers share data, code, and software and generally make their work as transparent as possible, it allows other researchers to verify and expand upon their work. Furthermore, it allows public officials to make informed decisions. In this study, we analyzed 535 preprint articles related to COVID-19 for eight transparency criteria and recorded study location and funding information. We found that individual researchers have lined up to help during this crisis, quickly tackling important public health questions, often without funding or support from outside organizations. However, most authors could improve their data sharing and scientific reporting practices. The contrast between researchers commitment to doing important research and their reporting practices reveals underlying weaknesses in the research communitys reporting habits, but not necessarily their science.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Josh Q Sumner", - "author_inst": "Ripeta, LLC" - }, - { - "author_name": "Leah Haynes", - "author_inst": "Ripeta, LLC" - }, - { - "author_name": "Sarah Nathan", - "author_inst": "Ripeta, LLC" - }, - { - "author_name": "Cynthia Hudson-Vitale", - "author_inst": "Ripeta, LLC" - }, - { - "author_name": "Leslie D McIntosh", - "author_inst": "Ripeta" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "health informatics" - }, { "rel_doi": "10.1101/2020.03.25.20042713", "rel_title": "World governments should protect their population from COVID-19 pandemic using Italy and Lombardy as precursor", @@ -1612267,6 +1610754,61 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.03.24.20042762", + "rel_title": "A model to estimate bed demand for COVID-19 related hospitalization", + "rel_date": "2020-03-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.24.20042762", + "rel_abs": "As of March 23, 2020 there have been over 354,000 confirmed cases of coronavirus disease 2019 (COVID-19) in over 180 countries, the World Health Organization characterized COVID-19 as a pandemic, and the United States (US) announced a national state of emergency.1, 2, 3 In parts of China and Italy the demand for intensive care (IC) beds was higher than the number of available beds.4, 5 We sought to build an accessible interactive model that could facilitate hospital capacity planning in the presence of significant uncertainty about the proportion of the population that is COVID-19+ and the rate at which COVID-19 is spreading in the population. Our approach was to design a tool with parameters that hospital leaders could adjust to reflect their local data and easily modify to conduct sensitivity analyses.\n\nWe developed a model to facilitate hospital planning with estimates of the number of Intensive Care (IC) beds, Acute Care (AC) beds, and ventilators necessary to accommodate patients who require hospitalization for COVID-19 and how these compare to the available resources. Inputs to the model include estimates of the characteristics of the patient population and hospital capacity. We deployed this model as an interactive online tool.6 The model is implemented in R 3.5, RStudio, RShiny 1.4.0 and Python 3.7. The parameters used may be modified as data become available, for use at other institutions, and to generate sensitivity analyses.\n\nWe illustrate the use of the model by estimating the demand generated by COVID-19+ arrivals for a hypothetical acute care medical center. The model calculated that the number of patients requiring an IC bed would equal the number of IC beds on Day 23, the number of patients requiring a ventilator would equal the number of ventilators available on Day 27, and the number of patients requiring an AC bed and coverage by the Medicine Service would equal the capacity of the Medicine service on Day 21.\n\nIn response to the COVID-19 epidemic, hospitals must understand their current and future capacity to care for patients with severe illness. While there is significant uncertainty around the parameters used to develop this model, the analysis is based on transparent logic and starts from observed data to provide a robust basis of projections for hospital managers. The model demonstrates the need and provides an approach to address critical questions about staffing patterns for IC and AC, and equipment capacity such as ventilators.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Teng Zhang", + "author_inst": "Stanford University School of Engineering" + }, + { + "author_name": "Kelly McFarlane", + "author_inst": "Stanford University Graduate School of Business, Harvard Medical School" + }, + { + "author_name": "Jacqueline Vallon", + "author_inst": "Stanford University School of Engineering" + }, + { + "author_name": "Linying Yang", + "author_inst": "Stanford University School of Engineering" + }, + { + "author_name": "Jin Xie", + "author_inst": "Stanford University School of Engineering" + }, + { + "author_name": "Jose Blanchet", + "author_inst": "Stanford University School of Engineering" + }, + { + "author_name": "Peter Glynn", + "author_inst": "Stanford University School of Engineering" + }, + { + "author_name": "Kristan Staudenmayer", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "Kevin Schulman", + "author_inst": "Stanford University School of Medicine" + }, + { + "author_name": "David Scheinker", + "author_inst": "Stanford University School of Engineering, Stanford University School of Medicine, Lucile Packard Children's Hospital" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.26.009803", "rel_title": "The potential SARS-CoV-2 entry inhibitor", @@ -1612675,33 +1611217,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.24.20042705", - "rel_title": "Mathematical modeling of COVID-19 transmission and mitigation strategies in the population of Ontario, Canada", - "rel_date": "2020-03-26", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.24.20042705", - "rel_abs": "BackgroundWe evaluated how non-pharmaceutical interventions could be used to control the COVID-19 pandemic and reduce the burden on the healthcare system.\n\nMethodsUsing an age-structured compartmental model of COVID-19 transmission in the population of Ontario, Canada, we compared a base case with limited testing, isolation, and quarantine to scenarios with: enhanced case finding; restrictive social distancing measures; or a combination of enhanced case finding and less restrictive social distancing. Interventions were either implemented for fixed durations or dynamically cycled on and off, based on projected ICU bed occupancy. We present median and credible intervals (CrI) from 100 replicates per scenario using a two-year time horizon.\n\nResultsWe estimated that 56% (95% CrI: 42-63%) of the Ontario population would be infected over the course of the epidemic in the base case. At the epidemic peak, we projected 107,000 (95% CrI: 60,760-149,000) cases in hospital and 55,500 (95% CrI: 32,700-75,200) cases in ICU. For fixed duration scenarios, all interventions were projected to delay and reduce the height of the epidemic peak relative to the base case, with restrictive social distancing estimated to have the greatest effect. Longer duration interventions were more effective. Dynamic interventions were projected to reduce the proportion of the population infected at the end of the two-year period. Dynamic social distancing interventions could reduce the median number of cases in ICU below current estimates of Ontarios ICU capacity.\n\nInterpretationWithout significant social distancing or a combination of moderate social distancing with enhanced case finding, we project that ICU resources would be overwhelmed. Dynamic social distancing could maintain health system capacity and also allow periodic psychological and economic respite for populations.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Ashleigh Tuite", - "author_inst": "University of Toronto" - }, - { - "author_name": "David N Fisman", - "author_inst": "University of Toronto" - }, - { - "author_name": "Amy L Greer", - "author_inst": "University of Guelph" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.24.20027730", "rel_title": "Moving-average based index to evaluate the epidemic trend of COVID-19 outbreak", @@ -1614033,6 +1612548,65 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.22.20040782", + "rel_title": "A comparative multi-centre study on the clinical and imaging features of comfirmed and uncomfirmed patients with COVID-19", + "rel_date": "2020-03-24", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.22.20040782", + "rel_abs": "BackgroundPrevious studies had described the differences in clinical characteristics between ICU and non-ICU patients. However, seldom study focused on confirmed and unconfirmed groups. Our aim was to compare clinical and imaging characteristics of COVID-19 patients outside Hubei province between confirmed and unconfirmed group.\n\nMethodsWe retrospectively enrolled 163 consecutive adult patients with suspected COVID-19 from three tertiary hospitals in two provinces outside Hubei province from January 12, 2020 to February 13, 2020 and the differences in epidemiological, clinical, laboratory and imaging characteristics between the two groups were compared.\n\nResultsThis study enrolled 163 patients with 62 confirmed cases and 101 unconfirmed cases. Most confirmed patients were clustered (31, 50.0%) and with definite epidemiological exposure. Symptoms of COVID-19 were nonspecific, largely fever and dry cough. Laboratory findings in confirmed group were characterized by normal or reduced white blood cell count, reduced the absolute value of lymphocytes, and elevated levels of C-reactive protein (CRP) and accelerated Erythrocyte sedimentation rate (ESR). The typical chest CT imaging features of patients with confirmed COVID-19 were peripherally distributed multifocal GGO with predominance in the lower lung lobe. Compared with unconfirmed patients, confirmed patients had significantly higher proportion of dry cough, leucopenia, lymphopenia and accelerated ESR (P<0.05); but not with alanine aminotransferase, aspartate aminotransferase, D-dimer, lactic dehydrogenase, and myoglobin (P>0.05). Proportion of peripheral, bilateral or lower lung distribution and multi-lobe involvement, GGO, crazy-paving pattern, air bronchogram and pleural thickening in the confirmed group were also higher (P<0.05).\n\nConclusionsSymptoms of COVID-19 were nonspecific. Leukopenia, lymphopenia and ESR, as well as chest CT could be used as a clue for clinical diagnosis of COVID-19.", + "rel_num_authors": 11, + "rel_authors": [ + { + "author_name": "Congliang Miao", + "author_inst": "Shanghai General Hospital, Shanghai Jiao Tong University" + }, + { + "author_name": "Jinqiang Zhuang", + "author_inst": "Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine" + }, + { + "author_name": "Mengdi Jin", + "author_inst": "Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine" + }, + { + "author_name": "Huanwen Xiong", + "author_inst": "High-tech Hospital, First Hospital Affiliated to Nanchang University" + }, + { + "author_name": "Peng Huang", + "author_inst": "People's Hospital of Yichun city" + }, + { + "author_name": "Qi Zhao", + "author_inst": "Shanghai General Hospital, Shanghai Jiao Tong University" + }, + { + "author_name": "Li Miao", + "author_inst": "High-tech Hospital, First Hospital Affiliated to Nanchang University" + }, + { + "author_name": "Jiang Du", + "author_inst": "Shanghai General Hospital, Shanghai Jiao Tong University" + }, + { + "author_name": "Xinying Yang", + "author_inst": "Shanghai General Hospital of Nanjing Medical University" + }, + { + "author_name": "Peijie Huang", + "author_inst": "Shanghai General Hospital, Shanghai Jiao Tong University" + }, + { + "author_name": "Jiang Hong", + "author_inst": "Shanghai General Hospital, Shanghai Jiao Tong University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.21.20040154", "rel_title": "Predicting the number of reported and unreported cases for the COVID-19 epidemic in South Korea, Italy, France and Germany", @@ -1614329,69 +1612903,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.22.20034504", - "rel_title": "High risk of infection caused posttraumatic stress symptoms in individuals with poor sleep quality: A study on influence of coronavirus disease (COVID-19) in China", - "rel_date": "2020-03-24", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.22.20034504", - "rel_abs": "The influence of the outbreak of coronavirus disease (COVID-19) on mental health was poorly understood. The present study aimed to exam sleep problems and posttraumatic stress symptoms (PTSS) in Chinese immediately after the massive outbreak of COVID-19. A total of 2027 Chinese participated in the present study. Wuhan-expose history, sleep quality and PTSS were measured with self-rating scales. Results showed that there were significant differences of PCL-5 and of sleep quality scores in different data-collection dates (ps<0.05). There were significant differences of PCL-5 scores (t=-2.93, p<0.05) and latency onset of sleep ({chi}2=9.77, p<0.05) between participants with and without Wuhan-expose history. The interaction effect of Wuhan exposure historyx sleep quality significantly influenced PCL-5 (ps<0.05). These results indicate that keeping good sleep quality in individuals with high infectious risk is a way to prevent PTSS.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Fan Zhang", - "author_inst": "Naval Medical University" - }, - { - "author_name": "Zhilei Shang", - "author_inst": "Naval Medical University" - }, - { - "author_name": "Haiying Ma", - "author_inst": "Naval Medical University" - }, - { - "author_name": "Yanpu Jia", - "author_inst": "Naval Medical University" - }, - { - "author_name": "Luna Sun", - "author_inst": "Naval Medical University" - }, - { - "author_name": "Xin Guo", - "author_inst": "Naval Medical University" - }, - { - "author_name": "Lili Wu", - "author_inst": "Naval Medical University" - }, - { - "author_name": "Zhuoer Sun", - "author_inst": "Naval Medical University" - }, - { - "author_name": "Yaoguang Zhou", - "author_inst": "Naval Medical University" - }, - { - "author_name": "Yan Wang", - "author_inst": "Naval Medical University" - }, - { - "author_name": "Nianqi Liu", - "author_inst": "Naval Medical University" - }, - { - "author_name": "Weizhi Liu", - "author_inst": "Naval Medical University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "psychiatry and clinical psychology" - }, { "rel_doi": "10.1101/2020.03.22.20040899", "rel_title": "Analysis of psychological state and clinical psychological intervention model of patients with COVID-19", @@ -1615723,6 +1614234,77 @@ "type": "PUBLISHAHEADOFPRINT", "category": "intensive care and critical care medicine" }, + { + "rel_doi": "10.1101/2020.03.16.20037259", + "rel_title": "High incidence of asymptomatic SARS-CoV-2 infection, Chongqing, China", + "rel_date": "2020-03-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.16.20037259", + "rel_abs": "BackgroundSARS-CoV-2 has been a global pandemic, but the emergence of asymptomatic patients has caused difficulties in the prevention of the epidemic. Therefore, it is significant to understand the epidemiological characteristics of asymptomatic patients with SARS-CoV-2 infection.\n\nMethodsIn this single-center, retrospective and observational study, we collected data from 167 patients with SARS-CoV-2 infection treated in Chongqing Public Health Medical Center (Chongqing, China) from January to March 2020. The epidemiological characteristics and variable of these patients were collected and analyzed.\n\nFindings82.04% of the SARS-CoV-2 infected patients had a travel history in Wuhan or a history of contact with returnees from Wuhan, showing typical characteristics of imported cases, and the proportion of severe Covid-19 patients was 13.2%, of which 59% were imported from Wuhan. For the patients who was returnees from Wuhan, 18.1% was asymptomatic patients. In different infection periods, compared with the proportion after 1/31/2020, the proportion of asymptomatic patient among SARS-CoV-2 infected patient was higher(19% VS 1.5%). In different age groups, the proportion of asymptomatic patient was the highest(28.6%) in children group under 14, next in elder group over 70 (27.3%). Compared with mild and common Covid-19 patients, the mean latency of asymptomatic was longer (11.25 days VS 8.86 days), but the hospital length of stay was shorter (14.3 days VS 16.96 days).\n\nConclusionThe SARS-CoV-2 prevention needs to focus on the screening of asymptomatic patients in the community with a history of contact with the imported population, especially for children and the elderly population.", + "rel_num_authors": 14, + "rel_authors": [ + { + "author_name": "Yang Tao", + "author_inst": "Beibei Tranditional Chinese Medical Hospital, Chongqing, 400000, China" + }, + { + "author_name": "Panke Cheng", + "author_inst": "Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China" + }, + { + "author_name": "Wen Chen", + "author_inst": "Army Medical University (Third Military Medical University)" + }, + { + "author_name": "Peng Wan", + "author_inst": "Beibei Tranditional Chinese Medical Hospital, Chongqing, 400000, China" + }, + { + "author_name": "Yaokai Chen", + "author_inst": "Chongqing Public Health Medical Center, Chongqing, 400000, China" + }, + { + "author_name": "Guodan Yuan", + "author_inst": "Chongqing Public Health Medical Center, Chongqing, 400000, China" + }, + { + "author_name": "Junjie Chen", + "author_inst": "Army Medical University (Third Military Medical University)" + }, + { + "author_name": "Da Huo", + "author_inst": "Army Medical University (Third Military Medical University)" + }, + { + "author_name": "Ge Guan", + "author_inst": "Army Medical University (Third Military Medical University)" + }, + { + "author_name": "Dayu Sun", + "author_inst": "Army Medical University (Third Military Medical University)" + }, + { + "author_name": "Ju Tan", + "author_inst": "Army Medical University (Third Military Medical University)" + }, + { + "author_name": "Guanyuan Yang", + "author_inst": "Army Medical University (Third Military Medical University)" + }, + { + "author_name": "Wen Zeng", + "author_inst": "Army Medical University (Third Military Medical University)" + }, + { + "author_name": "Chuhong Zhu", + "author_inst": "Army Medical University (Third Military Medical University), Chongqing 400038, China" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "emergency medicine" + }, { "rel_doi": "10.1101/2020.03.19.20039388", "rel_title": "Chinese and Italian COVID-19 outbreaks can be correctly described by a modified SIRD model", @@ -1615943,41 +1614525,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.19.20039404", - "rel_title": "Healthcare worker absenteeism, child care costs, and COVID-19 school closures: a simulation analysis", - "rel_date": "2020-03-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.19.20039404", - "rel_abs": "BackgroundSchool closures have been enacted as a measure of mitigation during the ongoing COVID-19 pandemic. It has been shown that school closures could cause absenteeism amongst healthcare workers with dependent children, but there remains a need for spatially granular analyses of the relationship between school closures and healthcare worker absenteeism to inform local community preparedness.\n\nMethodsWe provide national- and county-level simulations of school closures and unmet child care needs across the United States. We develop individual simulations using county-level demographic and occupational data, and model school closure effectiveness with age-structured compartmental models. We perform multivariate quasi-Poisson ecological regressions to find associations between unmet child care needs and COVID-19 vulnerability factors.\n\nResultsAt the national level, we estimate the projected rate of unmet child care needs for healthcare worker households to range from 7.5% to 8.6%, and the effectiveness of school closures to range from 3.2% (R0 = 4) to 7.2% (R0 = 2) reduction in fewer ICU beds at peak demand. At the county-level, we find substantial variations of projected unmet child care needs and school closure effects, ranging from 1.9% to 18.3% of healthcare worker households and 5.7% to 8.8% reduction in fewer ICU beds at peak demand (R0 = 2). We find significant positive associations between estimated levels of unmet child care needs and diabetes prevalence, county rurality, and race (p < 0.05). We estimate costs of absenteeism and child care and observe from our models that an estimated 71.1% to 98.8% of counties would find it less expensive to provide child care to all healthcare workers with children than to bear the costs of healthcare worker absenteeism during school closures.\n\nConclusionsSchool closures are projected to reduce peak ICU bed demand, but could disrupt healthcare systems through absenteeism, especially in counties that are already particularly vulnerable to COVID-19. Child care subsidies could help circumvent the ostensible tradeoff between school closures and healthcare worker absenteeism.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Elizabeth T Chin", - "author_inst": "Stanford University" - }, - { - "author_name": "Benjamin Q Huynh", - "author_inst": "Stanford University" - }, - { - "author_name": "Nathan C Lo", - "author_inst": "University of California, San Francisco" - }, - { - "author_name": "Trevor Hastie", - "author_inst": "Stanford University" - }, - { - "author_name": "Sanjay Basu", - "author_inst": "Harvard Medical School" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.20.20039537", "rel_title": "The Population Attributable Fraction (PAF) of cases due to gatherings and groups with relevance to COVID-19 mitigation strategies", @@ -1616877,6 +1615424,25 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.20.20039891", + "rel_title": "COVID-19 outbreak in Algeria: A mathematical model to predict the incidence", + "rel_date": "2020-03-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.20.20039891", + "rel_abs": "IntroductionSince December 29, 2019 a pandemic of new novel coronavirus-infected pneumonia named COVID-19 has started from Wuhan, China, has led to 254 996 confirmed cases until midday March 20, 2020. Sporadic cases have been imported worldwide, in Algeria, the first case reported on February 25, 2020 was imported from Italy, and then the epidemic has spread to other parts of the country very quickly with 139 confirmed cases until March 21, 2020.\n\nMethodsIt is crucial to estimate the cases number growth in the early stages of the outbreak, to this end, we have implemented the Alg-COVID-19 Model which allows to predict the incidence and the reproduction number R0 in the coming months in order to help decision makers.\n\nThe Alg-COVIS-19 Model initial equation 1, estimates the cumulative cases at t prediction time using two parameters: the reproduction number R0 and the serial interval SI.\n\nResultsWe found R0=2.55 based on actual incidence at the first 25 days, using the serial interval SI= 4,4 and the prediction time t=26. The herd immunity HI estimated is HI=61%. Also, The Covid-19 incidence predicted with the Alg-COVID-19 Model fits closely the actual incidence during the first 26 days of the epidemic in Algeria Fig. 1.A. which allows us to use it.\n\nO_FIG O_LINKSMALLFIG WIDTH=123 HEIGHT=200 SRC=\"FIGDIR/small/20039891v2_fig1.gif\" ALT=\"Figure 1\">\nView larger version (20K):\norg.highwire.dtl.DTLVardef@baae3org.highwire.dtl.DTLVardef@5cb4org.highwire.dtl.DTLVardef@1c65fb0org.highwire.dtl.DTLVardef@b41ec6_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 1.C_FLOATNO A: Alg-COVID-19 Model match to actual data (Cases number) of the first 26 days of epidemic. B: Alg-COVID-19 Model before and before (R0=2.55) and after mitigation (R0<2.55).\n\nC_FIG According to Alg-COVID-19 Model, the number of cases will exceed 5000 on the 42th day (April 7th) and it will double to 10000 on 46th day of the epidemic (April 11th), thus, exponential phase will begin (Table 1; Fig.1.B) and increases continuously until reaching a herd immunity of 61% unless serious preventive measures are considered.\n\nO_TBL View this table:\norg.highwire.dtl.DTLVardef@1506af6org.highwire.dtl.DTLVardef@9e6d5dorg.highwire.dtl.DTLVardef@11e014borg.highwire.dtl.DTLVardef@e7086dorg.highwire.dtl.DTLVardef@1da5599_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 1.C_FLOATNO O_TABLECAPTIONAlg-COVID-19 Model results for next weeks\n\nC_TABLECAPTION C_TBL DiscussionThis model is valid only when the majority of the population is vulnerable to COVID-19 infection, however, it can be updated to fit the new parameters values.", + "rel_num_authors": 1, + "rel_authors": [ + { + "author_name": "Mohamed HAMIDOUCHE Sr.", + "author_inst": "Pasteur Institute of Algeria" + } + ], + "version": "1", + "license": "cc_by", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.19.20033175", "rel_title": "Characteristics of patients with COVID-19 during epidemic ongoing outbreak in Wuhan, China", @@ -1617413,37 +1615979,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.21.001933", - "rel_title": "SARS-CoV-2, an evolutionary perspective of interaction with human ACE2 reveals undiscovered amino acids necessary for complex stability", - "rel_date": "2020-03-23", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.21.001933", - "rel_abs": "The emergence of SARS-CoV-2 has resulted in more than 200,000 infections and nearly 9,000 deaths globally so far. This novel virus is thought to have originated from an animal reservoir, and acquired the ability to infect human cells using the SARS-CoV cell receptor hACE2. In the wake of a global pandemic it is essential to improve our understanding of the evolutionary dynamics surrounding the origin and spread of a novel infectious disease. One way theory predicts selection pressures should shape viral evolution is to enhance binding with host cells. We first assessed evolutionary dynamics in select betacoronavirus spike protein genes to predict where these genomic regions are under directional or purifying selection between divergent viral lineages at various scales of relatedness. With this analysis, we determine a region inside the receptor-binding domain with putative sites under positive selection interspersed among highly conserved sites, which are implicated in structural stability of the viral spike protein and its union with human receptor hACE2. Next, to gain further insights into factors associated with coronaviruses recognition of the human host receptor, we performed modeling studies of five different coronaviruses and their potential binding to hACE2. Modeling results indicate that interfering with the salt bridges at hot spot 353 could be an effective strategy for inhibiting binding, and hence for the prevention of coronavirus infections. We also propose that a glycine residue at the receptor binding domain of the spike glycoprotein can have a critical role in permitting bat variants of the coronaviruses to infect human cells.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Vinicio Armijos-Jaramillo", - "author_inst": "Universidad de Las Americas-Quito" - }, - { - "author_name": "Justin Yeager", - "author_inst": "Universidad de Las Americas-Quito" - }, - { - "author_name": "Claire Muslin", - "author_inst": "Universidad de Las Americas-Quito" - }, - { - "author_name": "Yunierkis Perez-Castillo", - "author_inst": "Universidad de Las Americas-Quito" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.03.20.000885", "rel_title": "Emergence of SARS-CoV-2 through Recombination and Strong Purifying Selection", @@ -1618915,6 +1617450,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.15.20036756", + "rel_title": "Analysis of Epidemic Situation of New Coronavirus Infection at Home and Abroad Based on Rescaled Range (R/S) Method", + "rel_date": "2020-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.15.20036756", + "rel_abs": "11.1 BackgroundThe outbreak of the new coronavirus infection broke out in Wuhan City, Hubei Province in December 2019, and has spread to 97 countries and regions around the world. Apart from China, there are currently three other severely affected areas, namely Italy, South Korea, and Iran. This poses a huge threat to Chinas and even global public health security, challenges scientific research work such as disease surveillance and tracking, clinical treatment, and vaccine development, and it also brings huge uncertainty to the global economy. As of March 11, 2020, the epidemic situation in China is nearing its end, but the epidemic situation abroad is in the outbreak period. Italy has even taken measures to close the city nationwide, with a total of 118,020 cases of infection worldwide.\n\n1.2 MethodThis article selects the data of newly confirmed cases of COVID-19 at home and abroad as the data sample. Among them: the data of newly confirmed cases abroad is represented by Italy, and the span is from February 13 to March 10. The data of newly confirmed cases at home are divided into two parts: Hubei Province and other provinces except Hubei Province, spanning from January 23 to March 3, and with February 12 as the cutting point, it\"s divided into two periods, the growth period and the recession period. The rescaled range (R / S) analysis method and the dimensionless fractal Hurst exponent are used to measure the correlation of time series to determine whether the time series conforms to the fractal Brownian motion, that is, a biased random process. Contrast analysis of the meaning of H value in different stages and different overall H values in the same stage.\n\n1.3 ResultsBased on R / S analysis and calculated Hurst value of newly confirmed cases in Hubei and non-Hubei provinces, it was found that the H value of Hubei Province in the first stage was 0.574, which is greater than 0.5, indicating that the future time series has a positive correlation and Fractal characteristics; The H value in the second stage is 1.368, which is greater than 1, which indicates that the future epidemic situation is completely preventable and controllable, and the second stage has a downward trend characteristic, which indicates that there is a high probability that the future time series will decline. The H values of the first and second stages of non-Hubei Province are 0.223 and 0.387, respectively, which are both less than 0.5, indicating that the time series of confirmed cases in the future is likely to return to historical points, and the H value in the second stage is greater than that in the first stage, indicating that the time series of confirmed cases in the second stage is more long-term memory than the time series of confirmed cases in the first stage. The daily absolute number of newly confirmed cases in Italy was converted to the daily growth rate of confirmed cases to eliminate the volatility of the data. The H value was 1.853, which was greater than 1, indicating that the time series of future confirmed cases is similar to the trend of historical changes. The daily rate of change in cases will continue to rise.\n\n1.4 ConclusionAccording to the different interpretation of the H value obtained by the R / S analysis method, hierarchical isolation measures are adopted accordingly. When the H value is greater than 0.5, it indicates that the development of the epidemic situation in the area has more long-term memory, that is, when the number of confirmed cases in the past increases rapidly, the probability of the time series of confirmed cases in the future will continue the historical trend. Therefore, it is necessary to formulate strict anti-epidemic measures in accordance with the actual conditions of various countries, to detect, isolate, and treat early to reduce the base of infectious agents.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Xiaofeng Ji", + "author_inst": "Sichuan Academy of Social Sciences" + }, + { + "author_name": "Zhou Tang", + "author_inst": "Sichuan Academy of Social Sciences" + }, + { + "author_name": "Kejian Wang", + "author_inst": "Sichuan Academy of Social Sciences" + }, + { + "author_name": "Xianbin Li", + "author_inst": "Sichuan Academy of Social Sciences" + }, + { + "author_name": "Houqiang Li", + "author_inst": "Sichuan Academy of Social Sciences" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.16.20037036", "rel_title": "Transmissibility of 2019 Novel Coronavirus: zoonotic vs. human to human transmission, China, 2019-2020", @@ -1619323,25 +1617893,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.14.20035659", - "rel_title": "Maximum entropy method for estimating the reproduction number: An investigation for COVID-19 in China", - "rel_date": "2020-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.14.20035659", - "rel_abs": "The key parameter that characterizes the transmissibility of a disease is the reproduction number R. If it exceeds 1, the number of incident cases will inevitably grow over time, and a large epidemic is possible. To prevent the expansion of an epidemic, R must be reduced to a level below 1. To estimate the reproduction number, the probability distribution function of the generation interval of an infectious disease is required to be available; however, this distribution is often unknown. In this letter, given the incomplete information for the generation interval, we propose a maximum entropy method to estimate the reproduction number. Based on this method, given the mean value and variance of the generation interval, we first determine its probability distribution function and in turn estimate the real-time values of reproduction number of COVID-19 in China. By applying these estimated reproduction numbers into the susceptible-infectious-removed epidemic model, we simulate the evolutionary track of the epidemic in China, which is well in accordance with that of the real incident cases. The simulation results predict that Chinas epidemic will gradually tend to disappear by May 2020 if the quarantine measures can continue to be executed.", - "rel_num_authors": 1, - "rel_authors": [ - { - "author_name": "Yong Tao", - "author_inst": "Southwest University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.16.20034470", "rel_title": "Regaining perspective on SARS-CoV-2 molecular tracing and its implications", @@ -1620257,6 +1618808,69 @@ "type": "PUBLISHAHEADOFPRINT", "category": "palliative medicine" }, + { + "rel_doi": "10.1101/2020.03.17.20037515", + "rel_title": "A Tool to Early Predict Severe 2019-Novel Coronavirus Pneumonia (COVID-19) : A Multicenter Study using the Risk Nomogram in Wuhan and Guangdong, China", + "rel_date": "2020-03-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.17.20037515", + "rel_abs": "BackgroundDue to no reliable risk stratification tool for severe corona virus disease 2019 (COVID-19) patients at admission, we aimed to construct an effective model for early identifying cases at high risk of progression to severe COVID-19.\n\nMethodsIn this retrospective three-centers study, 372 non-severe COVID-19 patients during hospitalization were followed for more than 15 days after admission. Patients who deteriorated to severe or critical COVID-19 and patients who kept non-severe state were assigned to the severe and non-severe group, respectively. Based on baseline data of the two groups, we constructed a risk prediction nomogram for severe COVID-19 and evaluate its performance.\n\nResultsThe train cohort consisted of 189 patients, while the two independent validation cohorts consisted of 165 and 18 patients. Among all cases, 72 (19.35%) patients developed severe COVID-19. We found that old age, and higher serum lactate dehydrogenase, C-reactive protein, the coefficient of variation of red blood cell distribution width, blood urea nitrogen, direct bilirubin, lower albumin, are associated with severe COVID-19. We generated the nomogram for early identifying severe COVID-19 in the train cohort (AUC 0.912 [95% CI 0.846-0.978], sensitivity 85.71%, specificity 87.58%); in validation cohort (0.853 [0.790-0.916], 77.5%, 78.4%). The calibration curve for probability of severe COVID-19 showed optimal agreement between prediction by nomogram and actual observation. Decision curve and clinical impact curve analysis indicated that nomogram conferred high clinical net benefit.\n\nConclusionOur nomogram could help clinicians to early identify patients who will exacerbate to severe COVID-19, which will enable better centralized management and early treatment of severe patients.\n\nSummaryOlder age; higher LDH, CRP, RDW, DBIL, BUN; lower ALB on admission correlated with higher odds of severe COVID-19. An effective prognostic nomogram composed of 7 features could allow early identification of patients at risk of exacerbation to severe COVID-19.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Jiao Gong", + "author_inst": "Third Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Jingyi Ou", + "author_inst": "Guangzhou Eighth People's Hospital" + }, + { + "author_name": "Xueping Qiu", + "author_inst": "Zhongnan Hospital of Wuhan University" + }, + { + "author_name": "Yusheng Jie", + "author_inst": "Third Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Yaqiong Chen", + "author_inst": "Third Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Lianxiong Yuan", + "author_inst": "Third Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Jing Cao", + "author_inst": "Third Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Mingkai Tan", + "author_inst": "Guangzhou Eighth People's Hospital" + }, + { + "author_name": "Wenxiong Xu", + "author_inst": "Third Affiliated Hospital of Sun Yat-sen University" + }, + { + "author_name": "Fang Zheng", + "author_inst": "Zhongnan Hospital of Wuhan University" + }, + { + "author_name": "Yaling Shi", + "author_inst": "Clinical Laboratory of Guangzhou Eighth People's Hospital" + }, + { + "author_name": "Bo Hu", + "author_inst": "Third Affiliated Hospital of Sun Yat-sen University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.03.18.20038638", "rel_title": "Spatial Visualization of Cluster-Specific COVID-19 Transmission Network in South Korea During the Early Epidemic Phase", @@ -1620609,61 +1619223,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.19.20038844", - "rel_title": "A framework for identifying regional outbreak and spread of COVID-19 from one-minute population-wide surveys", - "rel_date": "2020-03-20", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.19.20038844", - "rel_abs": "Coronavirus infection spreads in clusters and therefore early identification of these clusters is critical for slowing down the spread of the virus. Here, we propose that daily population-wide surveys that assess the development of symptoms caused by the virus could serve as a strategic and valuable tool for identifying such clusters to inform epidemiologists, public health officials, and policy makers. We show preliminary results from a survey of over 58,000 Israelis and call for an international consortium to extend this concept in order to develop predictive models. We expect such data to allow: Faster detection of spreading zones and patients; Obtaining a current snapshot of the number of people in each area who have developed symptoms; Predicting future spreading zones several days before an outbreak occurs; Evaluating the effectiveness of the various social distancing measures taken, and their contribution to reduce the number of symptomatic people. Such information can provide a valuable tool for decision makers to decide which areas need strengthening of social distancing measures and which areas can be relieved. Preliminary analysis shows that in neighborhoods with confirmed COVID-19 patient history, more responders report on COVID-19 associated symptoms, demonstrating the potential utility of our approach for detection of outbreaks. Researchers from other countries including the U.S, India, Italy, Spain, Germany, Mexico, Finland, Sweden, Norway and several others have adopted our approach and we are collaborating to further improve it. We call with urgency for other countries to join this international consortium, and to share methods and data collected from these daily, simple, one-minute surveys.", - "rel_num_authors": 10, - "rel_authors": [ - { - "author_name": "Hagai Rossman", - "author_inst": "Weizmann institute of science" - }, - { - "author_name": "Ayya Keshet", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Smadar Shilo", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Amir Gavrieli", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Tal Bauman", - "author_inst": "Technion" - }, - { - "author_name": "Ori Cohen", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Ran Balicer", - "author_inst": "Clalit Research Institute" - }, - { - "author_name": "Benjamin Geiger", - "author_inst": "Weizmann Institute of Science" - }, - { - "author_name": "Yuval Dor", - "author_inst": "The Hebrew University of Jerusalem" - }, - { - "author_name": "Eran Segal", - "author_inst": "Weizmann Institute of Science" - } - ], - "version": "1", - "license": "cc_by_nc", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.17.20037572", "rel_title": "Incidence, clinical characteristics and prognostic factor of patients with COVID-19: a systematic review and meta-analysis", @@ -1621699,6 +1620258,61 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.15.20036392", + "rel_title": "Routes for COVID-19 importation in Brazil", + "rel_date": "2020-03-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.15.20036392", + "rel_abs": "HighlightThe global outbreak caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been declared a pandemic by the WHO. As the number of imported SARS-CoV-2 cases is on the rise in Brazil, we use incidence and historical air travel data to estimate the most important routes of importation into the country.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Darlan da Silva Candido", + "author_inst": "Department of Zoology, University of Oxford, United Kingdom." + }, + { + "author_name": "Alexander Watts", + "author_inst": "Department of Medicine, Division of Infectious Diseases, University of Toronto, Canada" + }, + { + "author_name": "Leandro Abade", + "author_inst": "Department of Zoology, University of Oxford, United Kingdom." + }, + { + "author_name": "Moritz UG Kraemer", + "author_inst": "Department of Zoology, University of Oxford, United Kingdom" + }, + { + "author_name": "Oliver G Pybus", + "author_inst": "Department of Zoology, University of Oxford, United Kingdom" + }, + { + "author_name": "Julio Croda", + "author_inst": "Laboratorio de Pesquisa em Ciencias da Saude, Universidade Federal da Grande Dourados, Dourados, Mato Grosso do Sul, Brazil" + }, + { + "author_name": "Wanderson de Oliveira", + "author_inst": "Secretaria de Vigilancia em Saude, Coordenacao Geral de Laboratorios de Saude Publica, Ministerio da Saude, Brasilia-DF, Brazil" + }, + { + "author_name": "Kamran Khan", + "author_inst": "Department of Medicine, Division of Infectious Diseases, University of Toronto, Canada" + }, + { + "author_name": "Ester C Sabino", + "author_inst": "Instituto Medicina Tropical, University of Sao Paulo, Brazil" + }, + { + "author_name": "Nuno R. Faria", + "author_inst": "University of Oxford" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.15.20036319", "rel_title": "The clinical and epidemiological features and hints of 82 confirmed COVID-19 pediatric cases aged 0-16 in Wuhan, China", @@ -1622215,29 +1620829,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.15.20036350", - "rel_title": "Coronavirus disease-19: Summary of 2,370 Contact Investigations of the First 30 Cases in the Republic of Korea", - "rel_date": "2020-03-18", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.15.20036350", - "rel_abs": "Between January 24 and March 10, of a total of 2,370 individuals who had contacted the first 30 cases of COVID-19, 13 were found to have COVID-19, resulting secondary attack rate of 0.55% (95% CI 0.31 - 0.96). Of 119 household contacts, 9 had infections resulting secondary attack rate of 7.56 (95% CI 3.73 - 14.26).", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "- Korea Centers for Disease Control and Prevention COVID-19 National Emergency Response Center", - "author_inst": "-" - }, - { - "author_name": "Young June Choe", - "author_inst": "Hallym University College of Medicine" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.16.20035105", "rel_title": "Acute myelitis after SARS-CoV-2 infection: a case report.", @@ -1623317,6 +1621908,33 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.03.14.20035964", + "rel_title": "Covid-19 pandemic: on a simple way to visualize the epidemic states and trajectories of some European countries, and to assess the effect of delays in official response", + "rel_date": "2020-03-17", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.14.20035964", + "rel_abs": "We present a self-synchronizing and robust method for comparing the progression of the Covid-19 epidemics among multiple countries. In their growth phase the epidemics show power law rather than exponential law time dependences. They are similar enough for the earlier China outbreak to guide other countries projections. The delayed reaction of European countries is shown to produce a significantly worse outcome compared to China.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Antoine Kevorkian", + "author_inst": "TEEM PHOTONICS" + }, + { + "author_name": "Thierry Grenet", + "author_inst": "CNRS" + }, + { + "author_name": "Hubert Gallee", + "author_inst": "IGE UGA-CNRS" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "public and global health" + }, { "rel_doi": "10.1101/2020.03.15.992438", "rel_title": "Computational analysis of microRNA-mediated interactions in SARS-CoV-2 infection", @@ -1623813,81 +1622431,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.10.986711", - "rel_title": "Efficient inactivation of SARS-CoV-2 by WHO-recommended hand rub formulations and alcohols", - "rel_date": "2020-03-17", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.10.986711", - "rel_abs": "The recent emergence of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing COVID-19 is a major burden for health care systems worldwide. It is important to address if the current infection control instructions based on active ingredients are sufficient. We therefore determined the virucidal activity of two alcohol-based hand rub solutions for hand disinfection recommended by the World Health Organization (WHO), as well as commercially available alcohols. Efficient SARS-CoV-2 inactivation was demonstrated for all tested alcohol-based disinfectants. These findings show the successful inactivation of SARS-CoV-2 for the first time and provide confidence in its use for the control of COVID-19.\n\nImportanceThe current COVID-19 outbreak puts a huge burden on the worlds health care systems. Without effective therapeutics or vaccines being available, effective hygiene measure are of utmost importance to prevent viral spreading. It is therefore crucial to evaluate current infection control strategies against SARS-CoV-2. We show the inactivation of the novel coronavirus for the first time and endorse the importance of disinfectant-based hand hygiene to reduce SARS-CoV-2 transmission.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Annika Kratzel", - "author_inst": "Institute of Virology and Immunology, Bern and Mittelh\u00e4usern, Switzerland" - }, - { - "author_name": "Daniel Todt", - "author_inst": "Department of Molecular and Medical Virology, Ruhr-University Bochum" - }, - { - "author_name": "Silvio Steiner", - "author_inst": "Institute of Virology and Immunology, Bern and Mittelh\u00e4usern, Switzerland" - }, - { - "author_name": "Mitra L Gultom", - "author_inst": "Institute of Virology and Immunology, Bern and Mittelh\u00e4usern, Switzerland" - }, - { - "author_name": "Tran Thi Nhu Thao", - "author_inst": "Institute of Virology and Immunology, Bern and Mittelh\u00e4usern, Switzerland" - }, - { - "author_name": "Nadine Ebert", - "author_inst": "Institute of Virology and Immunology" - }, - { - "author_name": "Melle Holwerda", - "author_inst": "Institute of Virology and Immunology, Bern and Mittelh\u00e4usern, Switzerland" - }, - { - "author_name": "Joerg Steinmann", - "author_inst": "University Hospital Essen" - }, - { - "author_name": "Daniela Niemeyer", - "author_inst": "Charit\u00e9" - }, - { - "author_name": "Ronald Dijkman", - "author_inst": "Institute of Virology and Immunology" - }, - { - "author_name": "G\u00fcnter Kampf", - "author_inst": "University Medicine Greifswald, Institute for Hygiene and Environmental Medicine, Greifswald, Germany" - }, - { - "author_name": "Christian Drosten", - "author_inst": "Charit\u00e9" - }, - { - "author_name": "Eike Steinmann", - "author_inst": "Ruhr University Bochum" - }, - { - "author_name": "Volker Thiel", - "author_inst": "University of Bern" - }, - { - "author_name": "Stephanie Pfaender", - "author_inst": "Department for Molecular & Medical Virology, Ruhr-Universit\u00e4t Bochum, Germany" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.03.14.20035980", "rel_title": "Indications for healthcare surge capacity in European countries facing an exponential increase in COVID19 cases", @@ -1624831,6 +1623374,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.11.20030957", + "rel_title": "Clinical features and outcomes of 2019 novel coronavirus-infected patients with cardiac injury", + "rel_date": "2020-03-16", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.11.20030957", + "rel_abs": "AimsTo explore the epidemiological and clinical features of 2019 novel coronavirus(2019-nCoV)-infected patients with cardiac injury.\n\nMethods and resultsData were collected from patients medical records, and we defined cardiac injury according to cardiac biomarker troponin I level > 0.03 g/L. Among the 291 patients, 15 (5.2%) showed evidence of cardiac injury. Of 15 hospitalized patients with cardiac injury, the median age was 65 years, and 11/15 (73.3%) were men. Underlying cardiovascular diseases in some patients were hypertension (n=7, 46.7%), coronary heart disease (n=3, 20%) and diabetes (n=3, 20%). The most common symptoms at illness onset in patients with cardiac injury were fever (n=11, 73.3%), cough (n=7, 46.7%), headache or fatigue (n=5, 33.3%) and dyspnea (n=4, 26.7%). These patients had higher systolic pressures, white blood cell count, neutrophil count, troponin I, brain natriuretic peptide, D-dimer and lower lymphocyte count, and platelet count, compared with patients without cardiac injury, respectively. Bilateral infiltrates on chest X-ray and elevated C-reactive protein occurred in all patients with cardiac injury. Compared with patients without cardiac injury, patients with cardiac injury were more likely to develop acute respiratory distress syndrome, and receive mechanical ventilation, continuous renal replacement therapy, extracorporeal membrane oxygenation and vasopressor therapy and be admitted to the intensive care unit.\n\nConclusionCardiac injury is a common condition among patients infected with 2019-nCoV. Compared with patients without cardiac injury, the clinical outcomes of patients with cardiac injury are relatively worse.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "youbin liu", + "author_inst": "Department of Cardiology, Guangzhou Eighth People's Hospital" + }, + { + "author_name": "Jinglong Li", + "author_inst": "Department of Cardiology, Guangzhou Eighth People's Hospital, Guangzhou, PR China" + }, + { + "author_name": "Dehui liu", + "author_inst": "Department of Cardiology, Guangzhou Eighth People's Hospital, Guangzhou, PR China" + }, + { + "author_name": "Huafeng Song", + "author_inst": "Department of Cardiology, Guangzhou Eighth People's Hospital, Guangzhou, PR China" + }, + { + "author_name": "Chunlin chen", + "author_inst": "Department of Cardiology, Guangzhou Eighth People's Hospital, Guangzhou, PR China" + }, + { + "author_name": "Mingfang lv", + "author_inst": "Department of Cardiology, Guangzhou Eighth People's Hospital, Guangzhou, PR China" + }, + { + "author_name": "Xing pei", + "author_inst": "Department of Cardiology, Guangzhou Eighth People's Hospital, Guangzhou, PR China" + }, + { + "author_name": "Zhongwei Hu", + "author_inst": "Department of Internal medicine, Guangzhou Eighth People's Hospital" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.07.20032052", "rel_title": "Duration of viral detection in throat and rectum of a patient with COVID-19", @@ -1625235,97 +1623825,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.11.20031096", - "rel_title": "Relationship between the ABO Blood Group and the COVID-19 Susceptibility", - "rel_date": "2020-03-16", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.11.20031096", - "rel_abs": "The novel coronavirus disease-2019 (COVID-19) has been spreading around the world rapidly and declared as a pandemic by WHO. Here, we compared the ABO blood group distribution in 2,173 patients with COVID-19 confirmed by SARS-CoV-2 test from three hospitals in Wuhan and Shenzhen, China with that in normal people from the corresponding regions. The results showed that blood group A was associated with a higher risk for acquiring COVID-19 compared with non-A blood groups, whereas blood group O was associated with a lower risk for the infection compared with non-O blood groups. This is the first observation of an association between the ABO blood type and COVID-19. It should be emphasized, however, that this is an early study with limitations. It would be premature to use this study to guide clinical practice at this time, but it should encourage further investigation of the relationship between the ABO blood group and the COVID-19 susceptibility.", - "rel_num_authors": 19, - "rel_authors": [ - { - "author_name": "Jiao Zhao", - "author_inst": "School of Medicine, Southern University of Science and Technology, Shenzhen, China" - }, - { - "author_name": "Yan Yang", - "author_inst": "National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen Third Peopl" - }, - { - "author_name": "Hanping Huang", - "author_inst": "Infection Disease Department, Wuhan Jinyintan Hospital, Wuhan, China" - }, - { - "author_name": "Dong Li", - "author_inst": "Renmin Hospital of Wuhan University, Wuhan 430060, China" - }, - { - "author_name": "Dongfeng Gu", - "author_inst": "School of Medicine, Southern University of Science and Technology, Shenzhen, China" - }, - { - "author_name": "Xiangfeng Lu", - "author_inst": "Department of Epidemiology, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China" - }, - { - "author_name": "Zheng Zhang", - "author_inst": "National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen Third Peopl" - }, - { - "author_name": "Lei Liu", - "author_inst": "National Clinical Research Center for Infectious Diseases, The Second Affiliated Hospital of Southern University of Science and Technology, Shenzhen Third Peopl" - }, - { - "author_name": "Ting Liu", - "author_inst": "Infection Disease Department, Wuhan Jinyintan Hospital, Wuhan, China" - }, - { - "author_name": "Yukun Liu", - "author_inst": "School of Statistics, East China Normal University, Shanghai, China" - }, - { - "author_name": "Yunjiao He", - "author_inst": "School of Medicine, Southern University of Science and Technology, Shenzhen, China" - }, - { - "author_name": "Bin Sun", - "author_inst": "School of Medicine, Southern University of Science and Technology, Shenzhen, China" - }, - { - "author_name": "Meilan Wei", - "author_inst": "School of Medicine, Southern University of Science and Technology, Shenzhen, China" - }, - { - "author_name": "Guangyu Yang", - "author_inst": "School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China" - }, - { - "author_name": "Xinghuan Wang", - "author_inst": "Zhongnan Hospital of Wuhan University" - }, - { - "author_name": "Li Zhang", - "author_inst": "Infection Disease Department, Wuhan Jinyintan Hospital, Wuhan, China" - }, - { - "author_name": "Xiaoyang Zhou", - "author_inst": "Renmin Hospital of Wuhan University, Wuhan 430060, China" - }, - { - "author_name": "Mingzhao Xing", - "author_inst": "School of Medicine, Southern University of Science and Technology, Shenzhen, China" - }, - { - "author_name": "Peng George Wang", - "author_inst": "School of Medicine, Southern University of Science and Technology, Shenzhen, China" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.11.20024901", "rel_title": "Estimation of the final size of the second phase of the coronavirus epidemic by the logistic model", @@ -1626627,6 +1625126,73 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.11.20034215", + "rel_title": "Estimation of instant case fatality rate of COVID-19 in Wuhan and Hubei based on daily case notification data", + "rel_date": "2020-03-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.11.20034215", + "rel_abs": "BackgroundThe outbreak of coronavirus disease 2019 (COVID-19) initially appeared and has most rapidly spread in Wuhan, China. The case fatality rate is the most direct indicator to assess the hazards of an infectious disease. We aimed to estimate the instant fatality rate and cure rate of COVID-19 in Wuhan City and its affiliated Hubei Province.\n\nMethodsWe collected the daily case notification data of COVID-19 from Dec 8, 2019 to Mar 10, 2020 in Wuhan City and Hubei Province officially announced by the Chinese authority. The numbers of daily confirmed/deaths/cured cases and the numbers of daily cumulative confirmed/deaths/cured cases were obtained. The death time and cure time of COVID-19 patients were calculated based on the dates of diagnosis, death and discharge of individual cases. Then the estimated diagnosis dates of deaths and cured cases were obtained on the basis of the median death or medium cure time, respectively. Finally, the instant fatality rate of COVID-19 was calculated according to the numbers of deaths and cured cases on the same estimated diagnosis dates.\n\nResultsFrom Jan 1, 2020 to Feb 22, 2020 in Wuhan City, the instant case fatality rate of COVID-19 was 3.4%[~]19.5% and the instant cured rate was 80.0%[~]96.6%. The average fatality rate reached 11.4% while the average cure rate was 88.6%. During the same period in Hubei Province, the instant case fatality rate was 3.8%[~]16.6% and the instant cured rate was 83.4%[~]96.6%. The average fatality rate and the average cure rate were 9.2% and 91.8%, respectively.\n\nConclusionsThe fatality rate and cure rate of COVID-19 in Wuhan City and Hubei Province were underestimated. Wuhan showed higher fatality rate and cure rate than the whole Hubei Province did.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Lei Cao", + "author_inst": "Xi'an Jiaotong University" + }, + { + "author_name": "Ting-ting Huang", + "author_inst": "Xi'an Jiaotong University" + }, + { + "author_name": "Jun-xia Zhang", + "author_inst": "Xi'an Jiaotong University" + }, + { + "author_name": "Qi Qin", + "author_inst": "Xi'an Jiaotong University" + }, + { + "author_name": "Si-yu Liu", + "author_inst": "Xi'an Jiaotong University" + }, + { + "author_name": "Hui-min Xue", + "author_inst": "Xi'an Jiaotong University" + }, + { + "author_name": "Ya-xin Gong", + "author_inst": "Xi'an Jiaotong University" + }, + { + "author_name": "Chang-hua Ning", + "author_inst": "Xi'an Jiaotong University" + }, + { + "author_name": "Xiao-tong Shen", + "author_inst": "Xian Jiaotong University" + }, + { + "author_name": "Jia-xin Yang", + "author_inst": "Xi'an Jiaotong University" + }, + { + "author_name": "Yan-ni Mi", + "author_inst": "Xi'an Jiaotong University" + }, + { + "author_name": "Xue Xiao", + "author_inst": "Xi'an Jiaotong University" + }, + { + "author_name": "Yongxiao Cao", + "author_inst": "Xi'an Jiaotong University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.10.20033761", "rel_title": "Inferring the number of COVID-19 cases from recently reported deaths", @@ -1627090,53 +1625656,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.11.20033159", - "rel_title": "Prolonged presence of SARS-CoV-2 in feces of pediatric patients during the convalescent phase", - "rel_date": "2020-03-13", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.11.20033159", - "rel_abs": "BackgroundSevere acute respiratory coronavirus 2 (SARS-CoV-2) is a newly identified virus which mainly spreads from person-to-person. Presence of SARS-CoV-2 has been constantly reported in stools of patients with coronavirus disease 2019 (COVID-19). However, there is a paucity of data concerning fecal shedding of the virus in pediatric patients.\n\nObjectiveTo investigate dynamic changes of SARS-CoV-2 in respiratory and fecal specimens in children with COVID-19.\n\nMethodsFrom January 17, 2020 to February 23, 2020, three pediatric cases of COVID-19 were reported in Qingdao, Shandong Province, China. Epidemiological, clinical, laboratory, and radiological characteristics and treatment data of these children were collected. Real-time fluorescence reverse-transcriptase-polymerase-chain reaction (RT-PCR) was performed to detect SARS-CoV-2 RNA in throat swabs and fecal specimens. Patients were followed up to March 10, 2020, the final date of follow-up, and dynamic profiles of RT-PCR results were closely monitored.\n\nResultsAll the three pediatric cases were household contacts of adults whose symptoms developed earlier. Severity of disease was mild to moderate and fever was the most consistent and predominant symptom at onset of illness of these children (two cases had body temperature higher than 38.5{degrees}C). All children showed increased lymphocytes (>4.4x109 /L) with normal white blood cell counts on admission. Radiological changes were not typical for COVID-19. All children showed good response to supportive treatment. Clearance of SARS-CoV-2 in respiratory tract occurred within two weeks after abatement of fever, whereas viral RNA remained positive in stools of pediatric patients for longer than 4 weeks. Two children had fecal SARS-CoV-2 turned negative 20 days after throat swabs showing negative, while that of another child lagged behind for 8 days.\n\nInterpretationSARS-CoV-2 may exist in gastrointestinal tract for a longer time than respiratory system. Persistent shedding of SARS-CoV-2 in stools of infected children indicates the potential for the virus to be transmitted through fecal excretion. Massive efforts should be made at all levels to prevent spreading of the infection among children after reopening of kindergartens and schools.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Yuhan Xing", - "author_inst": "The Chinese University of Hong Kong" - }, - { - "author_name": "Wei Ni", - "author_inst": "Qingdao Women and Childrens Hospital" - }, - { - "author_name": "Qin Wu", - "author_inst": "Qingdao Women and Childrens Hospital" - }, - { - "author_name": "Wenjie Li", - "author_inst": "Qingdao Women and Childrens Hospital" - }, - { - "author_name": "Guoju Li", - "author_inst": "Qingdao Women and Childrens Hospital" - }, - { - "author_name": "Jianning Tong", - "author_inst": "Qingdao Women and Childrens Hospital" - }, - { - "author_name": "Xiufeng Song", - "author_inst": "Qingdao Women and Childrens Hospital" - }, - { - "author_name": "Quansheng Xing", - "author_inst": "Qingdao Women and Children's Hospital" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.09.20033142", "rel_title": "Age specificity of cases and attack rate of novel coronavirus disease (COVID-19)", @@ -1628268,6 +1626787,53 @@ "type": "PUBLISHAHEADOFPRINT", "category": "health policy" }, + { + "rel_doi": "10.1101/2020.03.06.20032342", + "rel_title": "Early, low-dose and short-term application of corticosteroid treatment in patients with severe COVID-19 pneumonia: single-center experience from Wuhan, China", + "rel_date": "2020-03-12", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.06.20032342", + "rel_abs": "BackgroundSevere patients with 2019 novel coronavirus (2019-nCoV) pneumonia progressed rapidly to acute respiratory failure. We aimed to evaluate the definite efficacy and safety of corticosteroid in the treatment of severe COVID-19 pneumonia.\n\nMethodsForty-six hospitalized patients with severe COVID-19 pneumonia hospitalized at Wuhan Union Hospital from January 20 to February 25, 2020, were retrospectively reviewed. The patients were divided into two groups based on whether they received corticosteroid treatment. The clinical symptoms and chest computed tomography(CT) results were compared.\n\nResultsA total of 26 patients received intravenous administration of methylprednisolone with a dosage of 1-2mg/kg/d for 5-7 days, while the remaining patients not. There was no significant difference in age, sex, comorbidities, clinical or laboratory parameters between the two groups on admission. The average number of days for body temperature back to the normal range was significantly shorter in patients with administration of methylprednisolone when compared to those without administration of methylprednisolone (2.06{+/-}0.28 vs. 5.29{+/-}0.70, P=0.010). The patients with administration of methylprednisolone had a faster improvement of SpO2, while patients without administration of methylprednisolone had a significantly longer interval of using supplemental oxygen therapy (8.2days[IQR 7.0-10.3] vs. 13.5days(IQR 10.3-16); P<0.001). In terms of chest CT, the absorption degree of the focus was significantly better in patients with administration of methylprednisolone.\n\nConclusionOur data indicate that in patients with severe COVID-19 pneumonia, early, low-dose and short-term application of corticosteroid was associated with a faster improvement of clinical symptoms and absorption of lung focus.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Yin Wang", + "author_inst": "Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Weiwei Jiang", + "author_inst": "Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China" + }, + { + "author_name": "Qi He", + "author_inst": "Department of Gastroenterology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China" + }, + { + "author_name": "Cheng Wang", + "author_inst": "Department of Rheumatology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China" + }, + { + "author_name": "Baoju Wang", + "author_inst": "Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Pan Zhou", + "author_inst": "Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Nianguo Dong", + "author_inst": "Department of Cardiovascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Qiaoxia Tong", + "author_inst": "Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.09.20032045", "rel_title": "The effectiveness of full and partial travel bans against COVID-19 spread in Australia for travellers from China.", @@ -1629311,41 +1627877,6 @@ "type": "new results", "category": "biochemistry" }, - { - "rel_doi": "10.1101/2020.03.10.985150", - "rel_title": "A proposal of an alternative primer for the ARTIC Network's multiplex PCR to improve coverage of SARS-CoV-2 genome sequencing", - "rel_date": "2020-03-10", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.10.985150", - "rel_abs": "Since December 2019, the coronavirus disease 2019 (COVID-19) caused by a novel coronavirus SARS-CoV-2 has rapidly spread to almost every nation in the world. Soon after the pandemic was recognized by epidemiologists, a group of biologists comprising the ARTIC Network, has devised a multiplexed polymerase chain reaction (PCR) protocol and primer set for targeted whole-genome amplification of SARS-CoV-2. The ARTIC primer set amplifies 98 amplicons, which are separated only in two PCRs, across a nearly entire viral genome. The original primer set and protocol showed a fairly small amplification bias when clinical samples with relatively high viral loads were used. However, when samples viral load was low, several amplicons, especially amplicons 18 and 76, exhibited low coverage or complete dropout. We have determined that these dropouts were due to a dimer formation between the forward primer for amplicon 18, 18_LEFT, and the reverse primer for amplicon 76, 76_RIGHT. Replacement of 76_RIGHT with an alternatively designed primer was sufficient to produce a drastic improvement in coverage of both amplicons. Based on this result, we replaced 12 primers in total in the ARTIC primer set that were predicted to be involved in 14 primer interactions. The resulting primer set, version N1 (NIID-1), exhibits improved overall coverage compared to the ARTIC Networks original (V1) and modified (V3) primer set.", - "rel_num_authors": 5, - "rel_authors": [ - { - "author_name": "Kentaro Itokawa", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Tsuyoshi Sekizuka", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Masanori Hashino", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Rina Tanaka", - "author_inst": "National Institute of Infectious Diseases" - }, - { - "author_name": "Makoto Kuroda", - "author_inst": "National Institute of Infectious Diseases" - } - ], - "version": "1", - "license": "cc_by", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.03.08.982637", "rel_title": "Aerodynamic Characteristics and RNA Concentration of SARS-CoV-2 Aerosol in Wuhan Hospitals during COVID-19 Outbreak", @@ -1630381,6 +1628912,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.03.09.20032219", + "rel_title": "Data-driven discovery of clinical routes for severity detection in COVID-19 pediatric cases", + "rel_date": "2020-03-10", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.09.20032219", + "rel_abs": "The outbreak of COVID-19 epidemic has caused worldwide health concerns since Nov., 2019. A previous study described the demographic, epidemiologic, and clinical features for infected infants. However, compared with adult cases, little attention has been paid to the infected pediatric cases. Severity detection is challenging for children since most of children patients have mild symptoms no matter they are moderately or critically ill therein.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "Hui Yu", + "author_inst": "Huazhong University of Science and Technology" + }, + { + "author_name": "Jianbo Shao", + "author_inst": "Huazhong University of Science and Technology" + }, + { + "author_name": "Yuqi Guo", + "author_inst": "Huazhong University of Science and Technology" + }, + { + "author_name": "Yun Xiang", + "author_inst": "Huazhong University of Science and Technology" + }, + { + "author_name": "Chuan Sun", + "author_inst": "Huazhong University of Science and Technology" + }, + { + "author_name": "Ye Yuan", + "author_inst": "Huazhong University of Science and Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.03.08.20032821", "rel_title": "Clinical Characteristics of Two Human to Human Transmitted Coronaviruses: Corona Virus Disease 2019 versus Middle East Respiratory Syndrome Coronavirus.", @@ -1630793,153 +1629363,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.03.06.20031955", - "rel_title": "Transmission of corona virus disease 2019 during the incubation period may lead to a quarantine loophole", - "rel_date": "2020-03-08", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.06.20031955", - "rel_abs": "BackgroundThe ongoing outbreak of novel corona virus disease 2019 (COVID-19) in Wuhan, China, is arousing international concern. This study evaluated whether and when the infected but asymptomatic cases during the incubation period could infect others.\n\nMethodsWe collected data on demographic characteristics, exposure history, and symptom onset day of the confirmed cases, which had been announced by the Chinese local authorities. We evaluated the potential of transmission during the incubation period in 50 infection clusters, including 124 cases. All the secondary cases had a history of contact with their first-generation cases prior to symptom onset.\n\nResultsThe estimated mean incubation period for COVID-19 was 4.9 days (95% confidence interval [CI], 4.4 to 5.4) days, ranging from 0.8 to 11.1 days (2.5th to 97.5th percentile). The observed mean and standard deviation (SD) of serial interval was 4.1{+/-}3.3 days, with the 2.5th and 97.5th percentiles at -1 and 13 days. The infectious curve showed that in 73.0% of the secondary cases, their date of getting infected was before symptom onset of the first-generation cases, particularly in the last three days of the incubation period.\n\nConclusionsThe results indicated the transmission of COVID-9 occurs among close contacts during the incubation period, which may lead to a quarantine loophole. Strong and effective countermeasures should be implemented to prevent or mitigate asymptomatic transmission during the incubation period in populations at high risk.", - "rel_num_authors": 33, - "rel_authors": [ - { - "author_name": "Wei Xia", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Jiaqiang Liao", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Chunhui Li", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Yuanyuan Li", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Xi Qian", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Xiaojie Sun", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Hongbo Xu", - "author_inst": "Tongji School of Pharmacy, Huazhong University of Science and Technology" - }, - { - "author_name": "Gaga Mahai", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Xin Zhao", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Lisha Shi", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Juan Liu", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Ling Yu", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Meng Wang", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Qianqian Wang", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Asmagvl Namat", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Ying Li", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Jingyu Qu", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Qi Liu", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Xiaofang Lin", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Shuting Cao", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Shu Huan", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Jiying Xiao", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Fengyu Ruan", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Hanjin Wang", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Qing Xu", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Xingjuan Ding", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Xingjie Fang", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Feng Qiu", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Jiaolong Ma", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Yu Zhang", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Aizhen Wang", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Yuling Xing", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Shunqing Xu", - "author_inst": "School of Public Health, Tongji Medical College, Huazhong University of Science and Technology" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.06.20032177", "rel_title": "Evaluating the secondary transmission pattern and epidemic prediction of the COVID-19 in metropolitan areas of China", @@ -1631954,6 +1630377,53 @@ "type": "new results", "category": "microbiology" }, + { + "rel_doi": "10.1101/2020.03.04.976027", + "rel_title": "In silico study of the spike protein from SARS-CoV-2 interaction with ACE2: similarity with SARS-CoV, hot-spot analysis and effect of the receptor polymorphism", + "rel_date": "2020-03-07", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.04.976027", + "rel_abs": "The spread of COVID-19 caused by the SARS-CoV-2 outbreak has been growing since its first identification in December 2019. The publishing of the first SARS-CoV-2 genome made a valuable source of data to study the details about its phylogeny, evolution, and interaction with the host. Protein-protein binding assays have confirmed that Angiotensin-converting enzyme 2 (ACE2) is more likely to be the cell receptor through which the virus invades the host cell. In the present work, we provide an insight into the interaction of the viral spike Receptor Binding Domain (RBD) from different coronavirus isolates with host ACE2 protein. By calculating the binding energy score between RBD and ACE2, we highlighted the putative jump in the affinity from a progenitor form of SARS-CoV-2 to the current virus responsible for COVID-19 outbreak. Our result was consistent with previously reported phylogenetic analysis and corroborates the opinion that the interface segment of the spike protein RBD might be acquired by SARS-CoV-2 via a complex evolutionary process rather than a progressive accumulation of mutations. We also highlighted the relevance of Q493 and P499 amino acid residues of SARS-CoV-2 RBD for binding to human ACE2 and maintaining the stability of the interface. Moreover, we show from the structural analysis that it is unlikely for the interface residues to be the result of genetic engineering. Finally, we studied the impact of eight different variants located at the interaction surface of ACE2, on the complex formation with SARS-CoV-2 RBD. We found that none of them is likely to disrupt the interaction with the viral RBD of SARS-CoV-2.", + "rel_num_authors": 8, + "rel_authors": [ + { + "author_name": "Houcemeddine Othman", + "author_inst": "Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa." + }, + { + "author_name": "Zied Bouslama", + "author_inst": "Laboratory of veterinary epidemiology and microbiology LR16IPT03. Institut Pasteur of Tunis. University of Tunis El Manar, Tunis, Tunisia." + }, + { + "author_name": "Jean-Tristan Brandenburg", + "author_inst": "Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa." + }, + { + "author_name": "Jorge da Rocha", + "author_inst": "Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa." + }, + { + "author_name": "Yosr Hamdi", + "author_inst": "Laboratory of Biomedical Genomics and Oncogenetics, LR16IPT05, Pasteur Institute of Tunis, University of Tunis El Manar, Tunis, Tunisia." + }, + { + "author_name": "Kais Ghedira", + "author_inst": "Laboratory of Bioinformatics, Biomathematics and Biostatistics - LR16IPT09, Pasteur Institute of Tunis, University Tunis El Manar, Tunis, Tunisia." + }, + { + "author_name": "Najet-Srairi Abid", + "author_inst": "Universite de Tunis El Manar, Institut Pasteur de Tunis, LR11IPT08 Venins et Biomolecules Therapeutiques, 1002, Tunis, Tunisia." + }, + { + "author_name": "Scott Hazelhurst", + "author_inst": "Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences and School of Electrical and Information Engineering, University of the Witwaters" + } + ], + "version": "1", + "license": "cc_by_nd", + "type": "new results", + "category": "bioinformatics" + }, { "rel_doi": "10.1101/2020.03.04.976258", "rel_title": "Cryo-electron microscopy structure of the SADS-CoV spike glycoprotein provides insights into an evolution of unique coronavirus spike proteins", @@ -1632402,109 +1630872,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "public and global health" }, - { - "rel_doi": "10.1101/2020.03.04.20031005", - "rel_title": "Case fatality risk of novel coronavirus diseases 2019 in China", - "rel_date": "2020-03-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.04.20031005", - "rel_abs": "ObjectiveThe outbreak of novel coronavirus disease 2019 (COVID-19) imposed a substantial health burden in mainland China and remains a global epidemic threat. Our objectives are to assess the case fatality risk (CFR) among COVID-19 patients detected in mainland China, stratified by clinical category and age group.\n\nMethodsWe collected individual information on laboratory-confirmed COVID-19 cases from publicly available official sources from December 29, 2019 to February 23, 2020. We explored the risk factors associated with mortality. We used methods accounting for right-censoring and survival analyses to estimate the CFR among detected cases.\n\nResultsOf 12,863 cases reported outside Hubei, we obtained individual records for 9,651 cases, including 62 deaths and 1,449 discharged cases. The deceased were significantly older than discharged cases (median age: 77 vs 39 years, p<0.001). 58% (36/62) were male. Older age (OR 1.18 per year; 95%CI: 1.14 to 1.22), being male (OR 2.02; 95%CI: 1.02 to 4.03), and being treated in less developed economic regions (e.g., West and Northeast vs. East, OR 3.93; 95%CI: 1.74 to 8.85) were mortality risk factors. The estimated CFR was 0.89-1.24% among all cases. The fatality risk among critical patients was 2-fold higher than that among severe and critical patients, and 24-fold higher than that among moderate, severe and critical patients.\n\nConclusionsOur estimates of CFR based on laboratory-confirmed cases ascertained outside of Hubei suggest that COVID-19 is not as severe as severe acute respiratory syndrome and Middle East respiratory syndrome, but more similar to the mortality risk of 2009 H1N1 influenza pandemic in hospitalized patients. The fatality risk of COVID-19 is higher in males and increases with age. Our study improves the severity assessment of the ongoing epidemic and can inform the COVID-19 outbreak response in China and beyond.", - "rel_num_authors": 22, - "rel_authors": [ - { - "author_name": "Xiaowei Deng", - "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" - }, - { - "author_name": "Juan Yang", - "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" - }, - { - "author_name": "Wei Wang", - "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" - }, - { - "author_name": "Xiling Wang", - "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" - }, - { - "author_name": "Jiaxin Zhou", - "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" - }, - { - "author_name": "Zhiyuan Chen", - "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" - }, - { - "author_name": "Jing Li", - "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" - }, - { - "author_name": "Yinzi Chen", - "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" - }, - { - "author_name": "Han Yan", - "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" - }, - { - "author_name": "Juanjuan Zhang", - "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" - }, - { - "author_name": "Yongli Zhang", - "author_inst": "Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China" - }, - { - "author_name": "Yan Wang", - "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" - }, - { - "author_name": "Qi Qiu", - "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" - }, - { - "author_name": "Hui Gong", - "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" - }, - { - "author_name": "Xianglin Wei", - "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" - }, - { - "author_name": "Lili Wang", - "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" - }, - { - "author_name": "Kaiyuan Sun", - "author_inst": "Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA" - }, - { - "author_name": "Peng Wu", - "author_inst": "WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hon" - }, - { - "author_name": "Marco Ajelli", - "author_inst": "Bruno Kessler Foundation, Trento, Italy" - }, - { - "author_name": "Benjamin J. Cowling", - "author_inst": "WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hon" - }, - { - "author_name": "Cecile Viboud", - "author_inst": "Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, USA" - }, - { - "author_name": "Hongjie Yu", - "author_inst": "School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai, China" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.04.20031039", "rel_title": "Clinical characteristics of 101 non-surviving hospitalized patients with COVID-19: A single center, retrospective study", @@ -1633584,6 +1631951,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.03.02.20030049", + "rel_title": "Estimation of COVID-19 outbreak size in Italy based on international case exportations", + "rel_date": "2020-03-06", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.02.20030049", + "rel_abs": "Italy is currently experiencing an epidemic of COVID-19 which emerged in the Lombardy region 1. During the interval between February 25-29, 2020, we identified 46 cases of COVID-19 reported in 21 countries in Europe, Africa, North America, and South America which were either in individuals with recent travel from Italy, or who had presumed infection by a traveler from Italy 2. In six cases, in four of the affected countries (Switzerland, France, Austria, Croatia), land travel was a likely route of introduction, or was documented to have been the route of introduction2.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Ashleigh Tuite", + "author_inst": "University of Toronto" + }, + { + "author_name": "Victoria Ng", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "Erin Rees", + "author_inst": "Public Health Agency of Canada" + }, + { + "author_name": "David Fisman", + "author_inst": "University of Toronto" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.03.01.20029884", "rel_title": "Preliminary epidemiological analysis on children and adolescents with novel coronavirus disease 2019 outside Hubei Province in China: an observational study utilizing crowdsourced data", @@ -1634024,69 +1632422,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.03.03.20030593", - "rel_title": "Evolving Epidemiology and Impact of Non-pharmaceutical Interventions on the Outbreak of Coronavirus Disease 2019 in Wuhan, China", - "rel_date": "2020-03-06", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.03.03.20030593", - "rel_abs": "BACKGROUNDWe described the epidemiological features of the coronavirus disease 2019 (Covid-19) outbreak, and evaluated the impact of non-pharmaceutical interventions on the epidemic in Wuhan, China.\n\nMETHODSIndividual-level data on 25,961 laboratory-confirmed Covid-19 cases reported through February 18, 2020 were extracted from the municipal Notifiable Disease Report System. Based on key events and interventions, we divided the epidemic into four periods: before January 11, January 11-22, January 23 - February 1, and February 2-18. We compared epidemiological characteristics across periods and different demographic groups. We developed a susceptible-exposed-infectious-recovered model to study the epidemic and evaluate the impact of interventions.\n\nRESULTSThe median age of the cases was 57 years and 50.3% were women. The attack rate peaked in the third period and substantially declined afterwards across geographic regions, sex and age groups, except for children (age <20) whose attack rate continued to increase. Healthcare workers and elderly people had higher attack rates and severity risk increased with age. The effective reproductive number dropped from 3.86 (95% credible interval 3.74 to 3.97) before interventions to 0.32 (0.28 to 0.37) post interventions. The interventions were estimated to prevent 94.5% (93.7 to 95.2%) infections till February 18. We found that at least 59% of infected cases were unascertained in Wuhan, potentially including asymptomatic and mild-symptomatic cases.\n\nCONCLUSIONSConsiderable countermeasures have effectively controlled the Covid-19 outbreak in Wuhan. Special efforts are needed to protect vulnerable populations, including healthcare workers, elderly and children. Estimation of unascertained cases has important implications on continuing surveillance and interventions.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Chaolong Wang", - "author_inst": "Huazhong University of Science and Technology" - }, - { - "author_name": "Li Liu", - "author_inst": "Huazhong University of Science and Technology" - }, - { - "author_name": "Xingjie Hao", - "author_inst": "Huazhong University of Science and Technology" - }, - { - "author_name": "Huan Guo", - "author_inst": "Huazhong University of Science and Technology" - }, - { - "author_name": "Qi Wang", - "author_inst": "Huazhong University of Science and Technology" - }, - { - "author_name": "Jiao Huang", - "author_inst": "Huazhong University of Science and Technology" - }, - { - "author_name": "Na He", - "author_inst": "Fudan University" - }, - { - "author_name": "Hongjie Yu", - "author_inst": "Fudan University" - }, - { - "author_name": "Xihong Lin", - "author_inst": "Harvard University" - }, - { - "author_name": "An Pan", - "author_inst": "Huazhong University of Science and Technology" - }, - { - "author_name": "Sheng Wei", - "author_inst": "Huazhong University of Science and Technology" - }, - { - "author_name": "Tangchun Wu", - "author_inst": "Huazhong University of Science and Technology" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.03.03.20030353", "rel_title": "Epidemiological and clinical features of 291 cases with coronavirus disease 2019 in areas adjacent to Hubei, China: a double-center observational study", @@ -1635289,6 +1633624,117 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.02.29.20029322", + "rel_title": "Vicarious traumatization in the general public, members, and non-members of medical teams aiding in COVID-19 control", + "rel_date": "2020-03-03", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.29.20029322", + "rel_abs": "Since December 2019, more than 79,000 people have been diagnosed with infection of the Corona Virus Disease 2019 (COVID-19). A large number of medical staff were dispersed for Wuhan city and Hubei province to aid COVID-19 control. Psychological stress, especially vicarious traumatization (VT) caused by the COVID-19 pandemic, should not be ignored. To address this concern, the study employed a total of 214 general public (GP) and 526 nurses to evaluate VT scores via a mobile app-based questionnaire. Results showed that the VT scores slightly increased across periods of aiding COVID-19 control, although no statistical difference was noted (P = 0.083). However, the study found lower scores for VT in nurses [median = 69; interquartile range (IQR) = 56-85] than those of the GP (median = 75.5; IQR = 62-88.3) (P = 0.017). In addition, the VT scores for front-line nurses (FLNs; median = 64; IQR = 52-75), including scores for physiological and psychological responses, were significantly lower than those of non-front-line nurses (nFLNs; median = 75.5; IQR = 63-92) (P < 0.001). Interestingly, the VT scores of the GP were significantly higher than those of the FLNs (P < 0.001). However, no statistical difference was observed compared with those of nFLNs (P > 0.05). Importantly, nFLNs are more likely to suffer from VT, which might be related to two factors, namely, gender [odds ratio (OR) = 3.1717; 95% confidence interval (CI) = 4.247-18.808; P = 0.002] and fertility [OR = 2.072; 95%CI = 0.626-24.533; P = 0.039]. Therefore, increased attention should be paid to the psychological problems of the medical staff, especially nFLNs, and GP under the situation of the spread and control of COVID-19. Early strategies that aim to prevent and treat VT in medical staff and GP are extremely necessary.", + "rel_num_authors": 24, + "rel_authors": [ + { + "author_name": "Zhenyu Li", + "author_inst": "The First Affiliated Hospital of Nanjing Medical University" + }, + { + "author_name": "Jingwu Ge", + "author_inst": "The First Affiliated Hospital of Nanjing Medical University" + }, + { + "author_name": "Meiling Yang", + "author_inst": "The First Affiliated Hospital of Nanjing Medical University" + }, + { + "author_name": "Jianping Feng", + "author_inst": "The First Affiliated Hospital of Nanjing Medical University" + }, + { + "author_name": "Mei Qiao", + "author_inst": "The First Affiliated Hospital of Nanjing Medical University" + }, + { + "author_name": "Riyue Jiang", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Jiangjiang Bi", + "author_inst": "Huangzhong University of Science and Technology" + }, + { + "author_name": "Gaofeng Zhan", + "author_inst": "Huangzhong University of Science and Technology" + }, + { + "author_name": "Xiaolin Xu", + "author_inst": "Huangzhong University of Science and Technology" + }, + { + "author_name": "Long Wang", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Qin Zhou", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Chenliang Zhou", + "author_inst": "Renmin Hospital of Wuhan University" + }, + { + "author_name": "Yinbing Pan", + "author_inst": "The First Affiliated Hospital of Nanjing Medical University" + }, + { + "author_name": "Shijiang Liu", + "author_inst": "The First Affiliated Hospital of Nanjing Medical University" + }, + { + "author_name": "Haiwei Zhang", + "author_inst": "The First Affiliated Hospital of Nanjing Medical University" + }, + { + "author_name": "Jianjun Yang", + "author_inst": "The First Affiliated Hospital of Zhengzhou University" + }, + { + "author_name": "Bin Zhu", + "author_inst": "The Third Affiliated Hospital of Soochow University," + }, + { + "author_name": "Yimin Hu", + "author_inst": "The Second Affiliated Changzhou Hospital of Nanjing Medical University" + }, + { + "author_name": "Kenji Hashimoto", + "author_inst": "Chiba University Center for Forensic Mental Health" + }, + { + "author_name": "Yan Jia", + "author_inst": "The First Affiliated Hospital of Nanjing Medical University" + }, + { + "author_name": "Haofei Wang", + "author_inst": "The First Affiliated Hospital of Nanjing Medical University" + }, + { + "author_name": "Rong Wang", + "author_inst": "The First Affiliated Hospital of Nanjing Medical University" + }, + { + "author_name": "Cunming Liu", + "author_inst": "The First Affiliated Hospital of Nanjing Medical University" + }, + { + "author_name": "Chun Yang", + "author_inst": "The First Affiliated Hospital of Nanjing Medical University" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.02.29.20029413", "rel_title": "The spatiotemporal estimation of the dynamic risk and the international transmission of 2019 Novel Coronavirus (COVID-19) outbreak: A global perspective", @@ -1635645,69 +1634091,6 @@ "type": "new results", "category": "bioinformatics" }, - { - "rel_doi": "10.1101/2020.02.28.20029025", - "rel_title": "Clinical significance of IgM and IgG test for diagnosis of highly suspected COVID-19 infection", - "rel_date": "2020-03-03", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.28.20029025", - "rel_abs": "Quick, simple and accurate diagnosis of suspected COVID-19 is very important for the screening and therapy of patients. Although several methods were performed in clinical practice, however, the IgM and IgG diagnostic value evaluation was little performed. 57 suspected COVID-19 infection patients were enrolled in our study. 24 patients with positive and 33 patients with negative nucleic acid test. The positive rate of COVID-19 nucleic acid was 42.10%. The positive detection rate of combination of IgM and IgG for patients with COVID-19 negative and positive nucleic acid test was 72.73% and 87.50%. The results were significantly higher than the nucleic acid or IgM, IgG single detection. hsCRP in the COVID-19 nucleic acid negative group showed significantly higher than the positive groups (P=0.0298). AST in the COVID-19 IgM negative group showed significantly lower than the positive groups (P=0.0365). We provided a quick, simple, accurate aided detection method for the suspected patients and on-site screening in close contact with the population.", - "rel_num_authors": 12, - "rel_authors": [ - { - "author_name": "Xingwang Jia", - "author_inst": "Department of Clinical Laboratory Medicine, Shenzhen Hospital, Southern Medical University, Shenzhen, China" - }, - { - "author_name": "Pengjun Zhang", - "author_inst": "Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Interventional Therapy Department, Peking University Cancer Hospita" - }, - { - "author_name": "Yaping Tian", - "author_inst": "Department of Translational Medicine, Chinese PLA General Hospital, Beijing, China." - }, - { - "author_name": "Junli Wang", - "author_inst": "Department of Respiratory and Critical Care Medicine, Shenzhen Hospital, Southern Medical University, Shenzhen, China" - }, - { - "author_name": "Huadong Zeng", - "author_inst": "Department of Respiratory and Critical Care Medicine, Shenzhen Hospital, Southern Medical University, Shenzhen, China" - }, - { - "author_name": "Jun Wang", - "author_inst": "Department of Respiratory and Critical Care Medicine, Shenzhen Hospital, Southern Medical University, Shenzhen, China" - }, - { - "author_name": "Liu Jiao", - "author_inst": "Department of Clinical Laboratory Medicine, Shenzhen Hospital, Southern Medical University, Shenzhen, China" - }, - { - "author_name": "Zeyan Chen", - "author_inst": "Department of Clinical Laboratory Medicine, Shenzhen Hospital, Southern Medical University, Shenzhen, China" - }, - { - "author_name": "Lijun Zhang", - "author_inst": "Department of Clinical Laboratory Medicine, Shenzhen Hospital, Southern Medical University, Shenzhen, China." - }, - { - "author_name": "Haihong He", - "author_inst": "Department of Clinical Laboratory Medicine, Shenzhen Hospital, Southern Medical University, Shenzhen, China" - }, - { - "author_name": "Kunlun He", - "author_inst": "Key Laboratory of Ministry of Industry and Information Technology of Biomedical Engineering and Translational Medicine, Chinese PLA General Hospital, Beijing, C" - }, - { - "author_name": "Yajie Liu", - "author_inst": "Department of Neurology, Shenzhen Hospital, Southern Medical University, Shenzhen, China" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.03.02.972935", "rel_title": "Isolation and characterization of SARS-CoV-2 from the first US COVID-19 patient", @@ -1637207,6 +1635590,69 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.03.01.971499", + "rel_title": "Kallikrein 13: a new player in coronaviral infections.", + "rel_date": "2020-03-02", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.03.01.971499", + "rel_abs": "Human coronavirus HKU1 (HCoV-HKU1) is associated with respiratory disease and is prevalent worldwide, but in vitro model for virus replication is lacking. Interaction between the coronaviral spike (S) protein and its receptor is the major determinant of virus tissue and host specificity, but virus entry is a complex process requiring a concerted action of multiple cellular elements. Here, we show that KLK13 is required for the infection of the human respiratory epithelium and is sufficient to mediate the entry of HCoV-HKU1 to non-permissive RD cells. We also demonstrated HCoV-HKU1 S protein cleavage by KLK13 in the S1/S2 region, proving that KLK13 is the priming enzyme for this virus. Summarizing, we show for the first time that protease distribution and specificity predetermines the tissue and cell specificity of the virus and may also regulate interspecies transmission. It is also of importance that presented data may be relevant for the emerging coronaviruses, including SARS-CoV-2 and may help to understand the differences in their zoonotic potential.", + "rel_num_authors": 12, + "rel_authors": [ + { + "author_name": "Aleksandra Milewska", + "author_inst": "Malopolska Centre of Biotechnology, Jagiellonian University in Krakow, Poland" + }, + { + "author_name": "Katherine Falkowski", + "author_inst": "Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, Poland" + }, + { + "author_name": "Magdalena Kalinska", + "author_inst": "Malopolska Centre of Biotechnology, Jagiellonian University in Krakow, Poland" + }, + { + "author_name": "Ewa Bielecka", + "author_inst": "Malopolska Centre of Biotechnology, Jagiellonian University in Krakow, Poland" + }, + { + "author_name": "Antonina Naskalska", + "author_inst": "Malopolska Centre of Biotechnology, Jagiellonian University in Krakow, Poland" + }, + { + "author_name": "Pawel Mak", + "author_inst": "Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, Poland" + }, + { + "author_name": "Adam Lesner", + "author_inst": "Faculty of Chemistry, University of Gdansk, Poland" + }, + { + "author_name": "Marek Ochman", + "author_inst": "Department of Cardiac, Vascular and Endovascular Surgery and Transplantology, Medical University of Silesia in Katowice, Silesian Centre for Heart Diseases, Zab" + }, + { + "author_name": "Maciej Urlik", + "author_inst": "Department of Cardiac, Vascular and Endovascular Surgery and Transplantology, Medical University of Silesia in Katowice, Silesian Centre for Heart Diseases, Zab" + }, + { + "author_name": "Jan Potempa", + "author_inst": "Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University in Krakow, Poland" + }, + { + "author_name": "Tomasz Kantyka", + "author_inst": "Malopolska Centre of Biotechnology, Jagiellonian University in Krakow, Poland" + }, + { + "author_name": "Krzysztof Pyrc", + "author_inst": "Malopolska Centre of Biotechnology, Jagiellonian University in Krakow, Poland" + } + ], + "version": "1", + "license": "cc_no", + "type": "new results", + "category": "microbiology" + }, { "rel_doi": "10.1101/2020.02.27.968008", "rel_title": "Molecular Dynamics Simulations Indicate the COVID-19 Mpro Is Not a Viable Target for Small-Molecule Inhibitors Design", @@ -1637527,53 +1635973,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.02.28.20029173", - "rel_title": "Analysis on the Clinical Characteristics of 36 Cases of Novel Coronavirus Pneumonia in Kunming", - "rel_date": "2020-03-01", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.28.20029173", - "rel_abs": "ObjectiveTo analyze the clinical characteristics of patients with novel coronavirus pneumonia in Kunming City, and to study the correlation between nutritional status and immune function.\n\nMethodsClinical data of 36 patients with novel coronavirus pneumonia in isolation area of Kunming Third Peoples Hospital from January 31 to February 15, 2020 were collected, and the basic situation, clinical characteristics, laboratory examination and CT imaging characteristics were analyzed. Serum albumin (ALB), prealbumin (PAB), hypersensitive c-reactive protein (hs-crp), CD3T cells, CD4T cells, CD8T cells and normal control group were analyzed. A simple linear regression analysis of the relationship between proalbumin and T cell subpopulation counts in the blood of patients.\n\nResults(1) The patients with new coronavirus pneumonia in Kunming were mainly of common type. (2) 50% of the patients first symptoms were fever and cough; (3) The total number of white blood cells in peripheral blood was normal or decreased in 23 cases (79%), and the lymphocyte count decreased in 5 cases (13.89%), without anemia. Hypersensitive c-reactive protein increased in 19 (52.78%) cases, and procalcitonin increased in 1 case. Albumin decreased in 5 cases (13.89%), proalbumin decreased in 15 cases (41.67%), alanine transaminase increased slightly in 4 cases (11.11%), alanine transaminase increased slightly in 4 cases (11.11%), total bilirubin increased slightly in 11 cases (30.56%), and renal function and blood coagulation were normal. Absolute value of CD3+T cells is with a decrease in 21 cases (58.3%), CD4+T in 28 cases (77.8%), CD8+T in 17 cases (47.2%), and CD4+/ CD8+ inverse in 6 cases (16.7%). (4) The prealbumin, CD3 T cells, CD4 T cells and CD8 T cells in the new coronavirus pneumonia group were significantly lower than those in the normal control group, and the hypersensitive c-reactive protein was higher than that in the normal control group. (5) The levels of PAB in the serum of the patients were linearly correlated with hs-crp, CD3 T cells, CD4 T cells and CD8 T cells, and the correlation coefficients were -0.474, 0.558, 0.467 and 0.613, respectively, showing statistical differences.\n\nConclusionThe clinical characteristics of the novel coronavirus pneumonia in Kunming are different from those in Wuhan. The changes of serum proalbumin and T cell subsets are relatively obvious. Changes in serum proalbumin may contribute to the early warning of novel coronavirus pneumonia. The nutritional status of patients with common and mild pneumonia should be considered.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Haiyan Fu", - "author_inst": "1.Kunming Third People's Hospital Isolation Ward" - }, - { - "author_name": "Hongjuan Li", - "author_inst": "1.Kunming Third People's Hospital Isolation Ward" - }, - { - "author_name": "Xiaoqing Tang", - "author_inst": "1.Kunming Third People's Hospital Isolation Ward" - }, - { - "author_name": "Xiang Li", - "author_inst": "1.Kunming Third People's Hospital Isolation Ward" - }, - { - "author_name": "Jie Shen", - "author_inst": "1.Kunming Third People's Hospital Isolation Ward" - }, - { - "author_name": "Yujun Zhou", - "author_inst": "1.Kunming Third People's Hospital Isolation Ward" - }, - { - "author_name": "Bing Xu", - "author_inst": "1.Kunming Third People's Hospital Isolation Ward" - }, - { - "author_name": "Yu Luo", - "author_inst": "Kunming Third People's Hospital" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.27.20028027", "rel_title": "Prediction of survival for severe Covid-19 patients with three clinical features: development of a machine learning-based prognostic model with clinical data in Wuhan", @@ -1638492,6 +1636891,133 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.02.26.20028191", + "rel_title": "Clinical characteristics of 82 death cases with COVID-19", + "rel_date": "2020-02-27", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.26.20028191", + "rel_abs": "BackgroundA recently developing pneumonia caused by SARS-CoV-2 was originated in Wuhan, China, and has quickly spread across the world. We reported the clinical characteristics of 82 death cases with COVID-19 in a single center.\n\nMethodsClinical data on 82 death cases laboratory-confirmed as SARS-CoV-2 infection were obtained from a Wuhan local hospitals electronic medical records according to previously designed standardized data collection forms.\n\nResultsAll patients were local residents of Wuhan, and the great proportion of them were diagnosed as severe illness when admitted. Most of the death cases were male (65.9%). More than half of dead patients were older than 60 years (80.5%) and the median age was 72.5 years. The bulk of death cases had comorbidity (76.8%), including hypertension (56.1%), heart disease (20.7%), diabetes (18.3%), cerebrovascular disease (12.2%), and cancer (7.3%). Respiratory failure remained the leading cause of death (69.5%), following by sepsis syndrome/MOF (28.0%), cardiac failure (14.6%), hemorrhage (6.1%), and renal failure (3.7%). Furthermore, respiratory, cardiac, hemorrhage, hepatic, and renal damage were found in 100%, 89%, 80.5%, 78.0%, and 31.7% of patients, respectively. On the admission, lymphopenia (89.2%), neutrophilia (74.3%), and thrombocytopenia (24.3%) were usually observed. Most patients had a high neutrophil-to-lymphocyte ratio of >5 (94.5%), high systemic immune-inflammation index of >500 (89.2%), increased C-reactive protein level (100%), lactate dehydrogenase (93.2%), and D-dimer (97.1%). A high level of IL-6 (>10 pg/ml) was observed in all detected patients. Median time from initial symptom to death was 15 days (IQR 11-20), and a significant association between aspartate aminotransferase (p=0.002), alanine aminotransferase (p=0.037) and time from initial symptom to death were interestingly observed.\n\nConclusionOlder males with comorbidities are more likely to develop severe disease, even die from SARS-CoV-2 infection. Respiratory failure is the main cause of COVID-19, but either virus itself or cytokine release storm mediated damage to other organ including cardiac, renal, hepatic, and hemorrhage should be taken seriously as well.\n\nFundingNo founding.\n\nResearch in contextO_ST_ABSEvidence before this studyC_ST_ABSAs the seventh member of enveloped RNA coronavirus, severe acute respiratory syndrome coronavirus (SARS-CoV)-2 causes a cluster of severe respiratory disease which is similar to another two fatal coronavirus infection caused by SARS-CoV and Middle Eastern respiratory syndrome coronavirus (MERS-CoV). Through searching PubMed and the China National knowledge infrastructure databases up to February 20, 2020, no published article focusing on hospitalized dead patients was identified.\n\nAdded value of this studyWe conducted a single-center investigation involving 82 hospitalized death patients with COVID-19 and focused on their epidemiological and clinical characteristics. 66 of 82 (80.5%) of patients were older than 60 years and the median age was 72.5 years.\n\nThe bulk of death cases had comorbidity (76.8%). Respiratory failure remained the leading cause of death, following by sepsis syndrome/MOF, cardiac failure, hemorrhage, and renal failure. Most patients had a high neutrophil-to-lymphocyte ratio, high systemic immune-inflammation index, and increased levels of proinflammatory cytokines.\n\nImplications of all the available evidenceSARS-CoV-2 causes a cluster of severe respiratory illness which is similar to another two fatal coronavirus infection caused by SARS-CoV and MERS-CoV. Death is more likely to occur in older male patients with comorbidity. Infected patients might develop acute respiratory distress and respiratory failure which was the leading cause of death, but damages of other organs and systems, including cardiac, hemorrhage, hepatic, and renal also contribute to the death. These damages might be attributable to indirect cytokines storm initiated by immune system and direct attack from SARS-CoV-2 itself.", + "rel_num_authors": 28, + "rel_authors": [ + { + "author_name": "Bicheng Zhang", + "author_inst": "Department of Oncology, Eastern Campus, Renmin Hospital, Wuhan University" + }, + { + "author_name": "Xiaoyang Zhou", + "author_inst": "Cardiac Care Unit, Eastern Campus, Renmin Hospital, Wuhan University" + }, + { + "author_name": "Yanru Qiu", + "author_inst": "Department of Oncology, Eastern Campus, Renmin Hospital, Wuhan University" + }, + { + "author_name": "Fan Feng", + "author_inst": "Department of Oncology, Eastern Campus, Renmin Hospital, Wuhan University" + }, + { + "author_name": "Jia Feng", + "author_inst": "Department of Oncology, Eastern Campus, Renmin Hospital, Wuhan University" + }, + { + "author_name": "Yifan Jia", + "author_inst": "Department of Pain Management, Eastern Campus, Renmin Hospital, Wuhan University" + }, + { + "author_name": "Hengcheng Zhu", + "author_inst": "Department of Urology Surgery, Eastern Campus, Renmin Hospital, Wuhan University" + }, + { + "author_name": "Ke Hu", + "author_inst": "Department of Respiratory and Critical Care Medicine, Shouyi Campus, Renmin Hospital, Wuhan University" + }, + { + "author_name": "Jiasheng Liu", + "author_inst": "Department of Gastrointestinal Surgery, Eastern Campus, Renmin Hospital, Wuhan University" + }, + { + "author_name": "Zaiming Liu", + "author_inst": "Department of Neurosurgery, Eastern Campus, Renmin Hospital, Wuhan University" + }, + { + "author_name": "Shihong Wang", + "author_inst": "Department of Pediatric, Eastern Campus, Renmin Hospital, Wuhan University" + }, + { + "author_name": "Yiping Gong", + "author_inst": "Department of Breast, Eastern Campus, Renmin Hospital, Wuhan University" + }, + { + "author_name": "Chenliang Zhou", + "author_inst": "Intensive Care Unit, Eastern Campus, Renmin Hospital, Wuhan University" + }, + { + "author_name": "Ting Zhu", + "author_inst": "Department of Otolaryngology, Eastern Campus, Renmin Hospital, Wuhan University" + }, + { + "author_name": "Yanxiang Cheng", + "author_inst": "Department of Gynecology, Eastern Campus, Renmin Hospital, Wuhan University" + }, + { + "author_name": "Zhichao Liu", + "author_inst": "Department of Neurology, Eastern Campus, Renmin Hospital, Wuhan University" + }, + { + "author_name": "Hongping Deng", + "author_inst": "Department of Vascular Surgery, Eastern Campus, Renmin Hospital, Wuhan University" + }, + { + "author_name": "Fenghua Tao", + "author_inst": "Department of Orthopedics, Eastern Campus, Renmin Hospital, Wuhan University" + }, + { + "author_name": "Yijun Ren", + "author_inst": "Department of Orthopedics, Eastern Campus, Renmin Hospital, Wuhan University" + }, + { + "author_name": "Biheng Cheng", + "author_inst": "Department of Obstetrics, Eastern Campus, Renmin Hospital, Wuhan University" + }, + { + "author_name": "Ling Gao", + "author_inst": "Department of Endocrinology, Eastern Campus, Renmin Hospital, Wuhan University" + }, + { + "author_name": "Xiongfei Wu", + "author_inst": "Department of Nephrology, Eastern Campus, Renmin Hospital, Wuhan University" + }, + { + "author_name": "Lilei Yu", + "author_inst": "Department of Vasculocardiology, Eastern Campus, Renmin Hospital, Wuhan University" + }, + { + "author_name": "Zhixin Huang", + "author_inst": "Department of Gynecology, Eastern Campus, Renmin Hospital, Wuhan University" + }, + { + "author_name": "Zhangfan Mao", + "author_inst": "Department of Cardiothoracic Surgery, Eastern Campus, Renmin Hospital, Wuhan University" + }, + { + "author_name": "Qibin Song", + "author_inst": "Department of Oncology, Eastern Campus, Renmin Hospital, Wuhan University" + }, + { + "author_name": "Bo Zhu", + "author_inst": "Institute of Cancer, Xinqiao Hospital, Army Medical University" + }, + { + "author_name": "Jun Wang", + "author_inst": "The First Affiliated Hospital of Shandong First Medical University" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.02.26.20028225", "rel_title": "Clinical features and sexual transmission potential of SARS-CoV-2 infected female patients: a descriptive study in Wuhan, China", @@ -1639036,65 +1637562,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.25.20025643", - "rel_title": "Correlation Analysis Between Disease Severity and Inflammation-related Parameters in Patients with COVID-19 Pneumonia", - "rel_date": "2020-02-27", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.25.20025643", - "rel_abs": "AimThe new coronavirus (COVID-19) pneumonia outbreaking at the end of 2019 is highly contagious. Crude mortality rate reached 49% in critical patients. Inflammation matters on disease progression. This study analyzed blood inflammation indicators among mild, severe and critical patients, helping to identify severe or critical patients early.\n\nMethodsIn this cross-sectional study, 100 patients were included and divided to mild, severe or critical groups. Correlation of peripheral blood inflammation-related indicators with disease criticality was analyzed. Cut-off values for critically ill patients were speculated through the ROC curve.\n\nResultsSignificantly, disease severity was associated with age (R=-0.564, P<0.001), interleukin-2 receptor (IL2R) (R=-0.534, P<0.001), interleukin-6 (IL-6) (R=-0.535, P<0.001), interleukin-8 (IL-8) (R=-0.308, P<0.001), interleukin-10 (IL-10) (R=-0.422, P<0.001), tumor necrosis factor (TNF) (R=-0.322, P<0.001), C-reactive protein (CRP) (R=-0.604, P<0.001), ferroprotein (R=-0.508, P<0.001), procalcitonin (R=-0.650, P<0.001), white cell counts (WBC) (R=-0.54, P<0.001), lymphocyte counts (LC) (R=0.56, P<0.001), neutrophil count (NC) (R=-0.585, P<0.001) and eosinophil counts (EC) (R=0.299, P=0.01).\n\nConclusionWith following parameters such as age >67.5 years, IL2R >793.5U/mL, CRP >30.7ng/mL, ferroprotein >2252g/L, WBC>9.5*10^9/L or NC >7.305*10^9/L, the progress of COVID-19 to critical stage should be closely observed and possibly prevented. Inflammation is closely related to severity of COVID-19, and IL-6, TNF and IL-8 might be promising therapeutic targets.", - "rel_num_authors": 11, - "rel_authors": [ - { - "author_name": "Jing Gong", - "author_inst": "Department of Integrated Traditional Chinese and Western Medicine" - }, - { - "author_name": "Hui Dong", - "author_inst": "TongJiHospital" - }, - { - "author_name": "Song Qing Xia", - "author_inst": "TongJiHospital" - }, - { - "author_name": "Yi Zhao Huang", - "author_inst": "TongJiHospital" - }, - { - "author_name": "Dingkun Wang", - "author_inst": "TongJiHospital" - }, - { - "author_name": "Yan Zhao", - "author_inst": "TongJiHospital" - }, - { - "author_name": "Wenhua Liu", - "author_inst": "TongJiHospital" - }, - { - "author_name": "Shenghao Tu", - "author_inst": "TongJiHospital" - }, - { - "author_name": "Mingmin Zhang", - "author_inst": "TongJiHospital" - }, - { - "author_name": "Qi Wang", - "author_inst": "TongJiHospital" - }, - { - "author_name": "Fuer Lu", - "author_inst": "felu@tjh.tjmu.edu.cn" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.25.20027755", "rel_title": "Application and optimization of RT-PCR in diagnosis of SARS-CoV-2 infection", @@ -1640270,6 +1638737,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "allergy and immunology" }, + { + "rel_doi": "10.1101/2020.02.26.20028076", + "rel_title": "Case fatality rate of novel coronavirus disease 2019 in China", + "rel_date": "2020-02-26", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.26.20028076", + "rel_abs": "BackgroundA pandemic of coronavirus disease 2019 (COVID-19) which have caused more than 80 thousand persons infected globally is still ongoing. This study aims to calculate its case fatality rate (CFR).\n\nMethodsThe method, termed as converged CFR calculation, was based on the formula of dividing the number of known deaths by the number of confirmed cases T days before, where T was an average time period from case confirmation to death. It was found that supposing a T, if it was smaller (bigger) than the true T, calculated CFRs would gradually increase (decrease) to infinitely near the true T with time went on. According to the law, the true T value could be determined by trends of daily CFRs calculated with different assumed T values (left of true T is decreasing, right is increasing). Then the CFR could be calculated.\n\nResultsCFR of COVID-19 in China except Hubei Province was 0.8% to 0.9%. So far, the CFR had accurately predicted the death numbers more than 3 weeks. CFR in Hubei of China was 5.4% by which the calculated death number corresponded with the reported number for 2 weeks.\n\nConclusionThe method could be used for CFR calculating while pandemics are still ongoing. Dynamic monitoring of the daily CFRs trends could help outbreak-controller to have a clear vision in the timeliness of the case confirmation.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Rui Qi", + "author_inst": "Wuhan University" + }, + { + "author_name": "Chao Ye", + "author_inst": "Shandong Maternal and Child Health Care Hospital" + }, + { + "author_name": "Xiang-rong Qin", + "author_inst": "Wuhan University" + }, + { + "author_name": "Xue-Jie Yu", + "author_inst": "Wuhan University School of Health Sciences, State Key Laboratory of Virology, Wuhan University, Wuhan, Hubei Province, China." + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.21.20026229", "rel_title": "Epidemiological Development of Novel Coronavirus Pneumonia in China and Its Forecast", @@ -1640710,53 +1639208,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.23.20026864", - "rel_title": "Higher severity and mortality in male patients with COVID-19 independent of age and susceptibility", - "rel_date": "2020-02-25", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.23.20026864", - "rel_abs": "ImportanceThe recent outbreak of Novel Coronavirus (SARS-CoV-2) Disease (COVID-19) has put the world on alert, that is reminiscent of the SARS outbreak seventeen years ago.\n\nObjectiveWe aim to compare the severity and mortality between male and female patients with both COVID-19 and SARS, to explore the most useful prognostic factors for individualized assessment.\n\nDesign, Setting, and ParticipantsWe extracted the data from a case series of 43 hospitalized patients we treated, a public data set of the first 37 cases died of COVID-19 in Wuhan city and 1019 survived patients from six cities in China. We also analyzed the data of 524 patients with SARS, including 139 deaths, from Beijing city in early 2003.\n\nMain Outcomes and MeasuresSeverity and mortality.\n\nResultsOlder age and high number of comorbidities were associated with higher severity and mortality in patients with both COVID-19 and SARS. The percentages of older age ([≥]65 years) were much higher in the deceased group than in the survived group in patients with both COVID-19 (83.8 vs. 13.2, P<0.001) and SARS (37.4 vs. 4.9, P<0.001). In the case series, men tend to be more serious than women (P=0.035), although age was comparable between men and women. In the public data set, age was also comparable between men and women in the deceased group or the survived group in patients with COVID-19. Meanwhile, gender distribution was exactly symmetrical in the 1019 survivors of COVID-19. However, the percentage of male were higher in the deceased group than in the survived group (70.3 vs. 50.0, P=0.015). The gender role in mortality was also observed in SARS patients. Survival analysis showed that men (hazard ratio [95% CI] 1.47 [1.05-2.06, P= 0.025) had a significantly higher mortality rate than women in patients with SARS.\n\nConclusions and RelevanceOlder age and male gender are risk factors for worse outcome in patients with COVID. While men and women have the same susceptibility to both SARS-CoV-2 and SARS-CoV, men may be more prone to have higher severity and mortality independent of age and susceptibility.\n\nKey PointsO_ST_ABSQuestionC_ST_ABSAre men more susceptible to getting and dying from COVID-19?\n\nFindingsIn the case series, men tend to be more serious than women. In the public data set, the percentage of men were higher in the deceased group than in the survived group, although age was comparable between men and women.\n\nMeaningMale gender is a risk factor for worse outcome in patients with COVID independent of age and susceptibility.", - "rel_num_authors": 8, - "rel_authors": [ - { - "author_name": "Jian-Min Jin", - "author_inst": "Beijing Tongren Hospital, Capital Medical University" - }, - { - "author_name": "Peng Bai", - "author_inst": "Beijing Tongren Hospital, Capital Medical University" - }, - { - "author_name": "Wei He", - "author_inst": "Beijing Tongren Hospital, Capital Medical University" - }, - { - "author_name": "Fei Wu", - "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Xiao-Fang Liu", - "author_inst": "Beijing Tongren Hospital, Capital Medical University" - }, - { - "author_name": "De-Min Han", - "author_inst": "Beijing Tongren Hospital, Capital Medical University" - }, - { - "author_name": "Shi Liu", - "author_inst": "Union Hospital, Tongji Medical College, Huazhong University of Science and Technology" - }, - { - "author_name": "Jin-Kui Yang", - "author_inst": "Beijing Tongren Hospital, Capital Medical University" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.21.20026179", "rel_title": "2019 Novel Coronavirus can be detected in urine, blood, anal swabs and oropharyngeal swabs samples", @@ -1641840,6 +1640291,61 @@ "type": "new results", "category": "biochemistry" }, + { + "rel_doi": "10.1101/2020.02.20.20025957", + "rel_title": "From Isolation to Coordination: How Can Telemedicine Help Combat the COVID-19 Outbreak?", + "rel_date": "2020-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.20.20025957", + "rel_abs": "The rapid spread of Coronavirus disease 2019 (COVID-19) presents China with a critical challenge. As normal capacity of the Chinese hospitals is exceeded, healthcare professionals struggling to manage this unprecedented crisis face the difficult question of how best to coordinate the medical resources used in highly separated locations. Responding rapidly to this crisis, the National Telemedicine Center of China (NTCC), located in Zhengzhou, Henan Province, has established the Emergency Telemedicine Consultation System (ETCS), a telemedicine-enabled outbreak alert and response network. ETCS is built upon a doctor-to-doctor (D2D) approach, in which health services can be accessed remotely through terminals across hospitals. The system architecture of ETCS comprises three major architectural layers: (1) telemedicine service platform layer, (2) telemedicine cloud layer, and (3) telemedicine service application layer. Our ETCS has demonstrated substantial benefits in terms of the effectiveness of consultations and remote patient monitoring, multidisciplinary care, and prevention education and training.", + "rel_num_authors": 10, + "rel_authors": [ + { + "author_name": "Yunkai Zhai", + "author_inst": "The First Affiliated Hospital of Zhengzhou University; National Telemedicine Center of China; Zhengzhou University" + }, + { + "author_name": "Yichuan Wang", + "author_inst": "University of Sheffield" + }, + { + "author_name": "Minhao Zhang", + "author_inst": "University of Bristol" + }, + { + "author_name": "Jody Hoffer Gittell", + "author_inst": "Brandeis University" + }, + { + "author_name": "Shuai Jiang", + "author_inst": "The First Affiliated Hospital of Zhengzhou University; National Telemedicine Center of China" + }, + { + "author_name": "Baozhan Chen", + "author_inst": "The First Affiliated Hospital of Zhengzhou University; National Telemedicine Center of China" + }, + { + "author_name": "Fangfang Cui", + "author_inst": "The First Affiliated Hospital of Zhengzhou University; National Telemedicine Center of China" + }, + { + "author_name": "Xianying He", + "author_inst": "The First Affiliated Hospital of Zhengzhou University; National Telemedicine Center of China" + }, + { + "author_name": "Jie Zhao", + "author_inst": "The First Affiliated Hospital of Zhengzhou University; National Telemedicine Center of China" + }, + { + "author_name": "Xiaojun Wang", + "author_inst": "University of Bristol" + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "health systems and quality improvement" + }, { "rel_doi": "10.1101/2020.02.19.20024885", "rel_title": "Comparative study of the lymphocyte change between COVID-19 and non-COVID-19 pneumonia cases suggesting uncontrolled inflammation might not be the main reason of tissue injury", @@ -1642404,81 +1640910,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.02.22.20025460", - "rel_title": "Development and Evaluation of A CRISPR-based Diagnostic For 2019-novel Coronavirus", - "rel_date": "2020-02-23", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.22.20025460", - "rel_abs": "BackgroundThe recent outbreak of infections by the 2019 novel coronavirus (2019-nCoV), the third zoonotic CoV has raised great public health concern. The demand for rapid and accurate diagnosis of this novel pathogen brought significant clinical and technological challenges. Currently, metagenomic next-generation sequencing (mNGS) and reverse-transcription PCR (RT-PCR) are the most widely used molecular diagnostics for 2019-nCoV.\n\nMethods2019-nCoV infections were confirmed in 52 specimens by mNGS. Genomic information was analyzed and used for the design and development of an isothermal, CRISPR-based diagnostic for the novel virus. The diagnostic performance of CRISPR-nCoV was assessed and also compared across three technology platforms (mNGS, RT-PCR and CRISPR)\n\nResults2019-nCoVs sequenced in our study were conserved with the Wuhan strain, and shared certain genetic similarity with SARS-CoV. A high degree of variation in the level of viral RNA was observed in clinical specimens. CRISPR-nCoV demonstrated a near single-copy sensitivity and great clinical sensitivity with a shorter turn-around time than RT-PCR.\n\nConclusionCRISPR-nCoV presents as a promising diagnostic option for the emerging pathogen.", - "rel_num_authors": 15, - "rel_authors": [ - { - "author_name": "Tieying Hou", - "author_inst": "Laboratory Medicine, Provincial People's Hospital, Guangdong Academy of Medical Sciences Guangzhou, Guangdong 510000, China" - }, - { - "author_name": "Weiqi Zeng", - "author_inst": "Vision Medicals, Co., Ltd, Guangzhou, Guangdong 510000, China" - }, - { - "author_name": "Minling Yang", - "author_inst": "Vision Medicals, Co., Ltd, Guangzhou, Guangdong 510000, China" - }, - { - "author_name": "Wenjing Chen", - "author_inst": "Vision Medicals Co., Ltd, Guangzhou" - }, - { - "author_name": "Lili Ren", - "author_inst": "National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens; Christophe M\u00e9rieux Laboratory, Institute of Pathoge" - }, - { - "author_name": "Jingwen Ai", - "author_inst": "Department of Infectious Diseases, Huashan Hospital affiliated to Fudan University, Shanghai 200040, China" - }, - { - "author_name": "Ji Wu", - "author_inst": "Laboratory Medicine, Provincial People's Hospital, Guangdong Academy of Medical Sciences Guangzhou, Guangdong 510000, China" - }, - { - "author_name": "Yalong Liao", - "author_inst": "Laboratory Medicine, Provincial People's Hospital, Guangdong Academy of Medical Sciences Guangzhou, Guangdong 510000, China" - }, - { - "author_name": "Xuejing Gou", - "author_inst": "Vision Medicals, Co., Ltd, Guangzhou, Guangdong 510000, China" - }, - { - "author_name": "Yongjun Li", - "author_inst": "Vision Medicals, Co., Ltd, Guangzhou, Guangdong 510000, China" - }, - { - "author_name": "Xiaorui Wang", - "author_inst": "Vision Medicals, Co., Ltd, Guangzhou, Guangdong 510000, China" - }, - { - "author_name": "Hang Su", - "author_inst": "Vision Medicals, Co., Ltd, Guangzhou, Guangdong 510000, China" - }, - { - "author_name": "Bing Gu", - "author_inst": "Affiliated Hospital of Xuzhou Medical University" - }, - { - "author_name": "Jianwei Wang", - "author_inst": "NHC Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Pek" - }, - { - "author_name": "Teng Xu", - "author_inst": "Vision Medicals Co., Ltd, 31 Kefeng Rd, G10-301, Guangzhou 510000, China" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.20.20025536", "rel_title": "Clinical characteristics of 51 patients discharged from hospital with COVID-19 in Chongqing\uff0cChina", @@ -1643617,6 +1642048,81 @@ "type": "PUBLISHAHEADOFPRINT", "category": "gastroenterology" }, + { + "rel_doi": "10.1101/2020.02.20.20025338", + "rel_title": "COVID-19 in Wuhan: Immediate Psychological Impact on 5062 Health Workers", + "rel_date": "2020-02-23", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.20.20025338", + "rel_abs": "BACKGROUNDThe outbreak of COVID-19 has laid unprecedented psychological stress on health workers (HWs). We aimed to assess the immediate psychological impact on HWs at Tongji Hospital in Wuhan, China.\n\nMETHODSWe conducted a single-center, cross-sectional survey of HWs via online questionnaires between February 8th and 10th, 2020. We evaluated stress, depression and anxiety by Impact of Event Scale-Revised (IES-R), Patient Health Questionnaire-9 (PHQ-9), and Generalized Anxiety Disorder 7-item (GAD-7), respectively. We also designed a questionnaire to assess the effect of psychological protective measures taken by Tongji Hospital. Multivariate logistic regression was used to identify predictors of acute stress, depression, and anxiety.\n\nRESULTSWe received 5062 completed questionnaires (response rate, 77.1 percent). 1509 (29.8 percent), 681 (13.5 percent) and 1218 (24.1 percent) HWs reported stress, depression and anxiety symptoms. Women (hazard ratio[HR], 1.31; P=0.032), years of working> 10 years (HR, 2.02; P<0.001), concomitant chronic diseases (HR, 1.51; P<0.001), history of mental disorders (HR, 3.27; P<0.001), and family members or relatives confirmed or suspected (HR, 1.23; P=0.030) were risk factors for stress, whereas care provided by hospital and department administrators(odds ratio [OR], 0.76; P=0.024) and full coverage of all departments with protective measures (OR, 0.69; P=0.004) were protective factors.\n\nCONCLUSIONSWomen and those who have more than 10 years of working, concomitant chronic diseases, history of mental disorders, and family members or relatives confirmed or suspected are susceptible to stress, depression and anxiety among HWs during the COVID-19 pandemic. Psychological protective measures implemented by the hospital could be helpful.", + "rel_num_authors": 15, + "rel_authors": [ + { + "author_name": "Zhou Zhu", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Shabei Xu", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Hui Wang", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Zheng Liu", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Jianhong Wu", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Guo Li", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Jinfeng Miao", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Chenyan Zhang", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Yuan Yang", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Wenzhe Sun", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Suiqiang Zhu", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Yebin Fan", + "author_inst": "School of Computer Science and Technology, Huazhong University of Science and Technology" + }, + { + "author_name": "Junbo Hu", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Jihong Liu", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + }, + { + "author_name": "Wei Wang", + "author_inst": "Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "psychiatry and clinical psychology" + }, { "rel_doi": "10.1101/2020.02.21.20026146", "rel_title": "Public Exposure to Live Animals, Behavioural Change, and Support in Containment Measures in response to COVID-19 Outbreak: a population-based cross sectional survey in China", @@ -1643917,121 +1642423,6 @@ "type": "new results", "category": "genomics" }, - { - "rel_doi": "10.1101/2020.02.21.959817", - "rel_title": "Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform", - "rel_date": "2020-02-21", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.21.959817", - "rel_abs": "Reverse genetics has been an indispensable tool revolutionising our insights into viral pathogenesis and vaccine development. Large RNA virus genomes, such as from Coronaviruses, are cumbersome to clone and to manipulate in E. coli hosts due to size and occasional instability1-3. Therefore, an alternative rapid and robust reverse genetics platform for RNA viruses would benefit the research community. Here we show the full functionality of a yeast-based synthetic genomics platform for the genetic reconstruction of diverse RNA viruses, including members of the Coronaviridae, Flaviviridae and Paramyxoviridae families. Viral subgenomic fragments were generated using viral isolates, cloned viral DNA, clinical samples, or synthetic DNA, and reassembled in one step in Saccharomyces cerevisiae using transformation associated recombination (TAR) cloning to maintain the genome as a yeast artificial chromosome (YAC). T7-RNA polymerase has been used to generate infectious RNA, which was then used to rescue viable virus. Based on this platform we have been able to engineer and resurrect chemically-synthetized clones of the recent epidemic SARS-CoV-24 in only a week after receipt of the synthetic DNA fragments. The technical advance we describe here allows to rapidly responding to emerging viruses as it enables the generation and functional characterization of evolving RNA virus variants - in real-time - during an outbreak.", - "rel_num_authors": 25, - "rel_authors": [ - { - "author_name": "Tran Thi Nhu Thao", - "author_inst": "Institute of Virology and Immunology (IVI), Bern, Switzerland" - }, - { - "author_name": "Fabien Labroussaa", - "author_inst": "Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Nadine Ebert", - "author_inst": "Institute of Virology and Immunology (IVI), Bern, Switzerland" - }, - { - "author_name": "Hanspeter Stalder", - "author_inst": "Institute of Virology and Immunology (IVI), Bern, Switzerland" - }, - { - "author_name": "Jamine Portmann", - "author_inst": "Institute of Virology and Immunology (IVI), Bern, Switzerland" - }, - { - "author_name": "Jenna Kelly", - "author_inst": "Institute of Virology and Immunology (IVI), Bern, Switzerland" - }, - { - "author_name": "Silvio Steiner", - "author_inst": "Institute of Virology and Immunology (IVI), Bern, Switzerland" - }, - { - "author_name": "Melle Holwerda", - "author_inst": "Institute of Virology and Immunology (IVI), Bern, Switzerland" - }, - { - "author_name": "Annika Kratzel", - "author_inst": "Institute of Virology and Immunology (IVI), Bern, Switzerland" - }, - { - "author_name": "Mitra Gultom", - "author_inst": "Institute of Virology and Immunology (IVI), Bern, Switzerland" - }, - { - "author_name": "Laura Laloli", - "author_inst": "Insitute for Infectious Diseases, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Linda Huesser", - "author_inst": "Institute of Virology and Immunology (IVI), Bern, Switzerland" - }, - { - "author_name": "Manon Wider", - "author_inst": "Insitute for Infectious Diseases, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Stephanie Pfaender", - "author_inst": "Institute of Virology and Immunology (IVI), Bern, Switzerland" - }, - { - "author_name": "Dagny Hirt", - "author_inst": "Institute of Virology and Immunology (IVI), Bern, Switzerland" - }, - { - "author_name": "Valentina Cippa", - "author_inst": "Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Silvia Crespo-Pomar", - "author_inst": "Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Simon Schroeder", - "author_inst": "Institute of Virology, Charite-Universitaetsmedizin Berlin, corporatemember of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute " - }, - { - "author_name": "Doreen Muth", - "author_inst": "Institute of Virology, Charite-Universitaetsmedizin Berlin, corporatemember of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute " - }, - { - "author_name": "Daniela Niemeyer", - "author_inst": "Institute of Virology, Charite-Universitaetsmedizin Berlin, corporatemember of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute " - }, - { - "author_name": "Marcel A Mueller", - "author_inst": "Institute of Virology, Charite-Universitaetsmedizin Berlin, corporatemember of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute " - }, - { - "author_name": "Christian Drosten", - "author_inst": "Institute of Virology, Charite-Universitaetsmedizin Berlin, corporatemember of Freie Universitaet Berlin, Humboldt-Universitaet zu Berlin, and Berlin Institute " - }, - { - "author_name": "Ronald Dijkman", - "author_inst": "Insitute for Infectious Diseases, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Joerg Jores", - "author_inst": "Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland" - }, - { - "author_name": "Volker Thiel", - "author_inst": "Institute of Virology and Immunology (IVI), Bern, Switzerland" - } - ], - "version": "1", - "license": "cc_by_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.02.15.20023333", "rel_title": "The role of institutional trust in preventive and treatment-seeking behaviors during the 2019 novel coronavirus (2019-nCoV) outbreak among residents in Hubei, China", @@ -1645087,6 +1643478,41 @@ "type": "PUBLISHAHEADOFPRINT", "category": "nephrology" }, + { + "rel_doi": "10.1101/2020.02.18.20024570", + "rel_title": "Modeling and Prediction of the 2019 Coronavirus Disease Spreading in China Incorporating Human Migration Data", + "rel_date": "2020-02-20", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.18.20024570", + "rel_abs": "This study integrates the daily intercity migration data with the classic Susceptible-Exposed-Infected-Removed (SEIR) model to construct a new model suitable for describing the dynamics of epidemic spreading of Coronavirus Disease 2019 (COVID-19) in China. Daily intercity migration data for 367 cities in China are collected from Baidu Migration, a mobile-app based human migration tracking data system. Historical data of infected, recovered and death cases from official source are used for model fitting. The set of model parameters obtained from best data fitting using a constrained nonlinear optimization procedure is used for estimation of the dynamics of epidemic spreading in the coming weeks. Our results show that the number of infections in most cities in China will peak between mid February to early March 2020, with about 0.8%, less than 0.1% and less than 0.01% of the population eventually infected in Wuhan, Hubei Province and the rest of China, respectively.", + "rel_num_authors": 5, + "rel_authors": [ + { + "author_name": "Choujun Zhan", + "author_inst": "South China Normal University, Guangzhou, China" + }, + { + "author_name": "Chi K. Tse", + "author_inst": "City University of Hong Kong, Hong Kong" + }, + { + "author_name": "Yuxia Fu", + "author_inst": "Nanfang College of Sun Yat-Sen University, Guangzhou, China" + }, + { + "author_name": "Zhikang Lai", + "author_inst": "Nanfang College of Sun Yat-Sen University, Guangzhou, China" + }, + { + "author_name": "Haijun Zhang", + "author_inst": "Harbin Institute of Technology, Shenzhen, China" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.02.18.20024315", "rel_title": "Estimation of the epidemic properties of the 2019 novel coronavirus: A mathematical modeling study", @@ -1645455,33 +1643881,6 @@ "type": "new results", "category": "biophysics" }, - { - "rel_doi": "10.1101/2020.02.18.20021881", - "rel_title": "Association between 2019-nCoV transmission and N95 respirator use", - "rel_date": "2020-02-19", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.18.20021881", - "rel_abs": "2019-nCoV had caused pneumonia outbreak in Wuhan. Existing evidence have confirmed the human-to-human transmission of 2019-nCoV. We retrospectively collected infection data from 2 January to 22 January at six departments from Zhongnan Hospital of Wuhan University. In our study, we found N95 respirators, disinfection and hand washing can help to reduce the risk of 2019-nCoV infection in medical staffs. Our results call for re-emphasizing strict occupational protection code in battling this novel contagious disease. The risk of 2019-nCoV infection was higher in the open area than in the quarantined area. N95 may be more effective for 2019-nCoV infections.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Xinghuan Wang", - "author_inst": "Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China" - }, - { - "author_name": "Zhenyu Pan", - "author_inst": "Department of Infection Management, Zhongnan Hospital of Wuhan University, Wuhan, China" - }, - { - "author_name": "Zhenshun Cheng", - "author_inst": "Department of Respiratory medicine, Zhongnan Hospital of Wuhan University, Wuhan, China" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.02.16.20023903", "rel_title": "Clinical and immunologic features in severe and moderate forms of Coronavirus Disease 2019", @@ -1646501,6 +1644900,45 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.02.16.20023804", + "rel_title": "When will the battle against novel coronavirus end in Wuhan: a SEIR modeling analysis", + "rel_date": "2020-02-18", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.16.20023804", + "rel_abs": "Recent outbreak of 2019-nCoV in Wuhan raised serious public health concerns. By February 15, 2020 in Wuhan, the total number of confirmed infection cases has reached 37,914, and the number of deaths has reached 1123, accounting for 56.9% of the total confirmed cases and 73.7% of the total deaths in China. People are eager to know when the epidemic will be completely controlled and when peoples work and life will be on the right track. In this study we analyzed the epidemic dynamics and trend of 2019-nCoV in Wuhan by using the data after the closure of Wuhan city till February 12, 2020 based on the SEIR modeling method. The optimal parameters were estimated as R0=1.44 (interquartile range: 1.40-1.47),TI=14 (interquartile range: 14-14) and TE=3.0 (interquartile range: 2.8-3.1). Based on these parameters, the number of infected individuals in Wuhan city may reach the peak around February 19 at about 45,000 people. Once entering March, the epidemic would gradually decline, and end around the late March. It is worth noting that the above prediction is based on the assumption that the number of susceptible population N = 200,000 will not increase. If the epidemic situation is not properly controlled, the peak of infected number can be further increased and the peak time will be a little postponed. It was expected that the epidemic would subside in early March, and disappear gradually towards the late March.", + "rel_num_authors": 6, + "rel_authors": [ + { + "author_name": "lianglu zhang Sr.", + "author_inst": "Wuhan Ammunition Life-Tech Co., Ltd." + }, + { + "author_name": "kangkang wan Jr.", + "author_inst": "Wuhan Ammunition Life-Tech Co., Ltd." + }, + { + "author_name": "jing chen Sr.", + "author_inst": "Clinics of Oilcrops Research Institute, CAAS" + }, + { + "author_name": "changming lu Sr.", + "author_inst": "Wuhan Ammunition Life-Tech Co., Ltd" + }, + { + "author_name": "lanlan dong Jr.", + "author_inst": "Wuhan Ammunition Life-Tech Co., Ltd." + }, + { + "author_name": "zhicheng wu Sr.", + "author_inst": "Wuhan Ammunition Life-Tech Co., Ltd." + } + ], + "version": "1", + "license": "cc_no", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.15.20023440", "rel_title": "Evaluating new evidence in the early dynamics of the novel coronavirus COVID-19 outbreak in Wuhan, China with real time domestic traffic and potential asymptomatic transmissions", @@ -1646853,45 +1645291,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.02.14.20021535", - "rel_title": "Clinical Characteristics of 2019 Novel Infected Coronavirus Pneumonia\uff1aA Systemic Review and Meta-analysis", - "rel_date": "2020-02-17", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.14.20021535", - "rel_abs": "BackgroundA novel pneumonia associated with the 2019 coronavirus infected pneumonia (NCIP) suddenly broke out in Wuhan, China in December 2019. 37287 confirmed cases and 813 death case in China (Until 8th/Feb/2019) have been reported in just fortnight. Although this risky pneumonia with high infection rates and high mortality rates need to be resolved immediately, major gaps in our knowledge of clinical characters of it were still not be established. The aim of this study is to summaries and analysis the clinical characteristics of 2019-nCoV pneumonia.\n\nMethodsLiteratures have been systematically performed a search on PubMed, Embase, Web of Science, GreyNet International, and The Cochrane Library from inception up to February 8, 2020. The Newcastle-Ottawa Scale was used to assess quality, and publication bias was analyzed by Eggers test. In the single-arm meta-analysis, A fix-effects model was used to obtain a pooled incidence rate. We conducted subgroup analysis according to geographic region and research scale.\n\nResultsA total of nine studies including 356 patients were included in this study, the mean age was 52.4 years and 221 (62.1%) were male. The pooled incidences rate of symptoms as follows: pharyngalgia (12.2%, 95% CI: 0.087-0.167), diarrhea (9.2%, 95% CI: 0.062-0.133) and headache (8.9%, 95% CI: 0.063-0.125). Meanwhile, 5.7% (95% CI: 0.027-0.114) of patients were found without any symptoms although they were diagnosed by RT-PCR. In the terms of CT imaging examination, the most of patients showed bilateral mottling or ground-glass opacity, 8.6% (95% CI: 0.048-0.148) of patients with crazy-paving pattern, and 11.5% (95% CI: 0.064-0.197) of patients without obvious CT imaging presentations. The pooled incidence of mortality was 8.9% (95% CI: 0.062-0.126).\n\nConclusionsTo our knowledge, this is the first evidence-based medicine research to further elaborate the clinical characteristics of NCIP, which is beneficial to the next step of prevention and treatment.", - "rel_num_authors": 6, - "rel_authors": [ - { - "author_name": "Kai Qian", - "author_inst": "Kunming University of Science and Technology" - }, - { - "author_name": "Yi Deng", - "author_inst": "Daping Hospital, Army Medical University" - }, - { - "author_name": "Yonghang Tai", - "author_inst": "Yunnan Normal University" - }, - { - "author_name": "Jun Peng", - "author_inst": "The First People's Hospital of Yunnan Province" - }, - { - "author_name": "Hao Peng", - "author_inst": "The First People's Hospital of Yunnan Province" - }, - { - "author_name": "Lihong Jiang", - "author_inst": "The First People's Hospital of Yunnan Province" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.02.14.20022897", "rel_title": "Assessing the impact of reduced travel on exportation dynamics of novel coronavirus infection (COVID-19)", @@ -1647755,6 +1646154,37 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, + { + "rel_doi": "10.1101/2020.02.11.20022228", + "rel_title": "Single-cell RNA expression profiling of ACE2, the putative receptor of Wuhan 2019-nCoV, in the nasal tissue", + "rel_date": "2020-02-13", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.11.20022228", + "rel_abs": "A novel coronavirus (2019-nCoV) was first identified in Wuhan, Hubei Province, and then spreads to the other Provinces of China. WHO decides to determine a Public Health Emergency of International Concern (PHEIC) of 2019-nCoV. 2019-nCov was reported to share the same receptor, Angiotensin-converting enzyme 2 (ACE2), with SARS-Cov. Here based on the public single-cell RNA-Seq datasets, we analyzed the ACE2 RNA expression profile in the tissues at different locations of the respiratory tract. The result indicates that the ACE2 expression appears in nasal epithelial cells. We found that the size of this population of ACE2-expressing nasal epithelial cells is comparable with the size of the population of ACE2-expression type II alveolar cells (AT2) in the Asian sample reported by Yu Zhao et al. We further detected 2019-nCoV by polymerase chain reaction (PCR) from the nasal-swab and throat-swab of seven suspected cases. We found that 2019-nCoV tends to have a higher concentration in the nasal-swab comparing to the throat-swab, which could attribute to the ACE2-expressing nasal epithelial cells. We hope this study could be informative for virus-prevention strategy development, especially the treatment of nasal mucus.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "CHAO WU", + "author_inst": "Zhe Jiang University, China" + }, + { + "author_name": "Shufa Zheng", + "author_inst": "Zhe Jiang University" + }, + { + "author_name": "Yu Chen", + "author_inst": "Zhe Jiang University" + }, + { + "author_name": "Min Zheng", + "author_inst": "Zhe Jiang University" + } + ], + "version": "1", + "license": "cc_by_nc", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.02.11.20022186", "rel_title": "Data-Based Analysis, Modelling and Forecasting of the novel Coronavirus (2019-nCoV) outbreak", @@ -1648191,37 +1646621,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.02.11.20022095", - "rel_title": "Primary Care Practitioners' Response to 2019 Novel Coronavirus Outbreak in China", - "rel_date": "2020-02-12", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.11.20022095", - "rel_abs": "The emerging outbreak of the 2019 novel coronavirus (2019-nCoV) originated from Wuhan poses a great challenge to healthcare system in China.1 Primary care practitioners (PCPs) have an important role in district communicable disease control.2 However, because primary health-care system in China still needs to be substantially strengthened,3,4 whether PCPs are proactive and capable in responding to the outbreak remains unclear. Using an electronic questionnaire, we surveyed a national sample of PCPs to assess their response to novel coronavirus outbreak.", - "rel_num_authors": 4, - "rel_authors": [ - { - "author_name": "Zhijie Xu", - "author_inst": "Department of General Practice, Sir Run Run Shaw hospital, Zhejiang University School of Medicine" - }, - { - "author_name": "Yi Qian", - "author_inst": "Department of General Practice, Sir Run Run Shaw hospital, Zhejiang University School of Medicine" - }, - { - "author_name": "Lizheng Fang", - "author_inst": "Department of General Practice, Sir Run Run Shaw hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang Province" - }, - { - "author_name": "Mi Yao", - "author_inst": "Institute of Applied Health Research, University of Birmingham" - } - ], - "version": "1", - "license": "cc_no", - "type": "PUBLISHAHEADOFPRINT", - "category": "primary care research" - }, { "rel_doi": "10.1101/2020.02.11.20021956", "rel_title": "Ophthalmologic evidence against the interpersonal transmission of 2019 novel coronavirus through conjunctiva", @@ -1649161,6 +1647560,37 @@ "type": "new results", "category": "genomics" }, + { + "rel_doi": "10.1101/2020.02.08.20021311", + "rel_title": "Assessing the plausibility of subcritical transmission of 2019-nCoV in the United States", + "rel_date": "2020-02-11", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.08.20021311", + "rel_abs": "Rapid assessment of the transmission potential of an emerging or reemerging pathogen is a cornerstone of public health response. A simple approach is shown for using the number of disease introductions and secondary cases to determine whether the upper bound of the reproduction number exceeds the critical value of one.", + "rel_num_authors": 4, + "rel_authors": [ + { + "author_name": "Seth Blumberg", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Phoebe Lu", + "author_inst": "University of California, Los Angeles" + }, + { + "author_name": "Thomas M Lietman", + "author_inst": "University of California, San Francisco" + }, + { + "author_name": "Travis C Porco", + "author_inst": "University of California, San Francisco" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "epidemiology" + }, { "rel_doi": "10.1101/2020.02.07.939389", "rel_title": "The Pathogenicity of 2019 Novel Coronavirus in hACE2 Transgenic Mice", @@ -1649785,33 +1648215,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, - { - "rel_doi": "10.1101/2020.02.06.20020941", - "rel_title": "Analysis of the epidemic growth of the early 2019-nCoV outbreak using internationally confirmed cases", - "rel_date": "2020-02-09", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.02.06.20020941", - "rel_abs": "BackgroundOn January 23, 2020, a quarantine was imposed on travel in and out of Wuhan, where the 2019 novel coronavirus (2019-nCoV) outbreak originated from. Previous analyses estimated the basic epidemiological parameters using symptom onset dates of the confirmed cases in Wuhan and outside China.\n\nMethodsWe obtained information on the 46 coronavirus cases who traveled from Wuhan before January 23 and have been subsequently confirmed in Hong Kong, Japan, Korea, Macau, Singapore, and Taiwan as of February 5, 2020. Most cases have detailed travel history and disease progress. Compared to previous analyses, an important distinction is that we used this data to informatively simulate the infection time of each case using the symptom onset time, previously reported incubation interval, and travel history. We then fitted a simple exponential growth model with adjustment for the January 23 travel ban to the distribution of the simulated infection time. We used a Bayesian analysis with diffuse priors to quantify the uncertainty of the estimated epidemiological parameters. We performed sensitivity analysis to different choices of incubation interval and the hyperparameters in the prior specification.\n\nResultsWe found that our model provides good fit to the distribution of the infection time. Assuming the travel rate to the selected countries and regions is constant over the study period, we found that the epidemic was doubling in size every 2.9 days (95% credible interval [CrI], 2 days--4.1 days). Using previously reported serial interval for 2019-nCoV, the estimated basic reproduction number is 5.7 (95% CrI, 3.4--9.2). The estimates did not change substantially if we assumed the travel rate doubled in the last 3 days before January 23, when we used previously reported incubation interval for severe acute respiratory syndrome (SARS), or when we changed the hyperparameters in our prior specification.\n\nConclusionsOur estimated epidemiological parameters are higher than an earlier report using confirmed cases in Wuhan. This indicates the 2019-nCoV could have been spreading faster than previous estimates.", - "rel_num_authors": 3, - "rel_authors": [ - { - "author_name": "Qingyuan Zhao", - "author_inst": "University of Cambridge" - }, - { - "author_name": "Yang Chen", - "author_inst": "University of Michigan" - }, - { - "author_name": "Dylan S Small", - "author_inst": "University of Pennsylvania" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "epidemiology" - }, { "rel_doi": "10.1101/2020.02.06.20020974", "rel_title": "Clinical characteristics of 2019 novel coronavirus infection in China", @@ -1650931,6 +1649334,73 @@ "type": "new results", "category": "bioinformatics" }, + { + "rel_doi": "10.1101/2020.02.03.931766", + "rel_title": "Specific ACE2 Expression in Cholangiocytes May Cause Liver Damage After 2019-nCoV Infection", + "rel_date": "2020-02-04", + "rel_site": "bioRxiv", + "rel_link": "https://biorxiv.org/cgi/content/short/2020.02.03.931766", + "rel_abs": "A newly identified coronavirus, 2019-nCoV, has been posing significant threats to public health since December 2019. ACE2, the host cell receptor for severe acute respiratory syndrome coronavirus (SARS), has recently been demonstrated in mediating 2019-nCoV infection. Interestingly, besides the respiratory system, substantial proportion of SARS and 2019-nCoV patients showed signs of various degrees of liver damage, the mechanism and implication of which have not yet been determined. Here, we performed an unbiased evaluation of cell type specific expression of ACE2 in healthy liver tissues using single cell RNA-seq data of two independent cohorts, and identified specific expression in cholangiocytes. The results indicated that virus might directly bind to ACE2 positive cholangiocytes but not necessarily hepatocytes. This finding suggested the liver abnormalities of SARS and 2019-nCoV patients may not be due to hepatocyte damage, but cholangiocyte dysfunction and other causes such as drug induced and systemic inflammatory response induced liver injury. Our findings indicate that special care of liver dysfunction should be installed in treating 2019-nCoV patients during the hospitalization and shortly after cure.", + "rel_num_authors": 13, + "rel_authors": [ + { + "author_name": "Xiaoqiang Chai", + "author_inst": "Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invas" + }, + { + "author_name": "Longfei Hu", + "author_inst": "Singleron Biotechnologies, Yaogu Avenue 11, Nanjing, Jiangsu, China" + }, + { + "author_name": "Yan Zhang", + "author_inst": "Singleron Biotechnologies, Yaogu Avenue 11, Nanjing, Jiangsu, China" + }, + { + "author_name": "Weiyu Han", + "author_inst": "Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invas" + }, + { + "author_name": "Zhou Lu", + "author_inst": "Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invas" + }, + { + "author_name": "Aiwu Ke", + "author_inst": "Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invas" + }, + { + "author_name": "Jian Zhou", + "author_inst": "Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invas" + }, + { + "author_name": "Guoming Shi", + "author_inst": "Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invas" + }, + { + "author_name": "Nan Fang", + "author_inst": "Singleron Biotechnologies, Yaogu Avenue 11, Nanjing, Jiangsu, China" + }, + { + "author_name": "Jia Fan", + "author_inst": "Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invas" + }, + { + "author_name": "Jiabin Cai", + "author_inst": "Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invas" + }, + { + "author_name": "Jue Fan", + "author_inst": "Singleron Biotechnologies, Yaogu Avenue 11, Nanjing, Jiangsu, China" + }, + { + "author_name": "Fei Lan", + "author_inst": "Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University; Key Laboratory of Carcinogenesis and Cancer Invas" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "new results", + "category": "genomics" + }, { "rel_doi": "10.1101/2020.01.30.927889", "rel_title": "Machine intelligence design of 2019-nCoV drugs", @@ -1651187,105 +1649657,6 @@ "type": "PUBLISHAHEADOFPRINT", "category": "infectious diseases" }, - { - "rel_doi": "10.1101/2020.01.30.20019844", - "rel_title": "Early evaluation of the Wuhan City travel restrictions in response to the 2019 novel coronavirus outbreak", - "rel_date": "2020-02-02", - "rel_site": "medRxiv", - "rel_link": "https://medrxiv.org/cgi/content/short/2020.01.30.20019844", - "rel_abs": "Respiratory illness caused by a novel coronavirus (COVID-19) appeared in China during December 2019. Attempting to contain infection, China banned travel to and from Wuhan city on 23 January and implemented a national emergency response. Here we evaluate the spread and control of the epidemic based on a unique synthesis of data including case reports, human movement and public health interventions. The Wuhan shutdown slowed the dispersal of infection to other cities by an estimated 2.91 days (95%CI: 2.54-3.29), delaying epidemic growth elsewhere in China. Other cities that implemented control measures pre-emptively reported 33.3% (11.1-44.4%) fewer cases in the first week of their outbreaks (13.0; 7.1-18.8) compared with cities that started control later (20.6; 14.5-26.8). Among interventions investigated here, the most effective were suspending intra-city public transport, closing entertainment venues and banning public gatherings. The national emergency response delayed the growth and limited the size of the COVID-19 epidemic and, by 19 February (day 50), had averted hundreds of thousands of cases across China.\n\nOne sentence summaryTravel restrictions and the national emergency response delayed the growth and limited the size of the COVID-19 epidemic in China.", - "rel_num_authors": 21, - "rel_authors": [ - { - "author_name": "Huaiyu Tian", - "author_inst": "Beijing Normal University" - }, - { - "author_name": "Yonghong Liu", - "author_inst": "Beijing Normal University" - }, - { - "author_name": "Yidan Li", - "author_inst": "Beijing Normal University" - }, - { - "author_name": "Chieh-Hsi Wu", - "author_inst": "University of Southampton" - }, - { - "author_name": "Bin Chen", - "author_inst": "University of California Davis" - }, - { - "author_name": "Moritz U. G. Kraemer", - "author_inst": "University of Oxford" - }, - { - "author_name": "Bingying Li", - "author_inst": "Beijing Normal University" - }, - { - "author_name": "Jun Cai", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Bo Xu", - "author_inst": "Tsinghua University" - }, - { - "author_name": "Qiqi Yang", - "author_inst": "Beijing Normal University" - }, - { - "author_name": "Ben Wang", - "author_inst": "Beijing Normal University" - }, - { - "author_name": "Peng Yang", - "author_inst": "Beijing Center for Disease Prevention and Control" - }, - { - "author_name": "Yujun Cui", - "author_inst": "State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Yimeng Song", - "author_inst": "The University of Hong Kong" - }, - { - "author_name": "Pai Zheng", - "author_inst": "Peking University" - }, - { - "author_name": "Quanyi Wang", - "author_inst": "Beijing Center for Disease Prevention and Control" - }, - { - "author_name": "Ottar N Bjornstad", - "author_inst": "Penn State University" - }, - { - "author_name": "Ruifu Yang", - "author_inst": "Beijing Institute of Microbiology and Epidemiology" - }, - { - "author_name": "Bryan Grenfell", - "author_inst": "Princeton University" - }, - { - "author_name": "Oliver Pybus", - "author_inst": "University of Oxford" - }, - { - "author_name": "Christopher Dye", - "author_inst": "University of Oxford" - } - ], - "version": "1", - "license": "cc_by", - "type": "PUBLISHAHEADOFPRINT", - "category": "infectious diseases" - }, { "rel_doi": "10.1101/2020.01.30.20019877", "rel_title": "Reconciling early-outbreak preliminary estimates of the basic reproductive number and its uncertainty: a new framework and applications to the novel coronavirus (2019-nCoV) outbreak", @@ -1652129,6 +1650500,33 @@ "type": "PUBLISHAHEADOFPRINT", "category": "epidemiology" }, + { + "rel_doi": "10.1101/2020.01.27.20018986", + "rel_title": "The incubation period of 2019-nCoV infections among travellers from Wuhan, China", + "rel_date": "2020-01-28", + "rel_site": "medRxiv", + "rel_link": "https://medrxiv.org/cgi/content/short/2020.01.27.20018986", + "rel_abs": "Currently, a novel coronavirus 2019-nCoV causes an outbreak of viral pneumonia in Wuhan, China. Little is known about its epidemiological characteristics. Using the travel history and symptom onset of 88 confirmed cases that were detected outside Wuhan, we estimate the mean incubation period to be 6.4 (5.6 - 7.7, 95% CI) days, ranging from 2.1 to 11.1 days (2.5th to 97.5th percentile). These values help to inform case definitions for 2019-nCoV and appropriate durations for quarantine.", + "rel_num_authors": 3, + "rel_authors": [ + { + "author_name": "Jantien A. Backer", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Don Klinkenberg", + "author_inst": "National Institute for Public Health and the Environment" + }, + { + "author_name": "Jacco Wallinga", + "author_inst": "National Institute for Public Health and the Environment, Leiden University Medical Center" + } + ], + "version": "1", + "license": "cc_by_nc_nd", + "type": "PUBLISHAHEADOFPRINT", + "category": "infectious diseases" + }, { "rel_doi": "10.1101/2020.01.27.922443", "rel_title": "Breaking down of the healthcare system: Mathematical modelling for controlling the novel coronavirus (2019-nCoV) outbreak in Wuhan, China", @@ -1652488,29 +1650886,6 @@ "type": "new results", "category": "systems biology" }, - { - "rel_doi": "10.1101/2020.01.25.919688", - "rel_title": "Origin time and epidemic dynamics of the 2019 novel coronavirus", - "rel_date": "2020-01-26", - "rel_site": "bioRxiv", - "rel_link": "https://biorxiv.org/cgi/content/short/2020.01.25.919688", - "rel_abs": "The 2019 novel coronavirus (2019-nCoV) have emerged from Wuhan, China. Studying the epidemic dynamics is crucial for further surveillance and control of the outbreak. We employed a Bayesian framework to infer the time-calibrated phylogeny and the epidemic dynamics represented by the effective reproductive number (Re) changing over time from 33 genomic sequences available from GISAID. The time of the most recent common ancestor (MRCA) was December 17, 2019 (95% HPD: December 7, 2019 - December 23, 2019). The median estimate of Re shifted from 1.6 to 1.1 on around January 1, 2020. This study provides an early insight of the 2019-nCoV epidemic. However, due to limited amount of data, one should be cautious when interpreting the results at this stage.", - "rel_num_authors": 2, - "rel_authors": [ - { - "author_name": "Chi Zhang", - "author_inst": "IVPP, CAS" - }, - { - "author_name": "Mei Wang", - "author_inst": "PKU" - } - ], - "version": "1", - "license": "cc_by_nc_nd", - "type": "new results", - "category": "microbiology" - }, { "rel_doi": "10.1101/2020.01.24.919159", "rel_title": "2019-20 Wuhan coronavirus outbreak: Intense surveillance is vital for preventing sustained transmission in new locations",